2017
By land, air, and sea: hemipteran diversity through the genomic lens
Panfilio K.A., Angelini D.R., 24. Dec. 2017, Current Opinion in Insect Science 25:106-115, https://doi.org/10.1016/j.cois.2017.12.005
Background
Thanks to a recent spate of sequencing projects, the Hemiptera are the first hemimetabolous insect order to achieve a critical mass of species with sequenced genomes, establishing the basis for comparative genomics of the bugs. However, as the most speciose hemimetabolous order, there is still a vast swathe of the hemipteran phylogeny that awaits genomic representation across subterranean, terrestrial, and aquatic habitats, and with lineage-specific and developmentally plastic cases of both wing polyphenisms and flightlessness. In this review, we highlight opportunities for taxonomic sampling beyond obvious pest species candidates, motivated by intriguing biological features of certain groups as well as the rich research tradition of ecological, physiological, developmental, and particularly cytogenetic investigation that spans the diversity of the Hemiptera.
Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species
Mateos J.L., Tilmes V., Madrigal P., Severing E., Richter R., Rijkenberg C.W.M., Krajewski P. and Coupland G., 4. Dec. 2017, Proc. Natl. Acad. Sci. USA 114(51):E11037-E11046, DOI: 10.1073/pnas.1618075114
Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found that only 14% of their BSs were conserved in both species and that these contained a CArG-box that is recognized by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared with the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets, and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated (COR) genes were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were usually different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared with WT, and this correlated with reduced growth in pep1-1. Therefore, FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.
Adaptive benefits from small mutation supplies in an antibiotic resistance enzyme
Salverda M.L.M., Koomen J., Koopmanschap B., Zwart M.P., de Visser J.A.G.M., 28. Nov. 2017, Proc. Natl. Acad. Sci. USA 114:12773-12778, https://doi.org/10.1073/pnas.1712999114
Populations with large mutation supplies adapt via the “greedy” substitution of the fittest genotype available, leading to fast and repeatable short-term responses. At longer time scales, smaller mutation supplies may in theory lead to larger improvements when distant high-fitness genotypes more readily evolve from lower-fitness intermediates. Here we test for long-term adaptive benefits from small mutation supplies using in vitro evolution of an antibiotic-degrading enzyme in the presence of a novel antibiotic. Consistent with predictions, large mutant libraries cause rapid initial adaptation via the substitution of cohorts of mutations, but show later deceleration and convergence. Smaller libraries show on average smaller initial, but also more variable, improvements, with two lines yielding alleles with exceptionally high resistance levels. These two alleles share three mutations with the large-library alleles, which are known from previous work, but also have unique mutations. Replay evolution experiments and analyses of the adaptive landscape of the enzyme suggest that the benefit resulted from a combination of avoiding mutational cohorts leading to local peaks and chance. Our results demonstrate adaptive benefits from limited mutation supplies on a rugged fitness landscape, which has implications for artificial selection protocols in biotechnology and argues for a better understanding of mutation supplies in clinical settings.
Fitness cost of reassortment in human influenza
Mara Villa, Michael Lässig, PLOS Pathogens 13(11): e1006685, 7. November 2017, https://doi.org/10.1371/journal.ppat.1006685
Reassortment, which is the exchange of genome sequence between viruses co-infecting a host cell, plays an important role in the evolution of segmented viruses. In the human influenza virus, reassortment happens most frequently between co-existing variants within the same lineage. This process breaks genetic linkage and fitness correlations between viral genome segments, but the resulting net effect on viral fitness has remained unclear. In this paper, we determine rate and average selective effect of reassortment processes in the human influenza lineage A/H3N2. For the surface proteins hemagglutinin and neuraminidase, reassortant variants with a mean distance of at least 3 nucleotides to their parent strains get established at a rate of about 10−2 in units of the neutral point mutation rate. Our inference is based on a new method to map reassortment events from joint genealogies of multiple genome segments, which is tested by extensive simulations. We show that intra-lineage reassortment processes are, on average, under substantial negative selection that increases in strength with increasing sequence distance between the parent strains. The deleterious effects of reassortment manifest themselves in two ways: there are fewer reassortment events than expected from a null model of neutral reassortment, and reassortant strains have fewer descendants than their non-reassortant counterparts. Our results suggest that influenza evolves under ubiquitous epistasis across proteins, which produces fitness barriers against reassortment even between co-circulating strains within one lineage.
Recurrent Reverse Evolution Maintains Polymorphism after Strong Bottlenecks in Commensal Gut Bacteria
Sousa A., Ramiro R.S., Barroso-Batista J., Güleresi D., Lourenço M., Gordo I., 1. Nov. 2017, Mol Biol Evol. 34(11):2879-2892, https://doi.org/10.1093/molbev/msx221
The evolution of new strains within the gut ecosystem is poorly understood. We used a natural but controlled system to follow the emergence of intraspecies diversity of commensal Escherichia coli, during three rounds of adaptation to the mouse gut (∼1,300 generations). We previously showed that, in the first round, a strongly beneficial phenotype (loss-of-function for galactitol consumption; gat-negative) spread to >90% frequency in all colonized mice. Here, we show that this loss-of-function is repeatedly reversed when a gat-negative clone colonizes new mice. The regain of function occurs via compensatory mutation and reversion, the latter leaving no trace of past adaptation. We further show that loss-of-function adaptive mutants reevolve, after colonization with an evolved gat-positive clone. Thus, even under strong bottlenecks a regime of strong-mutation-strong-selection dominates adaptation. Coupling experiments and modeling, we establish that reverse evolution recurrently generates two coexisting phenotypes within the microbiota that can or not consume galactitol (gat-positive and gat-negative, respectively). Although the abundance of the dominant strain, the gat-negative, depends on the microbiota composition, gat-positive abundance is independent of the microbiota composition and can be precisely manipulated by supplementing the diet with galactitol. These results show that a specific diet is able to change the abundance of specific strains. Importantly, we find polymorphism for these phenotypes in indigenous Enterobacteria of mice and man. Our results demonstrate that natural selection can greatly overwhelm genetic drift at structuring the strain diversity of gut commensals and that competition for limiting resources may be a key mechanism for maintaining polymorphism in the gut.
Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology
Dylan H. Morris, Katelyn M. Gostic, Simone Pompei, Trevor Bedford, Marta Łuksza, Richard A. Neher, Bryan T. Grenfell, Michael Lässig, John W. McCauley, Trends in Microbiology, Volume 0 , Issue 0, 30. October 2017, http://dx.doi.org/10.1016/j.tim.2017.09.004
Seasonal influenza is controlled through vaccination campaigns. Evolution of influenza virus antigens means that vaccines must be updated to match novel strains, and vaccine effectiveness depends on the ability of scientists to predict nearly a year in advance which influenza variants will dominate in upcoming seasons. In this review, we highlight a promising new surveillance tool: predictive models. Developed through data-sharing and close collaboration between the World Health Organization and academic scientists, these models use surveillance data to make quantitative predictions regarding influenza evolution. Predictive models demonstrate the potential of applied evolutionary biology to improve public health and disease control. We review the state of influenza predictive modeling and discuss next steps and recommendations to ensure that these models deliver upon their considerable biomedical promise.
Phase and antigenic variation govern competition dynamics through positioning in bacterial colonies
Zöllner R., Oldewurtel E.R., Kouzel N., Maier B., 22. Sept. 2017, Sci. Rep. 12151, DOI:10.1038/s41598-017-12472-7
Cellular positioning towards the surface of bacterial colonies and biofilms can enhance dispersal,
provide a selective advantage due to increased nutrient and space availability, or shield interior
cells from external stresses. Little is known about the molecular mechanisms that govern bacterial positioning. Using the type IV pilus (T4P) of Neisseria gonorrhoeae, we tested the hypothesis that the processes of phase and antigenic variation govern positioning and thus enhance bacterial fitness in expanding gonococcal colonies. By independently tuning growth rate and T4P-mediated interaction forces, we show that the loss of T4P and the subsequent segregation to the front confers a strong selective advantage. Sequencing of the major pilin gene of the spatially segregated sub-populations and an investigation of the spatio-temporal population dynamics was carried out. Our findings indicate that pilin phase and antigenic variation generate a standing variation of pilin sequences within the inoculation zone, while variants associated with a non-piliated phenotype segregate to the front of the growing colony. We conclude that tuning of attractive forces by phase and antigenic variation is a powerful mechanism for governing the dynamics of bacterial colonies.
Decomposing the Site Frequency Spectrum: The Impact of Tree Topology on Neutrality Tests
Ferretti L., Ledda A., Wiehe T., Achaz G., Ramos-Onsins S.E., 1. Sept. 2017, Genetics 207: 229, https://doi.org/10.1534/genetics.116.188763
We investigate the dependence of the site frequency spectrum on the topological structure of genealogical trees. We show that basic population genetic statistics, for instance, estimators of θ or neutrality tests such as Tajima’s D, can be decomposed into components of waiting times between coalescent events and of tree topology. Our results clarify the relative impact of the two components on these statistics. We provide a rigorous interpretation of positive or negative values of an important class of neutrality tests in terms of the underlying tree shape. In particular, we show that values of Tajima’s D and Fay and Wu’s H depend in a direct way on a peculiar measure of tree balance, which is mostly determined by the root balance of the tree. We present a new test for selection in the same class as Fay and Wu’s H and discuss its interpretation and power. Finally, we determine the trees corresponding to extreme expected values of these neutrality tests and present formulas for these extreme values as a function of sample size and number of segregating sites.
Mutation supply and the repeatability of selection for antibiotic resistance.
Van Dijk T., Hwang S., Krug J., de Visser J.A.G.M., Zwart M.P., 21. Aug. 2017, Phys. Biol. 14:055005, DOI: 10.1088/1478-3975/aa7f36
Whether evolution can be predicted is a key question in evolutionary biology. Here we set out to better understand the repeatability of evolution, which is a necessary condition for predictability. We explored experimentally the effect of mutation supply and the strength of selective pressure on the repeatability of selection from standing genetic variation. Different sizes of mutant libraries of antibiotic resistance gene TEM-1 β-lactamase in Escherichia coli, generated by error-prone PCR, were subjected to different antibiotic concentrations. We determined whether populations went extinct or survived, and sequenced the TEM gene of the surviving populations. The distribution of mutations per allele in our mutant libraries followed a Poisson distribution. Extinction patterns could be explained by a simple stochastic model that assumed the sampling of beneficial mutations was key for survival. In most surviving populations, alleles containing at least one known large-effect beneficial mutation were present. These genotype data also support a model which only invokes sampling effects to describe the occurrence of alleles containing large-effect driver mutations. Hence, evolution is largely predictable given cursory knowledge of mutational fitness effects, the mutation rate and population size. There were no clear trends in the repeatability of selected mutants when we considered all mutations present. However, when only known large-effect mutations were considered, the outcome of selection is less repeatable for large libraries, in contrast to expectations. We show experimentally that alleles carrying multiple mutations selected from large libraries confer higher resistance levels relative to alleles with only a known large-effect mutation, suggesting that the scarcity of high-resistance alleles carrying multiple mutations may contribute to the decrease in repeatability at large library sizes.
Adaptive Evolution of Gene Expression in Drosophila
Armita Nourmohammad, Joachim Rambeau, Torsten Held, Viera Kovacova, Johannes Berg, Michael Lässig, Cell Reports, Volume 20, Issue 6, 1385 - 1395, 8. August 2017, http://dx.doi.org/10.1016/j.celrep.2017.07.033
Gene expression levels are important quantitative traits that link genotypes to molecular functions and fitness. In Drosophila, population-genetic studies have revealed substantial adaptive evolution at the genomic level, but the evolutionary modes of gene expression remain controversial. Here, we present evidence that adaptation dominates the evolution of gene expression levels in flies. We show that 64% of the observed expression divergence across seven Drosophila species are adaptive changes driven by directional selection. Our results are derived from time-resolved data of gene expression divergence across a family of related species, using a probabilistic inference method for gene-specific selection. Adaptive gene expression is stronger in specific functional classes, including regulation, sensory perception, sexual behavior, and morphology. Moreover, we identify a large group of genes with sex-specific adaptation of expression, which predominantly occurs in males. Our analysis opens an avenue to map system-wide selection on molecular quantitative traits independently of their genetic basis.
The Second Intron Is Essential for the Transcriptional Control of the Arabidopsis thaliana GLABRA3 Gene in Leaves
Friede A., Zhang B., Herberth S., Pesch M., Schrader A. and Hülskamp M., 1. Aug. 2016, Frontiers in Plant Science 8., https://doi.org/10.3389/fpls.2017.01382
The GLABRA3 gene is a major regulator of trichome patterning in Arabidopsis thaliana. The regulatory regions important for the trichome-specific expression of GL3 have not been characterized yet. In this study, we used a combination of marker and rescue constructs to determine the relevant promoter regions. We demonstrate that a 1 kb 5′ region combined with the second intron is sufficient to rescue the trichome mutant phenotype of gl3 egl3 mutants. Swap experiments of the second intron suggest that it is not sufficient to generally enhance the expression level of GL3. This implies that the second intron contains regulatory regions for the temporal and spatial regulation of GL3. The corresponding GUS-marker constructs revealed trichome-specific expression in young trichomes.
Inverse statistical problems: from the inverse Ising problem to data science
Nguyen H.C., Zecchina R., Berg J., Advances in Physics, 66:197-261, 29. June 2017, https://doi.org/10.1080/00018732.2017.1341604
Inverse problems in statistical physics are motivated by the challenges of ‘big data’ in different fields, in particular high-throughput experiments in biology. In inverse problems, the usual procedure of statistical physics needs to be reversed: Instead of calculating observables on the basis of model parameters, we seek to infer parameters of a model based on observations. In this review, we focus on the inverse Ising problem and closely related problems, namely how to infer the coupling strengths between spins given observed spin correlations, magnetizations, or other data. We review applications of the inverse Ising problem, including the reconstruction of neural connections, protein structure determination, and the inference of gene regulatory networks. For the inverse Ising problem in equilibrium, a number of controlled and uncontrolled approximate solutions have been developed in the statistical mechanics community. A particularly strong method, pseudolikelihood, stems from statistics. We also review the inverse Ising problem in the non-equilibrium case, where the model parameters must be reconstructed based on non-equilibrium statistics.
Evolution of commensal bacteria in the intestinal tract of mice
Sousa A., Frazão N., Ramiro R.S., Gordo I., 4. June. 2017, Current Opinion in Microbiology 38, 114-121, https://doi.org/10.1016/j.mib.2017.05.007
Hundreds of different bacterial species inhabit our intestines and contribute to our health status, with significant loss of species diversity typically observed in disease conditions. Within each microbial species a great deal of diversity is hidden and such intra-specific variation is also key to the proper homeostasis between the host and its microbial inhabitants. Indeed, it is at this level that new mechanisms of antibiotic resistance emerge and pathogenic characteristics evolve. Yet, our knowledge on intra-species variation in the gut is still limited and an understanding of the evolutionary mechanisms acting on it is extremely reduced. Here we review recent work that has begun to reveal that adaptation of commensal bacteria to the mammalian intestine may be fast and highly repeatable, and that the time scales of evolutionary and ecological change can be very similar in these ecosystems.
Genotypic Complexity of Fisher’s Geometric Model
Sungmin Hwang, Su-Chan Park, Joachim Krug, GENETICS, 2017 vol. 206 no. 2 1049-1079, 1. June 2017, https://doi.org/10.1534/genetics.116.199497
Fisher’s geometric model was originally introduced to argue that complex adaptations must occur in small steps because of pleiotropic constraints. When supplemented with the assumption of additivity of mutational effects on phenotypic traits, it provides a simple mechanism for the emergence of genotypic epistasis from the nonlinear mapping of phenotypes to fitness. Of particular interest is the occurrence of reciprocal sign epistasis, which is a necessary condition for multipeaked genotypic fitness landscapes. Here we compute the probability that a pair of randomly chosen mutations interacts sign epistatically, which is found to decrease with increasing phenotypic dimension n, and varies nonmonotonically with the distance from the phenotypic optimum. We then derive expressions for the mean number of fitness maxima in genotypic landscapes comprised of all combinations of L random mutations. This number increases exponentially with L, and the corresponding growth rate is used as a measure of the complexity of the landscape. The dependence of the complexity on the model parameters is found to be surprisingly rich, and three distinct phases characterized by different landscape structures are identified. Our analysis shows that the phenotypic dimension, which is often referred to as phenotypic complexity, does not generally correlate with the complexity of fitness landscapes and that even organisms with a single phenotypic trait can have complex landscapes. Our results further inform the interpretation of experiments where the parameters of Fisher’s model have been inferred from data, and help to elucidate which features of empirical fitness landscapes can be described by this model.
NLR locus-mediated trade-off between abiotic and biotic stress adaptation in Arabidopsis
Hirotaka Ariga, Taku Katori, Takashi Tsuchimatsu, Taishi Hirase, Yuri Tajima, Jane E. Parker, Rubén Alcázar, Maarten Koornneef, Owen Hoekenga, Alexander E. Lipka, Michael A. Gore, Hitoshi Sakakibara, Mikiko Kojima, Yuriko Kobayashi, Satoshi Iuchi, Masatomo Kobayashi, Kazuo Shinozaki, Yoichi Sakata, Takahisa Hayashi, Yusuke Saijo, Teruaki Taji, Nature Plants 3, Article number: 17072 (2017), 26. May 2017, doi:10.1038/nplants.2017.72
Osmotic stress caused by drought, salt or cold decreases plant fitness. Acquired stress tolerance defines the ability of plants to withstand stress following an initial exposure1. We found previously that acquired osmotolerance after salt stress is widespread among Arabidopsis thaliana accessions2. Here, we identify ACQOS as the locus responsible for ACQUIRED OSMOTOLERANCE. Of its five haplotypes, only plants carrying group 1 ACQOS are impaired in acquired osmotolerance. ACQOS is identical to VICTR, encoding a nucleotide-binding leucine-rich repeat (NLR) protein3. In the absence of osmotic stress, group 1 ACQOS contributes to bacterial resistance. In its presence, ACQOS causes detrimental autoimmunity, thereby reducing osmotolerance. Analysis of natural variation at the ACQOS locus suggests that functional and non-functional ACQOS alleles are being maintained due to a trade-off between biotic and abiotic stress adaptation. Thus, polymorphism in certain plant NLR genes might be influenced by competing environmental stresses.
Enhancer evolution and the origins of morphological novelty
Mark Rebeiz, Miltos Tsiantis,Science Direct Volume 45, August 2017, Pages 115–123, 18. May 2017, https://doi.org/10.1016/j.gde.2017.04.006.
A central goal of evolutionary biology is to understand the genetic origin of morphological novelties—i.e. anatomical structures unique to a taxonomic group. Elaboration of morphology during development depends on networks of regulatory genes that activate patterned gene expression through transcriptional enhancer regions. We summarize recent case studies and genome-wide investigations that have uncovered diverse mechanisms though which new enhancers arise. We also discuss how these enhancer-originating mechanisms have clarified the history of genetic networks underlying diversification of genital structures in flies, limbs and neural crest in chordates, and plant leaves. These studies have identified enhancers that were pivotal for morphological divergence and highlighted how novel genetic networks shaping form emerged from pre-existing ones.
The Protistan Microbiome of Grassland Soil: Diversity in the Mesoscale
Paul Christiaan Venter, Frank Nitsche, Anne Domonell, Peter Heger, Hartmut Arndt, In Protist, Volume 168, Issue 5, 2017, Pages 546-564, ISSN 1434-4610, April 2017, https://doi.org/10.1016/j.protis.2017.03.005.
Genomic data for less than one quarter of ∼1.8 million named species on earth exist in public databases like GenBank. Little information exists on the estimated one million small sized (1–100 μm) heterotrophic nanoflagellates and ciliates and their taxa-area relationship. We analyzed environmental DNA from 150 geo-referenced grassland plots representing topographical and land-use ranges typical for Central Europe. High through-put barcoding allowed the identification of operational taxonomic units (OTUs) at species level, with high pairwise identity to reference sequences (≥99.7%), but also the identification of sequences at the genus (≥97%) and class (≥80%) taxonomic level. Species richness analyses revealed, on average, 100 genus level OTUs (332 unique individual read (UIR) and 56 class level OTUs per gram of soil sample in the mesoscale (1–1 000 km). Database shortfalls were highlighted by increased uncertain taxonomic lineages at lower resolution (≥80% sequence identity). No single barcode occurred ubiquitously across all sites. Taxa-area relationships indicated that OTUs spread over the entire mesoscale were more similar than in the local scale and increased land-use (fertilization, mowing and grazing) promoted taxa-area separation. Only a small fraction of sequences strictly matched reference library sequences, suggesting a large protistan “dark matter” in soil which warrants further research.
Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data
Jiao W.B., Accinelli G.G., Hartwig B., Kiefer C., Baker D., Severing E., Willing E.M., Piednoel M., Woetzel S., Madrid-Herrero E.M., Huettel B., Hümann U., Reinhard R., Koch M.A., Swan D., Clavijo B., Coupland G. and Schneeberger K., 3. Feb. 2017, Genome Research 27:778-786, DOI: 10.1101/gr.213652.116
Long-read sequencing can overcome the weaknesses of short reads in the assembly of eukaryotic genomes; however, at present additional scaffolding is needed to achieve chromosome-level assemblies. We generated Pacific Biosciences (PacBio) long-read data of the genomes of three relatives of the model plant Arabidopsis thaliana and assembled all three genomes into only a few hundred contigs. To improve the contiguities of these assemblies, we generated BioNano Genomics optical mapping and Dovetail Genomics chromosome conformation capture data for genome scaffolding. Despite their technical differences, optical mapping and chromosome conformation capture performed similarly and doubled N50 values. After improving both integration methods, assembly contiguity reached chromosome-arm-levels. We rigorously assessed the quality of contigs and scaffolds using Illumina mate-pair libraries and genetic map information. This showed that PacBio assemblies have high sequence accuracy but can contain several misassemblies, which join unlinked regions of the genome. Most, but not all, of these misjoints were removed during the integration of the optical mapping and chromosome conformation capture data. Even though none of the centromeres were fully assembled, the scaffolds revealed large parts of some centromeric regions, even including some of the heterochromatic regions, which are not present in gold standard reference sequences.
Predicting evolution
Michael Lässig, Ville Mustonen, Aleksandra M. Walczak, Nature Ecology & Evolution, 21. Feb. 2017, doi:10.1038/s41559-017-0077
The face of evolutionary biology is changing: from reconstructing and analysing the past to predicting future evolutionary pro- cesses. Recent developments include prediction of reproducible patterns in parallel evolution experiments, forecasting the future of individual populations using data from their past, and controlled manipulation of evolutionary dynamics. Here we undertake a synthesis of central concepts for evolutionary predictions, based on examples of microbial and viral systems, can- cer cell populations, and immune receptor repertoires. These systems have strikingly similar evolutionary dynamics driven by the competition of clades within a population. These dynamics are the basis for models that predict the evolution of clade frequencies, as well as broad genetic and phenotypic changes. Moreover, there are strong links between prediction and control, which are important for interventions such as vaccine or therapy design. All of these are key elements of what may become a predictive theory of evolution.
Divergence of annual and perennial species in the Brassicaceae and the contribution of cis‐acting variation at FLC orthologues
Kiefer C., Severing E., Karl R., Bergonzi S., Koch M., Tresch A., Coupland G., 6. Mar. 2017, Molecular Ecology 26:3437-3457, DOI: 10.1111/mec.14084
Variation in life history contributes to reproductive success in different environments. Divergence of annual and perennial angiosperm species is an extreme example that has occurred frequently. Perennials survive for several years and restrict the duration of reproduction by cycling between vegetative growth and flowering, whereas annuals live for 1 year and flower once. We used the tribe Arabideae (Brassicaceae) to study the divergence of seasonal flowering behaviour among annual and perennial species. In perennial Brassicaceae, orthologues of FLOWERING LOCUS C (FLC), a floral inhibitor in Arabidopsis thaliana, are repressed by winter cold and reactivated in spring conferring seasonal flowering patterns, whereas in annuals, they are stably repressed by cold. We isolated FLC orthologues from three annual and two perennial Arabis species and found that the duplicated structure of the A. alpina locus is not required for perenniality. The expression patterns of the genes differed between annuals and perennials, as observed among Arabidopsis species, suggesting a broad relevance of these patterns within the Brassicaceae. Also analysis of plants derived from an interspecies cross of A. alpina and annual A. montbretiana demonstrated that cis‐regulatory changes in FLC orthologues contribute to their different transcriptional patterns. Sequence comparisons of FLC orthologues from annuals and perennials in the tribes Arabideae and Camelineae identified two regulatory regions in the first intron whose sequence variation correlates with divergence of the annual and perennial expression patterns. Thus, we propose that related cis‐acting changes in FLC orthologues occur independently in different tribes of the Brassicaceae during life history evolution.
2016
Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface
McKenna D.D., Panfilio K.A., Richards S., et al., 11. Nov. 2016, Genome Biology 2016 17:227, https://doi.org/10.1186/s13059-016-1088-8
Background
Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species. Complementary studies of genes encoding enzymes involved in digestion of woody plant tissues or detoxification of plant allelochemicals were undertaken with the genomes of 14 additional insects, including the newly sequenced emerald ash borer and bull-headed dung beetle.
Results
The Asian longhorned beetle genome encodes a uniquely diverse arsenal of enzymes that can degrade the main polysaccharide networks in plant cell walls, detoxify plant allelochemicals, and otherwise facilitate feeding on woody plants. It has the metabolic plasticity needed to feed on diverse plant species, contributing to its highly invasive nature. Large expansions of chemosensory genes involved in the reception of pheromones and plant kairomones are consistent with the complexity of chemical cues it uses to find host plants and mates.
Conclusions
Amplification and functional divergence of genes associated with specialized feeding on plants, including genes originally obtained via horizontal gene transfer from fungi and bacteria, contributed to the addition, expansion, and enhancement of the metabolic repertoire of the Asian longhorned beetle, certain other phytophagous beetles, and to a lesser degree, other phytophagous insects. Our results thus begin to establish a genomic basis for the evolutionary success of beetles on plants.
Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects
Pauli T., Vedder L., Dowling D., Petersen M., Meusemann K., Donath A., Peters R.S., Podsiadlowski L., Mayer C., Liu S., Zhou X., Heger P., Wiehe T., Hering L., Mayer G., Misof B., Niehuis O., 3. Nov. 2016, BMC Genomics 17:861, https://doi.org/10.1186/s12864-016-3205-1
Background
Body plan development in multi-cellular organisms is largely determined by homeotic genes. Expression of homeotic genes, in turn, is partially regulated by insulator binding proteins (IBPs). While only a few enhancer blocking IBPs have been identified in vertebrates, the common fruit fly Drosophila melanogaster harbors at least twelve different enhancer blocking IBPs. We screened recently compiled insect transcriptomes from the 1KITE project and genomic and transcriptomic data from public databases, aiming to trace the origin of IBPs in insects and other arthropods.
Results
Our study shows that the last common ancestor of insects (Hexapoda) already possessed a substantial number of IBPs. Specifically, of the known twelve insect IBPs, at least three (i.e., CP190, Su(Hw), and CTCF) already existed prior to the evolution of insects. Furthermore we found GAF orthologs in early branching insect orders, including Zygentoma (silverfish and firebrats) and Diplura (two-pronged bristletails). Mod(mdg4) is most likely a derived feature of Neoptera, while Pita is likely an evolutionary novelty of holometabolous insects. Zw5 appears to be restricted to schizophoran flies, whereas BEAF-32, ZIPIC and the Elba complex, are probably unique to the genus Drosophila. Selection models indicate that insect IBPs evolved under neutral or purifying selection.
Conclusions
Our results suggest that a substantial number of IBPs either pre-date the evolution of insects or evolved early during insect evolution. This suggests an evolutionary history of insulator binding proteins in insects different to that previously thought. Moreover, our study demonstrates the versatility of the 1KITE transcriptomic data for comparative analyses in insects and other arthropods.
A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut
Lourenço M., Ramiro R.S., Güleresi D., Barroso-Batista J., Xavier K.B., Gordo I., Sousa A., 3. Nov. 2016, PLoS Genetics 12 (11), https://doi.org/10.1371/journal.pgen.1006420
The relative role of drift versus selection underlying the evolution of bacterial species within the gut microbiota remains poorly understood. The large sizes of bacterial populations in this environment suggest that even adaptive mutations with weak effects, thought to be the most frequently occurring, could substantially contribute to a rapid pace of evolutionary change in the gut. We followed the emergence of intra-species diversity in a commensal Escherichia coli strain that previously acquired an adaptive mutation with strong effect during one week of colonization of the mouse gut. Following this first step, which consisted of inactivating a metabolic operon, one third of the subsequent adaptive mutations were found to have a selective effect as high as the first. Nevertheless, the order of the adaptive steps was strongly affected by a mutational hotspot with an exceptionally high mutation rate of 10−5. The pattern of polymorphism emerging in the populations evolving within different hosts was characterized by periodic selection, which reduced diversity, but also frequency-dependent selection, actively maintaining genetic diversity. Furthermore, the continuous emergence of similar phenotypes due to distinct mutations, known as clonal interference, was pervasive. Evolutionary change within the gut is therefore highly repeatable within and across hosts, with adaptive mutations of selection coefficients as strong as 12% accumulating without strong constraints on genetic background. In vivo competitive assays showed that one of the second steps (focA) exhibited positive epistasis with the first, while another (dcuB) exhibited negative epistasis. The data shows that strong effect adaptive mutations continuously recur in gut commensal bacterial species.
Coupled enhancer and coding sequence evolution of a homeobox gene shaped leaf diversity
Vuolo F., Mentink R.A., Hajheidari M., Bailey C.D., Filatov D.A., Tsiantis M., 25. Oct. 2016, Genes Dev. 30:2370-2375 doi: 10.1101/gad.290684.116
Here we investigate mechanisms underlying the diversification of biological forms using crucifer leaf shape as an example. We show that evolution of an enhancer element in the homeobox gene REDUCED COMPLEXITY (RCO) altered leaf shape by changing gene expression from the distal leaf blade to its base. A single amino acid substitution evolved together with this regulatory change, which reduced RCO protein stability, preventing pleiotropic effects caused by its altered gene expression. We detected hallmarks of positive selection in these evolved regulatory and coding sequence variants and showed that modulating RCO activity can improve plant physiological performance. Therefore, interplay between enhancer and coding sequence evolution created a potentially adaptive path for morphological evolution.
Importance of rare gene copy number alterations for personalized tumor characterization and survival analysis
M. Seifert, B. Friedrich, A. Beyer, Genome Biology, 3. Oct. 2016, DOI: 10.1186/s13059-016-1058-1
It has proven exceedingly difficult to ascertain rare copy number alterations (CNAs) that may have strong effects in individual tumors. We show that a regulatory network inferred from gene expression and gene copy number data of 768 human cancer cell lines can be used to quantify the impact of patient-specific CNAs on survival signature genes. A focused analysis of tumors from six tissues reveals that rare patient-specific gene CNAs often have stronger effects on signature genes than frequent gene CNAs. Further comparison to a related network-based approach shows that the integration of indirectly acting gene CNAs significantly improves the survival analysis.
Stem Cell Fate versus Differentiation: the Missing Link
Judith Nardmann, John W. Chandler, Wolfgang Werr, Trends in Plant Science , Volume 21 , Issue 9 , 725 - 727, Sept. 2016
The shoot apical meristem provides a microenvironment that ensures stem cell fate and proliferation via homeostasis between WUSCHEL (WUS) activity and CLAVATA signalling. New data from maize and arabidopsis reveal that an evolutionarily conserved signal deriving from primordium cells links WUS transcription to the morphogenetic programme.
A fast and simple LC-MS-based characterization of the flavonoid biosynthesis pathway for few seed(ling)s
B Jaegle, M K Uroic, X Holtkotte, C Lucas, A O Termath, H-G Schmalz, M Bucher, U Hoecker, M Hulskamp and A Schrader (2016), BMC plant biology, 16(1):190, DOI: 10.1186/s12870-016-0880-7
Background
I(Pro)anthocyanidins are synthesized by the flavonoid biosynthesis pathway with multi-layered regulatory control. Methods for the analysis of the flavonoid composition in plants are well established for different purposes. However, they typically compromise either on speed or on depth of analysis.
Results
In this work we combined and optimized different protocols to enable the analysis of the flavonoid biosynthesis pathway with as little as possible biological material. We chose core substances of this metabolic pathway that serve as a fingerprint to recognize alterations in the main branches of the pathway. We used a simplified sample preparation, two deuterated internal standards, a short and efficient LC separation, highly sensitive detection with tandem MS in multiple reaction monitoring (MRM) mode and hydrolytic release of the core substances to reduce complexity. The method was optimized for Arabidopsis thaliana seeds and seedlings. We demonstrate that one Col-0 seed/seedling is sufficient to obtain a fingerprint of the core substances of the flavonoid biosynthesis pathway. For comparative analysis of different genotypes, we suggest the use of 10 seed(lings). The analysis of Arabidopsis thaliana mutants affecting steps in the pathway revealed foreseen and unexpected alterations of the pathway. For example, HY5 was found to differentially regulate kaempferol in seeds vs. seedlings. Furthermore, our results suggest that COP1 is a master regulator of flavonoid biosynthesis in seedlings but not of flavonoid deposition in seeds.
Conclusions
TWhen sample numbers are high and the plant material is limited, this method effectively facilitates metabolic fingerprinting with one seed(ling), revealing shifts and differences in the pathway. Moreover the combination of extracted non-hydrolysed, extracted hydrolysed and non-extracted hydrolysed samples proved useful to deduce the class of derivative from which the individual flavonoids have been released.
Diminishing-returns epistasis among random beneficial mutations in a multicellular fungus
Schoustra S, Hwang S, Krug J, de Visser JAGM. Diminishing-returns epistasis among random beneficial mutations in a multicellular fungus. Proc. R. Soc. B 283: 20161376. Aug. 2016
Adaptive evolution ultimately is fuelled by mutations generating novel gen- etic variation. Non-additivity of fitness effects of mutations (called epistasis) may affect the dynamics and repeatability of adaptation. However, under- standing the importance and implications of epistasis is hampered by the observation of substantial variation in patterns of epistasis across empirical studies. Interestingly, some recent studies report increasingly smaller benefits of beneficial mutations once genotypes become better adapted (called diminishing-returns epistasis) in unicellular microbes and single genes. Here, we use Fisher’s geometric model (FGM) to generate analytical predictions about the relationship between the effect size of mutations and the extent of epistasis. We then test these predictions using the multicellular fungus Aspergillus nidulans by generating a collection of 108 strains in either a poor or a rich nutrient environment that each carry a beneficial mutation and constructing pairwise combinations using sexual crosses. Our results support the predictions from FGM and indicate negative epistasis among beneficial mutations in both environments, which scale with mutational effect size. Hence, our findings show the importance of diminishing-returns epistasis among beneficial mutations also for a multicellular organism, and suggest that this pattern reflects a generic constraint operating at diverse levels of biological organization.
The impact of Toxoplasma gondii on the mammalian genome
Urs B Müller, Jonathan C Howard, ScienceDirect 2016 Aug. doi:10.1016/j.mib.2016.04.009
Nobody doubts that infections have imposed specialisations on the mammalian genome. However sufficient information is usually missing to attribute a specific genomic modification to pressure from a specific pathogen. Recent studies on mechanisms of mammalian resistance against the ubiquitous protozoan parasite, Toxoplasma gondii, have shown that the small rodents presumed to be largely responsible for transmission of the parasite to its definitive host, the domestic cat, possess distinctive recognition proteins, and interferon-inducible effector proteins (IRG proteins) that limit the potential virulence of the parasite. The phylogenetic association of the recognition proteins, TLR11 and TLR12, with T. gondii resistance is weak, but there is evidence for reciprocal polymorphism between parasite virulence proteins and host IRG proteins that strongly suggests current or recent coevolution.
Global analysis of dorsoventral patterning in the wasp Nasonia reveals extensive incorporation of novelty in a regulatory network
Pers D., Buchta T., Özüak O., Wolff S., Pietsch J.M., Memon M.B., Roth S. and Lynch J.A., BMC Biology, 2016 14:63, 1. Aug. 2016, https://doi.org/10.1186/s12915-016-0285-y
Background
Gene regulatory networks (GRNs) underlie developmental patterning and morphogenetic processes, and changes in the interactions within the underlying GRNs are a major driver of evolutionary processes. In order to make meaningful comparisons that can provide significant insights into the evolution of regulatory networks, homologous networks from multiple taxa must be deeply characterized. One of the most thoroughly characterized GRNs is the dorsoventral (DV) patterning system of the Drosophila melanogaster embryo. We have developed the wasp Nasonia as a comparative DV patterning model because it has shown the convergent evolution of a mode of early embryonic patterning very similar to that of the fly, and it is of interest to know whether the similarity at the gross level also extends to the molecular level.
Results
We used RNAi to dorsalize and ventralize Nasonia embryos, RNAseq to quantify transcriptome-wide expression levels, and differential expression analysis to identify genes whose expression levels change in either RNAi case. This led to the identification of >100 genes differentially expressed and regulated along the DV axis. Only a handful of these genes are shared DV components in both fly and wasp. Many of those unique to Nasonia are cytoskeletal and adhesion molecules, which may be related to the divergent cell and tissue behavior observed at gastrulation. In addition, many transcription factors and signaling components are only DV regulated in Nasonia, likely reflecting the divergent upstream patterning mechanisms involved in producing the conserved pattern of cell fates observed at gastrulation. Finally, several genes that lack Drosophila orthologs show robust and distinct expression patterns. These include genes with vertebrate homologs that have been lost in the fly lineage, genes that are found only among Hymenoptera, and several genes that entered the Nasonia genome through lateral transfer from endosymbiotic bacteria.
Conclusions
Altogether, our results provide insights into how GRNs respond to new functional demands and how they can incorporate novel components.
Toll Genes Have an Ancestral Role in Axis Elongation
Matthew A. Benton, Matthias Pechmann, Nadine Frey, Dominik Stappert, Kai H. Conrads, Yen-Ta Chen, Evangelia Stamataki, Anastasios Pavlopoulos, Siegfried Roth, Cell Press, June 20, 2016, doi:10.1016/j.cub.2016.04.055
One of the key morphogenetic processes used during development is the controlled intercalation of cells between their neighbors. This process has been co-opted into a range of developmental events, and it also underlies an event that occurs in each major group of bilaterians: elongation of the embryo along the anterior-posterior axis. In Drosophila, a novel component of this process was recently discovered by Paré et al., who showed that three Toll genes function together to drive cell intercalation during germband extension. This finding raises the question of whether this role of Toll genes is an evolutionary novelty of flies or a general mechanism of embryonic morphogenesis. Here we show that the Toll gene function in axis elongation is, in fact, widely conserved among arthropods. First, we functionally demonstrate that two Toll genes are required for cell intercalation in the beetle Tribolium castaneum. We then show that these genes belong to a previously undescribed Toll subfamily and that members of this subfamily exhibit striped expression (as seen in Tribolium and previously reported in Drosophila) in embryos of six other arthropod species spanning the entire phylum. Last, we show that two of these Toll genes are required for normal morphogenesis during anterior-posterior embryo elongation in the spider Parasteatoda tepidariorum, a member of the most basally branching arthropod lineage. From our findings, we hypothesize that Toll genes had a morphogenetic function in embryo elongation in the last common ancestor of all arthropods, which existed over 550 million years ago.
The Footprint of Polygenic Adaptation on Stress-Responsive Cis-Regulatory Divergence in the Arabidopsis Genus
He F., Arce A., Schmitz G., Rico A., Beyer A. and de Meaux J., 11. June 2016, Mol Biol Evol. 33(8):2088-101, https://doi.org/10.1093/molbev/msw096
Adaptation of a complex trait often requires the accumulation of many modifications to finely tune its underpinning molecular components to novel environmental requirements. The investigation of cis-acting regulatory modifications can be used to pinpoint molecular systems partaking in such complex adaptations. Here, we identify cis-acting modifications with the help of an interspecific crossing scheme designed to distinguish modifications derived in each of the two sister species, Arabidopsis halleri and A. lyrata. Allele-specific expression levels were assessed in three environmental conditions chosen to reflect interspecific ecological differences: cold exposure, dehydration, and standard conditions. The functions described by Gene Ontology categories enriched in cis-acting mutations are markedly different in A. halleri and A. lyrata, suggesting that polygenic adaptation reshaped distinct polygenic molecular functions in the two species. In the A. halleri lineage, an excess of cis-acting changes affecting metal transport and homeostasis was observed, confirming that the well-known heavy metal tolerance of this species is the result of polygenic selection. In A. lyrata, we find a marked excess of cis-acting changes among genes showing a transcriptional response to cold stress in the outgroup species A. thaliana. The adaptive relevance of these changes will have to be validated. We finally observed that polygenic molecular functions enriched in derived cis-acting changes are more constrained at the amino acid level. Using the distribution of cis-acting variation to tackle the polygenic basis of adaptation thus reveals the contribution of mutations of small effect to Darwinian adaptation.
Fitness trade-offs in competence differentiation of Bacillus subtilis
Yüksel M., Power J.J., Ribbe J., Volkmann T., Maier B.,
Front. Microbiol. 7, 888 (2016)
In the stationary phase, Bacillus subtilis differentiates stochastically and transiently into the state of competence for transformation (K-state). The latter is associated with growth arrest, and it is unclear how the ability to develop competence is stably maintained, despite its cost. To quantify the effect differentiation has on the competitive fitness of B. subtilis, we characterized the competition dynamics between strains with different probabilities of entering the K-state. The relative fitness decreased with increasing differentiation probability both during the stationary phase and during outgrowth. When exposed to antibiotics inhibiting cell wall synthesis, transcription, and translation, cells that differentiated into the K-state showed a selective advantage compared to differentiation-deficient bacteria; this benefit did not require transformation. Although beneficial, the K-state was not induced by sub-MIC concentrations of antibiotics. Increasing the differentiation probability beyond the wt level did not significantly affect the competition dynamics with transient antibiotic exposure. We conclude that the competition dynamics are very sensitive to the fraction of competent cells under benign conditions but less sensitive during antibiotic exposure, supporting the picture of stochastic differentiation as a fitness trade-off.
Genome-wide identification of Tribolium dorsoventral patterning genes
Stappert D, Frey N, von Levetzow C, Roth S,
The Company of Biologists Ltd | Development (2016) 143, 2443-2454 doi:10.1242/dev.130641 May-Jun;17(3):198-219. doi: 10.1111/ede.12125.
The gene regulatory network controlling dorsoventral axis formation in insects has undergone drastic evolutionary changes. In Drosophila, a stable long-range gradient of Toll signalling specifies ventral cell fates and restricts BMP signalling to the dorsal half of the embryo. In Tribolium, however, Toll signalling is transient and only indirectly controls BMP signalling. In order to gain unbiased insights into the Tribolium network, we performed comparative transcriptome analyses of embryos with various dorsoventral pattering defects produced by parental RNAi for Toll and BMP signalling components. We also included embryos lacking the mesoderm (produced by Tc-twist RNAi) and characterized similarities and differences between Drosophila and Tribolium twist loss-of-function phenotypes. Using stringent conditions, we identified over 750 differentially expressed genes and analysed a subset with altered expression in more than one knockdown condition. We found new genes with localized expression and showed that conserved genes frequently possess earlier and stronger phenotypes than their Drosophila orthologues. For example, the leucine-rich repeat (LRR) protein Tartan, which has only a minor influence on nervous system development in Drosophila, is essential for early neurogenesis in Tribolium and the Tc-zinc-finger homeodomain protein 1 (Tc-zfh1), the orthologue of which plays a minor role in Drosophila muscle development, is essential for maintaining early Tc-twist expression, indicating an important function for mesoderm specification.
Adaptive evolution of complex innovations through stepwise metabolic niche expansion
Balázs Szappanos, Jonathan Fritzemeier, Bálint Csörgő, Viktória Lázár, Xiaowen Lu, Gergely Fekete, Balázs Bálint, Róbert Herczeg, István Nagy, Richard A. Notebaart, Martin J. Lercher, Csaba Pál, Balázs Papp, Nature Communications (2016) DOI: 10.1038/ncomms11607
A central challenge in evolutionary biology concerns the mechanisms by which complex metabolic innovations requiring multiple mutations arise. Here, we propose that metabolic innovations accessible through the addition of a single reaction serve as stepping stones towards the later establishment of complex metabolic features in another environment. We demonstrate the feasibility of this hypothesis through three complementary analyses. First, using genome-scale metabolic modelling, we show that complex metabolic innovations in Escherichia coli can arise via changing nutrient conditions. Second, using phylogenetic approaches, we demonstrate that the acquisition patterns of complex metabolic pathways during the evolutionary history of bacterial genomes support the hypothesis. Third, we show how adaptation of laboratory populations of E. coli to one carbon source facilitates the later adaptation to another carbon source. Our work demonstrates how complex innovations can evolve through series of adaptive steps without the need to invoke non-adaptive processes.
Energy efficiency trade-offs drive nucleotide usage in transcribed regions
Wei-Hua Chen, Guanting Lu, Peer Bork, Songnian Hu, Martin J. Lercher, Nature Communications (2016) DOI: 10.1038/ncomms11334
Efficient nutrient usage is a trait under universal selection. A substantial part of cellular resources is spent on making nucleotides. We thus expect preferential use of cheaper nucleotides especially in transcribed sequences, which are often amplified thousand-fold compared with genomic sequences. To test this hypothesis, we derive a mutation-selection-drift equilibrium model for nucleotide skews (strand-specific usage of ‘A’ versus ‘T’ and ‘G’ versus ‘C’), which explains nucleotide skews across 1,550 prokaryotic genomes as a consequence of selection on efficient resource usage. Transcription-related selection generally favours the cheaper nucleotides ‘U’ and ‘C’ at synonymous sites. However, the information encoded in mRNA is further amplified through translation. Due to unexpected trade-offs in the codon table, cheaper nucleotides encode on average energetically more expensive amino acids. These trade-offs apply to both strand-specific nucleotide usage and GC content, causing a universal bias towards the more expensive nucleotides ‘A’ and ‘G’ at non-synonymous coding sites.
On the Dependency of Cellular Protein Levels on mRNA Abundance
Liu Y., Beyer A., Aebersold R., 21. Apr. 2016, Cell 165(3):535-50, https://doi.org/10.1016/j.cell.2016.03.014
The question of how genomic information is expressed to determine phenotypes is of central importance for basic and translational life science research and has been studied by transcriptomic and proteomic profiling. Here, we review the relationship between protein and mRNA levels under various scenarios, such as steady state, long-term state changes, and short-term adaptation, demonstrating the complexity of gene expression regulation, especially during dynamic transitions. The spatial and temporal variations of mRNAs, as well as the local availability of resources for protein biosynthesis, strongly influence the relationship between protein levels and their coding transcripts. We further discuss the buffering of mRNA fluctuations at the level of protein concentrations. We conclude that transcript levels by themselves are not sufficient to predict protein levels in many scenarios and to thus explain genotype-phenotype relationships and that high-quality data quantifying different levels of gene expression are indispensable for the complete understanding of biological processes.
Loss of the interferon-γ-inducible regulatory immunity-related GTPase (IRG), Irgm1, causes activation of effector IRG proteins on lysosomes, damaging lysosomal function and predicting the dramatic susceptibility of Irgm1-deficient mice to infection
Maric-Biresev J., Hunn J.P., Krut O., Helms J.B., Martens S. and Howard J.C., 20. Apr. 2016, BMC Biol. 14:33 DOI 10.1186/s12915-016-0255-4
Background
The interferon-γ (IFN-γ)-inducible immunity-related GTPase (IRG), Irgm1, plays an essential role in restraining activation of the IRG pathogen resistance system. However, the loss of Irgm1 in mice also causes a dramatic but unexplained susceptibility phenotype upon infection with a variety of pathogens, including many not normally controlled by the IRG system. This phenotype is associated with lymphopenia, hemopoietic collapse, and death of the mouse.
Results
We show that the three regulatory IRG proteins (GMS sub-family), including Irgm1, each of which localizes to distinct sets of endocellular membranes, play an important role during the cellular response to IFN-γ, each protecting specific membranes from off-target activation of effector IRG proteins (GKS sub-family). In the absence of Irgm1, which is localized mainly at lysosomal and Golgi membranes, activated GKS proteins load onto lysosomes, and are associated with reduced lysosomal acidity and failure to process autophagosomes. Another GMS protein, Irgm3, is localized to endoplasmic reticulum (ER) membranes; in the Irgm3-deficient mouse, activated GKS proteins are found at the ER. The Irgm3-deficient mouse does not show the drastic phenotype of the Irgm1 mouse. In the Irgm1/Irgm3 double knock-out mouse, activated GKS proteins associate with lipid droplets, but not with lysosomes, and the Irgm1/Irgm3 −/− does not have the generalized immunodeficiency phenotype expected from its Irgm1 deficiency.
Conclusions
The membrane targeting properties of the three GMS proteins to specific endocellular membranes prevent accumulation of activated GKS protein effectors on the corresponding membranes and thus enable GKS proteins to distinguish organellar cellular membranes from the membranes of pathogen vacuoles. Our data suggest that the generalized lymphomyeloid collapse that occurs in Irgm1 −/− mice upon infection with a variety of pathogens may be due to lysosomal damage caused by off-target activation of GKS proteins on lysosomal membranes and consequent failure of autophagosomal processing.
Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal
Fritzemeier C.J., Hartleb D., Szappanos B., Papp B., Lercher M.J., 18. Apr. 2017, PLOS Computational Biology 13: e1005494, https://doi.org/10.1371/journal.pcbi.1005494
Energy metabolism is central to cellular biology. Thus, genome-scale models of heterotrophic unicellular species must account appropriately for the utilization of external nutrients to synthesize energy metabolites such as ATP. However, metabolic models designed for flux-balance analysis (FBA) may contain thermodynamically impossible energy-generating cycles: without nutrient consumption, these models are still capable of charging energy metabolites (such as ADP→ATP or NADP+→NADPH). Here, we show that energy-generating cycles occur in over 85% of metabolic models without extensive manual curation, such as those contained in the ModelSEED and MetaNetX databases; in contrast, such cycles are rare in the manually curated models of the BiGG database. Energy generating cycles may represent model errors, e.g., erroneous assumptions on reaction reversibilities. Alternatively, part of the cycle may be thermodynamically feasible in one environment, while the remainder is thermodynamically feasible in another environment; as standard FBA does not account for thermodynamics, combining these into an FBA model allows erroneous energy generation. The presence of energy-generating cycles typically inflates maximal biomass production rates by 25%, and may lead to biases in evolutionary simulations. We present efficient computational methods (i) to identify energy generating cycles, using FBA, and (ii) to identify minimal sets of model changes that eliminate them, using a variant of the GlobalFit algorithm.
Stem cell regulation by Arabidopsis WOX genes
Alicja Dolzblasz, Judith Nardmann, Elena Clerici, Barry Causier, Eric van der Graaff, Jinhui Chen, Brendan Davies, Wolfgang Werr, Thomas Laux, Molecular Plant (2016) DOI: http://dx.doi.org/10.1016/j.molp.2016.04.007
Gene amplification followed by functional diversification is a major force in evolution. A typical example of this is seen in the WUSCHEL-RELATED HOMEOBOX (WOX) gene family, named after the Arabidopsis stem cell regulator WUSCHEL. Here we analyze functional divergence in the WOX gene family. Members of the WUS clade, except the cambium stem cell regulator WOX4, can substitute for WUS function in shoot and floral stem cell maintenance to different degrees. Stem cell function of WUS requires a canonical WUS-box, necessary for interaction with TPL/TPR corepressors, whereas the repressive EAR domain is dispensable and the acidic domain seems only to be required for female fertility. In contrast to the WUS clade, members of the ancient WOX13 and the WOX9 clades cannot support stem cell maintenance. Although the homeodomains are interchangeable between WUS and WOX9 clade members, a WUS-compatible homeodomain together with canonical WUS-box is not sufficient for stem cell maintenance. Our results suggest that WOX function in shoot and floral meristems of Arabidopsis is restricted to the modern WUS clade, suggesting that stem cell control is a derived function. Yet undiscovered functional domains in addition to the homeodomain and the WUS-box are necessary for this function.
Arabidopsis thaliana DM2h (R8) within the Landsberg RPP1-like Resistance Locus Underlies Three Different Cases of EDS1-Conditioned Autoimmunity
Johannes Stuttmann , Nora Peine , Ana V. Garcia, Christine Wagner, Sayan R. Choudhury, Yiming Wang, Geo Velikkakam James, Thomas Griebel, Ruben Alcázar, Kenichi Tsuda, Korbinian Schneeberger, Jane E. Parker, PLoS Genet 12(4): e1005990. doi: 10.1371/journal.pgen.1005990
Plants have a large panel of nucleotide-binding/leucine rich repeat (NLR) immune receptors which monitor host interference by diverse pathogen molecules (effectors) and trigger disease resistance pathways. NLR receptor systems are necessarily under tight control to mitigate the trade-off between induced defenses and growth. Hence, mis-regulated NLRs often cause autoimmunity associated with stunting and, in severe cases, necrosis. Nucleocytoplasmic ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) is indispensable for effector-triggered and autoimmune responses governed by a family of Toll-Interleukin1-Receptor-related NLR receptors (TNLs). EDS1 operates coincidently or immediately downstream of TNL activation to transcriptionally reprogram cells for defense. We show here that low levels of nuclear-enforced EDS1 are sufficient for pathogen resistance in Arabidopsis thaliana, without causing negative effects. Plants expressing higher nuclear EDS1 amounts have the genetic, phenotypic and transcriptional hallmarks of TNL autoimmunity. In a screen for genetic suppressors of nuclear EDS1 autoimmunity, we map multiple, independent mutations to one gene, DM2h, lying within the polymorphic DANGEROUS MIX2 cluster of TNL RPP1-like genes from A. thaliana accession Landsberg erecta (Ler). The DM2 locus is a known hotspot for deleterious epistatic interactions leading to immune-related incompatibilities between A. thaliana natural accessions. We find that DM2hLer underlies two further genetic incompatibilities involving the RPP1-likeLer locus and EDS1. We conclude that the DM2hLer TNL protein and nuclear EDS1 cooperate, directly or indirectly, to drive cells into an immune response at the expense of growth. A further conclusion is that regulating the available EDS1 nuclear pool is fundamental for maintaining homeostatic control of TNL immune pathways.
Unique features of the bed bug, a global human ectoparasite, identified through genome sequencing
Benoit JB, Adelman ZN, Reinhardt K, Dolan A, Poelchau M, Jennings EC, Szuter EM, Hagan RW, Gujar H, Shukla JN, Zhu F, Mohan M, Nelson DR, Rosendale AJ, Derst C, Resnik V, Wernig S, Menegazzi P, Wegener C, Peschel N, Hendershot JM, Blenau W, Predel R, Johnston PR, Ioannidis P, Waterhouse RM, Nauen R, Schorn C, Ott MC, Maiwald F, Johnston JS, Gondhalekar AD, Scharf ME, Peterson BF, Raje KR, Hottel BA, Armisén D, Crumière AJ, Refki PN, Santos ME, Sghaier E, Viala S, Khila A, Ahn SJ, Childers C, Lee CY, Lin H, Hughes DS, Duncan EJ, Murali SC, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Wheeler D, Panfilio KA, Vargas Jentzsch IM, Vargo EL, Booth W, Friedrich M, Weirauch MT, Anderson MA, Jones JW, Mittapalli O, Zhao C, Zhou JJ, Evans JD, Attardo GM, Robertson HM, Zdobnov EM, Ribeiro JM, Gibbs RA, Werren JH, Palli SR, Schal C, Richards S, Nat. Commun. (2016), doi: 10.1038/ncomms10165
The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host-symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human-bed bug and symbiont-bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.
Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers
Pang T.Y., Lercher M.J., 9. Jan. 2017, Scientific Reports 7:40294, DOI: 10.1038/srep40294
Adaptation of bacteria occurs predominantly via horizontal gene transfer (HGT). While it is widely recognized that horizontal acquisitions frequently encompass multiple genes, it is unclear what the size distribution of successfully transferred DNA segments looks like and what evolutionary forces shape this distribution. Here, we identified 1790 gene family pairs that were consistently co-gained on the same branches across a phylogeny of 53 E. coli strains. We estimated a lower limit of their genomic distances at the time they were transferred to their host genomes; this distribution shows a sharp upper bound at 30 kb. The same gene-pairs can have larger distances (up to 70 kb) in other genomes. These more distant pairs likely represent recent acquisitions via transduction that involve the co-transfer of excised prophage genes, as they are almost always associated with intervening phage-associated genes. The observed distribution of genomic distances of co-transferred genes is much broader than expected from a model based on the co-transfer of genes within operons; instead, this distribution is highly consistent with the size distribution of supra-operonic clusters (SOCs), groups of co-occurring and co-functioning genes that extend beyond operons. Thus, we propose that SOCs form a basic unit of horizontal gene transfer.
Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN
Zacher B., Michel M., Schwalb B., Cramer P., Tresch A., Gagneur J., 5. Jan. 2017, PLoS One 12(1), doi: 10.1371/journal.pone.0169249
Accurate maps of promoters and enhancers are required for understanding transcriptional regulation. Promoters and enhancers are usually mapped by integration of chromatin assays charting histone modifications, DNA accessibility, and transcription factor binding. However, current algorithms are limited by unrealistic data distribution assumptions. Here we propose GenoSTAN (Genomic STate ANnotation), a hidden Markov model overcoming these limitations. We map promoters and enhancers for 127 cell types and tissues from the ENCODE and Roadmap Epigenomics projects, today’s largest compendium of chromatin assays. Extensive benchmarks demonstrate that GenoSTAN generally identifies promoters and enhancers with significantly higher accuracy than previous methods. Moreover, GenoSTAN-derived promoters and enhancers showed significantly higher enrichment of complex trait-associated genetic variants than current annotations. Altogether, GenoSTAN provides an easy-to-use tool to define promoters and enhancers in any system, and our annotation of human transcriptional cis-regulatory elements constitutes a rich resource for future research in biology and medicine.
2015
Interspecies Gene Transfer as a Method for Understanding the Genetic Basis for Evolutionary Change: Progress, Pitfalls, and Prospects
Nikolov LA, Tsiantis M.
Front Plant Sci. 2015 Dec 22;6:1135. doi: 10.3389/fpls.2015.01135. eCollection 2015
The recent revolution in high throughput sequencing and associated applications provides excellent opportunities to catalog variation in DNA sequences and gene expression between species. However, understanding the astonishing diversity of the Tree of Life requires understanding the phenotypic consequences of such variation and identification of those rare genetic changes that are causal to diversity. One way to study the genetic basis for trait diversity is to apply a transgenic approach and introduce genes of interest from a donor into a recipient species. Such interspecies gene transfer (IGT) is based on the premise that if a gene is causal to the morphological divergence of the two species, the transfer will endow the recipient with properties of the donor. Extensions of this approach further allow identifying novel loci for the diversification of form and investigating cis- and trans-contributions to morphological evolution. Here we review recent examples from both plant and animal systems that have employed IGT to provide insight into the genetic basis of evolutionary change. We outline the practice of IGT, its methodological strengths and weaknesses, and consider guidelines for its application, emphasizing the importance of phylogenetic distance, character polarity, and life history. We also discuss future perspectives for exploiting IGT in the context of expanding genomic resources in emerging experimental systems and advances in genome editing.
Horizontally transferred genes cluster spatially and metabolically
Dilthey A., Lercher M.J., 21. Dec. 2015, Biology Direct 10:72, https://doi.org/10.1186/s13062-015-0102-5
Background
Genomic uptake of DNA by prokaryotes often encompasses more than a single gene. In many cases, several horizontally transferred genes may be acquired together. Accordingly, we expect that horizontally transferred genes cluster spatially in the genome more often than expected if transfers were independent. Further, genes that depend on each other functionally may be unlikely to have beneficial fitness effects when taken up individually by a foreign genome. Hence, we also expect the co-acquisition of functionally related genes, resulting in the clustering of horizontally transferred genes in functional networks.
Results
Analysing spatial and metabolic clustering of recent horizontal (or lateral) gene transfers among 21 γ-proteobacteria, we confirm both predictions. When comparing two datasets of predicted transfers that differ in their expected false-positive rate, we find that the more stringent dataset shows a stronger enrichment of clustered pairs.
Conclusions
The enrichment of interdependent metabolic genes among predicted transfers supports a biologically significant role of horizontally transferred genes in metabolic adaptation. Our results further suggest that spatial and metabolic clustering may be used as a benchmark for methods that predict recent horizontal gene transfers.
Reviewers
This article was reviewed by Peter Gogarten in collaboration with Luiz Thiberio Rangel, and by Yuri Wolf.
The African Turquoise Killifish Genome Provides Insights into Evolution and Genetic Architecture of Lifespan
Dario Riccardo Valenzano, Bérénice A. Benayoun, Param Priya Singh, Elisa Zhang, Paul D. Etter, Chi-Kuo Hu, Mathieu Clément-Ziza, David Willemsen, Rongfeng Cui, Itamar Harel, Ben E. Machado, Muh-Ching Yee9, Sabrina C. Sharp, Carlos D. Bustamante, Andreas Beyer, Eric A. Johnson, Anne Brunet, Cell 2015, DOI: http://dx.doi.org/10.1016/j.cell.2015.11.008
Lifespan is a remarkably diverse trait ranging from a few days to several hundred years in nature, but the mechanisms underlying the evolution of lifespan differences remain elusive. Here we de novo assemble a reference genome for the naturally short-lived African turquoise killifish, providing a unique resource for comparative and experimental genomics. The identification of genes under positive selection in this fish reveals potential candidates to explain its compressed lifespan. Several aging genes are under positive selection in this short-lived fish and long-lived species, raising the intriguing possibility that the same gene could underlie evolution of both compressed and extended lifespans. Comparative genomics and linkage analysis identify candidate genes associated with lifespan differences between various turquoise killifish strains. Remarkably, these genes are clustered on the sex chromosome, suggesting that short lifespan might have co-evolved with sex determination. Our study provides insights into the evolutionary forces that shape lifespan in nature.
Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model
Julia Glas, Sebastian Dümcke, Benedikt Zacher, Don Poron3, Julien Gagneur and Achim Tresch, Nucl. Acids Res. (2015) doi: 10.1093/nar/gkv1184
Hidden Markov models (HMMs) have been extensively used to dissect the genome into functionally distinct regions using data such as RNA expression or DNA binding measurements. It is a challenge to disentangle processes occurring on complementary strands of the same genomic region. We present the double-stranded HMM (dsHMM), a model for the strand-specific analysis of genomic processes. We applied dsHMM to yeast using strand specific transcription data, nucleosome data, and protein binding data for a set of 11 factors associated with the regulation of transcription.The resulting annotation recovers the mRNA transcription cycle (initiation, elongation, termination) while correctly predicting strand-specificity and directionality of the transcription process. We find that pre-initiation complex formation is an essentially undirected process, giving rise to a large number of bidirectional promoters and to pervasive antisense transcription. Notably, 12% of all transcriptionally active positions showed simultaneous activity on both strands. Furthermore, dsHMM reveals that antisense transcription is specifically suppressed by Nrd1, a yeast termination factor.
Alternate wiring of a KNOXI genetic network underlies differences in leaf development of A. thaliana and C. hirsuta
Rast-Somssich MI, Broholm S, Jenkins H, Canales C, Vlad D, Kwantes M, Bilsborough G, Dello Ioio R, Ewing RM, Laufs P, Huijser P, Ohno C, Heisler MG, Hay A, Tsiantis M.
Genes Dev. 2015 Nov 15;29(22):2391-404. doi: 10.1101/gad.269050.115. Erratum in: Genes Dev. 2016 Jan 1;30(1):132
Two interrelated problems in biology are understanding the regulatory logic and predictability of morphological evolution. Here, we studied these problems by comparing Arabidopsis thaliana, which has simple leaves, and its relative, Cardamine hirsuta, which has dissected leaves comprising leaflets. By transferring genes between the two species, we provide evidence for an inverse relationship between the pleiotropy of SHOOTMERISTEMLESS (STM) and BREVIPEDICELLUS (BP) homeobox genes and their ability to modify leaf form. We further show that cis-regulatory divergence of BP results in two alternative configurations of the genetic networks controlling leaf development. In C. hirsuta, ChBP is repressed by the microRNA164A (MIR164A)/ChCUP-SHAPED COTYLEDON (ChCUC) module and ChASYMMETRIC LEAVES1 (ChAS1), thus creating cross-talk between MIR164A/CUC and AS1 that does not occur in A. thaliana. These different genetic architectures lead to divergent interactions of network components and growth regulation in each species. We suggest that certain regulatory genes with low pleiotropy are predisposed to readily integrate into or disengage from conserved genetic networks influencing organ geometry, thus rapidly altering their properties and contributing to morphological divergence.
Testing and Validation of Computational Methods for Mass Spectrometry
Gatto L., Hansen K.D., Hoopman M.R., Hermjakob H., Kohlbacher O., Beyer A., 9. Oct. 2015, J Prot. Res. DOI: 10.1021/acs.jproteome.5b00852.
High-throughput methods based on mass spectrometry (proteomics, metabolomics, lipidomics, etc.) produce a wealth of data that cannot be analyzed without computational methods. The impact of the choice of method on the overall result of a biological study is often underappreciated, but different methods can result in very different biological findings. It is thus essential to evaluate and compare the correctness and relative performance of computational methods. The volume of the data as well as the complexity of the algorithms render unbiased comparisons challenging. This paper discusses some problems and challenges in testing and validation of computational methods. We discuss the different types of data (simulated and experimental validation data) as well as different metrics to compare methods. We also introduce a new public repository for mass spectrometric reference data sets (http://compms.org/RefData) that contains a collection of publicly available data sets for performance evaluation for a wide range of different methods.
CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions
Amer Desouki A., Jarre F., Gelius-Dietrich G., Lercher M.J., 1. July 2015, Bioinformatics 31:2159-65, https://doi.org/10.1093/bioinformatics/btv096
Motivation: Constraint-based metabolic modeling methods such as Flux Balance Analysis (FBA) are routinely used to predict metabolic phenotypes, e.g. growth rates, ATP yield or the fitness of gene knockouts. One frequent difficulty of constraint-based solutions is the inclusion of thermodynamically infeasible loops (or internal cycles), which add nonbiological fluxes to the predictions.Results: We propose a simple postprocessing of constraint-based solutions, which removes internal cycles from any given flux distribution v(0) without disturbing other fluxes not involved in the loops. This new algorithm, termed CycleFreeFlux, works by minimizing the sum of absolute fluxes ||v||1 while (i) conserving the exchange fluxes and (ii) using the fluxes of the original solution to bound the new flux distribution. This strategy reduces internal fluxes until at least one reaction of every possible internal cycle is inactive, a necessary and sufficient condition for the thermodynamic feasibility of a flux distribution. If alternative representations of the input flux distribution in terms of elementary flux modes exist that differ in their inclusion of internal cycles, then CycleFreeFlux is biased towards solutions that maintain the direction given by v(0) and towards solutions with lower total flux ||v||1. Our method requires only one additional linear optimization, making it computationally very efficient compared to alternative strategies.Availability and implementation: We provide freely available R implementations for the enumeration of thermodynamically infeasible cycles as well as for cycle-free FBA solutions, flux variability calculations and random sampling of solution spaces.
The significance and scope of evolutionary developmental biology: a vision for the 21st century.
Moczek AP, Sears KE, Stollewerk A, Wittkopp PJ, Diggle P, Dworkin I, Ledon-Rettig C, Matus DQ,
Roth S, Abouheif E, Brown FD, Chiu CH, Cohen CS, Tomaso AW, Gilbert SF, Hall B, Love AC, Lyons
DC, Sanger TJ, Smith J, Specht C, Vallejo-Marin M, Extavour CG.
Evol Dev. 2015 May-Jun;17(3):198-219. doi: 10.1111/ede.12125.
Evolutionary developmental biology (evo-devo) has undergone dramatic transformations since
its emergence as a distinct discipline. This paper aims to highlight the scope, power, and
future promise of evo-devo to transform and unify diverse aspects of biology. We articulate
key questions at the core of eleven biological disciplines—from Evolution, Development,
Paleontology, and Neurobiology to Cellular and Molecular Biology, Quantitative Genetics,
Human Diseases, Ecology, Agriculture and Science Education, and lastly, Evolutionary
Developmental Biology itself—and discuss why evo-devo is uniquely situated to substantially
improve our ability to find meaningful answers to these fundamental questions. We posit that
the tools, concepts, and ways of thinking developed by evo-devo have profound potential to
advance, integrate, and unify biological sciences as well as inform policy decisions and
illuminate science education. We look to the next generation of evolutionary developmental
biologists to help shape this process as we confront the scientific challenges of the 21st
century.
Differential interaction forces govern bacterial sorting in early biofilms
Enno R Oldewurtel, Nadzeya Kouzel, Lena Dewenter, Katja Henseler, Berenike Maier, eLife
2015;4:e10811
Bacterial biofilms can generate micro-heterogeneity in terms of surface structures. However,
little is known about the associated changes in the physics of cell–cell interaction and its
impact on the architecture of biofilms. In this study, we used the type IV pilus of
Neisseria gonorrhoeae to test whether variation of surface structures induces cell-sorting.
We show that the rupture forces between pili are fine-tuned by post-translational
modification. Bacterial sorting was dependent on pilus post-translational modification and
pilus density. Active force generation was necessary for defined morphologies of mixed
microcolonies. The observed morphotypes were in remarkable agreement with the differential
strength of adhesion hypothesis proposing that a tug-of-war among surface structures of
different cells governs cell sorting. We conclude that in early biofilms the density and
rupture force of bacterial surface structures can trigger cell sorting based on similar
physical principles as in developing embryos.
The Toxoplasma gondii rhoptry protein ROP18 is an Irga6-specific
kinase and regulated by the dense granule protein GRA7.
Hermanns T., Müller UB., Könen-Waisman S., Howard JC., Steinfeldt
T. , Cell Microbiol. 2015 Aug 6. doi: 10.1111/cmi.12499 (2015)
In mice, avirulent strains (e.g. types II
and III) of the protozoan parasite Toxoplasma gondii are restricted by the immunity-related
GTPase (IRG) resistance system. Loading of IRG proteins onto the PVM is required for vacuolar
rupture resulting in parasite clearance. In virulent strain (e.g. type I) infections polymorphic
effector proteins ROP5 and ROP18 cooperate to phosphorylate and thereby inactivate mouse IRG
proteins to preserve PVM integrity. In this study we confirmed the dense granule protein GRA7 as
an additional component of the ROP5/ROP18 kinase complex and identified GRA7 association with
the PVM by direct binding to ROP5. The absence of GRA7 results in reduced phosphorylation of
Irga6 correlated with increased vacuolar IRG protein amounts and attenuated virulence. Earlier
work identified additional IRG proteins as targets of T. gondii ROP18 kinase. We show that the
only specific target of ROP18 among IRG proteins is in fact Irga6. Similarily, we demonstrate
that GRA7 is strictly an Irga6-specific virulence effector. This identifies T. gondii GRA7 as a
regulator for ROP18-specific inactivation of Irga6. The structural diversity of the IRG proteins
implies that certain family members constitute additional specific targets for other yet unknown
T. gondii virulence effectors.
Structure and evolutionary history of a large family of NLR proteins in the zebrafish
Kerstin Howe, Philipp H Schiffer, Julia Zielinski, Thomas Wiehe, Gavin K Laird, John Marioni, Onuralp Soylemez, Fyodor Kondrashov, Maria Leptin, Open Biology (2015) doi: http://dx.doi.org/10.1101/022061
NACHT- and Leucine-Rich-Repeat-containing domain (NLR) proteins act as cytoplasmic sensors for pathogen- and danger-associated molecular patterns and are found throughout the plant and animal kingdoms. In addition to having a small set of conserved NLRs, the genomes in some animal lineages contain massive expansions of this gene family. One of these arose in fishes, after the creation of a gene fusion that combined the core NLR domains with another domain used for immune recognition, the PRY/SPRY or B30.2 domain. We have analysed the expanded NLR gene family in zebrafish, which contains 368 genes, and studied its evolutionary history. The encoded proteins share a defining overall structure, but individual domains show different evolutionary trajectories. Our results suggest gene conversion homogenizes NACHT and B30.2 domain sequences among different gene subfamilies, however, the functional implications of its action remains unclear. The majority of the genes are located on the long arm of chromosome 4, interspersed with several other large multi-gene families, including a new family encoding proteins with multiple tandem arrays of Zinc fingers. This suggests that chromosome 4 may be a hotspot for rapid evolutionary change in zebrafish.
Multiple-Line Inference of Selection on Quantitative Traits
N. Riedel, B. S. Khatri, M. Lässig, and J. Berg; Genetics
September 2015 201:305-322; Early online July 2, 2015
Evolution of coexistence in a crowded microplate well
De Visser JAGM, Proceedings of the National Academy of Sciences USA, 112, 11148-11149 (2015)
Understanding what causes the emergence and maintenance of biological diversity has been a
central aim in biology ever since the dawn of the discipline. The realization that diversity
in microbial communities, such as those living in our guts and on our bodies, may affect our
health and that of the agricultural systems on which we depend has generated substantial
recent efforts to describe the extraordinary diversity of microbial communities. However,
efforts to understand the ecological and evolutionary mechanisms responsible for generating
and maintaining all this diversity have severely lagged behind those to describe it. This is
unfortunate and unnecessary. Microbes offer a great opportunity to rigorously test
hypotheses about these mechanisms in real time in controlled experiments in the laboratory.
As Frenkel et al. (1) show in PNAS, such experiments may also reveal novel mechanisms of
diversification and coexistence—in their case one where the avoidance of crowding plays a
key role.
The origin and maintenance of biological diversity requires natural selection operating in
heterogeneous environments (2, 3). In homogeneous environments with a single limiting
resource equally accessible to all individuals, natural selection will remove all but the
most superior competitor (4). However, in environments with temporal or spatial variation in
the type or amount of limiting resource, fitness trade-offs between adaptations to different
niches may lead to the stable maintenance of different genotypes through negative
frequency-dependent selection (5).
An important lesson from laboratory evolution studies with microbes is that virtually all
environments, even those designed to be homogeneous, such as chemostats, are heterogeneous
at the scale relevant for microbes. For instance, temporal variation in resource
availability occurs in serial transfer experiments in batch cultures with the opportunity
for specialist adaptation (6), potential resources inaccessible at the start of the
experiment may become available after evolutionary changes in the …
Dynamics of adaptation in experimental yeast populations exposed to gradual and abrupt change in
heavy metal concentration
Gorter FA, Aarts MMG, Zwaan BJ, de Visser JAGM, The American Naturalist, in press (2015)
Phase transition in random adaptive walks on correlated fitness landscapes
Su-Chan Park, Ivan G. Szendro, Johannes Neidhart and Joachim Krug, Physical Revivew E 91, 042707
(2015)
We study biological evolution on a random fitness landscape where correlations are
introduced through a linear fitness gradient of strength c. When selection is strong and
mutations rare the dynamics is a directed uphill walk that terminates at a local fitness
maximum. We analytically calculate the dependence of the walk length on the genome size L.
When the distribution of the random fitness component has an exponential tail, we find a
phase transition of the walk length D between a phase at small c, where walks are short
(D∼lnL), and a phase at large c, where walks are long (D∼L). For all other distributions
only a single phase exists for any c>0. The considered process is equivalent to a zero
temperature Metropolis dynamics for the random energy model in an external magnetic field,
thus also providing insight into the aging dynamics of spin glasses.
A random forest approach to capture genetic effects in the presence of population structure
Stephan J., Stegle O. and Beyer A., 25. June 2015, Nat. Commun. 6, 7432, DOI: 10.1038/ncomms8432
The accurate mapping of causal variants in genome-wide association studies requires the consideration of both, confounding factors (for example, population structure) and nonlinear interactions between individual genetic variants. Here, we propose a method termed ‘mixed random forest’ that simultaneously accounts for population structure and captures nonlinear genetic effects. We test the model in simulation experiments and show that the mixed random forest approach improves detection power compared with established approaches. In an application to data from an outbred mouse population, we find that mixed random forest identifies associations that are more consistent with prior knowledge than competing methods. Further, our approach allows predicting phenotypes from genotypes with greater accuracy than any of the other methods that we tested. Our results show that approaches that simultaneously account for both, confounding due to population structure and epistatic interactions, are important to fully explain the heritable component of complex quantitative traits.
Analysis of adaptive walks on NK fitness landscapes with different interaction schemes
Stefan Nowak and Joachim Krug, J. Stat. Mech. (2015) P06014
Fitness landscapes are genotype to fitness mappings commonly used in evolutionary biology
and computer science which are closely related to spin glass models. In this paper, we study
the NK model for fitness landscapes where the interaction scheme between genes can be
explicitly defined. The focus is on how this scheme influences the overall shape of the
landscape. Our main tool for the analysis are adaptive walks, an idealized dynamics by which
the population moves uphill in fitness and terminates at a local fitness maximum. We use
three different types of walks and investigate how their length (the number of steps
required to reach a local peak) and height (the fitness at the endpoint of the walk) depend
on the dimensionality and structure of the landscape. We find that the distribution of local
maxima over the landscape is particularly sensitive to the choice of interaction pattern.
Most quantities that we measure are simply correlated to the rank of the scheme, which is
equal to the number of nonzero coefficients in the expansion of the fitness landscape in
terms of Walsh functions.
Negative Epistasis and Evolvability in TEM-1 β-Lactamase—The Thin Line between an Enzyme's
Conformational Freedom and Disorder
Dellus-Gur E, Elias M, Caselli E, Prati F, Salverda MLM, de Visser JAGM, Fraser JS, Tawfik DS,
Journal of Molecular Biology, in press (2015)
Epistasis is a key factor in evolution since it determines which combinations of mutations
provide adaptive solutions and which mutational pathways toward these solutions are
accessible by natural selection. There is growing evidence for the pervasiveness of sign
epistasis—a complete reversion of mutational effects, particularly in protein evolution—yet
its molecular basis remains poorly understood. We describe the structural basis of sign
epistasis between G238S and R164S, two adaptive mutations in TEM-1 β-lactamase— an enzyme
that endows antibiotics resistance. Separated by 10 Å, these mutations initiate two separate
trajectories toward increased hydrolysis rates and resistance toward second and
third-generation cephalosporins antibiotics. Both mutations allow the enzyme's active site
to adopt alternative conformations and accommodate the new antibiotics. By solving the
corresponding set of crystal structures, we found that R164S causes local disorder whereas
G238S induces discrete conformations. When combined, the mutations in 238 and 164 induce
local disorder whereby nonproductive conformations that perturb the enzyme's catalytic
preorganization dominate. Specifically, Asn170 that coordinates the deacylating water
molecule is misaligned, in both the free form and the inhibitor-bound double mutant. This
local disorder is not restored by stabilizing global suppressor mutations and thus leads to
an evolutionary cul-de-sac. Conformational dynamism therefore underlines the reshaping
potential of protein's structures and functions but also limits protein evolvability because
of the fragility of the interactions networks that maintain protein structures.
From limbs to leaves: common themes in evolutionary diversification of organ form
Remco A. Mentink and Miltos Tsiantis, Front Genet. 2015; 6: 284
An open problem in
biology is to derive general principles that capture how morphogenesis evolved to generate
diverse forms in different organisms. Here we discuss recent work investigating the
morphogenetic basis for digit loss in vertebrate limbs and variation in form of marginal
outgrowths of angiosperm (flowering plant) leaves. Two pathways underlie digit loss in
vertebrate limbs. First, alterations to digit patterning arise through modification of
expression of the Patched 1 receptor, which senses the Sonic Hedgehog morphogen and limits its
mobility in the limb bud. Second, evolutionary changes to the degree of programmed cell death
between digits influence their development after their initiation. Similarly, evolutionary
modification of leaf margin outgrowths occurs via two broad pathways. First, species-specific
transcription factor expression modulates outgrowth patterning dependent on regulated transport
of the hormone auxin. Second, species-specific expression of the newly discovered REDUCED
COMPLEXITY homeodomain transcription factor influences growth between individual outgrowths
after their initiation. These findings demonstrate that in both plants and animals tinkering
with either patterning or post-patterning processes can cause morphological change. They also
highlight the considerable flexibility of morphological evolution and indicate that it may be
possible to derive broad principles that capture how morphogenesis evolved across complex
eukaryotes.
Keywords: evolution and development, leaflet formation, digit formation, patterning versus
post-patterning, morphological diversity
The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology
Schmitt-Engel, C., Schultheis, D., Schwirz, J., Ströhlein, N., Troelenberg, N., Majumdar, U.,
Dao, Van Anh, Grossmann, D., Richter, T., Tech, M., Dönitz, J., Gerischer, L., Theis, M.,
Schild, I., Trauner, J., Koniszewski, N.D.B., Küster, E., Kittelmann, S., Hu, Y., Lehmann, S.,
Siemanowski, J., Ulrich, J., Panfilio, K.A., Schröder, R., Morgenstern, B., Stanke, M.,
Buchhholz, F., Frasch, M., Roth, S., Wimmer, Ernst A., Schoppmeier, M., Klingler, M., and
Bucher, G. 2015 - Nat. Commun. 6: 7822
Genetic screens are powerful tools to identify the genes required for a given biological
process. However, for technical reasons, comprehensive screens have been restricted to very few
model organisms. Therefore, although deep sequencing is revealing the genes of ever more insect
species, the functional studies predominantly focus on candidate genes previously identified in
Drosophila, which is biasing research towards conserved gene functions. RNAi screens in other
organisms promise to reduce this bias. Here we present the results of the iBeetle screen, a
large-scale, unbiased RNAi screen in the red flour beetle, Tribolium castaneum, which identifies
gene functions in embryonic and postembryonic development, physiology and cell biology. The
utility of Tribolium as a screening platform is demonstrated by the identification of genes
involved in insect epithelial adhesion. This work transcends the restrictions of the candidate
gene approach and opens fields of research not accessible in Drosophila.
Natural genetic variation impacts expression levels of coding, non-coding, and antisense
transcripts in fission yeast.
Clément-Ziza M., Marsellach FX., Codlin S., Papadakis MA., Reinhardt S., Rodríguez-López M.,
Martin S., Marguerat S., Schmidt A., Lee E., Workman CT., Bähler J., Beyer A., Mol Syst Biol.
2014 Nov 28;10:764. doi: 10.15252/msb.20145123.
Our current understanding of how natural genetic variation affects gene expression beyond
well-annotated coding genes is still limited. The use of deep sequencing technologies for
the study of expression quantitative trait loci (eQTLs) has the potential to close this gap.
Here, we generated the first recombinant strain library for fission yeast and conducted an
RNA-seq-based QTL study of the coding, non-coding, and antisense transcriptomes. We show
that the frequency of distal effects (trans-eQTLs) greatly exceeds the number of local
effects (cis-eQTLs) and that non-coding RNAs are as likely to be affected by eQTLs as
protein-coding RNAs. We identified a genetic variation of swc5 that modifies the levels of
871 RNAs, with effects on both sense and antisense transcription, and show that this effect
most likely goes through a compromised deposition of the histone variant H2A.Z. The strains,
methods, and datasets generated here provide a rich resource for future studies.
Evolution of epithelial morphogenesis: phenotypic integration across multiple levels of
biological
organization
Horn, T., Hilbrant, M., and Panfilio, K.A., 2015 Front. Genet. 6: 303
Morphogenesis involves the dynamic reorganization of cell and tissue shapes to create the
three-dimensional body. Intriguingly, different species have evolved different morphogenetic
processes to achieve the same general outcomes during embryonic development. How are meaningful
comparisons between species made, and where do the differences lie? In this Perspective, we
argue
that examining the evolution of embryonic morphogenesis requires the simultaneous consideration
of
different levels of biological organization: (1) genes, (2) cells, (3) tissues, and (4) the
entire
egg, or other gestational context. To illustrate the importance of integrating these levels, we
use
the extraembryonic epithelia of insects—a lineage-specific innovation and evolutionary
hotspot—as an
exemplary case study. We discuss how recent functional data, primarily from RNAi experiments
targeting the Hox3/Zen and U-shaped group transcription factors, provide insights into
developmental
processes at all four levels. Comparisons of these data from several species both challenge and
inform our understanding of homology, in assessing how the process of epithelial morphogenesis
has
itself evolved.
Role of pleiotropy during adaptation of TEM-1 β-lactamase to two novel antibiotics.
Schenk MF, Witte S, Salverda MLM, Koopmanschap B, Krug J, de Visser JAGM, Evolutionary
Applications 8: 248-260 (2015)
Pleiotropy is a key feature of the genotype-phenotype map, and its form and extent have many
evolutionary implications, including for the dynamics of adaptation and the evolution of
specialization. Similarly, pleiotropic effects of antibiotic resistance mutations may affect
the evolution of antibiotic resistance in the simultaneous or fluctuating presence of
different antibiotics. Here, we study the role of pleiotropy during the in vitro adaptation
of the enzyme TEM-1 β-lactamase to two novel antibiotics, cefotaxime (CTX) and ceftazidime
(CAZ). We subject replicate lines for four rounds of evolution to selection with CTX and CAZ
alone, and in their combined and fluctuating presence. Evolved alleles show positive
correlated responses when selecting with single antibiotics. Nevertheless, pleiotropic
constraints are apparent from the effects of single mutations and from selected alleles
showing smaller correlated than direct responses and smaller responses after simultaneous
and fluctuating selection with both than with single antibiotics. We speculate that these
constraints result from structural changes in the oxyanion pocket surrounding the active
site, where accommodation of CTX and the larger CAZ is balanced against their positioning
with respect to the active site. Our findings suggest limited benefits from the combined or
fluctuating application of these related cephalosporins for containing antibiotic
resistance.
Gene transfer efficiency in gonococcal biofilms: role of biofilm age, and architecture, and
pilin antigenic variation
Kouzel, N., Oldewurtel, E.R., Maier, B., J. Bacteriol., JB.00171-15 in press (2015)
Evolution of CONSTANS Regulation and Function after Gene
Duplication produced a Photoperiodic Flowering Switch in the Brassicaceae
Simon S, Rühl M, de Montaigu A, Wötzel St, Coupland G, Molecular
Biology and Evolution, DOI: 10.1093/molbev/msv110 (2015)
Environmental control of flowering allows plant reproduction to occur under optimal
conditions and facilitates adaptation to different locations. At high latitude, flowering of
many plants is controlled by seasonal changes in day length. The photoperiodic flowering
pathway confers this response in the Brassicaceae, which colonized temperate latitudes after
divergence from the Cleomaceae, their subtropical sister family. The CONSTANS (CO)
transcription factor of Arabidopsis thaliana, a member of the Brassicaceae, is central to
the photoperiodic flowering response and shows characteristic patterns of transcription
required for day-length sensing. CO is believed to be widely conserved among flowering
plants, however we show that it arose after gene duplication at the root of the Brassicaceae
followed by divergence of transcriptional regulation and protein function. CO has two close
homologs, CONSTANS-LIKE1 (COL1) and COL2, which are related to CO by tandem duplication and
whole genome duplication, respectively. The single CO homolog present in the Cleomaceae
shows transcriptional and functional features similar to those of COL1 and COL2, suggesting
these were ancestral. We detect cis-regulatory and codon changes characteristic of CO and
use transgenic assays to demonstrate their significance in the day-length dependent
activation of the CO target gene FLOWERING LOCUS T. Thus, the function of CO as a potent
photoperiodic flowering switch evolved in the Brassicaceae after gene duplication. The
origin of CO may have contributed to the range expansion of the Brassicaceae and suggests
that in other families CO genes involved in photoperiodic flowering arose by convergent
evolution.
Dynamic BMP signaling polarized by Toll patterns the dorsoventral axis in a hemimetabolous
insect
Lena Sachs, Yen-Ta Chen, Axel Drechsler, Jeremy A Lynch, Kristen A Panfilio, Michael Lässig,
Johannes Berg, Siegfried Roth, DOI: http://dx.doi.org/10.7554/eLife.05502, Published May 12,
2015, Cite as eLife 2015;4:e05502
Toll-dependent patterning of the dorsoventral axis in Drosophila represents one of the best
understood gene regulatory networks. However, its evolutionary origin has remained elusive.
Outside the insects Toll is not known for a patterning function, but rather for a role in
pathogen defense. Here, we show that in the milkweed bug Oncopeltus fasciatus, whose lineage
split from Drosophila's more than 350 million years ago, Toll is only required to polarize a
dynamic BMP signaling network. A theoretical model reveals that this network has
self-regulatory properties and that shallow Toll signaling gradients are sufficient to
initiate axis formation. Such gradients can account for the experimentally observed twinning
of insect embryos upon egg fragmentation and might have evolved from a state of uniform Toll
activity associated with protecting insect eggs against pathogens.
2014
On the sub-permutations of pattern avoiding permutations
Disanto F, Wiehe T, Discrete mathematics, Volume 337, 28 December
2014, Pages 127–141 (2014)
There is a deep connection between
permutations and trees. Certain sub-structures of permutations, called sub-permutations,
bijectively map to sub-trees of binary increasing trees. This opens a powerful tool set to study
enumerative and probabilistic properties of sub-permutations and to investigate the
relationships between 'local' and 'global' features using the concept of pattern avoidance.
First, given a pattern {\mu}, we study how the avoidance of {\mu} in a permutation {\pi} affects
the presence of other patterns in the sub-permutations of {\pi}. More precisely, considering
patterns of length 3, we solve instances of the following problem: given a class of permutations
K and a pattern {\mu}, we ask for the number of permutations π∈Avn(μ) whose sub-permutations in
K satisfy certain additional constraints on their size. Second, we study the probability for a
generic pattern to be contained in a random permutation {\pi} of size n without being present in
the sub-permutations of {\pi} generated by the entry 1≤k≤n. These theoretical results can be
useful to define efficient randomized pattern-search procedures based on classical algorithms of
pattern-recognition, while the general problem of pattern-search is NP-complete.
Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol
II transcription cycle
Zacher B, Lidschreiber M, Cramer P, Gagneur J, Tresch A, DOI 10.15252/msb.20145654 | Published
online 19.12.2014 Molecular Systems Biology(2014)10:768
DNA replication, transcription and repair involve the recruitment of protein complexes that
change their composition as they progress along the genome in a directed or strand‐specific
manner. Chromatin immunoprecipitation in conjunction with hidden Markov models (HMMs) has
been instrumental in understanding these processes, as they segment the genome into discrete
states that can be related to DNA‐associated protein complexes. However, current HMM‐based
approaches are not able to assign forward or reverse direction to states or properly
integrate strand‐specific (e.g., RNA expression) with non‐strand‐specific (e.g., ChIP) data,
which is indispensable to accurately characterize directed processes. To overcome these
limitations, we introduce bidirectional HMMs which infer directed genomic states from
occupancy profiles de novo. Application to RNA polymerase II‐associated factors in yeast and
chromatin modifications in human T cells recovers the majority of transcribed loci, reveals
gene‐specific variations in the yeast transcription cycle and indicates the existence of
directed chromatin state patterns at transcribed, but not at repressed, regions in the human
genome. In yeast, we identify 32 new transcribed loci, a regulated initiation–elongation
transition, the absence of elongation factors Ctk1 and Paf1 from a class of genes, a
distinct transcription mechanism for highly expressed genes and novel DNA sequence motifs
associated with transcription termination. We anticipate bidirectional HMMs to significantly
improve the analyses of genome‐associated directed processes.
Adaptation in tunably rugged fitness landscapes: The Rough Mount Fuji Model
Johannes Neidhart, Ivan G. Szendro and Joachim Krug Genetics 198, 699-721 (2014)
Much of the current theory of adaptation is based on Gillespie’s mutational landscape model
(MLM), which assumes that the fitness values of genotypes linked by single mutational steps
are independent random variables. On the other hand, a growing body of empirical evidence
shows that real fitness landscapes, while possessing a considerable amount of ruggedness,
are smoother than predicted by the MLM. In the present article we propose and analyze a
simple fitness landscape model with tunable ruggedness based on the rough Mount Fuji (RMF)
model originally introduced by Aita et al. in the context of protein evolution. We provide a
comprehensive collection of results pertaining to the topographical structure of RMF
landscapes, including explicit formulas for the expected number of local fitness maxima, the
location of the global peak, and the fitness correlation function. The statistics of single
and multiple adaptive steps on the RMF landscape are explored mainly through simulations,
and the results are compared to the known behavior in the MLM model. Finally, we show that
the RMF model can explain the large number of second-step mutations observed on a highly fit
first-step background in a recent evolution experiment with a microvirid bacteriophage.
Empirical fitness landscapes and the predictability of evolution
J. Arjan G.M. de Visser and Joachim Krug, Nature Reviews Genetics 15, 480-490 (2014)
The genotype–fitness map (that is, the fitness landscape) is a key determinant of evolution,
yet it has mostly been used as a superficial metaphor because we know little about its
structure. This is now changing, as real fitness landscapes are being analysed by
constructing genotypes with all possible combinations of small sets of mutations observed in
phylogenies or in evolution experiments. In turn, these first glimpses of empirical fitness
landscapes inspire theoretical analyses of the predictability of evolution. Here, we review
these recent empirical and theoretical developments, identify methodological issues and
organizing principles, and discuss possibilities to develop more realistic fitness landscape
models.
Analysis of a Plant Complex Resistance Gene Locus Underlying Immune-Related Hybrid
Incompatibility and Its Occurrence in Nature
Alcázar R, von Reth M, Bauto J, Chae E, Weigel D, Koornneef M, Parker JE, PLOS Published:
December 11, 2014, DOI: 10.1371/journal.pgen.1004848
Mechanisms underlying speciation in plants include detrimental (incompatible) genetic
interactions between parental alleles that incur a fitness cost in hybrids. We reported on
recessive hybrid incompatibility between an Arabidopsis thaliana strain from Poland, Landsberg
erecta (Ler), and many Central Asian A. thaliana strains. The incompatible interaction is
determined by a polymorphic cluster of Toll/interleukin-1 receptor-nucleotide binding-leucine
rich repeat (TNL) RPP1 (Recognition of Peronospora parasitica1)-like genes in Ler and alleles of
the receptor-like kinase Strubbelig Receptor Family 3 (SRF3) in Central Asian strains Kas-2 or
Kond, causing temperature-dependent autoimmunity and loss of growth and reproductive fitness.
Here, we genetically dissected the RPP1-like Ler locus to determine contributions of individual
RPP1-like Ler (R1–R8) genes to the incompatibility. In a neutral background, expression of most
RPP1-like Ler genes, except R3, has no effect on growth or pathogen resistance. Incompatibility
involves increased R3 expression and engineered R3 overexpression in a neutral background
induces dwarfism and sterility. However, no individual RPP1-like Ler gene is sufficient for
incompatibility between Ler and Kas-2 or Kond, suggesting that co-action of at least two
RPP1-like members underlies this epistatic interaction. We find that the RPP1-like Ler haplotype
is frequent and occurs with other Ler RPP1-like alleles in a local population in Gorzów
Wielkopolski (Poland). Only Gorzów individuals carrying the RPP1-like Ler haplotype are
incompatible with Kas-2 and Kond, whereas other RPP1-like alleles in the population are
compatible. Therefore, the RPP1-like Ler haplotype has been maintained in genetically different
individuals at a single site, allowing exploration of forces shaping the evolution of RPP1-like
genes at local and regional population scales.
Identification of the Microsporidian Encephalitozoon cuniculi as a New Target of the IFNγ-Inducible IRG Resistance System
Marialice da Fonseca Ferreira-da-Silva , Helen Maria Springer-Frauenhoff , Wolfgang Bohne, Jonathan C. Howard , PLOS Published:
October 30, 2014, doi: 10.1371/journal.ppat.1004590
The IRG system of IFNγ-inducible GTPases constitutes a powerful resistance mechanism in mice against Toxoplasma gondii and two Chlamydia strains but not against many other bacteria and protozoa. Why only T. gondii and Chlamydia? We hypothesized that unusual features of the entry mechanisms and intracellular replicative niches of these two organisms, neither of which resembles a phagosome, might hint at a common principle. We examined another unicellular parasitic organism of mammals, member of an early-diverging group of Fungi, that bypasses the phagocytic mechanism when it enters the host cell: the microsporidian Encephalitozoon cuniculi. Consistent with the known susceptibility of IFNγ-deficient mice to E. cuniculi infection, we found that IFNγ treatment suppresses meront development and spore formation in mouse fibroblasts in vitro, and that this effect is mediated by IRG proteins. The process resembles that previously described in T. gondii and Chlamydia resistance. Effector (GKS subfamily) IRG proteins accumulate at the parasitophorous vacuole of E. cuniculi and the meronts are eliminated. The suppression of E. cuniculi growth by IFNγ is completely reversed in cells lacking regulatory (GMS subfamily) IRG proteins, cells that effectively lack all IRG function. In addition IFNγ-induced cells infected with E. cuniculi die by necrosis as previously shown for IFNγ-induced cells resisting T. gondii infection. Thus the IRG resistance system provides cell-autonomous immunity to specific parasites from three kingdoms of life: protozoa, bacteria and fungi. The phylogenetic divergence of the three organisms whose vacuoles are now known to be involved in IRG-mediated immunity and the non-phagosomal character of the vacuoles themselves strongly suggests that the IRG system is triggered not by the presence of specific parasite components but rather by absence of specific host components on the vacuolar membrane.
Ancient and diverged TGF-β signaling components in Nasonia vitripennis.
Özüak O, Buchta T, Roth S, Lynch JA, Dev Genes Evol. 2014 Dec;224(4-6):223-33. doi:
10.1007/s00427-014-0481-0. Epub 2014 Oct 11.
The transforming growth factor beta (TGF)-β signaling pathway and its modulators are
involved in many aspects of cellular growth and differentiation in all metazoa. Although
most of the core components of the pathway are highly conserved, many lineage-specific
adaptations have been observed including changes regarding paralog number, presence and
absence of modulators, and functional relevance for particular processes. In the parasitic
jewel wasp Nasonia vitripennis, the bone morphogenetic proteins (BMPs), one of the major
subgroups of the TGF-β superfamily, play a more fundamental role in dorsoventral (DV)
patterning than in all other insects studied so far. However, Nasonia lacks the BMP
antagonist Short gastrulation (Sog)/chordin, which is essential for polarizing the BMP
gradient along the DV axis in most bilaterian animals. Here, we present a broad survey of
TGF-β signaling in Nasonia with the aim to detect other lineage-specific peculiarities and
to identify potential mechanisms, which explain how BMP-dependent DV pattering occurs in the
early Nasonia embryo in the absence of Sog.
Dorsoventral polarity of the Nasonia embryo primarily relies on a BMP gradient formed without
input from Toll.
Özüak O, Buchta T, Roth S, Lynch JA, Curr Biol. 2014 Oct 20;24(20):2393-8. doi:
10.1016/j.cub.2014.08.035. Epub 2014 Oct 9.
In Drosophila, Toll signaling leads to a gradient of nuclear uptake of Dorsal with a peak at
the ventral egg pole and is the source for dorsoventral (DV) patterning and polarity of the
embryo. In contrast, Toll signaling plays no role in embryonic patterning in most animals,
while BMP signaling plays the major role. In order to understand the origin of the novelty
of the Drosophila system, we have examined DV patterning in Nasonia vitripennis (Nv), a
representative of the Hymenoptera and thus the most ancient branch points within the
Holometabola. We have previously shown that while the expression of several conserved DV
patterning genes is almost identical in Nasonia and Drosophila embryos at the onset of
gastrulation, the ways these patterns evolve in early embryogenesis are very different from
what is seen in Drosophila or the beetle Tribolium. In contrast to Drosophila or Tribolium,
we find that wasp Toll has a very limited ventral role, whereas BMP is required for almost
all DV polarity of the embryo, and these two signaling systems act independently of each
other to generate DV polarity. This result gives insights into how the Toll pathway could
have usurped a BMP-based DV patterning system in insects. In addition, our work strongly
suggests that a novel system for BMP activity gradient formation must be employed in the
wasp, since orthologs of crucial components of the fly system are either missing entirely or
lack function in the embryo.
Rapid identification of a natural knockout allele of ARMADILLO REPEAT-CONTAINING KINESIN1 that
causes root hair branching by mapping-by-sequencing.
Rishmawi L, Sun H, Schneeberger K, Hülskamp M, Schrader A, Plant Physiol. 2014
Nov;166(3):1280-7. doi: 10.1104/pp.114.244046. Epub 2014 Sep 23.
In Arabidopsis (Arabidopsis thaliana), branched root hairs are an indicator of defects in
root hair tip growth. Among 62 accessions, one accession (Heiligkreuztal2 [HKT2.4])
displayed branched root hairs, suggesting that this accession carries a mutation in a gene
of importance for tip growth. We determined 200- to 300-kb mapping intervals using a
mapping-by-sequencing approach of F2 pools from crossings of HKT2.4 with three different
accessions. The intersection of these mapping intervals was 80 kb in size featuring not more
than 36 HKT2.4-specific single nucleotide polymorphisms, only two of which changed the
coding potential of genes. Among them, we identified the causative single nucleotide
polymorphism changing a splicing site in ARMADILLO REPEAT-CONTAINING KINESIN1. The applied
strategies have the potential to complement statistical methods in high-throughput
phenotyping studies using different natural accessions to identify causative genes for
distinct phenotypes represented by only one or a few accessions.
Multidimensional epistasis and the transitory advantage of sex
Nowak S, Neidhart J, Szendro IG, Krug J, PLOS Computational
Biology 10(9): e1003836 (2014)
Identifying and quantifying the benefits of
sex and recombination is a long-standing problem in evolutionary theory. In particular,
contradictory claims have been made about the existence of a benefit of recombination on high
dimensional fitness landscapes in the presence of sign epistasis. Here we present a comparative
numerical study of sexual and asexual evolutionary dynamics of haploids on tunably rugged model
landscapes under strong selection, paying special attention to the temporal development of the
evolutionary advantage of recombination and the link between population diversity and the rate
of adaptation. We show that the adaptive advantage of recombination on static rugged landscapes
is strictly transitory. At early times, an advantage of recombination arises through the
possibility to combine individually occurring beneficial mutations, but this effect is reversed
at longer times by the much more efficient trapping of recombining populations at local fitness
peaks. These findings are explained by means of well-established results for a setup with only
two loci. In accordance with the Red Queen hypothesis the transitory advantage can be prolonged
indefinitely in fluctuating environments, and it is maximal when the environment fluctuates on
the same time scale on which trapping at local optima typically occurs.
Role of pleiotropy during adaptation of TEM-1 β-lactamase to two
novel antibiotics
Schenk MF, Witte S, Salverda MLM, Koopmanschap B, Krug J, de
Visser JAGM, Evolutionary Applications, early view (2014)
Pleiotropy is a key feature of the
genotype–phenotype map, and its form and extent have many evolutionary implications, including
for the dynamics of adaptation and the evolution of specialization. Similarly, pleiotropic
effects of antibiotic resistance mutations may affect the evolution of antibiotic resistance in
the simultaneous or fluctuating presence of different antibiotics. Here, we study the role of
pleiotropy during the in vitro adaptation of the enzyme TEM-1 β-lactamase to two novel
antibiotics, cefotaxime (CTX) and ceftazidime (CAZ). We subject replicate lines for four rounds
of evolution to selection with CTX and CAZ alone, and in their combined and fluctuating
presence. Evolved alleles show positive correlated responses when selecting with single
antibiotics. Nevertheless, pleiotropic constraints are apparent from the effects of single
mutations and from selected alleles showing smaller correlated than direct responses and smaller
responses after simultaneous and fluctuating selection with both than with single antibiotics.
We speculate that these constraints result from structural changes in the oxyanion pocket
surrounding the active site, where accommodation of CTX and the larger CAZ is balanced against
their positioning with respect to the active site. Our findings suggest limited benefits from
the combined or fluctuating application of these related cephalosporins for containing
antibiotic resistance.
Nonsense-mediated mRNA decay modulates immune receptor levels to
regulate plant antibacterial defense
Gloggnitzer J, Akimcheva S, Srinivasan A, Kusenda B, Riehs N,
Stampfl H, Bautor J, Dekrout B, Jonak C, Jiménez-Gómez JM, Parker JE, Riha K, Cell Host Microbe,
16(3):376-90 (2014)
Nonsense-mediated mRNA decay (NMD) is a
conserved eukaryotic RNA surveillance mechanism that degrades aberrant mRNAs. NMD impairment in
Arabidopsis is linked to constitutive immune response activation and enhanced antibacterial
resistance, but the underlying mechanisms are unknown. Here we show that NMD contributes to
innate immunity in Arabidopsis by controlling the turnover of numerous TIR domain-containing,
nucleotide-binding, leucine-rich repeat (TNL) immune receptor-encoding mRNAs. Autoimmunity
resulting from NMD impairment depends on TNL signaling pathway components and can be triggered
through deregulation of a single TNL gene, RPS6. Bacterial infection of plants causes
host-programmed inhibition of NMD, leading to stabilization of NMD-regulated TNL transcripts.
Conversely, constitutive NMD activity prevents TNL stabilization and impairs plant defense,
demonstrating that host-regulated NMD contributes to disease resistance. Thus, NMD shapes plant
innate immunity by controlling the threshold for activation of TNL resistance pathways.
Clonal interference and Muller's ratchet in spatial habitats
Otwinowski J, Krug J, Physical Biology 11:056003 (2014)
Competition between independently arising
beneficial mutations is enhanced in spatial populations due to the linear rather than
exponential growth of clones. Recent theoretical studies have pointed out that the resulting
fitness dynamics is analogous to a surface growth process, where new layers nucleate and spread
stochastically, leading to the build up of scale-invariant roughness. This scenario differs
qualitatively from the standard view of adaptation in that the speed of adaptation becomes
independent of population size while the fitness variance does not. Here we exploit recent
progress in the understanding of surface growth processes to obtain precise predictions for the
universal, non-Gaussian shape of the fitness distribution for one-dimensional habitats, which
are verified by simulations. When the mutations are deleterious rather than beneficial the
problem becomes a spatial version of Muller's ratchet. In contrast to the case of well-mixed
populations, the rate of fitness decline remains finite even in the limit of an infinite
habitat, provided the ratio [Formula: see text] between the deleterious mutation rate and the
square of the (negative) selection coefficient is sufficiently large. Using, again, an analogy
to surface growth models we show that the transition between the stationary and the moving state
of the ratchet is governed by directed percolation.
Adaptation in tunably rugged fitness landscapes: The Rough Mount Fuji Model
Neidhart J, Szendro IG, Krug J, (Submitted on 13 Feb 2014 (v1), last revised 1 Aug 2014
(this version, v2))
Much of the current theory of adaptation is based on Gillespie's mutational landscape
model (MLM), which assumes that the fitness values of genotypes linked by single
mutational steps are independent random variables. On the other hand, a growing body of
empirical evidence shows that real fitness landscapes, while possessing a considerable
amount of ruggedness, are smoother than predicted by the MLM. In the present article we
propose and analyse a simple fitness landscape model with tunable ruggedness based on
the Rough Mount Fuji (RMF) model originally introduced by Aita et al. [Biopolymers
54:64-79 (2000)] in the context of protein evolution. We provide a comprehensive
collection of results pertaining to the topographical structure of RMF landscapes,
including explicit formulae for the expected number of local fitness maxima, the
location of the global peak, and the fitness correlation function. The statistics of
single and multiple adaptive steps on the RMF landscape are explored mainly through
simulations, and the results are compared to the known behavior in the MLM model.
Finally, we show that the RMF model can explain the large number of second-step
mutations observed on a highly-fit first step backgound in a recent evolution experiment
with a microvirid bacteriophage [Miller et al., Genetics 187:185-202 (2011)].
Plant and animal glycolate oxidases have a common eukaryotic ancestor and convergently
duplicated to evolve long-chain 2-hydroxy acid oxidases.
Esser C, Kuhn A, Groth G, Lercher MJ, Maurino VG. Mol Biol Evol. 2014 May;31(5):1089-101.
doi: 10.1093/molbev/msu041. Epub 2014 Jan 9. PMID: 24408912
Glycolate oxidase (GOX) is a crucial enzyme of plant photorespiration. The encoding gene
is thought to have originated from endosymbiotic gene transfer between the eukaryotic
host and the cyanobacterial endosymbiont at the base of plantae. However, animals also
possess GOX activities. Plant and animal GOX belong to the gene family of
(L)-2-hydroxyacid-oxidases ((L)-2-HAOX). We find that all (L)-2-HAOX proteins in animals
and archaeplastida go back to one ancestral eukaryotic sequence; the sole exceptions are
green algae of the chlorophyta lineage. Chlorophyta replaced the ancestral eukaryotic
(L)-2-HAOX with a bacterial ortholog, a lactate oxidase that may have been obtained
through the primary endosymbiosis at the base of plantae; independent losses of this
gene may explain its absence in other algal lineages (glaucophyta, rhodophyta, and
charophyta). We also show that in addition to GOX, plants possess (L)-2-HAOX proteins
with different specificities for medium- and long-chain hydroxyacids (lHAOX), likely
involved in fatty acid and protein catabolism. Vertebrates possess lHAOX proteins acting
on similar substrates as plant lHAOX; however, the existence of GOX and lHAOX
subfamilies in both plants and animals is not due to shared ancestry but is the result
of convergent evolution in the two most complex eukaryotic lineages. On the basis of
targeting sequences and predicted substrate specificities, we conclude that the
biological role of plantae (L)-2-HAOX in photorespiration evolved by co-opting an
existing peroxisomal protein.
Evolutionary conservation of cold-induced antisense RNAs of
FLOWERING LOCUS C in Arabidopsis thaliana perennial relatives
Castaings L, Bergonzi S, Albani MC, Kemi U, Savolainen O, Coupland
G, Nature communications, DOI: 10.1038/ncomms5457 (2014)
Antisense RNA (asRNA) COOLAIR is expressed
at A. thaliana FLOWERING LOCUS C (FLC) in response to winter temperatures. Its contribution to
cold-induced silencing of FLC was proposed but its functional and evolutionary significance
remain unclear. Here we identify a highly conserved block containing the COOLAIR first exon and
core promoter at the 3' end of several FLC orthologues. Furthermore, asRNAs related to COOLAIR
are expressed at FLC loci in the perennials A. alpina and A. lyrata, although some splicing
variants differ from A. thaliana. Study of the A. alpina orthologue, PERPETUAL FLOWERING 1
(PEP1), demonstrates that AaCOOLAIR is induced each winter of the perennial life cycle.
Introduction of PEP1 into A. thaliana reveals that AaCOOLAIR cis-elements confer
cold-inducibility in this heterologous species while the difference between PEP1 and FLC mRNA
patterns depends on both cis-elements and species-specific trans-acting factors. Thus,
expression of COOLAIR is highly conserved, supporting its importance in FLC regulation.
Genome-wide quantitative analysis of DNA methylation from
bisulfite sequencing data
Akman K, Haaf T, Gravina S, Vijg J, Tresch A, Bioinformatics,
30(13) (2014)
Although many computer programs can perform
population genetics calculations, they are typically limited in the analyses and data input
formats they offer; few applications can process the large data sets produced by whole-genome
resequencing projects. Furthermore, there is no coherent framework for the easy integration of
new statistics into existing pipelines, hindering the development and application of new
population genetics and genomics approaches. Here, we present PopGenome, a population genomics
package for the R software environment (a de facto standard for statistical analyses). PopGenome
can efficiently process genome-scale data as well as large sets of individual loci. It reads DNA
alignments and single-nucleotide polymorphism (SNP) data sets in most common formats, including
those used by the HapMap, 1000 human genomes, and 1001 Arabidopsis genomes projects. PopGenome
also reads associated annotation files in GFF format, enabling users to easily define regions or
classify SNPs based on their annotation; all analyses can also be applied to sliding windows.
PopGenome offers a wide range of diverse population genetics analyses, including neutrality
tests as well as statistics for population differentiation, linkage disequilibrium, and
recombination. PopGenome is linked to Hudson's MS and Ewing's MSMS programs to assess
statistical significance based on coalescent simulations. PopGenome's integration in R
facilitates effortless and reproducible downstream analyses as well as the production of
publication-quality graphics. Developers can easily incorporate new analyses methods into the
PopGenome framework. PopGenome and R are freely available from CRAN (http://cran.r-project.org/)
for all major operating systems under the GNU General Public License.
PopGenome: an efficient Swiss army knife for population genomic
analyses in R
Pfeifer B, Wittelsbürger U, Ramos-Onsins SE, Lercher MJ, Mol Biol
Evol, 31(7):1929-36 (2014)
Although many computer programs can perform
population genetics calculations, they are typically limited in the analyses and data input
formats they offer; few applications can process the large data sets produced by whole-genome
resequencing projects. Furthermore, there is no coherent framework for the easy integration of
new statistics into existing pipelines, hindering the development and application of new
population genetics and genomics approaches. Here, we present PopGenome, a population genomics
package for the R software environment (a de facto standard for statistical analyses). PopGenome
can efficiently process genome-scale data as well as large sets of individual loci. It reads DNA
alignments and single-nucleotide polymorphism (SNP) data sets in most common formats, including
those used by the HapMap, 1000 human genomes, and 1001 Arabidopsis genomes projects. PopGenome
also reads associated annotation files in GFF format, enabling users to easily define regions or
classify SNPs based on their annotation; all analyses can also be applied to sliding windows.
PopGenome offers a wide range of diverse population genetics analyses, including neutrality
tests as well as statistics for population differentiation, linkage disequilibrium, and
recombination. PopGenome is linked to Hudson's MS and Ewing's MSMS programs to assess
statistical significance based on coalescent simulations. PopGenome's integration in R
facilitates effortless and reproducible downstream analyses as well as the production of
publication-quality graphics. Developers can easily incorporate new analyses methods into the
PopGenome framework. PopGenome and R are freely available from CRAN (http://cran.r-project.org/)
for all major operating systems under the GNU General Public License.
The role of photorespiration during the evolution of C4
photosynthesis in the genus Flaveria
Mallmann J, Heckmann D, Bräutigam A, Lercher MJ, Weber AP,
Westhoff P, Gowik U, Elife, doi:10.7554/eLife.02478 (2014)
C4 photosynthesis represents a most
remarkable case of convergent evolution of a complex trait, which includes the reprogramming of
the expression patterns of thousands of genes. Anatomical, physiological, and phylogenetic and
analyses as well as computational modeling indicate that the establishment of a photorespiratory
carbon pump (termed C2 photosynthesis) is a prerequisite for the evolution of C4. However, a
mechanistic model explaining the tight connection between the evolution of C4 and C2
photosynthesis is currently lacking. Here we address this question through comparative
transcriptomic and biochemical analyses of closely related C3, C3–C4, and C4 species, combined
with Flux Balance Analysis constrained through a mechanistic model of carbon fixation. We show
that C2 photosynthesis creates a misbalance in nitrogen metabolism between bundle sheath and
mesophyll cells. Rebalancing nitrogen metabolism requires anaplerotic reactions that resemble at
least parts of a basic C4 cycle. Our findings thus show how C2 photosynthesis represents a
pre-adaptation for the C4 system, where the evolution of the C2 system establishes important C4
components as a side effect.
Empirical fitness landscapes and the predictability of evolution
de Visser JAGM, Krug J, Nature Reviews Genetics, published online
(2014)
The genotype–fitness map (that is, the
fitness landscape) is a key determinant of evolution, yet it has mostly been used as a
superficial metaphor because we know little about its structure. This is now changing, as real
fitness landscapes are being analysed by constructing genotypes with all possible combinations
of small sets of mutations observed in phylogenies or in evolution experiments. In turn, these
first glimpses of empirical fitness landscapes inspire theoretical analyses of the
predictability of evolution. Here, we review these recent empirical and theoretical
developments, identify methodological issues and organizing principles, and discuss
possibilities to develop more realistic fitness landscape models.
Coiled-Coil Proteins Facilitated the Functional Expansion of the
Centrosome
Kuhn M, Hyman AA, Beyer A, PloS Computational Biology, published
online (2014)
Repurposing existing proteins for new
cellular functions is recognized as a main mechanism of evolutionary innovation, but its role in
organelle evolution is unclear. Here, we explore the mechanisms that led to the evolution of the
centrosome, an ancestral eukaryotic organelle that expanded its functional repertoire through
the course of evolution. We developed a refined sequence alignment technique that is more
sensitive to coiled coil proteins, which are abundant in the centrosome. For proteins with high
coiled-coil content, our algorithm identified 17% more reciprocal best hits than BLAST.
Analyzing 108 eukaryotic genomes, we traced the evolutionary history of centrosome proteins. In
order to assess how these proteins formed the centrosome and adopted new functions, we
computationally emulated evolution by iteratively removing the most recently evolved proteins
from the centrosomal protein interaction network. Coiled-coil proteins that first appeared in
the animal–fungi ancestor act as scaffolds and recruit ancestral eukaryotic proteins such as
kinases and phosphatases to the centrosome. This process created a signaling hub that is crucial
for multicellular development. Our results demonstrate how ancient proteins can be co-opted to
different cellular localizations, thereby becoming involved in novel functions.
Demography-adjusted tests of neutrality based on genome-wide SNP
data
Rafajlović M, Klassmann A, Eriksson A, Wiehe T, Mehlig B,
Theoretical Population Biology, Vol. 95, pp. 1–12 (2014)
Tests of the neutral evolution hypothesis
are usually built on the standard null model which assumes that mutations are neutral and the
population size remains constant over time. However, it is unclear how such tests are affected
if the last assumption is dropped. Here, we extend the unifying framework for tests based on the
site frequency spectrum, introduced by Achaz and Ferretti, to populations of varying size. Key
ingredients are the first two moments of the site frequency spectrum. We show how these moments
can be computed analytically if a population has experienced two instantaneous size changes in
the past. We apply our method to data from ten human populations gathered in the 1000 genomes
project, estimate their demographies and define demography-adjusted versions of Tajima’s DD, Fay
& Wu’s HH, and Zeng’s EE. Our results show that demography-adjusted test statistics facilitate
the direct comparison between populations and that most of the differences among populations
seen in the original unadjusted tests can be explained by their underlying demographies. Upon
carrying out whole-genome screens for deviations from neutrality, we identify candidate regions
of recent positive selection. We provide track files with values of the adjusted and unadjusted
tests for upload to the UCSC genome browser.
New tools in the box: An evolutionary synopsis of chromatin
insulators
Heger P, Wiehe T, Trends In Genetics, Vol. 30, Issue 5, p161–171
(2014)
Despite progress in understanding genome
organization and gene expression during the last decade, the evolutionary pathways that led to
the intricate patterns of gene expression in different cells of an organism are still poorly
understood. Important steps in this regulation take place at the level of chromatin, where the
(epi)genomic environment of a gene determines its expression in time and space. Although the
basic mechanisms of gene expression apply to all eukaryotes, multicellular organisms face the
additional challenge of coordinating gene expression during development. In this review we
summarize and put into evolutionary context current knowledge about chromatin insulators, an
important class of regulatory factors mediating these tasks. Our interpretation of historical
and recent findings points to a dynamic and ongoing evolution of insulator proteins
characterized by multiple instances of convergent evolution, gene loss, and binding site changes
in different organisms. The idea of two autonomously evolving insulator functions (as a barrier
element and an enhancer blocker) further suggests that the evolution of metazoans and their
enhancer-rich gene regulatory repertoire might be connected to the radiation of enhancer
blocking insulators. Although speculative at the moment, such coevolution might create tools for
complex gene regulation and therefore influence the evolutionary roadmaps of metazoans.
WOX13-like genes are required for reprogramming of leaf and protoplast cells into stem cells in the moss Physcomitrella patens
Sakakibara, K, Reisewitz, P, Aoyama, T, Friedrich, T, Ando, S, Sato, Y, Tamada, Y, Nishiyama, T, Hiwatashi, Y, Kurata, T, Ishikawa, M, Deguchi, H, Rensing, SA, Werr, W, Murata, T, Hasebe, M & Laux, T. , 141:1660-70. doi: 10.1242/dev.097444 (2014)
Many differentiated plant cells can dedifferentiate into stem cells, reflecting the remarkable developmental plasticity of plants. In the moss Physcomitrella patens, cells at the wound margin of detached leaves become reprogrammed into stem cells. Here, we report that two paralogous P. patens WUSCHEL-related homeobox 13-like (PpWOX13L) genes, homologs of stem cell regulators in flowering plants, are transiently upregulated and required for the initiation of cell growth during stem cell formation. Concordantly, Δppwox13l deletion mutants fail to upregulate genes encoding homologs of cell wall loosening factors during this process. During the moss life cycle, most of the Δppwox13l mutant zygotes fail to expand and initiate an apical stem cell to form the embryo. Our data show that PpWOX13L genes are required for the initiation of cell growth specifically during stem cell formation, in analogy to WOX stem cell functions in seed plants, but using a different cellular mechanism.
A predictive fitness model for influenza
Łuksza M, Lässig M, Nature, 507, 57-61 (2014)
The seasonal human influenza A (H3N2) virus
undergoes rapid evolution, which produces significant year-to-year sequence turnover in the
population of circulating strains. Adaptive mutations respond to human immune challenge and
occur primarily in antigenic epitopes, the antibody-binding domains of the viral surface protein
haemagglutinin. Here we develop a fitness model for haemagglutinin that predicts the evolution
of the viral population from one year to the next. Two factors are shown to determine the
fitness of a strain: adaptive epitope changes and deleterious mutations outside the epitopes. We
infer both fitness components for the strains circulating in a given year, using
population-genetic data of all previous strains. From fitness and frequency of each strain, we
predict the frequency of its descendent strains in the following year. This fitness model maps
the adaptive history of influenza A and suggests a principled method for vaccine selection. Our
results call for a more comprehensive epidemiology of influenza and other fast-evolving
pathogens that integrates antigenic phenotypes with other viral functions coupled by genetic
linkage.
Leaf Shape Evolution Through Duplication, Regulatory
Diversification, and Loss of a Homeobox Gene
Vlad D, Kierzkowski D, Rast MI, Vuolo F, Dello Ioio R, Galinha C,
Gan X, Hajheidari M, Hay A, Smith RS, Huijser P, Bailey CD, Tsiantis M, Science Vol. 343 no.
6172 pp. 780-783 (2014)
In this work, we investigate morphological
differences between Arabidopsis thaliana, which has simple leaves, and its relative Cardamine
hirsuta, which has dissected leaves comprising distinct leaflets. With the use of genetics,
interspecific gene transfers, and time-lapse imaging, we show that leaflet development requires
the REDUCED COMPLEXITY (RCO) homeodomain protein. RCO functions specifically in leaves, where it
sculpts developing leaflets by repressing growth at their flanks. RCO evolved in the
Brassicaceae family through gene duplication and was lost in A. thaliana, contributing to leaf
simplification in this species. Species-specific RCO action with respect to its paralog results
from its distinct gene expression pattern in the leaf base. Thus, regulatory evolution coupled
with gene duplication and loss generated leaf shape diversity by modifying local growth patterns
during organogenesis.
Innate resistance against Toxoplasma gondii: an evolutionary tale
of mice, cats, and men
Gazzinelli RT, Mendonça-Neto R, Lilue J, Howard J, Sher A, Cell
Host Microbe. 15(2):132-8 (2014)
Recent studies have revealed remarkable
species specificity of the Toll-like receptors (TLRs) TLR11 and TLR12 and the immunity-related
GTPase (IRG) proteins that are essential elements for detection and immune control of Toxoplasma
gondii in mice, but not in humans. The biological and evolutionary implications of these
findings for the T. gondii host-pathogen relationship and for human disease are discussed.
Periodic mRNA synthesis and degradation co‐operate during cell
cycle gene expression
Eser P, Demel C, Maier KC, Schwalb B, Pirkl N, Martin DE, Cramer
P, Tresch A, Mol Syst Biol. 10:717 (2014)
During the cell cycle, the levels of
hundreds of mRNAs change in a periodic manner, but how this is achieved by alterations in the
rates of mRNA synthesis and degradation has not been studied systematically. Here, we used
metabolic RNA labeling and comparative dynamic transcriptome analysis (cDTA) to derive mRNA
synthesis and degradation rates every 5 min during three cell cycle periods of the yeast
Saccharomyces
cerevisiae. A novel statistical model identified 479 genes that show periodic changes
in mRNA synthesis and generally also periodic changes in their mRNA degradation rates. Peaks of
mRNA degradation generally follow peaks of mRNA synthesis, resulting in sharp and high peaks of
mRNA levels at defined times during the cell cycle. Whereas the timing of mRNA synthesis is set
by upstream DNA motifs and their associated transcription factors (TFs), the synthesis rate of a
periodically expressed gene is apparently set by its core promoter.
Analysis of TTG1 function in Arabis alpina
Chopra D, Wolff H, Span J, Schellmann S, Coupland G, Albani MC,
Schrader A, Hülskamp M, BMC Plant Biology 2014; 14:16 (2014)
Background
In Arabidopsis thaliana (A. thaliana) the WD40 protein TRANSPARENT TESTA GLABRA1 (TTG1)
controls five traits relevant for the adaptation of plants to environmental changes
including the production of proanthocyanidin, anthocyanidin, seed coat mucilage, trichomes
and root hairs. The analysis of different Brassicaceae species suggests that the function of
TTG1 is conserved within the family.
Results
In this work, we studied the function of TTG1 in Arabis alpina (A. alpina). A comparison of
wild type and two Aattg1 alleles revealed that AaTTG1 is involved in the regulation of all
five traits. A detailed analysis of the five traits showed striking phenotypic differences
between A. alpina and A. thaliana such that trichome formation occurs also at later stages
of leaf development and that root hairs form at non-root hair positions.
Conclusions
The evolutionary conservation of the regulation of the five traits by TTG1 on the one hand
and the striking phenotypic differences make A. alpina a very interesting genetic model
system to study the evolution of TTG1-dependent gene regulatory networks at a functional
level.
Horizontal gene acquisitions by eukaryotes as drivers of adaptive
evolution
Schönknecht G, Weber AP, Lercher MJ, Bioessays, 36(1):9-20 (2014)
In contrast to vertical gene transfer from
parent to offspring, horizontal (or lateral) gene transfer moves genetic information between
different species. Bacteria and archaea often adapt through horizontal gene transfer. Recent
analyses indicate that eukaryotic genomes, too, have acquired numerous genes via horizontal
transfer from prokaryotes and other lineages. Based on this we raise the hypothesis that
horizontally acquired genes may have contributed more to adaptive evolution of eukaryotes than
previously assumed. Current candidate sets of horizontally acquired eukaryotic genes may just be
the tip of an iceberg. We have recently shown that adaptation of the thermoacidophilic red alga
Galdieria sulphuraria to its hot, acid, toxic-metal laden, volcanic environment was facilitated
by the acquisition of numerous genes from extremophile bacteria and archaea. Other recently
published examples of horizontal acquisitions involved in adaptation include ice-binding
proteins in marine algae, enzymes for carotenoid biosynthesis in aphids, and genes involved in
fungal metabolism. Editor's suggested further reading in BioEssays Jumping the fine LINE between
species: Horizontal transfer of transposable elements in animals catalyses genome evolution
Abstract.
2013
Speed Switching of Gonococcal Surface Motility Correlates with Proton Motive Force
Kurre, R., Kouzel, N., Ramakrishnan, K., Oldewurtel, E.R., Maier, B., PLoS ONE, 8(6), e67718
(2013)
Bacterial type IV pili are essential for adhesion to surfaces, motility, microcolony
formation, and horizontal gene transfer in many bacterial species. These polymers are strong
molecular motors that can retract at two different speeds. In the human pathogen Neisseria
gonorrhoeae speed switching of single pili from 2 µm/s to 1 µm/s can be triggered by oxygen
depletion. Here, we address the question how proton motive force (PMF) influences motor
speed. Using pHluorin expression in combination with dyes that are sensitive to
transmembrane ΔpH gradient or transmembrane potential ΔΨ, we measured both components of the
PMF at varying external pH. Depletion of PMF using uncouplers reversibly triggered switching
into the low speed mode. Reduction of the PMF by ≈ 35 mV was enough to trigger speed
switching. Reducing ATP levels by inhibition of the ATP synthase did not induce speed
switching. Furthermore, we showed that the strictly aerobic Myxococcus xanthus failed to
move upon depletion of PMF or oxygen, indicating that although the mechanical properties of
the motor are conserved, its regulatory inputs have evolved differently. We conclude that
depletion of PMF triggers speed switching of gonococcal pili. Although ATP is required for
gonococcal pilus retraction, our data indicate that PMF is an independent additional energy
source driving the high speed mode.
Universality and predictability in molecular quantitative
genetics
Nourmohammad A, Held T, Lässig M, Current Opinion in Genetics and
Development, Volume 23, Issue 6, Pages 684–693 (2013)
Molecular traits, such as gene expression
levels or protein binding affinities, are increasingly accessible to quantitative measurement by
modern high-throughput techniques. Such traits measure molecular functions and, from an
evolutionary point of view, are important as targets of natural selection. We review recent
developments in evolutionary theory and experiments that are expected to become building blocks
of a quantitative genetics of molecular traits. We focus on universal evolutionary
characteristics: these are largely independent of a trait's genetic basis, which is often at
least partially unknown. We show that universal measurements can be used to infer selection on a
quantitative trait, which determines its evolutionary mode of conservation or adaptation.
Furthermore, universality is closely linked to predictability of trait evolution across
lineages. We argue that universal trait statistics extends over a range of cellular scales and
opens new avenues of quantitative evolutionary systems biology.
Sybil--efficient constraint-based modelling in R
Gelius-Dietrich G, Desouki AA, Fritzemeier CJ, Lercher MJ, BMC
Syst Biol, 7:125 (2013)
BACKGROUND:
Constraint-based analyses of metabolic networks are widely used to simulate the properties of
genome-scale metabolic networks. Publicly available implementations tend to be slow, impeding
large scale analyses such as the genome-wide computation of pairwise gene knock-outs, or the
automated search for model improvements. Furthermore, available implementations cannot easily be
extended or adapted by users.
RESULTS:Here, we present sybil, an open
source software library for constraint-based analyses in R; R is a free, platform-independent
environment for statistical computing and graphics that is widely used in bioinformatics. Among
other functions, sybil currently provides efficient methods for flux-balance analysis (FBA),
MOMA, and ROOM that are about ten times faster than previous implementations when calculating
the effect of whole-genome single gene deletions in silico on a complete E. coli metabolic
model.
CONCLUSIONS:Due to the object-oriented architecture of sybil, users
can easily build analysis pipelines in R or even implement their own constraint-based
algorithms. Based on its highly efficient communication with different mathematical optimisation
programs, sybil facilitates the exploration of high-dimensional optimisation problems on small
time scales. Sybil and all its dependencies are open source. Sybil and its documentation are
available for download from the comprehensive R archive network (CRAN).
A Genomics-Based Classification of Human Lung Tumors
Seidel D et al., Science Translational Medicine, 5 (209) p.
209ra153 (2013)
We characterized genome alterations in 1255
clinically annotated lung tumors of all histological subgroups to identify genetically defined
and clinically relevant subtypes. More than 55% of all cases had at least one oncogenic genome
alteration potentially amenable to specific therapeutic intervention, including several
personalized treatment approaches that are already in clinical evaluation. Marked differences in
the pattern of genomic alterations existed between and within histological subtypes, thus
challenging the original histomorphological diagnosis. Immunohistochemical studies confirmed
many of these reassigned subtypes. The reassignment eliminated almost all cases of large cell
carcinomas, some of which had therapeutically relevant alterations. Prospective testing of our
genomics-based diagnostic algorithm in 5145 lung cancer patients enabled a genome-based
diagnosis in 3863 (75%) patients, confirmed the feasibility of rational reassignments of large
cell lung cancer, and led to improvement in overall survival in patients with EGFR-mutant or
ALK-rearranged cancers. Thus, our findings provide support for broad implementation of
genome-based diagnosis of lung cancer.
Evolutionary Accessibility of Modular Fitness Landscapes
Schmiegelt B, Krug J, Journal of Statistical Physics, October
2013, 1-22 (2013)
A fitness landscape is a mapping from the
space of genetic sequences, which is modeled here as a binary hypercube of dimension L, to the
real numbers. We consider random models of fitness landscapes, where fitness values are assigned
according to some probabilistic rule, and study the statistical properties of pathways to the
global fitness maximum along which fitness increases monotonically. Such paths are important for
evolution because they are the only ones that are accessible to an adapting population when
mutations occur at a low rate. The focus of this work is on the block model introduced by A.S.
Perelson and C.A. Macken (Proc. Natl. Acad. Sci. USA 92:9657, 1995) where the genome is
decomposed into disjoint sets of loci (‘modules’) that contribute independently to fitness, and
fitness values within blocks are assigned at random. We show that the number of accessible paths
can be written as a product of the path numbers within the blocks, which provides a detailed
analytic description of the path statistics. The block model can be viewed as a special case of
Kauffman’s NK-model, and we compare the analytic results to simulations of the NK-model with
different genetic architectures. We find that the mean number of accessible paths in the
different versions of the model are quite similar, but the distribution of the path number is
qualitatively different in the block model due to its multiplicative structure. A similar
statement applies to the number of local fitness maxima in the NK-models, which has been studied
extensively in previous works. The overall evolutionary accessibility of the landscape, as
quantified by the probability to find at least one accessible path to the global maximum, is
dramatically lowered by the modular structure.
Reciprocal virulence and resistance polymorphism in the
relationship between Toxoplasma gondii and the house mouse
Lilue J, Müller UB, Steinfeldt T, Howard JC, Elife. 2013 Oct
29;2:e01298 (2013)
Virulence in the ubiquitous intracellular
protozoon
Toxoplasma gondii for its natural intermediate host, the mouse, appears
paradoxical from an evolutionary standpoint because death of the mouse before encystment
interrupts the parasite life cycle. Virulent
T. gondii strains secrete kinases and
pseudokinases that inactivate the immunity-related GTPases (IRG proteins) responsible for mouse
resistance to avirulent strains. Such considerations stimulated a search for IRG alleles unknown
in laboratory mice that might confer resistance to virulent strains of
T. gondii. We
report that the mouse IRG system shows extraordinary polymorphic complexity in the wild. We
describe an IRG haplotype from a wild-derived mouse strain that confers resistance against
virulent parasites by interference with the virulent kinase complex. In such hosts virulent
strains can encyst, hinting at an explanation for the evolution of virulence polymorphism in
T. gondii.
Rate of Adaptation in Sexuals and Asexuals: A Solvable Model of
the Fisher–Muller Effect
Park SC, Krug J, Genetics November 1, 2013 vol. 195 no. 3 941-955
(2013)
The adaptation of large asexual populations
is hampered by the competition between independently arising beneficial mutations in different
individuals, which is known as clonal interference. In classic work, Fisher and Muller proposed
that recombination provides an evolutionary advantage in large populations by alleviating this
competition. Based on recent progress in quantifying the speed of adaptation in asexual
populations undergoing clonal interference, we present a detailed analysis of the Fisher–Muller
mechanism for a model genome consisting of two loci with an infinite number of beneficial
alleles each and multiplicative (nonepistatic) fitness effects. We solve the deterministic,
infinite population dynamics exactly and show that, for a particular, natural mutation scheme,
the speed of adaptation in sexuals is twice as large as in asexuals. This result is argued to
hold for any nonzero value of the rate of recombination. Guided by the infinite population
result and by previous work on asexual adaptation, we postulate an expression for the speed of
adaptation in finite sexual populations that agrees with numerical simulations over a wide range
of population sizes and recombination rates. The ratio of the sexual to asexual adaptation speed
is a function of population size that increases in the clonal interference regime and approaches
2 for extremely large populations. The simulations also show that the imbalance between the
numbers of accumulated mutations at the two loci is strongly suppressed even by a small amount
of recombination. The generalization of the model to an arbitrary number L of loci is briefly
discussed. If each offspring samples the alleles at each locus from the gene pool of the whole
population rather than from two parents, the ratio of the sexual to asexual adaptation speed is
approximately equal to L in large populations. A possible realization of this scenario is the
reassortment of genetic material in RNA viruses with L genomic segments.
Arabidopsis semidwarfs evolved from independent mutations in
GA20ox1, ortholog to green revolution dwarf alleles in rice and barley
Barboza L, Effgen S, Alonso-Blanco C, Kooke R, Keurentjes JJ,
Koornneef M, Alcázar R, Proc Natl Acad Sci USA. 2013 Sep 24;110(39):15818-23 (2013)
Understanding the genetic bases of natural
variation for developmental and stress-related traits is a major goal of current plant biology.
Variation in plant hormone levels and signaling might underlie such phenotypic variation
occurring even within the same species. Here we report the genetic and molecular basis of
semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests
demonstrate that independent loss-of-function mutations at GA locus 5 (GA5), which encodes
gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis, are
found in different populations from southern, western, and northern Europe; central Asia; and
Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness
without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of
purifying selection, whereas GA5 loss-of-function alleles can also exhibit patterns of positive
selection in specific populations as shown by Fay and Wu’s H statistics. These results suggest
that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in
nature. Furthermore, because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green
revolution genes, this study illustrates the occurrence of conserved adaptive evolution between
wild A.thaliana and domesticated plants.
Yule-generated trees constrained by node imbalance
Disanto F, Schlizio A, Wiehe T, Mathematical Biosciences (online
access) August 13 (2013)
The
Yule process generates a class
of binary trees which is fundamental to population genetic models and other applications in
evolutionary biology. In this paper, we introduce a family of sub-classes of ranked trees,
called Ω-trees, which are characterized by imbalance of internal nodes. The degree of imbalance
is defined by an integer 0⩽ω. For caterpillars, the extreme case of unbalanced trees, ω=0. Under
models of neutral evolution, for instance the Yule model, trees with small ω are unlikely to
occur by chance. Indeed, imbalance can be a signature of permanent selection pressure, such as
observable in the genealogies of certain pathogens. From a mathematical point of view it is
interesting to observe that the space of Ω-trees maintains several statistical invariants
although it is drastically reduced in size compared to the space of unconstrained Yule trees.
Using generating functions, we study here some basic combinatorial properties of Ω-trees. We
focus on the distribution of the number of subtrees with two leaves. We show that expectation
and variance of this distribution match those for unconstrained trees already for very small
values of ω.
Irgm1 (LRG-47), a regulator of cell-autonomous immunity, does not
localize to mycobacterial or listerial phagosomes in IFN-γ-induced mouse cells
Springer H, Schramm M, Taylor GA, Howard JC, J. Immunol. Epub July
10 (2013)
The IFN-inducible protein Irgm1 (LRG-47)
belongs to the family of immunity-related GTPases that function in cell-autonomous resistance
against intracellular pathogens in mice. Irgm1 deficiency is associated with a severe
immunodeficiency syndrome. The protein has been variously interpreted as a direct effector
molecule on bacterial phagosomes or on other organelles or as an inducer of autophagy. In this
study, we re-examined one of these claims, namely that Irgm1 targets mycobacterial and listerial
phagosomes. We found no colocalization of endogenous Irgm1, using two immunofluorescent staining
techniques, either in fibroblasts or in macrophages. We demonstrated the predicted existence of
two protein isoforms of Irgm1 derived from differential splicing and described immunological
reagents for their detection. Both Irgm1 isoforms localize to the Golgi apparatus and weakly to
mitochondria; however, only the long Irgm1 isoforms can be detected on endolysosomal membranes.
Together with the previous observation that the general immunodeficiency phenotype of Irgm1(-/-)
mice is reversed in Irgm1/Irgm3 double-deficient mice, our results argue against a direct
effector function of Irgm1 at the bacterial phagosome. We discuss these findings in the context
of evidence that Irgm1 functions as a negative regulator of other members of the
immunity-related GTPase protein family.
Fitness landscape of nucleosome positioning
Weghorn D, Lässig M, Proc. Natl. Acad. Sci., vol. 110 no. 27
10988-10993 (2013)
Histone–DNA complexes, so-called
nucleosomes, are the building blocks of DNA packaging in eukaryotic cells. The histone-binding
affinity of a local DNA segment depends on its elastic properties and determines its
accessibility within the nucleus, which plays an important role in the regulation of gene
expression. Here, we derive a fitness landscape for intergenic DNA segments in yeast as a
function of two molecular phenotypes: their elasticity-dependent histone affinity and their
coverage with transcription factor binding sites. This landscape reveals substantial selection
against nucleosome formation over a wide range of both phenotypes. We use it as the core
component of a quantitative evolutionary model for intergenic DNA segments. This model
consistently predicts the observed diversity of histone affinities within wild Saccharomyces
paradoxus populations, as well as the affinity divergence between neighboring Saccharomyces
species. Our analysis establishes histone binding and transcription factor binding as two
separable modes of sequence evolution, each of which is a direct target of natural selection.
Predicting C4 Photosynthesis Evolution: Modular, Individually
Adaptive Steps on a Mount Fuji Fitness Landscape
Heckmann D, Schulze S, Denton A, Gowik U, Westhoff P, Weber APM,
Lercher MJ, Cell 153, No. 6 (2013)
An ultimate goal of evolutionary biology is
the prediction and experimental verification of adaptive trajectories on macroevolutionary
timescales. This aim has rarely been achieved for complex biological systems, as models usually
lack clear correlates of organismal fitness. Here, we simulate the fitness landscape connecting
two carbon fixation systems: C3 photosynthesis, used by most plant species, and the C4 system,
which is more efficient at ambient CO2 levels and elevated temperatures and which repeatedly
evolved from C3. Despite extensive sign epistasis, C4 photosynthesis is evolutionarily
accessible through individually adaptive steps from any intermediate state. Simulations show
that biochemical subtraits evolve in modules; the order and constitution of modules confirm and
extend previous hypotheses based on species comparisons. Plant-species-designated C3-C4
intermediates lie on predicted evolutionary trajectories, indicating that they indeed represent
transitory states. Contrary to expectations, we find no slowdown of adaptation and no
diminishing fitness gains along evolutionary trajectories.
Successive gain of insulator proteins in arthropod evolution
Heger P, George R, Wiehe T, Evolution (online access) June 4
(2013)
Alteration of regulatory DNA elements or
their binding proteins may have drastic consequences for morphological evolution. Chromatin
insulators are one example of such proteins and play a fundamental role in organizing gene
expression. While a single insulator protein, CTCF (CCCTC-binding factor), is known in
vertebrates,
Drosophila melanogaster utilizes six additional factors. We studied the
evolution of these proteins and show here that—in contrast to the bilaterian-wide distribution
of CTCF—all other
D. melanogaster insulators are restricted to arthropods. The full set
is present exclusively in the genus
Drosophila whereas only two insulators, Su(Hw) and
CTCF, existed at the base of the arthropod clade and all additional factors have been acquired
successively at later stages. Secondary loss of factors in some lineages further led to the
presence of different insulator subsets in arthropods. Thus, the evolution of insulator proteins
within arthropods is an ongoing and dynamic process that reshapes and supplements the ancient
CTCF-based system common to bilaterians. Expansion of insulator systems may therefore be a
general strategy to increase an organism's gene regulatory repertoire and its potential for
morphological plasticity.
Patterning the dorsal-ventral axis of the wasp Nasonia
vitripennis: Novelty and Convergence
Buchta T, Özüak O, Stappert D, Roth S, Lynch JA, Dev Biol, Epub
ahead of print (2013)
Regulatory networks composed of interacting
genes are responsible for pattern formation and cell type specification in a wide variety of
developmental contexts. Evolution must act on these regulatory networks in order to change the
proportions, distribution, and characteristics of specified cells. Thus, understanding how these
networks operate in homologous systems across multiple levels of phylogenetic divergence is
critical for understanding the evolution of developmental systems. Among the most thoroughly
characterized regulatory networks is the dorsal-ventral patterning system of the fly Drosophila
melanogaster. Due to the thorough understanding of this system, it is an ideal starting point
for comparative analyses. Here we report an analysis of the DV patterning system of the wasp,
Nasonia vitripennis. This wasp undergoes a mode of long germ embryogenesis that is superficially
nearly identical to that of Drosophila, but one that was likely independently derived. We have
found that while the expression of genes just prior to the onset of gastrulation is almost
identical in Nasonia and Drosophila, both the upstream network responsible for generating this
pattern, and the downstream morphogenetic movements that it sets in motion, are significantly
diverged. From this we conclude that many network structures are available to evolution to
achieve particular developmental ends.
How epigenetic mutations can affect genetic evolution: Model and
mechanism
Klironomos F, Berg J, Collins S, Bioessays, 35 (6), 571-578 (2013)
We hypothesize that heritable epigenetic
changes can affect rates of fitness increase as well as patterns of genotypic and phenotypic
change during adaptation. In particular, we suggest that when natural selection acts on pure
epigenetic variation in addition to genetic variation, populations adapt faster, and adaptive
phenotypes can arise before any genetic changes. This may make it difficult to reconcile the
timing of adaptive events detected using conventional population genetics tools based on DNA
sequence data with environmental drivers of adaptation, such as changes in climate. Epigenetic
modifications are frequently associated with somatic cell differentiation, but recently
epigenetic changes have been found that can be transmitted over many generations. Here, we show
how the interplay of these heritable epigenetic changes with genetic changes can affect adaptive
evolution, and how epigenetic changes affect the signature of selection in the genetic record.
Symplesiomorphies in the WUSCHEL clade suggest that the last
common ancestor of seed plants contained at least four independent stem cell niches
Nardmann J, Werr W, New Phytologist, 199:1081-92. doi: 10.1111/nph.12343 (2013)
Evolutionary studies addressing plant
architecture have uncovered several significant dichotomies between lower and higher land plant
radiations, which are based on differences in meristem histology and function. Here, we assess
the establishment of different stem cell niches during land plant evolution based on genes of
the stem cell-promoting WUSCHEL (WUS) clade of the WOX (WUSCHEL-related homeobox) gene family.
WOX gene orthology was addressed by phylogenetic analyses of full-length WOX protein sequences
and cellular expression pattern studies indicate process homology. Gene amplifications in the
WUS clade were present in the last common ancestor (LCA) of extant gymnosperms and angiosperms.
Whereas the evolution of complex multicellular shoot and root meristems relates to members in
the WUS/WOX5 sub-branch, the evolution of marginal and plate meristems or the vascular cambium
is associated with gene duplications that gave rise to WOX3 and WOX4, respectively. A fourth WUS
clade member, WOX2, was apparently recruited for apical cell fate specification during early
embryogenesis. The evolution and functional interplay of WOX3 and WOX4 possibly promoted a novel
mode of leaf development, and evolutionary adaptations in their activities have contributed to
the great diversity in shape and architecture of leaves in seed plants.
Co-variation of germination and growth related traits across the
European latitudinal range of Arabidopsis thaliana
Debieu M, Tang C, Stich B, Effgen S, Josephs E, Schmitt J,
Nordborg M, Koornneef M, de Meaux J, PlosONE 8(5): e61075 (2013)
Life-history traits controlling the
duration and timing of developmental phases in the life cycle jointly determine fitness.
Therefore, life-history traits studied in isolation provide an incomplete view on the relevance
of life-cycle variation for adaptation. In this study, we examine genetic variation in traits
covering the major life history events of the annual species Arabidopsis thaliana: seed
dormancy, vegetative growth rate and flowering time. In a sample of 112 genotypes collected
throughout the European range of the species, both seed dormancy and flowering time follow a
latitudinal gradient independent of the major population structure gradient. This finding
confirms previous studies reporting the adaptive evolution of these two traits. Here, however,
we further analyze patterns of co-variation among traits. We observe that co-variation between
primary dormancy, vegetative growth rate and flowering time also follows a latitudinal cline. At
higher latitudes, vegetative growth rate is positively correlated with primary dormancy and
negatively with flowering time. In the South, this trend disappears. Patterns of trait
co-variation change, presumably because major environmental gradients shift with latitude. This
pattern appears unrelated to population structure, suggesting that changes in the coordinated
evolution of major life history traits is adaptive. Our data suggest that A. thaliana provides a
good model for the evolution of trade-offs and their genetic basis.
A TIR-NBS protein encoded by Arabidopsis Chilling Sensitive 1
(CHS1) limits chloroplast damage and cell death at low temperature
Zbierzak AM, Porfirova S, Griebel T, Melzer M, Parker JE, Dörmann
P, Plant J. 74: online (2013)
Survival of plants at low temperature
depends on mechanisms for limiting physiological damage and maintaining growth. We mapped the
chs1-1 (chilling sensitive1-1) mutation in Arabidopsis accession Columbia to the TIR-NBS gene
At1g17610. In chs1-1, a single amino acid exchange at the CHS1 N-terminus close to the conserved
TIR domain creates a stable mutant protein that fails to protect leaves against chilling stress.
The sequence of another TIR-NBS gene (At5g40090) named CHL1 (CHS1-like 1) is related to that of
CHS1. Over-expression of CHS1 or CHL1 alleviates chilling damage and enhances plant growth at
moderate (24°C) and chilling (13°C) temperatures, suggesting a role for both proteins in growth
homeostasis. chs1-1 mutants show induced salicylic acid production and defense gene expression
at 13°C, indicative of autoimmunity. Genetic analysis of chs1-1 in combination with defense
pathway mutants shows that chs1-1 chilling sensitivity requires the TIR-NBS-LRR and basal
resistance regulators encoded by EDS1 and PAD4 but not salicylic acid. By following the timing
of metabolic, physiological and chloroplast ultrastructural changes in chs1-1 leaves during
chilling, we have established that alterations in photosynthetic complexes and thylakoid
membrane integrity precede leaf cell death measured by ion leakage. At 24°C, the chs1-1 mutant
appears normal but produces a massive necrotic response to virulent Pseudomonas syringae pv.
tomato infection, although this does not affect bacterial proliferation. Our results suggest
that CHS1 acts at an intersection between temperature sensing and biotic stress pathway
activation to maintain plant performance over a range of conditions.
Coalescent tree imbalance and a simple test for selective sweeps
based on microsatellite variation
Li H, Wiehe T, Plos Computational Biology, 9(5): e1003060 (2013)
It is one of the major interests in
population genetics to contrast the properties and consequences of neutral and non-neutral modes
of evolution. As is well-known, positive Darwinian selection and genetic hitchhiking drastically
change the profile of genetic diversity compared to neutral expectations. The present-day
observable genetic diversity in a sample of DNA sequences depends on events in their
evolutionary history, and in particular on the shape of the underlying genealogical tree. In
this paper we study how the shape of coalescent trees is affected by the presence of positively
selected mutations. We define a measure of tree topology and study its properties under
scenarios of neutrality and positive selection. We show that this measure can reliably be
estimated from experimental data, and define an easy-to-compute statistical test of the neutral
evolution hypothesis. We apply this test to data from a population of the malaria parasite
Plasmodium
falciparum and confirm the signature of recent positive selection in the vicinity of a
drug resistance locus.
Patterns of Epistasis between Beneficial Mutations in an
Antibiotic Resistance Gene
Schenk MF, Szendro IG, Salverda ML, Krug J, de Visser JA, Mol Biol
Evol 30 (8): 1779-1787 (2013)
Understanding epistasis is central to
biology. For instance, epistatic interactions determine the topography of the fitness landscape
and affect the dynamics and determinism of adaptation. However, few empirical data are
available, and comparing results is complicated by confounding variation in the system and the
type of mutations used. Here, we take a systematic approach by quantifying epistasis in two sets
of four beneficial mutations in the antibiotic resistance enzyme TEM-1 β-lactamase. Mutations in
these sets have either large or small effects on cefotaxime resistance when present as single
mutations. By quantifying the epistasis and ruggedness in both landscapes, we find two general
patterns. First, resistance is maximal for combinations of two mutations in both fitness
landscapes and declines when more mutations are added due to abundant sign epistasis and a
pattern of diminishing returns with genotype resistance. Second, large-effect mutations interact
more strongly than small-effect mutations, suggesting that the effect size of mutations may be
an organizing principle in understanding patterns of epistasis. By fitting the data to simple
phenotype resistance models, we show that this pattern may be explained by the nonlinear
dependence of resistance on enzyme stability and an unknown phenotype when mutations have
antagonistically pleiotropic effects. The comparison to a previously published set of mutations
in the same gene with a joint benefit further shows that the enzyme's fitness landscape is
locally rugged but does contain adaptive pathways that lead to high resistance.
Exact results for the amplitude spectra of fitness landscapes
Neidhart J, Szendro I G, Krug J, J. Theor. Biol., Volume 332, 7
September 2013, Pages 218–227 (2013)
Starting from fitness correlation
functions, we calculate exact expressions for the amplitude spectra of fitness landscapes as
defined by P.F. Stadler [J. Math. Chem. 20, 1 (1996)] for common landscape models, including
Kauffman's NK-model, rough Mt. Fuji landscapes and general linear superpositions of such
landscapes. We further show that correlations decaying exponentially with Hamming distance yield
exponentially decaying spectra similar to those reported recently for a model of molecular
signal transduction. Finally, we compare our results for the model systems to the spectra of
various experimentally measured fitness landscapes. We claim that our analytical results should
be helpful when trying to interpret empirical data and guide the search for improved fitness
landscape models.
Developmental gene discovery in a hemimetabolous insect: de novo
assembly and annotation of a transcriptome for the cricket Gryllus bimaculatus
Zeng V, Ewen-Campen B, Horch HW, Roth S, Mito T, Extavour CG, PLoS
ONE 8(5): e61479 (2013)
Most genomic resources available for
insects represent the Holometabola, which are insects that undergo complete metamorphosis like
beetles and flies. In contrast, the Hemimetabola (direct developing insects), representing the
basal branches of the insect tree, have very few genomic resources. We have therefore created a
large and publicly available transcriptome for the hemimetabolous insect Gryllus bimaculatus
(cricket), a well-developed laboratory model organism whose potential for functional genetic
experiments is currently limited by the absence of genomic resources. cDNA was prepared using
mRNA obtained from adult ovaries containing all stages of oogenesis, and from embryo samples on
each day of embryogenesis. Using 454 Titanium pyrosequencing, we sequenced over four million raw
reads, and assembled them into 21,512 isotigs (predicted transcripts) and 120,805 singletons
with an average coverage per base pair of 51.3. We annotated the transcriptome manually for over
400 conserved genes involved in embryonic patterning, gametogenesis, and signaling pathways.
BLAST comparison of the transcriptome against the NCBI non-redundant protein database (nr)
identified significant similarity to nr sequences for 55.5% of transcriptome sequences, and
suggested that the transcriptome may contain 19,874 unique transcripts. For predicted
transcripts without significant similarity to known sequences, we assessed their similarity to
other orthopteran sequences, and determined that these transcripts contain recognizable protein
domains, largely of unknown function. We created a searchable, web-based database to allow
public access to all raw, assembled and annotated data. This database is to our knowledge the
largest de novo assembled and annotated transcriptome resource available for any hemimetabolous
insect. We therefore anticipate that these data will contribute significantly to more effective
and higher-throughput deployment of molecular analysis tools in Gryllus.
Cyanobacterial protease inhibitors lead to maternal transfer of
increased protease gene expression in Daphnia.
Schwarzenberger A, Von Elert E, Oecologia, Volume 172, Issue 1, pp
11-20 (2013)
Protease inhibitors (PIs) have frequently
been found in cyanobacterial blooms and have been shown to affect the major herbivore
Daphnia
by decreasing growth and inhibiting gut protease activity. However, it has been shown that a
clone of
Daphnia is able to respond to dietary PIs by increasing its protease gene
expression. Such an inducible response might be maternally transferred to the next generation.
Therefore, we tested a tolerant clone for maternal transfer of protease gene expression. When
exposed to the trypsin inhibitor-producing cyanobacterium Microcystis aeruginosa PCC7806 Mut,
Daphnia mothers and their untreated newborns showed an increase in trypsin gene
expression compared to naïve mothers grown on control food and their offspring. The maternally
transferred increase in gene expression was accompanied by a higher somatic growth rate of the
offspring generation from exposed mothers compared to offspring from naïve mothers. This higher
growth rate compensated for the lower dry mass of newborns from exposed mothers and led to the
same fitness as observed in the offspring of naïve mothers. In nature, clones that can
maternally transfer increased protease gene expression should have an advantage over clones that
cannot. The selection for such more tolerant clones by naturally occurring PIs might lead to
microevolution of natural
Daphnia populations, and to local adaptation in the long
term. This is the first study to show an adaptive maternal transfer of increased target gene
expression in an ecological context.
Exact enumeration of cherries and pitchforks in ranked trees
under the coalescent model.
Disanto F, Wiehe T, Mathematical Biosciences 242, 195-200 (2013)
We consider exact enumerations and
probabilistic properties of ranked trees when generated under the random coalescent process.
Using a new approach, based on generating functions, we derive several statistics such as the
exact probability of finding k cherries in a ranked tree of fixed size n. We then extend our
method to consider also the number of pitchforks. We find a recursive formula to calculate the
joint and conditional probabilities of cherries and pitchforks when the size of the tree is
fixed. These results provide insights into structural properties of coalescent trees under the
model of neutral evolution.
Interspecific differences between D. pulex and D. magna in
sensitivity to cyanobacteria with protease inhibitors
Kuster CJ, Von Elert E, Plos One 8 (5): e62658 (2013)
It is known that cyanobacteria negatively
affect herbivores due to their production of toxins such as protease inhibitors. In the present
study we investigated potential interspecific differences between two major herbivores, Daphnia
magna and Daphnia pulex, in terms of their tolerance to cyanobacteria with protease inhibitors.
Seven clones each of D. magna and of D. pulex were isolated from different habitats in Europe
and North America. To test for interspecific differences in the daphnids’ tolerance to
cyanobacteria, their somatic and population growth rates were determined for each D. magna and
D. pulex clone after exposure to varying concentrations of two Microcystis aeruginosa strains.
The M. aeruginosa strains NIVA and PCC− contained either chymotrypsin or trypsin inhibitors, but
no microcystins. Mean somatic and population growth rates on a diet with 20% NIVA were
significantly more reduced in D. pulex than in D. magna. On a diet with 10% PCC−, the population
growth of D. pulex was significantly more reduced than that of D. magna. This indicates that D.
magna is more tolerant to cyanobacteria with protease inhibitors than D. pulex. The reduction of
growth rates was possibly caused by an interference of cyanobacterial inhibitors with proteases
in the gut of Daphnia, as many other conceivable factors, which might have been able to explain
the reduced growth, could be excluded as causal factors. Protease assays revealed that the
sensitivities of chymotrypsins and trypsins to cyanobacterial protease inhibitors did not differ
between D. magna and D. pulex. However, D. magna exhibited a 2.3-fold higher specific
chymotrypsin activity than D. pulex, which explains the observed higher tolerance to
cyanobacterial protease inhibitors of D. magna. The present study suggests that D. magna may
control the development of cyanobacterial blooms more efficiently than D. pulex due to
differences in their tolerance to cyanobacteria with protease inhibitors.
Semi-automated 3D Leaf Reconstruction and Analysis of Trichome Patterning from Light Microscopic Images
H Failmezger, B Jaegle, A Schrader, M Hulskamp and A Tresch (2013), PLoS Comput Biol, 9(4):e1003029, DOI: 10.1371/journal.pcbi.1003029
Trichomes are leaf hairs that are formed by single cells on the leaf surface. They are known to be involved in pathogen resistance. Their patterning is considered to emerge from a field of initially equivalent cells through the action of a gene regulatory network involving trichome fate promoting and inhibiting factors. For a quantitative analysis of single and double mutants or the phenotypic variation of patterns in different ecotypes, it is imperative to statistically evaluate the pattern reliably on a large number of leaves. Here we present a method that enables the analysis of trichome patterns at early developmental leaf stages and the automatic analysis of various spatial parameters. We focus on the most challenging young leaf stages that require the analysis in three dimensions, as the leaves are typically not flat. Our software TrichEratops reconstructs 3D surface models from 2D stacks of conventional light-microscope pictures. It allows the GUI-based annotation of different stages of trichome development, which can be analyzed with respect to their spatial distribution to capture trichome patterning events. We show that 3D modeling removes biases of simpler 2D models and that novel trichome patterning features increase the sensitivity for inter-accession comparisons.
The effect of single recombination events on coalescent tree
height and shape
Ferretti L, Disanto F, Wiehe T, PLoS One, 8(4):e60123 (2013)
The coalescent with recombination is a
fundamental model to describe the genealogical history of DNA sequence samples from recombining
organisms. Considering recombination as a process which acts along genomes and which creates
sequence segments with shared ancestry, we study the influence of single recombination events
upon tree characteristics of the coalescent. We focus on properties such as tree height and tree
balance and quantify analytically the changes in these quantities incurred by recombination in
terms of probability distributions. We find that changes in tree topology are often relatively
mild under conditions of neutral evolution, while changes in tree height are on average quite
large. Our results add to a quantitative understanding of the spatial coalescent and provide the
neutral reference to which the impact by other evolutionary scenarios, for instance tree
distortion by selective sweeps, can be compared.
Seasonal succession of cyanobacterial protease inhibitors and
Daphnia magna genotypes in a eutrophic Swedish lake
Schwarzenberger A, D'hondt S, Vyverman W, Von Elert E, Aquatic
Sciences, Volume 75, Issue 3, pp 433-445 (2013)
Lakes are well known for having a pattern
of seasonal succession of phytoplankton and zooplankton. The succession of different taxa of
phytoplankton results in a succession of zooplankton taxa, and within the genus
Daphnia,
into a succession of different genotypes (clones). One cause for this succession of
Daphnia clones might be the production of digestive protease inhibitors by
cyanobacteria, which usually bloom in summer. Here we report seasonal changes in the frequency
and the abundance of
Daphnia magna haplotypes in a eutrophic lake, which developed a
chymotrypsin-inhibitor-producing cyanobacterial bloom in May. These seasonal changes were not
related to changes of biotic and abiotic lake parameters. However, a very high content of
chymotrypsin inhibitors was observed in May (but not in other months). This was assumed to have
exerted a strong punctual selection pressure on the
Daphnia population and on the
direct targets of the protease inhibitors, i.e. the digestive chymotrypsins of Daphnia.
Actually, D. magna from before and during the cyanobacterial bloom showed a different protease
pattern on activity stained SDS-PAGE in comparison to clones from the month after the bloom.
However, no difference in tolerance, measured as IC50 values, to inhibition by natural lake
seston from May was found between the clones from before and after the bloom. Thus, the
hypothesis that a seasonal adaptation of D. magna subpopulations from either April/May or June
might have occurred could not be proven. This suggests that the
Daphnia population
investigated here is locally adapted to cyanobacterial protease inhibitors.
Gene Transfer from Bacteria and Archaea Facilitated Evolution of
an Extremophilic Eukaryote
Schönknecht G, Chen WH, Ternes CM, Barbier GG, Shrestha RP,
Stanke M, Bräutigam A, Baker BJ, Banfield JF, Garavito RM, Carr K, Wilkerson C, Rensing SA,
Gagneul D, Dickenson NE, Oesterhelt C, Lercher MJ, Weber APM, Science, Vol. 339 no. 6124 pp.
1207-1210 (2013)
Some microbial eukaryotes, such as the
extremophilic red alga
Galdieria sulphuraria, live in hot, toxic metal-rich, acidic
environments. To elucidate the underlying molecular mechanisms of adaptation, we sequenced the
13.7-megabase genome of
G. sulphuraria. This alga shows an enormous metabolic
flexibility, growing either photoautotrophically or heterotrophically on more than 50 carbon
sources. Environmental adaptation seems to have been facilitated by horizontal gene transfer
from various bacteria and archaea, often followed by gene family expansion. At least 5% of
protein-coding genes of
G. sulphuraria were probably acquired horizontally. These
proteins are involved in ecologically important processes ranging from heavy-metal
detoxification to glycerol uptake and metabolism. Thus, our findings show that a pan-domain gene
pool has facilitated environmental adaptation in this unicellular eukaryote.
Co-option of a coordinate system defined by the EGFr and Dpp
pathways in the evolution of a morphological novelty
Vreede BM, Lynch JA, Roth S, Sucena E, Evodevo 4:7 (2013)
Background
Morphological innovation is an elusive and fascinating concept in evolutionary biology. A
novel structure may open up an array of possibilities for adaptation, and thus is
fundamental to the evolution of complex multicellular life. We use the respiratory
appendages on the dorsal-anterior side of the Drosophila eggshell as a model system for
morphological novelty. To study the co-option of genetic pathways in the evolution of this
novelty we have compared oogenesis and eggshell patterning in Drosophila melanogaster with
Ceratitis capitata, a dipteran whose eggs do not bear dorsal appendages.
Results
During the final stages of oogenesis, the appendages are formed by specific groups of cells
in the follicular epithelium of the egg chamber. These cells are defined via signaling
activity of the Dpp and EGFr pathways, and we find that both pathways are active in C.
capitata oogenesis. The transcription factor gene mirror is expressed downstream of EGFr
activation in a dorsolateral domain in the D. melanogaster egg chamber, but could not be
detected during C. capitata oogenesis. In D. melanogaster, mirror regulates the expression
of two important genes: broad, which defines the appendage primordia, and pipe, involved in
embryonic dorsoventral polarity. In C. capitata, broad remains expressed ubiquitously
throughout the follicular epithelium, and is not restricted to the appendage primordia.
Interestingly pipe expression did not differ between the two species.
Conclusions
Our analysis identifies both broad and mirror as important nodes that have been redeployed in
the Drosophila egg chamber patterning network in the evolution of a morphologically novel
feature. Further, our results show how pre-existing signals can provide an epithelium with a
spatial coordinate system, which can be co-opted for novel patterns.
Evolutionary dynamics and statistical physics
Fisher DS, Lässig M, Shraiman B, J. Stat. Mech. N01001 (2013)
This introductory article provides the
background to and motivation for this special issue and the relationship between evolutionary
dynamics and statistical physics.
Predictability of evolution depends nonmonotonically on
population size.
Szendro IG, Franke J, de Visser JAGM, Krug J, Proceedings Of The
National Academy Of Sciences Of The United States Of America 110, 571-576 (2013)
To gauge the relative importance of
contingency and determinism in evolution is a fundamental problem that continues to motivate
much theoretical and empirical research. In recent evolution experiments with microbes, this
question has been explored by monitoring the repeatability of adaptive changes in replicate
populations. Here, we present the results of an extensive computational study of evolutionary
predictability based on an experimentally measured eight-locus fitness landscape for the
filamentous fungus Aspergillus niger. To quantify predictability, we define entropy measures on
observed mutational trajectories and endpoints. In contrast to the common expectation of
increasingly deterministic evolution in large populations, we find that these entropies display
an initial decrease and a subsequent increase with population size N, governed, respectively, by
the scales Nμ and Nμ(2), corresponding to the supply rates of single and double mutations, where
μ denotes the mutation rate. The amplitude of this pattern is determined by μ. We show that
these observations are generic by comparing our findings for the experimental fitness landscape
to simulations on simple model landscapes.
Evolution of molecular phenotypes under stabilizing selection
Nourmohammad A, Schiffels S, Lässig M, Journal Of Statistical
Mechanics, P01012 (34 pages) (2013)
Molecular phenotypes are important links
between genomic information and organismic functions, fitness, and evolution. Complex
phenotypes, which are also called quantitative traits, often depend on multiple genomic loci.
Their evolution builds on genome evolution in a complicated way, which involves selection,
genetic drift, mutations and recombination. Here we develop a coarse-grained evolutionary
statistics for phenotypes, which decouples from details of the underlying genotypes. We derive
approximate evolution equations for the distribution of phenotype values within and across
populations. This dynamics covers evolutionary processes at high and low recombination rates,
that is, it applies to sexual and asexual populations. In a fitness landscape with a single
optimal phenotype value, the phenotypic diversity within populations and the divergence between
populations reach evolutionary equilibria, which describe stabilizing selection. We compute the
equilibrium distributions of both quantities analytically and we show that the ratio of mean
divergence and diversity depends on the strength of selection in a universal way: it is largely
independent of the phenotype's genomic encoding and of the recombination rate. This establishes
a new method for the inference of selection on molecular phenotypes beyond the genome level. We
discuss the implications of our findings for the predictability of evolutionary processes.
Quantitative analyses of empirical fitness landscapes
Szendro IG, Schenk MF, Franke J, Krug J, de Visser JAGM, Journal
Of Statistical Mechanics, P01005 (2013)
The concept of a fitness landscape is a
powerful metaphor that offers insight into various aspects of evolutionary processes and
guidance for the study of evolution. Until recently, empirical evidence on the ruggedness of
these landscapes was lacking, but since it became feasible to construct all possible genotypes
containing combinations of a limited set of mutations, the number of studies has grown to a
point where a classification of landscapes becomes possible. The aim of this review is to
identify measures of epistasis that allow a meaningful comparison of fitness landscapes and then
apply them to the empirical landscapes to discern factors that affect ruggedness. The various
measures of epistasis that have been proposed in the literature appear to be equivalent. Our
comparison shows that the ruggedness of the empirical landscape is affected by whether the
included mutations are beneficial or deleterious and by whether intra- or intergenic epistasis
is involved. Finally, the empirical landscapes are compared to landscapes generated with the
Rough Mt.\ Fuji model. Despite the simplicity of this model, it captures the features of the
experimental landscapes remarkably well.
2012
Antimicrobial effects of murine mesenchymal stromal cells
directed against Toxoplasma gondii and Neospora caninum: role of immunity-related GTPases (IRGs)
and guanylate-binding proteins (GBPs).
Spekker K, Leineweber M, Degrandi D, Ince V, Brunder S, Schmidt S
K, Stuhlsatz S, Howard J C, Schares G, Degistirici O, Meisel R et al., Medical Microbiology and
Immunology (2012)
Mesenchymal stromal cells (MSCs) have a
multilineage differentiation potential and provide immunosuppressive and antimicrobial
functions. Murine as well as human MSCs restrict the proliferation of T cells. However,
species-specific differences in the underlying molecular mechanisms have been described. Here,
we analyzed the antiparasitic effector mechanisms active in murine MSCs. Murine MSCs, in
contrast to human MSCs, could not restrict the growth of a highly virulent strain of Toxoplasma
gondii (BK) after stimulation with IFN-γ. However, the growth of a type II strain of T. gondii
(ME49) was strongly inhibited by IFN-γ-activated murine MSCs. Immunity-related GTPases (IRGs) as
well as guanylate-binding proteins (GBPs) contributed to this antiparasitic effect. Further
analysis showed that IFN-γ-activated mMSCs also inhibit the growth of Neospora caninum, a
parasite belonging to the apicomplexan group as well. Detailed studies with murine
IFN-γ-activated MSC indicated an involvement in IRGs like Irga6, Irgb6 and Irgd in the
inhibition of N. caninum. Additional data showed that, furthermore, GBPs like mGBP1 and mGBP2
could have played a role in the anti-N. caninum effect of murine MSCs. These data underline that
MSCs, in addition to their regenerative and immunosuppressive activity, function as
antiparasitic effector cells as well. However, IRGs are not present in the human genome,
indicating a species-specific difference in anti-T. gondii and anti-N. caninum effect between
human and murine MSCs.
Natural variation in small molecule-induced TIR-NB-LRR signaling
induces root growth arrest via EDS1- and PAD4-complexed R protein VICTR in Arabidopsis
Kim TH, Kunz HH, Bhattacharjee S, Hauser F, Park J, Engineer C,
Liu A, Ha T, Parker JE, Gassmann W, Schroeder JI, Plant Cell 24:5177-5192 (2012)
In a chemical genetics screen we identified
the small-molecule [5-(3,4-dichlorophenyl)furan-2-yl]-piperidine-1-ylmethanethione (DFPM) that
triggers rapid inhibition of early abscisic acid signal transduction via PHYTOALEXIN DEFICIENT4
(PAD4)- and ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1)-dependent immune signaling mechanisms.
However, mechanisms upstream of EDS1 and PAD4 in DFPM-mediated signaling remain unknown. Here,
we report that DFPM generates an Arabidopsis thaliana accession-specific root growth arrest in
Columbia-0 (Col-0) plants. The genetic locus responsible for this natural variant, VICTR
(VARIATION IN COMPOUND TRIGGERED ROOT growth response), encodes a TIR-NB-LRR (for
Toll-Interleukin1 Receptor–nucleotide binding–Leucine-rich repeat) protein. Analyses of T-DNA
insertion victr alleles showed that VICTR is necessary for DFPM-induced root growth arrest and
inhibition of abscisic acid–induced stomatal closing. Transgenic expression of the Col-0 VICTR
allele in DFPM-insensitive Arabidopsis accessions recapitulated the DFPM-induced root growth
arrest. EDS1 and PAD4, both central regulators of basal resistance and effector-triggered
immunity, as well as HSP90 chaperones and their cochaperones RAR1 and SGT1B, are required for
the DFPM-induced root growth arrest. Salicylic acid and jasmonic acid signaling pathway
components are dispensable. We further demonstrate that VICTR associates with EDS1 and PAD4 in a
nuclear protein complex. These findings show a previously unexplored association between a
TIR-NB-LRR protein and PAD4 and identify functions of plant immune signaling components in the
regulation of root meristematic zone-targeted growth arrest.
PEP1 of Arabis alpina Is Encoded by Two Overlapping Genes That
Contribute to Natural Genetic Variation in Perennial Flowering.
Albani MC, Castaings L, Wötzel S, Mateos JL, Wunder J, Wang R,
Reymond M, Coupland G, PLoS Genetics 8, e1003130 (2012)
Higher plants exhibit a variety of
different life histories. Annual plants live for less than a year and after flowering produce
seeds and senesce. By contrast perennials live for many years, dividing their life cycle into
episodes of vegetative growth and flowering. Environmental cues control key check points in both
life histories. Genes controlling responses to these cues exhibit natural genetic variation that
has been studied most in short-lived annuals. We characterize natural genetic variation
conferring differences in the perennial life cycle of Arabis alpina. Previously the accession
Pajares was shown to flower after prolonged exposure to cold (vernalization) and only for a
limited period before returning to vegetative growth. We describe five accessions of A. alpina
that do not require vernalization to flower and flower continuously. Genetic complementation
showed that these accessions carry mutant alleles at PERPETUAL FLOWERING 1 (PEP1), which encodes
a MADS box transcription factor orthologous to FLOWERING LOCUS C in the annual Arabidopsis
thaliana. Each accession carries a different mutation at PEP1, suggesting that such variation
has arisen independently many times. Characterization of these alleles demonstrated that in most
accessions, including Pajares, the PEP1 locus contains a tandem arrangement of a full length and
a partial PEP1 copy, which give rise to two full-length transcripts that are differentially
expressed. This complexity contrasts with the single gene present in A. thaliana and might
contribute to the more complex expression pattern of PEP1 that is associated with the perennial
life-cycle. Our work demonstrates that natural accessions of A. alpina exhibit distinct life
histories conferred by differences in PEP1 activity, and that continuous flowering forms have
arisen multiple times by inactivation of the floral repressor PEP1. Similar phenotypic variation
is found in other herbaceous perennial species, and our results provide a paradigm for how
characteristic perennial phenotypes might arise.
The arginine-rich N-terminal domain of ROP18 is necessary for
vacuole targeting and virulence of Toxoplasma gondii.
Fentress SJ, Steinfeldt T, Howard JC, Sibley LD, Cellular
Microbiology 14, 1921-1933 (2012)
Toxoplasma gondii uses specialized
secretory organelles called rhoptries to deliver virulence determinants into the host cell
during parasite invasion. One such determinant called rhoptry protein 18 (ROP18) is a
polymorphic serine/threonine kinase that phosphorylates host targets to modulate acute
virulence. Following secretion into the host cell, ROP18 traffics to the parasitophorous vacuole
membrane (PVM) where it is tethered to the cytosolic face of this host-pathogen interface.
However, the functional consequences of PVM association are not known. In this report, we show
that ROP18 mutants altered in an arginine-rich domain upstream of the kinase domain fail to
associate to the PVM following secretion from rhoptries. During infection, host cells upregulate
immunity-related GTPases that localize to and destroy the PVM surrounding the parasites. ROP18
disarms this host innate immune pathway by phosphorylating IRGs in a critical GTPase domain and
preventing loading on the PVM. Vacuole-targeting mutants of ROP18 failed to phosphorylate Irga6
and were unable to divert IRGs from the PVM, despite retaining intrinsic kinase activity. As a
consequence, these mutants were avirulent in a mouse model of acute toxoplasmosis. Thus, the
association of ROP18 with the PVM, mediated by its N-terminal arginine-rich domain, is critical
to its function as a virulence determinant.
GraphAlignment: Bayesian pairwise alignment of biological
networks
Kolář M, Meier J, Mustonen V, Lässig M, Berg J, BMC Systems
Biology, 6:144 doi:10.1186/1752-0509-6-144 (2012)
Background
With increased experimental availability and accuracy of bio-molecular networks, tools for
their comparative and evolutionary analysis are needed. A key component for such studies is
the alignment of networks.
Results
We introduce the Bioconductor package GraphAlignment for pairwise alignment of bio-molecular
networks. The alignment incorporates information both from network vertices and network
edges and is based on an explicit evolutionary model, allowing inference of all scoring
parameters directly from empirical data. We compare the performance of our algorithm to an
alternative algorithm, Græmlin 2.0.
On simulated data, GraphAlignment outperforms Græmlin 2.0 in several benchmarks except for
computational complexity. When there is little or no noise in the data, GraphAlignment is
slower than Græmlin 2.0. It is faster than Græmlin 2.0 when processing noisy data containing
spurious vertex associations. Its typical case complexity grows approximately as
𝒪(N2.6).
On empirical bacterial protein-protein interaction networks (PIN) and gene co-expression
networks, GraphAlignment outperforms Græmlin 2.0 with respect to coverage and specificity,
albeit by a small margin. On large eukaryotic PIN, Græmlin 2.0 outperforms
GraphAlignment.
Conclusions
The GraphAlignment algorithm is robust to spurious vertex associations, correctly resolves
paralogs, and shows very good performance in identification of homologous vertices defined
by high vertex and/or interaction similarity. The simplicity and generality of
GraphAlignment edge scoring makes the algorithm an appropriate choice for global alignment
of networks.
The chromatin insulator CTCF and the emergence of metazoan
diversity.
Heger P, Marin B, Bartkuhn M, Schierenberg E, Wiehe T, Proceedings
Of The National Academy Of Sciences Of The United States Of America 109, 17507-17512 (2012)
The great majority of metazoans belong to
bilaterian phyla. They diversified during a short interval in Earth's history known as the
Cambrian explosion, ~540 million years ago. However, the genetic basis of these events is poorly
understood. Here we argue that the vertebrate genome organizer CTCF (CCCTC-binding factor)
played an important role for the evolution of bilaterian animals. We provide evidence that the
CTCF protein and a genome-wide abundance of CTCF-specific binding motifs are unique to
bilaterian phyla, but absent in other eukaryotes. We demonstrate that CTCF-binding sites within
vertebrate and Drosophila Hox gene clusters have been maintained for several hundred million
years, suggesting an ancient origin of the previously known interaction between Hox gene
regulation and CTCF. In addition, a close correlation between the presence of CTCF and Hox gene
clusters throughout the animal kingdom suggests conservation of the Hox-CTCF link across the
Bilateria. On the basis of these findings, we propose the existence of a Hox-CTCF kernel as
principal organizer of bilaterian body plans. Such a kernel could explain (i) the formation of
Hox clusters in Bilateria, (ii) the diversity of bilaterian body plans, and (iii) the uniqueness
and time of onset of the Cambrian explosion.
Clonal interference in the evolution of influenza.
Strelkowa N, Lässig M, Genetics 192, 671-682 (2012)
The seasonal influenza A virus undergoes
rapid evolution to escape human immune response. Adaptive changes occur primarily in antigenic
epitopes, the antibody-binding domains of the viral hemagglutinin. This process involves
recurrent selective sweeps, in which clusters of simultaneous nucleotide fixations in the
hemagglutinin coding sequence are observed about every 4 years. Here, we show that influenza A
(H3N2) evolves by strong clonal interference. This mode of evolution is a red queen race between
viral strains with different beneficial mutations. Clonal interference explains and quantifies
the observed sweep pattern: we find an average of at least one strongly beneficial amino acid
substitution per year, and a given selective sweep has three to four driving mutations on
average. The inference of selection and clonal interference is based on frequency time series of
single-nucleotide polymorphisms, which are obtained from a sample of influenza genome sequences
over 39 years. Our results imply that mode and speed of influenza evolution are governed not
only by positive selection within, but also by background selection outside antigenic epitopes:
immune adaptation and conservation of other viral functions interfere with each other. Hence,
adapting viral proteins are predicted to be particularly brittle. We conclude that a
quantitative understanding of influenza's evolutionary and epidemiological dynamics must be
based on all genomic domains and functions coupled by clonal interference.
Molecular mechanisms of tolerance to cyanobacterial protease
inhibitors revealed by clonal differences in Daphnia magna.
Schwarzenberger A, Kuster CJ, Von Elert E, Molecular Ecology 21,
4898-4911 (2012)
Protease inhibitors of primary producers
are a major food quality constraint for herbivores. In nutrient-rich freshwater ecosystems, the
interaction between primary producers and herbivores is mainly represented by Daphnia and
cyanobacteria. Protease inhibitors have been found in many cyanobacterial blooms. These
inhibitors have been shown (both in vitro and in situ) to inhibit the most important group of
digestive proteases in the daphnid's gut, that is, trypsins and chymotrypsins. In this
study, we fed four different Daphnia magna genotypes with the trypsin-inhibitor-containing
cyanobacterial strain Microcystis aeruginosa PCC 7806 Mut. Upon exposure to dietary trypsin
inhibitors, all D. magna genotypes showed increased gene expression of digestive trypsins and
chymotrypsins. Exposure to dietary trypsin inhibitors resulted in increased activity of
chymotrypsins and reduced activity of trypsin. Strong intraspecific differences in tolerance of
the four D. magna genotypes to the dietary trypsin inhibitors were found. The degree of
tolerance depended on the D. magna genotype. The genotypes' tolerance was positively
correlated with the residual trypsin activity and the different IC(50) values of the trypsins.
On the genetic level, the different trypsin loci varied between the D. magna genotypes. The two
tolerant Daphnia genotypes that both originate from the same lake, which frequently produces
cyanobacterial blooms, clustered in a neighbour-joining phylogenetic tree based on the three
trypsin loci. This suggests that the genetic variability of trypsin loci was an important cause
for the observed intraspecific variability in tolerance to cyanobacterial trypsin inhibitors.
Based on these findings, it is reasonable to assume that such genetic variability can also be
found in natural populations and thus constitutes the basis for local adaptation of natural
populations to dietary protease inhibitors.
Evolutionary Accessibility in Tunably Rugged Fitness Landscapes
Franke J, Krug J, Journal of Statistical Physics, Volume 148,
Issue 4, pp 705-722 (2012)
The adaptive evolution of a population
under the influence of mutation and selection is strongly influenced by the structure of the
underlying fitness landscape, which encodes the interactions between mutations at different
genetic loci. Theoretical studies of such landscapes have been carried out for several decades,
but only recently experimental fitness measurements encompassing all possible combinations of
small sets of mutations have become available. The empirical studies have spawned new questions
about the accessibility of optimal genotypes under natural selection. Depending on population
dynamic parameters such as mutation rate and population size, evolutionary accessibility can be
quantified through the statistics of accessible mutational pathways (along which fitness
increases monotonically), or through the study of the basin of attraction of the optimal
genotype under greedy (steepest ascent) dynamics. Here we investigate these two measures of
accessibility in the framework of Kauffman's LK-model, a paradigmatic family of random fitness
landscapes with tunable ruggedness. The key parameter governing the strength of genetic
interactions is the number K of interaction partners of each of the L sites in the genotype
sequence. In general, accessibility increases with increasing genotype dimensionality L and
decreases with increasing number of interactions K. Remarkably, however, we find that some
measures of accessibility behave non-monotonically as a function of K, indicating a special role
of the most sparsely connected, non-trivial cases K=1 and 2. The relation between models for
fitness landscapes and spin glasses is also addressed.
Seasonal dynamics of sestonic protease inhibition: Impact on Daphnia
populations
Kuster CJ, Schwarzenberger A, Von Elert E, Hydrobiologia, Volume
172, Issue 1, pp 11-20 (2012)
Daphnia populations often show
rapid microevolutionary adaptation to environmental changes. Here, we investigated the
possibility that microevolution of
Daphnia populations could be driven by natural
sestonic Protease Inhibition (PI). We hypothesized that PI changes seasonally, which might lead
to concomitant changes in tolerance to PI in a co-occurring
Daphnia magna population.
In order to test this, seston from a eutrophic pond was sampled regularly over two successive
years. Extracts of these freeze-dried samples were used to determine their Inhibitory Potential
(IP) on D. magna gut proteases. In the summer seston the IP against chymotrypsins exceeded that
of spring seston 200-fold. In order to test for possible impacts on the co-existing D. magna
population, we isolated clones before (spring) and after (fall) the peak of the IP.
Microsatellite analyses revealed that the two subpopulations were genetically distinct.
Individual exposure of three clones from each population to varying concentrations of a
cyanobacterium that contains chymotrypsin inhibitors revealed a decrease in population and
somatic growth rate for each clone, but no seasonal effects on
Daphnia’s tolerance. In
order to include maternal effects, we conducted a multi-clonal competition experiment on various
cyanobacterial concentrations. However, no evidence for seasonally increased tolerance of D.
magna to dietary protease inhibitors could be found.
The genetic basis of flowering responses to seasonal cues.
Andrés F, Coupland G, Nature Reviews. Genetics 13, 627-639 (2012)
Plants respond to the changing seasons to
initiate developmental programmes precisely at particular times of year. Flowering is the best
characterized of these seasonal responses, and in temperate climates it often occurs in spring.
Genetic approaches in Arabidopsis thaliana have shown how the underlying responses to changes in
day length (photoperiod) or winter temperature (vernalization) are conferred and how these
converge to create a robust seasonal response. Recent advances in plant genome analysis have
demonstrated the diversity in these regulatory systems in many plant species, including several
crops and perennials, such as poplar trees. Here, we report progress in defining the diverse
genetic mechanisms that enable plants to recognize winter, spring and autumn to initiate flower
development.
Mean-field theory for the inverse Ising problem at low
temperatures
Nguyen HC, Berg J, Phys. Rev. Lett. 109, 050602 (2012)
The large amounts of data from molecular
biology and neuroscience have lead to a renewed interest in the inverse Ising problem: how to
reconstruct parameters of the Ising model (couplings between spins and external fields) from a
number of spin configurations sampled from the Boltzmann measure. To invert the relationship
between model parameters and observables (magnetizations and correlations), mean-field
approximations are often used, allowing the determination of model parameters from data.
However, all known mean-field methods fail at low temperatures with the emergence of multiple
thermodynamic states. Here, we show how clustering spin configurations can approximate these
thermodynamic states and how mean-field methods applied to thermodynamic states allow an
efficient reconstruction of Ising models also at low temperatures.
High-resolution melting analysis: a genotyping tool for
population studies on Daphnia
Kuster CJ, Von Elert E, Molecular Ecology Resources 12, 1048-1057
(2012)
Determining genetic variation at the DNA
level within and between natural populations is important for understanding the role of natural
selection on phenotypic traits, but many techniques of screening for genetic variation are
either cost intensive, not sensitive enough or too labour- and time-consuming. Here, we
demonstrate high-resolution melting analysis (HRMA) as a cost-effective and powerful tool for
screening variable target genes in natural populations. HRMA is based on monitoring the melting
of PCR amplicons. Owing to saturating concentrations of a dye that binds at high concentrations
to double-stranded DNA, it is possible to genotype high numbers of samples rapidly and
accurately. We analysed digestive trypsins of two
Daphnia magna populations as an
application example for HRMA. One population originated from a pond containing toxic
cyanobacteria that possibly produce protease inhibitors and the other from a pond without such
cyanobacteria. The hypothesis was that D. magna clones from ponds with cyanobacteria have
undergone selection by these inhibitors, which has led to different trypsin alleles. We first
sequenced pooled genomic PCR products of trypsins from both populations to identify variable DNA
sequences of active trypsins. Second, we screened variable DNA sequences of each D. magna clone
from both populations for single nucleotide polymorphisms via HRMA. The HRMA results revealed
that both populations exhibited phenotypic differences in the analysed trypsins. Our results
indicate that HRMA is a powerful genotyping tool for studying the variation of target genes in
response to selection within and between natural
Daphnia populations.
Inducible tolerance to dietary protease inhibitors in Daphnia
magna.
Von Elert E, Zitt A, Schwarzenberger A, The Journal Of
Experimental Biology 215, 2051-2059 (2012)
Daphnia has been shown to acquire tolerance
to cyanobacterial toxins within an animals' lifetime and to transfer this tolerance to the
next generation. Here we used a strain of the cyanobacterium Microcystis aeruginosa, which
contained two chymotrypsin inhibitors (BN920 and CP954), the green alga Scenedesmus obliquus as
reference food and a clone of D. magna to investigate the physiological mechanism of acquired
tolerance to these cyanobacterial toxins. The intracellular concentrations of CP954 and BN920
were 1550 and 120 μmol l(-1), respectively. When food suspensions of the green alga contained
>60% M. aeruginosa, growth rates of D. magna were reduced. When grown on the green alga,
three chymotrypsins ranging in mass from 16 to 22 kDa were distinguished in D. magna. Purified
BN920 and CP954 specifically inhibited D. magna chymotrypsins. Feeding with encapsulated BN920
resulted in growth depression in D. magna and replacement of the chymotrypsins by three
chymotrypsins with smaller molecular mass. With just 20% M. aeruginosa, the same changes in the
chymotrypsin pattern as with the pure inhibitor were observed. IC(50) values for inhibition of
chymotrypsins of D. magna growing on the green alga were 5.4 nmol l(-1) (BN920) and 7.4 nmol
l(-1) (CP954). When D. magna was grown on 20% M. aeruginosa, 2.2-fold higher IC(50) values were
observed. This indicated that increased tolerance to these dietary inhibitors was acquired
within an animal's lifetime by remodelling the digestive chymotrypsins, which in turn
serves as an intra-generational defence against these cyanobacterial inhibitors. This mechanism
might be relevant for the transfer of tolerance to the next generation through maternal effects.
Flagellin perception varies quantitatively in Arabidopsis
thaliana and its relatives.
Vetter MM, Kronholm I, He F, Häweker H, Reymond M, Bergelson J,
Robatzek S, de Meaux J, Molecular Biology And Evolution 29, 1655-1667 (2012)
Much is known about the evolution of plant
immunity components directed against specific pathogen strains: They show pervasive functional
variation and have the potential to coevolve with pathogen populations. However, plants are
effectively protected against most microbes by generalist immunity components that detect
conserved pathogen-associated molecular patterns (PAMPs) and control the onset of PAMP-triggered
immunity. In Arabidopsis thaliana, the receptor kinase flagellin sensing 2 (FLS2) confers
recognition of bacterial flagellin (flg22) and activates a manifold defense response. To
decipher the evolution of this system, we performed functional assays across a large set of A.
thaliana genotypes and Brassicaceae relatives. We reveal extensive variation in flg22
perception, most of which results from changes in protein abundance. The observed variation
correlates with both the severity of elicited defense responses and bacterial proliferation. We
analyzed nucleotide variation segregating at FLS2 in A. thaliana and detected a pattern of
variation suggestive of the rapid fixation of a novel adaptive allele. However, our study also
shows that evolution at the receptor locus alone does not explain the evolution of flagellin
perception; instead, components common to pathways downstream of PAMP perception likely
contribute to the observed quantitative variation. Within and among close relatives, PAMP
perception evolves quantitatively, which contrasts with the changes in recognition typically
associated with the evolution of R genes.
Genetic basis of adaptation in Arabidopsis thaliana: local
adaptation at the seed dormancy QTL DOG1.
Kronholm I, Picó FX, Alonso-Blanco C, Goudet J, de Meaux J,
Evolution 66, 2287-2302 (2012)
Local adaptation provides an opportunity to
study the genetic basis of adaptation and investigate the allelic architecture of adaptive
genes. We study delay of germination 1 (DOG1), a gene controlling natural variation in seed
dormancy in Arabidopsis thaliana and investigate evolution of dormancy in 41 populations
distributed in four regions separated by natural barriers. Using F(ST) and Q(ST) comparisons, we
compare variation at DOG1 with neutral markers and quantitative variation in seed dormancy.
Patterns of genetic differentiation among populations suggest that the gene DOG1 contributes to
local adaptation. Although Q(ST) for seed dormancy is not different from F(ST) for neutral
markers, a correlation with variation in summer precipitation supports that seed dormancy is
adaptive. We characterize dormancy variation in several F(2) -populations and show that a series
of functionally distinct alleles segregate at the DOG1 locus. Theoretical models have shown that
the number and effect of alleles segregatin at quantitative trait loci (QTL) have important
consequences for adaptation. Our results provide support to models postulating a large number of
alleles at quantitative trait loci involved in adaptation.
Mutation in TERMINAL FLOWER1 Reverses the Photoperiodic
Requirement for Flowering in the Wild Strawberry Fragaria vesca
Koskela EA, Mouhu K, Albani MC, Kurokura T, Rantanen M, Sargent
DJ, Battey NH, Coupland G, Elomaa P, Hytonen T, Plant Physiol 159, 1043-105 (2012)
Photoperiodic flowering has been
extensively studied in the annual short-day and long-day plants rice (Oryza sativa) and
Arabidopsis (Arabidopsis thaliana), whereas less is known about the control of flowering in
perennials. In the perennial wild strawberry, Fragaria vesca (Rosaceae), short-day and perpetual
flowering long-day accessions occur. Genetic analyses showed that differences in their flowering
responses are caused by a single gene, SEASONAL FLOWERING LOCUS, which may encode the F. vesca
homolog of TERMINAL FLOWER1 (FvTFL1). We show through high-resolution mapping and transgenic
approaches that FvTFL1 is the basis of this change in flowering behavior and demonstrate that
FvTFL1 acts as a photoperiodically regulated repressor. In short-day F. vesca, long photoperiods
activate FvTFL1 mRNA expression and short days suppress it, promoting flower induction. These
seasonal cycles in FvTFL1 mRNA level confer seasonal cycling of vegetative and reproductive
development. Mutations in FvTFL1 prevent long-day suppression of flowering, and the early
flowering that then occurs under long days is dependent on the F. vesca homolog of FLOWERING
LOCUS T. This photoperiodic response mechanism differs from those described in model annual
plants. We suggest that this mechanism controls flowering within the perennial growth cycle in
F. vesca and demonstrate that a change in a single gene reverses the photoperiodic requirements
for flowering.
Quantifying the adaptive potential of an antibiotic resistance
enzyme.
Schenk MF, Szendro IG, Krug J, de Visser JAGM, PLoS Genetics 8,
e1002783 (2012)
For a quantitative understanding of the
process of adaptation, we need to understand its "raw material," that is, the
frequency and fitness effects of beneficial mutations. At present, most empirical evidence
suggests an exponential distribution of fitness effects of beneficial mutations, as predicted
for Gumbel-domain distributions by extreme value theory. Here, we study the distribution of
mutation effects on cefotaxime (Ctx) resistance and fitness of 48 unique beneficial mutations in
the bacterial enzyme TEM-1 β-lactamase, which were obtained by screening the products of random
mutagenesis for increased Ctx resistance. Our contributions are threefold. First, based on the
frequency of unique mutations among more than 300 sequenced isolates and correcting for mutation
bias, we conservatively estimate that the total number of first-step mutations that increase Ctx
resistance in this enzyme is 87 [95% CI 75-189], or 3.4% of all 2,583 possible base-pair
substitutions. Of the 48 mutations, 10 are synonymous and the majority of the 38 non-synonymous
mutations occur in the pocket surrounding the catalytic site. Second, we estimate the effects of
the mutations on Ctx resistance by determining survival at various Ctx concentrations, and we
derive their fitness effects by modeling reproduction and survival as a branching process.
Third, we find that the distribution of both measures follows a Fréchet-type distribution
characterized by a broad tail of a few exceptionally fit mutants. Such distributions have
fundamental evolutionary implications, including an increased predictability of evolution, and
may provide a partial explanation for recent observations of striking parallel evolution of
antibiotic resistance.
Does the Bicoid gradient matter?
Roth S, Lynch J, Cell 149, 511-512 (2012)
The generation and interpretation of
positional information are key processes in developmental systems. In this issue, Chen et al.
report discoveries made in the Drosophila embryo that give new insights into how positional
information can be produced by patterning gradients.
Development. Making waves for segments.
Roth S, Panfilio KA, Science (New York, N.Y.) 336, 306-307 (2012)
Signals of speciation within Arabidopsis thaliana in comparison
with its relatives.
Alcázar R, Pecinka A, Aarts MGM, Fransz PF, Koornneef M, Current
Opinion In Plant Biology 15, 205-211 (2012)
The species within the now well-defined
Arabidopsis genus provide biological materials suitable to investigate speciation and the
development of reproductive isolation barriers between related species. Even within the model
species A. thaliana, genetic differentiation between populations due to environmental adaptation
or demographic history can lead to cases where hybrids between accessions are non-viable.
Experimental evidence supports the importance of genome duplications and genetic epistatic
interactions in the occurrence of reproductive isolation. Other examples of adaptation to
specific environments can be found in Arabidopsis relatives where hybridization and chromosome
doubling lead to new amphidiploid species. Molecular signals of speciation found in the
Arabidopsis genus should provide a better understanding of speciation processes in plants from a
genetic, molecular and evolutionary perspective.
Chance and risk in adaptive evolution.
Lässig M, Proceedings Of The National Academy Of Sciences Of The
United States Of America 109, 4719-4720 (2012)
Bethe-Peierls approximation and the inverse Ising problem
Chau Nguyen H, Berg J, Journal Of Statistical Mechanics 03, 004
(2012)
We apply the Bethe-Peierls approximation to
the inverse Ising problem and show how the linear response relation leads to a simple method for
reconstructing couplings and fields of the Ising model. This reconstruction is exact on tree
graphs, yet its computational expense is comparable to those of other mean-field methods. We
compare the performance of this method to the independent-pair, naive mean-field, and
Thouless-Anderson-Palmer approximations, the Sessak-Monasson expansion, and susceptibility
propagation on the Cayley tree, SK model and random graph with fixed connectivity. At low
temperatures, Bethe reconstruction outperforms all of these methods, while at high temperatures
it is comparable to the best method available so far (the Sessak-Monasson method). The
relationship between Bethe reconstruction and other mean-field methods is discussed.
Horizontal gene transfers as metagenomic gene duplications.
Grassi L, Caselle M, Lercher MJ, Lagomarsino MC, Molecular
BioSystems 8, 790-795 (2012)
While it is well accepted that horizontal
gene transfer plays an important role in the evolution and the diversification of prokaryotic
genomes, many questions remain open regarding its functional mechanisms of action and its
interplay with the extant genome. This study addresses the relationship between proteome
innovation by horizontal gene transfer and genome content in Proteobacteria. We characterize the
transferred genes, focusing on the protein domain compositions and their relationships with the
existing protein domain superfamilies in the genome. In agreement with previous observations, we
find that the protein domain architectures of horizontally transferred genes are significantly
shorter than the genomic average. Furthermore, protein domains that are more common in the total
pool of genomes appear to have a proportionally higher chance to be transferred. This suggests
that transfer events behave as if they were drawn randomly from a cross-genomic community gene
pool, much like gene duplicates are drawn from a genomic gene pool. Finally, horizontally
transferred genes carry domains of exogenous families less frequently for larger genomes,
although they might do it more than expected by chance.
Widespread interspecific divergence in cis-regulation of
transposable elements in the Arabidopsis genus.
He F, Zhang X, Hu J, Turck F, Dong X, Goebel U, Borevitz JO, de
Meaux J, Molecular Biology And Evolution 29, 1081-1091 (2012)
Transposable elements (TEs) are so abundant
and variable that they count among the most important mutational sources in genomes.
Nonetheless, little is known about the genetics of their variation in activity or silencing
across closely related species. Here, we demonstrate that regulation of TE genes can differ
dramatically between the two closely related Arabidopsis species A. thaliana and A. lyrata. In
leaf and floral tissues of F1 interspecific hybrids, about 47% of TEs show allele-specific
expression, with the A. lyrata copy being generally expressed at higher level. We confirm that
TEs are generally expressed in A. lyrata but not in A. thaliana. Allele-specific differences in
TE expression are associated with divergence in epigenetic modifications like DNA and histone
methylation between species as well as with sequence divergence. Our data demonstrate that A.
thaliana silences TEs much better than A. lyrata. For long terminal repeat retrotransposons,
these differences are more pronounced for younger insertions. Interspecific differences in TE
silencing may have a great impact on genome size changes.
Comparative genomics of Coccidian parasites differing in host
range and transmission strategy
Reid AJ, Vermont SJ, Cotton JA, Harris D, Hill-Cawthorne GA,
Könen-Waisman S, Latham S, Mourier T, Norton R, Quail M, Sanders M, Shanmugam D, Sohal A,
Wasmuth J, Brunk B, Grigg M, Howard JC, Parkinson J, Roos DS, Trees AJ, Berriman M, Pain A,
Wastling JM, PLoS Pathogens (3): e1002567 (2012)
Toxoplasma gondii is a zoonotic
protozoan parasite which infects nearly one third of the human population and is found in an
extraordinary range of vertebrate hosts. Its epidemiology depends heavily on horizontal
transmission, especially between rodents and its definitive host, the cat. Neospora caninum is a
recently discovered close relative of
Toxoplasma, whose definitive host is the dog.
Both species are tissue-dwelling Coccidia and members of the phylum Apicomplexa; they share many
common features, but Neospora neither infects humans nor shares the same wide host range as
Toxoplasma, rather it shows a striking preference for highly efficient vertical transmission in
cattle. These species therefore provide a remarkable opportunity to investigate mechanisms of
host restriction, transmission strategies, virulence and zoonotic potential. We sequenced the
genome of
N. caninum and transcriptomes of the invasive stage of both species,
undertaking an extensive comparative genomics and transcriptomics analysis. We estimate that
these organisms diverged from their common ancestor around 28 million years ago and find that
both genomes and gene expression are remarkably conserved. However, in N. caninum we identified
an unexpected expansion of surface antigen gene families and the divergence of secreted
virulence factors, including rhoptry kinases. Specifically we show that the rhoptry kinase ROP18
is pseudogenised in N. caninum and that, as a possible consequence, Neospora is unable to
phosphorylate host immunity-related GTPases, as
Toxoplasma does. This defense strategy
is thought to be key to virulence in
Toxoplasma. We conclude that the ecological niches
occupied by these species are influenced by a relatively small number of gene products which
operate at the host-parasite interface and that the dominance of vertical transmission in N.
caninum may be associated with the evolution of reduced virulence in this species.
Correlations of record events as a test for heavy-tailed
distributions.
Franke J, Wergen G, Krug J, Physical Review Letters 108, 064101
(2012)
A record is an entry in a time series that
is larger or smaller than all previous entries. If the time series consists of independent,
identically distributed random variables with a superimposed linear trend, record events are
positively (negatively) correlated when the tail of the distribution is heavier (lighter) than
exponential. Here we use these correlations to detect heavy-tailed behavior in small sets of
independent random variables. The method consists of converting random subsets of the data into
time series with a tunable linear drift and computing the resulting record correlations.
OGEE: an online gene essentiality database.
Chen W, Minguez P, Lercher MJ, Bork P, Nucleic Acids Research 40,
D901-6 (2012)
OGEE is an Online GEne Essentiality
database. Its main purpose is to enhance our understanding of the essentiality of genes. This is
achieved by collecting not only experimentally tested essential and non-essential genes, but
also associated gene features such as expression profiles, duplication status, conservation
across species, evolutionary origins and involvement in embryonic development. We focus on
large-scale experiments and complement our data with text-mining results. Genes are organized
into data sets according to their sources. Genes with variable essentiality status across data
sets are tagged as conditionally essential, highlighting the complex interplay between gene
functions and environments. Linked tools allow the user to compare gene essentiality among
different gene groups, or compare features of essential genes to non-essential genes, and
visualize the results. OGEE is freely available at http://ogeedb.embl.de.
The invention of WUS-like stem cell-promoting functions in plants
predates leptosporangiate ferns.
Nardmann J, Werr W, Plant Molecular Biology 78, 123-134 (2012)
The growth of land plants depends on stem
cell-containing meristems which show major differences in their architecture from basal to
higher plant species. In Arabidopsis, the stem cell niches in the shoot and root meristems are
promoted by WUSCHEL (WUS) and WOX5, respectively. Both genes are members of a non-ancestral
clade of the WUS-related homeobox (WOX) gene family, which is absent in extant bryophytes and
lycophytes. Our analyses of five fern species suggest that a single WUS orthologue was present
in the last common ancestor (LCA) of leptosporangiate ferns and seed plants. In the extant fern
Ceratopteris richardii, the WUS pro-orthologue marks the pluripotent cell fate of immediate
descendants of the root apical initial, so-called merophytes, which undergo a series of
stereotypic cell divisions and give rise to all cell types of the root except the root cap. The
invention of a WUS-like function within the WOX gene family in an ancestor of leptosporangiate
ferns and seed plants and its amplification and sub-functionalisation to different stem cell
niches might relate to the success of seed plants, especially angiosperms.
A Toxoplasma gondii pseudokinase inhibits host IRG resistance
proteins.
Fleckenstein MC, Reese ML, Könen-Waisman S, Boothroyd JC, Howard
JC, Steinfeldt T, PLoS Biology 10, e1001358 (2012)
The ability of mice to resist infection
with the protozoan parasite, Toxoplasma gondii, depends in large part on the function of members
of a complex family of atypical large GTPases, the interferon-gamma-inducible immunity-related
GTPases (IRG proteins). Nevertheless, some strains of T. gondii are highly virulent for mice
because, as recently shown, they secrete a polymorphic protein kinase, ROP18, from the rhoptries
into the host cell cytosol at the moment of cell invasion. Depending on the allele, ROP18 can
act as a virulence factor for T. gondii by phosphorylating and thereby inactivating mouse IRG
proteins. In this article we show that IRG proteins interact not only with ROP18, but also
strongly with the products of another polymorphic locus, ROP5, already implicated as a major
virulence factor from genetic crosses, but whose function has previously been a complete
mystery. ROP5 proteins are members of the same protein family as ROP18 kinases but are
pseudokinases by sequence, structure, and function. We show by a combination of genetic and
biochemical approaches that ROP5 proteins act as essential co-factors for ROP18 and present
evidence that they work by enforcing an inactive GDP-dependent conformation on the IRG target
protein. By doing so they prevent GTP-dependent activation and simultaneously expose the target
threonines on the switch I loop for phosphorylation by ROP18, resulting in permanent
inactivation of the protein. This represents a novel mechanism in which a pseudokinase
facilitates the phosphorylation of a target by a partner kinase by preparing the substrate for
phosphorylation, rather than by upregulation of the activity of the kinase itself.
Comparisons of the embryonic development of Drosophila,
Nasonia, and Tribolium
Lynch JA, El-Sherif E, Brown SJ, Wiley Interdisciplinary Reviews:
Developmental Biology, 1: 16–39 (2012)
Studying the embryogenesis of diverse
insect species is crucial to understanding insect evolution. Here, we review current advances in
understanding the development of two emerging model organisms: the wasp Nasonia vitripennis and
the beetle Tribolium castaneum in comparison with the well-studied fruit fly Drosophila
melanogaster. Although Nasonia represents the most basally branching order of holometabolous
insects, it employs a derived long germband mode of embryogenesis, more like that of Drosophila,
whereas Tribolium undergoes an intermediate germband mode of embryogenesis, which is more
similar to the ancestral mechanism. Comparing the embryonic development and genetic regulation
of early patterning events in these three insects has given invaluable insights into insect
evolution. The similar mode of embryogenesis of Drosophila and Nasonia is reflected in their
reliance on maternal morphogenetic gradients. However, they employ different genes as maternal
factors, reflecting the evolutionary distance separating them. Tribolium, on the other hand,
relies heavily on self-regulatory mechanisms other than maternal cues, reflecting its sequential
nature of segmentation and the need for reiterated patterning.
2011
Emergent neutrality in adaptive asexual evolution.
Schiffels S, Szöllosi GJ, Mustonen V, Lässig M, Genetics 189,
1361-1375 (2011)
In nonrecombining genomes, genetic linkage
can be an important evolutionary force. Linkage generates interference interactions, by which
simultaneously occurring mutations affect each other's chance of fixation. Here, we develop
a comprehensive model of adaptive evolution in linked genomes, which integrates interference
interactions between multiple beneficial and deleterious mutations into a unified framework. By
an approximate analytical solution, we predict the fixation rates of these mutations, as well as
the probabilities of beneficial and deleterious alleles at fixed genomic sites. We find that
interference interactions generate a regime of emergent neutrality: all genomic sites with
selection coefficients smaller in magnitude than a characteristic threshold have nearly random
fixed alleles, and both beneficial and deleterious mutations at these sites have nearly neutral
fixation rates. We show that this dynamic limits not only the speed of adaptation, but also a
population's degree of adaptation in its current environment. We apply the model to
different scenarios: stationary adaptation in a time-dependent environment and approach to
equilibrium in a fixed environment. In both cases, the analytical predictions are in good
agreement with numerical simulations. Our results suggest that interference can severely
compromise biological functions in an adapting population, which sets viability limits on
adaptive evolution under linkage.
Mathematics and biology: a Kantian view on the history of pattern
formation theory.
Roth S, Development Genes and Evolution 221, 255-279 (2011)
Driesch's statement, made around 1900,
that the physics and chemistry of his day were unable to explain self-regulation during
embryogenesis was correct and could be extended until the year 1972. The emergence of theories
of self-organisation required progress in several areas including chemistry, physics, computing
and cybernetics. Two parallel lines of development can be distinguished which both culminated in
the early 1970s. Firstly, physicochemical theories of self-organisation arose from theoretical
(Lotka 1910-1920) and experimental work (Bray 1920; Belousov 1951) on chemical oscillations.
However, this research area gained broader acceptance only after thermodynamics was extended to
systems far from equilibrium (1922-1967) and the mechanism of the prime example for a chemical
oscillator, the Belousov-Zhabotinski reaction, was deciphered in the early 1970s. Secondly,
biological theories of self-organisation were rooted in the intellectual environment of
artificial intelligence and cybernetics. Turing wrote his The chemical basis of morphogenesis
(1952) after working on the construction of one of the first electronic computers. Likewise,
Gierer and Meinhardt's theory of local activation and lateral inhibition (1972) was
influenced by ideas from cybernetics. The Gierer-Meinhardt theory provided an explanation for
the first time of both spontaneous formation of spatial order and of self-regulation that proved
to be extremely successful in elucidating a wide range of patterning processes. With the advent
of developmental genetics in the 1980s, detailed molecular and functional data became available
for complex developmental processes, allowing a new generation of data-driven theoretical
approaches. Three examples of such approaches will be discussed. The successes and limitations
of mathematical pattern formation theory throughout its history suggest a picture of the
organism, which has structural similarity to views of the organic world held by the philosopher
Immanuel Kant at the end of the eighteenth century.
The impact of temperature on balancing immune responsiveness and
growth in Arabidopsis.
Alcázar R, Parker JE, Trends In Plant Science 16, 666-675 (2011)
Plants have evolved polymorphic immune
receptors to recognize pathogens causing disease. However, triggering of resistance needs to be
tuned to the local environment to maintain a balance between defense and growth. We consider
here the impact of temperature as a key environmental factor influencing immune pathway
activation in Arabidopsis. Genetic compensatory and molecular buffering mechanisms affecting the
diversification, functionality and subcellular dynamics of immune receptors, reveal multiple
points at which temperature intersects with host resistance signaling systems, including a role
of at least one receptor in sensing temperature change. Analysis of temperature-dependent
autoimmunity caused by allelic mismatches in hybrids of evolutionary diverged Arabidopsis
accessions is illuminating processes by which plants maintain 'poise' between immune
responsiveness and fitness in natural populations.
Adaptive walks and extreme value theory.
Neidhart J, Krug J, Physical Review Letters 107, 178102 (2011)
We study biological evolution in a
high-dimensional genotype space in the regime of rare mutations and strong selection. The
population performs an uphill walk which terminates at local fitness maxima. Assigning fitness
randomly to genotypes, we show that the mean walk length is logarithmic in the number of
initially available beneficial mutations, with a prefactor determined by the tail of the fitness
distribution. This result is derived analytically in a simplified setting where the mutational
neighborhood is fixed during the adaptive process, and confirmed by numerical simulations.
The causes of epistasis (Review)
de Visser JAGM, Cooper TF, Elena SF, Proc. R. Soc. B vol. 278
3617-3624 (2011)
Since Bateson's discovery that genes can
suppress the phenotypic effects of other genes, gene interactions-called epistasis-have been the
topic of a vast research effort. Systems and developmental biologists study epistasis to
understand the genotype-phenotype map, whereas evolutionary biologists recognize the fundamental
importance of epistasis for evolution. Depending on its form, epistasis may lead to divergence
and speciation, provide evolutionary benefits to sex and affect the robustness and evolvability
of organisms. That epistasis can itself be shaped by evolution has only recently been realized.
Here, we review the empirical pattern of epistasis, and some of the factors that may affect the
form and extent of epistasis. Based on their divergent consequences, we distinguish between
interactions with or without mean effect, and those affecting the magnitude of fitness effects
or their sign. Empirical work has begun to quantify epistasis in multiple dimensions in the
context of metabolic and fitness landscape models. We discuss possible proximate causes (such as
protein function and metabolic networks) and ultimate factors (including mutation,
recombination, and the importance of natural selection and genetic drift). We conclude that, in
general, pleiotropy is an important prerequisite for epistasis, and that epistasis may evolve as
an adaptive or intrinsic consequence of changes in genetic robustness and evolvability.
Formation of regulatory modules by local sequence duplication.
Nourmohammad A, Lässig M, PLoS Computational Biology 7, e1002167
(2011)
Turnover of regulatory sequence and
function is an important part of molecular evolution. But what are the modes of sequence
evolution leading to rapid formation and loss of regulatory sites? Here we show that a large
fraction of neighboring transcription factor binding sites in the fly genome have formed from a
common sequence origin by local duplications. This mode of evolution is found to produce
regulatory information: duplications can seed new sites in the neighborhood of existing sites.
Duplicate seeds evolve subsequently by point mutations, often towards binding a different factor
than their ancestral neighbor sites. These results are based on a statistical analysis of 346
cis-regulatory modules in the Drosophila melanogaster genome, and a comparison set of intergenic
regulatory sequence in Saccharomyces cerevisiae. In fly regulatory modules, pairs of binding
sites show significantly enhanced sequence similarity up to distances of about 50 bp. We analyze
these data in terms of an evolutionary model with two distinct modes of site formation: (i)
evolution from independent sequence origin and (ii) divergent evolution following duplication of
a common ancestor sequence. Our results suggest that pervasive formation of binding sites by
local sequence duplications distinguishes the complex regulatory architecture of higher
eukaryotes from the simpler architecture of unicellular organisms.
Immunity-related GTPase M (IRGM) proteins influence the
localization of guanylate-binding protein 2 (GBP2) by modulating macroautophagy.
Traver MK, Henry SC, Cantillana V, Oliver T, Hunn JP, Howard JC,
Beer S, Pfeffer K, Coers J, Taylor GA, The Journal of Biological Chemistry 286, 30471-30480
(2011)
The immunity-related GTPases (IRGs) are a
family of proteins induced by interferon-γ that play a crucial role in innate resistance to
intracellular pathogens. The M subfamily of IRG proteins (IRGM) plays a profound role in this
context, in part because of the ability of its members to regulate the localization and
expression of other IRG proteins. We present here evidence that IRGM proteins affect the
localization of the guanylate-binding proteins (GBPs), a second family of interferon-induced
GTP-binding proteins that also function in innate immunity. Absence of Irgm1 or Irgm3 led to
accumulation of Gbp2 in intracellular compartments that were positive for both the
macroautophagy (hereafter referred to as autophagy) marker LC3 and the autophagic adapter
molecule p62/Sqstm1. Gbp2 was similarly relocalized in cells in which autophagy was impaired
because of the absence of Atg5. Both in Atg5- and IRGM-deficient cells, the IRG protein Irga6
relocalized to the same compartments as Gbp2, raising the possibility of a common regulatory
mechanism. However, other data indicated that Irga6, but not Gbp2, was ubiquitinated in
IRGM-deficient cells. Similarly, coimmunoprecipitation studies indicated that although Irgm3 did
interact directly with Irgb6, it did not interact with Gbp2. Collectively, these data suggest
that IRGM proteins indirectly modulate the localization of GBPs through a distinct mechanism
from that through which they regulate IRG protein localization. Further, these results suggest
that a core function of IRGM proteins is to regulate autophagic flux, which influences the
localization of GBPs and possibly other factors that instruct cell-autonomous immune resistance.
DOG1 expression is predicted by the seed-maturation environment
and contributes to geographical variation in germination in Arabidopsis thaliana
Chiang GCK, Bartsch M, Barua D, Nakayabashi K, Debieu M, Kronholm
I, Koornneef M, Soppe WJJ, Donohue K, de Meaux J, Molecular Ecology, 20: 3336-3349 (2011)
Seasonal germination timing of Arabidopsis
thaliana strongly influences overall life history expression and is the target of intense
natural selection. This seasonal germination timing depends strongly on the interaction between
genetics and seasonal environments both before and after seed dispersal. DELAY OF GERMINATION 1
(DOG1) is the first gene that has been identified to be associated with natural variation in
primary dormancy in A. thaliana. Here, we report interaccession variation in DOG1 expression and
document that DOG1 expression is associated with seed-maturation temperature effects on
germination; DOG1 expression increased when seeds were matured at low temperature, and this
increased expression was associated with increased dormancy of those seeds. Variation in DOG1
expression suggests a geographical structure such that southern accessions, which are more
dormant, tend to initiate DOG1 expression earlier during seed maturation and achieved higher
expression levels at the end of silique development than did northern accessions. Although
elimination of the synthesis of phytohormone abscisic acid (ABA) results in the elimination of
maternal temperature effects on dormancy, DOG1 expression predicted dormancy better than
expression of genes involved in ABA metabolism.
Evolutionary accessibility of mutational pathways.
Franke J, Klözer A, de Visser JAGM, Krug J, PLoS Computational
Biology 7, e1002134 (2011)
Functional effects of different mutations
are known to combine to the total effect in highly nontrivial ways. For the trait under
evolutionary selection ('fitness'), measured values over all possible combinations of
a set of mutations yield a fitness landscape that determines which mutational states can be
reached from a given initial genotype. Understanding the accessibility properties of fitness
landscapes is conceptually important in answering questions about the predictability and
repeatability of evolutionary adaptation. Here we theoretically investigate accessibility of the
globally optimal state on a wide variety of model landscapes, including landscapes with tunable
ruggedness as well as neutral 'holey' landscapes. We define a mutational pathway to be
accessible if it contains the minimal number of mutations required to reach the target genotype,
and if fitness increases in each mutational step. Under this definition accessibility is high,
in the sense that at least one accessible pathway exists with a substantial probability that
approaches unity as the dimensionality of the fitness landscape (set by the number of mutational
loci) becomes large. At the same time the number of alternative accessible pathways grows
without bounds. We test the model predictions against an empirical 8-locus fitness landscape
obtained for the filamentous fungus Aspergillus niger. By analyzing subgraphs of the full
landscape containing different subsets of mutations, we are able to probe the mutational
distance scale in the empirical data. The predicted effect of high accessibility is supported by
the empirical data and is very robust, which we argue reflects the generic topology of sequence
spaces. Together with the restrictive assumptions that lie in our definition of accessibility,
this implies that the globally optimal configuration should be accessible to genome wide
evolution, but the repeatability of evolutionary trajectories is limited owing to the presence
of a large number of alternative mutational pathways.
Genetic and evolutionary perspectives on the interplay between
plant immunity and development.
Alcázar R, Reymond M, Schmitz G, de Meaux J, Current Opinion In
Plant Biology 14, 378-384 (2011)
There is now ample evidence that plant
development, responses to abiotic environments, and immune responses are tightly intertwined in
their physiology. Thus optimization of the immune system during evolution will occur in
coordination with that of plant development. Two alternative and possibly complementary forces
are at play: genetic constraints due to the pleiotropic action of players in both systems, and
coevolution, if developmental changes modulate the cost-benefit balance of immunity. A current
challenge is to elucidate the ecological forces driving evolution of quantitative variation for
defense at molecular level. The analysis of natural co-variation for developmental and immunity
traits in Arabidopsis thaliana promises to bring important insights.
The IRG protein-based resistance mechanism in mice and its
relation to virulence in Toxoplasma gondii.
Howard JC, Hunn JP, Steinfeldt T, Current Opinion in Microbiology
14, 414-421 (2011)
IRG proteins (immunity-related GTPases)
provide an early defense mechanism in mice against the protozoal pathogen, Toxoplasma gondii.
This is a particularly suitable time to provide a brief review of this host-pathogen interaction
because the nature of the IRG resistance system, and to some extent its mode of action, have
become known in the past few years. Likewise, forward genetic screens have recently drawn
attention to a number of loci contributing to the differential virulence of T. gondii strains in
mice. It is now clear that at least some important virulence mechanisms exert their action
against components of the IRG resistance system. Thus these two mechanisms form the two poles of
a dynamic host-pathogen virulence-resistance relationship with interesting and accessible
properties.
Nonlinear fitness landscape of a molecular pathway.
Perfeito L, Ghozzi S, Berg J, Schnetz K, Lässig M, PLoS Genetics
7(7): e1002160 (2011)
Genes are regulated because their
expression involves a fitness cost to the organism. The production of proteins by transcription
and translation is a well-known cost factor, but the enzymatic activity of the proteins produced
can also reduce fitness, depending on the internal state and the environment of the cell. Here,
we map the fitness costs of a key metabolic network, the lactose utilization pathway in
Escherichia
coli. We measure the growth of several regulatory lac operon mutants in different
environments inducing expression of the lac genes. We find a strikingly nonlinear fitness
landscape, which depends on the production rate and on the activity rate of the lac proteins. A
simple fitness model of the lac pathway, based on elementary biophysical processes, predicts the
growth rate of all observed strains. The nonlinearity of fitness is explained by a feedback
loop: production and activity of the lac proteins reduce growth, but growth also affects the
density of these molecules. This nonlinearity has important consequences for molecular function
and evolution. It generates a cliff in the fitness landscape, beyond which populations cannot
maintain growth. In viable populations, there is an expression barrier of the lac genes, which
cannot be exceeded in any stationary growth process. Furthermore, the nonlinearity determines
how the fitness of operon mutants depends on the inducer environment. We argue that fitness
nonlinearities, expression barriers, and gene–environment interactions are generic features of
fitness landscapes for metabolic pathways, and we discuss their implications for the evolution
of regulation.
An integrated approach to characterize genetic interaction
networks in yeast metabolism.
Szappanos B, Kovacs K, Szamecz B, Honti F, Costanzo M,
Baryshnikova A, Gelius-Dietrich G, Lercher MJ, Jelasity M, Myers CL, Andrews BJ et al., Nature
Genetics 43, 656-662 (2011)
Although experimental and theoretical
efforts have been applied to globally map genetic interactions, we still do not understand how
gene-gene interactions arise from the operation of biomolecular networks. To bridge the gap
between empirical and computational studies, we i, quantitatively measured genetic interactions
between approximately 185,000 metabolic gene pairs in Saccharomyces cerevisiae, ii, superposed
the data on a detailed systems biology model of metabolism and iii, introduced a
machine-learning method to reconcile empirical interaction data with model predictions. We
systematically investigated the relative impacts of functional modularity and metabolic flux
coupling on the distribution of negative and positive genetic interactions. We also provide a
mechanistic explanation for the link between the degree of genetic interaction, pleiotropy and
gene dispensability. Last, we show the feasibility of automated metabolic model refinement by
correcting misannotations in NAD biosynthesis and confirming them by in vivo experiments.
Evolutionary advantage of small populations on complex fitness
landscapes.
Jain K, Krug J, Park S, Evolution 65, 1945-1955 (2011)
Recent experimental and theoretical studies
have shown that small asexual populations evolving on complex fitness landscapes may achieve a
higher fitness than large ones due to the increased heterogeneity of adaptive trajectories.
Here, we introduce a class of haploid three-locus fitness landscapes that allow the
investigation of this scenario in a precise and quantitative way. Our main result derived
analytically shows how the probability of choosing the path of the largest initial fitness
increase grows with the population size. This makes large populations more likely to get trapped
at local fitness peaks and implies an advantage of small populations at intermediate time
scales. The range of population sizes where this effect is operative coincides with the onset of
clonal interference. Additional studies using ensembles of random fitness landscapes show that
the results achieved for a particular choice of three-locus landscape parameters are robust and
also persist as the number of loci increases. Our study indicates that an advantage for small
populations is likely whenever the fitness landscape contains local maxima. The advantage
appears at intermediate time scales, which are long enough for trapping at local fitness maxima
to have occurred but too short for peak escape by the creation of multiple mutants.
Evolutionary genetics: evolution with foresight.
Salverda MLM, de Visser JAGM, Current Biology 21, R398-400 (2011)
Evolution has no foresight, but produces ad
hoc solutions by tinkering with available variation. A new study demonstrates how evolution
nevertheless prepares organisms for the future by increasing their evolvability.
The IFN-γ-inducible GTPase, Irga6, protects mice against
Toxoplasma gondii but not against Plasmodium berghei and some other intracellular pathogens
Liesenfeld O, Parvanova I, Zerrahn J, Han SJ, Heinrich F, Muñoz M,
Kaiser F, Aebischer T, Buch T, Waisman A, Reichmann G, Utermöhlen O, von Stebut E, von Loewenich
FD, Bogdan C, Specht S, Saeftel M, Hoerauf A, Mota MM, Könen-Waisman S, Kaufmann SH, Howard JC,
PLoS One, 6(6):e20568 (2011)
Clearance of infection with intracellular
pathogens in mice involves interferon-regulated GTPases of the IRG protein family. Experiments
with mice genetically deficient in members of this family such as Irgm1(LRG-47), Irgm3(IGTP),
and Irgd(IRG-47) has revealed a critical role in microbial clearance, especially for
Toxoplasma
gondii. The in vivo role of another member of this family, Irga6 (IIGP, IIGP1) has been
studied in less detail. We investigated the susceptibility of two independently generated mouse
strains deficient in Irga6 to in vivo infection with T. gondii, Mycobacterium tuberculosis,
Leishmania mexicana, L. major, Listeria monocytogenes, Anaplasma phagocytophilum and Plasmodium
berghei. Compared with wild-type mice, mice deficient in Irga6 showed increased susceptibility
to oral and intraperitoneal infection with T. gondii but not to infection with the other
organisms. Surprisingly, infection of Irga6-deficient mice with the related apicomplexan
parasite, P. berghei, did not result in increased replication in the liver stage and no Irga6
(or any other IRG protein) was detected at the parasitophorous vacuole membrane in IFN-γ-induced
wild-type cells infected with P. berghei in vitro. Susceptibility to infection with T. gondii
was associated with increased mortality and reduced time to death, increased numbers of
inflammatory foci in the brains and elevated parasite loads in brains of infected
Irga6-deficient mice. In vitro, Irga6-deficient macrophages and fibroblasts stimulated with
IFN-γ were defective in controlling parasite replication. Taken together, our results implicate
Irga6 in the control of infection with T. gondii and further highlight the importance of the IRG
system for resistance to this pathogen.
Bistability in two-locus models with selection, mutation, and
recombination.
Park S, Krug J, Journal Of Mathematical Biology 62, 763-788 (2011)
The evolutionary effect of recombination
depends crucially on the epistatic interactions between linked loci. A paradigmatic case where
recombination is known to be strongly disadvantageous is a two-locus fitness landscape
displaying reciprocal sign epistasis with two fitness peaks of unequal height. Although this
type of model has been studied since the 1960s, a full analytic understanding of the stationary
states of mutation-selection balance was not achieved so far. Focusing on the bistability
arising due to the recombination, we consider here the deterministic, haploid two-locus model
with reversible mutations, selection and recombination. We find analytic formulae for the
critical recombination probability r ( c ) above which two stable stationary solutions appear
which are localized on each of the two fitness peaks. We also derive the stationary genotype
frequencies in various parameter regimes. In particular, when the recombination rate is close to
r ( c ) and the fitness difference between the two peaks is small, we obtain a compact
description in terms of a cubic polynomial which is analogous to the Landau theory of physical
phase transitions.
Aa TFL1 confers an age-dependent response to vernalization in
perennial Arabis alpina.
Wang R, Albani MC, Vincent C, Bergonzi S, Luan M, Bai Y, Kiefer C,
Castillo R, Coupland G, The Plant Cell 23, 1307-1321 (2011)
Flowering of many plants is induced by
environmental signals, but these responses can depend on the age of the plant. Exposure of
Arabidopsis thaliana to vernalization (winter temperatures) at germination induces flowering,
whereas a close perennial relative Arabis alpina only responds if exposed when at least 5 weeks
old. We show that vernalization of these older A. alpina plants reduces expression of the floral
repressor PEP1 and activates the orthologs of the Arabidopsis flowering genes SOC1 (Aa SOC1) and
LFY (Aa LFY). By contrast, when younger plants are vernalized, PEP1 and Aa SOC1 mRNA levels
change as in older plants, but Aa LFY is not expressed. We demonstrate that A. alpina TFL1 (Aa
TFL1) blocks flowering and prevents Aa LFY expression when young plants are exposed to
vernalization. In addition, in older plants, Aa TFL1 increases the duration of vernalization
required for Aa LFY expression and flowering. Aa TFL1 has similar functions in axillary shoots,
thus ensuring that following a flowering episode vegetative branches are maintained to continue
the perennial life cycle. We propose that Aa TFL1 blocks flowering of young plants exposed to
vernalization by setting a threshold for a flowering pathway that is increased in activity as
the shoot ages, thus contributing to several perennial traits.
The phylogenetic origin of oskar coincided with the origin of
maternally provisioned germ plasm and pole cells at the base of the Holometabola.
Lynch JA, Ozüak O, Khila A, Abouheif E, Desplan C, Roth S, PLoS
Genetics 7, e1002029 (2011)
The establishment of the germline is a
critical, yet surprisingly evolutionarily labile, event in the development of sexually
reproducing animals. In the fly Drosophila, germ cells acquire their fate early during
development through the inheritance of the germ plasm, a specialized maternal cytoplasm
localized at the posterior pole of the oocyte. The gene oskar (osk) is both necessary and
sufficient for assembling this substance. Both maternal germ plasm and oskar are evolutionary
novelties within the insects, as the germline is specified by zygotic induction in basally
branching insects, and osk has until now only been detected in dipterans. In order to understand
the origin of these evolutionary novelties, we used comparative genomics, parental RNAi, and
gene expression analyses in multiple insect species. We have found that the origin of osk and
its role in specifying the germline coincided with the innovation of maternal germ plasm and
pole cells at the base of the holometabolous insects and that losses of osk are correlated with
changes in germline determination strategies within the Holometabola. Our results indicate that
the invention of the novel gene osk was a key innovation that allowed the transition from the
ancestral late zygotic mode of germline induction to a maternally controlled establishment of
the germline found in many holometabolous insect species. We propose that the ancestral role of
osk was to connect an upstream network ancestrally involved in mRNA localization and
translational control to a downstream regulatory network ancestrally involved in executing the
germ cell program.
Initial mutations direct alternative pathways of protein
evolution.
Salverda MLM, Dellus E, Gorter FA, Debets AJM, van der Oost J,
Hoekstra RF, Tawfik DS, de Visser JAGM, PLoS Genetics 7, e1001321 (2011)
Whether evolution is erratic due to random
historical details, or is repeatedly directed along similar paths by certain constraints,
remains unclear. Epistasis (i.e. non-additive interaction between mutations that affect fitness)
is a mechanism that can contribute to both scenarios. Epistasis can constrain the type and order
of selected mutations, but it can also make adaptive trajectories contingent upon the first
random substitution. This effect is particularly strong under sign epistasis, when the sign of
the fitness effects of a mutation depends on its genetic background. In the current study, we
examine how epistatic interactions between mutations determine alternative evolutionary
pathways, using in vitro evolution of the antibiotic resistance enzyme TEM-1 β-lactamase. First,
we describe the diversity of adaptive pathways among replicate lines during evolution for
resistance to a novel antibiotic (cefotaxime). Consistent with the prediction of epistatic
constraints, most lines increased resistance by acquiring three mutations in a fixed order.
However, a few lines deviated from this pattern. Next, to test whether negative interactions
between alternative initial substitutions drive this divergence, alleles containing initial
substitutions from the deviating lines were evolved under identical conditions. Indeed, these
alternative initial substitutions consistently led to lower adaptive peaks, involving more and
other substitutions than those observed in the common pathway. We found that a combination of
decreased enzymatic activity and lower folding cooperativity underlies negative sign epistasis
in the clash between key mutations in the common and deviating lines (Gly238Ser and Arg164Ser,
respectively). Our results demonstrate that epistasis contributes to contingency in protein
evolution by amplifying the selective consequences of random mutations.
Rare events in population genetics: stochastic tunneling in a
two-locus model with recombination.
Altland A, Fischer A, Krug J, Szendro IG, Physical Review Letters
106, 088101 (2011)
We study the evolution of a population in a
two-locus genotype space, in which the negative effects of two single mutations are
overcompensated in a high-fitness double mutant. We discuss how the interplay of finite
population size N and sexual recombination at rate r affects the escape times t(esc) to the
double mutant. For small populations demographic noise generates massive fluctuations in t(esc).
The mean escape time varies nonmonotonically with r, and grows exponentially as
lnt(esc)∼N(r-r(*))(3/2) beyond a critical value r(*).
The immunity-related GTPases in mammals: a fast-evolving
cell-autonomous resistance system against intracellular pathogens.
Hunn JP, Feng CG, Sher A, Howard JC, Mammalian Genome : Official
Journal Of The International Mammalian Genome Society 22, 43-54 (2011)
The immunity-related GTPases (IRGs) belong
to the family of large, interferon-inducible GTPases and constitute a cell-autonomous resistance
system essential for the control of vacuolar pathogens like Toxoplasma gondii in mice. Recent
results demonstrated that numerous IRG members accumulate collaboratively at the parasitophorous
vacuole of invading T. gondii leading to the destruction of the vacuole and the parasite and
subsequent necrotic host cell death. Complex regulatory interactions between different IRG
proteins are necessary for these processes. Disturbance of this finely balanced system, e.g., by
single genetic deficiency for the important negative regulator Irgm1 or the autophagic regulator
Atg5, leads to spontaneous activation of the effector IRG proteins when induced by IFNγ. This
activation has cytotoxic consequences resulting in a severe lymphopenia, macrophage defects, and
failure of the adaptive immune system in Irgm1-deficient mice. However, alternative functions in
phagosome maturation and induction of autophagy have been proposed for Irgm1. The IRG system has
been studied primarily in mice, but IRG genes are present throughout the mammalian lineage.
Interestingly, the number, type, and diversity of genes present differ greatly even between
closely related species, probably reflecting intimate host-pathogen coevolution driven by an
armed race between the IRG resistance proteins and pathogen virulence factors. IRG proteins are
targets for polymorphic T. gondii virulence factors, and genetic variation in the IRG system
between different mouse strains correlates with resistance and susceptibility to virulent T.
gondii strains.
The evolution of dorsal-ventral patterning mechanisms in insects.
Lynch JA, Roth S, Genes & Development 25, 107-118 (2011)
The gene regulatory network (GRN)
underpinning dorsal-ventral (DV) patterning of the Drosophila embryo is among the most
thoroughly understood GRNs, making it an ideal system for comparative studies seeking to
understand the evolution of development. With the emergence of widely applicable techniques for
testing gene function, species with sequenced genomes, and multiple tractable species with
diverse developmental modes, a phylogenetically broad and molecularly deep understanding of the
evolution of DV axis formation in insects is feasible. Here, we review recent progress made in
this field, compare our emerging molecular understanding to classical embryological experiments,
and suggest future directions of inquiry.
A gene's ability to buffer variation is predicted by its
fitness contribution and genetic interactions.
Wang G, Liu J, Wang W, Zhang H, Lercher MJ, PloS One 6, e17650
(2011)
BACKGROUND: Many single-gene knockouts
result in increased phenotypic (e.g., morphological) variability among the mutant's
offspring. This has been interpreted as an intrinsic ability of genes to buffer genetic and
environmental variation. A phenotypic capacitor is a gene that appears to mask phenotypic
variation: when knocked out, the offspring shows more variability than the wild type. Theory
predicts that this phenotypic potential should be correlated with a gene's knockout fitness
and its number of negative genetic interactions. Based on experimentally measured phenotypic
capacity, it was suggested that knockout fitness was unimportant, but that phenotypic capacitors
tend to be hubs in genetic and physical interaction networks. METHODOLOGY/PRINCIPAL FINDINGS: We
re-analyse the available experimental data in a combined model, which includes knockout fitness
and network parameters as well as expression level and protein length as predictors of
phenotypic potential. Contrary to previous conclusions, we find that the strongest predictor is
in fact haploid knockout fitness (responsible for 9% of the variation in phenotypic potential),
with an additional contribution from the genetic interaction network (5%); once these two
factors are taken into account, protein-protein interactions do not make any additional
contribution to the variation in phenotypic potential. CONCLUSIONS/SIGNIFICANCE: We conclude
that phenotypic potential is not a mysterious "emergent" property of cellular
networks. Instead, it is very simply determined by the overall fitness reduction of the organism
(which in its compromised state can no longer compensate for multiple factors that contribute to
phenotypic variation), and by the number (and presumably nature) of genetic interactions of the
knocked-out gene. In this light, Hsp90, the prototypical phenotypic capacitor, may not be
representative: typical phenotypic capacitors are not direct "buffers" of variation,
but are simply genes encoding central cellular functions.
The activation mechanism of Irga6, an interferon-inducible GTPase
contributing to mouse resistance against Toxoplasma gondii.
Pawlowski N, Khaminets A, Hunn JP, Papic N, Schmidt A, Uthaiah RC,
Lange R, Vopper G, Martens S, Wolf E, Howard JC et al., BMC Biology 9, 7 (2011)
BACKGROUND:The interferon-inducible
immunity-related GTPases (IRG proteins/p47 GTPases) are a distinctive family of GTPases that
function as powerful cell-autonomous resistance factors. The IRG protein, Irga6 (IIGP1),
participates in the disruption of the vacuolar membrane surrounding the intracellular parasite,
Toxoplasma gondii, through which it communicates with its cellular hosts. Some aspects of the
protein's behaviour have suggested a dynamin-like molecular mode of action, in that the
energy released by GTP hydrolysis is transduced into mechanical work that results in deformation
and ultimately rupture of the vacuolar membrane.RESULTS:Irga6 forms GTP-dependent oligomers in
vitro and thereby activates hydrolysis of the GTP substrate. In this study we define the
catalytic G-domain interface by mutagenesis and present a structural model, of how GTP
hydrolysis is activated in Irga6 complexes, based on the substrate-twinning reaction mechanism
of the signal recognition particle (SRP) and its receptor (SRα). In conformity with this model,
we show that the bound nucleotide is part of the catalytic interface and that the 3'hydroxyl
of the GTP ribose bound to each subunit is essential for trans-activation of hydrolysis of the
GTP bound to the other subunit. We show that both positive and negative regulatory interactions
between IRG proteins occur via the catalytic interface. Furthermore, mutations that disrupt the
catalytic interface also prevent Irga6 from accumulating on the parasitophorous vacuole membrane
of T. gondii, showing that GTP-dependent Irga6 activation is an essential component of the
resistance mechanism.CONCLUSIONS:The catalytic interface of Irga6 defined in the present
experiments can probably be used as a paradigm for the nucleotide-dependent interactions of all
members of the large family of IRG GTPases, both activating and regulatory. Understanding the
activation mechanism of Irga6 will help to explain the mechanism by which IRG proteins exercise
their resistance function. We find no support from sequence or G-domain structure for the idea
that IRG proteins and the SRP GTPases have a common phylogenetic origin. It therefore seems
probable, if surprising, that the substrate-assisted catalytic mechanism has been independently
evolved in the two protein families.
The effects of network neighbours on protein evolution.
Wang G, Lercher MJ, PloS One 6, e18288 (2011)
Interacting proteins may often experience
similar selection pressures. Thus, we may expect that neighbouring proteins in biological
interaction networks evolve at similar rates. This has been previously shown for protein-protein
interaction networks. Similarly, we find correlated rates of evolution of neighbours in networks
based on co-expression, metabolism, and synthetic lethal genetic interactions. While the
correlations are statistically significant, their magnitude is small, with network effects
explaining only between 2% and 7% of the variation. The strongest known predictor of the rate of
protein evolution remains expression level. We confirmed the previous observation that similar
expression levels of neighbours indeed explain their similar evolution rates in protein-protein
networks, and showed that the same is true for metabolic networks. In co-expression and
synthetic lethal genetic interaction networks, however, neighbouring genes still show somewhat
similar evolutionary rates even after simultaneously controlling for expression level, gene
essentiality and gene length. Thus, similar expression levels and related functions (as inferred
from co-expression and synthetic lethal interactions) seem to explain correlated evolutionary
rates of network neighbours across all currently available types of biological networks.
The maternal and early embryonic transcriptome of the milkweed
bug Oncopeltus fasciatus.
Ewen-Campen B, Shaner N, Panfilio KA, Suzuki Y, Roth S, Extavour
CG, BMC Genomics 12, 61 (2011)
BACKGROUND:Most evolutionary developmental
biology ("evo-devo") studies of emerging model organisms focus on small numbers of
candidate genes cloned individually using degenerate PCR. However, newly available sequencing
technologies such as 454 pyrosequencing have recently begun to allow for massive gene discovery
in animals without sequenced genomes. Within insects, although large volumes of sequence data
are available for holometabolous insects, developmental studies of basally branching
hemimetabolous insects typically suffer from low rates of gene discovery.RESULTS:We used 454
pyrosequencing to sequence over 500 million bases of cDNA from the ovaries and embryos of the
milkweed bug Oncopeltus fasciatus, which lacks a sequenced genome. This indirectly developing
insect occupies an important phylogenetic position, branching basal to Diptera (including fruit
flies) and Hymenoptera (including honeybees), and is an experimentally tractable model for
short-germ development. 2,087,410 reads from both normalized and non-normalized cDNA assembled
into 21,097 sequences (isotigs) and 112,531 singletons. The assembled sequences fell into 16,617
unique gene models, and included predictions of splicing isoforms, which we examined
experimentally. Discovery of new genes plateaued after assembly of ~1.5 million reads,
suggesting that we have sequenced nearly all transcripts present in the cDNA sampled. Many
transcripts have been assembled at close to full length, and there is a net gain of sequence
data for over half of the pre-existing O. fasciatus accessions for developmental genes in
GenBank. We identified 10,775 unique genes, including members of all major conserved metazoan
signaling pathways and genes involved in several major categories of early developmental
processes. We also specifically address the effects of cDNA normalization on gene discovery in
de novo transcriptome analyses.CONCLUSIONS:Our sequencing, assembly and annotation framework
provide a simple and effective way to achieve high-throughput gene discovery for organisms
lacking a sequenced genome. These data will have applications to the study of the evolution of
arthropod genes and genetic pathways, and to the wider evolution, development and genomics
communities working with emerging model organisms.[The sequence data from this study have been
submitted to GenBank under study accession number SRP002610
(http://www.ncbi.nlm.nih.gov/sra?term=SRP002610). Custom scripts generated are available at
http://www.extavourlab.com/protocols/index.html. Seven Additional files are available.].
2010
Natural variation at Strubbelig Receptor Kinase 3 drives
immune-triggered incompatibilities between Arabidopsis thaliana accessions.
Alcázar R, García AV, Kronholm I, de Meaux J, Koornneef M, Parker
JE, Reymond M, Nature Genetics 42, 1135-1139 (2010)
Accumulation of genetic incompatibilities
within species can lead to reproductive isolation and, potentially, speciation. In this study,
we show that allelic variation at SRF3 (Strubbelig Receptor Family 3), encoding a receptor-like
kinase, conditions the occurrence of incompatibility between Arabidopsis thaliana accessions.
The geographical distribution of SRF3 alleles reveals that allelic forms causing epistatic
incompatibility with a Landsberg erecta allele at the RPP1 resistance locus are present in A.
thaliana accessions in central Asia. Incompatible SRF3 alleles condition for an enhanced early
immune response to pathogens as compared to the resistance-dampening effect of compatible SRF3
forms in isogenic backgrounds. Variation in disease susceptibility suggests a basis for the
molecular patterns of a recent selective sweep detected at the SRF3 locus in central Asian
populations.
Significance analysis and statistical mechanics: an application
to clustering.
Łuksza M, Lässig M, Berg J, Physical Review Letters 105, 220601
(2010)
This Letter addresses the statistical
significance of structures in random data: given a set of vectors and a measure of mutual
similarity, how likely is it that a subset of these vectors forms a cluster with enhanced
similarity among its elements? The computation of this cluster p value for randomly distributed
vectors is mapped onto a well-defined problem of statistical mechanics. We solve this problem
analytically, establishing a connection between the physics of quenched disorder and
multiple-testing statistics in clustering and related problems. In an application to gene
expression data, we find a remarkable link between the statistical significance of a cluster and
the functional relationships between its genes.
Demographic history of Oceania inferred from genome-wide data.
Wollstein A, Lao O, Becker C, Brauer S, Trent RJ, Nürnberg P,
Stoneking M, Kayser M, Current Biology 20, 1983-1992 (2010)
BACKGROUND:The human history of Oceania
comprises two extremes: the initial colonizations of Near Oceania, one of the oldest
out-of-Africa migrations, and of Remote Oceania, the most recent expansion into unoccupied
territories. Genetic studies, mostly using uniparentally inherited DNA, have shed some light on
human origins in Oceania, particularly indicating that Polynesians are of mixed East Asian and
Near Oceanian ancestry. Here, we use ∼1 million single nucleotide polymorphisms (SNPs) to
investigate the demographic history of Oceania in a more detailed manner.RESULTS:We developed a
new approach to account for SNP ascertainment bias, used approximate Bayesian computation
simulations to choose the best-fitting model of population history, and estimated demographic
parameters. We find that the ancestors of Near Oceanians diverged from ancestral Eurasians ∼27
thousand years ago (kya), suggesting separate initial occupations of both territories. The
genetic admixture in Polynesian history between East Asians (∼87%) and Near Oceanians (∼13%)
occurred ∼3 kya, prior to the colonization of Polynesia. Fijians are of Polynesian (∼65%) and
additional Near Oceanian (∼35%) ancestry not found in Polynesians, with this admixture occurring
considerably after the initial settlement of Remote Oceania. Our data support a greater
contribution of East Asian women than men in the admixture history of Remote Oceania and
highlight population substructure in Polynesia and New Guinea.CONCLUSIONS:Despite the inherent
ascertainment bias, genome-wide SNP data provide new insights into the genetic history of
Oceana. Our approach to correct for ascertainment bias and obtain reliable inferences concerning
demographic history should prove useful in other such studies.
Novel modes of localization and function of nanos in the wasp
Nasonia.
Lynch JA, Desplan C, Development (Cambridge, England) 137,
3813-3821 (2010)
Abdominal patterning in Drosophila requires
the function of nanos (nos) to prevent translation of hunchback (hb) mRNA in the posterior of
the embryo. nos function is restricted to the posterior by the translational repression of mRNA
that is not incorporated into the posteriorly localized germ plasm during oogenesis. The wasp
Nasonia vitripennis (Nv) undergoes a long germ mode of development very similar to Drosophila,
although the molecular patterning mechanisms employed in these two organisms have diverged
significantly, reflecting the independent evolution of this mode of development. Here, we report
that although Nv nanos (Nv-nos) has a conserved function in embryonic patterning through
translational repression of hb, the timing and mechanisms of this repression are significantly
delayed in the wasp compared with the fly. This delay in Nv-nos function appears to be related
to the dynamic behavior of the germ plasm in Nasonia, as well as to the maternal provision of
Nv-Hb protein during oogenesis. Unlike in flies, there appears to be two functional populations
of Nv-nos mRNA: one that is concentrated in the oosome and is taken up into the pole cells
before evidence of Nv-hb repression is observed; another that forms a gradient at the posterior
and plays a role in Nv-hb translational repression. Altogether, our results show that, although
the embryonic patterning function of nos orthologs is broadly conserved, the mechanisms employed
to achieve this function are distinct.
Records and sequences of records from random variables with a
linear trend
Franke J, Wergen G, Krug J, J. Stat. Mech. P10013 (2010)
We consider records and sequences of
records drawn from discrete time series of the form $$X_{n}=Y_{n}+cn$$, where the $$Y_{n}$$ are
independent and identically distributed random variables and $$c$$ is a constant drift. For very
small and very large drift velocities, we investigate the asymptotic behavior of the probability
$$p_n(c)$$ of a record occurring in the $$n$$th step and the probability $$P_N(c)$$ that all
$$N$$ entries are records, i.e. that $$X_1 < X_2 < ... < X_N$$. Our work is motivated by the
analysis of temperature time series in climatology, and by the study of mutational pathways in
evolutionary biology.
Generation of distinct signaling modes via diversification of the
Egfr ligand-processing cassette.
Rousso T, Lynch J, Yogev S, Roth S, Schejter ED, Shilo B,
Development (Cambridge, England) 137, 3427-3437 (2010)
Egfr ligand processing in Drosophila
involves trafficking of the ligand precursor by the chaperone Star from the endoplasmic
reticulum (ER) to a secretory compartment, where the precursor is cleaved by the intramembrane
protease Rhomboid. Some of the Drosophila Rhomboids also reside in the ER, where they attenuate
signaling by premature cleavage of Star. The genome of the flour beetle Tribolium castaneum
contains a single gene for each of the ligand-processing components, providing an opportunity to
assess the regulation and impact of a simplified ligand-processing cassette. We find that the
central features of ligand retention, trafficking by the chaperone and cleavage by Rhomboid have
been conserved. The single Rhomboid is localized to both ER and secretory compartments. However,
we show that Tribolium Star is refractive to Rhomboid cleavage. Consequently, this
ligand-processing system effectively mediates long-range Egfr activation in the Tribolium
embryonic ventral ectoderm, despite ER localization of Rhomboid. Diversification of the Egfr
signaling pathway appears to have coupled gene duplication events with modulation of the
biochemical properties and subcellular localization patterns of Rhomboid proteases and their
substrates.
Evolution of extracellular Dpp modulators in insects: The roles
of tolloid and twisted-gastrulation in dorsoventral patterning of the Tribolium embryo.
Nunes da Fonseca R, van der Zee M, Roth S, Developmental Biology
345, 80-93 (2010)
The formation of the BMP gradient which
patterns the DV axis in flies and vertebrates requires several extracellular modulators like the
inhibitory protein Sog/Chordin, the metalloprotease Tolloid (Tld), which cleaves Sog/Chordin,
and the CR domain protein Twisted gastrulation (Tsg). While flies and vertebrates have only one
sog/chordin gene they possess several paralogues of tld and tsg. A simpler and probably
ancestral situation is observed in the short-germ beetle Tribolium castaneum (Tc), which
possesses only one tld and one tsg gene. Here we show that in T. castaneum tld is required for
early BMP signalling except in the head region and Tc-tld function is, as expected, dependent on
Tc-sog. In contrast, Tc-tsg is required for all aspects of early BMP signalling and acts in a
Tc-sog-independent manner. For comparison with Drosophila melanogaster we constructed fly
embryos lacking all early Tsg activity (tsg;;srw double mutants) and show that they still
establish a BMP signalling gradient. Thus, our results suggest that the role of Tsg proteins for
BMP gradient formation has changed during insect evolution.
EGF signaling and the origin of axial polarity among the insects.
Lynch JA, Peel AD, Drechsler A, Averof M, Roth S, Current Biology
20, 1042-1047 (2010)
The eggs of insects are unusual in that
they often have bilateral symmetry when they are laid, indicating that both anterior-posterior
(AP) and dorsal-ventral (DV) symmetries are broken during oogenesis. The molecular basis of this
process is well understood in Drosophila melanogaster, in which symmetry breaking events for
both axes depend on the asymmetric position of the oocyte nucleus and on germline-soma signaling
mediated by the Tgf alpha-like epidermal growth factor (EGF) ligand Gurken. Germline-soma
signaling interactions centered around the oocyte nucleus have been proposed in other insect
species, but the molecular nature of these interactions has not been elucidated. We have
examined the behavior of the oocyte nucleus and the function of EGF signaling components in the
ovaries of the wasp Nasonia vitripennis, the beetle Tribolium castaneum, and the cricket Gryllus
bimaculatus. We have found that EGF signaling has broadly conserved roles in mediating the
encapsulation of oocytes by the somatic follicle cell layer, in establishing polarity of the egg
chambers, and in setting up the DV axis of the embryo. These results provide insights into the
evolutionary origins of the unique strategy employed by insects to establish embryonic axial
polarity during oogenesis.
Genome-wide association study of 107 phenotypes in Arabidopsis
thaliana inbred lines.
Atwell S, Huang YS, Vilhjálmsson BJ, Willems G, Horton M, Li Y,
Meng D, Platt A, Tarone AM, Hu TT, Jiang R et al., Nature 465, 627-631 (2010)
Although pioneered by human geneticists as
a potential solution to the challenging problem of finding the genetic basis of common human
diseases, genome-wide association (GWA) studies have, owing to advances in genotyping and
sequencing technology, become an obvious general approach for studying the genetics of natural
variation and traits of agricultural importance. They are particularly useful when inbred lines
are available, because once these lines have been genotyped they can be phenotyped multiple
times, making it possible (as well as extremely cost effective) to study many different traits
in many different environments, while replicating the phenotypic measurements to reduce
environmental noise. Here we demonstrate the power of this approach by carrying out a GWA study
of 107 phenotypes in Arabidopsis thaliana, a widely distributed, predominantly self-fertilizing
model plant known to harbour considerable genetic variation for many adaptively important
traits. Our results are dramatically different from those of human GWA studies, in that we
identify many common alleles of major effect, but they are also, in many cases, harder to
interpret because confounding by complex genetics and population structure make it difficult to
distinguish true associations from false. However, a-priori candidates are significantly
over-represented among these associations as well, making many of them excellent candidates for
follow-up experiments. Our study demonstrates the feasibility of GWA studies in A. thaliana and
suggests that the approach will be appropriate for many other organisms.
Assessing the influence of adjacent gene orientation on the
evolution of gene upstream regions in Arabidopsis thaliana.
He F, Chen W, Collins S, Acquisti C, Goebel U, Ramos-Onsins S,
Lercher MJ, de Meaux J, Genetics 185, 695-701 (2010)
The orientation of flanking genes may
influence the evolution of intergenic regions in which cis-regulatory elements are likely to be
located: divergently transcribed genes share their 5' regions, resulting either in smaller
"private" spaces or in overlapping regulatory elements. Thus, upstream sequences of
divergently transcribed genes (bi-directional upstream regions, or URs) may be more constrained
than those of uni-directional gene pairs. We investigated this effect by analyzing nucleotide
variation segregating within and between Arabidopsis species. Compared to uni-directional URs,
bi-directional URs indeed display lower population mutation rate, as well as more low-frequency
polymorphisms. Furthermore, we find that bi-directional regions undergo selection for the
maintenance of intergenic distance. Altogether, however, we observe considerable variation in
evolutionary rates, with putative signatures of selection on two uni-directional upstream
regions.
Balanced nuclear and cytoplasmic activities of EDS1 are required
for a complete plant innate immune response
Garcia AV, Blanvillain-Baufumé S, Huibers R P, Wiermer M, Li G,
Gobbato E, Rietz S, Parker JE, PLoS Path 6: e1000970 (2010)
An important layer of plant innate immunity
to host-adapted pathogens is conferred by intracellular nucleotide-binding/oligomerization
domain-leucine rich repeat (NB-LRR) receptors recognizing specific microbial effectors.
Signaling from activated receptors of the TIR (Toll/Interleukin-1 Receptor)-NB-LRR class
converges on the nucleo-cytoplasmic immune regulator EDS1 (Enhanced Disease Susceptibility1). In
this report we show that a receptor-stimulated increase in accumulation of nuclear EDS1 precedes
or coincides with the EDS1-dependent induction and repression of defense-related genes. EDS1 is
capable of nuclear transport receptor-mediated shuttling between the cytoplasm and nucleus. By
enhancing EDS1 export from inside nuclei (through attachment of an additional nuclear export
sequence (NES)) or conditionally releasing EDS1 to the nucleus (by fusion to a glucocorticoid
receptor (GR)) in transgenic Arabidopsis we establish that the EDS1 nuclear pool is essential
for resistance to biotrophic and hemi-biotrophic pathogens and for transcriptional
reprogramming. Evidence points to post-transcriptional processes regulating receptor-triggered
accumulation of EDS1 in nuclei. Changes in nuclear EDS1 levels become equilibrated with the
cytoplasmic EDS1 pool and cytoplasmic EDS1 is needed for complete resistance and restriction of
host cell death at infection sites. We propose that coordinated nuclear and cytoplasmic
activities of EDS1 enable the plant to mount an appropriately balanced immune response to
pathogen attack.
Coordinated loading of IRG resistance GTPases on to the
Toxoplasma gondii parasitophorous vacuole.
Khaminets A, Hunn JP, Könen-Waisman S, Zhao YO, Preukschat D,
Coers J, Boyle JP, Ong Y, Boothroyd JC, Reichmann G, Howard JC et al., Cellular Microbiology 12,
939-961 (2010)
The immunity-related GTPases (IRGs)
constitute an interferon-induced intracellular resistance mechanism in mice against Toxoplasma
gondii. IRG proteins accumulate on the parasitophorous vacuole membrane (PVM), leading to its
disruption and to death of the parasite. How IRGs target the PVM is unknown. We show that
accumulation of IRGs on the PVM begins minutes after parasite invasion and increases for about 1
h. Targeting occurs independently of several signalling pathways and the microtubule network,
suggesting that IRG transport is diffusion-driven. The intensity of IRG accumulation on the PVM,
however, is reduced in absence of the autophagy regulator, Atg5. In wild-type cells IRG proteins
accumulate cooperatively on PVMs in a definite order reflecting a temporal hierarchy, with Irgb6
and Irgb10 apparently acting as pioneers. Loading of IRG proteins onto the vacuoles of virulent
Toxoplasma strains is attenuated and the two pioneer IRGs are the most affected. The polymorphic
rhoptry kinases, ROP16, ROP18 and the catalytically inactive proteins, ROP5A-D, are not
individually responsible for this effect. Thus IRG proteins protect mice against avirulent
strains of Toxoplasma but fail against virulent strains. The complex cooperative behaviour of
IRG proteins in resisting Toxoplasma may hint at undiscovered complexity also in virulence
mechanisms.
Epithelial reorganization events during late extraembryonic
development in a hemimetabolous insect.
Panfilio KA, Roth S, Developmental Biology 340, 100-115 (2010)
As extra-embryonic tissues, the amnion and
serosa are not considered to contribute materially to the insect embryo, yet they must execute
an array of morphogenetic movements before they are dispensable. In hemimetabolous insects,
these movements have been known for over a century, but they have remained virtually unexamined.
This study addresses late extraembryonic morphogenesis in the milkweed bug, Oncopeltus
fasciatus. Cell shape changes and apoptosis profiles are used to characterize the membranes as
they undergo a large repertoire of final reorganizational events that reposition the embryo
(katatrepsis), and eliminate the membranes themselves in an ordered fashion (dorsal closure). A
number of key features were identified. First, amnion-serosa "fusion" involves
localized apoptosis in the amnion and the formation of a supracellular actin purse string at the
amnion-serosa border. During katatrepsis, a 'focus' of serosal cells undergoes
precocious columnarization and may serve as an anchor for contraction. Lastly, dorsal closure
involves novel modifications of the amnion and embryonic flank that are without counterpart
during the well-known process of dorsal closure in the fruit fly Drosophila melanogaster. These
data also address the long-standing question of the final fate of the amnion: it undergoes
apoptosis during dorsal closure and thus is likely to be solely extraembryonic.
The earliest stages of adaptation in an experimental plant
population: strong selection on QTLS for seed dormancy.
Huang X, Schmitt J, Dorn L, Griffith C, Effgen S, Takao S,
Koornneef M, Donohue K, Molecular Ecology 19, 1335-1351 (2010)
Colonizing species may often encounter
strong selection during the initial stages of adaptation to novel environments. Such selection
is particularly likely to act on traits expressed early in development since early survival is
necessary for the expression of adaptive phenotypes later in life. Genetic studies of fitness
under field conditions, however, seldom include the earliest developmental stages. Using a new
set of recombinant inbred lines, we present a study of the genetic basis of fitness variation in
Arabidopsis thaliana in which genotypes, environments, and geographic location were manipulated
to study total lifetime fitness, beginning with the seed stage. Large-effect quantitative trait
loci (QTLs) for fitness changed allele frequency and closely approached 90% in some treatments
within a single generation. These QTLs colocated with QTLs for germination phenology when seeds
were dispersed following a schedule of a typical winter annual, and they were detected in two
geographic locations at different latitudes. Epistatically interacting loci affected both
fitness and germination in many cases. QTLs for field germination phenology colocated with known
QTLs for primary dormancy induction as assessed in laboratory tests, including the candidate
genes DOG1 and DOG6. Therefore fitness, germination phenology, and primary dormancy are
genetically associated at the level of specific chromosomal regions and candidate loci. Genes
associated with the ability to arrest development at early life stages and assess environmental
conditions are thereby likely targets of intense natural selection early in the colonization
process.
Fitness flux and ubiquity of adaptive evolution.
Mustonen V, Lässig M, Proceedings Of The National Academy Of
Sciences Of The United States Of America 107, 4248-4253 (2010)
Natural selection favors fitter variants in
a population, but actual evolutionary processes may decrease fitness by mutations and genetic
drift. How is the stochastic evolution of molecular biological systems shaped by natural
selection? Here, we derive a theorem on the fitness flux in a population, defined as the
selective effect of its genotype frequency changes. The fitness-flux theorem generalizes Fisher's
fundamental theorem of natural selection to evolutionary processes including mutations, genetic
drift, and time-dependent selection. It shows that a generic state of populations is adaptive
evolution: there is a positive fitness flux resulting from a surplus of beneficial over
deleterious changes. In particular, stationary nonequilibrium evolution processes are predicted
to be adaptive. Under specific nonstationary conditions, notably during a decrease in population
size, the average fitness flux can become negative. We show that these predictions are in
accordance with experiments in bacteria and bacteriophages and with genomic data in Drosophila.
Our analysis establishes fitness flux as a universal measure of adaptation in molecular
evolution.
A test of the neutral model of expression change in natural
populations of house mouse subspecies.
Staubach F, Teschke M, Voolstra CR, Wolf JBW, Tautz D, Evolution
64, 549-560 (2010)
Changes in expression of genes are thought
to contribute significantly to evolutionary divergence. To study the relative role of selection
and neutrality in shaping expression changes, we analyzed 24 genes in three different tissues of
the house mouse (Mus musculus). Samples from two natural populations of the subspecies M. m.
domesticus and M. m. musculus were investigated using quantitative PCR assays and sequencing of
the upstream region. We have developed an approach to quantify expression polymorphism within
such populations and to disentangle technical from biological variation in the data. We found a
correlation between expression polymorphism within populations and divergence between
populations. Furthermore, we found a correlation between expression polymorphism and sequence
polymorphism of the respective genes. These data are most easily interpreted within a framework
of a predominantly neutral model of gene expression change, where only a fraction of the changes
may have been driven by positive selection. Although most genes investigated were expressed in
all three tissues analyzed, significant changes of expression levels occurred predominantly in a
single tissue only. This adds to the notion that enhancer-specific effects or transregulatory
effects can modulate the evolution of gene expression in a tissue-specific way.
The speed of evolution in large asexual populations
Park S, Simon D, Krug J, J. Stat. Phys. 138, 381-410 (2010)
We consider an asexual biological
population of constant size N evolving in discrete time under the influence of selection and
mutation. Beneficial mutations appear at rate U and their selective effects s are drawn from a
distribution g(s). After introducing the required models and concepts of mathematical population
genetics, we review different approaches to computing the speed of logarithmic fitness increase
as a function of N, U and g(s). We present an exact solution of the infinite population size
limit and provide an estimate of the population size beyond which it is valid. We then discuss
approximate approaches to the finite population problem, distinguishing between the case of a
single selection coefficient, g(s)=δ(s−s b ), and a continuous distribution of selection
coefficients. Analytic estimates for the speed are compared to numerical simulations up to
population sizes of order 10^300.
Bayesian analysis of biological networks: clusters, motifs,
cross-species correlations
Berg J, Lässig M, in Statistical And Evolutionary Analysis Of
Biological Network Data, M. Stumpf and C. Wiuf (Eds.), Imperial College Press (2010)
An important part of the analysis of
bio-molecular networks is to detect different functional units. Different functions are
reflected in a different evolutionary dynamics, and hence in different statistical
characteristics of network parts. In this sense, the {\em global statistics} of a biological
network, e.g., its connectivity distribution, provides a background, and {\em local deviations}
from this background signal functional units. In the computational analysis of biological
networks, we thus typically have to discriminate between different statistical models governing
different parts of the dataset. The nature of these models depends on the biological question
asked. We illustrate this rationale here with three examples: identification of functional parts
as highly connected extit{network clusters}, finding extit{network motifs}, which occur in a
similar form at different places in the network, and the analysis of extit{cross-species network
correlations}, which reflect evolutionary dynamics between species.
Co-expression of neighbouring genes in Arabidopsis: separating
chromatin effects from direct interactions.
Chen W, de Meaux J, Lercher MJ, BMC Genomics 11, 178 (2010)
BACKGROUND:In all eukaryotic species
examined, genes that are chromosomal neighbours are more similar in their expression than random
gene pairs. Currently, it is still unclear how much of this local co-expression is caused by
direct transcriptional interactions, and how much is due to shared chromatin
environments.RESULTS:We analysed neighbouring genes in Arabidopsis thaliana. At large intergenic
distances (>400 bp), divergently and convergently transcribed gene pairs show very similar
levels of co-expression, mediated most likely by shared chromatin environments. At gene
distances below 400 bp, co-expression is strongly enhanced only for divergently transcribed gene
pairs, indicating bi-directional transcription from a single promoter. Conversely, co-expression
is suppressed for short convergently or uni-directionally transcribed pairs. This suppression
points to transcriptional interference concentrated at the 3' end, e.g., in the context of
transcription termination.CONCLUSIONS:Classifying linked gene pairs by their orientation, we are
able to partially tease apart the different levels of regional expression modulation. (i)
Regional chromatin characteristics modulate the accessibility for regulation and transcription,
regardless of gene orientation; the strength of this chromatin effect can be assessed from
divergently or convergently transcribed distant neighbours. (ii) Shared promoter regions up to
400 bp in length enhance the co-expression of close bi-directional neighbours. (iii)
Transcriptional interference of close neighbours is concentrated at the 3' ends of genes,
and reduces co-expression on average by 40%.
Comparative analysis of flowering in annual and perennial plants.
Albani MC, Coupland G, Current topics in developmental biology 91,
323-348 (2010)
In plants the switch from vegetative growth
to flowering involves a major transition in the development of the shoot apex. This transition
can occur once, in annual species, or repeatedly, in perennial plants. In annuals, flowering is
associated with senescence and death of the whole plant, whereas perennials flower in
consecutive years and maintain vegetative development after flowering. The perennial life
strategy depends on differential behavior of meristems on a single plant so that some remain in
the vegetative state while others undergo the floral transition. A. thaliana provides a powerful
model system for understanding the mechanisms of flowering in annuals. Here we review the events
that occur in the meristem of A. thaliana during the floral transition and compare these with
our understanding of flowering in perennial systems.
Conservation of MAP kinase activity and MSP genes in
parthenogenetic nematodes.
Heger P, Kroiher M, Ndifon N, Schierenberg E, BMC developmental
biology 10, 51 (2010)
BACKGROUND:MAP (mitogen-activated protein)
kinase activation is a prerequisite for oocyte maturation, ovulation and fertilisation in many
animals. In the hermaphroditic nematode Caenorhabditis elegans, an MSP (major sperm protein)
dependent pathway is utilised for MAP kinase activation and successive oocyte maturation with
extracellular MSP released from sperm acting as activator. How oocyte-to-embryo transition is
triggered in parthenogenetic nematode species that lack sperm, is not known.RESULTS:We
investigated two key elements of oocyte-to-embryo transition, MSP expression and MAP kinase
signaling, in two parthenogenetic nematodes and their close hermaphroditic relatives. While
activated MAP kinase is present in all analysed nematodes irrespective of the reproductive mode,
MSP expression differs. In contrast to hermaphroditic or bisexual species, we do not find MSP
expression at the protein level in parthenogenetic nematodes. However, genomic sequence analysis
indicates that functional MSP genes are present in several parthenogenetic
species.CONCLUSIONS:We present three alternative interpretations to explain our findings. (1)
MSP has lost its function as a trigger of MAP kinase activation and is not expressed in
parthenogenetic nematodes. Activation of the MAP kinase pathway is achieved by another, unknown
mechanism. Functional MSP genes are required for occasionally emerging males found in some
parthenogenetic species. (2) Because of long-term disadvantages, parthenogenesis is of recent
origin. MSP genes remained intact during this short interval although they are useless. As in
the first scenario, an unknown mechanism is responsible for MAP kinase activation. (3) The
molecular machinery regulating oocyte-to-embryo transition in parthenogenetic nematodes is
conserved with respect to C. elegans, thus requiring intact MSP genes. However, MSP expression
has been shifted to non-sperm cells and is reduced below the detection limits, but is still
sufficient to trigger MAP kinase activation and embryogenesis.
Gene expression and activity of digestive proteases in Daphnia:
effects of cyanobacterial protease inhibitors.
Schwarzenberger A, Zitt A, Kroth P, Mueller S, Von Elert E, BMC
Physiology 10, 6 (2010)
BACKGROUND:The frequency of cyanobacterial
blooms has increased worldwide, and these blooms have been claimed to be a major factor leading
to the decline of the most important freshwater herbivores, i.e. representatives of the genus
Daphnia. This suppression of Daphnia is partly attributed to the presence of biologically active
secondary metabolites in cyanobacteria. Among these metabolites, protease inhibitors are found
in almost every natural cyanobacterial bloom and have been shown to specifically inhibit Daphnia's
digestive proteases in vitro, but to date no physiological responses of these serine proteases
to cyanobacterial protease inhibitors in Daphnia have been reported in situ at the protein and
genetic levels.RESULTS:Nine digestive proteases were detected in D. magna using activity-stained
SDS-PAGE. Subsequent analyses by LC-MS/MS and database search led to the identification of
respective protease genes. D. magna responded to dietary protease inhibitors by up-regulation of
the expression of these respective proteases at the RNA-level and by the induction of new and
less sensitive protease isoforms at the protein level. The up-regulation in response to dietary
trypsin- and chymotrypsin-inhibitors ranged from 1.4-fold to 25.6-fold. These physiological
responses of Daphnia, i.e. up-regulation of protease expression and the induction of isoforms,
took place even after feeding on 20% cyanobacterial food for only 24 h. These physiological
responses proved to be independent from microcystin effects.CONCLUSION:Here for the first time
it was shown in situ that a D. magna clone responds physiologically to dietary cyanobacterial
protease inhibitors by phenotypic plasticity of the targets of these specific inhibitors, i.e.
Daphnia gut proteases. These regulatory responses are adaptive for D. magna, as they increase
the capacity for protein digestion in the presence of dietary protease inhibitors. The type and
extent of these responses in protease expression might determine the degree of growth reduction
in D. magna in the presence of cyanobacterial protease inhibitors. The rapid response of Daphnia
to cyanobacterial protease inhibitors supports the assumption that dietary cyanobacterial
protease inhibitors exert a strong selection pressure on Daphnia proteases themselves.
Influence of mutation rate on estimators of genetic
differentiation--lessons from Arabidopsis thaliana.
Kronholm I, Loudet O, de Meaux J, BMC Genetics 11, 33 (2010)
BACKGROUND:The analysis of molecular
variation within and between populations is crucial to establish strategies for conservation as
well as to detect the footprint of spatially heterogeneous selection. The traditional estimator
of genetic differentiation (F(ST)) has been shown to be misleading if genetic diversity is high.
Alternative estimators of F(ST) have been proposed, but their robustness to variation in
mutation rate is not clearly established. We first investigated the effect of mutation and
migration rate using computer simulations and examined their joint influence on Q(ST), a measure
of genetic differentiation for quantitative traits. We further used experimental data in natural
populations of Arabidopsis thaliana to characterize the effect of mutation rate on various
estimates of population differentiation. Since natural species exhibit various degrees of
self-fertilisation, we also investigated the effect of mating system on the different
estimators.RESULTS:If mutation rate is high and migration rate low, classical measures of
genetic differentiation are misleading. Only Phi(ST), an estimator that takes the mutational
distances between alleles into account, is independent of mutation rate, for all migration
rates. However, the performance of Phi(ST) depends on the underlying mutation model and
departures from this model cause its performance to degrade. We further show that Q(ST) has the
same bias. We provide evidence that, in A. thaliana, microsatellite variation correlates with
mutation rate. We thereby demonstrate that our results on estimators of genetic differentiation
have important implications, even for species that are well established models in population
genetics and molecular biology.CONCLUSIONS:We find that alternative measures of differentiation
like F'(ST) and D are not suitable for estimating effective migration rate and should not
be used in studies of local adaptation. Genetic differentiation should instead be measured using
an estimator that takes mutation rate into account, such as Phi(ST). Furthermore, in systems
where migration between populations is low, such as A. thaliana, Q(ST) < F(ST) cannot be
taken as evidence for homogenising selection as has been traditionally thought.
Localisation and mislocalisation of the interferon-inducible
immunity-related GTPase, Irgm1 (LRG-47) in mouse cells.
Zhao YO, Könen-Waisman S, Taylor GA, Martens S, Howard JC, PloS
One 5, e8648 (2010)
Irgm1 (LRG-47) is an interferon-inducible
Golgi membrane associated GTPase of the mouse whose disruption causes susceptibility to many
different intracellular pathogens. Irgm1 has been variously interpreted as a regulator of
homologous effector GTPases of the IRG family, a regulator of phagosome maturation and as an
initiator of autophagy in interferon-induced cells. We find that endogenous Irgm1 localises to
late endosomal and lysosomal compartments in addition to the Golgi membranes. The targeting
motif known to be required for Golgi localisation is surprisingly also required for
endolysosomal localisation. However, unlike Golgi localisation, localisation to the
endolysosomal system also requires the functional integrity of the nucleotide binding site, and
thus probably reflects transient activation. Golgi localisation is lost when Irgm1 is tagged at
either N- or C-termini with EGFP, while localisation to the endolysosomal system is relatively
favoured. N-terminally tagged Irgm1 localises predominantly to early endosomes, while
C-terminally tagged Irgm1 localises to late endosomes and lysosomes. Both these anomalous
distributions are reversed by inactivation of the nucleotide binding site, and the tagged
proteins both revert to Golgi membrane localisation. Irgm1 is the first IRG protein to be found
associated with the endolysosomal membrane system in addition to either Golgi (Irgm1 and Irgm2)
or ER (Irgm3) membranes, and we interpret the result to be in favour of a regulatory function of
IRGM proteins at cellular membrane systems. In future analyses it should be borne in mind that
tagging of Irgm1 leads to loss of Golgi localisation and enhanced localisation on endolysosomal
membranes, probably as a result of constitutive activation.
Phosphorylation of mouse immunity-related GTPase (IRG) resistance
proteins is an evasion strategy for virulent Toxoplasma gondii.
Steinfeldt T, Könen-Waisman S, Tong L, Pawlowski N, Lamkemeyer T,
Sibley LD, Hunn JP, Howard JC, PLoS Biology 8, e1000576 (2010)
Virulence of complex pathogens in mammals
is generally determined by multiple components of the pathogen interacting with the functional
complexity and multiple layering of the mammalian immune system. It is most unusual for the
resistance of a mammalian host to be overcome by the defeat of a single defence mechanism. In
this study we uncover and analyse just such a case at the molecular level, involving the
widespread intracellular protozoan pathogen Toxoplasma gondii and one of its most important
natural hosts, the house mouse (Mus musculus). Natural polymorphism in virulence of Eurasian T.
gondii strains for mice has been correlated in genetic screens with the expression of
polymorphic rhoptry kinases (ROP kinases) secreted into the host cell during infection. We show
that the molecular targets of the virulent allelic form of ROP18 kinase are members of a family
of cellular GTPases, the interferon-inducible IRG (immunity-related GTPase) proteins, known from
earlier work to be essential resistance factors in mice against avirulent strains of T. gondii.
Virulent T. gondii strain ROP18 kinase phosphorylates several mouse IRG proteins. We show that
the parasite kinase phosphorylates host Irga6 at two threonines in the nucleotide-binding
domain, biochemically inactivating the GTPase and inhibiting its accumulation and action at the
T. gondii parasitophorous vacuole membrane. Our analysis identifies the conformationally active
switch I region of the GTP-binding site as an Achilles' heel of the IRG protein
pathogen-resistance mechanism. The polymorphism of ROP18 in natural T. gondii populations
indicates the existence of a dynamic, rapidly evolving ecological relationship between parasite
virulence factors and host resistance factors. This system should be unusually fruitful for
analysis at both ecological and molecular levels since both T. gondii and the mouse are
widespread and abundant in the wild and are well-established model species with excellent
analytical tools available.
Spontaneous focal activation of invariant natural killer T (iNKT)
cells in mouse liver and kidney.
Zeng J, Howard JC, BMC Biology 8, 142 (2010)
BACKGROUND:Invariant natural killer T
(iNKT) cells differ from other T cells by their hyperactive effector T-cell status, in addition
to the expression of NK lineage receptors and semi-invariant T-cell receptors. It is generally
agreed that the immune phenotype of iNKT cells is maintained by repeated activation in
peripheral tissues although no explicit evidence for such iNKT cell activity in vivo has so far
been reported.RESULTS:We used an interferon (IFN)-γ-inducible cytoplasmic protein, Irga6, as a
histological marker for local IFN-γ production. Irga6 was intensely expressed in small foci of
liver parenchymal cells and kidney tubular epithelium. Focal Irga6 expression was unaffected by
germ-free status or loss of TLR signalling and was totally dependent on IFN-γ secreted by T
cells in the centres of expression foci. These were shown to be iNKT cells by diagnostic T cell
receptor usage and their activity was lost in both CD1 d and Jα-deficient mice.CONCLUSIONS:This
is the first report that supplies direct evidence for explicit activation events of NKT cells in
vivo and raises issues about the triggering mechanism and consequences for immune functions in
liver and kidney.
The mouse resistance protein Irgm1 (LRG-47): a regulator or an
effector of pathogen defense?
Hunn JP, Howard JC, PLoS Pathogens 6, e1001008 (2010)
2009
Adaptive gene regulatory networks
Stauffer F, Berg J, EPL 88, 48004 (2009)
Regulatory interactions between genes show
a large amount of cross-species variability, even when the underlying functions are conserved:
there are many ways to achieve the same function. Here we investigate the ability of regulatory
networks to reproduce given expression levels within a simple model of gene regulation. We find
an exponentially large space of regulatory networks compatible with a given set of expression
levels, giving rise to an extensive entropy of networks. Typical realisations of regulatory
networks are found to share a bias towards symmetric interactions, in line with empirical
evidence.
Brucella abortus induces Irgm3 and Irga6 expression via type-I
IFN by a MyD88-dependent pathway, without the requirement of TLR2, TLR4, TLR5 and TLR9.
Lapaque N, Muller A, Alexopoulou L, Howard JC, Gorvel J, Microbial
Pathogenesis 47, 299-304 (2009)
The innate immune system senses bacterial
pathogens by pattern recognition receptors, such as the well-characterised Toll-like Receptors
(TLR). The activation of TLR signalling cascades depends on several adaptor proteins, among
which MyD88 plays a key role in triggering innate immune responses. Here, we show in murine
macrophages that Brucella abortus triggers expression of the interferon-inducible resistance
proteins (IRGs, p47 GTPases) via type-I IFN secretion at late time points, when Brucella has
reached its replication niche. This induction requires the adaptor molecule MyD88 but does not
involve the TLRs normally implicated in sensing Gram-negative bacteria, namely TLR2, TLR4, TLR5
and TLR9. Brucella mutants lacking the functional VirB type-IV secretion system were not capable
of inducing Irgm3 and Irga6 expression, suggesting that the type-IV secretion system is part of
the triggering of the activation process. Our data suggest that Brucella is recognized
intracellularly by an unknown receptor, different from the conventional ones used for
Gram-negative sensing, but one that nevertheless signals through MyD88.
Estimating mutation distances from unaligned genomes.
Haubold B, Pfaffelhuber P, Domazet-Loso M, Wiehe T, Journal Of
Computational Biology 16, 1487-1500 (2009)
Abstract Alignment-free distance measures
are generally less accurate but more efficient than traditional alignment-based metrics. In the
context of genome sequence analysis, the efficiency gain is often so substantial that it
outweights the loss in accuracy. However, a further disadvantage of alignment-free distances is
that their relationship to evolutionary events such as substitutions is generally unknown. We
have therefore derived an estimator of the number of substitutions per site between two
unaligned DNA sequences, K(r). Simulations show that this estimator works well with "ideal"
data. We compare K(r) to two alternative alignment-free distances: a k-tuple distance and a
measure of relative entropy based on average common substring length. All three measures are
applied to 27 primate mitochondrial genomes, eight whole genomes of Streptococcus agalactiae
strains, and 12 whole genomes of Drosophila species. In each case, the cluster diagrams based on
K(r) are equivalent to or significantly better than those based on the two alternative measures.
This is due to the fact that in contrast to the alternative measures K(r) is derived from an
explicit model of evolution. The computation of K(r) is efficiently implemented in the program
kr, which can be downloaded freely from the internet.
Emergence of a new gene from an intergenic region.
Heinen TJAJ, Staubach F, Häming D, Tautz D, Current Biology 19,
1527-1531 (2009)
It is generally assumed that new genes
would arise by gene duplication mechanisms, because the signals for regulation and transcript
processing would be unlikely to evolve in parallel with a new gene function. We have identified
here a transcript in the house mouse (Mus musculus) that has arisen within the past 2.5-3.5
million years in a large intergenic region. The region is present in many mammals, including
humans, allowing us to exclude the involvement of gene duplication, transposable elements, or
other genome rearrangements, which are typically found for other cases of newly evolved genes.
The gene has three exons, shows alternative splicing, and is specifically expressed in
postmeiotic cells of the testis. The transcript is restricted to species within the genus Mus
and its emergence correlates with indel mutations in the 5' regulatory region of the
transcript. A recent selective sweep is associated with the transcript region in M. m. musculus
populations. A knockout in the laboratory strain BL6 results in reduced sperm motility and
reduced testis weight. Our results show that cryptic signals for transcript regulation and
processing exist in intergenic regions and can become the basis for the evolution of a new
functional gene.
Human Relationships Inferred from Genetic Variation
Lao O, Kayser M, Wiley Online Library (2009)
We humans are a diverse species, both at
the phenotypic and the genetic levels. The genetic diversity of current human populations has
been shaped by various demographic and evolutionary as well as some cultural factors. Thus,
studying how genetic variation is distributed through individuals around the world can provide
insights into (i) when and where our human ancestors first appeared on the planet, (ii) the
dynamics of admixture with other Homo species not existing anymore, (iii) migration waves that
brought humans across the world and (iv) processes of adaptations towards environmental and
other factors that shaped human genomes and phenotypic traits. Additionally, the quantification
of genetic variation between human populations provides data evidence for elucidating whether
humans can be classified according to genetically homogeneous groups or not, with implications
for medical and forensic studies. Hence, studying human genetic diversity is important for
better understanding of our past, presence and future
Discrete shoot and root stem cell-promoting WUS/WOX5 functions
are an evolutionary innovation of angiosperms.
Nardmann J, Reisewitz P, Werr W, Molecular Biology And Evolution
26, 1745-1755 (2009)
The morphologically diverse bodies of seed
plants comprising gymnosperms and angiosperms, which separated some 350 Ma, grow by the activity
of meristems containing stem cell niches. In the dicot model Arabidopsis thaliana, these are
maintained by the stem cell-promoting functions of WUS and WUSCHEL-related homeobox 5 (WOX5) in
the shoot and the root, respectively. Both genes are members of the WOX gene family, which has a
monophyletic origin in green algae. The establishment of the WOX gene phylogeny from basal land
plants through gymnosperms to basal and higher angiosperms reveals three major branches: a basal
clade consisting of WOX13-related genes present in some green algae and throughout all land
plant genomes, a second clade containing WOX8/9/11/12 homologues, and a modern clade restricted
to seed plants. The analysis of the origin of the modern branch in two basal angiosperms
(Amborella trichopoda and Nymphaea jamesoniana) and three gymnosperms (Pinus sylvestris, Ginkgo
biloba, and Gnetum gnemon) shows that all members of the modern clade consistently found in
monocots and dicots exist at the base of the angiosperm lineage, including WUS and WOX5
orthologues. In contrast, our analyses identify a single WUS/WOX5 homologue in all three
gymnosperm genomes, consistent with a monophyletic origin in the last common ancestor of
gymnosperms and angiosperms. Phylogenetic data, WUS- and WOX5-specific evolutionary signatures,
as well as the expression pattern and stem cell-promoting function of the single gymnosperm
WUS/WOX5 pro-orthologue in Arabidopsis indicate a gene duplication event followed by
subfunctionalization at the base of angiosperms.
Evolution of axis formation: mRNA localization, regulatory
circuits and posterior specification in non-model arthropods.
Nunes da Fonseca R, Lynch JA, Roth S, Current Opinion In Genetics
& Development 19, 404-411 (2009)
Drosophila melanogaster has been used as an
arthropod model to understand the establishment of embryonic axes. However, the long germ type
of embryogenesis in Drosophila is highly divergent from the ancestral, short germ mode seen in
most other arthropods. Therefore, broader sampling of other arthropod taxa is required to
understand the evolution of axial patterning mechanisms within this phylum. Here we describe
recent progress toward this end. First, we describe differing strategies for providing
patterning information along the anterior-posterior axis of arthropod embryos. Second, we
discuss the recent findings on dorso-ventral axis of beetles and spiders that highlight the
importance of regulatory interactions at the zygotic level. Third, recent discoveries of the
roles of Wnt signalling, the Notch/Delta pathway and caudal in establishing and patterning the
posterior embryonic region in spiders and beetles are described. In the end, we try to integrate
these new findings with non-model arthropods in a common framework and discuss the major gaps of
knowledge that should be addressed by future studies.
Exploring the effect of sex on empirical fitness landscapes.
de Visser JAGM, Park S, Krug J, The American Naturalist 174 Suppl
1, S15-30 (2009)
The nature of epistasis has important
consequences for the evolutionary significance of sex and recombination. Recent efforts to find
negative epistasis as a source of negative linkage disequilibrium and associated long-term
advantage to sex have yielded little support. Sign epistasis, where the sign of the fitness
effects of alleles varies across genetic backgrounds, is responsible for the ruggedness of the
fitness landscape, with several unexplored implications for the evolution of sex. Here, we
describe fitness landscapes for two sets of strains of the asexual fungus Aspergillus niger
involving all combinations of five mutations. We find that approximately 30% of the
single-mutation fitness effects are positive despite their negative effect in the wild-type
strain and that several local fitness maxima and minima are present. We then compare adaptation
of sexual and asexual populations on these empirical fitness landscapes by using simulations.
The results show a general disadvantage of sex on these rugged landscapes, caused by the
breakdown by recombination of genotypes on fitness peaks. Sex facilitates movement to the global
peak only for some parameter values on one landscape, indicating its dependence on the landscape's
topography. We discuss possible reasons for the discrepancy between our results and the reports
of faster adaptation of sexual populations.
Balance of Irgm protein activities determines IFN-gamma-induced
host defense.
Henry SC, Daniell XG, Burroughs AR, Indaram M, Howell DN, Coers J,
Starnbach MN, Hunn JP, Howard JC, Feng CG, Sher AEA, Journal Of Leukocyte Biology 85, 877-885
(2009)
The immunity-related GTPases (IRG), also
known as p47 GTPases, are a family of proteins that are tightly regulated by IFNs at the
transcriptional level and serve as key mediators of IFN-regulated resistance to intracellular
bacteria and protozoa. Among the IRG proteins, loss of Irgm1 has the most profound impact on
IFN-gamma-induced host resistance at the physiological level. Surprisingly, the losses of host
resistance seen in the absence of Irgm1 are sometimes more striking than those seen in the
absence of IFN-gamma. In the current work, we address the underlying mechanism. We find that in
several contexts, another protein in the IRG family, Irgm3, functions to counter the effects of
Irgm1. By creating mice that lack Irgm1 and Irgm3, we show that several phenotypes important to
host resistance that are caused by Irgm1 deficiency are reversed by coincident Irgm3 deficiency;
these include resistance to Salmonella typhimurium in vivo, the ability to affect
IFN-gamma-induced Salmonella killing in isolated macrophages, and the ability to regulate
macrophage adhesion and motility in vitro. Other phenotypes that are caused by Irgm1 deficiency,
including susceptibility to Toxoplasma gondii and the regulation of GKS IRG protein expression
and localization, are not reversed but exacerbated when Irgm3 is also absent. These data suggest
that members of the Irgm subfamily within the larger IRG family possess activities that can be
opposing or cooperative depending on the context, and it is the balance of these activities that
is pivotal in mediating IFN-gamma-regulated host resistance.
Modeling infectious disease in mice: co-adaptation and the role
of host-specific IFNgamma responses.
Coers J, Starnbach MN, Howard JC, PLoS Pathogens 5, e1000333
(2009)
Reentrant phase transition in a predator-prey model.
Sung-Guk H, Park S, Jun KB, Physical Review. E 79, 066114 (2009)
We numerically investigate the six-species
predator-prey game in complex networks as well as in d -dimensional regular hypercubic lattices
with d=1,2,...,6 . The food-web topology of the six species contains two directed loops, each of
which is composed of cyclically predating three species. As the mutation rate is lowered below
the well-defined phase transition point, the Z2 symmetry related with the interchange in the two
loops is spontaneously broken, and it has been known that the system develops the defensive
alliance in which three cyclically predating species defend each other against the invasion of
other species. In the Watts-Strogatz small-world network structure characterized by the rewiring
probability alpha , the phase diagram shows the reentrant behavior as alpha is varied,
indicating a twofold role of the shortcuts. In d -dimensional regular hypercubic lattices, the
system also exhibits the reentrant phase transition as d is increased. We identify universality
class of the phase transition and discuss the proper mean-field limit of the system.
Death and resurrection of the human IRGM gene.
Bekpen C, Marques-Bonet T, Alkan C, Antonacci F, Leogrande MB,
Ventura M, Kidd JM, Siswara P, Howard JC, Eichler EE, PLoS Genetics 5, e1000403 (2009)
Immunity-related GTPases (IRG) play an
important role in defense against intracellular pathogens. One member of this gene family in
humans, IRGM, has been recently implicated as a risk factor for Crohn's disease. We
analyzed the detailed structure of this gene family among primates and showed that most of the
IRG gene cluster was deleted early in primate evolution, after the divergence of the anthropoids
from prosimians ( about 50 million years ago). Comparative sequence analysis of New World and
Old World monkey species shows that the single-copy IRGM gene became pseudogenized as a result
of an Alu retrotransposition event in the anthropoid common ancestor that disrupted the open
reading frame (ORF). We find that the ORF was reestablished as a part of a polymorphic stop
codon in the common ancestor of humans and great apes. Expression analysis suggests that this
change occurred in conjunction with the insertion of an endogenous retrovirus, which altered the
transcription initiation, splicing, and expression profile of IRGM. These data argue that the
gene became pseudogenized and was then resurrected through a series of complex structural events
and suggest remarkable functional plasticity where alleles experience diverse evolutionary
pressures over time. Such dynamism in structure and evolution may be critical for a gene family
locked in an arms race with an ever-changing repertoire of intracellular parasites.
From fitness landscapes to seascapes: non-equilibrium dynamics of
selection and adaptation.
Mustonen V, Lässig M, Trends In Genetics 25, 111-119 (2009)
Evolution is a quest for innovation.
Organisms adapt to changing natural selection by evolving new phenotypes. Can we read this
dynamics in their genomes? Not every mutation under positive selection responds to a change in
selection: beneficial changes also occur at evolutionary equilibrium, repairing previous
deleterious changes and restoring existing functions. Adaptation, by contrast, is viewed here as
a non-equilibrium phenomenon: the genomic response to time-dependent selection. Our approach
extends the static concept of fitness landscapes to dynamic fitness seascapes. It shows that
adaptation requires a surplus of beneficial substitutions over deleterious ones. Here, we focus
on the evolution of yeast and Drosophila genomes, providing examples where adaptive evolution
can and cannot be inferred, despite the presence of positive selection.
Selection on cis-regulatory variation at B4galnt2 and its
influence on von Willebrand factor in house mice.
Johnsen JM, Teschke M, Pavlidis P, McGee BM, Tautz D, Ginsburg D,
Baines JF, Molecular Biology And Evolution 26, 567-578 (2009)
The RIIIS/J inbred mouse strain is a model
for type 1 von Willebrand disease (VWD), a common human bleeding disorder. Low von Willebrand
factor (VWF) levels in RIIIS/J are due to a regulatory mutation, Mvwf1, which directs a
tissue-specific switch in expression of a glycosyltransferase, B4GALNT2, from intestine to blood
vessel. We recently found that Mvwf1 lies on a founder allele common among laboratory mouse
strains. To investigate the evolutionary forces operating at B4galnt2, we conducted a survey of
DNA sequence polymorphism and microsatellite variation spanning the B4galnt2 gene region in
natural Mus musculus domesticus populations. Two divergent haplotypes segregate in these natural
populations, one of which corresponds to the RIIIS/J sequence. Different local populations
display dramatic differences in the frequency of these haplotypes, and reduced microsatellite
variability near B4galnt2 within the RIIIS/J haplotype is consistent with the recent action of
natural selection. The level and pattern of DNA sequence polymorphism in the 5' flanking
region of the gene significantly deviates from the neutral expectation and suggests that
variation in B4galnt2 expression may be under balancing selection and/or arose from a recently
introgressed allele that subsequently increased in frequency due to natural selection. However,
coalescent simulations indicate that the heterogeneity in divergence between haplotypes is
greater than expected under an introgression model. Analysis of a population where the RIIIS/J
haplotype is in high frequency reveals an association between this haplotype, the B4galnt2
tissue-specific switch, and a significant decrease in plasma VWF levels. Given these
observations, we propose that low VWF levels may represent a fitness cost that is offset by a
yet unknown benefit of the B4galnt2 tissue-specific switch. Similar mechanisms may account for
the variability in VWF levels and high prevalence of VWD in other mammals, including humans.
Toxoplasma gondii and the Immunity-Related GTPase (IRG)
resistance system in mice: a review.
Zhao YO, Rohde C, Lilue JT, Könen-Waisman S, Khaminets A, Hunn JP,
Howard JC, Memórias Do Instituto Oswaldo Cruz 104, 234-240 (2009)
The Immunity Related GTPases (IRG proteins)
constitute a large family of interferon-inducible proteins that mediate early resistance to
Toxoplasma gondii infection in mice. At least six members of this family are required for
resistance of mice to virulent T. gondii strains. Recent results have shown that the complexity
of the resistance arises from complex regulatory interactions between different family members.
The mode of action against T. gondii depends on the ability of IRG proteins to accumulate on the
parasitophorous vacuole of invading tachyzoites and to induce local damage to the vacuole
resulting in disruption of the vacuolar membrane. Virulent strains of T. gondii overcome the IRG
resistance system, probably by interfering with the loading of IRG proteins onto the
parasitophorous vacuole membrane. It may be assumed that T. gondii strains highly virulent for
mice will be disadvantaged in the wild due to the rapid extinction of the infected host, while
it is self-evident that susceptibility to virulent strains is disadvantageous to the mouse host.
We consider the possibility that this double disadvantage is compensated in wild populations by
segregating alleles with different resistance and susceptibility properties in the IRG system.
Incremental steps toward incompatibility revealed by Arabidopsis
epistatic interactions modulating salicylic acid pathway activation.
Alcázar R, García AV, Parker JE, Reymond M, Proceedings Of The
National Academy Of Sciences Of The United States Of America 106, 334-339 (2009)
Plant growth is influenced by genetic
factors and environmental cues. Genotype-by-environment interactions are governed by complex
genetic epistatic networks that are subject to natural selection. Here we describe a novel
epistatic interaction modulating growth in response to temperature common to 2 Arabidopsis
recombinant inbred line (RIL) populations (Ler x Kas-2 and Ler x Kond). At 14 degrees C, lines
with specific allele combinations at interacting loci (incompatible interactions) have severe
growth defects. These lines exhibit deregulated cell death programs and enhanced disease
resistance. At 20 degrees C, growth defects are suppressed, but a positive trait of enhanced
resistance is retained. Mapping of 1 interacting QTL to a cluster of RPP1-like TIR-NB-LRR genes
on chromosome 3 is consistent with our finding that environmentally conditioned epistasis
depends on activation of the salicylic acid (SA) stress signaling pathway. The nature of the
epistatic interaction conforms to the Dobzhansky-Muller model of genetic incompatibility with
incomplete penetrance for reproductive isolation. Variation in fitness of different incompatible
lines reveals the presence of additional modifiers in the genetic background. We propose that
certain interacting loci lead to an optimal balance between growth and resistance to pathogens
by modulating SA signaling under specific environments. This could allow the accumulation of
additional incompatibilities before reaching complete reproductive isolation.
Simulation of DNA sequence evolution under models of recent
directional selection.
Kim Y, Wiehe T, Briefings In Bioinformatics 10, 84-96 (2009)
Computer simulation is an essential tool in
the analysis of DNA sequence variation for mapping events of recent adaptive evolution in the
genome. Various simulation methods are employed to predict the signature of selection in
sequence variation. The most informative and efficient method currently in use is coalescent
simulation. However, this method is limited to simple models of directional selection.
Whole-population forward-in-time simulations are the alternative to coalescent simulations for
more complex models. The notorious problem of excessive computational cost in forward-in-time
simulations can be overcome by various simplifying amendments. Overall, the success of
simulations depends on the creative application of some population genetic theory to the
simulation algorithm.
A common and unstable copy number variant is associated with
differences in Glo1 expression and anxiety-like behavior.
Williams R, Lim JE, Harr B, Wing C, Walters R, Distler MG, Teschke
M, Wu C, Wiltshire T, Su AI, Sokoloff GEA, PloS One 4, e4649 (2009)
Glyoxalase 1 (Glo1) has been implicated in
anxiety-like behavior in mice and in multiple psychiatric diseases in humans. We used mouse
Affymetrix exon arrays to detect copy number variants (CNV) among inbred mouse strains and
thereby identified a approximately 475 kb tandem duplication on chromosome 17 that includes Glo1
(30,174,390-30,651,226 Mb; mouse genome build 36). We developed a PCR-based strategy and used it
to detect this duplication in 23 of 71 inbred strains tested, and in various outbred and
wild-caught mice. Presence of the duplication is associated with a cis-acting expression QTL for
Glo1 (LOD>30) in BXD recombinant inbred strains. However, evidence for an eQTL for Glo1 was
not obtained when we analyzed single SNPs or 3-SNP haplotypes in a panel of 27 inbred strains.
We conclude that association analysis in the inbred strain panel failed to detect an eQTL
because the duplication was present on multiple highly divergent haplotypes. Furthermore, we
suggest that non-allelic homologous recombination has led to multiple reversions to the
non-duplicated state among inbred strains. We show associations between multiple
duplication-containing haplotypes, Glo1 expression and anxiety-like behavior in both inbred
strain panels and outbred CD-1 mice. Our findings provide a molecular basis for differential
expression of Glo1 and further implicate Glo1 in anxiety-like behavior. More broadly, these
results identify problems with commonly employed tests for association in inbred strains when
CNVs are present. Finally, these data provide an example of biologically significant phenotypic
variability in model organisms that can be attributed to CNVs.
A dedicated promoter drives constitutive expression of the
cell-autonomous immune resistance GTPase, Irga6 (IIGP1) in mouse liver.
Zeng J, Parvanova IA, Howard JC, PloS One 4, e6787 (2009)
BACKGROUND:In general, immune effector
molecules are induced by infection.METHODOLOGY AND PRINCIPAL FINDINGS:However, strong
constitutive expression of the cell-autonomous resistance GTPase, Irga6 (IIGP1), was found in
mouse liver, contrasting with previous evidence that expression of this protein is exclusively
dependent on induction by IFNgamma. Constitutive and IFNgamma-inducible expression of Irga6 in
the liver were shown to be dependent on transcription initiated from two independent
untranslated 5' exons, which splice alternatively into the long exon encoding the
full-length protein sequence. Irga6 is expressed constitutively in freshly isolated hepatocytes
and is competent in these cells to accumulate on the parasitophorous vacuole membrane of
infecting Toxoplasma gondii tachyzoites.CONCLUSIONS AND SIGNIFICANCE:The role of constitutive
hepatocyte expression of Irga6 in resistance to parasites invading from the gut via the hepatic
portal system is discussed.
Differences in embryonic pattern formation between Caenorhabditis
elegans and its close parthenogenetic relative Diploscapter coronatus.
Lahl V, Schulze J, Schierenberg E, The International Journal Of
Developmental Biology 53, 507-515 (2009)
In order to evaluate the evolutionary
preservation of developmental programs during nematode embryogenesis, we searched for close
relatives of the model system Caenorhabditis elegans with deviant patterns. The
parthenogenetically reproducing species Diploscapter coronatus shows prominent differences to C.
elegans. While in the 2-cell stage of C. elegans a rotation of the nuclear/centrosome complex is
found only in the posterior P1 cell, in D. coronatus cell isolation indicates that rotation
takes place in a cell-autonomous manner in both blastomeres, resulting in a linear 4-cell array.
In C. elegans, the ABp cell becomes different from its ABa sister via a germline-induced
induction. In D. coronatus, AB daughters do not touch the germline but nevertheless execute
different fates, suggesting a cell-autonomous mechanism or signaling over distance. Laser
ablation experiments revealed that active migration of the EMS cell is required to transform the
linearly ordered blastomeres into a 3-dimensional embryo, and the difference can be most easily
explained with a heterochronic shift with respect to cell mobility. In D. coronatus, reversal of
cleavage polarity in the germline, typical for C. elegans, is absent. This results in four
different transient variants of posterior blastomeres which eventually merge into a single
pattern prior to the onset of gastrulation. This merging includes primordial germ cell
migrations of variable extent toward the gut precursor cell and suggests a specific cell-cell
recognition mechanism. Cell distribution in advanced embryos is essentially indistinguishable
between both species.
Loss of the insulator protein CTCF during nematode evolution.
Heger P, Marin B, Schierenberg E, BMC Molecular Biology 10, 84
(2009)
BACKGROUND:The zinc finger (ZF) protein
CTCF (CCCTC-binding factor) is highly conserved in Drosophila and vertebrates where it has been
shown to mediate chromatin insulation at a genomewide level. A mode of genetic regulation that
involves insulators and insulator binding proteins to establish independent transcriptional
units is currently not known in nematodes including Caenorhabditis elegans. We therefore
searched in nematodes for orthologs of proteins that are involved in chromatin
insulation.RESULTS:While orthologs for other insulator proteins were absent in all 35 analysed
nematode species, we find orthologs of CTCF in a subset of nematodes. As an example for these we
cloned the Trichinella spiralis CTCF-like gene and revealed a genomic structure very similar to
the Drosophila counterpart. To investigate the pattern of CTCF occurrence in nematodes, we
performed phylogenetic analysis with the ZF protein sets of completely sequenced nematodes. We
show that three ZF proteins from three basal nematodes cluster together with known CTCF proteins
whereas no zinc finger protein of C. elegans and other derived nematodes does so.CONCLUSION:Our
findings show that CTCF and possibly chromatin insulation are present in basal nematodes. We
suggest that the insulator protein CTCF has been secondarily lost in derived nematodes like C.
elegans. We propose a switch in the regulation of gene expression during nematode evolution,
from the common vertebrate and insect type involving distantly acting regulatory elements and
chromatin insulation to a so far poorly characterised mode present in more derived nematodes.
Here, all or some of these components are missing. Instead operons, polycistronic
transcriptional units common in derived nematodes, seemingly adopted their function.
Properties of Sequence Conservation in Upstream Regulatory and
Protein Coding Sequences among Paralogs in Arabidopsis thaliana
Richardson DN, Wiehe T, Comparative Genomics 5817, 217 (2009)
Whole genome duplication (WGD) has
catalyzed the formation of new species, genes with novel functions, altered expression patterns,
complexified signaling pathways and has provided organisms a level of genetic robustness. We
studied the long-term evolution and interrelationships of 5’ upstream regulatory sequences
(URSs), protein coding sequences (CDSs) and expression correlations (EC) of duplicated gene
pairs in Arabidopsis. Three distinct methods revealed significant evolutionary conservation
between paralogous URSs and were highly correlated with microarray-based expression correlation
of the respective gene pairs. Positional information on exact matches between sequences unveiled
the contribution of micro-chromosomal rearrangements on expression divergence. A three-way rank
analysis of URS similarity, CDS divergence and EC uncovered specific gene functional biases.
Transcription factor activity was associated with gene pairs exhibiting conserved URSs and
divergent CDSs, whereas a broad array of metabolic enzymes was found to be associated with gene
pairs showing diverged URSs but conserved CDSs.
Robustness and epistasis in mutation-selection models.
Wolff A, Krug J, Physical Biology 6, 036007 (2009)
We investigate the fitness advantage
associated with the robustness of a phenotype against deleterious mutations using deterministic
mutation-selection models of a quasispecies type equipped with a mesa-shaped fitness landscape.
We obtain analytic results for the robustness effect which become exact in the limit of infinite
sequence length. Thereby, we are able to clarify a seeming contradiction between recent rigorous
work and an earlier heuristic treatment based on mapping to a Schrödinger equation. We exploit
the quantum mechanical analogy to calculate a correction term for finite sequence lengths and
verify our analytic results by numerical studies. In addition, we investigate the occurrence of
an error threshold for a general class of epistatic landscapes and show that diminishing
epistasis is a necessary but not sufficient condition for error threshold behaviour.
Why didn't Darwin discover Mendel's laws?
Howard JC, Journal Of Biology 8, 15 (2009)
Darwin's focus on small quantitative
variations as the raw material of evolution may have prevented him from discovering the laws of
inheritance.
2008
Dynamic correlation between intrahost HIV-1 quasispecies
evolution and disease progression.
Lee HY, Perelson AS, Park S, Leitner T, PLoS Computational Biology
4, e1000240 (2008)
Quantifying the dynamics of intrahost HIV-1
sequence evolution is one means of uncovering information about the interaction between HIV-1
and the host immune system. In the chronic phase of infection, common dynamics of sequence
divergence and diversity have been reported. We developed an HIV-1 sequence evolution model that
simulated the effects of mutation and fitness of sequence variants. The amount of evolution was
described by the distance from the founder strain, and fitness was described by the number of
offspring a parent sequence produces. Analysis of the model suggested that the previously
observed saturation of divergence and decrease of diversity in later stages of infection can be
explained by a decrease in the proportion of offspring that are mutants as the distance from the
founder strain increases rather than due to an increase of viral fitness. The prediction of the
model was examined by performing phylogenetic analysis to estimate the change in the rate of
evolution during infection. In agreement with our modeling, in 13 out of 15 patients (followed
for 3-12 years) we found that the rate of intrahost HIV-1 evolution was not constant but rather
slowed down at a rate correlated with the rate of CD4+ T-cell decline. The correlation between
the dynamics of the evolutionary rate and the rate of CD4+ T-cell decline, coupled with our
HIV-1 sequence evolution model, explains previously conflicting observations of the
relationships between the rate of HIV-1 quasispecies evolution and disease progression.
Inferring the history of speciation in house mice from autosomal,
X-linked, Y-linked and mitochondrial genes.
Geraldes A, Basset P, Gibson B, Smith KL, Harr B, Yu H, Bulatova
N, Ziv Y, Nachman MW, Molecular Ecology 17, 5349-5363 (2008)
Patterns of genetic differentiation among
taxa at early stages of divergence provide an opportunity to make inferences about the history
of speciation. Here, we conduct a survey of DNA-sequence polymorphism and divergence at loci on
the autosomes, X chromosome, Y chromosome and mitochondrial DNA in samples of Mus domesticus, M.
musculus and M. castaneus. We analyzed our data under a divergence with gene flow model and
estimate that the effective population size of M. castaneus is 200,000-400,000, of M. domesticus
is 100,000-200,000 and of M. musculus is 60,000-120,000. These data also suggest that these
species started to diverge approximately 500,000 years ago. Consistent with this recent
divergence, we observed considerable variation in the genealogical patterns among loci. For some
loci, all alleles within each species formed a monophyletic group, while at other loci, species
were intermingled on the phylogeny of alleles. This intermingling probably reflects both
incomplete lineage sorting and gene flow after divergence. Likelihood ratio tests rejected a
strict allopatric model with no gene flow in comparisons between each pair of species. Gene flow
was asymmetric: no gene flow was detected into M. domesticus, while significant gene flow was
detected into both M. castaneus and M. musculus. Finally, most of the gene flow occurred at
autosomal loci, resulting in a significantly higher ratio of fixed differences to polymorphisms
at the X and Y chromosomes relative to autosomes in some comparisons, or just the X chromosome
in others, emphasizing the important role of the sex chromosomes in general and the X chromosome
in particular in speciation.
Identification of selective sweeps in closely related populations
of the house mouse based on microsatellite scans.
Teschke M, Mukabayire O, Wiehe T, Tautz D, Genetics 180, 1537-1545
(2008)
Genome scans of polymorphisms promise to
provide insights into the patterns and frequencies of positive selection under natural
conditions. The use of microsatellites as markers has the potential to focus on very recent
events, since in contrast to SNPs, their high mutation rates should remove signatures of older
events. We assess this concept here in a large-scale study. We have analyzed two population
pairs of the house mouse, one pair of the subspecies Mus musculus domesticus and the other of M.
m. musculus. A total of 915 microsatellite loci chosen to cover the whole genome were assessed
in a prescreening procedure, followed by individual typing of candidate loci. Schlötterer's
ratio statistics (lnRH) were applied to detect loci with significant deviations from patterns of
neutral expectation. For eight loci from each population pair we have determined the size of the
potential sweep window and applied a second statistical procedure (linked locus statistics). For
the two population pairs, we find five and four significant sweep loci, respectively, with an
average estimated window size of 120 kb. On the basis of the analysis of individual allele
frequencies, it is possible to identify the most recent sweep, for which we estimate an onset of
400-600 years ago. Given the known population history for the French-German population pair, we
infer that the average frequency of selective sweeps in these populations is higher than 1 in
100 generations across the whole genome. We discuss the implications for adaptation processes in
natural populations.
Regulatory interactions between IRG resistance GTPases in the
cellular response to Toxoplasma gondii.
Hunn JP, Koenen-Waisman S, Papic N, Schroeder N, Pawlowski N,
Lange R, Kaiser F, Zerrahn J, Martens S, Howard JC, The EMBO Journal 27, 2495-2509 (2008)
Members of the immunity-related GTPase
(IRG) family are interferon-inducible resistance factors against a broad spectrum of
intracellular pathogens including Toxoplasma gondii. The molecular mechanisms governing the
function and regulation of the IRG resistance system are largely unknown. We find that IRG
proteins function in a system of direct, nucleotide-dependent regulatory interactions between
family members. After interferon induction but before infection, the three members of the GMS
subfamily of IRG proteins, Irgm1, Irgm2 and Irgm3, which possess an atypical nucleotide-binding
site, regulate the intracellular positioning of the conventional GKS subfamily members, Irga6
and Irgb6. Following infection, the normal accumulation of Irga6 protein at the parasitophorous
vacuole membrane (PVM) is nucleotide dependent and also depends on the presence of all three GMS
proteins. We present evidence that an essential role of the GMS proteins in this response is
control of the nucleotide-bound state of the GKS proteins, preventing their GTP-dependent
activation before infection. Accumulation of IRG proteins at the PVM has previously been shown
to be associated with a block in pathogen replication: our results relate for the first time the
enzymatic properties of IRG proteins to their role in pathogen resistance.
Second-order moments of segregating sites under variable
population size.
Zivković D, Wiehe T, Genetics 180, 341-357 (2008)
The identification of genomic regions that
have been exposed to positive selection is a major challenge in population genetics. Since
selective sweeps are expected to occur during environmental changes or when populations are
colonizing a new habitat, statistical tests constructed on the assumption of constant population
size are biased by the co-occurrence of population size changes and selection. To delimit this
problem and gain better insights into demographic factors, theoretical results regarding the
second-order moments of segregating sites, such as the variance of segregating sites, have been
derived. Driven by emerging genomewide surveys, which allow the estimation of demographic
parameters, a generalized version of Tajima's D has been derived that takes into account a
previously estimated demographic scenario to test single loci for traces of selection against
the null hypothesis of neutral evolution under variable population size.
The role of the segmentation gene hairy in Tribolium.
Aranda M, Marques-Souza H, Bayer T, Tautz D, Development Genes and
Evolution 218, 465-477 (2008)
Hairy stripes in Tribolium are generated
during blastoderm and germ band extension, but a direct role for Tc-h in trunk segmentation was
not found. We have studied here several aspects of hairy function and expression in Tribolium,
to further elucidate its role. First, we show that there is no functional redundancy with other
hairy paralogues in Tribolium. Second, we cloned the hairy orthologue from Tribolium confusum
and show that its expression mimics that of Tribolium castaneum, implying that stripe expression
should be functional in some way. Third, we show that the dynamics of stripe formation in the
growth zone is not compatible with an oscillatory mechanism comparable to the one driving the
expression of hairy homologues in vertebrates. Fourth, we use parental RNAi experiments to study
Tc-h function and we find that mandible and labium are particularly sensitive to loss of Tc-h,
reminiscent of a pair-rule function in the head region. In addition, lack of Tc-h leads to cell
death in the gnathal region at later embryonic stages, resulting in a detachment of the head.
Cell death patterns are also altered in the midline. Finally, we have analysed the effect of
Tc-h knockdown on two of the target genes of hairy in Drosophila, namely fushi tarazu and
paired. We find that the trunk expression of Tc-h is required to regulate Tc-ftz, although
Tc-ftz is itself also not required for trunk segmentation in Tribolium. Our results imply that
there is considerable divergence in hairy function between Tribolium and Drosophila.
Energy-dependent fitness: a quantitative model for the evolution
of yeast transcription factor binding sites.
Mustonen V, Kinney J, Callan CG, Lässig M, Proceedings Of The
National Academy Of Sciences Of The United States Of America 105, 12376-12381 (2008)
We present a genomewide cross-species
analysis of regulation for broad-acting transcription factors in yeast. Our model for binding
site evolution is founded on biophysics: the binding energy between transcription factor and
site is a quantitative phenotype of regulatory function, and selection is given by a fitness
landscape that depends on this phenotype. The model quantifies conservation, as well as loss and
gain, of functional binding sites in a coherent way. Its predictions are supported by direct
cross-species comparison between four yeast species. We find ubiquitous compensatory mutations
within functional sites, such that the energy phenotype and the function of a site evolve in a
significantly more constrained way than does its sequence. We also find evidence for substantial
evolution of regulatory function involving point mutations as well as sequence insertions and
deletions within binding sites. Genes lose their regulatory link to a given transcription factor
at a rate similar to the neutral point mutation rate, from which we infer a moderate average
fitness advantage of functional over nonfunctional sites. In a wider context, this study
provides an example of inference of selection acting on a quantitative molecular trait.
Structurally different alleles of the ath-MIR824 microRNA
precursor are maintained at high frequency in Arabidopsis thaliana.
de Meaux J, Hu J, Tartler U, Goebel U, Proceedings Of The National
Academy Of Sciences Of The United States Of America 105, 8994-8999 (2008)
In plants and animals, gene expression can
be down-regulated at the posttranscriptional level by microRNAs (miRNAs), a class of small
endogenous RNA. Comparative analysis of miRNA content across species indicates continuous birth
and death of these loci in the course of evolution. However, little is known about the
microevolutionary dynamics of these genetic elements, especially in plants. In this article we
examine polymorphism at two miRNA-encoding loci in Arabidopsis thaliana, miR856 and miR824,
which are not found in rice or poplar. We compare their diversity to other miRNA-encoding loci
conserved across distant taxa. We find that levels of variation vary significantly across loci
and that the two recently derived loci harbor patterns of diversity deviating from neutrality.
miRNA miR856 shows a weak signature of a selective sweep whereas miR824 displays signs of
balancing selection. A detailed examination of structural variation among alleles found at the
miR824-encoding locus suggests nonrandom evolution of a thermoresistant substructure in the
precursor. Expression analysis of pre-miR824 and its target, AGL16, indicates that these
structural differences likely impact the processing of mature miR824. Our work highlights the
relevance of RNA structure in precursor sequence evolution, suggesting that the evolutionary
dynamics of miRNA-encoding loci is more complex than suggested by the constraints exerted on the
interaction between mature miRNA fragments and their target exon.
Chlamydia muridarum evades growth restriction by the
IFN-gamma-inducible host resistance factor Irgb10.
Coers J, Bernstein-Hanley I, Grotsky D, Parvanova I, Howard JC,
Taylor GA, Dietrich WF, Starnbach MN, Journal Of Immunology (Baltimore, Md. : 1950) 180,
6237-6245 (2008)
Chlamydiae are obligate intracellular
bacterial pathogens that exhibit a broad range of host tropism. Differences in host tropism
between Chlamydia species have been linked to host variations in IFN-gamma-mediated immune
responses. In mouse cells, IFN-gamma can effectively restrict growth of the human pathogen
Chlamydia trachomatis but fails to control growth of the closely related mouse pathogen
Chlamydia muridarum. The ability of mouse cells to resist C. trachomatis replication is largely
dependent on the induction of a family of IFN-gamma-inducible GTPases called immunity-related
GTPases or IRGs. In this study we demonstrate that C. muridarum can specifically evade
IRG-mediated host resistance. It has previously been suggested that C. muridarum inactivates the
IRG protein Irga6 (Iigp1) to dampen the murine immune response. However, we show that Irga6 is
dispensable for the control of C. trachomatis replication. Instead, an effective IFN-gamma
response to C. trachomatis requires the IRG proteins Irgm1 (Lrg47), Irgm3 (Igtp), and Irgb10.
Ectopic expression of Irgb10 in the absence of IFN-gamma is sufficient to reduce intracellular
growth of C. trachomatis but fails to restrict growth of C. muridarum, indicating that C.
muridarum can specifically evade Irgb10-driven host responses. Importantly, we find that Irgb10
protein intimately associates with inclusions harboring C. trachomatis but is absent from
inclusions formed by C. muridarum. These data suggest that C. muridarum has evolved a mechanism
to escape the murine IFN-gamma response by restricting access of Irgb10 and possibly other IRG
proteins to the inclusion.
The genome of the model beetle and pest Tribolium castaneum.
Tribolium Genome Sequencing Consortium, Richards S, Gibbs RA,
Weinstock GM, Brown SJ, Denell R, Beeman RW, Gibbs R, Beeman RW, Brown SJ, Bucher G et al.,
Nature 452, 949-955 (2008)
Tribolium castaneum is a member of the most
species-rich eukaryotic order, a powerful model organism for the study of generalized insect
development, and an important pest of stored agricultural products. We describe its genome
sequence here. This omnivorous beetle has evolved the ability to interact with a diverse
chemical environment, as shown by large expansions in odorant and gustatory receptors, as well
as P450 and other detoxification enzymes. Development in Tribolium is more representative of
other insects than is Drosophila, a fact reflected in gene content and function. For example,
Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila,
some being expressed in the growth zone crucial for axial elongation in short-germ development.
Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis
elegans, but nevertheless offers similar power for the elucidation of gene function and
identification of targets for selective insect control.
Self-regulatory circuits in dorsoventral axis formation of the
short-germ beetle Tribolium castaneum.
Nunes da Fonseca R, von Levetzow C, Kalscheuer P, Basal A, van der
Zee M, Roth S, Developmental cell 14, 605-615 (2008)
The rel/NF-kappaB transcription factor
Dorsal controls dorsoventral (DV) axis formation in Drosophila. A stable nuclear gradient of
Dorsal directly regulates approximately 50 target genes. In Tribolium castaneum (Tc), a beetle
with an ancestral type of embryogenesis, the Dorsal nuclear gradient is not stable, but rapidly
shrinks and disappears. We find that negative feedback accounts for this dynamic behavior:
Tc-Dorsal and one of its target genes activate transcription of the IkB homolog Tc-cactus,
terminating Dorsal function. Despite its transient role, Tc-Dorsal is strictly required to
initiate DV polarity, as in Drosophila. However, unlike in Drosophila, embryos lacking Tc-Dorsal
display a periodic pattern of DV cell fates along the AP axis, indicating that a self-organizing
ectodermal patterning system operates independently of mesoderm or maternal DV polarity cues.
Our results also elucidate how extraembryonic tissues are organized in short-germ embryos, and
how patterning information is transmitted from the early embryo to the growth zone.
TGFbeta signaling in Tribolium: vertebrate-like components in a
beetle.
van der Zee M, da Fonseca RN, Roth S, Development Genes and
Evolution 218, 203-213 (2008)
The cytokines of the TGFbeta superfamily
are highly conserved in evolution and elicit a diverse range of cellular responses in all
metazoa. In Drosophila, the signaling pathways of the two TGFbeta subfamilies, Activins and Bone
Morphogenetic Proteins (BMPs), have been well studied. To address the question of whether the
findings from Drosophila are representative of insects in general, we analyzed the components of
TGFbeta-signaling present in the genome of the beetle Tribolium castaneum. We were able to
identify orthologs of the BMPs Decapentaplegic and Glass bottom boat, of the Activins
Activinbeta and Dawdle, as well as orthologs of the less well-known ligands Myoglianin and
Maverick, together with orthologs of all TGFbeta receptors and cytoplasmic signal transducers
present in Drosophila. This indicates that the diversity of TGFbeta signaling components is
generally well conserved between Drosophila and Tribolium. However, the genome of the beetle-and
of the bee Apis mellifera-lacks an ortholog of the Drosophila BMP Screw but does contain a
vertebrate-like BMP10 homolog which is not found in Drosophila. Concerning BMP inhibitors,
Tribolium displays an even more vertebrate-like ensemble of components. We found two orthologs
of the vertebrate DAN family, Dan and Gremlin, and show embryonic expression of a
vertebrate-like BAMBI ortholog, all of which are absent in Drosophila. This suggests that
Tribolium might have retained a more ancestral composition of TGFbeta signaling components and
that TGFbeta signaling underwent considerable change in the Drosophila lineage. Tribolium is an
excellent model to study the function of these ancestral signaling components in insects.
Molecular evolution under fitness fluctuations.
Mustonen V, Lässig M, Physical Review Letters 100, 108101 (2008)
Molecular evolution is a stochastic process
governed by fitness, mutations, and reproductive fluctuations in a population. Here, we study
evolution where fitness itself is stochastic, with random switches in the direction of selection
at individual genomic loci. As the correlation time of these fluctuations becomes larger than
the diffusion time of mutations within the population, fitness changes from an annealed to a
quenched random variable. We show that the rate of evolution has its maximum in the crossover
regime, where both time scales are comparable. Adaptive evolution emerges in the quenched
fitness regime (evidence for such fitness fluctuations has recently been found in genomic data).
The joint statistical theory of reproductive and fitness fluctuations establishes a conceptual
connection between evolutionary genetics and statistical physics of disordered systems.
Delimiting the conserved features of hunchback function for the
trunk organization of insects.
Marques-Souza H, Aranda M, Tautz D, Development (Cambridge,
England) 135, 881-888 (2008)
The gap gene hunchback in Drosophila acts
during syncytial blastoderm stage via a short-range gradient and concentration-dependent
activation or repression of target genes. Orthologues of hunchback can be easily found in other
insects, but it has been unclear how well its functions are conserved. The segmentation process
in most insect embryos occurs under cellular conditions, which should not allow the formation of
diffusion-controlled transcription factor gradients. We have studied here in detail the function
of hunchback in the short germ embryo of Tribolium using parental RNAi and interaction with
possible target genes. We find that hunchback is a major regulator of the trunk gap genes and
Hox genes in Tribolium, but may only indirectly be required to regulate other segmentation
genes. The core function of hunchback appears to be the setting of the Ultrabithorax expression
border via a repression effect, and the activation of the Krüppel expression domain. These
regulatory effects are likely to be direct and are conserved between Drosophila and Tribolium.
We find no evidence for a classical gap phenotype in the form of loss of segments in the region
of expression of hunchback. However, the phenotypic effects in Tribolium are highly comparable
with those found for other short germ embryos, i.e. the core functions of hunchback in Tribolium
appear to be the same in these other insects, although they are evolutionarily more distant to
Tribolium, than Tribolium is to Drosophila. These results allow the disentanglement of the
conserved role of hunchback in insects from the derived features that have been acquired in the
lineage towards Drosophila. Given that the gap phenotype appears to occur only in long germ
embryos and that the main role of hunchback appears to be the regionalization of the embryo, it
may be appropriate to revive an alternative name for the class of gap genes, namely 'cardinal
genes'.
Integration of horizontally transferred genes into regulatory
interaction networks takes many million years.
Lercher MJ, Pal C, Molecular Biology And Evolution 25, 559-567
(2008)
Adaptation of bacteria to new or changing
environments is often associated with the uptake of foreign genes through horizontal gene
transfer. However, it has remained unclear how (and how fast) new genes are integrated into
their host's cellular networks. Combining the regulatory and protein interaction networks
of Escherichia coli with comparative genomics tools, we provide the first systematic analysis of
this issue. Genes transferred recently have fewer interaction partners compared to
nontransferred genes in both regulatory and protein interaction networks. Thus, horizontally
transferred genes involved in complex regulatory and protein-protein interactions are rarely
favored by selection. Only few protein-protein interactions are gained after the initial
integration of genes following the transfer event. In contrast, transferred genes are gradually
integrated into the regulatory network of their host over evolutionary time. During adaptation
to the host cellular environment, horizontally transferred genes recruit existing transcription
factors of the host, reflected in the fast evolutionary rates of the cis-regulatory regions of
transferred genes. Further, genes resulting from increasingly ancient transfer events show
increasing numbers of transcriptional regulators as well as improved coregulation with
interacting proteins. Fine-tuned integration of horizontally transferred genes into the
regulatory network spans more than 8-22 million years and encompasses accelerated evolution of
regulatory regions, stabilization of protein-protein interactions, and changes in codon usage.
Plant development revolves around axes.
Chandler J, Nardmann J, Werr W, Trends In Plant Science 13, 78-84
(2008)
Arabidopsis thaliana has become a paradigm
for dicot embryo development, despite its embryology being non-representative of dicots in
general. The recent cloning of heterologous genes involved in embryonic development from maize
and construction of robust phylogenies has shed light on the conservation of transcription
factor function and now facilitates a comparison of maize and Arabidopsis embryogenesis
orthology. In this review, we focus on a comparison of expression domains of WUSCHEL HOMEOBOX
LIKE (WOX), SHOOTMERISTEMLESS (STM), DORNROESCHEN (DRN) and CUP-SHAPED COTYLEDON (CUC) genes and
their role in axialization in both species, showing that despite significantly divergent modes
of embryogenesis, most notably in terms of axes and planes of symmetry, there is considerable
conservation of function as well as notable differences between maize and Arabidopsis.
Genome-wide analysis indicates more Asian than Melanesian
ancestry of Polynesians.
Kayser M, Lao O, Saar K, Brauer S, Wang X, Nürnberg P, Trent RJ,
Stoneking M, American Journal Of Human Genetics 82, 194-198 (2008)
Analyses of mitochondrial DNA (mtDNA) and
nonrecombining Y chromosome (NRY) variation in the same populations are sometimes concordant but
sometimes discordant. Perhaps the most dramatic example known of the latter concerns
Polynesians, in which about 94% of Polynesian mtDNAs are of East Asian origin, while about 66%
of Polynesian Y chromosomes are of Melanesian origin. Here we analyze on a genome-wide scale, to
our knowledge for the first time, the origins of the autosomal gene pool of Polynesians by
screening 377 autosomal short tandem repeat (STR) loci in 47 Pacific Islanders and compare the
results with those obtained from 44 Chinese and 24 individuals from Papua New Guinea. Our data
indicate that on average about 79% of the Polynesian autosomal gene pool is of East Asian origin
and 21% is of Melanesian origin. The genetic data thus suggest a dual origin of Polynesians with
a high East Asian but also considerable Melanesian component, reflecting sex-biased admixture in
Polynesian history in agreement with the Slow Boat model. More generally, these results also
demonstrate that conclusions based solely on uniparental markers, which are frequently used in
population history studies, may not accurately reflect the history of the autosomal gene pool of
a population.
Evolution in random fitness landscapes: the infinite sites model
Park S, Krug J, J. Stat. Mech. P04014
doi:10.1088/1742-5468/2008/04/P04014 (2008)
We consider the evolution of an asexually
reproducing population in an uncorrelated random fitness landscape in the limit of infinite
genome size, which implies that each mutation generates a new fitness value drawn from a
probability distribution g(w). This is the finite population version of Kingman's house of cards
model (Kingman 1978 J. Appl. Probab. 15 1). In contrast to Kingman's work, the focus here is on
unbounded distributions g(w) which lead to an indefinite growth of the population fitness. The
model is solved analytically in the limit of infinite population size and simulated numerically
for finite N. When the genome-wide mutation probability U is small, the long-time behavior of
the model reduces to a point process of fixation events, which is referred to as a diluted
record process (DRP). The DRP is similar to the standard record process except that a new record
candidate (a number that exceeds all previous entries in the sequence) is accepted only with a
certain probability that depends on the values of the current record and the candidate. We
develop a systematic analytic approximation scheme for the DRP. At finite U the fitness
frequency distribution of the population decomposes into a stationary part due to mutations and
a traveling wave component due to selection, which is shown to imply a reduction of the mean
fitness by a factor of 1−U compared to the limit.
From protein interactions to functional annotation: graph
alignment in Herpes.
Kolár M, Lässig M, Berg J, BMC Systems Biology 2, 90 (2008)
BACKGROUND:Sequence alignment is a prolific
basis of functional annotation, but remains a challenging problem in the 'twilight zone'
of high sequence divergence or short gene length. Here we demonstrate how information on gene
interactions can help to resolve ambiguous sequence alignments. We compare two distant Herpes
viruses by constructing a graph alignment, which is based jointly on the similarity of their
protein interaction networks and on sequence similarity. This hybrid method provides functional
associations between proteins of the two organisms that cannot be obtained from sequence or
interaction data alone.RESULTS:We find proteins where interaction similarity and sequence
similarity are individually weak, but together provide significant evidence of orthology. There
are also proteins with high interaction similarity but without any detectable sequence
similarity, providing evidence of functional association beyond sequence homology. The
functional predictions derived from our alignment are consistent with genomic position and gene
expression data.CONCLUSION:Our approach shows that evolutionary conservation is a powerful
filter to make protein interaction data informative about functional similarities between the
interacting proteins, and it establishes graph alignment as a powerful tool for the comparative
analysis of data from highly diverged species.
Many roads lead to Rome: different ways to construct a nematode
Schierenberg E, Schulze J, Evolving Pathways: Key Themes In
Evolutionary Developmental Biology. Cambridge University Press, Cambridge, 261-280 (2008)
The IRG proteins: a function in search of a mechanism.
Howard J, Immunobiology 213, 367-375 (2008)
The IRG proteins (p47 GTPases) constitute
one of the strongest resistance systems known to be active against intracellular pathogens in
mice. The proteins are induced by interferons and assemble on phagosomes and parasitophorous
vacuoles of a number of different micro-organisms in all cell types assayed. There are presently
three experimentally based views as to how they exert their cell-autonomous activity against
intracellular pathogens: blocking of interferon-mediated acceleration of phagosome maturation,
induction of autophagic membranes, and direct destruction of the parasitophorous vacuole
membrane. Failure of hemopoietic stem cells during infection is associated with targeted
deletion of one IRG protein, Irgm1. The significance of this non-cell-autonomous phenotype is
discussed.
2007
The evolution of plant regulatory networks: what Arabidopsis
cannot say for itself.
Nardmann J, Werr W, Current Opinion In Plant Biology 10, 653-659
(2007)
Genetic and molecular analyses in the dicot
model plant Arabidopsis thaliana have begun to shed some light on regulatory networks in plants.
However, comparisons with other species are necessary to validate networks identified in model
species on the evolutionary scale. Many key regulatory proteins are encoded by members of
transcription factor gene families. Orthologous genes can be identified by phylogenetic
reconstructions based on conserved protein domains and functionally substantiated by gene
expression patterns and mutant analyses. Recent comparative analyses of different pathways
involved in shoot meristem development reveal not only conservation from basal land plants to
angiosperms but also evolutionary freedom for significant adaptations in the course of plant
speciation.
Clonal interference in large populations.
Park S, Krug J, Proceedings Of The National Academy Of Sciences Of
The United States Of America 104, 18135-18140 (2007)
Clonal interference, the competition
between lineages arising from different beneficial mutations in an asexually reproducing
population, is an important factor determining the tempo and mode of microbial adaptation. The
standard theory of this phenomenon neglects the occurrence of multiple mutations as well as the
correlation between loss by genetic drift and clonal competition, which is questionable in large
populations. Working within the Wright-Fisher model with multiplicative fitness (no epistasis),
we determine the rate of adaptation asymptotically for very large population sizes and show that
the standard theory fails in this regime. Our study also explains the success of the standard
theory in predicting the rate of adaptation for moderately large populations. Furthermore, we
show that the nature of the substitution process changes qualitatively when multiple mutations
are allowed for, because several mutations can be fixed in a single fixation event. As a
consequence, the index of dispersion for counts of the fixation process displays a minimum as a
function of population size, whereas the origination process of fixed mutations becomes
completely regular for very large populations. We find that the number of mutations fixed in a
single event is geometrically distributed as in the neutral case. These conclusions are based on
extensive simulations combined with analytic results for the limit of infinite population size.
Cell-autonomous immunity to Toxoplasma gondii in mouse and man.
Könen-Waisman S, Howard JC, Microbes And Infection 9, 1652-1661
(2007)
The protozoan, Toxoplasma gondii, is a
natural pathogen of mouse and a zoonosis of man. Immunity against the pathogen is largely
mediated by interferon-stimulated cell-autonomous mechanisms that are strikingly different
between man and mouse. There are many poorly understood host and pathogen variables that affect
the outcome of infection.
Extensive additivity of gene expression differentiates subspecies
of the house mouse.
Rottscheidt R, Harr B, Genetics 177, 1553-1567 (2007)
We have studied different subspecies of the
house mouse and their reciprocal F(1) hybrids to estimate the within-locus mode of inheritance
for subspecies differences in gene expression in three tissues (brain, liver, and testis) of
male mice. This study investigates the mode of inheritance in crosses at a larger taxonomic
distance than has been previously systematically investigated. We found the vast majority of
transcripts to be additively expressed with only a few transcripts showing dominance or
overdominance in expression, except for one direction of one cross, which showed large
mis-expression in the testis. We suggest that, as time passes, more genes come to influence
expression, and if there is no directional dominance, additivity becomes increasingly more
likely, up to a threshold beyond which there is F(1) hybrid breakdown. Some previous studies on
different organisms have found a large degree of dominance, commonly at shorter taxonomic
differences. We surveyed these findings and show that the most consistent association exists
between the amount of additivity detected in a study and the expression analysis method (in
particular microarray platform), suggesting that at least some of the differences among studies
might be methodological. Most studies agree with ours in that within-locus additivity seems to
be general mode of inheritance for transcript expression. Differentially expressed transcripts
identified in our screen among subspecies of house mice are candidate genes that could be
involved in reproductive isolation between these subspecies.
WOX gene phylogeny in Poaceae: a comparative approach addressing
leaf and embryo development.
Nardmann J, Zimmermann R, Durantini D, Kranz E, Werr W, Molecular
Biology And Evolution 24, 2474-2484 (2007)
The phylogeny based on the homeodomain (HD)
amino acid sequence of the WOX (WUSCHEL-related homeobox gene family) was established in the 3
major radiations of the Poaceae family: Pooideae (Brachypodium distachyon), Bambusoideae (Oryza
sativa), and Panicoideae (Zea mays). The genomes of all 3 grasses contain an ancient duplication
in the WOX3 branch, and the cellular expression patterns in maize and rice indicate
subfunctionalization of paralogues during leaf development, which may relate to the architecture
of the grass leaf and the encircling of the stem. The use of maize WOX gene family members as
molecular markers in maize embryo development for the first time allowed us to visualize
cellular decisions in the maize proembryo, including specification of the shoot/root axis at an
oblique angle to the apical-basal polarity of the zygote. All molecular marker data are
compatible with the conclusion that the embryonic shoot/root axis comprises a discrete domain
from early proembryo stages onward. Novel cell fates of the shoot and the root are acquired
within this distinct morphogenic axis domain, which elongates and thus separates the shoot
apical meristem and root apical meristem (RAM) anlagen in the maize embryo.
The MADS-domain protein PPM2 preferentially occurs in gametangia
and sporophytes of the moss Physcomitrella patens.
Quodt V, Faigl W, Saedler H, Münster T, Gene 400, 25-34 (2007)
To date, the function of MADS-domain
transcription factors in non-seed plants remains largely elusive, although a number of genes
have been isolated and characterized from a variety of species. In our study we analyzed PPM2, a
classical MIKC-type MADS-box gene from the moss Physcomitrella patens, taking advantage of the
unique technical properties Physcomitrella offers in terms of efficient homologous
recombination. We determined mRNA and protein distribution and performed targeted disruption of
the genomic locus for functional analysis of PPM2. Despite weak ubiquitous expression, PPM2
protein is mostly found in male and female gametangia and basal parts of developing sporophytes.
Therefore, PPM2 seems to function in both the haploid and the diploid phase of the moss life
cycle. This situation reflects an evolutionary transition state of gene recruitment from an
ancestral gametophytic generation into a derived sporophytic generation which became dominating
in tracheophytes. However, a knock-out of the PPM2 gene did not cause visible phenotypical
changes in the respective structures. The implications of our findings for the understanding of
the evolutionary history of MADS-box transcription factors in plants are discussed.
Evolution of immunity and pathogens.
Howard JC, Jack RS, European Journal Of Immunology 37, 1721-1723
(2007)
The Cologne Spring Meeting of the Institute
of Genetics focuses on a different topic each year. In Spring 2007, the meeting focused on the
complex evolutionary relationships between hosts and pathogens.
Identification of a candidate genetic variant for the high
prevalence of type II diabetes in Polynesians.
Myles S, Hradetzky E, Engelken J, Lao O, Nürnberg P, Trent RJ,
Wang X, Kayser M, Stoneking M, European Journal Of Human Genetics 15, 584-589 (2007)
The prevalence of non-insulin-dependent
diabetes mellitus (type II diabetes) in Polynesia is among the highest recorded worldwide and is
substantially higher than in neighboring human populations. Such large differences in the
frequency of a phenotype between populations may be explained by large allele frequency
differences between populations in genes associated with the phenotype. To identify genes that
may explain the high between-population variation in type II diabetes prevalence in the Pacific,
we determined the frequency of 10 type II diabetes-associated alleles in 23 Polynesians, 23
highland New Guineans and 19 Han Chinese, calculated population-pairwise Fst values for each
allele and compared these values to the distribution of Fst values from approximately 100,000
SNPs from the same populations. The susceptibility allele in the PPARGC1A gene is at a frequency
of 0.717 in Polynesians, 0.368 in Chinese but is absent in the New Guineans. The striking
frequency difference between Polynesians and New Guineans is highly unusual (Fst=0.703, P=0.007)
and we therefore suggest that this allele may play a role in the large difference in type II
diabetes prevalence between Polynesians and neighboring populations.
A pooling approach to detect signatures of selective sweeps in
genome scans using microsatellites
Thomas M, Möller F, Wiehe T, Tautz D, Molecular Ecology Notes 7,
400-403 (2007)
We have evaluated a pooling approach that
can reduce the number of polymerase chain reactions in a screen for selective sweeps by more
than an order of magnitude. We show that the complex peak pattern that results from pooling of
all samples from a given population is a faithful reflection of the composite pattern of the
individual alleles, although with an under-representation of the larger alleles. Candidate loci
for selective sweeps can be identified by visual inspection of the pool patterns. We have also
implemented a software tool, which can find suitable microsatellite loci in the vicinity of
annotated genes.
Reduced X-linked diversity in derived populations of house mice.
Baines JF, Harr B, Genetics 175, 1911-1921 (2007)
Contrasting patterns of X-linked vs.
autosomal diversity may be indicative of the mode of selection operating in natural populations.
A number of observations have shown reduced X-linked (or Z-linked) diversity relative to
autosomal diversity in various organisms, suggesting a large impact of genetic hitchhiking.
However, the relative contribution of other forces such as population bottlenecks, variation in
reproductive success of the two sexes, and differential introgression remains unclear. Here, we
survey 13 loci, 6 X-linked and 7 autosomal, in natural populations of the house mouse (Mus
musculus) subspecies complex. We studied seven populations of three different subspecies, the
eastern house mouse M. musculus castaneus, the central house mouse M. m. musculus, and the
western house mouse M. m. domesticus, including putatively ancestral and derived populations for
each. All populations display lower diversity on the X chromosomes relative to autosomes, and
this effect is most pronounced in derived populations. To assess the role of demography, we fit
the demographic parameters that gave the highest likelihood of the data using coalescent
simulations. We find that the reduction in X-linked diversity is too large to be explained by a
simple demographic model in at least two of four derived populations. These observations are
also not likely to be explained by differences in reproductive success between males and
females. They are consistent with a greater impact of positive selection on the X chromosome,
and this is supported by the observation of an elevated K(A) and elevated K(A)/K(S) ratios on
the rodent X chromosome. A second contribution may be that the X chromosome less readily
introgresses across subspecies boundaries.
Deterministic and stochastic regimes of asexual evolution on
rugged fitness landscapes.
Jain K, Krug J, Genetics 175, 1275-1288 (2007)
We study the adaptation dynamics of an
initially maladapted asexual population with genotypes represented by binary sequences of length
L. The population evolves in a maximally rugged fitness landscape with a large number of local
optima. We find that whether the evolutionary trajectory is deterministic or stochastic depends
on the effective mutational distance d(eff) up to which the population can spread in genotype
space. For d(eff) = L, the deterministic quasi-species theory operates while for d(eff) < 1,
the evolution is completely stochastic. Between these two limiting cases, the dynamics are
described by a local quasi-species theory below a crossover time T(x) while above T(x) the
population gets trapped at a local fitness peak and manages to find a better peak via either
stochastic tunneling or double mutations. In the stochastic regime d(eff) < 1, we identify
two subregimes associated with clonal interference and uphill adaptive walks, respectively. We
argue that our findings are relevant to the interpretation of evolution experiments with
microbial populations.
Adaptations to fluctuating selection in Drosophila.
Mustonen V, Lässig M, Proceedings Of The National Academy Of
Sciences Of The United States Of America 104, 2277-2282 (2007)
Time-dependent selection causes the
adaptive evolution of new phenotypes, and this dynamics can be traced in genomic data. We have
analyzed polymorphisms and substitutions in Drosophila, using a more sensitive inference method
for adaptations than the standard population-genetic tests. We find evidence that selection
itself is strongly time-dependent, with changes occurring at nearly the rate of neutral
evolution. At the same time, higher than previously estimated levels of selection make adaptive
responses by a factor 10-100 faster than the pace of selection changes, ensuring that
adaptations are an efficient mode of evolution under time-dependent selection. The rate of
selection changes is faster in noncoding DNA, i.e., the inference of functional elements can
less be based on sequence conservation than for proteins. Our results suggest that selection
acts not only as a constraint but as a major driving force of genomic change.
Contrasting evolution of expression differences in the testis
between species and subspecies of the house mouse.
Voolstra C, Tautz D, Farbrother P, Eichinger L, Harr B, Genome
Research 17, 42-49 (2007)
Regulatory changes in genes involved in
reproduction are thought to be prime targets for divergence during speciation, since they are
expected to play an important role in sexual selection and sexual conflict. We used microarray
analysis of RNA from different wild populations of house mouse subspecies (including Mus m.
musculus, Mus m. domesticus, and Mus m. castaneus) and from the sister species Mus spretus to
test this assumption. A comparison of expression divergence in brain, liver/kidney, and testis
shows a major difference in the evolutionary dynamics of testis-related genes. While the
comparison between species confirms an excess in divergence in testis genes, we find that all
comparisons between subspecies yield only a very small number of genes with significantly
different expression levels in the testis. These results suggest that the early phase of the
speciation process may not be driven by regulatory changes in genes that are potential targets
of sexual selection, and that the divergence in these genes is only established during a later
phase of the speciation process.
Identification of selective sweeps using a dynamically adjusted
number of linked microsatellites.
Wiehe T, Nolte V, Zivković D, Schlötterer C, Genetics 175, 207-218
(2007)
There is currently large interest in
distinguishing the signatures of genetic variation produced by demographic events from those
produced by natural selection. We propose a simple multilocus statistical test to identify
candidate sites of selective sweeps with high power. The test is based on the variability
profile measured in an array of linked microsatellites. We also show that the analysis of
flanking markers drastically reduces the number of false positives among the candidates that are
identified in a genomewide survey of unlinked loci and find that this property is maintained in
many population-bottleneck scenarios. However, for a certain range of intermediately severe
population bottlenecks we find genomic signatures that are very similar to those produced by a
selective sweep. While in these worst-case scenarios the power of the proposed test remains
high, the false-positive rate reaches values close to 50%. Hence, selective sweeps may be hard
to identify even if multiple linked loci are analyzed. Nevertheless, the integration of
information from multiple linked loci always leads to a considerable reduction of the
false-positive rate compared to a genome scan of unlinked loci. We discuss the application of
this test to experimental data from Drosophila melanogaster.
MIKC* MADS-protein complexes bind motifs enriched in the proximal
region of late pollen-specific Arabidopsis promoters.
Verelst W, Saedler H, Münster T, Plant Physiology 143, 447-460
(2007)
The genome of Arabidopsis (Arabidopsis
thaliana) encodes over 100 MADS-domain transcription factors, categorized into five phylogenetic
subgroups. Most research efforts have focused on just one of these subgroups (MIKC(c)), whereas
the other four remain largely unexplored. Here, we report on five members of the so-called
Mdelta or Arabidopsis MIKC* (AtMIKC*) subgroup, which are predominantly expressed during the
late stages of pollen development. Very few MADS-box genes function in mature pollen, and from
this perspective, the AtMIKC* genes are therefore highly exceptional. We found that the AtMIKC*
proteins are able to form multiple heterodimeric complexes in planta, and that these protein
complexes exhibit a for the MADS-family unusual and high DNA binding specificity in vitro.
Compared to their occurrence in promoters genome wide, AtMIKC* binding sites are strongly
overrepresented in the proximal region of late pollen-specific promoters. By combining our
experimental data with in silico genomics and pollen transcriptomics approaches, we identified a
considerable number of putative direct target genes of the AtMIKC* transcription factor
complexes in pollen, many of which have known or proposed functions in pollen tube growth. The
expression of several of these predicted targets is altered in mutant pollen in which all
AtMIKC* complexes are affected, and in vitro germination of this mutant pollen is severely
impaired. Our data therefore suggest that the AtMIKC* protein complexes play an essential role
in transcriptional regulation during late pollen development.
Transcription of the putative maize orthologue of the Arabidopsis
DORNROSCHEN gene marks early asymmetry in the proembryo and during leaf initiation in the shoot
apical meristem.
Zimmermann R, Werr W, Gene Expression Patterns 7, 158-164 (2007)
A potential orthologue of the Arabidopsis
DORNROSCHEN (DRN) gene was isolated from maize based on phylogeny and expression patterns. ZmDRN
transcription provides a new marker for embryonic patterning and cellular differentiation in the
shoot apical meristem. In contrast to DRN expression in the 2-4-cell Arabidopsis embryo,
transcription of the maize orthologue is activated only in the late proembryo stage where
expression, however, marks the prospective scutellum domain such as DRN transcription
prepatterns cotyledon development in the Arabidopsis globular embryo. The scutellum is commonly
considered to be the grass specific organ, which is homologous to the pair of cotyledons in
dicots. Such as in Arabidopsis, ZmDRN transcriptional activity is linked to the anlagen of new
lateral organs in the maize apex. Striking with respect to the timing of cellular decisions
during leaf initiation is asymmetry established between adjacent cells at the very tip of the
shoot apical meristem.
From biophysics to evolutionary genetics: statistical aspects of
gene regulation.
Lässig M, BMC Bioinformatics 8 Suppl 6, S7 (2007)
This is an introductory review on how genes
interact to produce biological functions. Transcriptional interactions involve the binding of
proteins to regulatory DNA. Specific binding sites can be identified by genomic analysis, and
these undergo a stochastic evolution process governed by selection, mutations, and genetic
drift. We focus on the links between the biophysical function and the evolution of regulatory
elements. In particular, we infer fitness landscapes of binding sites from genomic data, leading
to a quantitative evolutionary picture of regulation.
MADS-complexes regulate transcriptome dynamics during pollen
maturation.
Verelst W, Twell D, de Folter S, Immink R, Saedler H, Münster T,
Genome Biology 8, R249 (2007)
BACKGROUND:Differentiation processes are
responsible for the diversity and functional specialization of the cell types that compose an
organism. The outcome of these processes can be studied at molecular, physiologic, and
biochemical levels by comparing different cell types, but the complexity and dynamics of the
regulatory processes that specify the differentiation are largely unexplored.RESULTS:Here we
identified the pollen-specific MIKC* class of MADS-domain transcription factors as major
regulators of transcriptome dynamics during male reproductive cell development in Arabidopsis
thaliana. Pollen transcript profiling of mutants deficient in different MIKC* protein complexes
revealed that they control a transcriptional switch that directs pollen maturation and that is
essential for pollen competitive ability. We resolved the functional redundancy among the MIKC*
proteins and uncovered part of the underlying network by identifying the non-MIKC* MADS-box
genes AGL18 and AGL29 as downstream regulators of a subset of the MIKC* MADS-controlled
genes.CONCLUSION:Our results provide a first, unique, and compelling insight into the complexity
of a transcription factor network that directs cellular differentiation during pollen
maturation, a process that is essential for male reproductive fitness in flowering plants.
2006
The shoot stem cell niche in angiosperms: expression patterns of
WUS orthologues in rice and maize imply major modifications in the course of mono- and dicot
evolution.
Nardmann J, Werr W, Molecular Biology And Evolution 23, 2492-2504
(2006)
In Arabidopsis, stem cell homeostasis in
the shoot apical meristem (SAM) is controlled by a feedback loop between WUS and CLV functions.
We have identified WUS orthologues in maize and rice by a detailed phylogenetic analysis of the
WOX gene family and subsequent cloning. A single WUS orthologue is present in the rice genome
(OsWUS), whereas the allotetraploid maize genome contains 2 WUS paralogues (ZmWUS1 and ZmWUS2).
None of the isolated grass WUS orthologues displays an organizing center-type expression pattern
in the vegetative SAM as in Arabidopsis. In contrast, the grass-specific expression patterns
relate to the specification of new phytomers consistent with the transcriptional expression
patterns of TD1 and FON1 (CLV1 orthologues of maize and rice, respectively). Moreover, the grass
WUS and CLV1 orthologues are coexpressed in all reproductive meristems, where fasciation and
supernumerary floral organs occur in td1 or fon1 loss-of-function mutants. The expression
patterns of WUS orthologues in both grass species compared with those of dicots imply that major
changes in WUS function, which are correlated with changes in CLV1 signaling, have occurred
during angiosperm evolution and raise doubts about the uniqueness of the WUS/CLV antagonism in
the maintenance of the shoot stem cell niche in grasses.
Cloning of DOG1, a quantitative trait locus controlling seed
dormancy in Arabidopsis.
Bentsink L, Jowett J, Hanhart CJ, Koornneef M, Proceedings Of The
National Academy Of Sciences Of The United States Of America 103, 17042-17047 (2006)
Genetic variation for seed dormancy in
nature is a typical quantitative trait controlled by multiple loci on which environmental
factors have a strong effect. Finding the genes underlying dormancy quantitative trait loci is a
major scientific challenge, which also has relevance for agriculture and ecology. In this study
we describe the identification of the DELAY OF GERMINATION 1 (DOG1) gene previously identified
as a quantitative trait locus involved in the control of seed dormancy. This gene was isolated
by a combination of positional cloning and mutant analysis and is absolutely required for the
induction of seed dormancy. DOG1 is a member of a small gene family of unknown molecular
function, with five members in Arabidopsis. The functional natural allelic variation present in
Arabidopsis is caused by polymorphisms in the cis-regulatory region of the DOG1 gene and results
in considerable expression differences between the DOG1 alleles of the accessions analyzed.
Melanesian and Asian origins of Polynesians: mtDNA and Y
chromosome gradients across the Pacific.
Kayser M, Brauer S, Cordaux R, Casto A, Lao O, Zhivotovsky LA,
Moyse-Faurie C, Rutledge RB, Schiefenhoevel W, Gil D, Lin AA et al., Molecular Biology And
Evolution 23, 2234-2244 (2006)
The human settlement of the Pacific Islands
represents one of the most recent major migration events of mankind. Polynesians originated in
Asia according to linguistic evidence or in Melanesia according to archaeological evidence. To
shed light on the genetic origins of Polynesians, we investigated over 400 Polynesians from 8
island groups, in comparison with over 900 individuals from potential parental populations of
Melanesia, Southeast and East Asia, and Australia, by means of Y chromosome (NRY) and
mitochondrial DNA (mtDNA) markers. Overall, we classified 94.1% of Polynesian Y chromosomes and
99.8% of Polynesian mtDNAs as of either Melanesian (NRY-DNA: 65.8%, mtDNA: 6%) or Asian
(NRY-DNA: 28.3%, mtDNA: 93.8%) origin, suggesting a dual genetic origin of Polynesians in
agreement with the "Slow Boat" hypothesis. Our data suggest a pronounced admixture
bias in Polynesians toward more Melanesian men than women, perhaps as a result of matrilocal
residence in the ancestral Polynesian society. Although dating methods are consistent with
somewhat similar entries of NRY/mtDNA haplogroups into Polynesia, haplotype sharing suggests an
earlier appearance of Melanesian haplogroups than those from Asia. Surprisingly, we identified
gradients in the frequency distribution of some NRY/mtDNA haplogroups across Polynesia and a
gradual west-to-east decrease of overall NRY/mtDNA diversity, not only providing evidence for a
west-to-east direction of Polynesian settlements but also suggesting that Pacific voyaging was
regular rather than haphazard. We also demonstrate that Fiji played a pivotal role in the
history of Polynesia: humans probably first migrated to Fiji, and subsequent settlement of
Polynesia probably came from Fiji.
Sog/Chordin is required for ventral-to-dorsal Dpp/BMP transport
and head formation in a short germ insect.
van der Zee M, Stockhammer O, von Levetzow C, Nunes da Fonseca R,
Roth S, Proceedings Of The National Academy Of Sciences Of The United States Of America 103,
16307-16312 (2006)
Bone morphogenetic protein (BMP) signaling
plays a major role in dorsoventral patterning in vertebrates and in Drosophila. Remarkably, in
Tribolium, a beetle with an ancestral type of insect development, early BMP/dpp exhibits
differential expression along the anteroposterior axis. However, the BMP/Dpp inhibitor
Sog/chordin is expressed ventrally and establishes a dorsal domain of BMP/Dpp activity by
transporting BMPs toward the dorsal side, like in Drosophila. Loss of Tribolium Sog not only
abolishes dorsoventral polarity in the ectoderm, but also leads to the complete absence of the
CNS. This phenotype suggests that sog is the main BMP antagonist in Tribolium, in contrast to
vertebrates and Drosophila, which possess redundant antagonists. Surprisingly, Sog also is
required for head formation in Tribolium, as are the BMP antagonists in vertebrates. Thus, in
Tribolium, the system of BMP and its antagonists is less complex than in Drosophila or
vertebrates and combines features from both, suggesting that it might represent an ancestral
state.
A change of expression in the conserved signaling gene MKK7 is
associated with a selective sweep in the western house mouse Mus musculus domesticus.
Harr B, Voolstra C, Heinen T J A J, Baines J F, Rottscheidt R,
Ihle S, Müller W, Bonhomme F, Tautz D, Journal Of Evolutionary Biology 19, 1486-1496 (2006)
Changes in gene expression are known to
occur between closely related species, but it is not yet clear how many of these are due to
random fixation of allelic variants or due to adaptive events. In a microarray survey between
subspecies of the Mus musculus complex, we identified the mitogen-activated
protein-kinase-kinase MKK7 as a candidate for change in gene expression. Quantitative PCR
experiments with multiple individuals from each subspecies confirmed a specific and significant
up-regulation in the testis of M. m. domesticus. Northern blot analysis shows that this is due
to a new transcript that is not found in other tissues, nor in M. m. musculus. A cis-trans test
via allele specific expression analysis of the MKK7 gene in F1 hybrids between domesticus and
musculus shows that the expression change is mainly caused by a mutation located in cis.
Nucleotide diversity was found to be significantly reduced in a window of at least 20 kb around
the MKK7 locus in domesticus, indicative of a selective sweep. Because the MKK7 gene is involved
in modulating a kinase signalling cascade in a stress response pathway, it seems a plausible
target for adaptive differences between subspecies, although the functional role of the new
testis-specific transcripts will need to be further studied.
A segmentation gene in tribolium produces a polycistronic mRNA
that codes for multiple conserved peptides.
Savard J, Marques-Souza H, Aranda M, Tautz D, Cell 126, 559-569
(2006)
Segmentation genes in insects are required
for generating the subdivisions of the early embryo. We describe here a new member of the gap
family of segmentation genes in the flour beetle Tribolium, mille-pattes (mlpt). mlpt knockdown
leads to transformation of the abdominal segments into thoracic segments, providing embryos with
up to ten pairs of legs. We show that there are crossregulatory interactions between mlpt and
the known gap genes in Tribolium, suggesting that mlpt is itself a gap gene. The mlpt gene
reveals an unusual structure, as it encodes a polycistronic mRNA that codes for four peptides.
mlpt appears to be the prototype of this previously unknown gene structure in eukaryotes, as we
find homologous genes with the same polycistronic arrangement in other insect genomes as well.
Cross-species analysis of biological networks by Bayesian
alignment.
Berg J, Lässig M, Proceedings Of The National Academy Of Sciences
Of The United States Of America 103, 10967-10972 (2006)
Complex interactions between genes or
proteins contribute a substantial part to phenotypic evolution. Here we develop an
evolutionarily grounded method for the cross-species analysis of interaction networks by
alignment, which maps bona fide functional relationships between genes in different organisms.
Network alignment is based on a scoring function measuring mutual similarities between networks,
taking into account their interaction patterns as well as sequence similarities between their
nodes. High-scoring alignments and optimal alignment parameters are inferred by a systematic
Bayesian analysis. We apply this method to analyze the evolution of coexpression networks
between humans and mice. We find evidence for significant conservation of gene expression
clusters and give network-based predictions of gene function. We discuss examples where
cross-species functional relationships between genes do not concur with sequence similarity.
Genomic islands of differentiation between house mouse
subspecies.
Harr B, Genome Research 16, 730-737 (2006)
Understanding the genes that contribute to
reproductive isolation is essential to understanding speciation, but isolating such genes has
proven very difficult. In this study I apply a multilocus test statistic to >10,000 SNP
markers assayed in wild-derived inbred strains of house mice to identify genomic regions of
elevated differentiation between two subspecies of house mice, Mus musculus musculus and M. m.
domesticus. Differentiation was high through approximately 90% of the X chromosome. In addition,
eight regions of high differentiation were identified on the autosomes, totaling 7.5% of the
autosomal genome. Regions of high differentiation were confirmed by direct sequencing of samples
collected from the wild. Some regions of elevated differentiation have an overrepresentation of
genes with host-pathogen interactions and olfaction. The most strongly differentiated region on
the X has previously been shown to fail to introgress across a hybrid zone between the two
subspecies. This survey indicates autosomal regions that should also be examined for
differential introgression across the hybrid zone, as containing potential genes causing hybrid
unfitness.
An integrated view of protein evolution.
Pal C, Papp B, Lercher MJ, Nature Reviews. Genetics 7, 337-348
(2006)
Why do proteins evolve at different rates?
Advances in systems biology and genomics have facilitated a move from studying individual
proteins to characterizing global cellular factors. Systematic surveys indicate that protein
evolution is not determined exclusively by selection on protein structure and function, but is
also affected by the genomic position of the encoding genes, their expression patterns, their
position in biological networks and possibly their robustness to mistranslation. Recent work has
allowed insights into the relative importance of these factors. We discuss the status of a
much-needed coherent view that integrates studies on protein evolution with biochemistry and
functional and structural genomics.
An analysis of signatures of selective sweeps in natural
populations of the house mouse.
Ihle S, Ravaoarimanana I, Thomas M, Tautz D, Molecular Biology And
Evolution 23, 790-797 (2006)
Population and locus-specific reduction of
variability of polymorphic loci could be an indication of positive selection at a linked site
(selective sweep) and therefore point toward genes that have been involved in recent
adaptations. Analysis of microsatellite variability offers a way to identify such regions and to
ask whether they occur more often than expected by chance. We studied four populations of the
house mouse (Mus musculus) to assess the frequency of such signatures of selective sweeps under
natural conditions. Three samples represent the subspecies Mus m. dometicus [corrected] and came
from Germany, France, and Cameroon. One sample came from Kazakhstan and constitutes a population
of the subspecies Mus m. [corrected] musculus. Mitochondrial D-loop sequences from all animals
confirm their respective assignments. Approximately 200 microsatellite loci were typed for up to
60 unrelated individuals from each population and evaluated for signs of selective sweeps on the
basis of Schlötterer's ln RV and ln RH statistics. Our data suggest that there are slightly
more signs of selective sweeps than would have been expected by chance alone in each of the
populations and also highlights some of the statistical challenges faced in genome scans for
detecting selection. Single-nucleotide polymorphism typing of one sweep signature in the M. m.
domesticus populations around the beta-defensin 6 locus confirms a lowered nucleotide diversity
in this region and limits the potential sweep region to about 20 kb. However, no amino acid
exchange has occurred in the coding region when compared to M. m. musculus. If this sweep
signature is due to a recent adaptation, it is expected that a regulatory change would have
caused it. Our data provide a framework for conducting a systematic whole genome scan for
signatures of selective sweeps in the mouse genome.
Chance and necessity in the evolution of minimal metabolic
networks.
Pal C, Papp B, Lercher MJ, Csermely P, Oliver SG, Hurst LD, Nature
440, 667-670 (2006)
It is possible to infer aspects of an
organism's lifestyle from its gene content. Can the reverse also be done? Here we consider
this issue by modelling evolution of the reduced genomes of endosymbiotic bacteria. The
diversity of gene content in these bacteria may reflect both variation in selective forces and
contingency-dependent loss of alternative pathways. Using an in silico representation of the
metabolic network of Escherichia coli, we examine the role of contingency by repeatedly
simulating the successive loss of genes while controlling for the environment. The minimal
networks that result are variable in both gene content and number. Partially different
metabolisms can thus evolve owing to contingency alone. The simulation outcomes do preserve a
core metabolism, however, which is over-represented in strict intracellular bacteria. Moreover,
differences between minimal networks based on lifestyle are predictable: by simulating their
respective environmental conditions, we can model evolution of the gene content in Buchnera
aphidicola and Wigglesworthia glossinidia with over 80% accuracy. We conclude that, at least for
the particular cases considered here, gene content of an organism can be predicted with
knowledge of its distant ancestors and its current lifestyle.
Egg development in parthenogenetic nematodes: variations in
meiosis and axis formation.
Lahl V, Sadler B, Schierenberg E, The International Journal Of
Developmental Biology 50, 393-398 (2006)
In the well studied model nematode
Caenorhabditis elegans entrance of the sperm induces an anterior-posterior polarity in the egg
and determines the orientation of the primary embryonic axis. Subsequently, fusion of two
haploid gamete nuclei results in a diploid zygote as a prerequisite for normal embryogenesis.
Here we analyze the establishment of embryonic polarity and diploidy in the absence of sperm in
three parthenogenetic nematode species from three different families, Diploscapter coronatus
(Diploscapteridae), Acrobeloides nanus (Cephalobidae) and Plectus sp. (Plectidae). We find that
they not only differ from C. elegans in these two aspects but also from each other, indicating
variant solutions for the same developmental challenges and supporting the view that the
parthenogenetic mode of reproduction has been acquired multiple times independently.
Embryological variation during nematode development.
Schierenberg E, WormBook : The Online Review Of C. Elegans
Biology, 1-13 (2006)
Early cell lineages and arrangement of
blastomeres in C. elegans are similar to the pattern found in Ascaris and other studied
nematodes leading to the assumption that embryonic development shows little variation within the
phylum Nematoda. However, analysis of a larger variety of species from various branches of the
phylogenetic tree demonstrate that prominent variations in crucial steps of early embryogenesis
exist among representatives of this taxon. So far, most of these variations have only been
studied on a descriptive level and thus essentially nothing is known about their molecular or
genetic basis. Nevertheless, it is obvious that the limited morphological diversity of the
freshly hatched juvenile and the uniformity of the basic body plan contrast with the many
modifications in the way a worm is generated from the egg cell. This chapter focuses on the
initial phase between egg activation and gastrulation and deals with the following aspects:
reproduction and diploidy, polarity, cleavage and germ line, cell lineages; cell cycles and
maternal contribution, cell-cell communication and cell specification, gastrulation.
The interferon-inducible GTPases.
Martens S, Howard J, Annual Review Of Cell And Developmental
Biology 22, 559-589 (2006)
Mammalian cells respond to interferons
(IFNs) secreted during infection by the transcriptional upregulation of as many as a thousand
genes. This remarkable transition prepares cells and organisms for resistance to infection, and
many IFN-regulated gene products are players in well-understood resistance programs. Oddly,
however, many of the most abundantly induced proteins are GTPases whose functions are not well
understood. Here we review the progress that has been made toward understanding the roles of
individual GTPase families in disease resistance and the hints of common mechanisms that are now
available.