Genome Mutational and Transcriptional Hotspots Are Traps for Duplicated Genes and Sources of Adaptations

[EN] Gene duplication generates new genetic material, which has been shown to lead to major innovations in unicellular and multicellular organisms. A whole-genome duplication occurred in the ancestor of Saccharomyces yeast species but 92% of duplicates returned to single-copy genes shortly after duplication. The persisting duplicated genes in Saccharomyces led to the origin of major metabolic innovations, which have been the source of the unique biotechnological capabilities in the Baker's yeast Saccharomyces cerevisiae. What factors have determined the fate of duplicated genes remains unknown. Here, we report the first demonstration that the local genome mutation and transcription rates determine the fate of duplicates. We show, for the first time, a preferential location of duplicated genes in the mutational and transcriptional hotspots of S. cerevisiae genome. The mechanism of duplication matters, with whole-genome duplicates exhibiting different preservation trends compared to small-scale duplicates. Genome mutational and transcriptional hotspots are rich in duplicates with large repetitive promoter elements. Saccharomyces cerevisiae shows more tolerance to deleterious mutations in duplicates with repetitive promoter elements, which in turn exhibit higher transcriptional plasticity against environmental perturbations. Our data demonstrate that the genome traps duplicates through the accelerated regulatory and functional divergence of their gene copies providing a source of novel adaptations in yeast.This study was supported by a grant (reference: FEDER-BFU2015-66073-P) from the Spanish Ministerio de Economia y Competitividad-FEDER and a grant (reference: ACOMP/2015/026) from the local government Conselleria de Educacion Investigacion, Cultura y Deporte, Generalitat Valenciana to M.A.F. C.T. was supported by a grant Juan de la Cierva from the Spanish Ministerio de Economia y Competitividad (reference: JCA-2012-14056).Fares Riaño, MA.; Sabater-Muñoz, B.; Toft, C. (2017). Genome Mutational and Transcriptional Hotspots Are Traps for Duplicated Genes and Sources of Adaptations. Genome Biology and Evolution. 9(5):1229-1240. https://doi.org/10.1093/gbe/evx085S1229124095Agier, N., & Fischer, G. (2011). The Mutational Profile of the Yeast Genome Is Shaped by Replication. Molecular Biology and Evolution, 29(3), 905-913. doi:10.1093/molbev/msr280Altschul, S. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389-3402. doi:10.1093/nar/25.17.3389Anders, S., & Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biology, 11(10). doi:10.1186/gb-2010-11-10-r106Berry, D. B., & Gasch, A. P. (2008). 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Coevolution analyses illuminate the dependencies between amino acid sites in the chaperonin system GroES-L

[EN] Background: GroESL is a heat-shock protein ubiquitous in bacteria and eukaryotic organelles. This evolutionarily conserved protein is involved in the folding of a wide variety of other proteins in the cytosol, being essential to the cell. The folding activity proceeds through strong conformational changes mediated by the co-chaperonin GroES and ATP. Functions alternative to folding have been previously described for GroEL in different bacterial groups, supporting enormous functional and structural plasticity for this molecule and the existence of a hidden combinatorial code in the protein sequence enabling such functions. Describing this plasticity can shed light on the functional diversity of GroEL. We hypothesize that different overlapping sets of amino acids coevolve within GroEL, GroES and between both these proteins. Shifts in these coevolutionary relationships may inevitably lead to evolution of alternative functions. Results: We conducted the first coevolution analyses in an extensive bacterial phylogeny, revealing complex networks of evolutionary dependencies between residues in GroESL. These networks differed among bacterial groups and involved amino acid sites with functional importance and others with previously unsuspected functional potential. Coevolutionary networks formed statistically independent units among bacterial groups and map to structurally continuous regions in the protein, suggesting their functional link. Sites involved in coevolution fell within narrow structural regions, supporting dynamic combinatorial functional links involving similar protein domains. Moreover, coevolving sites within a bacterial group mapped to regions previously identified as involved in folding-unrelated functions, and thus, coevolution may mediate alternative functions. Conclusions: Our results highlight the evolutionary plasticity of GroEL across the entire bacterial phylogeny. Evidence on the functional importance of coevolving sites illuminates the as yet unappreciated functional diversity of proteins.This study was supported by Science Foundation Ireland (10/RFP/GEN2685) and a grant from the Ministerio de Ciencia e Innovacion (BFU2009-12022) to MAF. MXRG is supported by the JAE DOC-2009, Ministerio de Ciencia e Innovacion. We thank two anonymous reviewers for useful comments to improve this study presentation.Ruíz González, MJ.; Fares Riaño, MA. (2013). Coevolution analyses illuminate the dependencies between amino acid sites in the chaperonin system GroES-L. BMC Evolutionary Biology. 13(156):1-13. https://doi.org/10.1186/1471-2148-13-15611313156Lund, P. A. (2009). Multiple chaperonins in bacteria – why so many? FEMS Microbiology Reviews, 33(4), 785-800. doi:10.1111/j.1574-6976.2009.00178.xRadford, S. E. (2006). GroEL: More than Just a Folding Cage. Cell, 125(5), 831-833. doi:10.1016/j.cell.2006.05.021Lin, Z., & Rye, H. S. (2006). 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The Role of Ancestral Duplicated Genes in Adaptation to Growth on Lactate, a Non-Fermentable Carbon Source for the Yeast Saccharomyces cerevisiae

[EN] The cell central metabolism has been shaped throughout evolutionary times when facing challenges from the availability of resources. In the budding yeast, Saccharomyces cerevisiae, a set of duplicated genes originating from an ancestral whole-genome and several coetaneous small-scale duplication events drive energy transfer through glucose metabolism as the main carbon source either by fermentation or respiration. These duplicates (~a third of the genome) have been dated back to approximately 100 MY, allowing for enough evolutionary time to diverge in both sequence and function. Gene duplication has been proposed as a molecular mechanism of biological innovation, maintaining balance between mutational robustness and evolvability of the system. However, some questions concerning the molecular mechanisms behind duplicated genes transcriptional plasticity and functional divergence remain unresolved. In this work we challenged S. cerevisiae to the use of lactic acid/lactate as the sole carbon source and performed a small adaptive laboratory evolution to this non-fermentative carbon source, determining phenotypic and transcriptomic changes. We observed growth adaptation to acidic stress, by reduction of growth rate and increase in biomass production, while the transcriptomic response was mainly driven by repression of the whole-genome duplicates, those implied in glycolysis and overexpression of ROS response. The contribution of several duplicated pairs to this carbon source switch and acidic stress is also discussed.This research was funded by Spanish National Plan for Scientific and Technical Research and Innovation from the Spanish Ministry of Economy and Competitiveness (MINECOFEDER), actually the Ministry of Science and Innovation (MCIN), Spanish Research Agency (AEI), MCIN/AEI/10.13039/501100011033 and ERDF A way of making Europe (FEDER "Una forma de hacer Europa") with grant number BFU2015-66073-P (to M.A.F.) and Generalitat Valenciana, Conselleria de Innovacion, Universidades y Sociedad Digital with grant number SEJI/2018/046 (to C.T.). F.M. was supported by a Spanish PhD Fellowship number FPI BES-2016-076677, from MCIN/AEI/10.13039/501100011033 and ESF "Investing in your future".Mattenberger, F.; Fares Riaño, MA.; Toft, C.; Sabater-Muñoz, B. (2021). The Role of Ancestral Duplicated Genes in Adaptation to Growth on Lactate, a Non-Fermentable Carbon Source for the Yeast Saccharomyces cerevisiae. International Journal of Molecular Sciences. 22(22):1-17. https://doi.org/10.3390/ijms222212293S117222

Expression properties exhibit correlated patterns with the fate of duplicated genes, their divergence, and transcriptional plasticity in Saccharomycotina

[EN] Gene duplication is an important source of novelties and genome complexity. What genes are preserved as duplicated through long evolutionary times can shape the evolution of innovations. Identifying factors that influence gene duplicability is therefore an important aim in evolutionary biology. Here, we show that in the yeast Saccharomyces cerevisiae the levels of gene expression correlate with gene duplicability, its divergence, and transcriptional plasticity. Genes that were highly expressed before duplication are more likely to be preserved as duplicates for longer evolutionary times and wider phylogenetic ranges than genes that were lowly expressed. Duplicates with higher expression levels exhibit greater divergence between their gene copies. Duplicates that exhibit higher expression divergence are those enriched for TATA-containing promoters. These duplicates also show transcriptional plasticity, which seems to be involved in the origin of adaptations to environmental stresses in yeast. While the expression properties of genes strongly affect their duplicability, divergence and transcriptional plasticity are enhanced after gene duplication. We conclude that highly expressed genes are more likely to be preserved as duplicates due to their promoter architectures, their greater tolerance to expression noise, and their ability to reduce the noise-plasticity conflict.We would like to thank members of Fares' Lab for a careful reading and discussion of the results in the manuscript. We are also grateful to colleagues at Trinity College for helpful discussions. This work was supported by a grant from the Spanish Ministerio de Economia y Competitividad (MINECO-FEDER; BFU2015-66073-P) to M.A.F. F.M. is supported by a PhD grant from the Spanish Ministerio de Economia y Competitividad (reference: BES-2016-076677). 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Molecular evolution of psbA gene in ferns: unraveling selective pressure and co-evolutionary

Background: The photosynthetic oxygen-evolving photo system II (PS II) produces almost the entire oxygen in the atmosphere. This unique biochemical system comprises a functional core complex that is encoded by psbA and other genes. Unraveling the evolutionary dynamics of this gene is of particular interest owing to its direct role in oxygen production. psbA underwent gene duplication in leptosporangiates, in which both copies have been preserved since. Because gene duplication is often followed by the non-fictionalization of one of the copies and its subsequent erosion, preservation of both psbA copies pinpoint functional or regulatory specialization events. The aim of this study was to investigate the molecular evolution of psbA among fern lineages. Results: We sequenced psbA, which encodes D1 protein in the core complex of PSII, in 20 species representing 8 orders of extant ferns; then we searched for selection and convolution signatures in psbA across the 11 fern orders. Collectively, our results indicate that: (1) selective constraints among D1 protein relaxed after the duplication in 4 leptosporangiate orders; (2) a handful positively selected codons were detected within species of single copy psbA, but none in duplicated ones; (3) a few sites among D1 protein were involved in co-evolution process which may intimate significant functional/structural communications between them. Conclusions: The strong competition between ferns and angiosperms for light may have been the main cause for a continuous fixation of adaptive amino acid changes in psbA, in particular after its duplication. Alternatively, a single psbA copy may have undergone bursts of adaptive changes at the molecular level to overcome angiosperms competition. The strong signature of positive Darwinian selection in a major part of D1 protein is testament to this. At the same time, species own two psbA copies hardly have positive selection signals among the D1 protein coding sequences. In this study, eleven co-evolving sites have been detected via different molecules, which may be more important than others.We thank Dr. Yefu Wang at State Key Laboratory of Virology, College of Life Sciences, Wuhan University, China, for the guidance for wording, and we also thank Bo Wang and Dr. Lei Gao at the Wuhan Botanical Garden, Chinese Academy of Sciences, China, for the experimental assistance. We thank Dr. Jianqiang Li at the Wuhan Botanical Garden, Chinese Academy of Sciences, China, for the advices on species sampling. We appreciate two anonymous reviewers and other editors for their helpful suggestions. The present work was financially supported by the National Nature Science Foundation of China (No. 30970290, 31070594), and by the Knowledge Innovation Program of the Chinese Academy of Sciences (No. KSCX2-EW-J-20, KSCX2-YW-Z-0940). Dr. Mario A. 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Arabidopsis Heat Stress-Induced Proteins Are Enriched in Electrostatically Charged Amino Acids and Intrinsically Disordered Regions

[EN] Comparison of the proteins of thermophilic, mesophilic, and psychrophilic prokaryotes has revealed several features characteristic to proteins adapted to high temperatures, which increase their thermostability. These characteristics include a profusion of disulfide bonds, salt bridges, hydrogen bonds, and hydrophobic interactions, and a depletion in intrinsically disordered regions. It is unclear, however, whether such differences can also be observed in eukaryotic proteins or when comparing proteins that are adapted to temperatures that are more subtly different. When an organism is exposed to high temperatures, a subset of its proteins is overexpressed (heat-induced proteins), whereas others are either repressed (heat-repressed proteins) or remain unaffected. Here, we determine the expression levels of all genes in the eukaryotic model system Arabidopsis thaliana at 22 and 37 degrees C, and compare both the amino acid compositions and levels of intrinsic disorder of heat-induced and heat-repressed proteins. We show that, compared to heat-repressed proteins, heat-induced proteins are enriched in electrostatically charged amino acids and depleted in polar amino acids, mirroring thermophile proteins. However, in contrast with thermophile proteins, heat-induced proteins are enriched in intrinsically disordered regions, and depleted in hydrophobic amino acids. Our results indicate that temperature adaptation at the level of amino acid composition and intrinsic disorder can be observed not only in proteins of thermophilic organisms, but also in eukaryotic heat-induced proteins; the underlying adaptation pathways, however, are similar but not the same.D.A.-P. and F.F. were supported by funds from the University of Nevada, Reno, and by pilot grants from Nevada INBRE (P20GM103440) and the Smooth Muscle Plasticity COBRE from the University of Nevada, Reno (5P30GM110767-04), both funded by the National Institute of General Medical Sciences (National Institutes of Health). M.X.R.-G. and M.A.F. were supported by grants from Science Foundation Ireland (12/IP/1637) and the Spanish Ministerio de Economia y Competitividad, Spain (MINECO-FEDER; BFU201236346 and BFU2015-66073-P) to MAF. MXRG was supported by a JAE DOC fellowship from the MINECO, Spain. 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Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations

Functional divergence is the process by which new genes and functions originate through the modification of existing ones. Both genetic and environmental factors influence the evolution of new functions, including gene duplication or changes in the ecological requirements of an organism. Novel functions emerge at the expense of ancestral ones and are generally accompanied by changes in the selective forces at constrained protein regions. We present software capable of analyzing whole proteomes, identifying putative amino acid replacements leading to functional change in each protein and performing statistical tests on all tabulated data. We apply this method to 750 complete bacterial proteomes to identify high-level patterns of functional divergence and link these patterns to ecological adaptations. Proteome-wide analyses of functional divergence in bacteria with different ecologies reveal a separation between proteins involved in information processing (Ribosome biogenesis etc.) and those which are dependent on the environment (energy metabolism, defense etc.). We show that the evolution of pathogenic and symbiotic bacteria is constrained by their association with the host, and also identify unusual events of functional divergence even in well-studied bacteria such as Escherichia coli. We present a description of the roles of phylogeny and ecology in functional divergence at the level of entire proteomes in bacteria.This study was supported by a grant from the Spanish Ministerio de Ciencia e Inovacion (BFU2009-12022) and a grant of the Research Frontiers Program (10/RFP/GEN2685) from Science Foundation Ireland. 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Survival and Innovation: The role of mutational robustness in evolution

[EN] Biological systems are resistant to perturbations caused by the environment and by the intrinsic noise of the system. Robustness to mutations is a particular aspect of robustness in which the phenotype is resistant to genotypic variation. Mutational robustness has been linked to the ability of the system to generate heritable genetic variation (a property known as evolvability). It is known that greater robustness leads to increased evolvability. Therefore, mechanisms that increase mutational robustness fuel evolvability. Two such mechanisms, molecular chaperones and gene duplication, have been credited with enormous importance in generating functional diversity through the increase of system's robustness to mutational insults. However, the way in which such mechanisms regulate robustness remains largely uncharacterized. In this review, I provide evidence in support of the role of molecular chaperones and gene duplication in innovation. Specifically, I present evidence that these mechanisms regulate robustness allowing unstable systems to survive long periods of time, and thus they provide opportunity for other mutations to compensate the destabilizing effects of functionally innovative mutations. The findings reported in this study set new questions with regards to the synergy between robustness mechanisms and how this synergy can alter the adaptive landscape of proteins. The ideas proposed in this article set the ground for future research in the understanding of the role of robustness in evolution. (C) 2014 Elsevier B.V. and Societe Francaise de Biochimie et Biologie Moleculaire (SFBBM).This study was supported by Science Foundation Ireland (grant reference: 12/IP/1673) and a grant from the Spanish Ministerio de Economia y Competitividad (BFU2009-12022) to MAF.Fares Riaño, MA. (2015). Survival and Innovation: The role of mutational robustness in evolution. Biochimie. 119:254-261. doi:10.1016/j.biochi.2014.10.019S25426111

Glycerol stress in Saccharomyces cerevisiae: Cellular responses and evolved adaptations

[EN] Glycerol synthesis is key to central metabolism and stress biology in Saccharomyces cerevisiae, yet the cellular adjustments needed to respond and adapt to glycerol stress are little understood. Here, we determined impacts of acute and chronic exposures to glycerol stress in S. cerevisiae. Glycerol stress can result from an increase of glycerol concentration in the medium due to the S. cerevisiae fermenting activity or other metabolic activities. Acute glycerol-stress led to a 50% decline in growth rate and altered transcription of more than 40% of genes. The increased genetic diversity in S. cerevisiae population, which had evolved in the standard nutrient medium for hundreds of generations, led to an increase in growth rate and altered transcriptome when such population was transferred to stressful media containing a high concentration of glycerol; 0.41 M (0.990 water activity). Evolution of S. cerevisiae populations during a 10-day period in the glycerol-containing medium led to transcriptome changes and readjustments to improve control of glycerol flux across the membrane, regulation of cell cycle, and more robust stress response; and a remarkable increase of growth rate under glycerol stress. Most of the observed regulatory changes arose in duplicated genes. These findings elucidate the physiological mechanisms, which underlie glycerol-stress response, and longer-term adaptations, in S. cerevisiae; they also have implications for enigmatic aspects of the ecology of this otherwise well-characterized yeast.This study was supported by grants from the Spanish Ministry of Economy and Competitiveness (Refs: BFU2012-36346, BFU2015-66073-P) and a grant from the local government Consellería de Educación, Investigación, Cultura y Deporte, Generalitat Valenciana (Ref: ACOMP/2012/098) to M.A.F.Mattenberger, F.; Sabater-Muñoz, B.; Hallsworth, JE.; Fares Riaño, MA. (2017). Glycerol stress in Saccharomyces cerevisiae: Cellular responses and evolved adaptations. Environmental Microbiology. 19(3):990-1007. https://doi.org/10.1111/1642-2920.13603S990100719

Group 1 LEA proteins, an ancestral plant protein group, are also present in other eukaryotes, and in the archeae and bacteria domains

[EN] Water is an essential element for living organisms, such that various responses have evolved to withstand water deficit in all living species. The study of these responses in plants has had particular relevance given the negative impact of water scarcity on agriculture. Among the molecules highly associated with plant responses to water limitation are the so-called late embryogenesis abundant (LEA) proteins. These proteins are ubiquitous in the plant kingdom and accumulate during the late phase of embryogenesis and in vegetative tissues in response to water deficit. To know about the evolution of these proteins, we have studied the distribution of group 1 LEA proteins, a set that has also been found beyond the plant kingdom, in Bacillus subtilis and Artemia franciscana. Here, we report the presence of group 1 LEA proteins in green algae (Chlorophyita and Streptophyta), suggesting that these group of proteins emerged before plant land colonization. By sequence analysis of public genomic databases, we also show that 34 prokaryote genomes encode group 1 LEA-like proteins; two of them belong to Archaea domain and 32 to bacterial phyla. Most of these microbes live in soil-associated habitats suggesting horizontal transfer from plants to bacteria; however, our phylogenetic analysis points to convergent evolution. Furthermore, we present data showing that bacterial group 1 LEA proteins are able to prevent enzyme inactivation upon freeze-thaw treatments in vitro, suggesting that they have analogous functions to plant LEA proteins. Overall, data in this work indicate that LEA1 proteins' properties might be relevant to cope with water deficit in different organisms.We thank Jaqueline Mazari for excellent technical assistance. We acknowledge to Paul Gaytan and Santiago Becerra from Oligonucleotide Synthesis and DNA Sequencing Facilities of the Instituto de Biotecnologia-UNAM for providing us with the oligonucleotides and DNA sequences used in this work. This work was partially supported by CONACyT-Mexico to AAC (50485 and 132258). C.C.-V. was supported by a PhD fellowship from CONACyT.Campos, F.; Cuevas-Velazquez, C.; Fares Riaño, MA.; Reyes, J.; Covarrubias, A. (2013). Group 1 LEA proteins, an ancestral plant protein group, are also present in other eukaryotes, and in the archeae and bacteria domains. Molecular Genetics and Genomics. 288(10):503-517. https://doi.org/10.1007/s00438-013-0768-2S50351728810Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. 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