Plasmids in the aphid endosymbiont Buchnera aphidicola with the smallest genomes. A puzzling evolutionary story.

Buchnera aphidicola, the primary endosymbiont of aphids, has undergone important genomic and biochemical changes as an adaptation to intracellular life. The most important structural changes include a drastic genome reduction and the amplification of genes encoding key enzymes for the biosynthesis of amino acids by their translocation to plasmids. Molecular characterization through different aphid subfamilies has revealed that the genes involved in leucine and tryptophan biosynthesis show a variable fate, since they can be located on plasmids or on the chromosome in different lineages. This versatility contrasts with the genomic stasis found in three distantly related B. aphidicola strains already sequenced. We present the analysis of three B. aphidicola strains (BTg, BCt and BCc) belonging to aphids from different tribes of the subfamily Lachninae, that was estimated to harbour the bacteria with the smallest genomes. The presence of both leucine and tryptophan plasmids in BTg, a chimerical leucine-tryptophan plasmid in BCt, and only a leucine plasmid in BCc, indicates the existence of many recombination events in a recA minus bacterium. In addition, these B. aphidicola plasmids are the simplest described in this species, indicating that plasmids are also involved in the genome shrinkage process

8th International Symposium on fruit flies of economic importance

Sabater Muñoz, B.; Urbaneja García, A.; Navarro Llopis, V. (2010). 8th International Symposium on fruit flies of economic importance. Editorial Universitat Politècnica de València. http://hdl.handle.net/10251/11200Archivo delegad

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). C.T. was supported by a grant Juan de la Cierva from the Spanish Ministerio de Economia y Competitividad (reference: JCA-2012-14056).Mattenberger, F.; Sabater-Muñoz, B.; Toft, C.; Sablok, G.; Fares Riaño, MA. (2017). Expression properties exhibit correlated patterns with the fate of duplicated genes, their divergence, and transcriptional plasticity in Saccharomycotina. DNA Research. 24(6):559-570. https://doi.org/10.1093/dnares/dsx025S559570246Ohno, S. (1999). Gene duplication and the uniqueness of vertebrate genomes circa 1970–1999. Seminars in Cell & Developmental Biology, 10(5), 517-522. doi:10.1006/scdb.1999.0332Lynch, M. (2000). The Evolutionary Fate and Consequences of Duplicate Genes. Science, 290(5494), 1151-1155. doi:10.1126/science.290.5494.1151Otto, S. P., & Whitton, J. (2000). Polyploid Incidence and Evolution. Annual Review of Genetics, 34(1), 401-437. doi:10.1146/annurev.genet.34.1.401Carretero-Paulet, L., & Fares, M. A. (2012). Evolutionary Dynamics and Functional Specialization of Plant Paralogs Formed by Whole and Small-Scale Genome Duplications. Molecular Biology and Evolution, 29(11), 3541-3551. doi:10.1093/molbev/mss162Cui, L. (2006). Widespread genome duplications throughout the history of flowering plants. Genome Research, 16(6), 738-749. doi:10.1101/gr.4825606Holub, E. B. (2001). The arms race is ancient history in Arabidopsis, the wildflower. Nature Reviews Genetics, 2(7), 516-527. doi:10.1038/35080508Lespinet, O. (2002). The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes. Genome Research, 12(7), 1048-1059. doi:10.1101/gr.174302Wendel, J. F. (2000). Plant Molecular Biology, 42(1), 225-249. doi:10.1023/a:1006392424384Soltis, D. E., Albert, V. A., Leebens-Mack, J., Bell, C. D., Paterson, A. H., Zheng, C., … Soltis, P. S. (2009). Polyploidy and angiosperm diversification. American Journal of Botany, 96(1), 336-348. doi:10.3732/ajb.0800079De Peer, Y. V. (2004). Computational approaches to unveiling ancient genome duplications. Nature Reviews Genetics, 5(10), 752-763. doi:10.1038/nrg1449Hoegg, S., Brinkmann, H., Taylor, J. S., & Meyer, A. (2004). Phylogenetic Timing of the Fish-Specific Genome Duplication Correlates with the Diversification of Teleost Fish. Journal of Molecular Evolution, 59(2), 190-203. doi:10.1007/s00239-004-2613-zGrant, S. G. N. (2016). The molecular evolution of the vertebrate behavioural repertoire. Philosophical Transactions of the Royal Society B: Biological Sciences, 371(1685), 20150051. doi:10.1098/rstb.2015.0051Green, S. A., & Bronner, M. E. (2013). Gene duplications and the early evolution of neural crest development. Seminars in Cell & Developmental Biology, 24(2), 95-100. doi:10.1016/j.semcdb.2012.12.006Conant, G. C., & Wolfe, K. H. (2007). Increased glycolytic flux as an outcome of whole‐genome duplication in yeast. Molecular Systems Biology, 3(1), 129. doi:10.1038/msb4100170Wolfe, K. H., & Shields, D. C. (1997). Molecular evidence for an ancient duplication of the entire yeast genome. Nature, 387(6634), 708-713. doi:10.1038/42711Fares, M. A., Keane, O. M., Toft, C., Carretero-Paulet, L., & Jones, G. W. (2013). The Roles of Whole-Genome and Small-Scale Duplications in the Functional Specialization of Saccharomyces cerevisiae Genes. PLoS Genetics, 9(1), e1003176. doi:10.1371/journal.pgen.1003176Blanc, G., & Wolfe, K. H. (2004). Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes. The Plant Cell, 16(7), 1667-1678. doi:10.1105/tpc.021345Blanc, G., & Wolfe, K. H. (2004). Functional Divergence of Duplicated Genes Formed by Polyploidy during Arabidopsis Evolution. The Plant Cell, 16(7), 1679-1691. doi:10.1105/tpc.021410Conant, G. C., & Wolfe, K. H. (2008). Turning a hobby into a job: How duplicated genes find new functions. Nature Reviews Genetics, 9(12), 938-950. doi:10.1038/nrg2482Fares, M. A., Byrne, K. P., & Wolfe, K. H. (2005). Rate Asymmetry After Genome Duplication Causes Substantial Long-Branch Attraction Artifacts in the Phylogeny of Saccharomyces Species. Molecular Biology and Evolution, 23(2), 245-253. doi:10.1093/molbev/msj027Freeling, M. (2009). Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition. Annual Review of Plant Biology, 60(1), 433-453. doi:10.1146/annurev.arplant.043008.092122Conant, G. C., Birchler, J. A., & Pires, J. C. (2014). Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time. Current Opinion in Plant Biology, 19, 91-98. doi:10.1016/j.pbi.2014.05.008Keane, O. M., Toft, C., Carretero-Paulet, L., Jones, G. W., & Fares, M. A. (2014). Preservation of genetic and regulatory robustness in ancient gene duplicates ofSaccharomyces cerevisiae. Genome Research, 24(11), 1830-1841. doi:10.1101/gr.176792.114Fares, M. A. (2015). The origins of mutational robustness. Trends in Genetics, 31(7), 373-381. doi:10.1016/j.tig.2015.04.008Gout, J.-F., & Lynch, M. (2015). Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization. Molecular Biology and Evolution, 32(8), 2141-2148. doi:10.1093/molbev/msv095Altschul, 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/25.17.3389Byrne, K. P. (2005). The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Research, 15(10), 1456-1461. doi:10.1101/gr.3672305Lohse, M., Bolger, A. M., Nagel, A., Fernie, A. R., Lunn, J. E., Stitt, M., & Usadel, B. (2012). RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Research, 40(W1), W622-W627. doi:10.1093/nar/gks540Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2009). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139-140. doi:10.1093/bioinformatics/btp616Anders, S., & Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biology, 11(10). doi:10.1186/gb-2010-11-10-r106Brion, C., Pflieger, D., Souali-Crespo, S., Friedrich, A., & Schacherer, J. (2016). Differences in environmental stress response among yeasts is consistent with species-specific lifestyles. Molecular Biology of the Cell, 27(10), 1694-1705. doi:10.1091/mbc.e15-12-0816Linde, J., Duggan, S., Weber, M., Horn, F., Sieber, P., Hellwig, D., … Kurzai, O. (2015). Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. Nucleic Acids Research, 43(3), 1392-1406. doi:10.1093/nar/gku1357Seoighe, C., & Wolfe, K. H. (1999). Yeast genome evolution in the post-genome era. Current Opinion in Microbiology, 2(5), 548-554. doi:10.1016/s1369-5274(99)00015-6Aury, J.-M., Jaillon, O., Duret, L., Noel, B., Jubin, C., Porcel, B. M., … Wincker, P. (2006). Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature, 444(7116), 171-178. doi:10.1038/nature05230Gout, J.-F., Kahn, D., & Duret, L. (2010). The Relationship among Gene Expression, the Evolution of Gene Dosage, and the Rate of Protein Evolution. PLoS Genetics, 6(5), e1000944. doi:10.1371/journal.pgen.1000944McGrath, C. L., Gout, J.-F., Doak, T. G., Yanagi, A., & Lynch, M. (2014). Insights into Three Whole-Genome Duplications Gleaned from theParamecium caudatumGenome Sequence. Genetics, 197(4), 1417-1428. doi:10.1534/genetics.114.163287McGrath, C. L., Gout, J.-F., Johri, P., Doak, T. G., & Lynch, M. (2014). Differential retention and divergent resolution of duplicate genes following whole-genome duplication. Genome Research, 24(10), 1665-1675. doi:10.1101/gr.173740.114Albert, F. W., Muzzey, D., Weissman, J. S., & Kruglyak, L. (2014). Genetic Influences on Translation in Yeast. PLoS Genetics, 10(10), e1004692. doi:10.1371/journal.pgen.1004692Gout, J.-F., Duret, L., & Kahn, D. (2009). Differential Retention of Metabolic Genes Following Whole-Genome Duplication. Molecular Biology and Evolution, 26(5), 1067-1072. doi:10.1093/molbev/msp026Papp, B., Pál, C., & Hurst, L. D. (2003). Dosage sensitivity and the evolution of gene families in yeast. Nature, 424(6945), 194-197. doi:10.1038/nature01771Qian, W., Liao, B.-Y., Chang, A. Y.-F., & Zhang, J. (2010). Maintenance of duplicate genes and their functional redundancy by reduced expression. Trends in Genetics, 26(10), 425-430. doi:10.1016/j.tig.2010.07.002Birchler, J. A., & Veitia, R. A. (2012). Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines. Proceedings of the National Academy of Sciences, 109(37), 14746-14753. doi:10.1073/pnas.1207726109Pu, S., Wong, J., Turner, B., Cho, E., & Wodak, S. J. (2008). Up-to-date catalogues of yeast protein complexes. Nucleic Acids Research, 37(3), 825-831. doi:10.1093/nar/gkn1005Scannell, D. R., Byrne, K. P., Gordon, J. L., Wong, S., & Wolfe, K. H. (2006). Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature, 440(7082), 341-345. doi:10.1038/nature04562Landry, C. R., Lemos, B., Rifkin, S. A., Dickinson, W. J., & Hartl, D. L. (2007). Genetic Properties Influencing the Evolvability of Gene Expression. Science, 317(5834), 118-121. doi:10.1126/science.1140247Lehner, B. (2010). Conflict between Noise and Plasticity in Yeast. PLoS Genetics, 6(11), e1001185. doi:10.1371/journal.pgen.1001185Mattenberger, F., Sabater-Muñoz, B., Hallsworth, J. E., & Fares, M. A. (2017). Glycerol stress inSaccharomyces cerevisiae: Cellular responses and evolved adaptations. Environmental Microbiology, 19(3), 990-1007. doi:10.1111/1462-2920.13603Mattenberger, F., Sabater-Muñoz, B., Toft, C., & Fares, M. A. (2016). The Phenotypic Plasticity of Duplicated Genes in Saccharomyces cerevisiae and the Origin of Adaptations. G3: Genes|Genomes|Genetics, 7(1), 63-75. doi:10.1534/g3.116.035329Blake, W. J., Balázsi, G., Kohanski, M. A., Isaacs, F. J., Murphy, K. F., Kuang, Y., … Collins, J. J. (2006). Phenotypic Consequences of Promoter-Mediated Transcriptional Noise. Molecular Cell, 24(6), 853-865. doi:10.1016/j.molcel.2006.11.003Raser, J. M. (2005). Noise in Gene Expression: Origins, Consequences, and Control. Science, 309(5743), 2010-2013. doi:10.1126/science.1105891Newman, J. R. S., Ghaemmaghami, S., Ihmels, J., Breslow, D. K., Noble, M., DeRisi, J. L., & Weissman, J. S. (2006). Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature, 441(7095), 840-846. doi:10.1038/nature04785Tirosh, I., Weinberger, A., Carmi, M., & Barkai, N. (2006). A genetic signature of interspecies variations in gene expression. Nature Genetics, 38(7), 830-834. doi:10.1038/ng181

El patrimonio construido de la marina auxiliante en El Cabanyal (Valencia) y su puesta en valor

Tras la realización de un estudio histórico y el análisis de la realidad arquitectónica y urbana del Cabanyal dentro del proyecto Patrimonio en Riesgo, se determinó como objetivo la documentación y puesta en valor del patrimonio construido de la Marina Auxiliante, por su valor histórico y arquitectónico, y su deficiente estado de conservación. Se han realizado un levantamiento arquitectónico, utilizando técnicas de escaneado láser 3D y rectificación fotográfica como apoyo a la metodología tradicional, y diferentes estudios patológicos, según las necesidades de cada edificio, pues presentan diferentes grados de deterioro como consecuencia de usos inadecuados, el envejecimiento y la erosión. La puesta en valor del conjunto pasa por la conservación de los edificios y su posible reutilización para un uso público.Muñoz Cosme, G.; Martín Domínguez, B.; Mestre Sabater, M. (2011). El patrimonio construido de la marina auxiliante en El Cabanyal (Valencia) y su puesta en valor. Arché. (6):357-364. http://hdl.handle.net/10251/34472357364

Molecular characterization of Cardinium, Rickettsia, Spiroplasma and Wolbachia in mite species from citrus orchards

Tetranychidae spider mites are considered key citrus pests in some production areas, especially Tetranychus urticae Koch. Over the past decades, pesticide overuse seems to have promoted T. urticae population selection in citrus orchards. However, the microbiota has also been pointed out as a plausible explanation for population structure or plant host specialisation observed in several arthropod species. In this work, we have determined the incidence of Cardinium, Rickettsia, Spiroplasma and Wolbachia as representatives of major distorter bacteria genera in Aplonobia histricina (Berlese), Eutetranychus banksi (McGregor), Eutetranychus orientalis (Klein), Panonychus citri (McGregor), Tetranychus evansi Baker and Pritchard, Tetranychus turkestani Ugarov and Nikolskii, and T. urticae populations from Spanish citrus orchards. Only Wolbachia was detected by PCR. The multilocus alignment approach and phylogenetic inference indicated that all detected Wolbachia belong to supergroup B. The deep analysis of each 16S rDNA, ftsZ and wsp gene sequences allowed identifying several phylogenetically diferent Wolbachia sequences. It probably indicates the presence of several diferent races or strains, all of them belonging to supergroup B. The wsp sequence typing analysis unveiled the presence of the two already identifed alleles (61 and 370) and allowed to contribute with fve new alleles, supporting the presence of diferent but related B-races in the studied mite populations. The results are discussed and related to T. urticae population structure, previously observed in Spanish citrus orchards

Fitness Trade-Offs Determine the Role of the Molecular Chaperonin GroEL in Buffering Mutations

Molecular chaperones fold many proteins and their mutated versions in a cell and can sometimes buffer the phenotypic effect of mutations that affect protein folding. Unanswered questions about this buffering include the nature of its mechanism, its influence on the genetic variation of a population, the fitness trade-offs constraining this mechanism, and its role in expediting evolution. Answering these questions is fundamental to understand the contribution of buffering to increase genetic variation and ecological diversification. Here, we performed experimental evolution, genome resequencing, and computational analyses to determine the trade-offs and evolutionary trajectories of Escherichia coli expressing high levels of the essential chaperonin GroEL. GroEL is abundantly present in bacteria, particularly in bacteria with large loads of deleterious mutations, suggesting its role in mutational buffering. We show that groEL overexpression is costly to large populations evolving in the laboratory, leading to groE expression decline within 66 generations. In contrast, populations evolving under the strong genetic drift characteristic of endosymbiotic bacteria avoid extinction or can be rescued in the presence of abundant GroEL. Genomes resequenced from cells evolved under strong genetic drift exhibited significantly higher tolerance to deleterious mutations at high GroEL levels than at native levels, revealing that GroEL is buffering mutations in these cells. GroEL buffered mutations in a highly diverse set of proteins that interact with the environment, including substrate and ion membrane transporters, hinting at its role in ecological diversification. Our results reveal the fitness trade-offs of mutational buffering and how genetic variation is maintained in population

The Molecular Chaperone DnaK Is a Source of Mutational Robustness

[EN] Molecular chaperones, also known as heat-shock proteins, refold misfolded proteins and help other proteins reach their native conformation. Thanks to these abilities, some chaperones, such as the Hsp90 protein or the chaperonin GroEL, can buffer the deleterious phenotypic effects of mutations that alter protein structure and function. Hsp70 chaperones use a chaperoning mechanism different from that of Hsp90 and GroEL, and it is not known whether they can also buffer mutations. Here, we show that they can. To this end, we performed a mutation accumulation experiment in Escherichia coli, followed by whole-genome resequencing. Overexpression of the Hsp70 chaperone DnaK helps cells cope with mutational load and completely avoid the extinctions we observe in lineages evolving without chaperone overproduction. Additionally, our sequence data show that DnaK overexpression increases mutational robustness, the tolerance of its clients to nonsynonymous nucleotide substitutions. We also show that this elevated mutational buffering translates into differences in evolutionary rates on intermediate and long evolutionary time scales. Specifically, we studied the evolutionary rates of DnaK clients using the genomes of E. coli, Salmonella enterica, and 83 other gamma-proteobacteria. We find that clients that interact strongly with DnaK evolve faster than weakly interacting clients. Our results imply that all three major chaperone classes can buffer mutations and affect protein evolution. They illustrate how an individual protein like a chaperone can have a disproportionate effect on the evolution of a proteome.The authors thank Xiaoshu Chen and Jianzhi Zhang for kindly providing us with the gene expression data. This work was supported by the Forschungskredit program of the University of Zurich (grant FK-14-076 to J.A.), the Swiss National Science Foundation (grant 31003A_146137 to A.W.), the University Priority Research Program in Evolutionary Biology at the University of Zurich (to A.W.), the Science Foundation Ireland (grant 12/IP/1673 to M.A.F.), and the Spanish Ministerio de Economia y Competitividad (grant BFU2012-36346 to M.A.F.). We posted an earlier version of this paper in bioRxiv (doi: http://dx.doi.org/10.1101/040600) on 22 February 2016.Aguilar-Rodríguez, J.; Sabater-Munoz, B.; Montagud-Martinez, R.; Berlanga, V.; Alvarez-Ponce, D.; Wagner, A.; Fares Riaño, MA. (2016). The Molecular Chaperone DnaK Is a Source of Mutational Robustness. Genome Biology and Evolution. 8(9):2979-2991. https://doi.org/10.1093/gbe/evw176S297929918

Essentiality Is a Strong Determinant of Protein Rates of Evolution during Mutation Accumulation Experiments in Escherichia coli

[EN] The Neutral Theory of Molecular Evolution is considered the most powerful theory to understand the evolutionary behavior of proteins. One of the main predictions of this theory is that essential proteins should evolve slower than dispensable ones owing to increased selective constraints. Comparison of genomes of different species, however, has revealed only small differences between the rates of evolution ofessential and nonessential proteins. In some analyses, these differences vanish once confounding factors are controlled for, whereas in other cases essentiality seems to have an independent, albeit small, effect. It has been argued that comparing relatively distant genomes may entail a number of limitations. For instance, many of the genes that are dispensable in controlled lab conditions may be essential in some of the conditions faced in nature. Moreover, essentiality can change during evolution, and rates of protein evolution are simultaneously shaped by a variety of factors, whose individual effects are difficult to isolate. Here, we conducted two parallel mutation accumulation experiments in Escherichia coli, during 5,500–5,750 generations, and compared the genomes at different points of the experiments. Our approach (a short-term experiment, under highly controlled conditions) enabled us to overcome many of the limitations of previous studies. We observed that essential proteins evolved substantially slower than nonessential ones during our experiments. Strikingly, rates of protein evolution were only moderately affected by expression level and protein length.We are grateful to Kais Fares, Maria Prats-Escriche and Victor Berlanga-Laparra for technical assistance with the evolution experiments. We are also grateful to the Editor and two anonymous referees for helpful comments. This work was supported by grants from the Spanish Ministerio de Economia y Competitividad (BFU2009-12022, BFU2012-36346, and BFU2015-66073-P) and Science Foundation Ireland (12/IP/1673) to M.A.F. D.A.-P. was partially supported by funds from the University of Nevada, Reno. C.T. was supported by a European Molecular Biology Organization long-term fellowship (EMBO ALTF 730-2011) and a Juan de la Cierva fellowship from the Ministerio de Economia y Competitividad (JCA-2012-14056). M.X.R.-G. was partially supported by a JAE DOC fellowship from the Ministerio de Economia y Competitividad, Spain.Alvarez-Ponce, D.; Sabater-Munoz, B.; Toft, C.; Ruíz-González, MJ.; Fares Riaño, MA. (2016). Essentiality Is a Strong Determinant of Protein Rates of Evolution during Mutation Accumulation Experiments in Escherichia coli. Genome Biology and Evolution. 8(9):2914-2927. https://doi.org/10.1093/gbe/evw205S291429278

Chance and necessity in the genome evolution of endosymbiotic bacteria of insects

[EN] An open question in evolutionary biology is how does the selection¿drift balance determine the fates of biological interactions. We searched for signatures of selection and drift in genomes of five endosymbiotic bacterial groups known to evolve under strong genetic drift. Although most genes in endosymbiotic bacteria showed evidence of relaxed purifying selection, many genes in these bacteria exhibited stronger selective constraints than their orthologs in free-living bacterial relatives. Remarkably, most of these highly constrained genes had no role in the host¿symbiont interactions but were involved in either buffering the deleterious consequences of drift or other host-unrelated functions, suggesting that they have either acquired new roles or their role became more central in endosymbiotic bacteria. Experimental evolution of Escherichia coli under strong genetic drift revealed remarkable similarities in the mutational spectrum, genome reduction patterns and gene losses to endosymbiotic bacteria of insects. Interestingly, the transcriptome of the experimentally evolved lines showed a generalized deregulation of the genome that affected genes encoding proteins involved in mutational buffering, regulation and amino acid biosynthesis, patterns identical to those found in endosymbiotic bacteria. Our results indicate that drift has shaped endosymbiotic associations through a change in the functional landscape of bacterial genes and that the host had only a small role in such a shiftThis work was supported by Science Foundation Ireland (12/IP/1637) and grants from the Spanish Ministerio de Economia y Competitividad (MINECO-FEDER; BFU2012-36346 and BFU2015-66073-P) to MAF. DAP and CT were supported by Juan de la Cierva fellowships from MINECO (references: JCI-2011-11089 and JCA-2012-14056, respectively). DAP is supported by funds from the University of Nevada, Reno, NV, USA.Sabater-Muñoz, B.; Toft, C.; Alvarez-Ponce, D.; Fares Riaño, MA. (2017). Chance and necessity in the genome evolution of endosymbiotic bacteria of insects. The ISME Journal. 11(6):1291-1304. https://doi.org/10.1038/ismej.2017.18S12911304116Aguilar-Rodriguez J, Sabater-Munoz B, Montagud-Martinez R, Berlanga V, Alvarez-Ponce D, Wagner A et al. (2016). The molecular chaperone DnaK is a source of mutational robustness. Genome Biol Evol 8: 2979–2991.Alvarez-Ponce D, Sabater-Munoz B, Toft C, Ruiz-Gonzalez MX, Fares MA . (2016). Essentiality is a strong determinant of protein rates of evolution during mutation accumulation experiments in Escherichia coli. Genome Biol Evol 8: 2914–2927.Anders S, Huber W . (2010). Differential expression analysis for sequence count data. Genome Biol 11: R106.Archibald J . (2014) One Plus One Equals One: Symbiosis and the Evolution of Complex Life. Oxford University Press: Oxford, UK.Aussel L, Loiseau L, Hajj Chehade M, Pocachard B, Fontecave M, Pierrel F et al. (2014). ubiJ, a new gene required for aerobic growth and proliferation in macrophage, is involved in coenzyme Q biosynthesis in Escherichia coli and Salmonella enterica serovar Typhimurium. J Bacteriol 196: 70–79.Baumann P, Baumann L, Clark MA . (1996). Levels of Buchnera aphidicola chaperonin groEL during growth of the aphid Schizaphis graminum. Curr Microbiol 32: 7.Benjamini Y, Yekutieli Y . (2005). False discovery rate controlling confidence intervals for selected parameters. J Am Stat Assoc 100: 10.Bennett GM, Moran NA . (2015). Heritable symbiosis: the advantages and perils of an evolutionary rabbit hole. Proc Natl Acad Sci USA 112: 10169–10176.Bermingham J, Rabatel A, Calevro F, Vinuelas J, Febvay G, Charles H et al. (2009). Impact of host developmental age on the transcriptome of the symbiotic bacterium Buchnera aphidicola in the pea aphid (Acyrthosiphon pisum. Appl Environ Microbiol 75: 7294–7297.Bogumil D, Dagan T . (2010). Chaperonin-dependent accelerated substitution rates in prokaryotes. Genome Biol Evol 2: 602–608.Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S et al. (2009). AmiGO: online access to ontology and annotation data. Bioinformatics 25: 288–289.Chen Z, Wang Y, Li Y, Li Y, Fu N, Ye J et al. (2012). Esre: a novel essential non-coding RNA in Escherichia coli. FEBS Lett 586: 1195–1200.Clark JW, Hossain S, Burnside CA, Kambhampati S . (2001). Coevolution between a cockroach and its bacterial endosymbiont: a biogeographical perspective. Proc Biol Sci 268: 393–398.Dale C, Wang B, Moran N, Ochman H . (2003). Loss of DNA recombinational repair enzymes in the initial stages of genome degeneration. Mol Biol Evol 20: 1188–1194.Deatherage DE, Barrick JE . (2014). Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol Biol 1151: 165–188.Douglas AE . (2003). The nutritional physiology of aphids. Adv Insect Physiol 31: 68.Fares MA, Barrio E, Sabater-Munoz B, Moya A . (2002a). The evolution of the heat-shock protein GroEL from Buchnera, the primary endosymbiont of aphids, is governed by positive selection. Mol Biol Evol 19: 1162–1170.Fares MA, Ruiz-Gonzalez MX, Moya A, Elena SF, Barrio E . (2002b). Endosymbiotic bacteria: groEL buffers against deleterious mutations. Nature 417: 398.Gancedo C, Flores CL, Gancedo JM . (2016). The expanding landscape of moonlighting proteins in yeasts. Microbiol Mol Biol Rev 80: 765–777.Gerardo NM, Altincicek B, Anselme C, Atamian H, Barribeau SM, de Vos M et al. (2010). Immunity and other defenses in pea aphids, Acyrthosiphon pisum. Genome Biol 11: R21.Gomez-Valero L, Latorre A, Silva FJ . (2004). The evolutionary fate of nonfunctional DNA in the bacterial endosymbiont Buchnera aphidicola. Mol Biol Evol 21: 2172–2181.Gomez-Valero L, Silva FJ, Christophe Simon J, Latorre A . (2007). Genome reduction of the aphid endosymbiont Buchnera aphidicola in a recent evolutionary time scale. Gene 389: 87–95.Gonzalez-Domenech CM, Belda E, Patino-Navarrete R, Moya A, Pereto J, Latorre A . (2012). Metabolic stasis in an ancient symbiosis: genome-scale metabolic networks from two Blattabacterium cuenoti strains, primary endosymbionts of cockroaches. BMC Microbiol 12 (Suppl 1): S5.Hansen AK, Moran NA . (2011). Aphid genome expression reveals host-symbiont cooperation in the production of amino acids. Proc Natl Acad Sci USA 108: 2849–2854.Hansen AK, Moran NA . (2014). The impact of microbial symbionts on host plant utilization by herbivorous insects. Mol Ecol 23: 1473–1496.Henderson B, Fares MA, Lund PA . (2013). Chaperonin 60: a paradoxical, evolutionarily conserved protein family with multiple moonlighting functions. Biol Rev Camb Philos Soc 88: 955–987.Humphreys NJ, Douglas AE . (1997). Partitioning of symbiotic bacteria between generations of an insect: a quantitative study of a Buchnera sp. in the pea aphid (Acyrthosiphon pisum reared at different temperatures. Appl Environ Microbiol 63: 3294–3296.International Aphid Genomics Consortium. (2010). Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biol 8: e1000313.Kadibalban AS, Bogumil D, Landan G, Dagan T . (2016). DnaK-dependent accelerated evolutionary rate in prokaryotes. Genome Biol Evol 8: 1590–1599.Katoh K, Standley DM . (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30: 772–780.Kelkar YD, Ochman H . (2013). Genome reduction promotes increase in protein functional complexity in bacteria. Genetics 193: 303–307.Koga R, Meng XY, Tsuchida T, Fukatsu T . (2012). Cellular mechanism for selective vertical transmission of an obligate insect symbiont at the bacteriocyte-embryo interface. Proc Natl Acad Sci USA 109: E1230–E1237.Kuo CH, Moran NA, Ochman H . (2009). The consequences of genetic drift for bacterial genome complexity. Genome Res 19: 1450–1454.Kuo CH, Ochman H . (2009). Deletional bias across the three domains of life. Genome Biol Evol 1: 145–152.Law R, Lewis DH . (1983). Biotic environments and the maintenance of sex-some evidence from mutualistic symbioses. Biol J Linnean Soc 20: 28.Liu XD, Xie L, Wei Y, Zhou X, Jia B, Liu J et al. (2014). Abiotic stress resistance, a novel moonlighting function of ribosomal protein RPL44 in the halophilic fungus Aspergillus glaucus. Appl Environ Microbiol 80: 4294–4300.Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M et al. (2012). RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res 40: W622–W627.Macdonald SJ, Lin GG, Russell CW, Thomas GH, Douglas AE . (2012). The central role of the host cell in symbiotic nitrogen metabolism. Proc Biol Sci 279: 2965–2973.McClure R, Balasubramanian D, Sun Y, Bobrovskyy M, Sumby P, Genco CA et al. (2013). Computational analysis of bacterial RNA-Seq data. Nucleic Acids Res 41: e140.McCutcheon JP, Moran NA . (2012). Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol 10: 13–26.McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Loso T, Douglas AE et al. (2013). Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci USA 110: 3229–3236.Mira A, Ochman H, Moran NA . (2001). Deletional bias and the evolution of bacterial genomes. Trends Genet 17: 589–596.Moran NA . (1996). Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc Natl Acad Sci USA 93: 2873–2878.Moran NA, Dunbar HE, Wilcox JL . (2005). Regulation of transcription in a reduced bacterial genome: nutrient-provisioning genes of the obligate symbiont Buchnera aphidicola. J Bacteriol 187: 4229–4237.Moran NA, McCutcheon JP, Nakabachi A . (2008). Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet 42: 165–190.Moran NA, McLaughlin HJ, Sorek R . (2009). The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 323: 379–382.Nakabachi A, Ishida K, Hongoh Y, Ohkuma M, Miyagishima SY . (2014). Aphid gene of bacterial origin encodes a protein transported to an obligate endosymbiont. Curr Biol 24: R640–R641.Nilsson AI, Koskiniemi S, Eriksson S, Kugelberg E, Hinton JC, Andersson DI . (2005). Bacterial genome size reduction by experimental evolution. Proc Natl Acad Sci USA 102: 12112–12116.Patino-Navarrete R, Moya A, Latorre A, Pereto J . (2013). Comparative genomics of Blattabacterium cuenoti: the frozen legacy of an ancient endosymbiont genome. Genome Biol Evol 5: 351–361.Pettersson ME, Berg OG . (2007). Muller's ratchet in symbiont populations. Genetica 130: 199–211.Price DR, Feng H, Baker JD, Bavan S, Luetje CW, Wilson AC . (2014). Aphid amino acid transporter regulates glutamine supply to intracellular bacterial symbionts. Proc Natl Acad Sci USA 111: 320–325.Reyes-Prieto M, Vargas-Chavez C, Latorre A, Moya A . (2015). SymbioGenomesDB: a database for the integration and access to knowledge on host-symbiont relationships. Database 2015: bav109 (1–8).Robinson MD, McCarthy DJ, Smyth GK . (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139–140.Sabater-Muñoz B, Prats-Escriche M, Montagud-Martinez R, Lopez-Cerdan A, Toft C, Aguilar-Rodriguez J et al. (2015). Fitness trade-offs determine the role of the molecular chaperonin groel in buffering mutations. Mol Biol Evol 32: 2681–2693.Schlicker A, Domingues FS, Rahnenfuhrer J, Lengauer T . (2006). A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics 7: 302.Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H . (2000). Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407: 81–86.Supek F, Bosnjak M, Skunca N, Smuc T . (2011). REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE 6: e21800.Tamas I, Klasson L, Canback B, Naslund AK, Eriksson AS, Wernegreen JJ et al. (2002). 50 million years of genomic stasis in endosymbiotic bacteria. Science 296: 2376–2379.Toft C, Fares MA . (2008). The evolution of the flagellar assembly pathway in endosymbiotic bacterial genomes. Mol Biol Evol 25: 2069–2076.van Ham RC, Kamerbeek J, Palacios C, Rausell C, Abascal F, Bastolla U et al. (2003). Reductive genome evolution in Buchnera aphidicola. Proc Natl Acad Sci USA 100: 581–586.Wernegreen JJ . (2002). Genome evolution in bacterial endosymbionts of insects. Nat Rev Genet 3: 850–861.Wernegreen JJ . (2011). Reduced selective constraint in endosymbionts: elevation in radical amino acid replacements occurs genome-wide. PLoS One 6: e28905.Williams TA, Fares MA . (2010). The effect of chaperonin buffering on protein evolution. Genome Biol Evol 2: 609–619.Yang Z . (2007). PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586–1591