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Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations

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Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations

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Nombre: Caffrey;WILLIAMS;Jiang ...
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dc.contributor.author Caffrey, Brian E. es_ES
dc.contributor.author Williams, Tom A. es_ES
dc.contributor.author Jiang, Xiaowei es_ES
dc.contributor.author Toft, Christina es_ES
dc.contributor.author Hokamp, Karsten es_ES
dc.contributor.author Fares Riaño, Mario Ali es_ES
dc.date.accessioned 2016-01-13T10:47:20Z
dc.date.available 2016-01-13T10:47:20Z
dc.date.issued 2012-04
dc.identifier.issn 1932-6203
dc.identifier.uri http://hdl.handle.net/10251/59792
dc.description.abstract 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. es_ES
dc.description.sponsorship 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. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. en_EN
dc.language Inglés es_ES
dc.publisher Public Library of Science es_ES
dc.relation.ispartof PLoS ONE es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Detecting Positive Selection es_ES
dc.subject Amino-acid sites es_ES
dc.subject Bartonella-Bacilliformis es_ES
dc.subject Escherichia coli es_ES
dc.subject Genome sequence es_ES
dc.subject Molecular adaptation es_ES
dc.subject Statistical methods es_ES
dc.subject Maximum likelihood es_ES
dc.subject Gene duplication es_ES
dc.subject Cog database es_ES
dc.title Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1371/journal.pone.0035659
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//BFU2009-12022/ES/Impacto De La Duplicacion Genomica En La Innovacion Y Geometria Funcional De Arabidopsis Thaliana/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/SFI/SFI Research Frontiers Programme (RFP)/10%2FRFP%2FGEN2685/IE/Understanding the Role of Heat-Shock Proteins in Evolutionary Innovation/ en_EN
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes es_ES
dc.description.bibliographicCitation Caffrey, BE.; Williams, TA.; Jiang, X.; Toft, C.; Hokamp, K.; Fares Riaño, MA. (2012). Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations. PLoS ONE. 7:35659-35659. https://doi.org/10.1371/journal.pone.0035659 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion http://dx.doi.org/10.1371/journal.pone.0035659 es_ES
dc.description.upvformatpinicio 35659 es_ES
dc.description.upvformatpfin 35659 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 7 es_ES
dc.relation.senia 233111 es_ES
dc.identifier.pmid 22563391 en_EN
dc.identifier.pmcid PMC3338524 en_EN
dc.contributor.funder Ministerio de Ciencia e Innovación es_ES
dc.description.references Conant, 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/nrg2482 es_ES
dc.description.references Lynch, M. (2000). The Evolutionary Fate and Consequences of Duplicate Genes. Science, 290(5494), 1151-1155. doi:10.1126/science.290.5494.1151 es_ES
dc.description.references Pinto, G., Mahler, D. L., Harmon, L. J., & Losos, J. B. (2008). Testing the island effect in adaptive radiation: rates and patterns of morphological diversification in Caribbean and mainland Anolis lizards. Proceedings of the Royal Society B: Biological Sciences, 275(1652), 2749-2757. doi:10.1098/rspb.2008.0686 es_ES
dc.description.references Lynch, M., & Katju, V. (2004). The altered evolutionary trajectories of gene duplicates. Trends in Genetics, 20(11), 544-549. doi:10.1016/j.tig.2004.09.001 es_ES
dc.description.references Innan, H., & Kondrashov, F. (2010). The evolution of gene duplications: classifying and distinguishing between models. Nature Reviews Genetics, 11(2), 97-108. doi:10.1038/nrg2689 es_ES
dc.description.references Moran, N. A. (2002). Microbial Minimalism. Cell, 108(5), 583-586. doi:10.1016/s0092-8674(02)00665-7 es_ES
dc.description.references Toft, C., Williams, T. A., & Fares, M. A. (2009). Genome-Wide Functional Divergence after the Symbiosis of Proteobacteria with Insects Unraveled through a Novel Computational Approach. PLoS Computational Biology, 5(4), e1000344. doi:10.1371/journal.pcbi.1000344 es_ES
dc.description.references Dykhuizen, D. E. (1998). Antonie van Leeuwenhoek, 73(1), 25-33. doi:10.1023/a:1000665216662 es_ES
dc.description.references Gans, J. (2005). Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil. Science, 309(5739), 1387-1390. doi:10.1126/science.1112665 es_ES
dc.description.references Pikuta, E. V., Hoover, R. B., & Tang, J. (2007). Microbial Extremophiles at the Limits of Life. Critical Reviews in Microbiology, 33(3), 183-209. doi:10.1080/10408410701451948 es_ES
dc.description.references Pace, N. R. (1997). A Molecular View of Microbial Diversity and the Biosphere. Science, 276(5313), 734-740. doi:10.1126/science.276.5313.734 es_ES
dc.description.references Dyall, S. D. (2004). Ancient Invasions: From Endosymbionts to Organelles. Science, 304(5668), 253-257. doi:10.1126/science.1094884 es_ES
dc.description.references Zhang, J. (2003). Evolution by gene duplication: an update. Trends in Ecology & Evolution, 18(6), 292-298. doi:10.1016/s0169-5347(03)00033-8 es_ES
dc.description.references Lynch, M., & Conery, J. S. (2003). The Origins of Genome Complexity. Science, 302(5649), 1401-1404. doi:10.1126/science.1089370 es_ES
dc.description.references Ochman, H., Lawrence, J. G., & Groisman, E. A. (2000). Lateral gene transfer and the nature of bacterial innovation. Nature, 405(6784), 299-304. doi:10.1038/35012500 es_ES
dc.description.references McKenzie, G. J., Harris, R. S., Lee, P. L., & Rosenberg, S. M. (2000). The SOS response regulates adaptive mutation. Proceedings of the National Academy of Sciences, 97(12), 6646-6651. doi:10.1073/pnas.120161797 es_ES
dc.description.references Dagan, T., & Martin, W. (2006). Genome Biology, 7(10), 118. doi:10.1186/gb-2006-7-10-118 es_ES
dc.description.references Kimura, M. (1983). The Neutral Theory of Molecular Evolution. doi:10.1017/cbo9780511623486 es_ES
dc.description.references Yang, Z., & Bielawski, J. P. (2000). Statistical methods for detecting molecular adaptation. Trends in Ecology & Evolution, 15(12), 496-503. doi:10.1016/s0169-5347(00)01994-7 es_ES
dc.description.references Suzuki, Y., & Gojobori, T. (1999). A method for detecting positive selection at single amino acid sites. Molecular Biology and Evolution, 16(10), 1315-1328. doi:10.1093/oxfordjournals.molbev.a026042 es_ES
dc.description.references Yang, Z., & Nielsen, R. (2002). Codon-Substitution Models for Detecting Molecular Adaptation at Individual Sites Along Specific Lineages. Molecular Biology and Evolution, 19(6), 908-917. doi:10.1093/oxfordjournals.molbev.a004148 es_ES
dc.description.references Fares, M. A., Elena, S. F., Ortiz, J., Moya, A., & Barrio, E. (2002). A Sliding Window-Based Method to Detect Selective Constraints in Protein-Coding Genes and Its Application to RNA Viruses. Journal of Molecular Evolution, 55(5), 509-521. doi:10.1007/s00239-002-2346-9 es_ES
dc.description.references Suzuki, Y. (2004). New Methods for Detecting Positive Selection at Single Amino Acid Sites. Journal of Molecular Evolution, 59(1). doi:10.1007/s00239-004-2599-6 es_ES
dc.description.references Zhang, J. (2004). Frequent False Detection of Positive Selection by the Likelihood Method with Branch-Site Models. Molecular Biology and Evolution, 21(7), 1332-1339. doi:10.1093/molbev/msh117 es_ES
dc.description.references Suzuki, Y. (2004). Three-Dimensional Window Analysis for Detecting Positive Selection at Structural Regions of Proteins. Molecular Biology and Evolution, 21(12), 2352-2359. doi:10.1093/molbev/msh249 es_ES
dc.description.references Zhang, J. (2005). Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level. Molecular Biology and Evolution, 22(12), 2472-2479. doi:10.1093/molbev/msi237 es_ES
dc.description.references Berglund, A.-C., Wallner, B., Elofsson, A., & Liberles, D. A. (2005). Tertiary Windowing to Detect Positive Diversifying Selection. Journal of Molecular Evolution, 60(4), 499-504. doi:10.1007/s00239-004-0223-4 es_ES
dc.description.references Gu, X. (1999). Statistical methods for testing functional divergence after gene duplication. Molecular Biology and Evolution, 16(12), 1664-1674. doi:10.1093/oxfordjournals.molbev.a026080 es_ES
dc.description.references Gu, X. (2001). Mathematical Modeling for Functional Divergence after Gene Duplication. Journal of Computational Biology, 8(3), 221-234. doi:10.1089/10665270152530827 es_ES
dc.description.references Gu, X. (2006). A Simple Statistical Method for Estimating Type-II (Cluster-Specific) Functional Divergence of Protein Sequences. Molecular Biology and Evolution, 23(10), 1937-1945. doi:10.1093/molbev/msl056 es_ES
dc.description.references Williams, T. A., Codoñer, F. M., Toft, C., & Fares, M. A. (2010). Two chaperonin systems in bacterial genomes with distinct ecological roles. Trends in Genetics, 26(2), 47-51. doi:10.1016/j.tig.2009.11.009 es_ES
dc.description.references Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., … Natale, D. A. (2003). BMC Bioinformatics, 4(1), 41. doi:10.1186/1471-2105-4-41 es_ES
dc.description.references Lake, J. A. (1999). GENOMICS:Mix and Match in the Tree of Life. Science, 283(5410), 2027-2028. doi:10.1126/science.283.5410.2027 es_ES
dc.description.references Mushegian, A. R., & Koonin, E. V. (1996). A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proceedings of the National Academy of Sciences, 93(19), 10268-10273. doi:10.1073/pnas.93.19.10268 es_ES
dc.description.references Azuma, Y., & Ota, M. (2009). An evaluation of minimal cellular functions to sustain a bacterial cell. BMC Systems Biology, 3(1). doi:10.1186/1752-0509-3-111 es_ES
dc.description.references Crick, F. H. C. (1968). The origin of the genetic code. Journal of Molecular Biology, 38(3), 367-379. doi:10.1016/0022-2836(68)90392-6 es_ES
dc.description.references Lund, 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.x es_ES
dc.description.references Kampinga, H. H., Dynlacht, J. R., & Dikomey, E. (2004). Mechanism of radiosensitization by hyperthermia (43°C) as derived from studies with DNA repair defective mutant cell lines. International Journal of Hyperthermia, 20(2), 131-139. doi:10.1080/02656730310001627713 es_ES
dc.description.references Laszlo, A. (1992). The effects of hyperthermia on mammalian cell structure and function. Cell Proliferation, 25(2), 59-87. doi:10.1111/j.1365-2184.1992.tb01482.x es_ES
dc.description.references Kregel, K. C. (2002). Invited Review: Heat shock proteins: modifying factors in physiological stress responses and acquired thermotolerance. Journal of Applied Physiology, 92(5), 2177-2186. doi:10.1152/japplphysiol.01267.2001 es_ES
dc.description.references Lepock, J. R. (1997). Protein Denaturation During Heat Shock. Advances in Molecular and Cell Biology, 223-259. doi:10.1016/s1569-2558(08)60079-x es_ES
dc.description.references Degnan, P. H. (2005). Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects. Genome Research, 15(8), 1023-1033. doi:10.1101/gr.3771305 es_ES
dc.description.references Gil, R., Sabater-Munoz, B., Latorre, A., Silva, F. J., & Moya, A. (2002). Extreme genome reduction in Buchnera spp.: Toward the minimal genome needed for symbiotic life. Proceedings of the National Academy of Sciences, 99(7), 4454-4458. doi:10.1073/pnas.062067299 es_ES
dc.description.references Perez-Brocal, V., Gil, R., Ramos, S., Lamelas, A., Postigo, M., Michelena, J. M., … Latorre, A. (2006). A Small Microbial Genome: The End of a Long Symbiotic Relationship? Science, 314(5797), 312-313. doi:10.1126/science.1130441 es_ES
dc.description.references 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(6800), 81-86. doi:10.1038/35024074 es_ES
dc.description.references Tamas, I. (2002). 50 Million Years of Genomic Stasis in Endosymbiotic Bacteria. Science, 296(5577), 2376-2379. doi:10.1126/science.1071278 es_ES
dc.description.references Van Ham, R. C. H. J., Kamerbeek, J., Palacios, C., Rausell, C., Abascal, F., Bastolla, U., … Moya, A. (2003). Reductive genome evolution in Buchnera aphidicola. Proceedings of the National Academy of Sciences, 100(2), 581-586. doi:10.1073/pnas.0235981100 es_ES
dc.description.references Nakabachi, A., Yamashita, A., Toh, H., Ishikawa, H., Dunbar, H. E., Moran, N. A., & Hattori, M. (2006). The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella. Science, 314(5797), 267-267. doi:10.1126/science.1134196 es_ES
dc.description.references Baron, C. (2010). Antivirulence drugs to target bacterial secretion systems. Current Opinion in Microbiology, 13(1), 100-105. doi:10.1016/j.mib.2009.12.003 es_ES
dc.description.references Douglas, A. E. (1998). Nutritional Interactions in Insect-Microbial Symbioses: Aphids and Their Symbiotic BacteriaBuchnera. Annual Review of Entomology, 43(1), 17-37. doi:10.1146/annurev.ento.43.1.17 es_ES
dc.description.references Sandström, J., Telang, A., & Moran, N. . (2000). Nutritional enhancement of host plants by aphids — a comparison of three aphid species on grasses. Journal of Insect Physiology, 46(1), 33-40. doi:10.1016/s0022-1910(99)00098-0 es_ES
dc.description.references Anderson, B. E., & Neuman, M. A. (1997). Bartonella spp. as emerging human pathogens. Clinical Microbiology Reviews, 10(2), 203-219. doi:10.1128/cmr.10.2.203 es_ES
dc.description.references Dramsi, S., & Cossart, P. (1998). INTRACELLULAR PATHOGENS AND THE ACTIN CYTOSKELETON. Annual Review of Cell and Developmental Biology, 14(1), 137-166. doi:10.1146/annurev.cellbio.14.1.137 es_ES
dc.description.references Dehio, C. (2001). Bartonella interactions with endothelial cells and erythrocytes. Trends in Microbiology, 9(6), 279-285. doi:10.1016/s0966-842x(01)02047-9 es_ES
dc.description.references Ihler, G. M. (1996). Bartonella bacilliformis: dangerous pathogen slowly emerging from deep background. FEMS Microbiology Letters, 144(1), 1-11. doi:10.1111/j.1574-6968.1996.tb08501.x es_ES
dc.description.references Fricke, W. F., Wright, M. S., Lindell, A. H., Harkins, D. M., Baker-Austin, C., Ravel, J., & Stepanauskas, R. (2008). Insights into the Environmental Resistance Gene Pool from the Genome Sequence of the Multidrug-Resistant Environmental Isolate Escherichia coli SMS-3-5. Journal of Bacteriology, 190(20), 6779-6794. doi:10.1128/jb.00661-08 es_ES
dc.description.references Ren, C.-P., Beatson, S. A., Parkhill, J., & Pallen, M. J. (2005). The Flag-2 Locus, an Ancestral Gene Cluster, Is Potentially Associated with a Novel Flagellar System from Escherichia coli. Journal of Bacteriology, 187(4), 1430-1440. doi:10.1128/jb.187.4.1430-1440.2005 es_ES
dc.description.references Manges, A. R., Johnson, J. R., Foxman, B., O’Bryan, T. T., Fullerton, K. E., & Riley, L. W. (2001). Widespread Distribution of Urinary Tract Infections Caused by a Multidrug-ResistantEscherichia coliClonal Group. New England Journal of Medicine, 345(14), 1007-1013. doi:10.1056/nejmoa011265 es_ES
dc.description.references Cascales, E., & Christie, P. J. (2003). The versatile bacterial type IV secretion systems. Nature Reviews Microbiology, 1(2), 137-149. doi:10.1038/nrmicro753 es_ES
dc.description.references Bailey, S., Ward, D., Middleton, R., Grossmann, J. G., & Zambryski, P. C. (2006). Agrobacterium tumefaciens VirB8 structure reveals potential protein-protein interaction sites. Proceedings of the National Academy of Sciences, 103(8), 2582-2587. doi:10.1073/pnas.0511216103 es_ES
dc.description.references Altenhoff, A. M., & Dessimoz, C. (2009). Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods. PLoS Computational Biology, 5(1), e1000262. doi:10.1371/journal.pcbi.1000262 es_ES
dc.description.references Roth, A. C., Gonnet, G. H., & Dessimoz, C. (2008). Algorithm of OMA for large-scale orthology inference. BMC Bioinformatics, 9(1). doi:10.1186/1471-2105-9-518 es_ES
dc.description.references Schneider, A., Dessimoz, C., & Gonnet, G. H. (2007). OMA Browser Exploring orthologous relations across 352 complete genomes. Bioinformatics, 23(16), 2180-2182. doi:10.1093/bioinformatics/btm295 es_ES
dc.description.references Tatusov, R. L. (2001). The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Research, 29(1), 22-28. doi:10.1093/nar/29.1.22 es_ES
dc.description.references Lima, T., Auchincloss, A. H., Coudert, E., Keller, G., Michoud, K., Rivoire, C., … Bairoch, A. (2009). HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Research, 37(Database), D471-D478. doi:10.1093/nar/gkn661 es_ES
dc.description.references Gascuel, O. (1997). BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Molecular Biology and Evolution, 14(7), 685-695. doi:10.1093/oxfordjournals.molbev.a025808 es_ES
dc.description.references Benjamini, Y., & Hochberg, Y. (1995). Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society: Series B (Methodological), 57(1), 289-300. doi:10.1111/j.2517-6161.1995.tb02031.x es_ES
dc.description.references Dutheil, J., Gaillard, S., Bazin, E., Glémin, S., Ranwez, V., Galtier, N., & Belkhir, K. (2006). BMC Bioinformatics, 7(1), 188. doi:10.1186/1471-2105-7-188 es_ES
dc.description.references Gu, X., & Vander Velden, K. (2002). DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics, 18(3), 500-501. doi:10.1093/bioinformatics/18.3.500 es_ES
dc.description.references Stamatakis, A., Ludwig, T., & Meier, H. (2004). RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics, 21(4), 456-463. doi:10.1093/bioinformatics/bti191 es_ES
dc.description.references Yang, Z. (2007). PAML 4: Phylogenetic Analysis by Maximum Likelihood. Molecular Biology and Evolution, 24(8), 1586-1591. doi:10.1093/molbev/msm088 es_ES
dc.description.references Baron, C. (2006). VirB8: a conserved type IV secretion system assembly factor and drug targetThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Membrane Proteins in Health and Disease. Biochemistry and Cell Biology, 84(6), 890-899. doi:10.1139/o06-148 es_ES


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