- -

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

RiuNet: Institutional repository of the Polithecnic University of Valencia

Share/Send to

Cited by

Statistics

  • Estadisticas de Uso

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

Show full item record

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

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/59792

Files in this item

Item Metadata

Title: Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations
Author: Caffrey, Brian E. Williams, Tom A. Jiang, Xiaowei Toft, Christina Hokamp, Karsten Fares Riaño, Mario Ali
UPV Unit: 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
Issued date:
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 ...[+]
Subjects: Detecting Positive Selection , Amino-acid sites , Bartonella-Bacilliformis , Escherichia coli , Genome sequence , Molecular adaptation , Statistical methods , Maximum likelihood , Gene duplication , Cog database
Copyrigths: Reconocimiento (by)
Source:
PLoS ONE. (issn: 1932-6203 )
DOI: 10.1371/journal.pone.0035659
Publisher:
Public Library of Science
Publisher version: http://dx.doi.org/10.1371/journal.pone.0035659
Project ID:
info:eu-repo/grantAgreement/MICINN//BFU2009-12022/ES/Impacto De La Duplicacion Genomica En La Innovacion Y Geometria Funcional De Arabidopsis Thaliana/
info:eu-repo/grantAgreement/SFI/SFI Research Frontiers Programme (RFP)/10%2FRFP%2FGEN2685/IE/Understanding the Role of Heat-Shock Proteins in Evolutionary Innovation/
Thanks:
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 ...[+]
Type: Artículo

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

Lynch, M. (2000). The Evolutionary Fate and Consequences of Duplicate Genes. Science, 290(5494), 1151-1155. doi:10.1126/science.290.5494.1151

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 [+]
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

Lynch, M. (2000). The Evolutionary Fate and Consequences of Duplicate Genes. Science, 290(5494), 1151-1155. doi:10.1126/science.290.5494.1151

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

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

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

Moran, N. A. (2002). Microbial Minimalism. Cell, 108(5), 583-586. doi:10.1016/s0092-8674(02)00665-7

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

Dykhuizen, D. E. (1998). Antonie van Leeuwenhoek, 73(1), 25-33. doi:10.1023/a:1000665216662

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

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

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

Dyall, S. D. (2004). Ancient Invasions: From Endosymbionts to Organelles. Science, 304(5668), 253-257. doi:10.1126/science.1094884

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

Lynch, M., & Conery, J. S. (2003). The Origins of Genome Complexity. Science, 302(5649), 1401-1404. doi:10.1126/science.1089370

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

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

Dagan, T., & Martin, W. (2006). Genome Biology, 7(10), 118. doi:10.1186/gb-2006-7-10-118

Kimura, M. (1983). The Neutral Theory of Molecular Evolution. doi:10.1017/cbo9780511623486

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

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

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

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

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

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

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

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

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

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

Gu, X. (2001). Mathematical Modeling for Functional Divergence after Gene Duplication. Journal of Computational Biology, 8(3), 221-234. doi:10.1089/10665270152530827

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Tamas, I. (2002). 50 Million Years of Genomic Stasis in Endosymbiotic Bacteria. Science, 296(5577), 2376-2379. doi:10.1126/science.1071278

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

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

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

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

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

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

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

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

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

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

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

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

Cascales, E., & Christie, P. J. (2003). The versatile bacterial type IV secretion systems. Nature Reviews Microbiology, 1(2), 137-149. doi:10.1038/nrmicro753

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

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

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

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

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

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

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

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

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

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

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

Yang, Z. (2007). PAML 4: Phylogenetic Analysis by Maximum Likelihood. Molecular Biology and Evolution, 24(8), 1586-1591. doi:10.1093/molbev/msm088

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

[-]

recommendations

 

This item appears in the following Collection(s)

Show full item record