Evolutionary dynamics of insertion sequences in relation to the evolutionary histories of the chromosome and symbiotic plasmid genes of Rhizobium etli populations

Applied and Environmental Microbiology

Volumn 76, Issue 19, 2010, Pages 6504-6513

  Lozano, Luis ^a   Hernández González, Ismael ^a   Bustos, Patricia ^a   Santamaría, Rosa I ^a   Souza, Valeria ^b   Young, J Peter W ^c   Dávila, Guillermo ^a   González, Víctor ^a  

^a INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

^b INSTITUTO DE ECOLOGÍA   (Mexico)

^c UNIVERSITY OF YORK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CONTEXT CONSERVATION; EVOLUTIONARY DYNAMICS; EVOLUTIONARY HISTORY; GENETIC DIFFERENTIATION; GENETIC ELEMENTS; GEOGRAPHICAL ORIGINS; HIGHER-DEGREE; HOUSEKEEPING GENE; INSERTION SEQUENCES; ME-XICO; NITROGEN FIXING BACTERIA; NUCLEOTIDE DIVERSITY; POPULATION GENETIC ANALYSIS; PRESENCE/ABSENCE; RECOMBINATION EVENTS; RHIZOBIUM ETLI; RHIZOBIUM STRAIN;

MICROBIOLOGY; NITROGEN FIXATION;

GENES;

BACTERIAL DNA; BACTERIAL PROTEIN;

BACTERIUM; CHROMOSOME; DIVERGENCE; EVOLUTIONARY THEORY; GENE; GENETIC DIFFERENTIATION; PLASMID; RECOMBINATION; SYMBIOSIS;

ARTICLE; BACTERIAL CHROMOSOME; CHEMISTRY; CLUSTER ANALYSIS; DNA SEQUENCE; GENETIC POLYMORPHISM; GENETICS; MEXICO; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASMID; POLYMERASE CHAIN REACTION; RHIZOBIUM ETLI; SEQUENCE HOMOLOGY; TRANSPOSON;

BACTERIAL PROTEINS; CHROMOSOMES, BACTERIAL; CLUSTER ANALYSIS; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; EVOLUTION, MOLECULAR; MEXICO; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLASMIDS; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; RHIZOBIUM ETLI; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY;

BACTERIA (MICROORGANISMS); PROKARYOTA; RHIZOBIACEAE; RHIZOBIUM; RHIZOBIUM ETLI;

EID: 78049295691     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01001-10     Document Type: Article

References (44)

1. Altschul, S., T. Madden, A. Schaffer, J. Zhang, Z. Zhang, W. Millar, and D. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Amadou, C., G. Pascal, S. Mangenot, M. Glew, C. Bontemps, D. Capela, S. Carrere, S. Cruveiller, C. Dossat, A. Lajus, M. Marchetti, V. Poinsot, B. Rouy, Z. Servin, M. Saad, C. Schenowitz, V. Barbe, J. Batut, C. Medigue, and C. Masson-Boivin. 2008. Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Res. 18: 1472-1483.
3. Bailly, X., I. Olivieri, S. De Mita, J. C. Cleyet-Marel, and G. Bena. 2006. Recombination and selection shape the molecular diversity pattern of nitrogen-fixing Sinorhizobium sp. associated to Medicago. Mol. Ecol. 15:2719-2734.
4. Chandler, M., and J. Mahillon. 2002. Insertion sequences revisited, p. 305-366. In L. Craig et al. (ed.), Mobile DNA II. ASM Press, Washington, DC.
5. Crossman, L. C., S. Castillo-Ramírez, C. McAnnula, L. Lozano, G. S. Vernikos, J. L. Acosta, Z. F. Ghazoui, I. Hernández-González, G. Meakin, A. W. Walker, M. F. Hynes, J. P. Young, J. A. Downie, D. Romero, A. W. Johnston, G. Dávila, J. Parkhill, and V. González. 2008. A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria. PloS ONE 3:e2567.
6. Doolittle, W. F., and C. Sapienza. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284:601-603.
7. Edgar, R. 2004. MUSCLE: a multiple sequence alignment method withreduced time and space complexity. BMC Bioinform. 5:113.
8. Escobar-Páramo, P., S. Ghosh, and J. DiRuggiero. 2005. Evidence for genetic drift in the diversification of a geographically isolated population of the hyperthermophilic archaeon Pyrococcus. Mol. Biol. Evol. 22:2297-2303.
9. Filée, J., P. Siguier, and M. Chandler. 2007. Insertion sequence diversity in Archea. Microbiol. Mol. Biol. Rev. 71:121-157.
10. Flores, M., L. Morales, M. Avila, P. Bustos, V. González, D. Garcia, Y. Mora, X. Guo, J. Collado-Vides, D. Piñero, G. Davila, J. Mora, and R. Palacios. 2005. Diversification of DNA sequences in the symbiotic genome of Rhizobium etli. J. Bacteriol. 187:7185-7192.
11. Freiberg, C., R. Fellay, A. Bairoch, W. J. Broughton, A. Rosenthal, and X. Perret. 1997. Molecular basis of symbiosis between Rhizobium and legumes. Nature 387:394-401.
12. Galibert, F., T. M. Finan, S. R. Long, A. Puhler, P. Abola, F. Ampe, F. Barloy-Hubler, M. J. Barnett, A. Becker, P. Boistard, G. Bothe, M. Boutry, L. Bowser, J. Buhrmester, E. Cadieu, D. Capela, P. Chain, A. Cowie, R. W. Davis, S. Dreano, N. A. Federspiel, R. F. Fisher, S. Gloux, T. Godrie, A. Goffeau, B. Golding, J. Gouzy, M. Gurjal, I. Hernandez-Lucas, A. Hong, L. Huizar, R. W. Hyman, T. Jones, D. Kahn, M. L. Kahn, S. Kalman, D. H. Keating, E. Kiss, C. Komp, V. Lelaure, D. Masuy, C. Palm, M. C. Peck, T. M. Pohl, D. Portetelle, B. Purnelle, U. Ramsperger, R. Surzycki, P. Thebault, M. Vandenbol, F. J. Vorholter, S. Weidner, D. H. Wells, K. Wong, K. C. Yeh, and J. Batut. 2001. The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293:668-672.
13. Gasca, J. 2004. Genética de poblaciones de Rhizobium etli asociado a Phaseolus vulgaris en dos localidades del bajío mexicano. B.S. thesis. Istituto de Ecología, Universidad Nacional Autónoma de México, Mexico DF, Mexico.
14. González, V., R. Santamaría, P. Bustos, I. Hernandez-González, A. Medrano- Soto, G. Moreno-Hagelsieb, S. Janga, M. Ramirez, V. Jiménez-Jacinto, J. Collado-Vides, and G. Davila. 2006. The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. Proc. Natl. Acad. Sci. U. S. A. 103:3834-3839.
15. González, V., J. L. Acosta, R. Santamaría, P. Bustos, J. L. Fernandez, I. Hernandez-González, R. Diza, M. Flores, R. Palacios, J. Mora, and G. Davila. 2010. Conserved symbiotic plasmid DNA sequences in the multireplicon pangenomic structure of Rhizobium etli. Appl. Environ. Microbiol. 76:1604-1614.
16. Guindon, S., and O. Gascuel. 2002. Efficient biased estimation of evolutionary distances when substitution rates vary across sites. Mol. Biol. Evol. 19:534-543.
17. Huson, D. H., and D. Bryant. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23:254-267.
18. Kalia, A., A. K. Mukhopadhyay, G. Dailide, Y. Ito, T. Azuma, B. C. Wong, and D. E. Berg. 2004. Evolutionary dynamics of insertion sequences in Helicobacter pylori. J. Bacteriol. 186:7508-7520.
19. Kaneko, T., Y. Nakamura, S. Sato, E. Asamizu, T. Kato, S. Sasamoto, A. Watanabe, K. Idesawa, A. Ishikawa, K. Kawashima, T. Kimura, Y. Kishida, C. Kiyokawa, M. Kohara, M. Matsumoto, A. Matsuno, Y. Mochizuki, S. Nakayama, N. Nakazaki, S. Shimpo, M. Sugimoto, C. Takeuchi, M. Yamada, and S. Tabata. 2000. Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res. 7:331-338.
20. Kaneko, T., Y. Nakamura, S. Sato, K. Minamisawa, T. Uchiumi, S. Sasamoto, A. Watanabe, K. Idesawa, M. Iriguchi, K. Kawashima, M. Kohara, M. Matsumoto, S. Shimpo, H. Tsuruoka, T. Wada, M. Yamada, and S. Tabata. 2002. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 9:189-197. (Pubitemid 36307023)
21. Kidwell, M. G., and D. R. Lisch. 2002. Transposable elements as sources of genomic variation, p. 305-366. In L. Craig et al. (ed.), Mobile DNA II. ASM Press, Washington, DC.
22. Korber, B. 2000. HIV signature and sequence variation analysis, p. 55-72. In A. G. Rodrigo and G. H. Learn (ed.), Computational analysis of HIV molecular sequences. Kluwer Academic Publishers, Dordrecht, Netherlands.
23. Kurtz, S., A. Phullippy, A. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S. Salzberg. 2004. Versatile and open software for comparing large genomes. Genome Biol. 5:R12.
24. Kwak, M., and P. Gepts. 2009. Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae). Theor. Appl. Genet. 118:979-992.
25. Lenski, R., C. Winkwirth, and M. Riley. 2003. Rates of DNA sequence evolution in experimental populations of Escherichia coli during 20,000 generations, J. Mol. Evol. 56:498-508.
26. Librado, P., and J. Rozas. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452.
27. Mahillon, J., C. Léonard, and M. Chandler. 1999. IS elements as constituents of bacterial genomes. Res. Microbiol. 150:675-687.
28. Martin, D. P., C. Williamson, and D. Posada. 2005. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21:260-262.
29. Papadopoulos, D., D. Schneider, J. Meier-Eis, W. Arber, R. E. Lenski, M. Blot, et al. 1999. Genomic evolution during a 10,000-generation experiement with bacteria. Proc. Natl. Acad. Sci. U. S. A. 96:3807-3812.
30. Pérez-Mendoza, D., A. Dominguez-Ferreras, S. Munoz, M. J. Soto, J. Olivares, S. Brom, L. Girard, J. A. Herrera-Cervera, and J. Sanjuan. 2004. Identification of functional mob regions in Rhizobium etli: evidence for self-transmissibility of the symbiotic plasmid pRetCFN42d. J. Bacteriol. 186: 5753-5761.
31. Posada, D., and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.
32. Ramsay, J. P., J. T. Sullivan, G. S. Stuart, I. L. Lamont, and C. W. Ronson. 2006. Excision and transfer of the Mesorhizobium loti R7A symbiosis island requires an integrase IntS, a novel recombination directionality factor RdfS, and a putative relaxase Rlxs. Mol. Microbiol. 62:723-734.
33. Rodríguez-Navarro, D., A. Buendia, M. Camacho, M. Lucas, and C. Santamaria. 2000. Characterization of Rhizobium spp. Bean isolates from southwest Spain. Soil Biol. Biochem. 32:1601-1613.
34. Schneider, D., and R. Lenski. 2004. Dynamics of insertion sequence elements during experimental evolution of bacteria. Res. Microbiol. 155:319-327.
35. Siguier, P., J. Filée, and M. Chandler. 2006. Insertion sequences in prokaryotic genomes. Curr. Opin. Microbiol. 9:1-6.
36. Silva, C., P. Vinuesa, L. Eguiarte, E. Martínez-Romero, and V. Souza. 2003. Rhizobium etli and Rhizobium gallicum nodulate common bean (Phaseolus vulgaris) in a traditionally managed milpa plot in Mexico: population genetics and biogeographic implications. Appl. Environ. Microbiol. 69:884-893.
37. Silva, C., P. Vinuesa, L. Eguiarte, V. Souza, and E. Martínez- Romero. 2005. Evolutionary genetics and biogeographic structure of Rhizobium gallicum sensu lato, a widely distributed bacterial symbiont of diverse legumes. Mol. Ecol. 14:4033-4050.
38. Slatkin, M. 1985. Genetic differentiation of transposable elements under mutation and unbiased gene conversion. Genetics 110:145-158.
39. Sullivan, J. T., and C. W. Ronson. 1998. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. Proc. Natl. Acad. Sci. U. S. A. 95:5145-5149.
40. Sullivan, J. T., J. R. Trzebiatowski, R. W. Cruickshank, J. Gouzy, S. D. Brown, R. M. Elliot, D. J. Fleetwood, N. G. McCallum, U. Rossbach, G. S. Stuart, J. E. Weaver, R. J. Webby, F. J. De Bruijn, and C. W. Ronson. 2002. Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A. J. Bacteriol. 184:3086-3095.
41. Touchon, M., and E. Rocha. 2007. Causes of insertion sequences abundance in prokaryotic genomes. Mol. Biol. Evol. 4:969-981.
42. Wagner, A. 2006. Periodic extinctions of transposable elements in bacterial lineales: evidence from intragenomic variation in multiple genomes. Mol. Biol. Evol. 23:723-733.
43. Young, J. P., L. C. Crossman, A. W. Johnston, N. R. Thomson, Z. F. Ghazoui, K. H. Hull, M. Wexler, A. R. Curson, J. D. Todd, P. S. Poole, T. H. Mauchline, A. K. East, M. A. Quail, C. Churcher, C. Arrowsmith, I. Cherevach, T. Chillingworth, K. Clarke, A. Cronin, P. Davis, A. Fraser, Z. Hance, H. Hauser, K. Jagels, S. Moule, K. Mungall, H. Norbertczak, E. Rabbinowitsch, M. Sanders, M. Simmonds, S. Whitehead, and J. Parkhill. 2006. The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol. 7:R34.
44. Zeigler, D. R. 2003. Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int. J. Syst. Evol. Microbiol. 53:1893-1900.