Divergence among genes encoding the elongation factor Tu of Yersinia species

Journal of Bacteriology

Volumn 190, Issue 22, 2008, Pages 7548-7558

  Isabel, Sandra ^a   Leblanc, Éric ^a   Boissinot, Maurice ^a   Boudreau, Dominique K ^a   Grondin, Myrian ^a   Picard, François J ^a   Martel, Eric A ^a   Parham, Nicholas J ^a   Chain, Patrick S G ^b,c,d   Bader, Douglas E ^e   Mulvey, Michael R ^f   Bryden, Louis ^f   Roy, Paul H ^a   Ouellette, Marc ^a   Bergeron, Michel G ^a  

^a LAVAL UNIVERSITY   (Canada)

^b LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^c DOE JOINT GENOME INSTITUTE   (United States)

^d Michigan State University ^*  (United States)

^e DEFENCE RESEARCH AND DEVELOPMENT CANADA   (Canada)

^f PUBLIC HEALTH AGENCY OF CANADA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ELONGATION FACTOR TU;

ARTICLE; CLADISTICS; CONTROLLED STUDY; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENETIC TREE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; YERSINIA;

ENTEROBACTERIACEAE; YERSINIA;

EID: 55549106103     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.01067-08     Document Type: Article

References (63)

1. Abdulkarim, F., and D. Hughes. 1996. Homologous recombination between the tuf genes of Salmonella typhimurium. J. Mol. Biol. 260:506-522.
2. Achtman, M., K. Zurth, G. Morelli, G. Torrea, A. Guiyoule, and E. Carniel. 1999. Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA 96:14043-14048.
3. Arwidsson, O., and D. Hughes. 2004. Evidence against reciprocal recombination as the basis for tuf gene conversion in Salmonella enterica serovar Typhimurium. J. Mol. Biol. 338:463-467.
4. Bell, K. S., M. Sebaihia, L. Pritchard, M. T. Holden, L. J. Hyman, M. C. Holeva, N. R. Thomson, S. D. Bentley, L. J. Churcher, K. Mungall, R. Atkin, N. Bason, K. Brooks, T. Chillingworth, K. Clark, J. Doggett, A. Fraser, Z. Hance, H. Hauser, K. Jagels, S. Moule, H. Norbertczak, D. Ormond, C. Price, M. A. Quail, M. Sanders, D. Walker, S. Whitehead, G. P. Salmond, P. R. Birch, J. Parkhill, and I. K. Toth. 2004. Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. Proc. Natl. Acad. Sci. USA 101:11105-11110.
5. Berchtold, H., L. Reshetnikova, C. O. Reiser, N. K. Schirmer, M. Sprinzl, and R. Hilgenfeld. 1993. Crystal structure of active elongation factor Tu reveals major domain rearrangements. Nature 365:126-132.
6. Bercovier, H., H. H. Mollaret, J. M. Alonso, J. Brault, G. R. Fanning, A. G. Steigerwalt, and D. J. Brenner. 1980. Intra- and interspecies relatedness of Yersinia pestis by DNA hybridization and its relationship to Yersinia pseudotuberculosis. Curr. Microbiol. 4:225-229.
7. Bryant, D., and V. Moulton. 2004. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 21:255-265.
8. Caldas, T., A. El Yaagoubi, and G. Richarme. 1998. Chaperone properties of bacterial elongation factor EF-Tu. J. Biol. Chem. 273:11478-11482.
9. Chain, P. S., E. Carniel, F. W. Larimer, J. Lamerdin, P. O. Stoutland, W. M. Regala, A. M. Georgescu, L. M. Vergez, M. L. Land, V. L. Motin, R. R. Brubaker, J. Fowler, J. Hinnebusch, M. Marceau, C. Medigue, M. Simonet, V. Chenal-Francisque, B. Souza, D. Dacheux, J. M. Elliott, A. Derbise, L. J. Hauser, and E. Garcia. 2004. Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA 101:13826-13831.
10. Chain, P. S., P. Hu, S. A. Malfatti, L. Radnedge, F. Larimer, L. M. Vergez, P. Worsham, M. C. Chu, and G. L. Andersen. 2006. Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. J. Bacteriol. 188:4453-4463.
11. Chenna, R., H. Sugawara, T. Koike, R. Lopez, T. J. Gibson, D. G. Higgins, and J. D. Thompson. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31:3497-3500.
12. Cilia, V., B. Lafay, and R. Christen. 1996. Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at specific level. Mol. Biol. Evol. 13:451-461.
13. Coenye, T., and P. Vandamme. 2003. Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes. FEMS Microbiol. Lett. 228:45-49.
14. Demarta, A., S. De Respinis, M. Dolina, and R. Peduzzi. 2004. Molecular typing of Yersinia frederiksenii strains by means of 16S rDNA and gyrB genes sequence analyses. FEMS Microbiol. Lett. 238:423-428.
15. Deng, W., V. Burland, G. Plunkett III, A. Boutin, G. F. Mayhew, P. Liss, N. T. Perna, D. J. Rose, B. Mau, S. Zhou, D. C. Schwartz, J. D. Fetherston, L. E. Lindler, R. R. Brubaker, G. V. Plano, S. C. Straley, K. A. McDonough, M. L. Nilles, J. S. Matson, F. R. Blattner, and R. D. Perry. 2002. Genome sequence of Yersinia pestis KIM. J. Bacteriol. 184:4601-4611.
16. Dolina, M., V. Gaia, and R. Peduzzi. 1995. Molecular typing of Yersinia frederiksenii strains by means of ribotyping and DNA-DNA hybridization. Contrib. Microbiol. Immunol. 13:140-144.
17. Dolina, M., and R. Peduzzi. 1993. Population genetics of human, animal, and environmental Yersinia strains. Appl. Environ. Microbiol. 59:442-450.
18. Duchaud, E., C. Rusniok, L. Frangeul, C. Buchrieser, A. Givaudan, S. Taourit, S. Bocs, C. Boursaux-Eude, M. Chandler, J. F. Charles, E. Dassa, R. Derose, S. Derzelle, G. Freyssinet, S. Gaudriault, C. Medigue, A. Lanois, K. Powell, P. Siguier, R. Vincent, V. Wingate, M. Zouine, P. Glaser, N. Boemare, A. Danchin, and F. Kunst. 2003. The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens. Nat. Biotechnol. 21:1307-1313.
19. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
20. Grunberg-Manago, M. 1996. Regulation of the expression of aminoacyl-tRNA synthetases and translation factors, 2nd ed., vol. 2. ASM Press, Washington, DC.
21. Han, Y., J. Qiu, Z. Guo, H. Gao, Y. Song, D. Zhou, and R. Yang. 2007. Comparative transcriptomics in Yersinia pestis: a global view of environmental modulation of gene expression. BMC Microbiol. 7:96.
22. Hashimoto, J. G., B. S. Stevenson, and T. M. Schmidt. 2003. Rates and consequences of recombination between rRNA operons. J. Bacteriol. 185:966-972.
23. Heidelberg, J. F., J. A. Eisen, W. C. Nelson, R. A. Clayton, M. L. Gwinn, R. J. Dodson, D. H. Haft, E. K. Hickey, J. D. Peterson, L. Umayam, S. R. Gill, K. E. Nelson, T. D. Read, H. Tettelin, D. Richardson, M. D. Ermolaeva, J. Vamathevan, S. Bass, H. Qin, I. Dragoi, P. Sellers, L. McDonald, T. Utterback, R. D. Fleishmann, W. C. Nierman, O. White, S. L. Salzberg, H. O. Smith, R. R. Colwell, J. J. Mekalanos, J. C. Venter, and C. M. Fraser. 2000. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406:477-483.
24. Henikoff, S., and J. G. Henikoff. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89:10915-10919.
25. Howard, S. L., M. W. Gaunt, J. Hinds, A. A. Witney, R. Stabler, and B. W. Wren. 2006. Application of comparative phylogenomics to study the evolution of Yersinia enterocolitica and to identify genetic differences relating to pathogenicity. J. Bacteriol. 188:3645-3653.
26. Hughes, D. 2000. Co-evolution of the tuf genes links gene conversion with the generation of chromosomal inversions. J. Mol. Biol. 297:355-364.
27. Huson, D. H., and D. Bryant. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23:254-267.
28. Ibrahim, A., B. M. Goebel, W. Liesack, M. Griffiths, and E. Stackebrandt. 1993. The phylogeny of the genus Yersinia based on 16S rDNA sequences. FEMS Microbiol. Lett. 114:173-177.
29. International Journal of Systematic and Evolutionary Microbiology. 2000. IJSEM validation list no. 75. 50:1415-1417.
30. International Journal of Systematic Bacteriology. 1981. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. List no. 7. Int. J. Syst. Bacteriol. 31:382-383.
31. Judicial Commission of the International Committee on Systematic Bacteriology. 1985. Opinion 60. Rejection of the name Yersinia pseudotuberculosis subsp. pestis (van Loghen) Bercovieri et al. 1981 and conversion of the name Yersinia pestis (Lehmann and Neumann) van Loghem 1944 for the plague bacillus. Int. J. Syst. Bacteriol. 35:540.
32. Ke, D., M. Boissinot, A. Huletsky, F. J. Picard, J. Frenette, M. Ouellette, P. H. Roy, and M. G. Bergeron. 2000. Evidence for horizontal gene transfer in evolution of elongation factor Tu in enterococci. J. Bacteriol. 182:6913-6920.
33. Kellogg, D. E., I. Rybalkin, S. Chen, N. Mukhamedova, T. Vlasik, P. D. Siebert, and A. Chenchik. 1994. TaqStart Antibody™: "hot start" PCR facilitated by a neutralizing monoclonal antibody directed against Taq DNA polymerase. BioTechniques 16:2888-2893.
34. Kloepper, T. H., and D. H. Huson. 2008. Drawing explicit phylogenetic networks and their integration into SplitsTree. BMC Evol. Biol. 8:22.
35. Kondrashov, F. A., T. A. Gurbich, and P. K. Vlasov. 2007. Selection for functional uniformity of tuf duplicates in gamma-proteobacteria. Trends Genet. 23:215-218.
36. Kotetishvili, M., A. Kreger, G. Wauters, J. G. Morris, Jr., A. Sulakvelidze, and O. C. Stine. 2005. Multilocus sequence typing for studying genetic relationships among Yersinia species. J. Clin. Microbiol. 43:2674-2684.
37. Reference deleted.
38. Kushiro, M., M. Shimizu, and K. Tomita. 1987. Molecular cloning and sequence determination of the tuf gene coding for the elongation factor Tu of Thermus thermophilus HB8. Eur. J. Biochem. 170:93-98.
39. Lathe, W. C., III, and P. Bork. 2001. Evolution of tuf genes: ancient duplication, differential loss and gene conversion. FEBS Lett. 502:113-116.
40. Liao, X., T. Ying, H. Wang, J. Wang, Z. Shi, E. Feng, K. Wei, Y. Wang, X. Zhang, L. Huang, G. Su, and P. Huang. 2003. A two-dimensional proteome map of Shigella flexneri. Electrophoresis 24:2864-2882.
41. Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
42. Martineau, F., F. J. Picard, D. Ke, S. Paradis, P. H. Roy, M. Ouellette, and M. G. Bergeron. 2001. Development of a PCR assay for identification of staphylococci at genus and species levels. J. Clin. Microbiol. 39:2541-2547.
43. Mattatall, N. R., and K. E. Sanderson. 1996. Salmonella typhimurium LT2 possesses three distinct 23S rRNA intervening sequences. J. Bacteriol. 178:2272-2278.
44. McClelland, M., K. E. Sanderson, J. Spieth, S. W. Clifton, P. Latreille, L. Courtney, S. Porwollik, J. Ali, M. Dante, F. Du, S. Hou, D. Layman, S. Leonard, C. Nguyen, K. Scott, A. Holmes, N. Grewal, E. Mulvaney, E. Ryan, H. Sun, L. Florea, W. Miller, T. Stoneking, M. Nhan, R. Waterston, and R. K. Wilson. 2001. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413:852-856.
45. Merhej, V., T. Adekambi, I. Pagnier, D. Raoult, and M. Drancourt. 2008. Yersinia massiliensis sp. nov., isolated from fresh water. Int. J. Syst. Evol. Microbiol. 58:779-784.
46. Neubauer, H., A. Stojanka, H. Andreas, F. Ernst-J.ürgen, and M. Hermann. 2000. Yersina enterocolitica 16S rRNA gene types belong to the same genospecies but form three homology groups. Int. J. Med. Microbiol. 290:61-64.
47. Paradis, S., M. Boissinot, N. Paquette, S. D. Bélanger, E. A. Martel, D. K. Boudreau, F. J. Picard, M. Ouelette, P. H. Roy, and M. G. Bergeron. 2005. Phylogeny of the Enterobacteriaceae based on genes encoding elongation factor TU and F-ATPase β-subunit. Int. J. Syst. Evol. Microbiol. 55:2013-2025.
48. Parkhill, J., B. W. Wren, N. R. Thomson, R. W. Titball, M. T. Holden, M. B. Prentice, M. Sebaihia, K. D. James, C. Churcher, K. L. Mungall, S. Baker, D. Basham, S. D. Bentley, K. Brooks, A. M. Cerdeno-Tarraga, T. Chillingworth, A. Cronin, R. M. Davies, P. Davis, G. Dougan, T. Feltwell, N. Hamlin, S. Holroyd, K. Jagels, A. V. Karlyshev, S. Leather, S. Moule, P. C. Oyston, M. Quail, K. Rutherford, M. Simmonds, J. Skelton, K. Stevens, S. Whitehead, and B. G. Barrell. 2001. Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413:523-527.
49. Prentice, M. B., and L. Rahalison. 2007. Plague. Lancet 369:1196-1207.
50. Sprague, L. D., and H. Neubauer. 2005. Yersinia aleksiciae sp. nov. Int. J. Syst. Evol. Microbiol. 55:831-835.
51. Sprague, L. D., H. C. Scholz, S. Amann, H. J. Busse, and H. Neubauer. 2008. Yersinia similis sp. nov. Int. J. Syst. Evol. Microbiol. 58:952-958.
52. Sulakvelidze, A. 2000. Yersiniae other than Y. enterocolitica, Y. pseudotuberculosis, and Y. pestis: the ignored species. Microbes Infect. 2:497-513.
53. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
54. Tamura, K., and S. Kumar. 2002. Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Mol. Biol. Evol. 19:1727-1736.
55. Tamura, K., M. Nei, and S. Kumar. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl. Acad. Sci. USA 101:11030-11035.
56. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
57. Thomson, N. R., S. Howard, B. W. Wren, M. T. Holden, L. Crossman, G. L. Challis, C. Churcher, K. Mungall, K. Brooks, T. Chillingworth, T. Feltwell, Z. Abdellah, H. Hauser, K. Jagels, M. Maddison, S. Moule, M. Sanders, S. Whitehead, M. A. Quail, G. Dougan, J. Parkhill, and M. B. Prentice. 2006. The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081. PLoS Genet. 2:e206.
58. Ursing, J., and S. Aleksic. 1995. Yersinia frederiksenii, a genotypically heterogeneous species with few differential characteristics. Contrib. Microbiol. Immunol. 13:112-116.
59. Walsh, J. B. 1987. Sequence-dependent gene conversion: can duplicated genes diverge fast enough to escape conversion? Genetics 117:543-557.
60. Wayne, L. G. 1986. Actions of the Judicial Commission of the International Committee on Systematic Bacteriology on requests for opinions published in 1983 and 1984. Int. J. Syst. Bacteriol. 36:357-358.
61. Welch, R. A., V. Burland, G. Plunkett III, P. Redford, P. Roesch, D. Rasko, E. L. Buckles, S. R. Liou, A. Boutin, J. Hackett, D. Stroud, G. F. Mayhew, D. J. Rose, S. Zhou, D. C. Schwartz, N. T. Perna, H. L. Mobley, M. S. Donnenberg, and F. R. Blattner. 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 99:17020-17024.
62. Williams, J. E. 1984. Proposal to reject the new combination Yersina pseudotuberculosis subsp. pestis for violation of the first principle of the International Code of Nomenclature of Bacteria: request for an opinion. Int. J. Syst. Bacteriol. 34:268-269.
63. Zhou, D., Z. Tong, Y. Song, Y. Han, D. Pei, X. Pang, J. Zhai, M. Li, B. Cui, Z. Qi, L. Jin, R. Dai, Z. Du, J. Wang, Z. Guo, J. Wang, P. Huang, and R. Yang. 2004. Genetics of metabolic variations between Yersinia pestis biovars and the proposal of a new biovar, microtus. J. Bacteriol. 186:5147-5152.