Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: A comparative genomics approach

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 15, 2006, Pages 5977-5982

  Chen, Swaine L ^a   Hung, Chia Seui ^a,c   Xu, Jian ^a   Reigstad, Christopher S ^a   Magrini, Vincent ^a   Sabo, Aniko ^a,d   Blasiar, Darin ^a   Bieri, Tamberlyn ^a   Meyer, Rekha R ^a   Ozersky, Philip ^a   Armstrong, Jon R ^a   Fulton, Robert S ^a   Latreille, J Phillip ^a   Spieth, John ^a   Hooton, Thomas M ^b   Mardis, Elaine R ^a   Hultgren, Scott J ^a   Gordon, Jeffrey I ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c Sequoia Sciences Inc   (United States)

^d BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

Ecogenomics; Uropathogenic Escherichia coli

Indexed keywords

DNA;

ADAPTATION; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CASE REPORT; CELL SURFACE; COMPARATIVE GENOMICS; CYSTITIS; DNA METABOLISM; ECOGENOMICS; ECOLOGICAL GENETICS; ENVIRONMENT; GENE ENVIRONMENT INTERACTION; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC SELECTION; GENOMICS; HUMAN; MATHEMATICAL ANALYSIS; MAXIMUM LIKELIHOOD METHOD; MICROFLORA; NONHUMAN; NUCLEOTIDE SEQUENCE; NUTRIENT UPTAKE; PRIORITY JOURNAL; UNINDEXED SEQUENCE; URINARY TRACT INFECTION; UROPATHOGENIC ESCHERICHIA COLI; VALIDATION PROCESS;

CHROMOSOMES, BACTERIAL; ESCHERICHIA COLI; ESCHERICHIA COLI INFECTIONS; GENOME, BACTERIAL; HUMANS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; RECOMBINATION, GENETIC; SELECTION (GENETICS); URINARY TRACT INFECTIONS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 33645827531     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0600938103     Document Type: Article

References (63)

1. McFeters, G. A., Barry, J. P. & Howington, J. P. (1993) Water Res. 27, 645-650.
2. Keseler, I. M., Collado-Vides, J., Gama-Castro, S., Ingraham, J., Paley, S., Paulsen, I. T., Peralta-Gil, M. & Karp, P. D. (2005) Nucleic Acids Res. 33, D334-D337.
3. Blattner, F. R., Plunkett, G., 3rd, Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., et al. (1997) Science 277, 1453-1474.
4. Welch, R. A., Burland, V., Plunkett, G., 3rd, Redford, P., Roesch, P., Rasko, D., Buckles, E. L., Liou, S. R., Boutin, A., Hackett, J., et al. (2002) Proc. Natl. Acad. Sci. USA 99, 17020-17024.
5. Perna, N. T., Plunkett, G., 3rd, Burland, V., Mau, B., Glasner, J. D., Rose, D. J., Mayhew, G. F., Evans, P. S., Gregor, J., Kirkpatrick, H. A., et al. (2001) Nature 409, 529-533.
6. Hayashi, T., Makino, K., Ohnishi, M., Kurokawa, K., Ishii, K., Yokoyama, K., Han, C. G., Ohtsubo, E., Nakayama, K., Murata, T., et al. (2001) DNA Res. 8, 11-22.
7. Wei, J., Goldberg, M. B., Burland, V., Venkatesan, M. M., Deng, W., Fournier, G., Mayhew, G. F., Plunkett, G., 3rd, Rose, D. J., Darling, A., et al. (2003) Infect. Immun. 71, 2775-2786.
8. Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., Wang, J., Liu, H., Yang, J., Yang, F., et al. (2002) Nucleic Acids Res. 30, 4432-4441.
9. Tettelin, H., Masignani, V., Cieslewicz, M. J., Donati, C., Medini, D., Ward, N. L., Angiuoli, S. V., Crabtree, J., Jones, A. L., Durkin, A. S., et al. (2005) Proc. Natl. Acad. Sci. USA 102, 13950-13955.
10. Mulvey, M. A., Lopez-Boado, Y. S., Wilson, C. L., Roth, R., Parks, W. C., Heuser, J. & Hultgren, S. J. (1998) Science 282, 1494-1497.
11. Martinez, J. J., Mulvey, M. A., Schilling, J. D., Pinkner, J. S. & Hultgren, S. J. (2000) EMBO J. 19, 2803-2812.
12. Justice, S. S., Hung, C., Theriot, J. A., Fletcher, D. A., Anderson, G. G., Footer, M. J. & Hultgren, S. J. (2004) Proc. Natl. Acad. Sci. USA 101, 1333-1338.
13. Anderson, G. G., Palermo, J. J., Schilling, J. D., Roth, R., Heuser, J. & Hultgren, S. J. (2003) Science 301, 105-107.
14. Mulvey, M. A., Schilling, J. D. & Hultgren, S. J. (2001) Infect. Immun. 69, 4572-4579.
15. Zhang, L., Foxman, B., Manning, S. D., Tallman, P. & Marrs, C. F. (2000) Infect. Immun. 68, 2009-2015.
16. Guyer, D. M., Kao, J. S. & Mobley, H. L. (1998) Infect. Immun. 66, 4411-4417.
17. Sannes, M. R., Kuskowski, M. A., Owens, K., Gajewski, A. & Johnson, J. R. (2004) J. Infect. Dis. 190, 2121-2128.
18. Srinivasan, U., Foxman, B. & Marrs, C. F. (2003) J. Clin. Microbiol. 41, 285-289.
19. Sokurenko, E. V., Chesnokova, V., Dykhuizen, D. E., Ofek, I., Wu, X. R., Krogfelt, K. A., Struve, C., Schembri, M. A. & Hasty, D. L. (1998) Proc. Natl. Acad. Sci. USA 95, 8922-8926.
20. Kreitman, M. (2000) Annu. Rev. Genom. Hum. Genet. 1, 539-559.
21. Fay, J. C. & Wu, C. I. (2003) Annu. Rev. Genom. Hum. Genet. 4, 213-235.
22. Yang, Z. & Nielsen, R. (2002) Mol. Biol. Evol. 19, 908-917.
23. Suzuki, Y. & Nei, M. (2001) Mol. Biol. Evol. 18, 2179-2185.
24. Guttman, D. S. & Dykhuizen, D. E. (1994) Science 266, 1380-1383.
25. Feil, E. J., Maiden, M. C., Achtman, M. & Spratt, B. G. (1999) Mol. Biol. Evol. 16, 1496-1502.
26. Wiuf, C., Christensen, T. & Kein, J. (2001) Mol. Biol. Evol. 18, 1929-1939.
27. Jakobsen, I. B. & Easteal, S. (1996) Comput. Appl. Biosci. 12, 291-295.
28. Feil, E. J. & Spratt, B. G. (2001) Annu. Rev. Microbiol. 55, 561-590.
29. Anisimova, M., Nielsen, R. & Yang, Z. (2003) Genetics 164, 1229-1236.
30. Suzuki, Y. & Nei, M. (2004) Mol. Biol. Evol. 21, 914-921.
31. Posada, D. (2002) Mol. Biol. Evol. 19, 708-717.
32. Wong, W. S., Yang, Z., Goldman, N. & Nielsen, R. (2004) Genetics 168, 1041-1051.
33. Anisimova, M., Bielawski, J. P. & Yang, Z. (2002) Mol. Biol. Evol. 19, 950-958.
34. Anisimova, M., Bielawski, J. P. & Yang, Z. (2001) Mol. Biol. Evol. 18, 1585-1592.
35. Denamur, E., Bonacorsi, S., Giraud, A., Duriez, P., Hilali, F., Amorin, C., Bingen, E., Andremont, A., Picard, B., Taddei, F., et al. (2002) J. Bacteriol. 184, 605-609.
36. Labat, F., Pradillon, O., Garry, L., Peuchmaur, M., Fantin, B. & Denamur, E. (2005) FEMS Immunol. Med. Microbiol. 44, 317-321.
37. Viswanathan, M., Burdett, V., Baitinger, C., Modrich, P. & Lovett, S. T. (2001) J. Biol. Chem. 276, 31053-31058.
38. Burdett, V., Baitinger, C., Viswanathan, M., Lovett, S. T. & Modrich, P. (2001) Proc. Natl. Acad. Sci. USA 98, 6765-6770.
39. Dermic, D., Halupecki, E., Zahradka, D. & Petranovic, M. (2005) Res. Microbiol. 156, 304-311.
40. Fitzpatrick, D. A., Creevey, C. J. & McInerney, J. O. (2005) J. Mol. Evol. 61, 90-98.
41. Finlay, B. B. & Falkow, S. (1997) Microbiol Mol. Biol. Rev. 61, 136-169.
42. Murray, G. L., Attridge, S. R. & Morona, R. (2003) Mol. Microbiol. 47, 1395-1406.
43. West, N. P., Sansonetti, P., Mounier, J., Exley, R. M., Parsot, C., Guadagnini, S., Prevost, M. C., Prochnicka-Chalufour, A., Delepierre, M., Tanguy, M., et al. (2005) Science 307, 1313-1317.
44. Svanborg, C., Godaly, G. & Hedlund, M. (1999) Curr. Opin. Microbiol. 2, 99-105.
45. Pece, S., Giuliani, G., Di Leo, A., Fumarola, D., Antonaci, S. & Jirillo, E. (1997) Recent Prog. Med. 88, 237-241.
46. Roux, A., Beloin, C. & Ghigo, J. M. (2005) J. Bacteriol. 187, 1001-1013.
47. Nikaido, H. (1996) in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, eds. NeidHardt, F. C., Curtiss, R., Ingraham, J. L., Lin, E. C. C., Low, K. B., Magasanik, B., Reznikoff, W. S., Riley, M., Schaecter, M. & Umbarger, H. E. (Am. Soc. Microbiol., Washington, DC), pp. 29-47.
48. Snyder, J. A., Haugen, B. J., Buckles, E. L., Lockatell, C. V., Johnson, D. E., Donnenberg, M. S., Welch, R. A. & Mobley, H. L. (2004) Infect. Immun. 72, 6373-6381.
49. Batchelor, E., Walthers, D., Kenney, L. J. & Goulian, M. (2005) J. Bacteriol. 187, 5723-5731.
50. Bernardini, M. L., Sanna, M. G., Fontaine, A. & Sansonetti, P. J. (1993) Infect. Immun. 61, 3625-3635.
51. Heidrich, C., Templin, M. F., Ursinus, A., Merdanovic, M., Berger, J., Schwarz, H., de Pedro, M. A. & Holtje, J. V. (2001) Mol. Microbiol. 41, 167-178.
52. Katayama, T., Takata, M. & Sekimizu, K. (1997) Mol. Microbiol. 26, 687-697.
53. Nurse, P., Levine, C., Hassing, H. & Marians, K. J. (2003) J. Biol. Chem. 278, 8653-8660.
54. Weinberg, E. D. (1978) Microbiol. Rev. 42, 45-66.
55. Janke, B., Dobrindt, U., Hacker, J. & Blum-Oehler, G. (2001) FEMS Microbiol. Lett. 199, 61-66.
56. Woodrow, G. C., Young, I. G. & Gibson, F. (1979) Biochim. Biophys. Acta 582, 145-153.
57. Zhang, Z. & Gerstein, M. (2003) J. Biol. 2, 11.1-11.4.
58. Wagner, G. P., Fried, C., Prohaska, S. J. & Stadler, P. F. (2004) Mol. Biol. Evol. 21, 2116-2121.
59. Lee, W. & Chen, S. L. (2002) BioTechniques 33, 1334-1341.
60. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994) Nucleic Acids Res. 22, 4673-4680.
61. Sawyer, S. (1989) Mol. Biol. Evol. 6, 526-538.
62. Felsenstein, J. (1989) Cladistics 5, 164-166.
63. Yang, Z. (1997) Comput. Appl. Biosci. 13, 555-556.