Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T

Infection and Immunity

Volumn 71, Issue 5, 2003, Pages 2775-2786

  Wei, J ^a   Goldberg, M B ^b   Burland, V ^a   Venkatesan, M M ^c   Deng, W ^a   Fournier, G ^b   Mayhew, G F ^a   Plunkett III, G ^a   Rose, D J ^a   Darling, A ^a   Mau, B ^a   Perna, N T ^a   Payne, S M ^d   Runyen Janecky, L J ^d   Zhou, S ^a   Schwartz, D C ^a   Blattner, F R ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

^c WALTER REED ARMY INSTITUTE OF RESEARCH   (United States)

^d UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL STRAIN; BACTERIAL VIRULENCE; COMPARATIVE GENOMIC HYBRIDIZATION; DIARRHEA; DYSENTERY; ESCHERICHIA COLI; GENE INSERTION; GENE REARRANGEMENT; GENE SEQUENCE; HORIZONTAL GENE TRANSFER; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEROTYPE; SHIGELLA FLEXNERI;

BASE SEQUENCE; DNA TRANSPOSABLE ELEMENTS; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMICS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLASMIDS; SHIGELLA FLEXNERI;

EID: 0242416999     PISSN: 00199567     EISSN: None     Source Type: Journal    
DOI: 10.1128/IAI.71.5.2775-2786.2003     Document Type: Article

References (73)

1. Aderem, A., and R. J. Ulevitch. 2000. Toll-like receptors in the induction of the innate immune response. Nature 406:782-787.
2. Al-Hasani, K., I. R. Henderson, H. Sakellaris, K. Rajakumar, T. Grant, J. P. Nataro, R. Robins-Browne, and B. Adler. 2000. The sigA gene which is borne on the she pathogenicity island of Shigella flexneri 2a encodes an exported cytopathic protease involved in intestinal fluid accumulation. Infect. Immun. 68:2457-2463.
3. Anderson, R. J., M. F. Pasetti, M. B. Sztein, M. M. Levine, and F. R. Noriega. 2000. ΔguaBA attenuated Shigella flexneri2a strain CVD 1204 as a Shigella vaccine and as a live mucosal delivery system for fragment C of tetanus toxin. Vaccine 18:2193-2202.
4. Blattner, F. R., G. Plunkett III, C. A. Bloch, N. T. Perna, V. Burland, M. Riley, J. Collado-Vides, J. D. Glasner, C. K. Rode, G. F. Mayhew, J. Gregor, N. W. Davis, H. A. Kirkpatrick, M. A. Goeden, D. J. Rose, B. Mau, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453-1474.
5. Brenner, D. J., G. R. Fanning, A. G. Steigerwalt, I. Ørskov, and F. Ørskov. 1972. Polynucleotide sequence relatedness among three groups of pathogenic Escherichia coli strains. Infect. Immun. 6:308-315.
6. Buchanan, S. G., and N. J. Gay. 1996. Structural and functional diversity in the leucine-rich repeat family of proteins. Prog. Biophys. Mol. Biol. 65:1-44.
7. Burland, V., D. L. Daniels, G. Plunkett III, and F. R. Blattner. 1993. Genome sequencing on both strands: the Janus strategy. Nucleic Acids Res. 21:3385-3390.
8. Buysse, J. M., A. B. Hartman, N. Strockbine, and M. Venkatesan. 1995. Genetic polymorphism of the ipaH multicopy antigen gene in Shigella spps. and enteroinvasive Escherichia coli. Microb. Pathog. 19:335-349.
9. Cossart, P., J. Pizarro-Cerda, and M. Lecuit. 2003. Invasion of mammalian cells by Listeria monocytogenes: functional mimicry to subvert cellular functions. Trends Cell Biol. 13:23-31.
10. 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.
11. Deng, W., S.-R. Liou, G. Plunkett III, G. F. Mayhew, D. J. Rose, V. Burland, V. Kodoyianni, D. C. Schwartz, and F. R. Blattner. 2003. Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J. Bacteriol. 185:2330-2337.
12. Devico, A. L., T. R. Fouts, M. T. Shata, R. Kamin-Lewis, G. K. Lewis, and D. M. Hone. 2002. Development of an oral prime-boost strategy to elicit broadly neutralizing antibodies against HIV-1. Vaccine 20:1968-1974.
13. Eisen, J. A., J. F. Heidelberg, O. White, and S. L. Salzberg. 2000. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biol. 1(6):0011.1-0011.9. [Online.] http://genomebiology.com.
14. Fennelly, G. J., S. A. Khan, M. A. Abadi, T. F. Wild, and B. R. Bloom. 1999. Mucosal DNA vaccine immunization against measles with a highly attenuated Shigella flexneri vector. J. Immunol. 162:1603-1610.
15. Fernandez, I. M., M. Silva, R. Schuch, W. A. Walker, A. M. Siber, A. T. Maurelli, and B. A. McCormick. 2001. Cadaverine prevents the escape of Shigella flexneri from the phagolysosome: a connection between bacterial dissemination and neutrophil transepithelial signaling. J. Infect. Dis. 184: 743-753.
16. 7.8 facilitates escape of virulent bacteria from the endocytic vacuoles of mouse and human macrophages. Infect. Immun. 68:3608-3619.
17. Formal, S. B., E. V. Oaks, R. E. Olsen, M. Wingfield-Eggleston, P. J. Snoy, and J. P. Cogan. 1991. Effect of prior infection with virulent Shigella flexneri 2a on the resistance of monkeys to subsequent infection with Shigella sonnei. J. Infect. Dis. 164:533-537.
18. 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.
19. Garcia-Martinez, J., I. Bescos, J. J. Rodriguez-Sala, and F. Rodriguez-Valera. 2001. RISSC: a novel database for ribosomal 16S-23S RNA genes spacer regions. Nucleic Acids Res. 29:178-180.
20. Grosdent, N., I. Maridonneau-Parini, M.-P. Sory, and G. R. Cornelis. 2002. Role of Yops and adhesins in resistance of Yersinia enterocolitica to phagocytosis. Infect. Immun. 70:4165-4176.
21. Henderson, I. R., J. Czeczulin, C. Eslava, F. Noriega, and J. P. Nataro. 1999. Characterization of Pic, a secreted protease of Shigella flexneri and enteroaggregative Escherichia coli. Infect. Immun. 67:5587-5596.
22. Hong, M., Y. Gleason, E. E. Wyckoff, and S. M. Payne. 1998. Identification of two Shigella flexneri chromosomal loci involved in intercellular spreading. Infect. Immun. 66:4700-4710.
23. Hong, M., and S. M. Payne. 1997. Effect of mutations in Shigella flexneri chromosomal and plasmid-encoded lipopolysaccharide genes on invasion and serum resistance. Mol. Microbiol. 24:779-791.
24. Isberg, R. R., D. L. Voorhis, and S. Falkow. 1987. Identification of invasin: a protein that allows enteric bacteria to penetrate cultured mammalian cells. Cell 50:769-778.
25. Jin, Q., Z. Yuan, J. Xu, Y. Wang, Y. Shen, W. Lu, J. Wang, H. Liu, J. Yang, F. Yang, X. Zhang, J. Zhang, G. Yang, H. Wu, D. Qu, J. Dong, L. Sun, Y. Xue, A. Zhao, Y. Gao, J. Zhu, B. Kan, K. Ding, S. Chen, H. Cheng, Z. Yao, B. He, R. Chen, D. Ma, B. Qiang, Y. Wen, Y. Hou, and J. Yu. 2002. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 30:4432-4441.
26. Kjemtrup, S., Z. Nimchuk, and J. L. Dangl. 2000. Effector proteins of phytopathogenic bacteria: bifunctional signals in virulence and host recognition. Curr. Opin. Microbiol. 3:73-78.
27. Kobe, B., and A. V. Kajava. 2001. The leucine-rich repeat as a protein recognition motif. Curr. Opin. Struct. Biol. 11:725-732.
28. Kohara, Y., K. Akiyama, and K. Isono. 1987. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50:495-508.
29. Kotloff, K. L., F. Noriega, G. A. Losonsky, M. B. Sztein, S. S. Wasserman, J. P. Nataro, and M. M. Levine. 1996. Safety, immunogenicity, and transmissibility in humans of CVD 1203, a live oral Shigella flexneri 2a vaccine candidate attenuated by deletions in aroA and virG. Infect. Immun. 64:4542-4548.
30. Kotloff, K. L., F. R. Noriega, T. Samandari, M. B. Sztein, G. A. Losonsky, J. P. Nataro, W. D. Picking, E. M. Barry., and M. M. Levine. 2000. Shigella flexneri 2a strain CVD 1207, with specific deletions in virG, sen, set, and guaBA, is highly attenuated in humans. Infect. Immun. 68:1034-1039.
31. Kotloff, K. L., D. N. Taylor, M. B. Sztein, S. S. Wasserman, G. A. Losonsky, J. P. Nataro, M. Venkatesan, A. Hartman, W. D. Picking, D. E. Katz, J. D. Campbell, M. M. Levine, and T. L. Hale. 2002. Phase I evaluation of ΔvirG Shigella sonnei live, attenuated, oral vaccine strain WRSS1 in healthy adults. Infect. Immun. 70:2016-2021.
32. Kotloff, K. L., J. P. Winickoff, B. Ivanoff, J. D. Clemens, D. L. Swerdlow, P. J. Sansonetti, G. K. Adak, and M. M. Levine. 1999. Global burden of Shigella infections: implications for vaccine development and implementation of control strategies. Bull. W. H. O. 77:651-666.
33. LaBrec, E. H., H. Schneider, T. J. Magnani, and S. B. Formal. 1964. Epithelial cell penetration as an essential step in the pathogenesis of bacillary dysentery. J. Bacteriol. 88:1503-1518.
34. Lan, R., B. Lumb, D. Ryan, and P. R. Reeves. 2001. Molecular evolution of large virulence plasmid in Shigella clones and enteroinvasive Escherichia coli. Infect. Immun. 69:6303-6309.
35. Lavie, M., E. Shillington, C. Eguiluz, N. Grimsley, and C. Boucher. 2002. PopP1, a new member of the YopJ/AvrRxw family of type III effector proteins, acts as a host-specificity factor and modulates aggressiveness of Ralstonia solanaceanim. Mol. Plant-Microbe Interact. 15:1058-1068.
36. Lecuit, M., S. Dramsi, C. Gottardi, M. Fedor-Chaiken, B. Gumbiner, and P. Cossart. 1999. A single amino acid in E-cadherin responsible for host specificity towards the human pathogen Listeria monocytogenes. EMBO J. 18: 3956-3963.
37. Lecuit, M., S. Vandormael-Pournin, J. Lefort, M. Huerre, P. Gounon, C. Dupuy, C. Babinet, and P. Cossart. 2001. A transgenic model for listeriosis: role of internalin in crossing the intestinal barrier. Science 292:1722-1725.
38. Lim, A., E. T. Dimalanta, K. D. Potamousis, G. Yen, J. Apodoca, C. Tao, J. Lin, R. Qi, J. Skiadas, A. Ramanathan, N. T. Perna, G. Plunkett III, V. Burland, B. Mau, J. Hackett, F. R. Blattner, T. S. Anantharaman, B. Mishra, and D. C. Schwartz. 2001. Shotgun optical maps of the whole Escherichia coli O157:H7 genome. Genome Res. 11:1584-1593.
39. Liu, S. L., and K. E. Sanderson. 1995. Rearrangements in the genome of the bacterium Salmonella typhi. Proc. Natl. Acad. Sci. USA 92:1018-1022.
40. Lowe, T. M., and S. R. Eddy. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
41. Luck, S. N., S. A. Turner, K. Rajakumar, H. Sakellaris, and B. Adler. 2001. Ferric dicitrate transport system (Fec) of Shigella flexneri 2a YSH6000 is encoded on a novel pathogenicity island carrying multiple antibiotic resistance genes. Infect. Immun. 69:6012-6021.
42. Lukashin, A. V., and M. Borodovsky. 1998. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 26:1107-1115.
43. Mahillon, J., and M. Chandler. 1998. Insertion sequences. Microbiol. Mol. Biol. Rev. 62:725-774.
44. Mahillon, J., H. A. Kirkpatrick, H. L. Kijenski, C. A. Bloch, C. K. Rode, G. F. Mayhew, D. J. Rose, G. Plunkett III, V. Burland, and F. R. Blattner. 1998. Subdivision of the Escherichia coli K-12 genome for sequencing: manipulation and DNA sequence of transposable elements introducing unique restriction sites. Gene 223:47-54.
45. Matsutani, S., and E. Ohtsubo. 1993. Distribution of the Shigella sonnei insertion elements in Enterobacteriaceae. Gene 127:111-115.
46. Maurelli, A. T., R. E. Fernandez, C. A. Bloch, C. K. Rode, and A. Fasano. 1998. "Black holes" and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli. Proc. Natl. Acad. Sci. USA 95:3943-3948.
47. Mavris, M., P. A. Manning, and R. Morona. 1997. Mechanism of bacteriophage Sfll-mediated serotype conversion in Shigella flexneri. Mol. Microbiol. 26:939-950.
48. Mirold, S., W. Rabsch, H. Tschape, and W. D. Hardt. 2001. Transfer of the Salmonella type III effector SopE between unrelated phage families. J. Mol. Biol. 312:7-16.
49. Mogull, S. A., L. J. Runyen-Janecky, M. Hong, and S. M. Payne. 2001. dksA is required for intercellular spread of Shigella flexneri via an RpoS-independent mechanism. Infect. Immun. 69:5742-5751.
50. Mounier, J., T. Vasselon, R. Hellio, M. Lesourd, and P. J. Sansonetti. 1992. Shigella flexneri enters human colonic Caco-2 epithelial cells through the basolateral pole. Infect. Immun. 60:237-248.
51. Nhieu, G. T., and P. J. Sansonetti. 1999. Mechanism of Shigella entry into epithelial cells. Curr. Opin. Microbiol. 2:51-55.
52. Ochman, H., and N. A. Moran. 2001. Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292:1096-1099.
53. Ohtsubo, H., K. Nyman, W. Doroszkiewicz, and E. Ohtsubo. 1981. Multiple copies of iso-insertion sequences of IS1 in Shigella dysenteriae chromosome. Nature 292:640-643.
54. Perna, N. T., G. Plunkett III, V. Burland, B. Mau, J. D. Glasner, D. J. Rose, G. F. Mayhew, P. S. Evans, J. Gregor, H. A. Kirkpatrick, G. Posfai, J. Hackett, S. Klink, A. Boutin, Y. Shao, L. Miller, E. J. Grotbeck, N. W. Davis, A. Lim, E. T. Dimalanta, K. D. Potamousis, J. Apodaca, T. S. Anantharaman, J. Lin, G. Yen, D. C. Schwartz, R. A. Welch, and F. R. Blattner. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529-533.
55. Plunkett, G., III, D. J. Rose, T. J. Durfee, and F. R. Blattner. 1999. Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product. J. Bacteriol. 181:1767-1778.
56. Pupo, G. M., D. K. Karaolis, R. Lan, and P. R. Reeves. 1997. Evolutionary relationships among pathogenic and nonpathogenic Escherichia coli strains inferred from multilocus enzyme electrophoresis and mdh sequence studies. Infect. Immun. 65:2685-2692.
57. Pupo, G. M., R. Lan, and P. R. Reeves. 2000. Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc. Natl. Acad. Sci. USA 97:10567-10572.
58. Purdy, G. E., and S. M. Payne. 2001. The SHI-3 iron transport island of Shigella boydii 0-1392 carries the genes for aerobactin synthesis and transport. J. Bacteriol. 183:4176-4182.
59. Robin, G., D. Cohen, N. Orr, I. Markus, R. Slepon, S. Ashkenazi, and Y. Keisari. 1997. Characterization and quantitative analysis of serum IgG class and subclass response to Shigella sonnei and Shigella flexneri 2a lipopolysaccharide following natural Shigella infection. J. Infect. Dis. 175:1128-1133.
60. Runyen-Janecky, L. J., and S. M. Payne. 2002. Identification of chromosomal Shigella flexneri genes induced by the eukaryotic intracellular environment. Infect. Immun. 70:4379-4388.
61. Sansonetti, P. J., D. J. Kopecko, and S. B. Formal. 1982. Involvement of a plasmid in the invasive ability of Shigella flexneri. Infect. Immun. 35:852-860.
62. Sherburne, C. K., T. D. Lawley, M. W. Gilmour, F. R. Blattner, V. Burland, E. Grotbeck, D. J. Rose, and D. E. Taylor. 2000. The complete DNA sequence and analysis of R27, a large IncHI plasmid from Salmonella typhi that is temperature sensitive for transfer. Nucleic Acids Res. 28:2177-2186.
63. Sizemore, D. R., A. A. Branstrom, and J. C. Sadoff. 1995. Attenuated Shigella as a DNA delivery vehicle for DNA-mediated immunization. Science 270: 299-302.
64. Sokurenko, E. V., D. L. Hasty, and D. E. Dykhuizen. 1999. Pathoadaptive mutations: gene loss and variation in bacterial pathogens. Trends Microbiol. 7:191-195.
65. Stevenson, G., A. Kessler, and P. R. Reeves. 1995. A plasmid-borne Oantigen chain length determinant and its relationship to other chain length determinants. FEMS Microbiol. Lett. 125:23-30.
66. Townsend, S. M., N. E. Kramer, R. Edwards, S. Baker, N. Hamlin, M. Simmonds, K. Stevens, S. Maloy, J. Parkhill, G. Dougan, and A. J. Bäumler. 2001. Salmonella enterica serovar Typhi possesses a unique repertoire of fimbrial gene sequences. Infect. Immun. 69:2894-2901.
67. 9.8 is secreted from bacteria within mammalian cells and transported to the nucleus. J. Biol. Chem. 276:32071-32079.
68. Venkatesan, M. M., J. M. Buysse, and A. B. Hartman. 1991. Sequence variation in two ipaH genes of Shigella flexneri 5 and homology to the LRG-like family of proteins. Mol. Microbiol. 5:2435-2445.
69. Venkatesan, M. M., M. B. Goldberg, D. J. Rose, E. J. Grotbeck, V. Burland, and F. R. Blattner. 2001. Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri. Infect. Immun. 69:3271-3285.
70. Vokes, S. A., S. A. Reeves, A. G. Torres, and S. M. Payne. 1999. The aerobactin iron transport system genes in Shigella flexneri are present within a pathogenicity island. Mol. Microbiol. 33:63-73.
71. Wang, L., W. Qu, and P. R. Reeves. 2001. Sequence analysis of four Shigella boydii O-antigen loci: implication for Escherichia coli and Shigella relationships. Infect. Immun. 69:6923-6930.
72. Way, S. S., A. C. Borczuk, and M. B. Goldberg. 1999. Thymic independence of adaptive immunity to the intracellular pathogen Shigella flexneri serotype 2a. Infect. Immun. 67:3970-3979.
73. 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. T. Mobley, M. S. Donnenberg, and F. R. Blattner. 2002. Extensive mosaic structure revealed by the complete genome sequence of a uropathogenic strain of Escherichia coli. Proc. Natl. Acad. Sci. USA 99:17020-17024.