Chapter 2 : Genomes: a Tale of Convergent Evolution and Specialization through IS Expansion and Genome Reduction

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Although all species share similar pathogenic properties, each species exhibits peculiar epidemiological characteristics. , , and are most common in developing countries, whereas is more prevalent in developed countries. A remarkable difference between and genomes is the presence of pseudogenes in the former. The second remarkable feature of the genome is the presence of enormous copies of IS elements, which are likely the cause of genomic rearrangements, including deletions, inversions, and translocations that may effectively disrupt the colinearity among different genomes. After the acquisition of the ancestral forms of the virulence plasmid by /enteroinvasive (EIEC), genome reduction by inactivation of the pathway-specific antivirulence loci (AVL) is vital for adaptation in the cytosolic niche. Similar to obligate pathogens, reduced selection pressure might have played an important role in genome reduction, which may have further accelerated terminal evolution and resulted in the increased host specificity. Numerous genes responsible for cell motility cell envelope, carbohydrate transport, and metabolism that are present in were frequently lost in . A combination of various strategies using the basic information provided by genomic research will be helpful in efficient control and prevention of infections.

Citation: Yang J, Sangal V, Jin Q, Yu J. 2011. Genomes: a Tale of Convergent Evolution and Specialization through IS Expansion and Genome Reduction, p 23-39. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch2
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Figure 1

Evolutionary path of /EIEC from diverse origins of Acquisition of virulence plasmid and pathway-specific reductions are two decisive events in the pathoadaption path. Diverse genomewide reduction occurs because of reduced effectiveness of purifying selection in the cell cytosol. IS expansion and consequent genome rearrangements played a major role in both pathway-specific and genomewide reduction. Formation of pseudogenes is one other mechanism resulting in genome decay.

Citation: Yang J, Sangal V, Jin Q, Yu J. 2011. Genomes: a Tale of Convergent Evolution and Specialization through IS Expansion and Genome Reduction, p 23-39. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch2
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1. 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: 24572463.
2. Aranda, K. R., U. Fagundes-Neto, and, I. C. Scaletsky. 2004. Evaluation of multiplex PCRs for diagnosis of infection with diarrheagenic Escherichia coli and Shigella spp. J. Clin. Micro-biol. 42: 58495853.
3. Ashida, H.,, T. Toyotome,, T. Nagai, and, C. Sasakawa. 2007. Shigella chromosomal IpaH proteins are secreted via the type III secretion system and act as effectors. Mol. Microbiol. 63: 680693.
4. Backert, S., and, T. F. Meyer. 2006. Type IV secretion systems and their effectors in bacterial pathogenesis. Curr. Opin. Microbiol. 9: 207217.
5. Baumler, A. J.,, T. L. Norris,, T. Lasco,, W. Voight,, R. Reissbrodt,, W. Rabsch, and, F. Heffron. 1998. IroN, a novel outer membrane siderophore receptor characteristic of Salmonella enter-ica. J. Bacteriol. 180: 14461453.
6. Bin, W.,, M. Liu,, J. Peng,, L. Sun,, X. Xu,, J. Zhang, and, Q. Jin. 2006. Construction, detection and microarray analysis on Shigella dysenteriae a1 IroN, ShuA single, double mutants. Sci. China C Life Sci. 49: 251258.
7. Brandal, L. T.,, B. A. Lindstedt,, L. Aas,, T. L. Stavnes,, J. Lassen, and, G. Kapperud. 2007. Octaplex PCR and fluorescence-based capillary electrophoresis for identification of human diarrheagenic Escherichia coli and Shigella spp. J. Microbiol. Methods 68: 331341.
8. Buchrieser, C.,, P. Glaser,, C. Rusniok,, H. Nedjari,, H. D’Hauteville, F. Kunst, P. Sansonetti, and, C. Parsot. 2000. The virulence plas-mid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri. Mol. Microbiol. 38: 760771.
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: 1382613831.
10. Chen, S. L.,, C. S. Hung,, J. Xu,, C. S. Reigstad,, V. Magrini,, A. Sabo,, D. Blasiar,, T. Bieri,, R. R. Meyer,, P. Ozersky,, J. R. Armstrong,, R. S. Fulton,, J. P. Latreille,, J. Spieth,, T. M. Hooton,, E. R. Mardis,, S. J. Hultgren, and, J. I. Gordon. 2006. Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc. Natl. Acad. Sci. USA 103: 59775982.
11. Cheng, F.,, J. Wang,, J. Peng,, J. Yang,, H. Fu,, X. Zhang,, Y. Xue,, W. Li,, Y. Chu, and, Q. Jin. 2007. Gene expression profiling of the pH response in Shigella flexneri 2a. FEMS Microbiol. Lett. 270: 1220.
12. Choi, S. Y.,, Y. S. Jeon,, J. H. Lee,, B. Choi,, S. H. Moon,, L. von Seidlein,, J. D. Clemens,, G. Dougan,, J. Wain,, J. Yu,, J. C. Lee,, S. Y. Seol,, B. K. Lee,, J. H. Song,, M. Song,, C. Czerkinsky,, J. Chun, and, D. W. Kim. 2007. Multilocus sequence typing analysis of Shigella flexneri isolates collected in Asian countries. J. Med. Microbiol. 56: 14601466.
13. Eitel, J., and, P. Dersch. 2002. The YadA protein of Yersinia pseudotuberculosis mediates high-efficiency uptake into human cells under environmental conditions in which invasin is repressed. Infect. Immun. 70: 48804891.
14. El Karoui, M.,, V. Biaudet,, S. Schbath, and, A. Gruss. 1999. Characteristics of Chi distribution on different bacterial genomes. Res. Microbiol. 150: 579587.
15. Escobar-Paramo, P.,, O. Clermont,, A. B. Blanc-Potard,, H. Bui,, C. Le Bouguenec, and, F. Denamur. 2004. A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli. Mol. Biol. Evol. 21: 10851094.
16. Fasano, A.,, F. R. Noriega,, D. R. Maneval,, Jr., S. Chana-songcram, R. Russell, S. Guandalini, and, M. M. Levine. 1995. Shigella enterotoxin 1: an enterotoxin of Shigella flexneri 2a active in rabbit small intestine in vivo and in vitro. J. Clin. Invest.. 95: 28532861.
17. Fernandez-Prada, C. M.,, D. L. Hoover,, B. D. Tall,, A. B. Hartman,, J. Kopelowitz, and, M. M. Venkatesan. 2000. Shigella flexneri IpaH(7.8) facilitates escape of virulent bacteria from the endocytic vacuoles of mouse and human macrophages. Infect. Immun. 68: 36083619.
18. Fu, H.,, W. Leng,, J. Wang,, W. Zhang,, J. Peng,, L. Wang, and, Q. Jin. 2007. Transcriptional profile induced by furazolidone treatment of Shigella flexneri. Appl. Microbiol. Biotechnol. 77: 657667.
19. Fukiya, S.,, H. Mizoguchi,, T. Tobe, and, H. Mori. 2004. Extensive genomic diversity in pathogenic Escherichia coli and Shigella strains revealed by comparative genomic hybridization microarray. J. Bacteriol. 186: 39113921.
20. Gohmann, S.,, P. A. Manning,, C. A. Alpert,, M. J. Walker, and, K. N. Timmis. 1994. Lipopolysaccharide O-antigen biosynthesis in Shigella dysenteriae serotype 1: analysis of the plas-mid-carried rfp determinant. Microb. Pathog. 16: 5364.
21. Halpern, D.,, H. Chiapello,, S. Schbath,, S. Robin,, C. Hennequet-Antier, A. Gruss, and, M. El Karoui. 2007. Identification of DNA motifs implicated in maintenance of bacterial core genomes by predictive modeling. PLoS Genet. 3: 16141621.
22. Hayashi, T.,, K. Makino,, M. Ohnishi,, K. Kurokawa,, K. Ishii,, K. Yokoyama,, C. G. Han,, E. Ohtsubo,, K. Nakayama,, T. Murata,, M. Tanaka,, T. Tobe,, T. Iida,, H. Takami,, T. Honda,, C. Sasakawa,, N. Ogasawara,, T. Yasunaga,, S. Kuhara,, T. Shiba,, M. Hattori, and, H. Shinagawa. 2001. Complete genome sequence of entero-hemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8: 1122.
23. 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: 55875596.
24. Hershberg, R.,, H. Tang, and, D. A. Petrov. 2007. Reduced selection leads to accelerated gene loss in Shigella. Genome Biol. 8: R164.
25. Holt, K. E.,, J. Parkhill,, C. J. Mazzoni,, P. Roumagnac,, F. X. Weill,, I. Goodhead,, R. Rance,, S. Baker,, D. J. Maskell,, J. Wain,, C. Dolecek,, M. Achtman, and, G. Dougan. 2008. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat. Genet. 40: 987993.
26. Jennison, A. V.,, R. Raqib, and, N. K. Verma. 2006. Immunoproteome analysis of soluble and membrane proteins of Shigella flexneri 2457T. World J. Gastroenterol. 12: 66836688.
27. Jeong, H. J.,, E. S. Jang,, B. I. Han,, K. H. Lee,, M. S. Ock,, H. H. Kong,, D. I. Chung,, S. Y. Seol,, D. T. Cho, and, H. S. Yu. 2007. Acanthamoeba: could it be an environmental host of Shigella? Exp. Parasitol. 115: 181186.
28. Jiang, Y.,, F. Yang,, X. Zhang,, J. Yang,, L. Chen,, Y. Yan,, H. Nie,, Z. Xiong,, J. Wang,, J. Dong,, Y. Xue,, X. Xu,, Y. Zhu,, S. Chen, and, Q. Jin. 2005. The complete sequence and analysis of the large virulence plasmid pSS of Shigella sonnei. Plasmid 54: 149159.
29. Jin, L. Q.,, J. W. Li,, S. Q. Wang,, F. H. Chao,, X. W. Wang, and, Z. Q. Yuan. 2005. Detection and identification of intestinal pathogenic bacteria by hybridization to oligonucleotide mi-croarrays. World J. Gastroenterol. 11: 76157619.
30. 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 0157. Nucleic Acids Res. 30: 44324441.
31. Kakinuma, K.,, M. Fukushima, and, R. Kawaguchi. 2003. Detection and identification of Escherichia coli, Shigella, and Salmonella by microarrays using the gyrB gene. Biotechnol. Bioeng. 83: 721728.
32. Keusch, G. X,, G. F. Grady,, L. J. Mata, and, J. McIver. 1972. The pathogenesis of Shigella diarrhea. I. Enterotoxin production by Shigella dysenteriae I. J. Clin. Invest. 51: 12121218.
33. 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. World Health Organ. 77: 651666.
34. Kuzminov, A. 1995. Collapse and repair of replication forks in Escherichia coli. Mol. Microbiol. 16: 373384.
35. Lan, R.,, M. C. Alles,, K. Donohoe,, M. B. Martinez, and, P. R. Reeves. 2004. Molecular evolutionary relationships of en-teroinvasive Escherichia coli and Shigella spp. Infect. Immun. 72: 50805088.
36. Le Gall, X,, P. Darlu,, P. Escobar-Paramo, B. Picard, and, E. Denamur. 2005. Selection-driven transcriptome polymorphism in Escherichia coli/Shigella. Nat. Rev. Genet. 9: 165178.
37. Levine, M. M.,, K. L. Kotloff,, E. M. Barry,, M. F. Pasetti, and, M. B. Sztein. 2007. Clinical trials of Shigella vaccines: two steps forward and one step back on a long, hard road. Nat. Rev. Microbiol. 5: 540553.
38. Li, Y.,, B. Cao,, B. Liu,, D. Liu,, Q. Gao,, X. Peng,, J. Wu,, D. A. Bastin,, L. Feng, and, L. Wang. 2009. Molecular detection of all 34 distinct O-antigen forms of Shigella. J. Med. Microbiol. 58: 6981.
39. Li, Y.,, D. Liu,, B. Cao,, W. Han,, Y. Liu,, F. Liu,, X. Guo,, D. A. Bastin,, L. Feng, and, L. Wang. 2006. Development of a serotype-specific DNA microarray for identification of some Shigella and pathogenic Escherichia coli strains. J. Clin. Microbiol. 44: 43764383.
40. Liu, M.,, H. Liu,, L. Sun,, J. Dong,, Y. Xue,, S. Chen, and, Q. Jin. 2005. Construction, detection and microarray analysis on the Shigella flexneri 2a sitC mutant. Sci. China C Life Sci. 48: 228240.
41. Lucchini, S.,, H. Liu,, Q. Jin,, J. C. Hinton, and, J. Yu. 2005. Transcriptional adaptation of Shigella flexneri during infection of macrophages and epithelial cells: insights into the strategies of a cytosolic bacterial pathogen. Infect. Immun. 73: 88102.
42. Maurelli, A. T,, B. Baudry,, H. d’Hauteville,, X L. Hale, and, P. J. Sansonetti. 1985. Cloning of plasmid DNA sequences involved in invasion of HeLa cells by Shigella flexneri. Infect. Immun. 49: 164171.
43. Maurelli, A. X,, 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: 39433948.
44. Moss, J. E.,, X J. Cardozo,, A. Zychlinsky, and, E. A. Groisman. 1999. The selC-associated SHI-2 pathogenicity island of Shigella flexneri. Mol. Microbiol. 33: 7483.
45. Nakata, N.,, X. Tobe,, I. Fukuda,, X Suzuki,, K. Komatsu,, M. Yoshikawa, and, C. Sasakawa. 1993. The absence of a surface protease, OmpT, determines the intercellular spreading ability of Shigella: the relationship between the ompT and kcpA loci. Mol. Microbiol. 9: 459468.
46. Nataro, J. P., and, J. B. Kaper. 1998. Diarrheagenic Escherichia coli. Clin. Microbiol. Rev. 11: 142201.
47. Nie, H.,, F. Yang,, X. Zhang,, J. Yang,, L. Chen,, J. Wang,, Z. Xiong,, J. Peng,, L. Sun,, J. Dong,, Y. Xue,, X. Xu,, S. Chen,, Z. Yao,, Y. Shen, and, Q. Jin. 2006. Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a. BMC Genomics 7: 173.
48. Niyogi, S. K. 2005. Shigellosis. J. Microbiol. 43: 133143.
49. Parkhill, J.,, M. Sebaihia,, A. Preston,, L. D. Murphy,, N. Thomson,, D. E. Harris,, M. X Holden,, C. M. Churcher,, S. D. Bentley,, K. L. Mungall,, A. M. Cerdeno-Tarraga,, L. Temple,, K. James,, B. Harris,, M. A. Quail,, M. Achtman,, R. Atkin,, S. Baker,, D. Basham,, N. Bason,, I. Cherevach,, X Chillingworth,, M. Collins,, A. Cronin,, P. Davis,, J. Doggett,, X Feltwell,, A. Goble,, N. Hamlin,, H. Hauser,, S. Holroyd,, K. Jagels,, S. Leather,, S. Moule,, H. Norberczak,, S. O’Neil,, D. Ormond,, C. Price,, E. Rabbinowitsch,, S. Rutter,, M. Sanders,, D. Saunders,, K. Seeger,, S. Sharp,, M. Simmonds,, J. Skelton,, R. Squares,, S. Squares,, K. Stevens,, L. Unwin,, S. Whitehead,, B. G. Barrell, and, D. J. Maskell. 2003. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat. Genet. 35: 3240.
50. Peng, J.,, X. Zhang,, J. Yang,, J. Wang,, E. Yang,, W. Bin,, C. Wei,, M. Sun, and, Q. Jin. 2006. The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella. BMC Genomics 7: 218.
51. Price, M. N.,, E. J. Alm, and, A. P. Arkin. 2005. Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication. Nucleic Acids Res. 33: 32243234.
52. Prunier, A. L.,, R. Schuch,, R. E. Fernandez, and, A. X Maurelli. 2007. Genetic structure of the nadA and nadB antivirulence loci in Shigella spp. J. Bacteriol. 189: 64826486.
53. Prunier, A. L.,, R. Schuch,, R. E. Fernandez,, K. L. Mumy,, H. Kohler,, B. A. McCormick, and, A. X Maurelli. 2007. nadA and nadB of Shigella flexneri 5a are antivirulence loci responsible for the synthesis of quinolinate, a small molecule inhibitor of Shigella pathogenicity. Microbiology 153: 23632372.
54. 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: 1056710572.
55. 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: 41764182.
56. Rajakumar, K.,, C. Sasakawa, and, B. Adler. 1997. Use of a novel approach, termed island probing, identifies the Shigella flexneri she pathogenicity island which encodes a homolog of the immu-noglobulin A protease-like family of proteins. Infect. Immun. 65: 46064614.
57. Ranjbar, R.,, A. Aleo,, G. M. Giammanco,, A. M. Dionisi,, N. Sadeghifard, and, C. Mammina. 2007. Genetic relatedness among isolates of Shigella sonnei carrying class 2 integrons in Tehran, Iran, 2002-2003. BMC Infect. Dis. 7: 62.
58. Rocha, E. P. 2006. Inference and analysis of the relative stability of bacterial chromosomes. Mol. Biol. Evol. 23: 513522.
59. Rocha, E. P., and, A. Danchin. 2003. Gene essentiality determines chromosome organisation in bacteria. Nucleic Acids Res. 31: 65706577.
60. Roumagnac, P.,, F. X. Weill,, C. Dolecek,, S. Baker,, S. Brisse,, N. X Chinh,, T. A. Le,, C. J. Acosta,, J. Farrar,, G. Dougan, and, M. Achtman. 2006. Evolutionary history of Salmonella typhi. Science 314: 13011304.
61. Sandkvist, M.,, L. O. Michel,, L. P. Hough,, V. M. Morales,, M. Bagdasarian,, M. Koomey,, V. J. DiRita, and, M. Bagdasarian. 1997. General secretion pathway (eps) genes required for toxin secretion and outer membrane biogenesis in Vibrio cholerae. J. Bacteriol. 179: 69947003.
62. Sansonetti, P. J.,, T. L. Hale,, G. J. Dammin,, C. Kapfer,, H. H. Collins, Jr., and, S. B. Formal. 1983. Alterations in the pathogenicity of Escherichia coli K-12 after transfer of plasmid and chromosomal genes from Shigella flexneri. Infect. Immun. 39: 13921402.
63. Sasakawa, C.,, B. Adler,, T. Tobe,, N. Okada,, S. Nagai,, K. Ko-matsu, and, M. Yoshikawa. 1989. Functional organization and nucleotide sequence of virulence Region-2 on the large virulence plasmid in Shigella flexneri 2a. Mol. Microbiol. 3: 11911201.
64. Schmid, Y.,, G. A. Grassl,, O. T. Buhler,, M. Skurnik,, I. B. Autenrieth, and, E. Bohn. 2004. Yersinia enterocolitica ad-hesin A induces production of interleukin-8 in epithelial cells. Infect. Immun. 72: 67806789.
65. Schroeder, G. N., and, H. Hilbi. 2008. Molecular pathogenesis of Shigella spp.: controlling host cell signaling, invasion, and death by type III secretion. Clin. Microbiol. Rev. 21: 134156.
66. Seol, S. Y.,, Y. T. Kim,, Y. S. Jeong,, J. Y. Oh,, H. Y. Kang,, D. C. Moon,, J. Kim,, Y. C. Lee,, D. T. Cho, and, J. C. Lee. 2006. Molecular characterization of antimicrobial resistance in Shigella sonnei isolates in Korea. J. Med. Microbiol. 55: 871877.
67. 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: 21772186.
68. Siguier, P., J. Filee, and, M. Chandler. 2006. Insertion sequences in prokaryotic genomes. Curr. Opin. Microbiol. 9: 526531.
69. Singer, A. U.,, J. R. Rohde,, R. Lam,, T. Skarina,, O. Kagan,, R. Dileo,, N. Y. Chirgadze,, M. E. Cuff,, A. Joachimiak,, M. Tyers,, P. J. Sansonetti,, C. Parsot, and, A. Savchenko. 2008. Structure of the Shigella T3SS effector IpaH defines a new class of E3 ubiquitin ligases. Nat. Struct. Mol. Biol. 15: 12931301.
70. Swanson, M. S., and, B. K. Hammer. 2000. Legionella pneu-mophila pathogesesis: a fateful journey from amoebae to mac-rophages. Annu. Rev. Microbiol. 54: 567613.
71. Tauschek, M.,, R. J. Gorrell,, R. A. Strugnell, and, R. M. Robins-Browne. 2002. Identification of a protein secretory pathway for the secretion of heat-labile enterotoxin by an entero-toxigenic strain of Escherichia coli. Proc. Natl. Acad. Sci. USA 99: 70667071.
72. Toyotome, T.,, T. Suzuki,, A. Kuwae,, T. Nonaka,, H. Fukuda,, S. Imajoh-Ohmi,, T. Toyofuku,, M. Hori, and, C. Sasakawa. 2001. Shigella protein IpaH(9.8) is secreted from bacteria within mammalian cells and transported to the nucleus. J. Biol. Chem. 276: 3207132079.
73. Turlan, C., and, M. Chandler. 1995. IS1-mediated intramolecular rearrangements: formation of excised transposon circles and replicative deletions. EMBO J. 14: 54105421.
74. 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: 32713285.
75. von Seidlein, L.,, D. R. Kim,, M. Ali,, H. Lee,, X. Wang,, V. D. Thiem,, G. Canh do,, W. Chaicumpa,, M. D. Agtini,, A. Hossain,, Z. A. Bhutta,, C. Mason,, O. Sethabutr,, K. Talukder,, G. B. Nair,, J. L. Deen,, K. Kotloff, and, J. Clemens. 2006. A multicentre study of Shigella diarrhoea in six Asian countries: disease burden, clinical manifestations, and microbiology. PLoS Med. 3: e353.
76. Wagner, A. 2006. Periodic extinctions of transposable elements in bacterial lineages: evidence from intragenomic variation in multiple genomes. Mol. Biol. Evol. 23: 723733.
77. Warren, B. R.,, M. E. Parish, and, K. R. Schneider. 2006. Shigella as a foodborne pathogen and current methods for detection in food. Crit. Rev. Food Sci. Nutr. 46: 551567.
78. Wei, C.,, J. Peng,, Z. Xiong,, J. Yang,, J. Wang, and, Q. Jin. 2008. Subproteomic tools to increase genome annotation complexity. Proteomics 8: 42094213.
79. Wei, C.,, J. Yang,, J. Zhu,, X. Zhang,, W. Leng,, J. Wang,, Y. Xue,, L. Sun,, W. Li,, J. Wang, and, Q. Jin. 2006. Comprehensive pro-teomic analysis of Shigella flexneri 2a membrane proteins. J. Proteome Res. 5: 18601865.
80. Wei, H. L.,, Y. W. Wang,, C. C. Li,, S. K. Tung, and, C. S. Chiou. 2007. Epidemiology and evolution of genotype and antimicrobial resistance of an imported Shigella sonnei clone circulating in central Taiwan. Diagn. Microbiol. Infect. Dis. 58: 469475.
81. Wei, J.,, M. B. Goldberg,, V. Burland,, M. M. Venkatesan,, W. Deng,, G. Fournier,, G. F. Mayhew,, G. Plunkett, III,, D. J. Rose,, A. Darling,, B. Mau,, N. T. Perna,, S. M. Payne,, L. J. Runyen-Janecky,, S. Zhou,, D. C. Schwartz, and, F. R. Blattner. 2003. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect. Immun. 71: 27752786.
82. Wyckoff, E. E.,, D. Duncan,, A. G. Torres,, M. Mills,, K. Maase, and, S. M. Payne. 1998. Structure of the Shigella dysenteriae haem transport locus and its phylogenetic distribution in enteric bacteria. Mol. Microbiol. 28: 11391152.
83. Yang, F. ,, J. Yang,, X. Zhang,, L. Chen,, Y. Jiang,, Y. Yan,, X. Tang,, J. Wang,, Z. Xiong,, J. Dong,, Y. Xue,, Y. Zhu,, X. Xu,, L. Sun,, S. Chen,, H. Nie,, J. Peng,, J. Xu,, Y. Wang,, Z. Yuan,, Y. Wen,, Z. Yao,, Y. Shen,, B. Qiang,, Y. Hou,, J. Yu, and, Q. Jin. 2005. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res. 33: 64456458.
84. Yang, J.,, L. Chen,, L. Sun,, J. Yu, and, Q. Jin. 2008. VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics. Nucleic Acids Res. 36: D539D542.
85. Yang, J.,, H. Nie,, L. Chen,, X. Zhang,, F. Yang,, X. Xu,, Y. Zhu,, J. Yu, and, Q. Jin. 2007. Revisiting the molecular evolutionary history of Shigella spp. J. Mol. Evol. 64: 7179.
86. Yang, J.,, J. Wang,, Z. J. Yao,, Q. Jin,, Y. Shen, and, R. Chen. 2003. GenomeComp: a visualization tool for microbial genome comparison. J. Microbiol. Methods 54: 423426.
87. Yang, Y. G.,, M. K. Song,, S. J. Park, and, S. W. Kim. 2007. Direct detection of Shigella flexneri and Salmonella typhimurium in human feces by real-time PCR. J. Microbiol. Biotechnol. 17: 16161621.
88. Ying, T.,, H. Wang,, M. Li,, J. Wang,, J. Wang,, Z. Shi,, E. Feng,, X. Liu,, G. Su,, K. Wei,, X. Zhang,, P. Huang, and, L. Huang. 2005. Immunoproteomics of outer membrane proteins and extracellular proteins of Shigella flexneri 2a 2457T. Proteomics 5: 47774793.
89. Ying, T. Y.,, J. J. Wang,, H. L. Wang,, E. L. Feng,, K. H. Wei,, L. Y. Huang,, P. T. Huang, and, C. F. Huang. 2005. Immunoproteomics of membrane proteins of Shigella flexneri 2a 2457T. World J. Gastroenterol. 11: 68806883.
90. Zhu, Y.,, H. Li,, L. Hu,, J. Wang,, Y. Zhou,, Z. Pang,, L. Liu, and, F. Shao. 2008. Structure of a Shigella effector reveals a new class of ubiquitin ligases. Nat. Struct. Mol. Biol. 15: 13021308.


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Table 1

Summary of ongoing /EIEC genome sequencing projects (as of December 2008)

Citation: Yang J, Sangal V, Jin Q, Yu J. 2011. Genomes: a Tale of Convergent Evolution and Specialization through IS Expansion and Genome Reduction, p 23-39. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch2
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Table 2

Characteristics of complete genome sequences

Citation: Yang J, Sangal V, Jin Q, Yu J. 2011. Genomes: a Tale of Convergent Evolution and Specialization through IS Expansion and Genome Reduction, p 23-39. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch2
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Table 3

IS elements identified in genomes

Citation: Yang J, Sangal V, Jin Q, Yu J. 2011. Genomes: a Tale of Convergent Evolution and Specialization through IS Expansion and Genome Reduction, p 23-39. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch2
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Table 4

Known and putative virulence factors in the

Citation: Yang J, Sangal V, Jin Q, Yu J. 2011. Genomes: a Tale of Convergent Evolution and Specialization through IS Expansion and Genome Reduction, p 23-39. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch2
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Table 5

Inactivated genes relevant to biochemical reactions used in identification

Citation: Yang J, Sangal V, Jin Q, Yu J. 2011. Genomes: a Tale of Convergent Evolution and Specialization through IS Expansion and Genome Reduction, p 23-39. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch2

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