Genetic structure and chromosomal integration site of the cryptic prophage CP-1639 encoding Shiga toxin 1

Microbiology

Volumn 151, Issue 3, 2005, Pages 941-950

  Creuzberg, Kristina ^a   Köhler, Bernd ^b   Hempel, Helena ^a   Schreier, Peter ^c   Jacobs, Enno ^a   Schmidt, Herbert ^a,d  

^a DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

^b UNIVERSITY OF WÜRZBURG   (Germany)

^c UNIVERSITY OF WÜRZBURG   (Germany)

^d UNIVERSITY OF HOHENHEIM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CAPSID PROTEIN; DNA FRAGMENT; INTEGRASE; VEROTOXIN 1;

3' UNTRANSLATED REGION; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CONTROLLED STUDY; DNA FLANKING REGION; DNA INTEGRATION; DNA SEQUENCE; ESCHERICHIA COLI; GENE INSERTION; GENE LIBRARY; GENE LOCATION; GENETIC ASSOCIATION; GENETIC CODE; GENETIC VARIABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROPHAGE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SEROTYPE;

CHROMOSOME MAPPING; CHROMOSOMES, BACTERIAL; ESCHERICHIA COLI; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; PROPHAGES; RNA, BACTERIAL; SEQUENCE ANALYSIS, DNA; SEROTYPING; SHIGA-LIKE TOXIN I; VIRUS INTEGRATION;

ESCHERICHIA COLI; MIRIDAE;

EID: 15844364940     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.27632-0     Document Type: Article

References (72)

1. Acheson, D. W., Reidl, J., Zhang, X., Keusch, G. T., Mekalanos, J. J. & Waldor, M. K. (1998). In vivo transduction with Shiga toxin 1-encoding phage. Infect Immun 66, 4496-4498.
2. Beutin, L., Krause, G., Zimmermann, S., Kaulfuss, S. & Gleier, K. (2004). Characterization of Shiga toxin-producing Escherichia coli strains isolated from human patients in Germany over a 3-year period. J Clin Microbiol 42, 1099-1108.
3. Bielaszewska, M., Fell, M., Greune, L., Prager, R., Fruth, A., Tschäpe, H., Schmidt, M. A. & Karch, H. (2004). Characterization of cytolethal distending toxin genes and expression in shiga toxin- producing Escherichia coli strains of non-O157 serogroups. Infect Immun 72, 1812-1816.
4. Bitzan, M. & te Loo, D. M. (2003). Interaction of Shiga toxin with endothelial cells. Methods Mol Med 73, 243-262.
5. Blanco, J. E., Blanco, M., Alonso, M. P., Mora, A., Dahbi, G., Coira, M. A. & Blanco, J. (2004). Serotypes, virulence genes, and intimin types of Shiga toxin (verotoxin)-producing Escherichia coli isolates from human patients: prevalence in Lugo, Spain, from 1992 through 1999. J Clin Microbiol 42, 311-319.
6. Blattner, F. R., Plunkett, G., III, Bloch, C. A. & 14 other authors (1997). The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1474.
7. Brunder, W., Schmidt, H., Frosch, M. & Karch, H. (1999). The large plasmids of Shiga-toxin-producing Escherichia coli (STEC) are highly variable genetic elements. Microbiology 145 1005-1014.
8. Campbell, A. (1994). Comparative molecular biology of lambdoid phages. Annu Rev Microbiol 48, 193-222.
9. Caprioli, A., Tozzi, A. E., Rizzoni, G. & Karch, H. (1997). Non-O157 Shiga toxin-producing Escherichia coli infections in Europe. Emerg Infect Dis 3, 578-579.
10. Casjens, S., Winn-Stapley, D. A., Gilcrease, E. B., Morona, R., Kuhlewein, C., Chua, J. E., Manning, P. A., Inwood, W. & Clark, A. J. (2004). The chromosome of Shigella flexneri bacteriophage Sf6: complete nucleotide sequence, genetic mosaicism, and DNA packaging. J Mol Biol 339, 379-394.
11. Cebula, T. A., Payne, W. L. & Feng, P. (1995). Simultaneous identification of strains of Escherichia coli serotype O157:H7 and their Shiga-like toxin type by mismatch amplification mutation assay-multiplex PCR. J Clin Microbiol 33, 248-250.
12. Deng, W., Burland, V., Plunkett, G., III & 18 other authors (2002). Genome sequence of Yersinia pestis KIM. J Bacteriol 184, 4601-4611.
13. Friedrich, A. W., Bielaszewska, M., Zhang, W. L., Pulz, M., Kuczius, T., Ammon, A. & Karch, H. (2002). Escherichia coli harboring Shiga toxin 2 gene variants: frequency and association with clinical symptoms. J Infect Dis 185, 74-84.
14. Friedrich, A. W., Borell, J., Bielaszewska, M., Fruth, A., Tschäpe, H. & Karch, H. (2003). Shiga toxin 1c-producing Escherichia coli strains: phenotypic and genetic characterization and association with human disease. J Clin Microbiol 41, 2448-2453.
15. Gross, R., Arico, B. & Rappuoli, R. (1989). Families of bacterial signal-transducing proteins. Mol Microbiol 3, 1661-1667.
16. Hall, T. A. (2004). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95-98.
17. Hayashi, T., Makino, K., Ohnishi, M. & 19 other authors (2001). Complete genome sequence of enterohemorrhagic Escherichia coli O157 : H7 and genomic comparison with a laboratory strain K-12. DNA Res 8, 11-22.
18. Herold, S., Karch, H. & Schmidt H. (2004). Shiga toxin-encoding phages-genomes in motion. Int J Med Microbiol 294 115-121.
19. Jacewicz, M. S., Acheson, D. W., Binion, D. G., West G. A., Lincicome, L. L., Fiocchi, C. & Keusch, G. T. (1999). Responses of human intestinal microvascular endothelial cells to Shiga toxins 1 and 2 and pathogenesis of hemorrhagic colitis. Infect Immun 67, 1439-1444.
20. Kaneko, K., Kiyokawa, N., Ohtomo, Y., Nagaoka, R., Yamashiro, Y., Taguchi, T., Mori, T., Fujimoto, J. & Takeda, T. (2001). Apoptosis of renal tubular cells in Shiga-toxin-mediated hemolytic uremic syndrome. Nephron 87, 182-185.
21. Kaper, J. B. (1998). Enterohemorrhagic Escherichia coli. Curr Opin Microbiol 1, 103-108.
22. Karch, H., Schmidt H., Janetzki-Mittmann, C., Scheef, J. & Kröger, M. (1999). Shiga toxins even when different are encoded at identical positions in the genomes of related temperate bacteriophages. Mol Gen Genet 262, 600-607.
23. lox3. J Bacteriol 185 6463-6466.
24. Leung, P. H., Peiris, J. S., Ng, W. W., Robins-Browne, R. M., Bettelheim, K. A. & Yam, W. C. (2003). A newly discovered verotoxin variant, VT2g, produced by bovine verocytotoxigenic Escherichia coli. Appl Environ Microbiol 69, 7549-7553.
25. Levin, B. R. & Bergstrom, C. T. (2000). Bacteria are different: observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes. Proc Natl Acad Sci U S A 97, 6981-6985.
26. Lukashin, A. V. & Borodovsky, M. (1998). GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 26, 1107-1115.
27. Makino, K., Yokoyama, K., Kubota, Y. & 15 other authors (1999). Complete nucleotide sequence of the prophage VT2-Sakai carrying the verotoxin 2 genes of the enterohemorrhagic Escherichia coli O157:H7 derived from the Sakai outbreak. Genes Genet Syst 74, 227-239.
28. Matsutani, S. & Ohtsubo, E. (1990). Complete sequence of IS629. Nucleic Acids Res 18, 1899.
29. McDonough, M. A., Butterton, J. R., Macrina, F. L. & 14 other authors (1999). Spontaneous tandem amplification and deletion of the shiga toxin operon in Shigella dysenteriae 1. Mol Microbiol 34, 1058-1069.
30. Melton-Celsa, A. R., Darnell, S. C. & O'Brien, A. D. (1996). Activation of Shiga-like toxins by mouse and human intestinal mucus correlates with virulence of enterohemorrhagic Escherichia coli O91: H21 isolates in orally infected, streptomycin-treated mice. Infect Immun 64, 1569-1576.
31. Misselwitz, J., Karch, H., Bielazewska, M., John, U., Ringelmann, F., Ronnefarth, G. & Patzer, L. (2003). Cluster of hemolytic-uremic syndrome caused by Shiga toxin-producing Escherichia coli O26:H11. Pediatr Infect Dis 22, 349-354.
32. Muniesa, M., Recktenwald, J., Bielaszewska, M., Karch, H. & Schmidt, H. (2000). Characterization of a shiga toxin 2e-converting bacteriophage from an Escherichia coli strain of human origin. Infect Immun 68, 4850-4855.
33. Nataro, J. P. & Kaper, J. B. (1998). Diarrheagenic Escherichia coli. Clin Microbiol Rev 11, 142-201.
34. Neely, M. N. & Friedman, D. I. (998). Functional and genetic analysis of regulatory regions of coliphage H-19B: location of Shiga-like toxin and lysis genes suggest a role for phage functions in toxin release. Mol Microbiol 28, 1255-1267.
35. O'Brien, A. D. & Holmes, R. K. (1987). Shiga and Shiga-like toxins. Microbiol Rev 51, 206-220.
36. O'Brien, A. D., Lively, T. A., Chang, T. W. & Gorbach, S. L. (1983). Purification of Shigella dysenteriae 1 (Shiga)-like toxin from Escherichia coli O157:H7 strain associated with haemorrhagic colitis. Lancet 2, 573.
37. O'Brien, A. D., Newland, J. W., Miller, S. F., Holmes, R. K., Smith, H. W. & Formal, S. B. (1984). Shiga-like toxin-converting phages from Escherichia coli strains that cause hemorrhagic colitis or infantile diarrhea. Science 226, 694-696.
38. O'Loughlin, E. V. & Robins-Browne, R. M. (2001). Effect of Shiga toxin and Shiga-like toxins on eukaryotic cells. Microbes Infect 3, 493-507.
39. Perna, N. T., Plunkett, G., III, Burland, V. & 25 other authors (2001). Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409, 529-533.
40. Pierard, D., Muyldermans, G., Moriau, L., Stevens, D. & Lauwers, S. (1998). Identification of new verocytotoxin type 2 variant B-subunit genes in human and animal Escherichia coli isolates. J Clin Microbiol 36, 3317-3322.
41. Plunkett, G., III, Rose, D. J., Durfee, T. J. & Blattner, F. R. (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.
42. Pridmore, R. D. (1987). New and versatile cloning vectors with kanamycin-resistance marker. Gene 56, 309-312.
43. Recktenwald, J. & Schmidt, H. (2002). The nucleotide sequence of Shiga toxin (Stx) 2e-encoding phage phiP27 is not related to other Stx phage genomes, but the modular genetic structure is conserved. Infect 70, 1896-1908.
44. Riley, L. W., Remis, R. S., Helgerson, S. D. & 9 other authors (1983). Hemorrhagic colitis associated with a rare Escherichia coli serotype. N Engl J Med 308, 681-685.
45. Rüssmann, H., Schmidt, H., Caprioll, A. & Karch, H. (1994a). Highly conserved B-subunit genes of Shiga-like toxin II variants found in Escherichia coli O157 strains. FEMS Microbiol Lett 118, 335-340.
46. Rüssmann, H., Schmidt, H., Heesemann, J., Caprioli, A. & Karch, H. (1994b). Variants of Shiga-like toxin II constitute a major toxin component in Escherichia coli O157 strains from patients with haemolytic uraemic syndrome. J Med Microbiol 40 338-343.
47. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning. a Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
48. Sato, T., Shimizu, T., Watarai, M., Kobayashi, M., Kano, S., Hamabata, T., Takeda, Y. & Yamasaki, S. (2003a). Distinctiveness of the genomic sequence of Shiga toxin 2-converting phage isolated from Escherichia coli O157:H7 Okayama strain as compared to other Shiga toxin 2-converting phages. Gene 309, 35-48.
49. Sato, T., Shimizu, T., Watarai, M., Kobayashi, M., Kano, S., Hamabata, T., Takeda, Y. & Yamasaki, S. (2003b). Genome analysis of a novel Shiga toxin 1 (Stx1)-converting phage which is closely related to Stx2-converting phages but not to other Stx1-converting phages. J Bacteriol 185, 3966-3971.
50. Schmidt H. (2001). Shiga-toxin-converting bacteriophages. Res Microbiol 152, 687-695.
51. Schmidt, H., Rüssmann, H., Schwarzkopf, A., Aleksic, S., Heesemann, J. & Karch, H. (1994). Prevalence of attaching and effacing Escherichia coli in stool samples from patients and controls. Zentbl Bakteriol 281, 201-213.
52. Schmidt, H., Bielaszewska, M. & Karch, H. (1999a). Transduction of enteric Escherichia coli isolates with a derivative of Shiga toxin 2-encoding bacteriophage phi3538 isolated from Escherichia coli O157:H7. Appl Environ Microbiol 65, 3855-3861.
53. Schmidt, H., Geitz, C., Tarr, P. I., Frosch, M. & Karch, H. (1999b). Non-O157:H7 pathogenic Shiga toxin-producing Escherichia coli: phenotypic and genetic profiling of virulence traits and evidence for clonality. J Infect Dis 179, 115-123.
54. Schmidt, H., Scheef, J., Huppertz, H. I., Frosch, M. & Karch, H. (1999c). Escherichia coli O157:H7 and O157:H- strains that do not produce Shiga toxin: phenotypic and genetic characterization of isolates associated with diarrhea and hemolytic-uremic syndrome. J Clin Microbiol 37, 3491-3496.
55. Schmidt, H., Scheef, J., Morabito, S., Caprioll, A., Wieler, L. H. & Karch, H. (2000). A new Shiga toxin 2 variant (Stx2f) from Escherichia coli isolated from pigeons. Appl Environ Microbiol 66, 1205-1208.
56. - strain E32511. Infect Immun 59, 1065-1073.
57. Scotland, S. M., Smith, H. R., Willshaw, G. A. & Rowe, B. (1983). Vero cytotoxin production in strain of Escherichia coli is determined by genes carried on bacteriophage. Lancet 2, 216.
58. Staden, R. & MacLachlan, A. D. (1982). Codon preference and its use in identifying protein coding regions in long DNA sequences. Nucleic Acids Res 10, 141-156.
59. Strauch, E., Lurz, R. & Beutin, L. (2001). Characterization of a Shiga toxin-encoding temperate bacteriophage of Shigella sonnei. Infect Immun 69, 7588-7595.
60. Thomas, A., Cheasty, T., Chart H. & Rowe, B. (1994). Isolation of Vero cytotoxin-producing Escherichia coli serotypes O9ab:H- and O101:H-carrying VT2 variant gene sequences from a patient with haemolytic uraemic syndrome. Eur J Clin Microbiol Infect Dis 13, 1074-1076.
61. Toth, I., Schmidt, H., Dow, M., Malik, A., Oswald, E. & Nagy, B. (2003). Transduction of porcine enteropathogenic Escherichia coli with a derivative of a Shiga toxin 2-encoding bacteriophage in a porcine ligated ileal loop system. Appl Environ Microbiol 69, 7242-7247.
62. Tozzi, A. E., Caprioli, A., Minelli, F. & 8 other authors (2003). Shiga toxin-producing Escherichia coli infections associated with hemolytic uremic syndrome, Italy, 1988-2000. Emerg Infect Dis 9, 106-108.
63. Unkmeir, A. & Schmidt, H. (2000). Structural analysis of phage-borne stx genes and their flanking sequences in shiga toxin-producing Escherichia coli and Shigella dysenteriae type 1 strains. Infect Immun 68, 4856-4864.
64. Wagner, P. L. & Waldor, M. K. (2002). Bacteriophage control of bacterial virulence. Infect Immun 70, 3985-3993.
65. Wagner, P. L., Neely, M. N., Zhang, X., Acheson, D. W., Waldor, M. K. & Friedman, D. I. (2001). Role for a phage promoter in Shiga toxin 2 expression from a pathogenic Escherichia coli strain. J Bacteriol 183, 2081-2085.
66. Wells, J. G., Davis, B. R., Wachsmuth, I. K., Riley, L. W., Remis, R. S., Sokolow, R. & Morris, G. K. (1983). Laboratory investigation of hemorrhagic colitis outbreaks associated with a rare Escherichia coli serotype. J Clin Microbiol 18, 512-520.
67. Williams, K. P. (2003). Traffic at the tmRNA gene. J Bacteriol 185, 1059-1070.
68. Williams, J. M., Boyd, B., Nutikka, A., Lingwood, C. A., Barnett Foster, D. E., Milford, D. V. & Taylor, C. M. (1999). A comparison of the effects of verocytotoxin-1 on primary human renal cell cultures. Toxicol Lett 105, 47-57.
69. Willshaw, G. A., Smith, H. R., Scotland, S. M., Field, A. M. & Rowe, B. (1987). Heterogeneity of Escherichia coli phages encoding Vero cytotoxins: comparison of cloned sequences determining VT1 and VT2 and development of specific gene probes. J Gen Microbiol 133, 1309-1317.
70. Zhang, W. L., Bielaszewska, M., Liesegang, A., Tschäpe, H., Schmidt, H., Bitzan, M. & Karch, H. (2000). Molecular characteristics and epidemiological significance of Shiga toxin-producing Escherichia coli O26 strains. J Clin Microbiol 38, 2134-2140.
71. 1c) in Escherichia coli strains isolated from humans. J Clin Microbiol 40, 1441-1446.
72. Zoja, C., Morigi, M. & Remuzzi, G. (2001). The role of the endothelium in hemolytic uremic syndrome. J Nephrol 14, 58-62.