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. 1996 Sep;64(9):3736–3743. doi: 10.1128/iai.64.9.3736-3743.1996

Two pathogenicity islands in uropathogenic Escherichia coli J96: cosmid cloning and sample sequencing.

D L Swenson 1, N O Bukanov 1, D E Berg 1, R A Welch 1
PMCID: PMC174287  PMID: 8751923

Abstract

Many of the virulence genes of pathogenic strains of Escherichia coli are carried in large multigene chromosomal segments called pathogenicity islands (PAIs) that are absent from normal fecal and laboratory K-12 strains of this bacterium. We are studying PAIs in order to better understand factors that govern virulence and to assess how such DNA segments are gained or lost during evolution. The isolation and sample sequencing of a set of 11 cosmid clones that cover all of one and much of a second large PAI in the uropathogenic E. coli J96 are described. These PAIs were mapped to the 64- and 94-min regions of the E. coli K-12 chromosome, which differ from the locations of three PAIs identified in other pathogenic E. coli strains. Analysis of the junction sequences with E. coli K-12-like DNAs showed that the insert at 94 min is within the 3' end of a phenylalanine tRNA gene, pheR, and is flanked by a 135-bp imperfect direct repeat. Analysis of the one junction recovered from the insert at 64 min indicated that it lies near another tRNA gene, pheV. To identify possible genes unique to these PAIs, 100 independent subclones of the cosmids were made by PstI digestion and ligation into a pBS+ plasmid and used in one-pass sample DNA sequencing from primer binding sites at the cloning site in the vector DNA. Database searches of the J96 PAI-specific sequences identified numerous instances in which the cloned DNAs shared significant sequence similarities to adhesins, toxins, and other virulence determinants of diverse pathogens. Several likely insertion sequence elements (IS100, IS630, and IS911) and conjugative R1 plasmid and P4 phage genes were also found. We propose that such mobile genetic elements may have facilitated the spread of virulence determinants within PAIs among bacteria.

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Selected References

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  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Bachmann B. J. Linkage map of Escherichia coli K-12, edition 8. Microbiol Rev. 1990 Jun;54(2):130–197. doi: 10.1128/mr.54.2.130-197.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bahrani F. K., Massad G., Lockatell C. V., Johnson D. E., Russell R. G., Warren J. W., Mobley H. L. Construction of an MR/P fimbrial mutant of Proteus mirabilis: role in virulence in a mouse model of ascending urinary tract infection. Infect Immun. 1994 Aug;62(8):3363–3371. doi: 10.1128/iai.62.8.3363-3371.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Barenkamp S. J., Leininger E. Cloning, expression, and DNA sequence analysis of genes encoding nontypeable Haemophilus influenzae high-molecular-weight surface-exposed proteins related to filamentous hemagglutinin of Bordetella pertussis. Infect Immun. 1992 Apr;60(4):1302–1313. doi: 10.1128/iai.60.4.1302-1313.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Blum G., Falbo V., Caprioli A., Hacker J. Gene clusters encoding the cytotoxic necrotizing factor type 1, Prs-fimbriae and alpha-hemolysin form the pathogenicity island II of the uropathogenic Escherichia coli strain J96. FEMS Microbiol Lett. 1995 Feb 15;126(2):189–195. doi: 10.1111/j.1574-6968.1995.tb07415.x. [DOI] [PubMed] [Google Scholar]
  6. Blum G., Ott M., Lischewski A., Ritter A., Imrich H., Tschäpe H., Hacker J. Excision of large DNA regions termed pathogenicity islands from tRNA-specific loci in the chromosome of an Escherichia coli wild-type pathogen. Infect Immun. 1994 Feb;62(2):606–614. doi: 10.1128/iai.62.2.606-614.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bukanov N. O., Berg D. E. Ordered cosmid library and high-resolution physical-genetic map of Helicobacter pylori strain NCTC11638. Mol Microbiol. 1994 Feb;11(3):509–523. doi: 10.1111/j.1365-2958.1994.tb00332.x. [DOI] [PubMed] [Google Scholar]
  8. Caprioli A., Falbo V., Roda L. G., Ruggeri F. M., Zona C. Partial purification and characterization of an escherichia coli toxic factor that induces morphological cell alterations. Infect Immun. 1983 Mar;39(3):1300–1306. doi: 10.1128/iai.39.3.1300-1306.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Caprioli A., Falbo V., Ruggeri F. M., Baldassarri L., Bisicchia R., Ippolito G., Romoli E., Donelli G. Cytotoxic necrotizing factor production by hemolytic strains of Escherichia coli causing extraintestinal infections. J Clin Microbiol. 1987 Jan;25(1):146–149. doi: 10.1128/jcm.25.1.146-149.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Cheetham B. F., Katz M. E. A role for bacteriophages in the evolution and transfer of bacterial virulence determinants. Mol Microbiol. 1995 Oct;18(2):201–208. doi: 10.1111/j.1365-2958.1995.mmi_18020201.x. [DOI] [PubMed] [Google Scholar]
  11. Delisse-Gathoye A. M., Locht C., Jacob F., Raaschou-Nielsen M., Heron I., Ruelle J. L., de Wilde M., Cabezon T. Cloning, partial sequence, expression, and antigenic analysis of the filamentous hemagglutinin gene of Bordetella pertussis. Infect Immun. 1990 Sep;58(9):2895–2905. doi: 10.1128/iai.58.9.2895-2905.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Falbo V., Famiglietti M., Caprioli A. Gene block encoding production of cytotoxic necrotizing factor 1 and hemolysin in Escherichia coli isolates from extraintestinal infections. Infect Immun. 1992 Jun;60(6):2182–2187. doi: 10.1128/iai.60.6.2182-2187.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Falbo V., Pace T., Picci L., Pizzi E., Caprioli A. Isolation and nucleotide sequence of the gene encoding cytotoxic necrotizing factor 1 of Escherichia coli. Infect Immun. 1993 Nov;61(11):4909–4914. doi: 10.1128/iai.61.11.4909-4914.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Fetherston J. D., Perry R. D. The pigmentation locus of Yersinia pestis KIM6+ is flanked by an insertion sequence and includes the structural genes for pesticin sensitivity and HMWP2. Mol Microbiol. 1994 Aug;13(4):697–708. doi: 10.1111/j.1365-2958.1994.tb00463.x. [DOI] [PubMed] [Google Scholar]
  15. Fetherston J. D., Schuetze P., Perry R. D. Loss of the pigmentation phenotype in Yersinia pestis is due to the spontaneous deletion of 102 kb of chromosomal DNA which is flanked by a repetitive element. Mol Microbiol. 1992 Sep;6(18):2693–2704. doi: 10.1111/j.1365-2958.1992.tb01446.x. [DOI] [PubMed] [Google Scholar]
  16. Fives-Taylor P. M., Macrina F. L., Pritchard T. J., Peene S. S. Expression of Streptococcus sanguis antigens in Escherichia coli: cloning of a structural gene for adhesion fimbriae. Infect Immun. 1987 Jan;55(1):123–128. doi: 10.1128/iai.55.1.123-128.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Fonstein M., Haselkorn R. Chromosomal structure of Rhodobacter capsulatus strain SB1003: cosmid encyclopedia and high-resolution physical and genetic map. Proc Natl Acad Sci U S A. 1993 Mar 15;90(6):2522–2526. doi: 10.1073/pnas.90.6.2522. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Ganeshkumar N., Hannam P. M., Kolenbrander P. E., McBride B. C. Nucleotide sequence of a gene coding for a saliva-binding protein (SsaB) from Streptococcus sanguis 12 and possible role of the protein in coaggregation with actinomyces. Infect Immun. 1991 Mar;59(3):1093–1099. doi: 10.1128/iai.59.3.1093-1099.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Gibson T. J., Rosenthal A., Waterston R. H. Lorist6, a cosmid vector with BamHI, NotI, ScaI and HindIII cloning sites and altered neomycin phosphotransferase gene expression. Gene. 1987;53(2-3):283–286. doi: 10.1016/0378-1119(87)90017-5. [DOI] [PubMed] [Google Scholar]
  20. Hacker J., Bender L., Ott M., Wingender J., Lund B., Marre R., Goebel W. Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extraintestinal Escherichia coli isolates. Microb Pathog. 1990 Mar;8(3):213–225. doi: 10.1016/0882-4010(90)90048-u. [DOI] [PubMed] [Google Scholar]
  21. Hacker J. Genetic determinants coding for fimbriae and adhesins of extraintestinal Escherichia coli. Curr Top Microbiol Immunol. 1990;151:1–27. doi: 10.1007/978-3-642-74703-8_1. [DOI] [PubMed] [Google Scholar]
  22. Hagberg L., Hull R., Hull S., Falkow S., Freter R., Svanborg Edén C. Contribution of adhesion to bacterial persistence in the mouse urinary tract. Infect Immun. 1983 Apr;40(1):265–272. doi: 10.1128/iai.40.1.265-272.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. High N. J., Hales B. A., Jann K., Boulnois G. J. A block of urovirulence genes encoding multiple fimbriae and hemolysin in Escherichia coli O4:K12:H-. Infect Immun. 1988 Feb;56(2):513–517. doi: 10.1128/iai.56.2.513-517.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Hull R., Bieler S., Falkow S., Hull S. Chromosomal map position of genes encoding P adhesins in uropathogenic Escherichia coli. Infect Immun. 1986 Feb;51(2):693–695. doi: 10.1128/iai.51.2.693-695.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Hull S. I., Bieler S., Hull R. A. Restriction fragment length polymorphism and multiple copies of DNA sequences homologous with probes for P-fimbriae and hemolysin genes among uropathogenic Escherichia coli. Can J Microbiol. 1988 Mar;34(3):307–311. doi: 10.1139/m88-056. [DOI] [PubMed] [Google Scholar]
  26. Hultgren S. J., Abraham S., Caparon M., Falk P., St Geme J. W., 3rd, Normark S. Pilus and nonpilus bacterial adhesins: assembly and function in cell recognition. Cell. 1993 Jun 4;73(5):887–901. doi: 10.1016/0092-8674(93)90269-v. [DOI] [PubMed] [Google Scholar]
  27. Knapp S., Hacker J., Jarchau T., Goebel W. Large, unstable inserts in the chromosome affect virulence properties of uropathogenic Escherichia coli O6 strain 536. J Bacteriol. 1986 Oct;168(1):22–30. doi: 10.1128/jb.168.1.22-30.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Kohara Y., Akiyama K., Isono K. 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. 1987 Jul 31;50(3):495–508. doi: 10.1016/0092-8674(87)90503-4. [DOI] [PubMed] [Google Scholar]
  29. Krishnan B. R., Jamry I., Berg D. E., Berg C. M., Chaplin D. D. Construction of a genomic DNA 'feature map' by sequencing from nested deletions: application to the HLA class I region. Nucleic Acids Res. 1995 Jan 11;23(1):117–122. doi: 10.1093/nar/23.1.117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Krogfelt K. A. Bacterial adhesion: genetics, biogenesis, and role in pathogenesis of fimbrial adhesins of Escherichia coli. Rev Infect Dis. 1991 Jul-Aug;13(4):721–735. doi: 10.1093/clinids/13.4.721. [DOI] [PubMed] [Google Scholar]
  31. Lee C. A. Pathogenicity islands and the evolution of bacterial pathogens. Infect Agents Dis. 1996 Jan;5(1):1–7. [PubMed] [Google Scholar]
  32. Lindberg F. P., Lund B., Normark S. Genes of pyelonephritogenic E. coli required for digalactoside-specific agglutination of human cells. EMBO J. 1984 May;3(5):1167–1173. doi: 10.1002/j.1460-2075.1984.tb01946.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Low D., David V., Lark D., Schoolnik G., Falkow S. Gene clusters governing the production of hemolysin and mannose-resistant hemagglutination are closely linked in Escherichia coli serotype O4 and O6 isolates from urinary tract infections. Infect Immun. 1984 Jan;43(1):353–358. doi: 10.1128/iai.43.1.353-358.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Lund B., Marklund B. I., Strömberg N., Lindberg F., Karlsson K. A., Normark S. Uropathogenic Escherichia coli can express serologically identical pili of different receptor binding specificities. Mol Microbiol. 1988 Mar;2(2):255–263. doi: 10.1111/j.1365-2958.1988.tb00027.x. [DOI] [PubMed] [Google Scholar]
  35. Lutwyche P., Rupps R., Cavanagh J., Warren R. A., Brooks D. E. Cloning, sequencing, and viscometric adhesion analysis of heat-resistant agglutinin 1, an integral membrane hemagglutinin from Escherichia coli O9:H10:K99. Infect Immun. 1994 Nov;62(11):5020–5026. doi: 10.1128/iai.62.11.5020-5026.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. McDaniel T. K., Jarvis K. G., Donnenberg M. S., Kaper J. B. A genetic locus of enterocyte effacement conserved among diverse enterobacterial pathogens. Proc Natl Acad Sci U S A. 1995 Feb 28;92(5):1664–1668. doi: 10.1073/pnas.92.5.1664. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Mills D. M., Bajaj V., Lee C. A. A 40 kb chromosomal fragment encoding Salmonella typhimurium invasion genes is absent from the corresponding region of the Escherichia coli K-12 chromosome. Mol Microbiol. 1995 Feb;15(4):749–759. doi: 10.1111/j.1365-2958.1995.tb02382.x. [DOI] [PubMed] [Google Scholar]
  38. Minshew B. H., Jorgensen J., Counts G. W., Falkow S. Association of hemolysin production, hemagglutination of human erythrocytes, and virulence for chicken embryos of extraintestinal Escherichia coli isolates. Infect Immun. 1978 Apr;20(1):50–54. doi: 10.1128/iai.20.1.50-54.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Mobley H. L., Jarvis K. G., Elwood J. P., Whittle D. I., Lockatell C. V., Russell R. G., Johnson D. E., Donnenberg M. S., Warren J. W. Isogenic P-fimbrial deletion mutants of pyelonephritogenic Escherichia coli: the role of alpha Gal(1-4) beta Gal binding in virulence of a wild-type strain. Mol Microbiol. 1993 Oct;10(1):143–155. doi: 10.1111/j.1365-2958.1993.tb00911.x. [DOI] [PubMed] [Google Scholar]
  40. Mühldorfer I., Hacker J. Genetic aspects of Escherichia coli virulence. Microb Pathog. 1994 Mar;16(3):171–181. doi: 10.1006/mpat.1994.1018. [DOI] [PubMed] [Google Scholar]
  41. O'Hanley P., Lalonde G., Ji G. Alpha-hemolysin contributes to the pathogenicity of piliated digalactoside-binding Escherichia coli in the kidney: efficacy of an alpha-hemolysin vaccine in preventing renal injury in the BALB/c mouse model of pyelonephritis. Infect Immun. 1991 Mar;59(3):1153–1161. doi: 10.1128/iai.59.3.1153-1161.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Ochman H., Groisman E. A. The evolution of invasion by enteric bacteria. Can J Microbiol. 1995 Jul;41(7):555–561. doi: 10.1139/m95-074. [DOI] [PubMed] [Google Scholar]
  43. Orskov F., Orskov I. Escherichia coli serotyping and disease in man and animals. Can J Microbiol. 1992 Jul;38(7):699–704. [PubMed] [Google Scholar]
  44. Palmer K. L., Munson R. S., Jr Cloning and characterization of the genes encoding the hemolysin of Haemophilus ducreyi. Mol Microbiol. 1995 Dec;18(5):821–830. doi: 10.1111/j.1365-2958.1995.18050821.x. [DOI] [PubMed] [Google Scholar]
  45. Poole K., Schiebel E., Braun V. Molecular characterization of the hemolysin determinant of Serratia marcescens. J Bacteriol. 1988 Jul;170(7):3177–3188. doi: 10.1128/jb.170.7.3177-3188.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Portnoy D. A., Falkow S. Virulence-associated plasmids from Yersinia enterocolitica and Yersinia pestis. J Bacteriol. 1981 Dec;148(3):877–883. doi: 10.1128/jb.148.3.877-883.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Reiter W. D., Palm P., Yeats S. Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res. 1989 Mar 11;17(5):1907–1914. doi: 10.1093/nar/17.5.1907. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Ritter A., Blum G., Emödy L., Kerenyi M., Böck A., Neuhierl B., Rabsch W., Scheutz F., Hacker J. tRNA genes and pathogenicity islands: influence on virulence and metabolic properties of uropathogenic Escherichia coli. Mol Microbiol. 1995 Jul;17(1):109–121. doi: 10.1111/j.1365-2958.1995.mmi_17010109.x. [DOI] [PubMed] [Google Scholar]
  49. Salvi R. J., Ahroon W., Saunders S. S., Arnold S. A. Evoked potentials: computer-automated threshold-tracking procedure using an objective detection criterion. Ear Hear. 1987 Jun;8(3):151–156. [PubMed] [Google Scholar]
  50. Sampson J. S., O'Connor S. P., Stinson A. R., Tharpe J. A., Russell H. Cloning and nucleotide sequence analysis of psaA, the Streptococcus pneumoniae gene encoding a 37-kilodalton protein homologous to previously reported Streptococcus sp. adhesins. Infect Immun. 1994 Jan;62(1):319–324. doi: 10.1128/iai.62.1.319-324.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Welch R. A., Dellinger E. P., Minshew B., Falkow S. Haemolysin contributes to virulence of extra-intestinal E. coli infections. Nature. 1981 Dec 17;294(5842):665–667. doi: 10.1038/294665a0. [DOI] [PubMed] [Google Scholar]
  52. Welch R. A., Falkow S. Characterization of Escherichia coli hemolysins conferring quantitative differences in virulence. Infect Immun. 1984 Jan;43(1):156–160. doi: 10.1128/iai.43.1.156-160.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Welch R. A., Hull R., Falkow S. Molecular cloning and physical characterization of a chromosomal hemolysin from Escherichia coli. Infect Immun. 1983 Oct;42(1):178–186. doi: 10.1128/iai.42.1.178-186.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Welch R. A., Pellett S. Transcriptional organization of the Escherichia coli hemolysin genes. J Bacteriol. 1988 Apr;170(4):1622–1630. doi: 10.1128/jb.170.4.1622-1630.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Welch R. A. Pore-forming cytolysins of gram-negative bacteria. Mol Microbiol. 1991 Mar;5(3):521–528. doi: 10.1111/j.1365-2958.1991.tb00723.x. [DOI] [PubMed] [Google Scholar]

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