Complete DNA sequence and detailed analysis of the Yersinia pestis KIM5 plasmid encoding murine toxin and capsular antigen

Infection and Immunity

Volumn 66, Issue 12, 1998, Pages 5731-5742

  Lindler, Luther E ^a   Plano, Gregory V ^b   Burland, Valerie ^c   Mayhew, George F ^c   Blattner, Frederick R ^c  

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

^b UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ANTIGEN; BACTERIAL TOXIN; VIRULENCE FACTOR;

ARTICLE; BACTERIAL VIRULENCE; BACTERIOPHAGE; DNA SEQUENCE; GENE REPLICATION; GENE TRANSFER; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLASMID; PRIORITY JOURNAL; SEQUENCE ANALYSIS; YERSINIA PESTIS;

YERSINIA PESTIS;

EID: 0031796312     PISSN: 00199567     EISSN: None     Source Type: Journal    
DOI: 10.1128/iai.66.12.5731-5742.1998     Document Type: Article

References (101)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Bercovier, H., H. H. Mollaret, J. M. Alonso, J. Brault, G. R. Fanning, A. G. Steigerwalt, and D. J. Brenner. 1980. Intra-and interspecies relatedness of Yersinia pestis by deoxyribonucleic acid hybridization and its relationship to Yersinia pseudotuberculosis. Curr. Microbiol. 4:225-229.
3. Beuzon, C. R., and J. Casadesus. 1997. Conserved structure of IS200 elements in Salmonella. Nucleic Acids Res. 25:1355-1361.
4. Birnboim, H. C., and J. Doly. 1979. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 7:1513-1523.
5. 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. Kirpatrick, M. A. Goeden, D. J. Rose, R. Mau, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453-1462.
6. Borodovsky, M., and J. McIninch. 1993. Genmark: parallel gene recognition for both DNA strands. Comput. Chem. 17:123-133.
7. Boyd, E. F., C. W. Hill, S. M. Rich, and D. L. Hartl. 1996. Mosaic structure of plasmids from natural populations of Escherichia coli. Genetics 143: 1091-1100.
8. Brubaker, R. R. 1972. The genus Yersinia: biochemistry and genetics of virulence. Curr. Top. Microbiol. 57:111-158.
9. ++. Rev. Infect. Dis. 5: S748-S758.
10. Brubaker, R. R. 1991. Factors promoting acute and chronic diseases caused by yersiniae. Clin. Microbiol. Rev. 4:309-324.
11. Brubaker, R. R., E. D. Beesley, and M. J. Surgalla. 1965. Pasturella pestis: role of pesticin I and iron in experimental plague. Science 149:422-424.
12. 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.
13. Burland, V., G. Plunkett III, H. J. Sofia, D. L. Daniels, and F. R. Blattner. 1995. Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes. Nucleic Acids Res. 23:2105-2119.
14. Burland, V., Y. Shao, N. T. Perna, G. Plunkett III, H. J. Sofia, and F. R. Blattner. The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7. Submitted for publication.
15. Butler, T. 1983. Plague and other yersinia infections, p. 111-159. In W. B. Greenbugh III and T. C. Merigan (ed.), Current topics in infectious disease. Plenum Press, New York, N.Y.
16. Cameron, B., C. Guilhot, F. Blanche, L. Cauchois, M. C. Rouyez, S. Rigault, S. Levy-Schil, and J. Crouzet. 1991. Genetic and sequence analysis of the Pseudomonas denitrificans DNA fragment containing two cob genes. J. Bacteriol. 173:6058-6065.
17. Cerin, H., and J. Hackett. 1993. The parVP region of the Salmonella typhimurium virulence plasmid pSLT contains four loci required for incompatibility and partition. Plasmid 30:30-38.
18. Chattoraj, D. K., and T. D. Schneider. 1997. Replication control of plasmid P1 and its host chromosome: the common ground. Prog. Nucleic Acid Res. Mol. Biol. 57:145-186.
19. Chattoraj, D. K., K. M. Snyder, and A. L. Abeles. 1985. P1 plasmid replication: multiple functions of RepA protein at the origin. Proc. Natl. Acad. Sci. USA 82:2588-2592.
20. Cheng, Q., E. A. Campbell, A. M. Naughton, S. Johnson, and H. R. Masure. 1997. The com locus controls genetic transformation in Streptococcus pneumoniae. Mol. Microbiol. 23:683-692.
21. Chilley, P. M., and B. M. Wilkins. 1995. Distribution of the ardA family of antirestriction genes on conjugative plasmids. Microbiology 141:2157-2164.
22. Davis, M. A., and S. J. Austin. 1988. Recognition of the P1 plasmid centromere analog involves binding of the ParB protein and is modified by a specific host factor. EMBO J. 7:1881-1888.
23. Davis, M. A., K. A. Martin, and S. J. Austin. 1992. Biochemical activities of the ParA partition protein of the P1 plasmid. Mol. Microbiol. 6:1141-1147.
24. De Chateau, M., and L. Bjorck. 1996. Identification of interdomain sequences promoting the intronless evolution of a bacterial protein family. Proc. Natl. Acad. Sci. USA 93:8490-8495.
25. Donelson, J. E., B. O. L. Duke, D. Moser, W. Zeng, N. E. Erondu, R. Lucius, A. Renz, M. Karam, and G. Z. Flores. 1988. Construction of Onchocerca volvulus cDNA libraries and partial characterization of the cDNA for a major antigen. Mol. Biochem. Parasitol. 31:241-250.
26. Doolittle, R. F. 1995. The multiplicity of domains in proteins. Annu. Rev. Biochem. 64:287-314.
27. Drozdov, I. G., A. P. Anisimov, S. V. Samoilova, I. N. Yezhov, S. A. Yeremin, A. V. Karlyshev, V. M. Krasilniova, and V. I. Kravchenko. 1995. Virulent non-capsulate Yersinia pestis variants constructed by insertion mutagenesis. J. Med. Microbiol. 42:264-268.
28. Du, Y., E. Galyov, and A. Forsberg. 1995. Genetic analysis of virulence determinants unique to Yersinia pestis. Contrib. Microbiol. Immunol. 13: 321-324.
29. Dutreix, M., A. Backman, J. Celerier, M. M. Bagdasarian, S. Sommer, A. Bailone, R. Devoret, and M. Bagdasatian. 1988. Identification of psiB genes of plasmids F and R6-5. Molecular basis for psiB enhanced expression in plasmid R6-5. Nucleic Acids Res. 16:10669-10679.
30. Ferber, D. M., and R. R. Brubaker. 1981. Plasmids in Yersinia pestis. Infect. Immun. 31:839-841.
31. Filippov, A. A., N. S. Solodovnikov, L. M. Kookleva, and O. A. Protsenko. 1990. Plasmid content in Yersinia pestis strains of different origin. FEMS Microbiol. Lett. 67:45-48.
32. Frey, J., R. Meier, D. Gygi, and J. Nicolet. 1991. Nucleotide sequence of the hemolysin I gene from Actinobacillus pleuropneumoniae. Infect. Immun. 59: 3026-3032.
33. Frost, L. S., K. Ippen-Ihler, and R. A. Skurry. 1994. Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol. Rev. 58:162-210.
34. Gabant, P., A. O. Chahdi, and M. Couturier. 1994. Nucleotide sequence and replication characteristics of RepHI1B: a replicon specific to the In-cHI1 plasmids. Plasmid 31:111-120.
35. Galjart, N. J., N. Sivasubramanian, and B. A. Federici. 1987. Plasmid localization, cloning and sequence of the gene encoding a 27.3-kilodalton cytolytic protein from Bacillus thuringiensis subspecies morrisoni (PG14). Curr. Microbiol. 16:171-177.
36. Galyov, E. E., A. V. Karlyshev, T. V. Chernoskaya, D. A. Dolgikh, O. Y. Smirnov, K. I. Volkovoy, V. M. Abramov, and V. P. Zav'yalov. 1991. Expression of the envelope antigen F1 of Yersinia pestis is mediated by the product of caf1M gene having homology with the chaperone protein PapD of Escherichia coli. FEBS Lett. 286:79-82.
37. Galyov, E. E., O. Y. Smirnov, A. V. Karlishev, K. I. Volkovoy, A. I. Denesyuk, I. V. Nazimov, K. S. Rubtsov, V. M. Dalvadyanz, and V. P. Zav'yalov. 1990. Nucleotide sequence of the Yersinia pestis gene encoding F1 antigen and the primary structure of the protein. Putative T and B cell epitopes. FEBS Lett. 277:230-232.
38. Goodrich, J. A., M. L. Schwartz, and W. R. McClure. 1990. Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF). Nucleic Acids Res. 18:4993-5000.
39. Hacker, J., G. Blum-Oehler, I. Muhldorfer, and H. Tschape. 1997. Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol. Microbiol. 23:1089-1097.
40. Hanekamp, T. D. Kobayashi, S. Hayes, and M. M. Stayton. 1997. Avirulence gene D of Pseudomonas syringae pv. tomato may have undergone horizontal gene transfer. FEBS Lett. 415:40-44.
41. Harlan, D. M., J. M. Graff, D. J. Stumpo, R. L. Eddy, Jr., T. B. Stows, J. M. Boyle and P. J. Blackshear. 1991. The human myristoylated alanine-rich C kinase substrate (MARCKS) gene. Analysis of its gene product, promoter and chromosomal localization. J. Biol. Chem. 266:14399-14405.
42. Hayes, F., and S. J. Austin. 1993. Specificity determinants of the P1 and P7 centromere analogs. Proc. Natl. Acad. Sci. USA 90:9228-9232.
43. Hayes, F., and S. J. Austin. 1994. Topological scanning of the P1 plasmid partition site. J. Mol. Biol. 243:190-198.
44. Herzer, P. J., S. Inouye, and M. Inouye. 1992. Retron-Ec107 is inserted into the Escherichia coli genome by replacing a palindromic 34bp intergenic sequence. Mol. Microbiol. 6:345-354.
45. Hofman, K., and W. Stoffel. 1993. Tmbase - a database of membrane spanning protein segmants. Biol. Chem. 347:166-172.
46. Hu, P., J. Elliott, P. McCready, E. Skowronski, J. Garnes, A. Kobayashi, R. R. Brubaker, and E. Garcia. 1998. Structural organization of virulence-associated plasmids of Yersinia pestis. J. Bacteriol. 180:5192-5202.
47. Humphreys, G. O., G. A. Willshaw, and E. S. Anderson. 1975. A simple method for the preparation of large quantities of pure plasmid DNA. Biochim. Biophys. Acta 383:457-463.
48. 12, p. 551-556. In F. C. Neidhardt, J. L. Ingraham, B. Magasanik, K. B. Low, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: cellular and molecular biology. American Society for Microbiology, Washington, D.C.
49. Jones, A. J., P. T. Barth, and B. M. Wilkins. 1992. Zygotic induction of plasmid ssb and psiB genes following conjugative transfer of IncI1 plasmid ColIb-P9. Mol. Microbiol. 6:605-613.
50. Karlyshev, A. V., E. E. Galyov, V. M. Abramov, and V. P. Zav'yalov. 1992. Caf1R gene and its role in the regulation of capsule formation of Y. pestis. FEBS Lett. 305:37-40.
51. Koltsova, E. G., Y. G. Suchkov, and S. A. Lebedeva. 1975. Transmission of a bacteriocinogenic factor in Pasturella pestis. Sov. Genet. 7:507-510.
52. Krause, M., J. Harwood, J. Fierer, and D. Guiney. 1991. Genetic analysis of homology between the virulence plasmids of Salmonella dublin and Yersinia pseudotuberculosis. Infect. Immun. 59:1860-1863.
53. Lampson, B. C., S. Inouye, and M. Inouye. 1991. msDNA of bacteria. Prog. Nucleic Acid Res. Mol. Biol. 40:1-24.
54. Lanka, E., and B. M. Wilkins. 1995. DNA processing reactions in bacterial conjugation. Annu. Rev. Biochem. 64:141-169.
55. Lewis, P. J., and J. Errington. 1997. Direct evidence for active segregation of oriC regions on the Bacillus subtilis chromosome and co-localization with the SpoOJ partitioning protein. Mol. Microbiol. 25:945-954.
56. Lipman, D., S. Altschul, and J. Kececioglu. 1989. A tool for multiple sequence alignment. Proc. Natl. Acad. Sci. USA 86:4412-4415.
57. Ludtke, D. N., and S. J. Austin. 1987. The plasmid-maintenance functions of the P7 prophage. Plasmid 18:93-98.
58. Matsutani, S., H. Ohtsubo, Y. Maeda, and E. Ohtsubo. 1987. Isolation and characterization of IS elements repeated in the bacterial chromosome. J. Mol. Biol. 196:445-455.
59. McDonough, K. A., A. M. Barnes, T. J. Quan, J. Montenieri, and S. Falkow. 1993. Mutation in the pla gene of Yersinia pestis alters the course of plague bacillus-flea (Siphonaptera: ceratophyllidae) interaction. J. Med. Entomol. 30:772-780.
60. McDonough, K. A., and J. M. Hare. 1997. Homology with a repeated Yersinia pestis DNA sequence IS100 correlates with pesticin sensitivity in Yersinia pseudotuberculosis. J. Bacteriol. 179:2081-2085.
61. Mercado-Blanco, J., and J. Olivares. 1994. A protein involved in stabilization of a large non-symbiotic plasmid of Rhizobium meliloti shows homology to eukaryotic cytoskeletal proteins and DNA binding proteins. Gene 139: 133-134.
62. Mercado-Blanco, J., and J. Olivares. 1994. The large non-symbiotic plasmid pRmeGR4a of Rhizobium meliloti GR4 encodes a protein involved in replication that has homology with the RepC protein of Agrobacterium plasmids. Plasmid 32:75-79.
63. Millon, 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. Subdivision of the Escherichia coli K-12 genome for sequencing: manipulation and DNA sequence of transposable elements introducing unique restriction sites. Submitted for publication.
64. Moore, R. L., and R. R. Brubaker. 1975. Hybridization of deoxyribonucleic acid sequences of Yersinia enterocolitica and other selected members of Enterobacteriaceae. Int. J. Syst. Bacteriol. 25:336-339.
65. Mukhopadhyay, G., K. M. Carr, J. M. Kaguni, and D. K. Chattoraj. 1993. Open-complex formation by the host initiator, DnaA, at the origin of P1 plasmid replication. EMBO J. 12:4547-4554.
66. Nagai, S., T. Yagihashi, and A. Ishihama. 1993. DNA sequence of an allelic variant of the Actinobacillus pleuropneumoniae-RTX-toxin I (ApxIA) from serotype 10. Microb. Pathog. 15:485-495.
67. Nakai, K., and M. Kanehisa. 1991. Expert system for predicting protein localization sites in Gram-negative bacteria. Proteins Struct. Funct. Genet. 11:95-110.
68. Nakayama, S., T. Kaneko, H. Ishimaru, H. Moriwaki, and K. Mizobuchi. 1994. Cloning, sequencing and expression of bacteriophage BF23 late genes 24 and 25 encoding tail proteins. J. Bacteriol. 176:7280-7290.
69. Olsen, C. H., F. R. Blattner, and D. L. Daniels. 1991. Simultaneous preparation of up to 768 single-stranded DNAs for use as templates in DNA sequencing. Methods 3:27-32.
70. Pal, S. K., R. J. Mason, and D. K. Chattoraj. 1986. P1 plasmid replication. Role of initiator titration in copy number control. J. Mol. Biol. 20:275-285.
71. Perna, N. T., G. F. Mayhew, G. Posfai, S. Elliot, M. S. Donnenberg, J. B. Kaper, and F. R. Blattner. 1998. Molecular evolution of the pathogemcity island from enterohemorrhagic Escherichia coli O157:H7. Infect. Immun. 66:3810-3817.
72. Perry, R. D., M. L. Pendrak, and P. Schuetze. 1990. Identification and cloning of the hemin storage locus involved in the pigmentation phenotype of Yersinia pestis. J. Bacteriol. 172:5929-5937.
73. Portnoy, D. A., and R. J. Martinez. 1985. Role of a plasmid in the pathogenicity of Yersinia species. Curr. Top. Microbiol. Immunol. 118:29-51.
74. Protsenko, O. A., P. I. Anisimov, O. T. Mosarov, N. P. Donnov, Y. A. Popov, and A. M. Kokushkin. 1983. Detection and characterization of Yersinia pestis plasmids determining pesticin I, fraction I antigen and mouse toxin synthesis. Genetika 19:1081-1090.
75. Protsenko, O. A., A. A. Filippov, and V. V. Kutyrev. 1991. Integration of the plasmid encoding the synthesis of capsular antigen and murine toxin into Yersinia pestis chromosome. Microb. Pathog. 11:123-128.
76. Radnedge, L., M. A. Davis, and S. J. Austin. 1996. P1 and P7 plasmid partition: ParB protein bound to its partition site makes a separate discriminator contact with the DNA that determines species specificity. EMBO J. 15:115-1162.
77. Rajakumar, K., C. Sasakawa, and B. Adler. 1997. Shigella flexneri she pathogenicity island which encodes a homolog of the immunoglobulin A protease-like family of proteins. Infect. Immun. 65:4606-4614.
78. Rakin, A., and J. Heesemann. 1995. Virulence-associated fyuA/irp2 gene cluster of Yersinia enterocolitica biotype 1B carries a novel insertion sequence IS1328. FEMS Microbiol. Lett. 129:287-292.
79. Romantschuk, M., G. Y. Richter, P. Mikhopadhyay, and D. Mills. 1991. IS801, an insertion sequence element isolated from Pseudomonas syringae pathovar phaseolicola. Mol. Microbiol. 5:617-622.
80. Ryan, M. C., R. Tizard, D. R. VanDevanter, and W. G. Carter. 1994. Cloning of the Lam3 gene encoding the alpha 3 chain of the adhesive ligand epiligrin: expression in wound repair. J. Biol. Chem. 269:22779-22787.
81. Samoilova, S. V., L. V. Somoilova, I. N. Yezhov, I. G. Drozdov, and A. P. Anisimov. 1996. Virulence of pPST+ and pPST-strains of Yersinia pestis for guinea pigs. J. Med. Microbiol. 45:440-444.
82. Sanger, F., A. R. Coulson, G. F. Hong, D. F. Hill, and G. B. Peterson. 1982. Nucleotide sequence of bacteriophage lambda DNA. J. Mol. Biol. 162: 729-773.
83. Schauer, D. B., and S. Falkow. 1993. Attaching and effacing locus of a Citrobacter freundii biotype that causes transmissible murine colonic hyperplasia. Infect. Immun. 61:2486-2492.
84. Schofield, J. P., D. S. Jones, and J. N. Forrest, Jr. 1991. Identification of C-type natriuretic peptide in heart of spiny dogfish shark (Squalus acanthias). Am. J. Physiol. 261:F734-F739.
85. Shapiro, J. A. 1992. Natural genetic engineering in evolution. Genetika 86: 99-111.
86. Shine, J., and L. Dalgarno. The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc. Natl. Acad. Sci. USA 71:1342-1346.
87. Simonet, M., B. Riot, N. Fortineau, and P. Berche. 1996. Invasin production by Yersinia pestis is abolished by insertion of an IS200-like element within the inv gene. Infect. Immun. 64:375-379.
88. Singer, M. F. 1995. Unusual reverse transcriptases. J. Biol. Chem. 270: 24623-24626.
89. Smith, C. A., M. Pinkney, D. G. Guiney, and C. M. Thomas. 1993. The ancestral IncP replication system consisted of contiguous oriV and trfA segments as deduced from a comparison of the nucleotide sequences of diverse IncP plasmids. J. Gen. Microbiol. 139:1761-1766.
90. Sodeinde, O. A., and J. D. Goguen. 1988. Genetic analysis of the 9.5-kilobase virulence plasmid of Yersinia pestis. Infect. Immun. 56:2743-2748.
91. Sodeinde, O. A., Y. V. B. K. Subrahmanyam, K. Stark, T. Quan, Y. Bao, and J. D. Goguen. 1992. A surface protease and the invasive character of plague. Science 258:1004-1007.
92. Straley, S. C. 1988. The plasmid-encoded outer-membrane proteins of Yersinia pestis. Rev. Infect. Dis. 10:5323-5326.
93. +2 response virulence regulon of human-pathogenic yersiniae. Microb. Pathog. 10:87-91.
94. Stralev, S. C., and R. R. Brubaker. 1981. Cytoplasmic and membrane proteins of yersiniae cultivated under conditions simulating mammalian intracellular environment. Proc. Natl. Acad. Sci. USA 78:1224-1228.
95. Temin, H. M. 1989. Reverse transcriptases: retrons in bacteria. Nature 339: 254-255.
96. Vidal, F., C. Baudoin, C. Miquel, M. F. Galliano, A. M. Christiano, J. Uitto, J. P. Ortonne, and G. Meneguzzi. 1995. Cloning of the laminin alpha 3 chain gene (LAMA3) and identification of a homozygous deletion in a patient with Herlitz junctional epidermolysis bullosa. Genomics 30:273-280.
97. Welkos, S. L., K. M. Davis, L. M. Pitt, P. L. Worsham, and A. M. Friedlander. 1995. Studies on the contribution of the F1 capsule-associated plasmid pFra to the virulence of Yersinia pestis. Contrib. Microbiol. Immunol. 13:299-305.
98. Willetts, N., and R. Skurry. 1987. Structure and function of the F factor and mechanism of conjugation, p. 1,110-1,133. In F. C. Neidhardt, J. L. Ingraham, B. Magasanik, K. B. Low, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: cellular and molecular biology American Society for Microbiology, Washington, D.C.
99. Wolf, M. K., and E. C. Boedeker. 1990. Cloning of the genes for AF/R1 pill from rabbit enteroadherent Escherichia coli RDEC-1 and DNA sequence of the major structural subunit. Infect. Immun. 58:1124-1128.
100. Zhang, D., and D. J. Miller. 1995. Characterization of a novel non-muscle myosin-related protein from Onchocerca gobsoni. Int. J. Parasitol. 25:1385-1391.
101. Zitman, D., and R. Ben-Gurion. 1972. Transduction of Pasturella pestis. Virology 47:513-516.