A new ColE1-like plasmid group revealed by comparative analysis of the replication proficient fragments of Vibrionaceae plasmids

Journal of Microbiology and Biotechnology

Volumn 20, Issue 8, 2010, Pages 1163-1178

  Pan, Li ^a   Leung, P C ^a   Gu, Ji Dong ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Compatibility; Plasmids; Replication; Replication initiation; RNA; Vibrio

Indexed keywords

BACTERIAL RNA; COMPLEMENTARY RNA;

ARTICLE; BIOINFORMATICS; COMPARATIVE STUDY; CONTROLLED STUDY; DNA REPLICATION; GENETIC ORGANIZATION; GENETIC RECOMBINATION; GENETIC REGULATION; MOLECULAR CLONING; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; POLYMERASE CHAIN REACTION; REPLICON; SEQUENCE ANALYSIS; SOUTHERN BLOTTING; VIBRIONACEAE;

CARNATION LATENT VIRUS; VIBRIO; VIBRIONACEAE;

EID: 77957088557     PISSN: 10177825     EISSN: 17388872     Source Type: Journal    
DOI: 10.4014/jmb.1003.03007     Document Type: Article

References (86)

1. Barbieri, E., L. Falzano, C. Fiorentini, A. Pianetti, W. Baffone, A. Fabbri, et al. 1999. Occurrence, diversity, and pathogenicity of halophilic Vibrio spp. and non-O1 Vibrio cholerae from estuarine waters along the Italian Adriatic coast. Appl. Environ. Microbiol. 65: 2748-2753.
2. Bistue, A. J. C. S., F. A. Martn, A. Petroni, D. Faccone, M. Galas, M. E. Tolmasky, and A. Zorreguieta. 2006. Vibrio cholerae InV117, a class 1 integron harboring aac(6_)-Ib and blaCTX-M-2, is linked to transposition genes. Antimicrob. Agents Chemother. 50: 1903-1907.
3. Blakely, G. W. and D. J. Sherratt. 1994. Interactions of the sitespecific recombinases XerC and XerD with the recombination site dif. Nucl. Acids Res. 22: 5613-5620.
4. Blakely, G., G. May, R. McCulloch, L. K. Arciszewska, M. Burke, S. T. Lovett, and D. J. Sherratt. 1993. Two related recombinases are required for site-specific recombination at dif and cer in E. coli K12. Cell 75: 351-361.
5. Blakely, G. W., A. O. Davidson, and D. J. Sherratt. 2000. Sequential strand exchange by XerC and XerD during sitespecific recombination at dif. J. Biol. Chem. 275: 9930-9936.
6. Bjorklof, K., A. Souniemi, K. Haahtela, and M. Romantschuk. 1995. High-frequency of conjugation versus plasmid segregation of RP1 in epiphytic Pseudomonas syringae population. Microbiology 141: 2719-2727.
7. Buell, C. R., V. Joardar, M. Lindeberg, J. Selengut, I. T. Paulsen, M. L. Gwinn, et al. 2003. The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc. Natl. Acad. Sci. U.S.A. 100: 10181-10186.
8. Cao, V., T. Lambert, and P. Courvalin. 2002. ColE1-like plasmid pIP843 of Klebsiella pneumoniae encoding extendedspectrum- β-lactamase CTX-M-17. Antimicrob. Agents Chemother. 46: 1212-1217.
9. Carla, B., P. J. Wilderman, C. W. Dorsey, and L. A. Actis. 1999. Analysis of the replication elements of the pMJ101 plasmid from the fish pathogen Vibrio ordalii. Plasmid 42: 20-30.
10. Castagnoli, L., M. Scarpa, M. Kokkinidis, D. W. Banner, D. Tsernoglou, and G. Cesareni. 1989. Genetic and structural analysis of the ColE 1 Rop (Rom) protein. EMBO J. 8: 621-629.
11. Catherine, J. P. and C. I. Kado. 1998. Characterization of pUCD5000 involved in pink disease color formation by Pantoea citrea. Plasmid 40: 169-173.
12. Ceccarelli, D., A. M. Salvia, J. Sami, P. Cappuccinelli, and M. M. Colombo. 2006. New cluster of plasmid-located class 1 integrons in Vibrio cholerae O1 and a dfrA15 cassette-containing integron in Vibrio parahaemolyticus isolated in Angola. Antimicrob. Agents Chemother. 50: 2493-2499.
13. Cesareni, G., M. Helmer-Citterich, and L. Castagnoli. 1991. Control of ColE1 plasmid replication by antisense RNA. Trends Genet. 7: 230-235.
14. Chan, P. T., H. Ohmori, J. I. Tomizawa, and J. Lebowitz. 1985. Nucleotide sequence and gene organization of ColE1 DNA. J. Biol. Chem. 260: 8925-8935.
15. Chang, C. F., P. E. Hung, and Y. F. Chang. 1998. Molecular characterization of a plasmid isolated from Riemerella anatipestifer. Avian Pathol. 27: 339-345.
16. Chen, C. Y., K. M. Wu, Y. C. Chang, C. H. Chang, H. C. Tsai, T. L. Liao, et al. 2003. Comparative genome analysis of Vibrio vulnificus, a marine pathogen. Genome Res. 13: 2577-2587.
17. Chen, C. Y., G. W. Nace, B. Solow, and P. Fratamico. 2007. Complete nucleotide sequences of 84.5- and 3.2-kb plasmids in the multi-antibiotic resistant Salmonella enterica serovar Typhimurium U302 strain G8430. Plasmid 57: 29-43.
18. Cho, J. C. and S. J. Giovannoni. 2004. Oceanicola granulosus gen. nov., sp. nov. and Oceanicola batsensis sp. nov., poly-β-hydroxybutyrate-producing marine bacteria in the order 'Rhodobacterales'. Int. J. Syst. Evol. Microbiol. 54: 1129-1136.
19. Colloms, S. D., R. McCulloch, K. Grant, L. Neilson, and D. J. Sherratt. 1996. Xer-mediated site-specific recombination in vitro. EMBO J. 15: 1172-1181.
20. Del Solar, G., R. Giraldo, M. J. Ruiz-Echevarria, M. Espinosa, and R. Diaz-Orejas. 1998. Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 62: 434-464.
21. Denner, E. B. M., D. Vybiral, U. R. Fischer, B. Velimirov, and H. J. Busse. 2002. Vibrio calviensis sp. nov., a halophilic, facultatively oligotrophic 0.2 micron-filterable marine bacterium. Int. J. Syst. Evol. Microbiol. 52: 549-553.
22. Dery, K. J., R. Chavideh, V. Waters, R. Chamorro, L. S. Tolmasky, and M. E. Tolmasky. 1997. Characterization of the replication and mobilization regions of the multiresistance Klebsiella pneumoniae plasmid pJHCMW1. Plasmid 38: 97-105.
23. Di Lorenzo, M., M. Stork, M. E. Tolmasky, L. A. Actis, D. Farrell, T. J. Welch, et al. 2003. Complete sequence of virulence plasmid pJM1 from the marine fish pathogen Vibrio anguillarum strain 775. J. Bacteriol. 185: 5822-5830.
24. do Vale, A., M. T. Silva, N. M. S. dos Santos, D. S. Nascimento, P. Reis-Rodrigues, C. Costa-Ramos, A. E. Ellis, and J. E. Azevedo. 2005. AIP56, a novel plasmid-encoded virulence factor of Photobacterium damselae subsp. Piscicida with apoptogenic activity against sea bass macrophages and neutrophils. Mol. Microbiol. 58: 1025-1038.
25. Dunn, A. K., D. S. Millikan, D. M. Adin, J. L. Bose, and E. V. Stabb. 2006. New rfp- and pES213-derived tools for analyzing symbiotic Vibrio fischeri reveal patterns of infection and lux expression in situ. Appl. Environ. Microbiol. 72: 802-810.
26. Dunn, A. K., M. O. Martin, and E. V. Stabb. 2005. Characterization of pES213, a small mobilizable plasmid from Vibrio fischeri. Plasmid 54: 114-134.
27. Eguchi, Y. and J. I. Tomizawa. 1990. Complex formed by complementary RNA stem-loops and its stabilization by a protein: Function of ColE1 Rom protein. Cell 60: 199-209.
28. Garcia-Vallve, S., E. Guzman, M. A. Montero, and A. Romeu. 2003. HGTDB: A database of putative horizontally transferred genes in prokaryotic complete genomes. Nucl. Acids Res. 31: 187-189.
29. Guhathakurta, A., I. Viney, and D. J. Sherratt. 1996. Accessory proteins impose site selectivity during ColE1 dimer resolution. Mol. Microbiol. 20: 613-620.
30. Gurtler, V. and V. A. Stanisich. 1996. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142: 3-16.
31. Hazen, T. H., D. Wu, J. A. Eisen, and P. A. Sobecky. 2007. Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp. Appl. Environ. Microbiol. 73: 7703-7710.
32. Heidelberg, J. F., K. B. Heidelberg, and R. R. Colwell. 2002. Seasonality of Chesapeake Bay bacterioplankton species. Appl. Environ. Microbiol. 68: 5488-5497.
33. Hjerde, E., M. S. Lorentzen, M. T. Holden, K. Seeger, S. Paulsen, N. Bason, et al. 2008. The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay. BMC Genomics 9: 616-629.
34. Hodgman, T. C., H. Griffiths, and D. K. Summers. 1998. Nucleoprotein architecture and ColE1 dimer resolution: A hypothesis. Mol. Microbiol. 29: 545-558.
35. Hoffmann, B., E. Strauch, C. Gewinner, H. Nattermann, and B. Appel. 1998. Characterization of plasmid regions of foodborne Yersinia enterocolitica biogroup 1A strains hybridizing to the Yersinia enterocolitica virulence plasmid. Syst. Appl. Microbiol. 21: 201-211.
36. Itoh, T. and J. I. Tomizawa. 1980. Formation of an RNA primer for initiation of replication of ColE1 DNA by ribonuclease H. Proc. Natl. Acad. Sci. U.S.A. 77: 2450-2454.
37. O:54 (O:54 antigen biosynthesis) gene cluster from Salmonella enterica serovar Borreze. J. Bacteriol. 177: 5247-5253.
38. Kim, M. J., I. Hirono, K. Kurokawa, T. Maki, J. Hawke, H. Kondo, M. D. Santos, and T. Aoki. 2008. Complete DNA sequence and analysis of the transferable multiple-drug resistance plasmids (R plasmids) from Photobacterium damselae subsp. piscicida isolates collected in Japan and the United States. Antimicrob. Agents Chemother. 52: 606-611.
39. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5: 150-163.
40. Lee, C. T., C. Amaro, K. M. Wu, E. Valiente, Y. F. Chang, S. F. Tsai, C. H. Chang, and L. I. Hor. 2008. A common virulence plasmid in biotype 2 Vibrio vulnificus and its dissemination aided by a conjugal plasmid. J. Bacteriol. 190: 1638-1648.
41. Leslie, N. R. and D. J. Sherratt. 1995. Site-specific recombination in the replication terminus region of Escherichia coli: Functional replacement of dif. EMBO J. 14: 1561-1570.
42. Mandel, M. J., M. S. Wollenberg, E. V. Stabb, K. L. Visick, and E. G. Ruby. 2009. A single regulatory gene is sufficient to alter bacterial host range. Nature 458: 215-218.
43. Maniatis, T., E. F. Fritsch, and J. Sambrook. 1982. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
44. Masukata, H. and J. I. Tomizawa. 1986. Control of primer formation for ColEl plasmid replication: Conformational change of the primer transcript. Cell 44: 125-136.
45. Masukata, H. and J. I. Tomizawa. 1990. A mechanism of formation of a persistent hybrid between elongating RNA and template DNA. Cell 62: 331-338.
46. Mikiewicz, D., B. Wróbel, G. W grzyn, and A. P ucienniczak. 1997. Isolation and characterization of a ColE1-like plasmid from Enterobacter agglomerans with a novel variant of rom gene. Plasmid 38: 210-219.
47. Mruk, I., M. Sektas, and T. Kaczorowski. 2001. Characterization of pEC156, a ColE1-type plasmid from Escherichia coli E1585-68 that carries genes of the EcoVIII restriction-modification system. Plasmid 46: 128-139.
48. Nakamura, Y., T. Itoh, H. Matsuda, and T. Gojobori. 2004. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat. Genet. 36: 760-766.
49. Nomura, N., M. Yamashita, and Y. Murooka. 1996. Genetic organization of a DNA-processing region required for mobilization of a non-self-transmissible plasmid, pEC3, isolated from Erwinia carotovora subsp. carotovora. Gene 170: 57-62.
50. Ortigosa, M., C. Esteve, and M. J. Pujalte. 1989. Vibrio species in seawater and mussels: Abundance and numerical taxonomy. Syst. Appl. Microbiol. 12: 316-325.
51. Pan, J. C., R. Ye, H. Q. Wang, H. Q. Xiang, W. Zhang, X. F. Yu, D. M. Meng, and Z. S. He. 2008. Vibrio cholerae O139 multiple-drug resistance mediated by Yersinia pestis pIP1202- like conjugative plasmids. Antimicrob. Agents Chemother. 52: 3829-3836.
52. Predki, P. F., L. M. Nayak, M. B. C. Gottlieb, and L. Regan. 1995. Dissecting RNA-protein interactions: RNA-RNA recognition by Rop. Cell 80: 41-50.
53. Purdy, A., F. Rohwer, R. Edwards, F. Azam, and D. H. Bartlett. 2005. A glimpse into the expanded genome content of Vibrio cholerae through identification of genes present in environmental strains. J. Bacteriol. 187: 2992-3001.
54. Rajpara, N., A. Patel, N. Tiwari, J. Bahuguna, A. Antony, I. Choudhury, et al. 2009. Mechanism of drug resistance in a clinical isolate of Vibrio fluvialis: Involvement of multiple plasmids and integrons. Int. J. Antimicrob. Agents 34: 220-225.
55. Reynaud, Y., D. Saulnier, D. Mazel, C. Goarant, and F. Le Roux. 2008. Correlation between detection of a plasmid and high-level virulence of Vibrio nigripulchritudo, a pathogen of the shrimp Litopenaeus stylirostris. Appl. Environ. Microbiol. 74: 3038-3047.
56. Rijavec, M., M. Budi, P. Mrak, M. Müller-Premru, Z. Podlesek, and D. Žgur-Bertok. 2007. Prevalence of ColE1-like plasmids and colicin K production among uropathogenic Escherichia coli strains and quantification of inhibitory activity of colicin K. Appl. Environ. Microbiol. 73: 1029-1032.
57. Riley, M. A., L. Cadavid, M. S. Collett, M. N. Neely, M. D. Adams, C. M. Phillips, J. V. Neel, and D. Friedman. 2000. The newly characterized colicin Y provides evidence of positive selection in pore-former colicin diversification. Microbiology 146: 1671-1677.
58. Riley, M. A., T. Pinou, J. E. Wertz, Y. Tan, and C. M. Valletta. 2001. Molecular characterization of the klebicin B plasmid of Klebsiella pneumoniae. Plasmid 45: 209-221.
59. Rozhon, W. M., E. K. Petutschnig, and C. Jonak. 2006. Isolation and characterization of pHW15, a small cryptic plasmid from Rahnella genomospecies 2. Plasmid 56: 202-215.
60. Sambrook, J., E. F. Fritsch, and T. Maniatis (eds.). 1989. Small scale preparations of plasmid DNA, pp. 125-131. In: Molecular Cloning: A Laboratory Manual, 2nd Ed. Cold Spring Harbor Laboratory Press, N.Y.
61. Seizer, G., T. Som, T. Itoh, and J. Tomizawa. 1983. The origin of replication of plasmid p15A and comparative studies on the nucleotide sequences around the origin of related plasmids. Cell 32: 119-129.
62. Sia, E. A., R. C. Roberts, C. Easter, D. R. Helinski, and D. H. Figuriski. 1995. Different relative importance of the par operons and the effect of conjugal transfer on the maintenance of the intact promiscuous plasmid RK2. J. Bacteriol. 177: 2789-2797.
63. Sobecky, P. A., T. J. Mincer, M. C. Chang, and D. R. Helinski. 1997. Plasmids isolated from marine sediment microbial communities contain replication and incompatibility regions unrelated to those of known plasmid groups. Appl. Environ. Microbiol. 63: 888-895.
64. Sobecky, P. A., T. J. Mincer, M. C. Chang, A. Toukdarian, and D. R. Helinski. 1998. Isolation of broad-host-range replicons from marine sediment bacteria. Appl. Environ. Microbiol. 64: 2822-2830.
65. Sorum, H., M. C. Roberts, and J. H. Crosa. 1992. Identification and cloning of a tetracycline resistance gene from the fish pathogen Vibrio salmonicida. Antimicrob. Agents Chemother. 36: 611-615.
66. Stalker, D. M., R. Kolter, and D. R. Helinski. 1982. Plasmid R6K DNA replication. I. Complete nucleotide sequence of an autonomously replicating segment. J. Mol. Biol. 161: 33-43.
67. Stirling, C. J., S. D. Colloms, J. F. Collins, G. Szatmari, and D. J. Sherratt. 1989. xerB, an Escherichia coli gene required for plasmid ColE1 site-specific recombination, is identical to pepA, encoding aminopeptidase A, a protein with substantial similarity to bovine lens leucine aminopeptidase. EMBO J. 8: 1623-1627.
68. Stirling, C. J., G. Stewart, and D. J. Sherratt. 1988. Multicopy plasmid stability in Escherichia coli requires host-encoded functions that lead to plasmid site-specific recombination. Mol. Gen. Genet. 214: 80-84.
69. Stirling, C. J., G. Szatmari, G. Stewart, M. C. M. Smith, and D. J. Sherratt. 1988. The arginine repressor is essential for plasmidstabilizing site-specific recombination at the ColE1 cer locus. EMBO J. 7: 4389-4395.
70. Strauch, E., I. Voigt, H. Broll, and B. Appel. 2000. Use of a plasmid of a Yersinia enterocolitica biogroup 1A strain for the construction of cloning vectors. J. Biotechnol. 79: 63-72.
71. Summers, D. K. and D. J. Sherratt. 1988. Resolution of ColE1 dimers requires a DNA sequence implicated in the threedimensional organization of the cer site. EMBO J. 7: 851-858.
72. Tamm, J. and B. Polisky. 1985. Characterization of the ColEl primer-RNA1 complex: Analysis of a domain of ColE1 RNA1 necessary for its interaction with primer RNA. Proc. Natl. Acad. Sci. U.S.A. 82: 2257-2261.
73. Thompson, F. L., T. Iida, and J. Swings. 2004. Biodiversity of vibrios. Microbiol. Mol. Biol. Rev. 68: 403-431.
74. Tolmasky, M. E., L. A. Actis, and J. H. Crosa. 1995. A histidine decarboxylase gene encoded by the Vibrio anguillarum plasmid pJM1 is essential for virulence: Histamine is a precursor in the biosynthesis of anguibactin. Mol. Microbiol. 15: 87-95.
75. Tomizawa, J. I. 1984. Control of ColE1 plasmid replication: The process of binding of RNA I to the primer transcript. Cell 38: 861-867.
76. Tomizawa, J. I. 1985. Control of ColE1 plasmid replication: Initial interaction of RNA I and the primer transcript is reversible. Cell 40: 527-535.
77. Tomizawa, J. I. and T. Itoh. 1981. Plasmid ColE1 incompatibility determined by interaction of RNA I with primer transcript. Proc. Natl. Acad. Sci. U.S.A. 78: 6096-6100.
78. Valiente, E., C. T. Lee, L. I. Hor, B. Fouz, and C. Amaro. 2008. Role of the metalloprotease Vvp and the virulence plasmid pR99 of Vibrio vulnificus serovar E in surface colonization and fish virulence. Environ. Microbiol. 10: 328-338.
79. Vezzi, A., S. Campanaro, M. D'Angelo, F. Simonato, N. Vitulo, F. M. Lauro, et al. 2005. Life at depth: Photobacterium profundum genome sequence and expression analysis. Science 307: 1459-1461.
80. Watson, N. 1988. A new revision of the sequence of plasmid pBR322. Gene 70: 399-403.
81. Wu, H. Z., H. Z. Zhang, C. X. Lu, N. Liang, H. Y. Jin, Y. Ma, and Y. X. Zhang. 2003. DNA sequencing of a plasmid with virulence from marine fish pathogen Vibrio anguillarum. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao 35: 956-959. (In Chinese.)
82. Wu, J. J., W. C. Ko, C. S. Chiou, H. M. Chen, L. R. Wang, and J. J. Yan. 2008. Emergence of Qnr determinants in human Salmonella isolates in Taiwan. J. Antimicrob. Chemother. 62: 1269-1272.
83. Yacoubi, B. E., A. M. Brunings, Q. Yuan, S. Shankar, and D. W. Gabriel. 2007. In planta horizontal transfer of a major pathogenicity effector gene. Appl. Environ. Microbiol. 73: 1612-1621.
84. Zhang, R. and J. D. Gu. 2009. Complete sequence of plasmid pMP1 from the marine environmental Vibrio vulnificus and location of its replication origin. Mar. Biotechnol. 11: 456-462.
85. Zhang, R. F., Y. L. Wang, P. C. Leung, and J. D. Gu. 2007. PVC, a small cryptic plasmid from the environmental isolate of Vibrio cholerae MP-1. J. Microbiol. 45: 193-198.
86. Zuker, M. and P. Steigler. 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucl. Acids Res. 9: 133-148.