1887

Abstract

The antibiotic-multiresistance IncF plasmid pRSB107 was isolated by a transformation-based approach from activated-sludge bacteria of a wastewater-treatment plant. It confers resistance to ampicillin, penicillin G, chloramphenicol, erythromycin, kanamycin, neomycin, streptomycin, sulfonamides, tetracycline and trimethoprim and against mercuric ions. Complete sequencing of this plasmid revealed that it is 120 592 bp in size and has a G+C content of 53·1 mol%. The plasmid backbone is composed of three replicons, RepFIA, RepFIB and RepFII, which are almost identical to corresponding regions located on the F-plasmid and on R100. The three replicons encode replication initiation () and replication control, multimer resolution (), post-segregational killing of plasmid-free cells () and active plasmid partitioning ( locus). Part of the F-leading region and remnants of the F-homologous DNA-transfer () module complete the pRSB107 backbone. Plasmid pRSB107 contains a complex, highly mosaic 35 991 bp antibiotic-resistance region consisting of a Tn- and a Tn-derivative and a chloramphenicol-resistance module. The Tn derivative is composed of a mercury-resistance region (), a Tn-like kanamycin/neomycin-resistance transposon, a streptomycin/sulfonamide-resistance module, remnants of the -lactam-resistance transposon Tn, a macrolide-resistance module flanked by copies of IS and IS, remnants of Tn integrating a class 1 integron and the Tn-specific transposition module. A truncated version of the tetracycline-resistance transposon Tn and the chloramphenicol acetyltransferase gene complete the pRSB107 resistance region. In addition to antibiotic resistance, pRSB107 encodes the following putative virulence-associated functions: (i) an aerobactin iron-acquisition siderophore system (/); (ii) a putative high-affinity Fe uptake system which was previously identified on a pathogenicity island of and in the genome of the phytopathogen subsp. SCRI1043; (iii) an -glycerol-3-phosphate transport system (); and (iv) the virulence-associated genes having a possible function in stable plasmid inheritance. All the accessory modules are framed by insertion sequences, indicating that pRSB107 was gradually assembled by integration of different horizontally acquired DNA segments via transposition or homologous recombination.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.27773-0
2005-04-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/micro/151/4/mic1511095.html?itemId=/content/journal/micro/10.1099/mic.0.27773-0&mimeType=html&fmt=ahah

References

  1. Bateman A., Coin L., Durbin R. 10 other authors 2004; The Pfam protein families database. Nucleic Acids Res 32: Database issue) D138–D141 [CrossRef]
    [Google Scholar]
  2. Belogurov A. A., Delver E. P., Rodzevich O. V. 1993; Plasmid pKM101 encodes two nonhomologous antirestriction proteins (ArdA and ArdB) whose expression is controlled by homologous regulatory sequences. J Bacteriol 175:4843–4850
    [Google Scholar]
  3. Bergquist P. L., Saadi S., Maas W. K. 1986; Distribution of basic replicons having homology with RepFIA, RepFIB, and RepFIC among IncF group plasmids. Plasmid 15:19–34 [CrossRef]
    [Google Scholar]
  4. Blàzquez J., Navas A., Gonzalo P., Martinez J. L., Baquero F. 1996; Spread and evolution of natural plasmids harboring transposon Tn5. FEMS Microbiol Ecol 19:63–71 [CrossRef]
    [Google Scholar]
  5. Bonacorsi S. P., Clermont O., Tinsley C., Le Gall I., Beaudoin J. C., Elion J., Nassif X., Bingen E. 2000; Identification of regions of the Escherichia coli chromosome specific for neonatal meningitis-associated strains. Infect Immun 68:2096–2101 [CrossRef]
    [Google Scholar]
  6. Boyd E. F., Hill C. W., Rich S. M., Hartl D. L. 1996; Mosaic structure of plasmids from natural populations of Escherichia coli. Genetics 143:1091–1100
    [Google Scholar]
  7. Burlage R. S., Bemis L. A., Layton A. C., Sayler G. S., Larimer F. 1990; Comparative genetic organization of incompatibility group P degradative plasmids. J Bacteriol 172:6818–6825
    [Google Scholar]
  8. Burland V., Shao Y., Perna N. T., Plunkett G., Sofia H. J., Blattner F. R. 1998; The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157 : H7. Nucleic Acids Res 26:4196–4204 [CrossRef]
    [Google Scholar]
  9. Cavalli L. L., Lederberg J., Lederberg E. M. 1953; An infective factor controlling sex compatibility in Bacterium coli. J Gen Microbiol 8:89–103 [CrossRef]
    [Google Scholar]
  10. Chalmers R., Sewitz S., Lipkow K., Crellin P. 2000; Complete nucleotide sequence of Tn10. J Bacteriol 182:2970–2972 [CrossRef]
    [Google Scholar]
  11. Chen Y. T., Chang H. Y., Lai Y. C., Pan C. C., Tsai S. F., Peng H. L. 2004; Sequencing and analysis of the large virulence plasmid pLVPK of Klebsiella pneumoniae CG43. Gene 337:189–198 [CrossRef]
    [Google Scholar]
  12. Davies J. 1994; Inactivation of antibiotics and the dissemination of resistance genes. Science 264:375–382 [CrossRef]
    [Google Scholar]
  13. Davison J. 1999; Genetic exchange between bacteria in the environment. Plasmid 42:73–91 [CrossRef]
    [Google Scholar]
  14. de Lorenzo V., Neilands J. B. 1986; Characterization of iucA and iucC genes of the aerobactin system of plasmid ColV-K30 inEscherichia coli. J Bacteriol 167:350–355
    [Google Scholar]
  15. de Lorenzo V., Bindereif A., Paw B. H., Neilands J. B. 1986; Aerobactin biosynthesis and transport genes of plasmid ColV-K30 in Escherichia coli K-12. J Bacteriol 165:570–578
    [Google Scholar]
  16. Di Lorenzo M., Stork M., Tolmasky M. E. 9 other authors 2003; Complete sequence of virulence plasmid pJM1 from the marine fish pathogen Vibrio anguillarum strain 775. J Bacteriol 185:5822–5830 [CrossRef]
    [Google Scholar]
  17. Dröge M., Pühler A., Selbitschka W. 1998; Horizontal gene transfer as a biosafety issue: a natural phenomenon of public concern. J Biotechnol 64:75–90 [CrossRef]
    [Google Scholar]
  18. Dröge M., Pühler A., Selbitschka W. 2000; Phenotypic and molecular characterization of conjugative antibiotic resistance plasmids isolated from bacterial communities of activated sludge. Mol Gen Genet 263:471–482 [CrossRef]
    [Google Scholar]
  19. Engelberg-Kulka H., Glaser G. 1999; Addiction modules and programmed cell death and antideath in bacterial cultures. Annu Rev Microbiol 53:43–70 [CrossRef]
    [Google Scholar]
  20. Gerdes K., Moller-Jensen J., Bugge Jensen R. 2000; Plasmid and chromosome partitioning: surprises from phylogeny. Mol Microbiol 37:455–466
    [Google Scholar]
  21. Gibbs M. D., Spiers A. J., Bergquist P. L. 1993; RepFIB: a basic replicon of large plasmids. Plasmid 29:165–179 [CrossRef]
    [Google Scholar]
  22. Grant S. G., Jessee J., Bloom F. R., Hanahan D. 1990; Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proc Natl Acad Sci U S A 87:4645–4649 [CrossRef]
    [Google Scholar]
  23. Herrero M., de Lorenzo V., Neilands J. B. 1988; Nucleotide sequence of the iucD gene of the pColV-K30 aerobactin operon and topology of its product studied withphoA and lacZ gene fusions. J Bacteriol 170:56–64
    [Google Scholar]
  24. Heuer H., Szczepanowski R., Schneiker S., Top E. M, Pühler A., Schlüter A. 2004; The complete sequences of plasmids pB2 and pB3 provide evidence for a recent ancestor of the IncP-1β group without any accessory genes. Microbiology 150:3591–3599 [CrossRef]
    [Google Scholar]
  25. Hu K. H., Liu E., Dean K., Gingras M., DeGraff W., Trun N. J. 1996; Overproduction of three genes leads to camphor resistance and chromosome condensation in Escherichia coli. Genetics 143:1521–1532
    [Google Scholar]
  26. Hynes M. F., Simon R., Pühler A. 1985; The development of plasmid-free strains of Agrobacterium tumefaciens by using incompatibility with a Rhizobium meliloti plasmid to eliminate Patc58. Plasmid 13:99–105 [CrossRef]
    [Google Scholar]
  27. Kawasaki Y., Matsunaga F., Kano Y., Yura T., Wada C. 1996; The localized melting of mini-F origin by the combined action of the mini-F initiator protein (RepE) and HU and DnaA of Escherichia coli. Mol Gen Genet 253:42–49 [CrossRef]
    [Google Scholar]
  28. Koonin E. V. 1994; Conserved sequence pattern in a wide variety of phosphoesterases. Protein Sci 3:356–358
    [Google Scholar]
  29. Kurtz S., Choudhuri J. V., Ohlebusch E., Schleiermacher C., Stoye J., Giegerich R. 2001; REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29:4633–4642 [CrossRef]
    [Google Scholar]
  30. Lane D., de Feyter R., Kennedy M., Phua S. H., Semon D. 1986; D protein of miniF plasmid acts as a repressor of transcription and as a site-specific resolvase. Nucleic Acids Res 14:9713–9728
    [Google Scholar]
  31. Lawley T. D., Klimke W. A., Gubbins M. J., Frost L. S. 2003; F factor conjugation is a true type IV secretion system. FEMS Microbiol Lett 224:1–15 [CrossRef]
    [Google Scholar]
  32. Lawlor K. M., Daskaleros P. A., Robinson R. E., Payne S. M. 1987; Virulence of iron transport mutants of Shigella flexneri and utilization of host iron compounds. Infect Immun 55:594–599
    [Google Scholar]
  33. Levi S., Santambrogio P., Cozzi A., Rovida E., Corsi B., Tamborini E., Spada S., Albertini A., Arosio P. 1994; The role of the L-chain in ferritin iron incorporation. Studies of homo and heteropolymers. J Mol Biol 238:649–654 [CrossRef]
    [Google Scholar]
  34. Liebert C. A., Hall R. M., Summers A. O. 1999; Transposon Tn21, flagship of the floating genome. Microbiol Mol Biol Rev 63:507–522
    [Google Scholar]
  35. Luck S. N., Turner S. A., Rajakumar K., Sakellaris H., Adler B. 2001; Ferric dicitrate transport system (Fec) of Shigella flexneri 2a YSH6000 is encoded on a novel pathogenicity island carrying multiple antibiotic resistance genes. Infect Immun 69:6012–6021 [CrossRef]
    [Google Scholar]
  36. Manwaring N. P., Skurray R. A., Firth N. 1999; Nucleotide sequence of the F plasmid leading region. Plasmid 41:219–225 [CrossRef]
    [Google Scholar]
  37. Martinez B., Tomkins J., Wackett L. P., Wing R., Sadowsky M. J. 2001; Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J Bacteriol 183:5684–5697 [CrossRef]
    [Google Scholar]
  38. Mazel D., Davies J. 1999; Antibiotic resistance in microbes. Cell Mol Life Sci 56:742–754 [CrossRef]
    [Google Scholar]
  39. McLoughlin S. Y., Jackson C., Liu J. W., Ollis D. L. 2004; Growth of Escherichia coli coexpressing phosphotriesterase and glycerophosphodiester phosphodiesterase, using paraoxon as the sole phosphorus source. Appl Environ Microbiol 70:404–412 [CrossRef]
    [Google Scholar]
  40. Meyer F., Goesmann A., McHardy A. C. 8 other authors 2003; GenDB – an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 31:2187–2195 [CrossRef]
    [Google Scholar]
  41. Miller J. H. 1972 Experiments in Molecular Genetics Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  42. Mirwaldt C., Korndorfer I., Huber R. 1995; The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2·5 Å resolution. J Mol Biol 246:227–239 [CrossRef]
    [Google Scholar]
  43. Moss J. E., Cardozo T. J., Zychlinsky A., Groisman E. A. 1999; The selC-associated SHI-2 pathogenicity island of Shigella flexneri. Mol Microbiol 33:74–83 [CrossRef]
    [Google Scholar]
  44. Nassif X., Mazert M. C., Mounier J., Sansonetti P. J. 1987; Evaluation with an iuc : : Tn10 mutant of the role of aerobactin production in the virulence ofShigella flexneri. Infect Immun 55:1963–1969
    [Google Scholar]
  45. Neidhardt F. C., Bloch P. L., Smith D. F. 1974; Culture medium for enterobacteria. J Bacteriol 119:736–747
    [Google Scholar]
  46. Nomura N., Masai H., Inuzuka M. 7 other authors 1991; Identification of eleven single-strand initiation sequences (ssi) for priming of DNA replication in the F, R6K, R100 and ColE2 plasmids. Gene 108:15–22 [CrossRef]
    [Google Scholar]
  47. Ohtsubo H., Ryder T. B., Maeda Y., Armstrong K., Ohtsubo E. 1986; DNA replication of the resistance plasmid R100 and its control. Adv Biophys 21:115–133 [CrossRef]
    [Google Scholar]
  48. Pansegrau W., Lanka E., Barth P. T. 7 other authors 1994; Complete nucleotide sequence of Birmingham IncP alpha plasmids. Compilation and comparative analysis. J Mol Biol 239:623–663 [CrossRef]
    [Google Scholar]
  49. Partridge S. R., Hall R. M. 2003; In34, a complex In5 family class 1 integron containing orf513 and dfrA10. Antimicrob Agents Chemother 47:342–349 [CrossRef]
    [Google Scholar]
  50. Perez-Casal J. F., Gammie A. E., Crosa J. H. 1989; Nucleotide sequence analysis and expression of the minimum REPI replication region and incompatibility determinants of pColV-K30. J Bacteriol 171:2195–2201
    [Google Scholar]
  51. Pullinger G. D., Lax A. J. 1992; A Salmonella dublin virulence plasmid locus that affects bacterial growth under nutrient-limited conditions. Mol Microbiol 6:1631–1643 [CrossRef]
    [Google Scholar]
  52. Saadi S., Maas W. K., Hill D. F., Bergquist P. L. 1987; Nucleotide sequence analysis of RepFIC, a basic replicon present in IncFI plasmids P307 and F, and its relation to the RepA replicon of IncFII plasmids. J Bacteriol 169:1836–1846
    [Google Scholar]
  53. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Labolatory Manual Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  54. Sansonetti P. J., Kopecko D. J., Formal S. B. 1982; Involvement of a plasmid in the invasive ability of Shigella flexneri. Infect Immun 35:852–860
    [Google Scholar]
  55. Scherzinger E., Haring V., Lurz R., Otto S. 1991; Plasmid RSF1010 DNA replication in vitro promoted by purified RSF1010 RepA, RepB and RepC proteins. Nucleic Acids Res 19:1203–1211 [CrossRef]
    [Google Scholar]
  56. Schlüter A., Heuer H., Szczepanowski R., Forney L. J., Thomas C. M., Top E. M, Pühler A. 2003; The 64 508 bp IncP-1β antibiotic multiresistance plasmid pB10 isolated from a waste-water treatment plant provides evidence for recombination between members of different branches of the IncP-1β group. Microbiology 149:3139–3153 [CrossRef]
    [Google Scholar]
  57. Schmidt H., Henkel B., Karch H. 1997; A gene cluster closely related to type II secretion pathway operons of gram-negative bacteria is located on the large plasmid of enterohemorrhagic Escherichia coli O157 strains. FEMS Microbiol Lett 148:265–272 [CrossRef]
    [Google Scholar]
  58. Simon R., Priefer U., Pühler A. 1983; A broad host range mobilization system for in vivo genetic-engineering-transposon mutagenesis in gram-negative bacteria. Bio/Technology 1:784–791 [CrossRef]
    [Google Scholar]
  59. Smalla K., Sobecky P. A. 2002; The prevalence and diversity of mobile genetic elements in bacterial communities of different environmental habitats: insights gained from different methodological approaches. FEMS Microbiol Ecol 42:165–175 [CrossRef]
    [Google Scholar]
  60. Sorsa L. J., Dufke S., Schubert S. 2004; Identification of novel virulence-associated loci in uropathogenic Escherichia coli by suppression subtractive hybridization. FEMS Microbiol Lett 230:203–208 [CrossRef]
    [Google Scholar]
  61. Spiers A. J., Bhana N., Bergquist P. L. 1993; Regulatory interactions between RepA, an essential replication protein, and the DNA repeats of RepFIB from plasmid P307. J Bacteriol 175:4016–4024
    [Google Scholar]
  62. Staden R. 1996; The Staden sequence analysis package. Mol Biotechnol 5:233–241 [CrossRef]
    [Google Scholar]
  63. Stearman R., Yuan D. S., Yamaguchi-Iwai Y., Klausner R. D., Dancis A. 1996; A permease-oxidase complex involved in high-affinity iron uptake in yeast. Science 271:1552–1557 [CrossRef]
    [Google Scholar]
  64. Szczepanowski R., Krahn I., Linke B., Goesmann A., Pühler A., Schlüter A. 2004; Antibiotic multiresistance plasmid pRSB101 isolated from a wastewater treatment plant is related to plasmids residing in phytopathogenic bacteria and carries eight different resistance determinants including a multidrug transport system. Microbiology 150:3613–3630 [CrossRef]
    [Google Scholar]
  65. Takase H., Nitanai H., Hoshino K., Otani T. 2000; Impact of siderophore production on Pseudomonas aeruginosa infections in immunosuppressed mice. Infect Immun 68:1834–1839 [CrossRef]
    [Google Scholar]
  66. Tatusov R. L., Natale D. A., Garkavtsev I. V. 7 other authors 2001; The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29:22–28 [CrossRef]
    [Google Scholar]
  67. Tauch A., Bischoff N., Goesmann A., Meyer F, Schlüter A., Pühler A. 2003; The 79,370-bp conjugative plasmid pB4 consists of an IncP-1beta backbone loaded with a chromate resistance transposon, the strA-strB streptomycin resistance gene pair, the oxacillinase gene bla(NPS-1), and a tripartite antibiotic efflux system of the resistance-nodulation-division family. Mol Genet Genomics 268:570–584
    [Google Scholar]
  68. Tennstedt T., Szczepanowski R., Braun S., Pühler A., Schlüter A. 2003; Occurrence of integron-associated resistance gene cassettes located on antibiotic resistance plasmids isolated from a wastewater treatment plant. FEMS Microbiol Ecol 45:239–252 [CrossRef]
    [Google Scholar]
  69. Tennstedt T., Szczepanowski R., Krahn I., Pühler A., Schlüter A. 2005; Sequence of the 68,869 bp IncP-1α plasmid pTB11 from a waste-water treatment plant reveals a highly conserved backbone, a Tn402-like integron and other transposable elements. Plasmid doi: 10.1016/j.plasmid.2004.09.004 http://dx.doi.org/10.1016/j.plasmid.2004.09.004
    [Google Scholar]
  70. Uga H., Matsunaga F., Wada C. 1999; Regulation of DNA replication by iterons: an interaction between the ori2 and incC regions mediated by RepE-bound iterons inhibits DNA replication of mini-F plasmid in Escherichia coli. EMBO J 18:3856–3867 [CrossRef]
    [Google Scholar]
  71. Venkatesan M. M., Goldberg M. B., Rose D. J., Grotbeck E. J., Burland V., Blattner F. R. 2001; Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri. Infect Immun 69:3271–3285 [CrossRef]
    [Google Scholar]
  72. Wain J., Diem Nga L. T., Kidgell C. 9 other authors 2003; Molecular analysis of IncHI1 antimicrobial resistance plasmids from Salmonella serovar Typhi strains associated with typhoid fever. Antimicrob Agents Chemother 47:2732–2739 [CrossRef]
    [Google Scholar]
  73. Wei J., Goldberg M. B., Burland V. 14 other authors 2003; Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect Immun 71:2775–2786 [CrossRef]
    [Google Scholar]
  74. Womble D. D., Rownd R. H. 1988; Genetic and physical map of plasmid NR1: comparison with other IncFII antibiotic resistance plasmids. Microbiol Rev 52:433–451
    [Google Scholar]
  75. Womble D. D., Sampathkumar P., Easton A. M., Luckow V. A., Rownd R. H. 1985; Transcription of the replication control region of the IncFII R-plasmid NR1 in vitro and in vivo. J Mol Biol 181:395–410 [CrossRef]
    [Google Scholar]
  76. Zhang L., Foxman B., Manning S. D., Tallman P., Marrs C. F. 2000; Molecular epidemiologic approaches to urinary tract infection gene discovery in uropathogenic Escherichia coli. Infect Immun 68:2009–2015 [CrossRef]
    [Google Scholar]
  77. Zzaman S., Abhyankar M. M., Bastia D. 2004; Reconstitution of F factor DNA replication in vitro with purified proteins. J Biol Chem 279:17404–17410 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.27773-0
Loading
/content/journal/micro/10.1099/mic.0.27773-0
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error