The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established α, β and δ sub-groups

Plasmid

Volumn 58, Issue 1, 2007, Pages 31-43

  Bahl, Martin Iain ^a   Hansen, Lars Hestbjerg ^a   Goesmann, Alexander ^b   Sørensen, Søren J ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b BIELEFELD UNIVERSITY   (Germany)

Author keywords

Antibiotic resistance; IncP 1; Integron; Plasmid; Transposable element

Indexed keywords

KANAMYCIN; NALIDIXIC ACID; RIFAMPICIN; SPECTINOMYCIN; STREPTOMYCIN; TETRACYCLINE; TRIMETHOPRIM;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENETICS; BACTERIAL STRAIN; DNA ISOLATION; INTEGRON; INVERTED REPEAT; MICROENVIRONMENT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASMID; SOIL;

BACTERIA; DRUG RESISTANCE, MULTIPLE, BACTERIAL; EVOLUTION, MOLECULAR; PHYLOGENY; PLASMIDS; SOIL MICROBIOLOGY;

DELTAPROTEOBACTERIA;

EID: 34249872978     PISSN: 0147619X     EISSN: 10959890     Source Type: Journal    
DOI: 10.1016/j.plasmid.2006.11.007     Document Type: Article

References (41)

1. Adamczyk M., and Jagura-Burdzy G. Spread and survival of promiscuous IncP-1 plasmids. Acta Biochim. Pol. 50 (2003) 425-453
2. Agersø Y., and Sandvang D. Class 1 integrons and tetracycline resistance genes in alcaligenes, arthrobacter, and Pseudomonas spp. isolated from pigsties and manured soil. Appl. Environ. Microbiol. 71 (2005) 7941-7947
3. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
4. Bergstrom M., Hermansson M., and Dahlberg C. Isolation and sequencing of the replication region of plasmid pBFp1 isolated from a marine biofilm. Plasmid 51 (2004) 179-184
5. Casadaban M.J., and Cohen S.N. Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J. Mol. Biol. 138 (1980) 179-207
6. Chikami G.K., Guiney D.G., Schmidhauser T.J., and Helinski D.R. Comparison of 10 IncP plasmids: homology in the regions involved in plasmid replication. J. Bacteriol. 162 (1985) 656-660
7. De Gelder L., Vandecasteele F.P., Brown C.J., Forney L.J., and Top E.M. Plasmid donor affects host range of promiscuous IncP-1beta plasmid pB10 in an activated-sludge microbial community. Appl. Environ. Microbiol. 71 (2005) 5309-5317
8. Dennis J.J. The evolution of IncP catabolic plasmids. Curr. Opin. Biotechnol. 16 (2005) 291-298
9. Droge M., Pühler A., and Selbitschka W. Phenotypic and molecular characterization of conjugative antibiotic resistance plasmids isolated from bacterial communities of activated sludge. Mol. Gen. Genet. 263 (2000) 471-482
10. Galtier N., and Lobry J.R. Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J. Mol. Evol. 44 (1997) 632-636
11. Gstalder M.E., Faelen M., Mine N., Top E.M., Mergeay M., and Couturier M. Replication functions of new broad host range plasmids isolated from polluted soils. Res. Microbiol. 154 (2003) 499-509
12. Haines A.S., Jones K., Cheung M., and Thomas C.M. The IncP-6 plasmid Rms149 consists of a small mobilizable backbone with multiple large insertions. J. Bacteriol. 187 (2005) 4728-4738
13. Hall R.M., Brown H.J., Brookes D.E., and Stokes H.W. Integrons found in different locations have identical 5′ ends but variable 3′ ends. J. Bacteriol. 176 (1994) 6286-6294
14. Hansen L.H., Johannesen E., Burmølle M., Sørensen A.H., and Sørensen S.J. Plasmid-encoded multidrug efflux pump conferring resistance to olaquindox in Escherichia coli. Antimicrob. Agents Chemother. 48 (2004) 3332-3337
15. Harada K.M., Aso Y., Hashimoto W., Mikami B., and Murata K. Sequence and analysis of the 46.6-kb plasmid pA1 from Sphingomonas sp. A1 that corresponds to the typical IncP-1beta plasmid backbone without any accessory gene. Plasmid 56 (2006) 11-23
16. Heuer H., Szczepanowski R., Schneiker S., Pühler A., Top E.M., and Schlüter A. The complete sequences of plasmids pB2 and pB3 provide evidence for a recent ancestor of the IncP-1beta group without any accessory genes. Microbiology 150 (2004) 3591-3599
17. Hill K.E., Weightman A.J., and Fry J.C. Isolation and screening of plasmids from the epilithon which mobilize recombinant plasmid pD10. Appl. Environ. Microbiol. 58 (1992) 1292-1300
18. Kholodii G.Y., Mindlin S.Z., Bass I.A., Yurieva O.V., Minakhina S.V., and Nikiforov V.G. Four genes, two ends, and a res region are involved in transposition of Tn5053: a paradigm for a novel family of transposons carrying either a mer operon or an integron. Mol. Microbiol. 17 (1995) 1189-1200
19. Klockgether J., Reva O., Larbig K., and Tummler B. Sequence analysis of the mobile genome island pKLC102 of Pseudomonas aeruginosa C. J. Bacteriol. 186 (2004) 518-534
20. Lawrence J.G., and Ochman H. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95 (1998) 9413-9417
21. Levy S.B. Antibiotic resistance: consequences of inaction. Clin. Infect. Dis. 33 Suppl.3 (2001) 124-129
22. Liebert C.A., Hall R.M., and Summers A.O. Transposon Tn21, flagship of the floating genome. Microbiol. Mol. Biol. Rev. 63 (1999) 507-522
23. Meyer F., Goesmann A., McHardy A.C., Bartels D., Bekel T., Clausen J., Kalinowski J., Linke B., Rupp O., Giegerich R., and Pühler A. GenDB-an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 31 (2003) 2187-2195
24. Miller J.H. Experiments in Molecular Genetics (1972), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
25. Pansegrau W., Lanka E., Barth P.T., Figurski D.H., Guiney D.G., Haas D., Helinski D.R., Schwab H., Stanisich V.A., and Thomas C.M. Complete nucleotide sequence of Birmingham IncP alpha plasmids. Compilation and comparative analysis. J. Mol. Biol. 239 (1994) 623-663
26. Radstrom P., Skold O., Swedberg G., Flensburg J., Roy P.H., and Sundstrom L. Transposon Tn5090 of plasmid R751, which carries an integron, is related to Tn7, Mu, and the retroelements. J. Bacteriol. 176 (1994) 3257-3268
27. Recchia G.D., and Hall R.M. Gene cassettes: a new class of mobile element. Microbiology 141 (1995) 3015-3027
28. Rocha E.P., and Danchin A. Base composition bias might result from competition for metabolic resources. Trends Genet. 18 (2002) 291-294
29. Schlüter A., Heuer H., Szczepanowski R., Forney L.J., Thomas C.M., Pühler A., and Top E.M. The 64 508 bp IncP-1beta antibiotic multiresistance plasmid pB10 isolated from a waste-water treatment plant provides evidence for recombination between members of different branches of the IncP-1beta group. Microbiology 149 (2003) 3139-3153
30. Sengeløv G., Kristensen K.J., Sørensen A.H., Kroer N., and Sørensen S.J. Effect of genomic location on horizontal transfer of a recombinant gene cassette between Pseudomonas strains in the rhizosphere and spermosphere of barley seedlings. Curr. Microbiol. 42 (2001) 160-167
31. Smit E., Wolters A., and van Elsas J.D. Self-transmissible mercury resistance plasmids with gene-mobilizing capacity in soil bacterial populations: influence of wheat roots and mercury addition. Appl. Environ. Microbiol. 64 (1998) 1210-1219
32. Sørensen S.J., and Jensen L.E. Transfer of plasmid RP4 in the spermosphere and rhizoshere of barley seedling. Antonie van Leeuwenhoek 73 (1998) 69-77
33. Sueoka N. Directional mutation pressure, mutator mutations, and dynamics of molecular evolution. J. Mol. Evol. 37 (1993) 137-153
34. Swofford, D.L., 2002. PAUP*: Phylogentic analysis using parsimony (* and other methods). Version 4. Sinaur Associates, Sunderland, Massachusetts.
35. Szpirer C., Top E., Couturier M., and Mergeay M. Retrotransfer or gene capture: a feature of conjugative plasmids, with ecological and evolutionary significance. Microbiology 145 (1999) 3321-3329
36. Tauch A., Schlüter A., Bischoff N., Goesmann A., Meyer F., and Pühler A. 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 (2003) 570-584
37. Tennstedt T., Szczepanowski R., Krahn I., Pühler A., and Schlüter A. Sequence of the 68,869 bp IncP-1alpha plasmid pTB11 from a waste-water treatment plant reveals a highly conserved backbone, a Tn402-like integron and other transposable elements. Plasmid 53 (2005) 218-238
38. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
39. Thorsted P.B., Macartney D.P., Akhtar P., Haines A.S., Ali N., Davidson P., Stafford T., Pocklington M.J., Pansegrau W., Wilkins B.M., Lanka E., and Thomas C.M. Complete sequence of the IncPbeta plasmid R751: implications for evolution and organisation of the IncP backbone. J. Mol. Biol. 282 (1998) 969-990
40. van Passel, M.W., Bart, A., Luyf, A.C., van Kampen, A.H., van der Ende, A., 2006. Compositional discordance between prokaryotic plasmids and host chromosomes. BMC Genomics. 7:26 (E. published).
41. Vedler E., Vahter M., and Heinaru A. The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. J. Bacteriol. 186 (2004) 7161-7174