The evolution of IncP catabolic plasmids

Current Opinion in Biotechnology

Volumn 16, Issue 3 SPEC. ISS., 2005, Pages 291-298

  Dennis, Jonathan J ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CYTOLOGY; DNA SEQUENCES; GENE TRANSFER; METABOLISM;

CATABOLIC PATHWAYS; CATABOLIC PLASMIDS; GENE CAPTURE; GENOME SEQUENCES;

BIOTECHNOLOGY;

ANTIBIOTIC RESISTANCE; BACTERIAL GENOME; BACTERIAL STRAIN; DEGRADATION; ENVIRONMENT; EVOLUTION; GENE INSERTION; GENE SEQUENCE; GENE TRANSFER; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PRIORITY JOURNAL; PSEUDOMONAS; REVIEW; SEQUENCE ANALYSIS;

EID: 20444417458     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2005.04.002     Document Type: Review

References (51)

1. M. Feldgarden, N. Byrd, and F.M. Cohan Gradual evolution in bacteria: evidence from Bacillus systematics Microbiology 149 2003 3565 3573
2. H. Ochman, and N.A. Moran Genes lost and found: evolution of bacterial pathogenesis and symbiosis Science 292 2001 1096 1099
3. C.M. Fraser, J. Eisen, R.D. Fleischmann, K.A. Ketchum, and S. Peterson Comparitive genomics and understanding of microbial biology Emerg Infect Dis 6 2000 505 512
4. J.A. Eisen Horizonal gene transfer among microbial genomes: new insights from complete genome analysis Curr Opin Genet Dev 10 2000 606 611
5. J.G. Lawrence, and H. Ochman Reconciling the many faces of lateral gene transfer Trends Microbiol 10 2002 1 4
6. J.R. van der Meer, and V. Sentchilo Genomic islands and the evolution of catabolic pathways in bacteria Curr Opin Biotechnol 14 2003 248 254
7. D. Springael, and E.M. Top Horizontal gene transfer and microbial adaptation to xenobiotics: new types of mobile genetic elements and lessons from ecological studies Trends Microbiol 12 2004 53 58
8. C.M. Thomas Paradigms of plasmid organization Mol Microbiol 37 2000 485 491
9. C. Szpirer, E.M. Top, M. Couturier, and M. Mergeay Retrotransfer or gene capture: a feature of conjugative plasmids, with ecological and evolutionary significance Microbiology 145 1999 3321 3329
10. E.L. Zechner, F. de la Cruz, R. Eisenbrandt, A.M. Grahn, G. Koraimann, E. Lanka, G. Muth, W. Pansegrau, C.M. Thomas, and B.M. Wilkins Conjugative-DNA transfer processes C.M. Thomas The Horizontal Gene Pool: Bacterial Plasmids and Gene Spread 2000 Harwood Amsterdam 87 174
11. J.J. Dennis, and G.J. Zylstra Complete sequence and genetic organization of pDTG1, the 83 kilobase naphthalene degradation plasmid from Pseudomonas putida strain NCIB 9816-4 J Mol Biol 341 2004 753 768
12. A. Greated, L. Lambertsen, P.A. Williams, and C.M. Thomas Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida Environ Microbiol 4 2002 856 871
13. A. Greated, M. Titok, R. Krasowiak, R.J. Fairclough, and C.M. Thomas The replication and stable-inheritance functions of IncP-9 plasmid pM3 Microbiology 146 2000 2249 2258
14. M. Jahnke, T. El-Banna, R. Klintworth, and G. Auling Mineralization of orthanilic acid is a plasmid-associated trait in Alcaligenes cp O-1 J Gen Microbiol 136 1990 2241 2249
15. K.M. Yen, and C.M. Serdar Genetics of naphthalene catabolism in pseudomonads Crit Rev Microbiol 15 1988 247 268
16. P.R. Lehrbach, I. McGregor, J.M. Ward, and P. Broda Molecular relationships between Pseudomonas Inc P-9 degradative plasmids TOL, NAH, and SAL Plasmid 10 1983 164 174
17. K.E. Nelson, C. Weinel, I.T. Paulsen, R.J. Dodson, H. Hilbert, V.A. Martins dos Santos, D.E. Fouts, S.R. Gill, M. Pop, and M. Holmes Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440 Environ Microbiol 4 2002 799 808
18. S. Haryama Codon usage patterns suggest independent evolution of two catabolic operons on toluene-degradative plasmid TOL pWW0 of Pseudomonas putida J Mol Evol 38 1994 328 335
19. W. Li, J. Shi, X. Wang, Y. Han, W. Tong, L. Ma, B. Liu, and B. Cai Complete nucleotide sequence and organization of the naphthalene catabolic plasmid pND6-1 from Pseudomonas sp. strain ND6 Gene 336 2004 231 240
20. H. Nojiri, H. Sekiguchi, K. Maeda, M. Urata, S. Nakai, T. Yoshida, H. Habe, and T. Omori Genetic characterization and evolutionary implications of a car gene cluster in the carbazole degrader Pseudomonas sp. strain CA10 J Bacteriol 183 2001 3663 3679
21. K. Maeda, H. Nojiri, M. Shintani, T. Yoshida, H. Habe, and T. Omori Complete nucleotide sequence of carbazole/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676 J Mol Biol 326 2003 21 33 An excellent description of a large IncP-7 plasmid and resident catabolic transposon, with comments about the evolutionary significance derived from plasmid genome comparisons.
22. H. Nojiri, M. Shintani, and T. Omori Divergence of mobile genetic elements involved in the distribution of xenobiotic-catabolic capacity Appl Microbiol Biotechnol 64 2004 154 174 A very good review of a broad topic including sections on catabolic plasmids, transposons, and conjugative transposons. It serves as a comprehensive review of the field, yet also contains several unpublished observations that enhance the readability and modernity of the presented information.
23. H.M. Tan Bacterial catabolic transposons Appl Microbiol Biotechnol 51 1999 1 12
24. M. Tsuda, and T. Iino Naphthalene degrading genes on plasmid NAH7 are on a defective transposon Mol Gen Genet 223 1990 33 39
25. M.C. Ronchel, M.A. Ramos-Diaz, and J.L. Ramos Retrotransfer of DNA in the rhizosphere Environ Microbiol 2 2000 319 323
26. E.M. Top, Y. Moenne-Loccoz, T. Pembroke, and C.M. Thomas Phenotypic traits conferred by plasmids C.M. Thomas The Horizontal Gene Pool: Bacterial Plasmids and Gene Spread 1995 Harwood New York 249 285
27. W. Pansegrau, E. Lanka, P.T. Barth, D.H. Figurski, D.G. Guiney, D. Haas, D.R. Helinski, H. Schwab, V.A. Stanisich, and C.M. Thomas Complete nucleotide sequence of Birmingham IncP α plasmids. Compilation and comparative analysis J Mol Biol 239 1994 623 663
28. P.B. Thorsted, D.P. Macartney, P. Akhtar, A.S. Haines, N. Ali, P. Davidson, T. Stafford, M.J. Pocklington, W. Pansegrau, and B.M. Wilkins Complete sequence of the IncP β plasmid R751: implications for evolution and organisation of the IncP backbone J Mol Biol 282 1998 969 990
29. A. Tauch, A. Schluter, N. Bischoff, A. Goesmann, F. Meyer, and A. Puhler The 79,370-bp conjugative plasmid pB4 consists of an IncP-1β 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
30. A. Schluter, H. Heuer, R. Szczepanowski, L.J. Forney, C.M. Thomas, A. Puhler, and E.M. Top The 64508 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 2003 3139 3153
31. B. Martinez, J. Tomkins, L.P. Wackett, R. Wing, and M.J. Sadowsky Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP J Bacteriol 183 2001 5684 5697
32. M. Sota, H. Kawasaki, and M. Tsuda Structure of haloacetate-catabolic IncP-1β plasmid pUO1 and genetic mobility of its residing haloacetate-catabolic transposon J Bacteriol 185 2003 6741 6745
33. N. Trefault, R. De la Iglesia, A.M. Molina, M. Manzano, T. Ledger, D. Perez-Pantoja, M.A. Sanchez, M. Stuardo, and B. Gonzalez Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways Environ Microbiol 6 2004 655 668
34. T. Tralau, A.M. Cook, and J. Ruff Map of the IncP1 β plasmid pTSA encoding the widespread genes (tsa) for p-toluenesulfonate degradation in Comamonas testosteroni T-2 Appl Environ Microbiol 67 2001 1508 1516
35. R.P. Poh, A.R. Smith, and I.J. Bruce Complete characterisation of Tn5530 from Burkholderia cepacia strain 2a (pIJB1) and studies of 2,4- dichlorophenoxyacetate uptake by the organism Plasmid 48 2002 1 12
36. S. Beil, K.N. Timmis, and D.H. Pieper Genetic and biochemical analyses of the tec operon suggest a route for evolution of chlorobenzene degradation genes J Bacteriol 181 1999 341 346
37. A.C. Layton, J. Sanseverino, W. Wallace, C. Corcoran, and G.S. Sayler Evidence for 4-chlorobenzoic acid dehalogenation mediated by plasmids related to pSS50 Appl Environ Microbiol 58 1992 399 402
38. H. Heuer, R. Szczepanowski, S. Schneiker, A. Puhler, E.M. Top, and A. Schluter 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 2004 3591 3599 This noteworthy paper contains the first description of an IncP-1β plasmid that does not contain an insertion in the oriV-trfA region. Although ostensibly insignificant, this finding implies the existence of 'unloaded' cryptic plasmids that may exist within cells, available for gene capture or sampling.
39. E. Vedler, M. Vahter, and A. Heinaru 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 A thorough analysis of an IncP-1 plasmid showing that not only does it have a single large tfd catabolic transposon inserted at only one of the three possible sites, it also contains a noncanonical IncP-1β plasmid backbone.
40. E.M. Top, and D. Springael The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds Curr Opin Biotechnol 14 2003 262 269
41. G.A. Jacoby, L. Sutton, L. Knobel, and P. Mammen Properties of IncP-2 plasmids of Pseudomonas spp Antimicrob Agents Chemother 24 1983 168 175
42. N. Boone, J. Goris, P. de Vos, W. Verstraete, and E.M. Top Genetic diversity among 3-chloroaniline- and aniline-degrading strains of the Comamonadaceae Appl Environ Microbiol 67 2001 1107 1115
43. T. Murata, M. Ohnishi, T. Ara, J. Kaneko, C.G. Han, Y.F. Li, K. Takashima, H. Nojima, K. Nakayama, and A. Kaji Complete nucleotide sequence of plasmid Rts1: implications for evolution of large plasmid genomes J Bacteriol 184 2002 3194 3202
44. D. Boltner, C. MacMahon, J.T. Pembroke, P. Strike, and A.M. Osborn R391: a conjugative integrating mosaic comprised of phage, plasmid, and transposon elements J Bacteriol 184 2002 5158 5169
45. M.W. Gilmour, N.R. Thomson, M. Sanders, J. Parkhill, and D.E. Taylor The complete nucleotide sequence of the resistance plasmid R478: defining the backbone components of incompatibility group H conjugative plasmids through comparative genomics Plasmid 52 2004 182 202
46. J. Klockgether, O. Reva, K. Larbig, and B. Tummler Sequence analysis of the mobile genome island pKLC102 of Pseudomonas aeruginosa C J Bacteriol 186 2004 518 534
47. A.M. Osborn, and D. Boltner When phages, plasmids, and transposons collide: genomic islands, and conjugative- and mobilizable- transposons as a mosaic continuum Plasmid 48 2002 202 212 A thought-provoking review on conjugative transposons, phage, genomic islands and how to differentiate them from one another.
48. A. Toussaint, C. Merlin, S. Monchy, M. Abderrafi Benotmane, R. Leplae, M. Mergeay, and D. Springael The biphenyl- and 4-chlorobiphenyl-catabolic transposon Tn4371, a member of a new family of genomic islands related to IncP and Ti plasmids Appl Environ Microbiol 69 2003 4837 4845
49. L.E. Bryan, S.D. Semaka, H.M. Van Den Eizen, J.E. Kinnear, and R.L.S. Whitehouse Characteristics of R931 and other Pseudomonas aeruginosa R factors Antimicrob Agents Chemother 3 1973 625 637
50. K.E. Hill, A.J. Weightman, and C.J. Fry Isolation and screening plasmids from the epilithon which mobilize recombinant plasmid D10 Appl Environ Microbiol 58 1992 1292 1300
51. J.B. Hansen, and R.H. Olsen Isolation of large bacterial plasmids and characterization of the P2 incompatibility group plasmids pMG1 and pMG5 J Bacteriol 135 1978 227 238