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Plasmid-Mediated Tolerance Toward Environmental Pollutants

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  • Authors: Ana Segura1, Lázaro Molina2, Juan Luis Ramos3
  • Editors: Marcelo E. Tolmasky4, Juan Carlos Alonso5
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Estación Experimental del Zaidin (CSIC), Environmental Protection Department, Profesor Albareda, 1, 18008 Granada, Spain; 2: CIDERTA, Laboratorio de Investigación y Control Agroalimentario (LICAH), Parque Huelva Empresarial, 21007 Huelva, Spain; 3: Estación Experimental del Zaidin (CSIC), Environmental Protection Department, Profesor Albareda, 1, 18008 Granada, Spain; 4: California State University, Fullerton, CA; 5: Centro Nacional de Biotecnología, Cantoblanco, Madrid, Spain
  • Source: microbiolspec November 2014 vol. 2 no. 6 doi:10.1128/microbiolspec.PLAS-0013-2013
  • Received 04 February 2014 Accepted 05 February 2014 Published 07 November 2014
  • Ana Segura, ana.segura@eez.csic.es
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  • Abstract:

    The survival capacity of microorganisms in a contaminated environment is limited by the concentration and/or toxicity of the pollutant. Through evolutionary processes, some bacteria have developed or acquired mechanisms to cope with the deleterious effects of toxic compounds, a phenomenon known as tolerance. Common mechanisms of tolerance include the extrusion of contaminants to the outer media and, when concentrations of pollutants are low, the degradation of the toxic compound. For both of these approaches, plasmids that encode genes for the degradation of contaminants such as toluene, naphthalene, phenol, nitrobenzene, and triazine or are involved in tolerance toward organic solvents and heavy metals, play an important role in the evolution and dissemination of these catabolic pathways and efflux pumps. Environmental plasmids are often conjugative and can transfer their genes between different strains; furthermore, many catabolic or efflux pump genes are often associated with transposable elements, making them one of the major players in bacterial evolution. In this review, we will briefly describe catabolic and tolerance plasmids and advances in the knowledge and biotechnological applications of these plasmids.

  • Citation: Segura A, Molina L, Ramos J. 2014. Plasmid-Mediated Tolerance Toward Environmental Pollutants. Microbiol Spectrum 2(6):PLAS-0013-2013. doi:10.1128/microbiolspec.PLAS-0013-2013.

Key Concept Ranking

Mobile Genetic Elements
0.72136563
Outer Membrane Proteins
0.45943847
Polycyclic Aromatic Hydrocarbons
0.4540851
Integral Membrane Proteins
0.43568507
0.72136563

References

1. Segura A, Rojas A, Hurtado A, Huertas MJ, Ramos JL. 2003. Comparative genomic analysis of solvent extrusion pumps in Pseudomonas strains exhibiting different degrees of solvent tolerance. Extremophiles 7:371–376. [PubMed][CrossRef]
2. Williams PA, Jones RM, Zysltra GJ. 2004. Genomics of catabolic plasmids, p 165–195. In Ramos JL (ed), Pseudomonas, vol 1. Kluwer Academic, Plenum Publishers, New York. [CrossRef]
3. Ogawa N, Chackrabarty AM, Zaborina O. 2004. Degradative plasmids, p 341–392. In Funnell BE, Phillips GJ (ed), Plasmid Biology. ASM Press, Washington, DC. [CrossRef]
4. Springael D, Top EM. 2004. Horizontal gene transfer and microbial adaptation to xenobiotics: new types of mobile genetic elements and lessons from ecological studies. Trends Microbiol 12:53–58. [PubMed][CrossRef]
5. Jones BV, Marchesi JR. 2007. Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat Methods 4:55–61. [PubMed][CrossRef]
6. Parales RE, Parales JV, Pelletier DA, Ditty JL. 2008. Diversity of microbial toluene degradation pathways. Adv Appl Microbiol 64:1–73. [PubMed][CrossRef]
7. Bertini L, Calafaro V, Proietti S, Caporale C, Capasso P, Caruso C, Di Donato A. 2013. Deepening TOL and TAU catabolic pathways of Pseudomonas sp. OX1: Cloning, sequencing and characterization of the lower pathways. Biochimie 95:241–250. [PubMed][CrossRef]
8. Williams PA, Murray K. 1974. Metabolism of benzoate and the methylbenzoates by Pseudomonas putida (arvilla) mt-2: evidence for the existence of a TOL plasmid. J Bacteriol 120:416–423. [PubMed]
9. Greated A, Lambertsen L, Williams PA, Thomas CM. 2002. Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Environ Microbiol 4:856–871. [PubMed][CrossRef]
10. Gallegos MT, Williams PA, Ramos JL. 1997. Transcriptional control of the multiple catabolic pathways encoded on the TOL plasmid pWW53 of Pseudomonas putida MT53. J Bacteriol 179:5024–5029. [PubMed]
11. Ramos JL, Marques S, Timmis KN. 1997. Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annu Rev Microbiol 51:341–371. [PubMed][CrossRef]
12. Silva-Roche R, de Lorenzo V. 2013. The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space. Env Microbiol 15:271–286. [PubMed][CrossRef]
13. Bayley SA, Duggleby CJ, Worsey MJ, Williams PA, Hardy KB, Broda P. 1977. Two modes of loss of the Tol function from Pseudomonas putida mt-2. Mol Gen Genet 154:203–204. [PubMed][CrossRef]
14. Muñoz R, Hernández M, Segura A, Gouveia J, Rojas A, Ramos JL, Villaverde S. 2009. Continuous cultures of Pseudomonas putida mt-2 overcome catabolic function loss under real case operating conditions. Appl Microbiol Biotech 83:189–198. [PubMed][CrossRef]
15. Tsuda M, Iino T. 1987. Genetic analysis of a transposon carrying toluene degrading genes on a TOL plasmid pWW0. Mol Gen Genet 210:270–276. [PubMed][CrossRef]
16. Tsuda M, Iino T. 1988. Identification and characterization of Tn4653, a transposon covering the toluene transposon Tn4651 on TOL plasmid pWW0. Mol Gen Genet 213:72–77. [PubMed][CrossRef]
17. Williams PA, Jones RM, Shaw LE. 2002. A third transposable element, ISPpu12, from the toluene-xylene catabolic plasmid pWW0 of Pseudomonas putida mt-2. J Bacteriol 184:6572–6580. [PubMed][CrossRef]
18. Williams PA, Worsey MJ. 1976. Ubiquity of plasmids in coding for toluene and xylene metabolism in soil bacteria: evidence for the existence of new TOL plasmids. J Bacteriol 125:818–828. [PubMed]
19. Keil H, Keil S, Pickup W, Williams PA. 1985. Evolutionary conservation of genes coding for meta pathway enzymes within TOL plasmids pWW0 and pWW53. J Bacteriol 164:887–895. [PubMed]
20. Chatfield LK, Williams PA. 1986. Naturally occurring TOL plasmids in Pseudomonas strains carry either two homologous or two nonhomologous catechol 2,3-oxygenase genes. J Bacteriol 168:878–885. [PubMed]
21. Sentchilo VS, Perebituk AN, Zehnder AJ, van der Meer JR. 2000. Molecular diversity of plasmids bearing genes that encode toluene and xylene metabolism in Pseudomonas strains isolated from different contaminated sites in Belarus. Appl Environ Microbiol 66:2842–2852. [PubMed][CrossRef]
22. Yano H, Garruto CE, Sota M, Ohtsubo Y, Nagata Y, Zylstra GJ, Williams PA, Tsuda M. 2007. Complete sequence determination combined with analysis of transposition/site-specific recombination events to explain genetic organization of IncP-7 TOL plasmid pWW53 and related mobile genetic elements. J Mol Biol 369:11–26. [PubMed][CrossRef]
23. Yano H, Miyakoshi M, Ohshima K, Tabata M, Nagata Y, Hattori M, Tsuda M. 2010. Complete nucleotide sequence of TOL plasmid pDK1 provides evidence for evolutionary history of IncP-7 catabolic plasmids. J Bacteriol 192:4337–4347. [PubMed][CrossRef]
24. Shields MS, Reagin MJ, Gerger RR, Campbell R, Somerville C. 1995. TOM, a new aromatic degradative plasmid from Burkholderia (Pseudomonas) cepacia G4. Appl Environ Microbiol 61:1352–1356. [PubMed]
25. Shields MS, Montgomery SO, Cuskey SM, Chapman PJ, Pritchard PH. 1991. Mutants of Pseudomonas cepacia G4 defective in catabolism of aromatic compounds and trichloroethylene. Appl Environ Microbiol 57:1935–1941. [PubMed]
26. Nelson MJK, Montgomery SO, Mahaffey WR, Pritchard PH. 1987. Biodegradation of trichloroethylene and involvement of an aromatic biodegradative pathway. Appl Environ Microbiol 53:949–954. [PubMed]
27. Molina L, Duque E, Gómez MJ, Krell T, Lacal J, García-Puente A, García,V, Matilla MA, Ramos JL, Segura A. 2011. The pGRT1 plasmid of Pseudomonas putida DOT-T1E encodes functions relevant for survival under harsh conditions in the environment. Environ Microbiol 13:2315–2327. [PubMed][CrossRef]
28. Rheinwald JG, Chakrabarty AM, Gunsalus IC. 1973. A transmissible plasmid controlling camphor oxidation in Pseudomonas putida. Proc Natl Acad Sci USA 70:885–889. [PubMed][CrossRef]
29. Dunn NW, Gunsalus IC. 1973. Transmissible plasmid coding early enzymes of naphthalene oxidation in Pseudomonas putida. J Bacteriol 114:974–979. [PubMed]
30. Yen KM, Gunsalus IC. 1982. Plasmid gene organization: naphthalene/salicylate oxidation. Proc Natl Acad Sci USA 79:874–879. [PubMed][CrossRef]
31. Yen KM, Serdar CM. 1988. Genetics of naphthalene catabolism in pseudomonads. Crit Rev Microbiol 15:247–268. [PubMed][CrossRef]
32. Denome SA, Stanley DC, Olson ES, Young KD. 1993. Metabolism of dibenzothiophene and naphthalene in Pseudomonas strains: complete DNA sequence of upper naphthalene catabolic pathway. J Bacteriol 175:6890–6901. [PubMed]
33. Simon MJ, Osslund TD, Saunders R, Ensley BD, Suggs S, Harcourt A, Suen WC, Cruden DL, Gibson DT, Zylstra GJ. 1993. Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strains G7 and NCIB 9816-4. Gene 127:31–37. [PubMed][CrossRef]
34. Eaton RW. 1994. Organization and evolution of naphthalene catabolic pathways: sequence of the DNA encoding 2-hydroxy-chromene-2-carboxylate isomerase and trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from the NAH7 plasmid. J Bacteriol 176:7757–7762. [PubMed]
35. Grimm AC, Harwood CS. 1999. NahY, a catabolic plasmid-encoded receptor required for chemotaxis of Pseudomonas putida to the aromatic hydrocarbon naphthalene. J Bacteriol 181:3310–3316. [PubMed]
36. Schell MA, Sukordhaman M. 1989. Evidence that the transcription activator encoded by the Pseudomonas putida nahR gene is evolutionarily related to the transcription activators encoded by the Rhizobium nodD genes. J Bacteriol 171:1952–1959. [PubMed]
37. Dennis JJ, Zylstra GJ. 2004. Complete sequence and genetic organization of pDTG1, the 83 kilobase naphthalene degradation plasmid from Pseudomonas putida strain NCIB 9816-4. J Mol Biol 341:753–768. [PubMed][CrossRef]
38. Li W, Shi J, Wang X, Han Y, Tong W, Ma L, Liu B, Cai B. 2004. Complete nucleotide sequence and organization of the naphthalene catabolic plasmid pND6-1 from Pseudomonas sp. strain ND6. Gene 336:231–240. [PubMed][CrossRef]
39. Sota M, Yano H, Ono A, Miyazaki R, Ishii H, Genka H, Top EM, Tsuda M. 2006. Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn4655 suggests catabolic gene spread by a tyrosine recombinase. J Bacteriol 188:4057–4067. [PubMed][CrossRef]
40. Tsuda M, Iino T. 1990. Naphthalene degrading genes on plasmid NAH7 are on a defective transposon. Mol Gen Genet 223:33–39. [PubMed][CrossRef]
41. Sanseverino J, Applegate BM, King JMH, Sayler GS. 1993. Plasmid-mediated mineralization of naphthalene, phenanthrene and anthracene. Appl Environ Microbiol 59:1931–1937. [PubMed]
42. Kiyohara H, Nagao K. 1978. The catabolism of phenanthrene and naphthalene in bacteria. J Gen Microbiol 105:69–75. [CrossRef]
43. Laurie AD, Lloyd-Jones G. 1999. The phn genes of Burkholderia sp. strain RP007 constitute a divergent gene cluster for polycyclic aromatic hydrocarbon catabolism. J Bacteriol 181:531–540. [PubMed]
44. Pinyakong O, Habe H, Omori T. 2003. The unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (PAHs) J Gen Appl Microbiol 49:1–19. [PubMed][CrossRef]
45. Basta T, Keck A, Klein J, Stolz A. 2004. Detection and characterization of conjugative degradative plasmids in xenobiotic-degrading Sphingomonas strains. J Bacteriol 186:3862–3872. [PubMed][CrossRef]
46. Romine MF, Stillwell LC, Wong K-K, Thurston SJ, Sisk EC, Sensen C, Gaasterland T, Fredrickson JK, Saffer JD. 1999. Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. J Bacteriol 181:1585–1602. [PubMed]
47. Feng X, Ou X-L, Ogram A. 1997. Plasmid-mediated mineralization of carbofuran by Sphingomonas sp. CF-06. Appl Environ Microbiol 63:1332–1337. [PubMed]
48. Basta I, Buerger S, Stolz A. 2005. Structural and replicative diversity of large plasmids from sphingomonads that degrade polycyclic aromatic compounds and xenobiotics. Microbiology 151:2025–2037. [PubMed][CrossRef]
49. Keck A, Conradt D, Mahler A, Stolz A, Mattes R, Klein J. 2006. Identification and functional analysis of the genes for naphthalenesulfonate catabolism by Sphingomonas xenophaga BN6. Microbiology 152:1929–1940. [PubMed][CrossRef]
50. Maeda K, Nojiri H, Shintani M, Yoshida T, Habe H, Omori T. 2003. 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 326:21–33. [PubMed][CrossRef]
51. Takahasi Y, Shintani M, Yamane H, Nojiri H. 2009. The complete nucleotide sequence of pCAR2: pCAR2 and pCAR1 were structurally identical IncP-7 carbazole degradative plasmids. Biosci Biotechnol Biochem 73:744–746. [PubMed][CrossRef]
52. Shintani M, Urata M, Inoue K, Eto K, Habe H, Omori T, Yamane H, Nojiri H. 2007. The Sphingomonas plasmid pCAR3 is involved in complete mineralization of carbazole. J Bacteriol 189:2007–2020. [PubMed][CrossRef]
53. Nam J-W, Nojiri H, Noguchi H, Uchimura H, Yoshida T. Habe H, Yamane H, Omori T. 2002. Purification and characterization of carbazole 1,9a-dioxigenase, a three-component dioxygenase system of Pseudomonas resinovorans strain CA10. Appl Environ Microbiol 68:5882–5890. [CrossRef]
54. Nojiri H. 2012. Structural and molecular genetic analyses of the bacterial carbazole degradation system. Biosci Biotechnol Biochem 76:1–18. [PubMed][CrossRef]
55. Ashikawa Y, Fujimoto Z, Usami Y, Inoue K, Noguchi H, Yamane H, Nojiri H. 2012. Structural insight into the substrate- and dioxygen-binding manner in the catalytic cycle of Rieske nonheme iron oxygenase system, carbazole 1,9a-dioxygenase. BMC Struct Biol 12:15. doi:10.1186/1472-6807-12-15. [PubMed][CrossRef]
56. Shintani M, Matsumoto T, Yoshikawa H, Yamane H, Ohkuma M, Nojiri H. 2011. DNA rearrangement has occurred in the carbazole-degradative plasmid pCAR1 and the chromosome of its unsuitable host, Pseudomonas fluorescens PF0-1. Microbiology 157:3405–3416. [PubMed][CrossRef]
57. Solinas F, Marconi AM, Ruzzi M, Zennaro E. 1995. Characterization and sequence of a novel insertion sequence, IS1162, from Pseudomonas fluorescens. Gene 155:77–82. [PubMed][CrossRef]
58. Schneiker S, Kosier B, Puhler A, Selbitschka W. 1999. The Sinorhizobium meliloti insertion sequence (IS) element ISRm14 is related to a previously unrecognized IS element located adjacent to the Escherichia coli locus of enterocyte effacement (LEE) pathogenicity island. Curr Microbiol 39:274–281. [PubMed][CrossRef]
59. Yao CC, Wong DTS, Poh CL. 1998. IS1491 from Pseudomonas alcaligenes NCIB 9867: characterization and distribution among Pseudomonas species. Plasmid 39:187–195. [PubMed][CrossRef]
60. Nojiri H, Sekiguchi H, Maeda K, Urata M, Nakai S, Yoshida T, Habe H, Omori T. 2001. Genetic characterization and evolutionary implications of a car gene cluster in carbazole degrader Pseudomonas sp. strain CA10. J Bacteriol 183:3663–3679. [PubMed][CrossRef]
61. Overhage J, Sielker S, Hombrug S, Parschat K, Fetzner S. 2005. Identification of large linear plasmids in Arthrobacter spp. encoding the degradation of quinaldine to anthranilate. Microbiology 151:491–500. [PubMed][CrossRef]
62. Parschat K, Hauer B, Kappl R, Kraft R, Hüttermann J, Fetzner S. 2003. Gene cluster of Arthrobacter ilicis Rü61a involved in the degradation of quinaldine to anthranilate. Characterization and functional expression of the quinaldine 4-oxidase qoxLMS genes. J Biol Chem 278:27483–27494. [PubMed][CrossRef]
63. Parschat K, Overhage J, Strittmatter AW, Henne A, Gottschalk G, Fetzner S. 2007. Complete nucleotide sequence of the 113-kilobase linear catabolic plasmid pAL1 of Arthrobacter nitroguajacolicus Rü61a and transcriptional analysis of genes involved in quinaldine degradation. J Bacteriol 189:3855–3867. [PubMed][CrossRef]
64. Niewerth H, Schuldes J, Parschat K, Kiefer P, Vorholt JA, Daniel R, Fetzner S. 2012. Complete genome sequence and metabolic potential of the quinaldine-degrading bacterium Arthrobacter sp. Rue61a. BMC Genomics 13:534. doi:10.1186/1471-2164-13-534. [PubMed][CrossRef]
65. Niewerth H, Parschat K, Rauschenberg M, Ravoo BJ, Fetzner S. 2013. The PaaX-type repressor MeqR2 of Arthrobacter sp. strain Rue61a, involved in the regulation of quinaldine catabolism, binds to its own promoter and to catabolic promoters and specifically responds to anthraniloyl coenzyme A. J Bacteriol. 195:1068–1080. [PubMed][CrossRef]
66. Wu W, Leblanc SKD, Piktel J, Jensen SE, Roy KL. 2006. Prediction and functional analysis of the replication origin of the linear plasmid pSCL2 in Streptomyces clavuligerus. Can J Microbiol 52:293–300. [PubMed][CrossRef]
67. Don RH, Pemberton JM. 1981. Properties of six pesticide degradation plasmids isolated from Alcaligenes paradoxus and Alcaligenes eutrophus. J Bacteriol 145:681–686. [PubMed]
68. Laemmli CM, Leveau JHJ, Zehnder AJB, van der Meer JR. 2000. Characterization of a second tfd gene cluster for chlorophenol and chlorocatechol metabolism on plasmid pJP4 in Ralstonia eutropha JMP134 (pJP4). J Bacteriol 182:4165–4172. [PubMed][CrossRef]
69. Pérez-Pantoja D, Guzmán L, Manzano M, Pieper DH, González B. 2000. Role of tfdCIDIEIFI and tfdDIICIIEIIFII gene modules in catabolism of 3-chlorobenzoate by Ralstonia eutropha JMP134 (pJP4). Appl Environ Microbiol 66:1602–1608. [PubMed][CrossRef]
70. Trefault N, De la Iglesia R, Molina AM, Manzano M, Ledger T, Perez-Pantoja D, Sánchez MA, Stuardo M, Gonzalez B. 2004. 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 6:655–668. [PubMed][CrossRef]
71. Vedler E, Vahter M, Heinaru A. 2004. 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 186:7161–7174. [PubMed][CrossRef]
72. Poh RP-C, Smith ARW, Bruce IJ. 2002. Complete characterization of Tn5530 from Burkholderia cepacia strain 2a (pIJB1) and studies of 2,4-dichlorophenoxyacetate uptake by the organism. Plasmid 48:1–12. [PubMed][CrossRef]
73. Tsoi TV, Plotnikova EG, Cole JR, Guerin WF, Bagdasarian M, Tiedje JM. 1999. Cloning, expression and nucleotide sequence of the Pseudomonas aeruginosa 142 ohb genes coding for oxygenolytic ortho dehalogenation of halobenzoates. Appl Environ Microbiol 65:2151–2162. [PubMed]
74. Hickey WJ, Sabat G, Yuroff AS, Arment AR, Perez-Lesher J. 2001. Cloning, nucleotide sequencing and functional analysis of a novel, mobile cluster of biodegradation genes from Pseudomonas aeruginosa strain JB2. Appl Environ Microbiol 67:4603–4609. [PubMed][CrossRef]
75. de Souza ML, Sadowsky MJ, Seffernick J, Martinez B, Wackett LP. 1998. The atrazine catabolism genes are widespread and highly conserved. J Bacteriol 180:1951–1954. [PubMed]
76. de Souza ML, Wackett LP, Sadowsky MJ. 1998. The atzABC genes encoding atrazine catabolism are located on a self-transmissible plasmid in Pseudomonas sp. strain ADP. Appl Environ Microbiol 64:2323–2326. [PubMed]
77. Martinez B, Tomkins J, Wackett LP, Wing R, Sadowsky MJ. 2001. Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J Bacteriol 183:5684–5697. [PubMed][CrossRef]
78. Król JE, Penrod JT, McCaslin H, Rogers LM, Yano H, Stancik AD, Dejonghe W, Brown CJ, Parales RE, Wuertz S, Top EM. 2011. Role of IncP-1ß plasmids pWDL7::rfp and pNB8c in chloroaniline catabolism as determined by genomic and functional analyses. Appl Environ Microbiol 78:828–838. [PubMed][CrossRef]
79. Wu JF, Sun CW, Jiang CY, Liu ZP, Liu SJ. 2005. A novel 2-aminophenol 1,6-dioxygenase involved in the degradation of p-chloronitrobenzene by Comamonas strain CNB-1 purification, properties, genetic cloning and expression in Escherichia coli. Arch Microbiol 183:1–8. [PubMed][CrossRef]
80. Wu JF, Jiang CY, Wang BJ, Ma YF, Liu ZP, Liu SJ. 2006. Novel partial reductive pathway for 4-chloronitrobenzene and nitrobenzene degradation in Comamonas sp. strain CNB-1. Appl Environ Microbiol 72:1759–1765. [PubMed][CrossRef]
81. Liu L, Wu JF, Ma YF, Wang SY, Zhao GP, Liu SJ. 2007. A novel deaminase involved in chloronitrobenzene and nitrobenzene degradation with Comamonas sp. strain CNB-1. J Bacteriol 189:2677–2682. [PubMed][CrossRef]
82. Ma YF, Wu JF, Wang SY, Jiang CY, Zhang Y, Qi SW, Liu L, Zhao GP, Liu SJ. 2007. Nucleotide sequence of plasmid pCNB1 from Comamonas strain CNB-1 reveals novel genetic organization and evolution for 4-chloronitrobenzene degradation. Appl Environ Microbiol 73:4477–4483. [PubMed][CrossRef]
83. Nagata Y, Kamakura M, Endo R, Miyazaki R, Ohtsubo Y, Tsuda M. 2006. Distribution of γ-hexachlorocyclohexane-degrading genes on three replicons in Sphingobium japonicum UT26. FEMS Microbiol Lett 256:112–118. [PubMed][CrossRef]
84. Miyazaki R, Sato Y, Ito M, Ohtsubo Y, Nagata Y, Tsuda M. 2006. Complete nucleotide sequence of an exogenously isolated plasmid pLB1, involved in γ-hexachlorocyclohexane degradation. Appl Environ Microbiol 72:6923–6933. [PubMed][CrossRef]
85. Smalla K, Osborn AM, Wellington EMH. 2000. Isolation and characterization of plasmids from bacteria, p 207–248. In Thomas CM (ed), The Horizontal Gene Pool–Bacterial Plasmids and Gene Spread. Harwood Academic Publishers, Amsterdam, The Netherlands. [CrossRef]
86. Junker F, Cook AM. 1997. Conjugative plasmids and the degradation of arylsulfonates in Comamonas testosteroni. Appl Environ Microbiol 63:2403–2410. [PubMed]
87. Tralau T, Cook AM, Ruff J. 2001. Map of the IncP1ß plasmid pTSA encoding the widespread genes (tsa) for p-toluenesulfonate degradation in Comamonas testosteroni T-2. Appl Environ Microbiol 67:1508–1516. [PubMed][CrossRef]
88. Kivisaar MA, Habicht JK, Heinaru AL. 1989. Degradation of phenol and m-toluate in Pseudomonas sp. strain EST1001 and its Pseudomonas putida transconjugants is determined by a multiplasmid system. J Bacteriol 171:5111–5116. [PubMed]
89. Kivisaar M, Hõrak R, Kasak L, Heinaru A, Habicht J. 1990. Selection of independent plasmids determining phenol degradation in Pseudomonas putida and the cloning and expression of genes encoding phenol monooxygenase and catechol 1,2-dioxygenase. Plasmid 24:25–36. [PubMed][CrossRef]
90. Kallastu A, Hõrak R, Kivisaar M. 1998. Identification and characterization of IS1411, a new insertion sequence which causes transcriptional activation of the phenol degradation genes in Pseudomonas putida. J Bacteriol 180:5306–5312. [PubMed]
91. Peters M, Heinaru E, Talpsep E, Wand H, Stottmeister U, Heinaru A, Nurk A. 1997. Acquisition of a deliberately introduced phenol degradation operon, pheBA, by different indigenous Pseudomonas species. Appl Environ Microbiol 63:4899–4906. [PubMed]
92. Shingler V, Franklin FC, Tsuda M, Holroyd D, Bagdasarian M. 1989. Molecular analysis of a plasmid-encoded phenol hydroxylase from Pseudomonas CF600. J Gen Microbiol. 135:1083–1092. [PubMed]
93. Powlowski J, Shingler V. 1994. Genetics and biochemistry of phenol degradation by Pseudomonas sp. CF600. Biodegradation 5:219–236. [PubMed][CrossRef]
94. van Beilen JB, Wubbolts MG, Witholt B. 1994. Genetics of alkane oxidation by Pseudomonas oleovorans. Biodegradation 5:161–174. [PubMed][CrossRef]
95. van Beilen JB, Panke S, Lucchini S, Franchini AG, Röthlisberger M, Witholt B. 2001. Analysis of Pseudomonas putida alkane degradation gene clusters and flanking insertion sequences: evolution and regulation of the alk genes. Microbiology 147:1621–1630. [PubMed]
96. Dinamarca MA, Aranda-Olmedo I, Puyet A, Rojo F. 2003. Expression of the Pseudomonas putida OCT plasmid alkane degradation pathway is modulated by two different global control signals: evidence from continuous cultures. J Bacteriol. 185:4772–4778. [PubMed][CrossRef]
97. Sikkema J, de Bont JA, Poolman B. 1995. Mechanisms of membrane toxicity of hydrocarbons. Microbiol Rev 59:201–222. [PubMed]
98. Udaondo Z, Molina L, Daniels C, Gómez MJ, Molina-Henares MA, Matilla MA, Roca A, Fernández M, Duque E, Segura A, Ramos JL. 2013. Metabolic potential of the organic-solvent tolerant Pseudomonas putida DOT-T1E deduced from its annotated genome. Microb Biotechnol 6:598–611. [PubMed][CrossRef]
99. Ramos JL, Duque E, Huertas MJ, Haïdour A. 1995. Isolation and expansion of the catabolic potential of a Pseudomonas putida strain able to grow in the presence of high concentrations of aromatic hydrocarbons. J Bacteriol 177:3911–3916. [PubMed]
100. Mosqueda G, Ramos-Gonzalez MI, Ramos JL. 1999. Toluene metabolism by the solvent tolerant Pseudomonas putida DOT-T1 strain, and its role in solvent impermeabilization. Gene 232:69–76. [PubMed][CrossRef]
101. Udaondo Z, Duque E. Fernández M, Molina L, de la Torre J, Bernal P, Niqui JL, Pini C, Roca A, Matilla MA, Molina-Henares MA, Silva-Jiménez H, Navarro-Avilés G, Busch, A, Lacal J, Krell T, Segura A, Ramos JL. 2012. Analysis of solvent tolerance in Pseudomonas putida DOT-T1E based on its genome sequence and a collection of mutants. FEBS Lett 586:2932–2938. [PubMed][CrossRef]
102. Rodríguez-Herva JJ, García V, Hurtado A, Segura A, Ramos JL. 2007. The ttgGHI solvent efflux pump operon of Pseudomonas putida DOT-T1E is located on a large self-transmissible plasmid. Environ Microbiol 9:1550–1561. [PubMed][CrossRef]
103. Segura A, Molina L, Fillet S, Krell T, Bernal P, Muñoz-Rojas J, Ramos JL. 2012. Solvent tolerance in Gram-negative bacteria. Curr Opin Biotechnol 23:415–421. [PubMed][CrossRef]
104. Rojas A, Duque E, Mosqueda G, Golden G, Hurtado A, Ramos JL, Segura A. 2001. Three efflux pumps are required to provide efficient tolerance to toluene to toluene in Pseudomonas putida DOT-TIE. J Bacteriol 183:3967–3973. [PubMed][CrossRef]
105. Blair JM, Piddock LJ. 2009 Structure, function and inhibition of RND efflux pumps in Gram-negative bacteria: an update. Curr Opin Microbiol 5:512–519. [PubMed][CrossRef]
106. Hinchliffe P, Symmons MF, Hughes C, Koronakis V. 2013. Structure and operation of bacterial tripartite pumps. Annu Rev Microbiol 67:221–242. [PubMed][CrossRef]
107. Murakami S, Nakashima R, Yamashita E, Yamaguchi A. 2002. Crystal structure of bacterial multidrug efflux transporter AcrB. Nature 419:587–593. [PubMed][CrossRef]
108. Sennhauser G, Bukowska MA, Briand C, Grütter MG. 2009. Crystal structure of the multidrug exporter MexB from Pseudomonas aeruginosa. J Mol Biol 389:134–145. [PubMed][CrossRef]
109. Koronakis V, Sharff A, Koronakis E, Luisi B, Hughes C. 2000. Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export. Nature 405:914–919. [PubMed][CrossRef]
110. Nikaido H, Zgurskaya HI. 2001 AcrAB and related multidrug efflux pumps of Escherichia coli. J Mol Microbiol Biotechnol 3:215–218. [PubMed]
111. Symmons MF, Bokma E, Koronakis E, Hughes C, Koronakis V. 2009. The assembled structure of a complete tripartite bacterial multidrug efflux pump. Proc Natl Acad SciUSA 106:7173–7178. [PubMed][CrossRef]
112. Ramos J L, Duque E, Godoy P, Segura A. 1998. Efflux pumps involved in toluene tolerance in Pseudomonas putida DOT-T1E. J Bacteriol 180:3323–3329. [PubMed]
113. Mosqueda G, Ramos JL. 2000. A set of genes encoding a second toluene efflux system in Pseudomonas putida DOT-T1E is linked to the tod genes for toluene metabolism. J Bacteriol 182:937–943. [PubMed][CrossRef]
114. Rojas A, Segura A, Guazzaroni ME, Terán W, Hurtado A, Gallegos MT, Ramos JL. 2003. In vivo and in vitro evidence that TtgV is the specific regulator of the TtgGHI multidrug and solvent efflux pump of Pseudomonas putida. J Bacteriol 185:4755–4763. [PubMed][CrossRef]
115. Lacal J, Muñoz-Martínez F, Reyes-Darías JA, Duque E, Matilla M, Segura A, Calvo JJ, Jímenez-Sánchez C, Krell T, Ramos JL. 2011. Bacterial chemotaxis towards aromatic hydrocarbons in Pseudomonas. Environ Microbiol 13:1733–1744. [PubMed][CrossRef]
116. Miyakoshi M, Shintani M, Terabayashi T, Kai S, Yamane H, Nojiri H. 2007. Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J Bacteriol 189:6849–6860. [PubMed][CrossRef]
117. Iwaki H, Muraki T, Ishihara S, Hasegawa Y, Rankin KN, Sulea T, Boyd J, Lau PC. 2007. Characterization of a pseudomonad 2-nitrobenzoate nitroreductase and its catabolic pathway-associated 2-hydroxylaminobenzoate mutase and a chemoreceptor involved in 2-nitrobenzoate chemotaxis. J Bacteriol 189:3502–3514. [PubMed][CrossRef]
118. Yoakum GH, Cole RS. 1977. Role of ATP in removal of psoralen cross-links from DNA of Escherichia coli permeabilized by treatment with toluene. J Biol Chem 252:7023–7030. [PubMed]
119. Rahmati S, Yang S, Davidson AL, Zechiedrich EL. 2002. Control of the AcrAB multidrug efflux pump by quorum-sensing regulator SdiA. Mol Microbiol 43:677–685. [PubMed][CrossRef]
120. Nikaido E, Yamaguchi A, Nishino K. 2008. AcrAB multidrug efflux pump regulation in Salmonella enterica serovar Typhimurium by RamA in response to environmental signals. J Biol Chem 283:24245–24253. [PubMed][CrossRef]
121. Haines AS, Jones K, Batt SM, Kosheleva IA, Thomas CM. 2007. Sequence of plasmid pBS228 and reconstruction of the IncP-1a phylogeny. Plasmid 58:76–83. [PubMed][CrossRef]
122. Kvint K, Nachin L, Diez A, Nyström T. 2003. The bacterial universal stress protein: function and regulation. Curr Opin Microbiol 6:140–145. [PubMed][CrossRef]
123. Nachin L, Nannmark U, Nyström T. 2005. Differential roles of the universal stress proteins of Escherichia coli in oxidative stress resistance, adhesion, and motility. J Bacteriol 187:6265–6272. [PubMed][CrossRef]
124. Xiong J, Alexander DC, Ma JH, Déraspe M, Low DE, Jamieson FB, Roy PH. 2013. Complete sequence of pOZ176, a 500-kilobase IncP-2 plasmid encoding IMP-9-mediated carbapenem resistance, from outbreak isolate Pseudomonas aeruginosa 96. Antimicrob Agents Chemother 57:3775–3782. [PubMed][CrossRef]
125. Kieboom J, Dennis JJ, de Bont JA, Zylstra GJ. 1998. Identification and molecular characterization of an efflux pump involved in Pseudomonas putida S12 solvent tolerance. J Biol Chem 273:85–91. [PubMed][CrossRef]
126. Lacal J, Reyes-Darias JA, García-Fontana C, Ramos JL, Krell T. 2013. Tactic responses to pollutants and their potential to increase biodegradation efficiency. J Appl Microbiol 114:923–933. [PubMed][CrossRef]
127. Kuc J. 1995. Phytoalexins, stress metabolism, and disease resistance in plants. Annu Rev Phytopathol 33:275–297. [PubMed][CrossRef]
128. Spaink HP. 1995. The molecular basis of infection and nodulation by rhizobia: the ins and outs of sympathogenesis. Annu Rev Phytopathol 33:345–368. [PubMed][CrossRef]
129. Rao JR, Cooper JE. 1994. Rhizobia catabolize nod gene-inducing flavonoids via C-ring fission mechanisms. J Bacteriol 176:5409–5413. [PubMed]
130. González-Pasayo R, Martínez-Romero E. 2000. Multiresistance genes of Rhizobium etli CFN42. Mol Plant Microbe Interact 13:572–577. [PubMed][CrossRef]
131. Gonzalez V, Santamaria RI, Bustos P, Hernandez-Gonzalez I, Medrano-Soto A, Moreno-Hagelsieb G, Janga, SC, Ramirez MA, Jimenez-Jacinto V, Collado-Vides J, Davila G. 2006. The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. Proc Natl Acad Sci USA 103:3834–3839. [PubMed][CrossRef]
132. Mann MS, Dragovic Z, Schirrmacher G, Lütke-Eversloh T. 2012. Over-expression of stress protein-encoding genes helps Clostridium acetobutylicum to rapidly adapt to butanol stress. Biotechnol Lett 34:1643–1649. [PubMed][CrossRef]
133. Streit WR, Schmitz RA, Perret X, Staehelin C, Deakin WJ, Raasch C, Liesegang H, Broughton WJ. 2004. An evolutionary hot spot: the pNGR234b replicon of Rhizobium sp. strain NGR234. J Bacteriol 186:535–542. [CrossRef]
134. Lim JS, Choi BS, Choi AY, Kim KD, Kim DI, Choi IY, Ka JO. 2012. Complete genome sequence of the fenitrothion-degrading Burkholderia sp. strain YI23. J Bacteriol 194:896. doi:10.1128/JB.06479-11. [CrossRef]
135. Janssen PJ, Van Houdt R, Moors H, Monsieurs P, Morin N, Michaux A, Benotmane MA, Leys N, Vallaeys T. Lapidus A, Monchy S, Médigue C, Taghavi S, McCorkle S, Dunn J, van der Lelie D, Mergeay M. 2010. The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS One 5:e10433. doi:10.1371/journal.pone.0010433. [CrossRef]
136. Ma Z, Jacobsen FE, Giedroc DP. 2009. Metal transporters and metal sensors: How coordination chemistry controls bacterial metal homeostasis. Chem Rev 13:4644–4681. [PubMed][CrossRef]
137. Adriano DC. 2001. Trace Elements in Terrestrial Environments: Biogeochemistry, Bioavailability, and Risks of Metals. Springer-Verlag, New York, NY. [CrossRef]
138. Mergeay M, Nies D, Schlegel HG, Gerits J, Charles P, Van Gijsegem F. 1985. Alcaligenes eutrophus CH34 is a facultative chemolithotroph with plasmid-bound resistance to heavy metals. J Bacteriol 162:328–334. [PubMed]
139. Monchy S, Benotmane MA, Janssen P, Vallaeys T, Taghavi S, van der Lelie D, Mergeay M. 2007. Plasmids pMOL28 and pMOL30 of Cupriavidus metallidurans are specialized in the maximal viable response to heavy metals. J Bacteriol 189:7417–7425. [PubMed][CrossRef]
140. Nies DH. 2003. Efflux-mediated heavy metal resistance in prokaryotes. FEMS Microbiol Rev 27:313–339. [PubMed][CrossRef]
141. Paulsen IT, Saier MH, Jr. 1997. A novel family of ubiquitous heavy metal ion transport proteins. J Membr Biol 156:99–103. [PubMed][CrossRef]
142. Munkelt D, Grass G, Nies DH. 2004. The chromosomally encoded cation diffusion facilitator proteins DmeF and FieF from Wautersia metallidurans CH34 are transporters of broad metal specificity. J Bacteriol 186:8036–8043. [PubMed][CrossRef]
143. Ramírez-Díaz MI, Díaz-Pérez C, Vargas E, Riveros-Rosas H, Campos-García J, Cervantes C. 2008. Mechanisms of bacterial resistance to chromium compounds. Biometals 21:321–332. [PubMed][CrossRef]
144. Henne KL, Nakatsu CH, Thompson DK, Konopka AE. 2009. High-level chromate resistance in Arthrobacter sp. strain FB24 requires previously uncharacterized accessory genes. BMC Microbiol 16:199. doi:10.1186/1471-2180-9-199. [PubMed][CrossRef]
145. Chen YF, Chao H, Zhou NY. 2014. The catabolism of 2,4-xylenol and p-cresol share the enzymes for the oxidation of para-methyl group in Pseudomonas putida NCIMB 9866. Appl Microbiol Biotechnol 98:1349–1356. [PubMed][CrossRef]
146. Misra TK. 1992. Bacterial resistances to inorganic mercury salts and organomercurials. Plasmid 27:4–16. [PubMed][CrossRef]
147. Diels L, Faelen M, Mergeay M, Nies D. 1985. Mercury transposons from plasmids governing multiple resistance to heavy metals in Alcaligenes eutrophus CH34. Arch Intern Physiol Biochem 93:27–28.
148. Silver S, Phung LT. 1996. Bacterial heavy metal resistance: new surprises. Annu Rev Microbiol 50:753–789. [PubMed][CrossRef]
149. Nascimento AM, Chartone-Souza E. 2003. Operon mer: bacterial resistance to mercury and potential for bioremediation of contaminated environments. Genet Mol Res 2:92–101. [PubMed]
150. Boon N, Goris J, De Vos P, Verstraete W, Top EM. 2001. Genetic diversity among 3-chloroaniline- and aniline-degrading strains of the Comamonadaceae. Appl Environ Microbiol 67:1107–1115. [PubMed][CrossRef]
151. Schwartz E, Henne A, Cramm R, Eitinger T, Friedrich B, Gottschalk G. 2003. Complete nucleotide sequence of pHG1: a Rastonia eutropha H16 megaplasmid encoding key enzymes of H(2)-based lithoautotrophy and anaerobiosis. J Mol Biol 332:369–383. [CrossRef]
152. Chen WM, Moulin L, Bontemps C, Vandamme P, Bena G, Boivin-Masson C. 2003. Legume symbiotic nitrogen fixation by beta-proteobacteria is widespread in nature. J Bacteriol 185:7266–7272. [PubMed][CrossRef]
153. Roselli S, Nadalig T, Vuilleumier S, Bringel F. 2013. The 380 Kbp pCMU01 plasmid encodes chloromethane utilization genes and redundant genes for vitamin B12- and tetrahydrofolate-dependent chloromethane metabolism in Methylobacterium extorquens CM4: A proteomic and bioinformatics study. PLoS One 8:e56598. doi:10.1371/journal.pone.0056598. [CrossRef]
154. Liesegang H, Lemke K, Siddiqui RA, Schlegel HG. 1993. Characterization of the inducible nickel and cobalt resistance determinant cnr from pMOL28 of Alcaligenes eutrophus CH34. J Bacteriol 175:767–778. [PubMed]
155. Schmidt T, Schlegel HG. 1994. Combined nickel-cobalt-cadmium resistance encoded by the ncc locus of Alcaligenes xylosoxidans 31A. J Bacteriol 176:7045–7054. [PubMed]
156. Silver S, Gupta A, Matsui K, Lo JF. 1999. Resistance to Ag(I) Cations in bacteria: environments, genes and proteins. Met Based Drugs 6:315–320. [PubMed][CrossRef]
157. Monchy S, Benotmane MA, Wattiez R, van Aelst S, Auquier V, Borremans B, Mergeay M, Taghavi S, van der Lelie D, Vallaeys T. 2006. Transcriptomic and proteomic analyses of the pMOL30-encoded copper resistance in Cupriavidus metallidurans strain CH34. Microbiology 152:1765–1776. [PubMed][CrossRef]
158. Mealman TD, Blackburn NJ, McEvoy MM. 2012. Metal export by CusCFBA, the periplasmic Cu(I)/Ag(I) transport system of Escherichia coli. Curr Top Membr 69:163–196. [PubMed][CrossRef]
159. Copley SD, Rokicki J, Turner P, Daligault H, Nolan M, Land M. 2012. The whole genome sequence of Sphingobium chlorophenolicum L-1: insights into the evolution of the pentachlorophenol degradation pathway. Genome Biol Evol 4:184–198. [PubMed][CrossRef]
160. Tabata M, Ohtsubo Y, Ohhata S, Tsuda M, Nagata Y. 2013. Complete genome sequence of the γ-hexachlorocyclohexane-degrading bacterium Sphingomonas sp. strain MM-1. Genome Announc 1:pii e00247-13. doi:10.1128/genomeA.00247-13. [PubMed][CrossRef]
161. Gómez-Sanz E, Kadlec K, Feßler AT, Zaragoza M, Torre, C, Schwarz S. 2013. Novel erm(T)-carrying multiresistance plasmids from porcine and human isolates of methicillin-resistant Staphylococcus aureus ST398 that also harbor cadmium and copper resistance determinants. Antimicrob Agents Chemother 57:3275–3282. [PubMed][CrossRef]
162. Bender CL, Cooksey DA. 1987. Molecular cloning of copper resistance genes from Pseudomonas syringae pv. tomato. J Bacteriol 169:470–474. [PubMed]
163. Gutiérrez-Barranquero JA, de Vicente A, Carrión VJ, Sundin GW, Cazorla FM. 2013. Recruitment and rearrangement of three different genetic determinants into a conjugative plasmid increase copper resistance in Pseudomonas syringae. Appl Environ Microbiol 79:1028–1033. [PubMed][CrossRef]
164. Shin SH, Kim S, Kim JY, Lee S, UmY, Oh MK, Kim YR, Lee J, Yang KS. 2012. Complete genome sequence of the 2,3-butanediol-producing Klebsiella pneumoniae strain KCTC 2242. J Bacteriol 194:2736–2737. [PubMed][CrossRef]
165. Diels L, Mergeay M. 1990. DNA probe-mediated detection of resistance bacteria from soils highly polluted by heavy metals. Appl Environ Microbiol 56:1485–1491. [PubMed]
166. Slyemi D, Bonnefoy V. 2012. How prokaryotes deal with arsenic. Environ Microbiol Reports 4:571–586. [PubMed]
167. Dhuldhaj UP, Yadav IC, Singh S, Sharma NK. 2013. Microbial interactions in the arsenic cycle: adoptive strategies and applications in environmental management. Rev Environ Cont Toxicol 224:1–38. [PubMed][CrossRef]
168. Volland S, Rachinger M, Strittmatter A, Daniel R, Gottschalk G, Meyer O. 2011. Complete genome sequences of the chemolithoautotrophic Oligotropha carboxidovorans strains OM4 and OM5. J Bacteriol 193:5043. doi:10.1128/JB.05619-11. [PubMed][CrossRef]
169. Vogel TM. 1996. Bioaugmentation as a soil bioremediation approach. Curr Opin Biotechnol 7:311–316. [PubMed][CrossRef]
170. Top EM, Springael D, Boon N. 2002. Catabolic mobile genetic elements and their potential use in bioaugmentation of polluted soils and waters. FEMS Microbiol Ecol 42:199–208. [PubMed][CrossRef]
171. Ikuma K, Gunsch CK. 2012. Genetic bioaugmentation as an effective method for in situ bioremediation. Functionality of catabolic plasmids following conjugal transfers. Bioengineered 3:236–241. [PubMed][CrossRef]
172. Jussila MM, Zhao J, Souminen L, Lindström K. 2007. TOL plasmid transfer during bacterial conjugation in vitro and rhizoremediation of oil compounds in vivo. Environ Pollut 146:510–524. [PubMed][CrossRef]
173. Ramos-Gonzalez MI, Duque E, Ramos JL. 1991. Conjugational transfer of recombinant DNA in cultures and in soils: host range of Pseudomonas putida TOL plasmids. Appl Environ Microbiol 57:3020–3027. [PubMed]
174. Molbak L, Licht TR, Kvist T, Kroer N, Andersen SR. 2003. Plasmid transfer from Pseudomonas putida to the indigenous bacteria on alfalfa sprouts: characterization, direct quantification and in situ location of transconjugant cells. Appl Environ Microbiol 69:5536–5542. [PubMed][CrossRef]
175. Ikuma K, Holzem RM, Gunsch CK. 2012. Impacts of organic carbon availability and recipient bacteria characteristics on the potential for TOL plasmid genetic bioaugmentation on soil slurries. Chemosphere 89:158–163. [PubMed][CrossRef]
176. Ikuma K, Gunsch CK. 2013. Functionality of the TOL plasmid under varying environmental conditions following conjugal transfer. Appl Microbiol Biotechnol 97:395–408. [PubMed][CrossRef]
177. Pinedo CA, Smets BF. 2005. Conjugal TOL transfer from Pseudomonas putida to Pseudomonas aeruginosa: effects of restriction proficiency, toxicant exposure, cell density ratios, and conjugation detection method on observed transfer efficiencies. Appl Environ Microbiol 71:51–57. [PubMed][CrossRef]
178. Daane LL, Molina J, Sadowsky MJ. 1997. Plasmid transfer between spatially separated donor and recipient bacteria en earthworm-containing soil microcosms. Appl Environ Microbiol 63:679–686. [PubMed]
179. Wuertz S, Okabe S, Hausner M. 2004. Microbial communities and their interactions in biofilm systems: an overview. Water Sci Technol 49:327–336. [PubMed]
180. Mohan SV, Falkentoft C, Nancharaiah YV, McSwain Sturm BS, Wattiau P, Wilderer PA, Wuertz S, Hausner M. 2009. Bioaugmentation of microbial communities in laboratory and pilot scale sequencing batch biofilm reactors using the TOL plasmid. Bioresour Technol 100:1746–1753. [PubMed][CrossRef]
181. Neilson JW, Josephson KL, Pepper IL, Arnold RB, Di Giovanni GD, Sinclair NA. 1994. Frequency of horizontal gene transfer of a large catabolic plasmid (pJP4) in soil. Appl Environ Microbiol 60:4053–4058. [PubMed]
182. Molina L, Ramos C, Duque E, Ronchel MC, Garcöla JM, Wyke L, Ramos JL. 2000. Survival of Pseudomonas putida KT2440 in soil and in the rhizosphere of plants under greenhouse and environmental conditions. Soil Biol Biochem 32:315–321. [CrossRef]
183. Mackova M, Dowling D, Macek T (ed). 2006. Phytoremediation and Rhizoremediation. Theoretical Background. Series: Focus on Biotechnology. Springer, New York, NY. [CrossRef]
184. Walker TS, Bais HP, Grotewold E, Vivanco JM. 2003. Root exudation and rhizosphere biology. Plant Physiol 132:44–51. [PubMed][CrossRef]
185. Matilla MA, Espinosa-Urgel M, Rodriguez-Hervá JJ, Ramos JL, Ramos-González MI. 2007. Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere. Genome Biol 8:R179. doi:10.1186/gb-2007-8-9-r179. [PubMed][CrossRef]
186. López-Guerrero MG, Ormeño-Orrillo E, Acosta JL, Mendoza-Vargas A, Rogel MA, Ramírez MA, Rosenblueth M, Martínez-Romero J, Martínez-Romero E. 2012. Rhizobial extrachromosomal replicon variability, stability and expression in natural niches. Plasmid 68:149–158. [PubMed][CrossRef]
187. Barac T, Taghavi S, Borremans B, Provoost A, Oeyen L, Colpaert JV, Vangronsveld J, van der Lelie D. 2004. Engineered endophytic bacteria improve phytoremediation of water-soluble, volatile, organic pollutants. Nat Biotech 22:583–588. [PubMed][CrossRef]
188. Taghavi S, Barac T, Greenberg B, Borremans B, Vangronsveld J, van der Lelie D. 2005. Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene. Appl Environ Microbiol 71:8500–8505. [PubMed][CrossRef]
189. Lilley AK, Bailey MJ. 1997. Impact of plasmid pQBR103 acquisition and carriage on the phytosphere fitness of Pseudomonas fluorescens SBW25: burden and benefit. Appl Environ Microbiol 63:1584–1587. [PubMed]
190. Tett A, Spiers AJ, Crossman LC, Ager D, Ciric L, Dow, JM, Fry JC, Harris D, Lilley A, Oliver A, Parkhill J, Quail MA, Rainey PB, Saunders NJ, Seeger K, Snyder LA, Squares R, Thomas CM, Turner SL, Zhang XX, Field D, Bailey MJ. 2007. Sequence-based analysis of pQBR103; a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet. ISME J 1:331–340. [PubMed]
191. Bale MJ, Fry JC, Day MJ. 1987. Plasmid transfer between strains of Pseudomonas aeruginosa on membrane filters attached to river stones. J Gen Microbiol 133:3099–3107. [PubMed]
192. Top EM, Holben WE, Forney LJ. 1995. Characterization of diverse 2,4-dichlorophenoxyacetic acid-degradative plasmids isolated from soil by complementation. Appl Environ Microbiol 61:1691–1698. [PubMed]
193. Lilley AK, Bailey MJ. 1997. The acquisition of indigenous plasmids by a generically marked pseudomonad population colonizing the sugar beet phytosphere is related to local environmental conditions. Appl Environ Microbiol 63:1577–1583. [PubMed]
194. Dahlberg C, Linberg C, Torsvik VL, Hermansson M. 1997. Conjugative plasmids isolated from bacteria in marine environments show various degrees of homology to each other and are not closely related to well characterized plasmids. Appl Environ Microbiol 63:4692–4697. [PubMed]
195. Ono A, Miyazaki R, Sota M, Ohtsubo Y, Nagata Y, Tsuda M. 2007. Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches. Appl Microbiol Biotechnol 74:501–510. [PubMed][CrossRef]
196. Kav AB, Sasson G, Jami E, Doron-Faigenboim A, Benhar I, Mizrahi I. 2012. Insights into the bovine rumen plasmidome. Proc Natl Acad Sci USA 109:5452–5457. [PubMed][CrossRef]
197. Nojiri H. 2013. Impact of catabolic plasmids on host cell physiology. Curr Opin Biotech 24:423–430. [PubMed][CrossRef]
198. Diaz-Ricci JC, Hernández ME. 2000. Plasmid effects on Escherichia coli metabolism. Crit Rev Biotechnol 20:79–108. [PubMed][CrossRef]
199. Miyakoshi M, Shitani M, Inoue K, Terabayashi T, Sai F, Ohkuma M, Nojiri H, Nagata Y. Tsuda M. 2012. ParI, an orphan ParA family protein from Pseudomonas putida KT2440-specific genomic island, interferes with the partition system of IncP-7 plasmids. Environ Microbiol 14:2946–2959. [PubMed][CrossRef]
200. Shintani M, Takahashi Y, Tokumaru H, Kadota K, Hara H, Miyakoshi M, Naito K, Yamane H, Nishida H, Nojiri H. 2010. Response of the Pseudomonas host chromosomal transcriptome to carriage of the IncP-7 plasmid pCAR1. Environ Microbiol 12:1413–1426. [PubMed]
201. Shintani M, Tokumaru H, Takahasi Y, Miyakoshi M, Yamane H, Nishida H, Nojiri H. 2011. Alterations of RNA maps of IncP-7 plasmid pCAR1 in various Pseudomonas bacteria. Plasmid 66:85–92. [PubMed][CrossRef]
202. Fernández M, Niqui-Arroyo JL, Conde S, Ramos JL, Duque E. 2012. Enhanced tolerance to naphthalene and enhanced rhizoremediation performance for Pseudomonas putida KT2440 via the NAH7 catabolic plasmid. Appl Environ Microbiol 78:5104–5110. [PubMed][CrossRef]
203. Yun CS, Suzuki C, Naito K, Takeda T, Takahashi Y, Sai F, Terabayashi T, Miyakoshi M, Shintani M, Nishida H, Yamane H, Nojiri H. 2010. Pmr, a histone-like protein H1 (H-NS) family protein encoded by the IncP-7 plasmid pCAR1, is a key global regulator that alters host function. J Bacteriol 192:4720–4731. [PubMed][CrossRef]
204. Rescalli E, Saini S, Bartocci C, Rychlewski L, de Lorenzo V, Bertoni G. 2004. Novel physiological modulation of the Pu promoter of TOL plasmid: negative regulatory role of the TurA protein of Pseudomonas putida in the response to suboptimal growth temperatures. J Biol Chem 279:7777–7784. [PubMed][CrossRef]
205. Bathe S, Mohan TV, Wuertz S, Hausner M. 2004. Bioaugmentation of a sequencing batch biofilm reactor by horizontal gene transfer. Water Sci Technol 49:337–344. [PubMed]
206. De Gelder L, Vandecasteele FP, Brown CJ, Forney LJ, Top EM. 2005. Plasmid donor affects host range of promiscuous IncP-1 beta plasmid pB10 in an activated-sludge microbial community. Appl Environ Microbiol 71:5309–5317. [PubMed][CrossRef]
207. Smalla K, Sobecky PA. 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. [PubMed][CrossRef]
208. Ma H, Katzenmeyer KN, Bryers JD. 2013. Non-invasive in situ monitoring and quantification of TOL plasmid segregational loss within Pseudomonas putida biofilms. Biotech Bioeng 110:2949–2958. [PubMed][CrossRef]
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/content/journal/microbiolspec/10.1128/microbiolspec.PLAS-0013-2013
2014-11-07
2017-08-17

Abstract:

The survival capacity of microorganisms in a contaminated environment is limited by the concentration and/or toxicity of the pollutant. Through evolutionary processes, some bacteria have developed or acquired mechanisms to cope with the deleterious effects of toxic compounds, a phenomenon known as tolerance. Common mechanisms of tolerance include the extrusion of contaminants to the outer media and, when concentrations of pollutants are low, the degradation of the toxic compound. For both of these approaches, plasmids that encode genes for the degradation of contaminants such as toluene, naphthalene, phenol, nitrobenzene, and triazine or are involved in tolerance toward organic solvents and heavy metals, play an important role in the evolution and dissemination of these catabolic pathways and efflux pumps. Environmental plasmids are often conjugative and can transfer their genes between different strains; furthermore, many catabolic or efflux pump genes are often associated with transposable elements, making them one of the major players in bacterial evolution. In this review, we will briefly describe catabolic and tolerance plasmids and advances in the knowledge and biotechnological applications of these plasmids.

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FIGURE 1

Degradation pathways of mono- and biaromatic compounds. Major intermediates of the pathways are depicted. Genes or operons in different plasmids are colored to indicate their role: blue for toluene degradation genes, pink for naphthalene degradation genes, and yellow for biphenyl degradation genes. In green are the genes that can function in different degradation pathways. Genes and operons are not drawn to scale. Operon organization in some cases has not been experimentally demonstrated. doi:10.1128/microbiolspec.PLAS-0013-2013.f1

Source: microbiolspec November 2014 vol. 2 no. 6 doi:10.1128/microbiolspec.PLAS-0013-2013
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FIGURE 2

Degradation pathways for heteroaromatic compounds. Major intermediates of the pathways are depicted. Genes or operons in different plasmids are shown in different colors. Genes and operons are not drawn to scale. doi:10.1128/microbiolspec.PLAS-0013-2013.f2

Source: microbiolspec November 2014 vol. 2 no. 6 doi:10.1128/microbiolspec.PLAS-0013-2013
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FIGURE 3

Degradation pathways for chloroaromatic compounds. Major intermediates of the pathways are depicted. Genes or operons in different plasmids are shown in different colors. Genes and operons are not drawn to scale. doi:10.1128/microbiolspec.PLAS-0013-2013.f3

Source: microbiolspec November 2014 vol. 2 no. 6 doi:10.1128/microbiolspec.PLAS-0013-2013
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FIGURE 4

Schematic representation of Tn-like region (A) and second region encoding stress resistance genes in pGRT1 (B). In red are indicated transposition-related genes, in green are stress-related functions, and in blue are putative recombinases or integrases. doi:10.1128/microbiolspec.PLAS-0013-2013.f4

Source: microbiolspec November 2014 vol. 2 no. 6 doi:10.1128/microbiolspec.PLAS-0013-2013
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