Mobile Catabolic Genetic Elements in Pseudomonads

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Biodegradative Bacteria

Abstract

Bacterial capabilities to degrade various recalcitrant compounds are often encoded on mobile genetic elements (MGEs) such as transposons, plasmids, and integrative and conjugative elements (ICEs). The movement of the transposons and consequently induced rearrangements of genome in a cell and the intercellular transfer of the latter two MGEs greatly facilitate rapid adaptation and evolution of the host cells and wide dissemination of catabolic genes and gene clusters in a variety of phylogenetically distinct environmental bacteria. This chapter summarizes how MGEs participate in the emergence of degradative bacteria based on the earlier and recent findings and analysis of catabolic MGEs in pseudomonads.

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References

  • Chandler M, Mahillon J (2002) Insertion sequences revisited. In: Craig NL, Craigie R, Gellert M, Lambowitz AM (eds) Mobile DNA II. ASM, Washington, DC, pp 305–366

    Google Scholar 

  • 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  CAS  Google Scholar 

  • Dennis JJ (2005) The evolution of IncP catabolic plasmids. Curr Opin Biotechnol 16:291–298

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Devers M, Rouard N, Martin-Laurent F (2008) Fitness drift of an atrazine-degrading population under atrazine selection pressure. Environ Microbiol 10:676–684

    Article  PubMed  CAS  Google Scholar 

  • Dunn N, Gunsalus IC (1973) Transmissible plasmid coding early enzymes of naphthalene oxidation in Pseudomonas putida. J Bacteriol 114:974–979

    PubMed  CAS  Google Scholar 

  • Durland RH, Helinski DR (1987) The sequence encoding the 43-kilodalton trfA protein is required for efficient replication or maintenance of minimal RK2 replicons in Pseudomonas aeruginosa. Plasmid 18:164–169

    Google Scholar 

  • Frost LS, Leplae R, Summers AO, Toussaint A (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Micro 3:722–732

    Article  CAS  Google Scholar 

  • Gaillard M, Vallaeys T, Vorhölter FJ, Minoia M, Werlen C, Sentchilo V, Pühler A, van der Meer JR (2006) The clc element of Pseudomonas sp. strain B13, a genomic island with various catabolic properties. J Bacteriol 188:1999–2013

    Article  PubMed  CAS  Google Scholar 

  • 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  CAS  Google Scholar 

  • Genka H, Nagata Y, Tsuda M (2002) Site-specific recombination system encoded by toluene catabolic transposon Tn4651. J Bacteriol 184:4757–4766

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Grindley NDF (2002) The movement of Tn3-like elements: transposition and cointegrate resolution. In: Craig NL, Craigie R, Gellert M, Lambowitz AM (eds) Mobile DNA II. ASM, Washington, DC, pp 272–302

    Google Scholar 

  • Hansen JB, Olsen RH (1978) IncP2 group of Pseudomonas, a class of uniquely large plasmids. Nature 274:715–717

    Google Scholar 

  • Heinaru E, Vedler E, Jutkina J, Aava M, Heinaru A (2009) Conjugal transfer and mobilization capacity of the completely sequenced naphthalene plasmid pNAH20 from multiplasmid strain Pseudomonas fluorescens PC20. FEMS Microbiol Ecol 70:563–574

    Article  PubMed  CAS  Google Scholar 

  • Heuer H, Smalla K (2012) Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol Rev 36:1083–1104

    Article  PubMed  CAS  Google Scholar 

  • Hickey WJ, Chen S, Zhao J (2012) The phn Island: a new genomic island encoding catabolism of polynuclear aromatic hydrocarbons. Front Microbiol 3:125

    Article  PubMed  Google Scholar 

  • Hill KE, Weightman AJ, Fry JC (1992) Isolation and screening of plasmids from the epilithon which mobilize recombinant plasmid pD10. Appl Environ Microbiol 58:1292–1300

    Google Scholar 

  • Hõrak R, Kivisaar M (1998) Expression of the transposase gene tnpA of Tn4652 is positively affected by integration host factor. J Bacteriol 180:2822–2829

    PubMed  Google Scholar 

  • Hõrak R, Kivisaar M (1999) Regulation of the transposase of Tn4652 by the transposon-encoded protein TnpC. J Bacteriol 181:6312–6318

    PubMed  Google Scholar 

  • Ilves H, Hõrak R, Kivisaar M (2001) Involvement of σS in starvation-induced transposition of Pseudomonas putida transposon Tn4652. J Bacteriol 183:5445–5448

    Article  PubMed  CAS  Google Scholar 

  • Ilves H, Hõrak R, Teras R, Kivisaar M (2004) IHF is the limiting host factor in transposition of Pseudomonas putida transposon Tn4652 in stationary phase. Mol Microbiol 51:1773–1785

    Article  PubMed  CAS  Google Scholar 

  • Inoue K, Miyazaki R, Ohtsubo Y, Nagata Y, Tsuda M (2013) Inhibitory effect of Pseudomonas putida nitrogen-related phosphotransferase system on conjugative transfer of IncP-9 plasmid from Escherichia coli. FEMS Microbiol Lett 345:102–109

    Google Scholar 

  • Izmalkova TY, Mavrodi DV, Sokolov SL, Kosheleva IA, Smalla K, Thomas CM, Boronin AM (2006) Molecular classification of IncP-9 naphthalene degradation plasmids. Plasmid 56:1–10

    Article  PubMed  CAS  Google Scholar 

  • Jeenes DJ, Williams PA (1982) Excision and integration of degradative pathway genes from TOL plasmid pWW0. J Bacteriol 150:188–194

    PubMed  CAS  Google Scholar 

  • Juhas M, van der Meer JR, Gaillard M, Harding RM, Hood DW, Crook DW (2009) Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev 33:376–393

    Article  PubMed  CAS  Google Scholar 

  • Keil H, Keil S, Pickup RW, Williams PA (1985a) Evolutionary conservation of genes coding for meta pathway enzymes within TOL plasmids pWW0 and pWW53. J Bacteriol 164:887–895

    PubMed  CAS  Google Scholar 

  • Keil H, Lebens MR, Williams PA (1985b) TOL plasmid pWW15 contains two nonhomologous, independently regulated catechol 2,3-oxygenase genes. J Bacteriol 163:248–255

    PubMed  CAS  Google Scholar 

  • Keil H, Keil S, Williams PA (1987) Molecular analysis of regulatory and structural xyl genes of the TOL plasmid p WW53–4. J Gen Microbiol 133:1149–1158

    PubMed  CAS  Google Scholar 

  • Kholodii GY, Yurieva OV, Gorlenko Z, Mindlin SZ, Bass IA, Lomovskaya OL, Kopteva AV, Nikiforov VG (1997) Tn5041: a chimeric mercury resistance transposon closely related to the toluene degradative transposon Tn4651. Microbiology 143:2549–2556

    Article  PubMed  CAS  Google Scholar 

  • Kivisaar M (2004) Transposition and other mutational processes in Pseudomonas. In: Ramos JL (ed) Pseudomonas, vol 1. Kluwer Academic/Plenum, New York, pp 261–316

    Chapter  Google Scholar 

  • Klockgether J, Wurdemann D, Reva O, Wiehlmann L, Tummler B (2007) Diversity of the abundant pKLC102/PAGI-2 family of genomic islands in Pseudomonas aeruginosa. J Bacteriol 189:2443–2459

    Article  PubMed  CAS  Google Scholar 

  • Król JE, Penrod JT, McCaslin H, Rogers LM, Yano H, Stancik AD, Dejonghe W, Brown CJ, Parales RE, Wuertz S, Top EM (2012) Role of IncP-1β plasmids pWDL7::rfp and pNB8c in chloroaniline catabolism as determined by genomic and functional analyses. Appl Environ Microbiol 78:828–838

    Article  PubMed  Google Scholar 

  • Kunz DA, Chapman PJ (1981) Isolation and characterization of spontaneously occurring TOL plasmid mutants of Pseudomonas putida HS1. J Bacteriol 146:952–964

    PubMed  CAS  Google Scholar 

  • Lehrbach PR, Ward J, Meulien P, Broda P (1982) Physical map** of TOL plasmids pWWO and pND2 and various R plasmid-TOL derivatives from Pseudomonas spp. J Bacteriol 152:1280–1283

    PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Liebert CA, Hall RM, Summers AO (1999) Transposon Tn21, flagship of the floating genome. Microbiol Mol Biol Rev 63:507–522

    PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Minakhina S, Kholodii G, Mindlin S, Yurieva O, Nikiforov V (1999) Tn5053 family transposons are res site hunters sensing plasmidal res sites occupied by cognate resolvases. Mol Microbiol 33:1059–1068

    Article  PubMed  CAS  Google Scholar 

  • Miyazaki R, Sato Y, Ito M, Ohtsubo Y, Nagata Y, Tsuda M (2006) Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in gamma-hexachlorocyclohexane degradation. Appl Environ Microbiol 72:6923–6933

    Article  PubMed  CAS  Google Scholar 

  • Miyazaki R, Ohtsubo Y, Nagata Y, Tsuda M (2008) Characterization of the traD operon of naphthalene-catabolic plasmid NAH7: a host-range modifier in conjugative transfer. J Bacteriol 190:6281–6289

    Article  PubMed  CAS  Google Scholar 

  • Miyazaki R, Minoia M, Pradervand N, Sentchilo V, Sulser S, Reinhard F, van der Meer JR (2012) The clc element and related genomic islands in Proteobacteria. In: Roberts AP, Mullany P (eds) Bacterial integrative mobile genetic elements. Landes Bioscience, Austin, pp 261–272

    Google Scholar 

  • Nakazawa T (2002) Travels of a Pseudomonas, from Japan around the world. Environ Microbiol 4:782–786

    Article  PubMed  CAS  Google Scholar 

  • Nishi A, Tominaga K, Furukawa K (2000) A 90-kilobase conjugative chromosomal element coding for biphenyl and salicylate catabolism in Pseudomonas putida KF715. J Bacteriol 182:1949–1955

    Article  PubMed  CAS  Google Scholar 

  • Nojiri H, Shintani M, Omori T (2004) Divergence of mobile genetic elements involved in the distribution of xenobiotic-catabolic capacity. Appl Microbiol Biotechnol 64:154–174

    Article  PubMed  CAS  Google Scholar 

  • Norman A, Hansen LH, Sørensen SJ (2009) Conjugative plasmids: vessels of the communal gene pool. Philos Trans R Soc Lond B Biol Sci 364:2275–2289

    Article  PubMed  CAS  Google Scholar 

  • Ohtsubo Y, Ishibashi Y, Naganawa H, Hirokawa S, Atobe S, Nagata Y, Tsuda M (2012a) Conjugal transfer of polychlorinated biphenyl/biphenyl degradation genes in Acidovorax sp. strain KKS102, which are located on an integrative and conjugative element. J Bacteriol 194:4237–4248

    Article  PubMed  CAS  Google Scholar 

  • Ohtsubo Y, Maruyama F, Mitsui H, Nagata Y, Tsuda M (2012b) Complete genome sequence of Acidovorax sp. KKS102, a polychlorinated biphenyl-degrading strain. J Bacteriol 194:6970–6971

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Petrovski S, Stanisich VA (2011) Embedded elements in the IncP1-β plasmids R772 and R906 can be mobilized and can serve as a source of diverse and novel elements. Microbiology 157:1714–1725

    Article  PubMed  CAS  Google Scholar 

  • Qiu X, Gurkar AU, Lory S (2006) Interstrain transfer of the large pathogenicity island (PAPI-1) of Pseudomonas aeruginosa. Proc Natl Acad Sci USA 103:19830–19835

    Article  PubMed  CAS  Google Scholar 

  • Rajeev L, Malanowska K, Gardner JF (2009) Challenging a paradigm: the role of DNA homology in tyrosine recombinase reactions. Microbiol Mol Biol Rev 73:300–309

    Article  PubMed  CAS  Google Scholar 

  • Ramos JL, Marqués 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 51:341–373

    Article  PubMed  CAS  Google Scholar 

  • Ravatn R, Zehnder AJ, van der Meer JR (1998) Low-frequency horizontal transfer of an element containing the chlorocatechol degradation genes from Pseudomonas sp. strain B13 to Pseudomonas putida F1 and to indigenous bacteria in laboratory-scale activated-sludge microcosms. Appl Environ Microbiol 64:2126–2132

    PubMed  CAS  Google Scholar 

  • Riuz R, Aranda-Olmedo MI, Domíniquez-Cuevas P, Ramos-Gonzalez MI, Marqués S (2004) Transcriptional regulation of the toluene catabolic pathways. In: Ramos JL (ed) Pseudomonas, vol 2. Kluwer Academic/Plenum, New York, pp 509–537

    Google Scholar 

  • Roberts AP, Chandler M, Courvalin P, Guedon G, Mullany P, Pembroke T, Rood JI, Smith CJ, Summers AO, Tsuda M, Berg DE (2008) Revised nomenclature for transposable genetic elements. Plasmid 60:167–173

    Article  PubMed  CAS  Google Scholar 

  • Ryan MP, Pembroke JT, Adley CC (2009) Novel Tn4371-ICE like element in Ralstonia pickettii and genome mining for comparative elements. BMC Microbiol 9:242

    Article  PubMed  Google Scholar 

  • Sen D, Van der Auwera GA, Rogers LM, Thomas CM, Brown CJ, Top EM (2011) Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes. Appl Environ Microbiol 77:7975–7983

    Article  PubMed  CAS  Google Scholar 

  • Sen D, Brown CJ, Top EM, Sullivan J (2013) Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees. Mol Biol Evol 30:154–166

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Sevastsyanovich YR, Krasowiak R, Bingle LE, Haines AS, Sokolov SL, Kosheleva IA, Leuchuk AA, Titok MA, Smalla K, Thomas CM (2008) Diversity of IncP-9 plasmids of Pseudomonas. Microbiology 154:2929–2941

    Article  PubMed  CAS  Google Scholar 

  • Shaw LE, Williams PA (1988) Physical and functional map** of two cointegrate plasmids derived from RP4 and TOL plasmid pDK1. J Gen Microbiol 134:2463–2474

    PubMed  CAS  Google Scholar 

  • Shintani M, Nojiri H (2013) Mobile genetic elements (MGEs) carrying catabolic genes. In: Malik A, Grohmann E, Alves M (eds) Management of microbial resources in the environment. Springer, Netherlands, pp 167–214

    Chapter  Google Scholar 

  • Sørensen SJ, Bailey M, Hansen LH, Kroer N, Wuertz S (2005) Studying plasmid horizontal transfer in situ: a critical review. Nat Rev Micro 3:700–710

    Article  Google Scholar 

  • Sota M, Endo M, Nitta K, Kawasaki H, Tsuda M (2002) Characterization of a class II defective transposon carrying two haloacetate dehalogenase genes from Delftia acidovorans plasmid pUO1. Appl Environ Microbiol 68:2307–2315

    Article  PubMed  CAS  Google Scholar 

  • Sota M, Kawasaki H, Tsuda M (2003) Structure of haloacetate-catabolic IncP-1β plasmid pUO1 and genetic mobility of its residing haloacetate-catabolic transposon. J Bacteriol 185:6741–6745

    Article  PubMed  CAS  Google Scholar 

  • Sota M, Yano H, Nagata Y, Ohtsubo Y, Genka H, Anbutsu H, Kawasaki H, Tsuda M (2006a) Functional analysis of unique class II insertion sequence IS1071. Appl Environ Microbiol 72:291–297

    Article  PubMed  CAS  Google Scholar 

  • Sota M, Yano H, Ono A, Miyazaki R, Ishii H, Genka H, Top EM, Tsuda M (2006b) 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

    Article  PubMed  CAS  Google Scholar 

  • Sota M, Tsuda M, Yano H, Suzuki H, Forney LJ, Top EM (2007) Region-specific insertion of transposons in combination with selection for high plasmid transferability and stability accounts for the structural similarity of IncP-1 plasmids. J Bacteriol 189:3091–3098

    Article  PubMed  CAS  Google Scholar 

  • Sota M, Yano H, Tsuda M (2008) Bacterial class II catabolic transposons. In: Yoshida Y, Aoki M (eds) DNA transposable elements research. Nova Science, New York, pp 23–67

    Google Scholar 

  • Springael D, Kreps S, Mergeay M (1993) Identification of a catabolic transposon, Tn4371, carrying biphenyl and 4-chlorobiphenyl degradation genes in Alcaligenes eutrophus A5. J Bacteriol 175:1674–1681

    PubMed  CAS  Google Scholar 

  • Suenaga H, Koyama Y, Miyakoshi M, Miyazaki R, Yano H, Sota M, Ohtsubo Y, Tsuda M, Miyazaki K (2009) Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis. ISME J 3:1335–1348

    Article  PubMed  CAS  Google Scholar 

  • Teras R, Hõrak R, Kivisaar M (2000) Transcription from fusion promoters generated during transposition of transposon Tn4652 is positively affected by integration host factor in Pseudomonas putida. J Bacteriol 182:589–598

    Article  PubMed  CAS  Google Scholar 

  • Teras R, Jakovleva J, Kivisaar M (2009) Fis negatively affects binding of Tn4652 transposase by out-competing IHF from the left end of Tn4652. Microbiology 155:1203–1214

    Article  PubMed  CAS  Google Scholar 

  • Thomas CM, Haines A (2004) Plasmids of the genus Pseudomonas. In: Ramos JL (ed) Pseudomonas, vol 1. Kluwer Academic/Plenum, New York, pp 197–231

    Chapter  Google Scholar 

  • Thomas CM, Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Micro 3:711–721

    Article  CAS  Google Scholar 

  • Toleman MA, Walsh TR (2011) Combinatorial events of insertion sequences and ICE in Gram-negative bacteria. FEMS Microbiol Rev 35:912–935

    Article  PubMed  CAS  Google Scholar 

  • Top E, de Smet I, Verstraete W, Dijkmans R. Mergeay M (1994) Exogenous isolation of mobilizing plasmids from polluted soils and sludges. Appl Environ Microbiol 60:831–839

    Google Scholar 

  • Top EM, Springael D (2003) The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr Opin Biotechnol 14:262–269

    Article  PubMed  CAS  Google Scholar 

  • Toussaint A, Merlin C, Monchy S, Benotmane MA, Leplae R, Mergeay M, Springael D (2003) 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 69:4837–4845

    Article  PubMed  CAS  Google Scholar 

  • Trefault N, De la Iglesia R, Molina AM, Manzano M, Ledger T, Pérez-Pantoja D, Sánchez MA, Stuardo M, González 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

    Article  PubMed  CAS  Google Scholar 

  • Tsuda M, Genka H (2001) Identification and characterization of Tn4656, a novel class II transposon carrying a set of toluene-degrading genes from TOL plasmid pWW53. J Bacteriol 183:6215–6224

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Tsuda M, Iino T (1990) Naphthalene degrading genes on plasmid NAH7 are on a defective transposon. Mol Gen Genet 223:33–39

    Article  PubMed  CAS  Google Scholar 

  • Tsuda M, Minegishi K, Iino T (1989) Toluene transposons Tn4651 and Tn4653 are class II transposons. J Bacteriol 171:1386–1393

    PubMed  CAS  Google Scholar 

  • Tsuda M, Tan HM, Nishi A, Furukawa K (1999) Mobile catabolic genes in bacteria. J Biosci Bioeng 87:401–410

    Article  PubMed  CAS  Google Scholar 

  • van der Meer JR, Sentchilo V (2003) Genomic islands and the evolution of catabolic pathways in bacteria. Curr Opin Biotechnol 14:248–254

    Article  PubMed  Google Scholar 

  • van Houdt R, Toussaint A, Ryan MP, Pembroke JT, Meargy M, Adley CC (2012) The Tn4731 ICE family of bacterial mobile genetic elements. In: Roberts AP, Mullany P (eds) Bacterial integrative mobile genetic elements. Landes Bioscience, Austin, pp 179–200

    Google Scholar 

  • Vanhooff V, Galloy C, Agaisse H, Lereclus D, Revet B, Hallet B (2006) Self-control in DNA site-specific recombination mediated by the tyrosine recombinase TnpI. Mol Microbiol 60:617–629

    Article  PubMed  CAS  Google Scholar 

  • 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  CAS  Google Scholar 

  • 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  CAS  Google Scholar 

  • Williams PA, Rheinallt MJ, Zylstra GJ (2004) Genomics of catabolic plasmids. In: Ramos JL (ed) Pseudomonas, vol 1. Kluwer Academic/Plenum, New York

    Google Scholar 

  • Yano H, Deckert GE, Rogers LM, Top EM (2012) Roles of long and short replication initiation proteins in the fate of IncP-1 plasmids. J Bacteriol 194:1533–1543

    Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Yano H, Genka H, Ohtsubo Y, Nagata Y, Top EM, Tsuda M (2013) Cointegrate-resolution of toluene-catabolic transposon Tn4651: determination of crossover site and the segment required for full resolution activity. Plasmid 69:24–35

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

We are grateful to all of our collaborators. Our works were supported by Grants-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology, Japan.

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Correspondence to Masataka Tsuda .

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Tsuda, M., Ohtsubo, Y., Yano, H. (2014). Mobile Catabolic Genetic Elements in Pseudomonads. In: Nojiri, H., Tsuda, M., Fukuda, M., Kamagata, Y. (eds) Biodegradative Bacteria. Springer, Tokyo. https://doi.org/10.1007/978-4-431-54520-0_5

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