1887

Abstract

Analysis of the complete nucleotide sequence of plasmid pM7012 from 2,4-dichlorophenoxyacetic-acid (2,4-D)-degrading bacterium sp. M701 revealed that the plasmid had 582 142 bp, with 541 putative protein-coding sequences and 39 putative tRNA genes for the transport of the standard 20 aa. pM7012 contains sequences homologous to the regions involved in conjugal transfer and plasmid maintenance found in plasmids byi_2p from sp. YI23 and pBVIE01 from sp. G4. No relaxase gene was found in any of these plasmids, although genes for a type IV secretion system and type IV coupling proteins were identified. Plasmids with no relaxase gene have been classified as non-mobile plasmids. However, nucleotide sequences with a high level of similarity to the genes for plasmid transfer, plasmid maintenance, 2,4-D degradation and arsenic resistance contained on pM7012 were also detected in eight other megaplasmids (~600 or 900 kb) found in seven strains and a strain of , which were isolated as 2,4-D-degrading bacteria in Japan and the United States. These results suggested that the 2,4-D degradation megaplasmids related to pM7012 are mobile and distributed across various bacterial species worldwide, and that the plasmid group could be distinguished from known mobile plasmid groups.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.074369-0
2014-03-01
2019-11-14
Loading full text...

Full text loading...

/deliver/fulltext/micro/160/3/525.html?itemId=/content/journal/micro/10.1099/mic.0.074369-0&mimeType=html&fmt=ahah

References

  1. Abe T., Ikemura T., Sugahara J., Kanai A., Ohara Y., Uehara H., Kinouchi M., Kanaya S., Yamada Y.. & other authors ( 2011;). tRNADB-CE 2011: tRNA gene database curated manually by experts. . Nucleic Acids Res 39: (Database), D210–D213. [CrossRef][PubMed]
    [Google Scholar]
  2. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J.. ( 1997;). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. . Nucleic Acids Res 25:, 3389–3402. [CrossRef][PubMed]
    [Google Scholar]
  3. Bælum J., Jacobsen C. S., Holben W. E.. ( 2010;). Comparison of 16S rRNA gene phylogeny and functional tfdA gene distribution in thirty-one different 2,4-dichlorophenoxyacetic acid and 4-chloro-2-methylphenoxyacetic acid degraders. . Syst Appl Microbiol 33:, 67–70. [CrossRef][PubMed]
    [Google Scholar]
  4. Bugreev D. V., Nevinsky G. A.. ( 2009;). Structure and mechanism of action of type IA DNA topoisomerases. . Biochemistry (Mosc) 74:, 1467–1481. [CrossRef][PubMed]
    [Google Scholar]
  5. Carattoli A., Bertini A., Villa L., Falbo V., Hopkins K. L., Threlfall E. J.. ( 2005;). Identification of plasmids by PCR-based replicon typing. . J Microbiol Methods 63:, 219–228. [CrossRef][PubMed]
    [Google Scholar]
  6. Chain P. S. G., Denef V. J., Konstantinidis K. T., Vergez L. M., Agulló L., Reyes V. L., Hauser L., Córdova M., Gómez L.. & other authors ( 2006;). Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. . Proc Natl Acad Sci U S A 103:, 15280–15287. [CrossRef][PubMed]
    [Google Scholar]
  7. Chan P. P., Lowe T. M.. ( 2009;). GtRNAdb: a database of transfer RNA genes detected in genomic sequence. . Nucleic Acids Res 37: (Database), D93–D97. [CrossRef][PubMed]
    [Google Scholar]
  8. Chinalia F. A., Regali-Seleghin M. H., Correa E. M.. ( 2007;). 2,4-D toxicity: cause, effect and control. . Terr Aquatic Environ Toxicol 1:, 24–33.
    [Google Scholar]
  9. Couturier M., Bex F., Bergquist P. L., Maas W. K.. ( 1988;). Identification and classification of bacterial plasmids. . Microbiol Rev 52:, 375–395.[PubMed]
    [Google Scholar]
  10. de la Cruz F., Frost L. S., Meyer R. J., Zechner E. L.. ( 2010;). Conjugative DNA metabolism in Gram-negative bacteria. . FEMS Microbiol Rev 34:, 18–40. [CrossRef][PubMed]
    [Google Scholar]
  11. Don R. H., Pemberton J. M.. ( 1981;). Properties of six pesticide degradation plasmids isolated from Alcaligenes paradoxus and Alcaligenes eutrophus. . J Bacteriol 145:, 681–686.[PubMed]
    [Google Scholar]
  12. Finn R. D., Mistry J., Tate J., Coggill P., Heger A., Pollington J. E., Gavin O. L., Gunasekaran P., Ceric G.. & other authors ( 2010;). The Pfam protein families database. . Nucleic Acids Res 38: (Database), D211–D222. [CrossRef][PubMed]
    [Google Scholar]
  13. Fisher P. R., Appleton J., Pemberton J. M.. ( 1978;). Isolation and characterization of the pesticide-degrading plasmid pJP1 from Alcaligenes paradoxus. . J Bacteriol 135:, 798–804.[PubMed]
    [Google Scholar]
  14. Francia M. V., Varsaki A., Garcillán-Barcia M. P., Latorre A., Drainas C., de la Cruz F.. ( 2004;). A classification scheme for mobilization regions of bacterial plasmids. . FEMS Microbiol Rev 28:, 79–100. [CrossRef][PubMed]
    [Google Scholar]
  15. Francisco P. Jr, Ogawa N., Suzuki K., Miyashita K.. ( 2001;). The chlorobenzoate dioxygenase genes of Burkholderia sp. strain NK8 involved in the catabolism of chlorobenzoates. . Microbiology 147:, 121–133.[PubMed]
    [Google Scholar]
  16. Garcillán-Barcia M. P., Francia M. V., de la Cruz F.. ( 2009;). The diversity of conjugative relaxases and its application in plasmid classification. . FEMS Microbiol Rev 33:, 657–687. [CrossRef][PubMed]
    [Google Scholar]
  17. Götz A., Pukall R., Smit E., Tietze E., Prager R., Tschäpe H., van Elsas J. D., Smalla K.. ( 1996;). Detection and characterization of broad-host-range plasmids in environmental bacteria by PCR. . Appl Environ Microbiol 62:, 2621–2628.[PubMed]
    [Google Scholar]
  18. Guglielmini J., Quintais L., Garcillán-Barcia M. P., de la Cruz F., Rocha E. P.. ( 2011;). The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. . PLoS Genet 7:, e1002222. [CrossRef][PubMed]
    [Google Scholar]
  19. Harrison P. W., Lower R. P. J., Kim N. K. D., Young J. P. W.. ( 2010;). Introducing the bacterial ‘chromid’: not a chromosome, not a plasmid. . Trends Microbiol 18:, 141–148. [CrossRef][PubMed]
    [Google Scholar]
  20. Hasebe A., Tsushima S., Iida S.. ( 1998;). Isolation and characterization of IS1416 from Pseudomonas glumae, a new member of the IS3 family. . Plasmid 39:, 196–204. [CrossRef][PubMed]
    [Google Scholar]
  21. Hayes F., Barillà D.. ( 2006;). The bacterial segrosome: a dynamic nucleoprotein machine for DNA trafficking and segregation. . Nat Rev Microbiol 4:, 133–143. [CrossRef][PubMed]
    [Google Scholar]
  22. Kim D. U., Kim M. S., Lim J. S., Ka J. O.. ( 2013;). Widespread occurrence of the tfd-II genes in soil bacteria revealed by nucleotide sequence analysis of 2,4-dichlorophenoxyacetic acid degradative plasmids pDB1 and p712. . Plasmid 69:, 243–248. [CrossRef][PubMed]
    [Google Scholar]
  23. Lawley T. D., Klimke W. A., Gubbins M. J., Frost L. S.. ( 2003;). F factor conjugation is a true type IV secretion system. . FEMS Microbiol Lett 224:, 1–15. [CrossRef][PubMed]
    [Google Scholar]
  24. Lawley T., Wilkins B. M., Frost L. S.. ( 2004;). Bacterial conjugation in gram-negative bacteria. . In Plasmid Biology, pp. 203–226. Edited by Funnell B. E., Phillips G. J... Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  25. Li S., Zhao H., Li Y., Niu S., Cai B.. ( 2012;). Complete genome sequence of the naphthalene-degrading Pseudomonas putida strain ND6. . J Bacteriol 194:, 5154–5155. [CrossRef][PubMed]
    [Google Scholar]
  26. Li S., Zhao H., Li Y., Niu S., Cai B.. ( 2013;). Complete nucleotide sequence of plasmid pND6-2 from Pseudomonas putida ND6 and characterization of conjugative genes. . Gene 512:, 148–156. [CrossRef][PubMed]
    [Google Scholar]
  27. Lim J. S., Choi B. S., Choi A. Y., Kim K. D., Kim D. I., Choi I. Y., Ka J. O.. ( 2012;). Complete genome sequence of the fenitrothion-degrading Burkholderia sp. strain YI23. . J Bacteriol 194:, 896. [CrossRef][PubMed]
    [Google Scholar]
  28. Mergeay M., Monchy S., Janssen P., Houdt R. V., Leys N.. ( 2009;). Megaplasmids in Cupriavidus genus and metal resistance. . In Microbial Megaplasmids, pp. 209–238. Edited by Schwartz E... Berlin:: Springer;. [CrossRef]
    [Google Scholar]
  29. Molina L., Bernal P., Udaondo Z., Segura A., Ramos J. L.. ( 2013;). Complete genome sequence of a Pseudomonas putida clinical isolate, strain H8234. . Genome Announc 1:, e00496-13. [CrossRef][PubMed]
    [Google Scholar]
  30. Monchy S., Benotmane M. A., 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. [CrossRef][PubMed]
    [Google Scholar]
  31. Ng J., Wyndham R. C.. ( 1993;). Is1071-mediated recombinational equilibrium in Alcaligenes sp. BR60 carrying the 3-chlorobenzoate catabolic transposon Tn5271. . Can J Microbiol 39:, 92–100. [CrossRef]
    [Google Scholar]
  32. 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. [CrossRef][PubMed]
    [Google Scholar]
  33. Ogawa N., Miyashita K.. ( 1995;). Recombination of a 3-chlorobenzoate catabolic plasmid from Alcaligenes eutrophus NH9 mediated by direct repeat elements. . Appl Environ Microbiol 61:, 3788–3795.[PubMed]
    [Google Scholar]
  34. Ogawa N., Chakrabarty A. M., Zaborina O.. ( 2004;). Degradative plasmids. . In Plasmid Biology, pp. 341–376. Edited by Funnell B. E., Phillips G. J... Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  35. Ormeño-Orrillo E., Rogel M. A., Chueire L. M. O., Tiedje J. M., Martínez-Romero E., Hungria M.. ( 2012;). Genome sequences of Burkholderia sp. strains CCGE1002 and H160, isolated from legume nodules in Mexico and Brazil. . J Bacteriol 194:, 6927. [CrossRef][PubMed]
    [Google Scholar]
  36. Pansegrau W., Schröder W., Lanka E.. ( 1993;). Relaxase (TraI) of IncP α plasmid RP4 catalyzes a site-specific cleaving-joining reaction of single-stranded DNA. . Proc Natl Acad Sci U S A 90:, 2925–2929. [CrossRef][PubMed]
    [Google Scholar]
  37. Pemberton J. M., Fisher P. R.. ( 1977;). 2,4-D plasmids and persistence. . Nature 268:, 732–733. [CrossRef][PubMed]
    [Google Scholar]
  38. Pérez-Mendoza D., Sepúlveda E., Pando V., Muñoz S., Nogales J., Olivares J., Soto M. J., Herrera-Cervera J. A., Romero D.. & other authors ( 2005;). Identification of the rctA gene, which is required for repression of conjugative transfer of rhizobial symbiotic megaplasmids. . J Bacteriol 187:, 7341–7350. [CrossRef][PubMed]
    [Google Scholar]
  39. Pérez-Pantoja D., Donoso R., Agulló L., Córdova M., Seeger M., Pieper D. H., González B.. ( 2012;). Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderiales. . Environ Microbiol 14:, 1091–1117. [CrossRef][PubMed]
    [Google Scholar]
  40. Poh R. P., Smith A. R., Bruce I. J.. ( 2002;). Complete characterisation of Tn5530 from Burkholderia cepacia strain 2a (pIJB1) and studies of 2,4-dichlorophenoxyacetate uptake by the organism. . Plasmid 48:, 1–12. [CrossRef][PubMed]
    [Google Scholar]
  41. Ravatn R., Studer S., Springael D., Zehnder A. J. B., van der Meer J. R.. ( 1998;). Chromosomal integration, tandem amplification, and deamplification in Pseudomonas putida F1 of a 105-kilobase genetic element containing the chlorocatechol degradative genes from Pseudomonas sp. strain B13. . J Bacteriol 180:, 4360–4369.[PubMed]
    [Google Scholar]
  42. Roberts A. P., Chandler M., Courvalin P., Guédon G., Mullany P., Pembroke T., Rood J. I., Smith C. J., Summers A. O.. & other authors ( 2008;). Revised nomenclature for transposable genetic elements. . Plasmid 60:, 167–173. [CrossRef][PubMed]
    [Google Scholar]
  43. Sakai Y., Ogawa N., Fujii T., Sugahara K., Miyashita K., Hasebe A.. ( 2007;). 2,4-Dichrolophenoxyacetic acid-degrading genes from bacteria isolated from soil in Japan: spread of Burkholderia cepacia RASC-type degrading genes harbored on large plasmids. . Microbes Environ 22:, 145–156. [CrossRef]
    [Google Scholar]
  44. Sambrook J., Russell D. W.. ( 2001;). Molecular Cloning: A Laboratory Manual, , 3rd edn.. Cold Spring Harbor, NY:: Cold Spring Harbor Laboratory Press;.
    [Google Scholar]
  45. Sato Y., Nishihara H., Yoshida M., Watanabe M., Rondal J. D., Concepcion R. N., Ohta H.. ( 2006;). Cupriavidus pinatubonensis sp. nov. and Cupriavidus laharis sp. nov., novel hydrogen-oxidizing, facultatively chemolithotrophic bacteria isolated from volcanic mudflow deposits from Mt. Pinatubo in the Philippines. . Int J Syst Evol Microbiol 56:, 973–978. [CrossRef][PubMed]
    [Google Scholar]
  46. Schattner P., Brooks A. N., Lowe T. M.. ( 2005;). The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. . Nucleic Acids Res 33: (Web Server), W686–W689. [CrossRef][PubMed]
    [Google Scholar]
  47. Shintani M., Yano H., Habe H., Omori T., Yamane H., Tsuda M., Nojiri H.. ( 2006;). Characterization of the replication, maintenance, and transfer features of the IncP-7 plasmid pCAR1, which carries genes involved in carbazole and dioxin degradation. . Appl Environ Microbiol 72:, 3206–3216. [CrossRef][PubMed]
    [Google Scholar]
  48. Silver S., Phung L. T.. ( 2005;). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. . Appl Environ Microbiol 71:, 599–608. [CrossRef][PubMed]
    [Google Scholar]
  49. Smillie C., Garcillán-Barcia M. P., Francia M. V., Rocha E. P. C., de la Cruz F.. ( 2010;). Mobility of plasmids. . Microbiol Mol Biol Rev 74:, 434–452. [CrossRef][PubMed]
    [Google Scholar]
  50. Sota M., Yano H., Nagata Y., Ohtsubo Y., Genka H., Anbutsu H., Kawasaki H., Tsuda M.. ( 2006;). Functional analysis of unique class II insertion sequence IS1071. . Appl Environ Microbiol 72:, 291–297. [CrossRef][PubMed]
    [Google Scholar]
  51. Takami H., Nakasone K., Hirama C., Takaki Y., Masui N., Fuji F., Nakamura Y., Inoue A.. ( 1999;). An improved physical and genetic map of the genome of alkaliphilic Bacillus sp. C-125. . Extremophiles 3:, 21–28. [CrossRef][PubMed]
    [Google Scholar]
  52. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S.. ( 2011;). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28:, 2731–2739. [CrossRef][PubMed]
    [Google Scholar]
  53. Taylor D. E., Gibreel A., Lawley T. D., Tracz D. M.. ( 2004;). Antibiotic resistance plasmids. . In Plasmid Biology, pp. 473–491. Edited by Funnell B. E., Phillips G. J... Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  54. Tonso N. L., Matheson V. G., Holben W. E.. ( 1995;). Polyphasic characterization of a suite of bacterial isolates capable of degrading 2,4-D. . Microb Ecol 30:, 3–24. [CrossRef][PubMed]
    [Google Scholar]
  55. Toussaint A., Merlin C., Monchy S., Benotmane M. A., 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. [CrossRef][PubMed]
    [Google Scholar]
  56. Trefault N., De la Iglesia R., Molina A. M., Manzano M., Ledger T., Pérez-Pantoja D., Sánchez M. A., 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. [CrossRef][PubMed]
    [Google Scholar]
  57. Tuffin I. M., Hector S. B., Deane S. M., Rawlings D. E.. ( 2006;). Resistance determinants of a highly arsenic-resistant strain of Leptospirillum ferriphilum isolated from a commercial biooxidation tank. . Appl Environ Microbiol 72:, 2247–2253. [CrossRef][PubMed]
    [Google Scholar]
  58. Vallaeys T., Fulthorpe R. R., Wright A. M., Soulas G.. ( 1996;). The metabolic pathway of 2,4-dichlorophenoxyacetic acid degradation involves different families of tfdA and tfdB genes according to PCR-RFLP analysis. . FEMS Microbiol Ecol 20:, 163–172. [CrossRef]
    [Google Scholar]
  59. van der Meer J. R.. ( 2008;). Genomics and molecular biology: A genomic view on the evolution of catabolic pathways and bacterial adaptation to xenobiotic compounds. . In Microbial Biodegradation, pp. 219–267. Edited by Díaz E... Wymondham:: Caister Academic Press;.
    [Google Scholar]
  60. 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. [CrossRef][PubMed]
    [Google Scholar]
  61. Weilharter A., Mitter B., Shin M. V., Chain P. S. G., Nowak J., Sessitsch A.. ( 2011;). Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN. . J Bacteriol 193:, 3383–3384. [CrossRef][PubMed]
    [Google Scholar]
  62. Xia X. S., Aathithan S., Oswiecimska K., Smith A. R., Bruce I. J.. ( 1998;). A novel plasmid pIJB1 possessing a putative 2,4-dichlorophenoxyacetate degradative transposon Tn5530 in Burkholderia cepacia strain 2a. . Plasmid 39:, 154–159. [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.074369-0
Loading
/content/journal/micro/10.1099/mic.0.074369-0
Loading

Data & Media loading...

Supplements

Supplementary material 

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