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Genome Analysis of Naphthalene-Degrading Pseudomonas sp. AS1 Harboring the Megaplasmid pAS1

  • Kim, Jisun (Laboratory of Molecular Environmental Microbiology, Department of Environmental Sciences and Ecological Engineering, Korea University) ;
  • Park, Woojun (Laboratory of Molecular Environmental Microbiology, Department of Environmental Sciences and Ecological Engineering, Korea University)
  • 투고 : 2017.09.01
  • 심사 : 2017.11.21
  • 발행 : 2018.02.28

초록

Polycyclic aromatic hydrocarbons (PAHs), including naphthalene, are widely distributed in nature. Naphthalene has been regarded as a model PAH compound for investigating the mechanisms of bacterial PAH biodegradation. Pseudomonas sp. AS1 isolated from an arseniccontaminated site is capable of growing on various aromatic compounds such as naphthalene, salicylate, and catechol, but not on gentisate. The genome of strain AS1 consists of a 6,126,864 bp circular chromosome and the 81,841 bp circular plasmid pAS1. Pseudomonas sp. AS1 has multiple dioxygenases and related enzymes involved in the degradation of aromatic compounds, which might contribute to the metabolic versatility of this isolate. The pAS1 plasmid exhibits extremely high similarity in size and sequences to the well-known naphthalene-degrading plasmid pDTG1 in Pseudomonas putida strain NCIB 9816-4. Two gene clusters involved in the naphthalene degradation pathway were identified on pAS1. The expression of several nah genes on the plasmid was upregulated by more than 2-fold when naphthalene was used as a sole carbon source. Strains have been isolated at different times and places with different characteristics, but similar genes involved in the degradation of aromatic compounds have been identified on their plasmids, which suggests that the transmissibility of the plasmids might play an important role in the adaptation of the microorganisms to mineralize the compounds.

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참고문헌

  1. Nayak AS, Veeranagouda Y, Lee K, Karegoudar TB. 2009. Metabolism of acenaphthylene via 1,2-dihydroxynaphthalene and catechol by Stenotrophomonas sp. RMSK. Biodegradation 20: 837-843. https://doi.org/10.1007/s10532-009-9271-1
  2. Park W, Jeon CO, Cadillo H, DeRito C, Madsen EL. 2004. Survival of naphthalene-degrading Pseudomonas putida NCIB 9816-4 in naphthalene-amended soils: toxicity of naphthalene and its metabolites. Appl. Microbiol. Biotechnol. 64: 429-435. https://doi.org/10.1007/s00253-003-1420-6
  3. Peng RH, Xiong AS, Xue Y, Fu XY, Gao F, Zhao W, et al. 2008. Microbial biodegradation of polyaromatic hydrocarbons. FEMS Microbiol. Rev. 32: 927-955.
  4. Volkering F, Breure AM, Sterkenburg A, van Andel JG. 1992. Microbial degradation of polycyclic aromatic hydrocarbons: effect of substrate availability on bacterial growth kinetics. Appl. Microbiol. Biotechnol. 36: 548-552.
  5. Cerniglia CE. 1984. Microbial metabolism of polycyclic aromatic hydrocarbons. Adv. Appl. Microbiol. 30: 31-71.
  6. Heitkamp MA, Cerniglia CE. 1988. Mineralization of polycyclic aromatic hydrocarbons by a bacterium isolated from sediment below an oil field. Appl. Environ. Microbiol. 54: 1612-1614.
  7. Kang YS, Kim YJ, Jeon CO, Park W. 2006. Characterization of naphthalene-degrading Pseudomonas species isolated from pollutant-contaminated sites: oxidative stress during their growth on naphthalene. J. Microbiol. Biotechnol. 16: 1819-1825.
  8. Seo H, Kim J, Jung J, Jin HM, Jeon CO, Park W. 2012. Complexity of cell-cell interactions between Pseudomonas sp. AS1 and Acinetobacter oleivorans DR1: metabolic commensalism, biofilm formation and quorum quenching. Res. Microbiol. 163: 173-181. https://doi.org/10.1016/j.resmic.2011.12.003
  9. 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.
  10. Kang YS, Lee Y, Jung H, Jeon CO, Madsen EL, Park W. 2007. Overexpressing antioxidant enzymes enhances naphthalene biodegradation in Pseudomonas sp. strain As1. Microbiology 153: 3246-3254. https://doi.org/10.1099/mic.0.2007/008896-0
  11. Park W, Padmanabhan P, Padmanabhan S, Zylstra GJ, Madsen EL. 2002. nahR, encoding a LysR-type transcriptional regulator, is highly conserved among naphthalene-degrading bacteria isolated from a coal tar waste-contaminated site and in extracted community DNA. Microbiology 148: 2319-2329. https://doi.org/10.1099/00221287-148-8-2319
  12. Simon MJ, Osslund TD, S aunders R, E nsley BD, Suggs S , Harcourt A, et al. 1993. Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida s trai ns G7 and NCIB 9816-4. Gene 127: 31-37. https://doi.org/10.1016/0378-1119(93)90613-8
  13. Yen KM, Serdar CM. 1988. Genetics of naphthalene catabolism in pseudomonads. Crit. Rev. Microbiol. 15: 247-268. https://doi.org/10.3109/10408418809104459
  14. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, et al. 2016. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 44: D279-D285. https://doi.org/10.1093/nar/gkv1344
  15. Tatusov RL, Galperin MY, Natale DA, Koonin EV. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28: 33-36. https://doi.org/10.1093/nar/28.1.33
  16. Galperin MY, Makarova KS, Wolf YI, Koonin EV. 2015. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 43: D261-D269. https://doi.org/10.1093/nar/gku1223
  17. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. 2016. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44: D457-D462. https://doi.org/10.1093/nar/gkv1070
  18. Barrangou R, Fremaux C, Deveau H, Ri chards M, Boyaval P, Moineau S, et al. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315: 1709-1712.
  19. Kim J, Park C, Imlay JA, Park W. 2017. Lineage-specific SoxR-mediated regulation of an endoribonuclease protects non-enteric bacteria from redox-active compounds. J. Biol. Chem. 292: 121-133. https://doi.org/10.1074/jbc.M116.757500
  20. Andersen SM, Johnsen K, Sorensen J, Nielsen P, Jacobsen CS. 2000. Pseudomonas frederiksbergensis sp. nov., isolated from soil at a coal gasification site. Int. J. Syst. Evol. Microbiol. 50: 1957-1964. https://doi.org/10.1099/00207713-50-6-1957
  21. Ruiz ON, Brown LM, Striebich RC, Mueller SS, Gunasekera TS. 2015. Draft genome sequence of Pseudomonas frederiksbergensis SI8, a psychrotrophic aromatic-degrading bacterium. Genome Announc. 3: e00811-e00815.
  22. Davison J. 1999. Genetic exchange between bacteria in the environment. Plasmid 42: 73-91. https://doi.org/10.1006/plas.1999.1421
  23. Lawrence JG. 1997. Selfish operons and speciation by gene transfer. Trends Microbiol. 5: 355-359. https://doi.org/10.1016/S0966-842X(97)01110-4
  24. 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. https://doi.org/10.1128/AEM.69.9.5536-5542.2003

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  2. Variability in Assembly of Degradation Operons for Naphthalene and its derivative, Carbaryl, Suggests Mobilization through Horizontal Gene Transfer vol.10, pp.8, 2018, https://doi.org/10.3390/genes10080569