Browse > Article
http://dx.doi.org/10.7845/kjm.2014.4038

Characterization of a Small Cryptic Plasmid from Pseudomonas nitroreducens Strain TX1  

Nguyen, Ngoc Tuan (Department of Life Sciences, National Central University)
Lee, Kyoung (Department of Microbiology and Biomedical Institute at CWNU, Changwon National University)
Kang, Ju Beom (Department of Microbiology and Biomedical Institute at CWNU, Changwon National University)
Huang, Shir-Ly (Department of Life Sciences, National Central University)
Publication Information
Korean Journal of Microbiology / v.50, no.3, 2014 , pp. 210-215 More about this Journal
Abstract
Pseudomonas nitroreducens TX1 was isolated from a rice field drainage in Taiwan. The bacterium is of special interest because of its capability to use a group of nonionic surfactants such as alkylphenol polyethoxylates even at high concentrations as a sole carbon source. In this study, a small cryptic circular plasmid, pTX1, was characterized from P. nitroreducens TX1. It is 2,286 bp in length with a GC content of 63.3% and harbors three open reading frames, $Rep_{pTX1}$ and functionally unidentified ORF1 and ORF2. The predicted $rep_{pTX1}$ gene product is homologous to Rep proteins of plasmids belonging to the pC194/pUB110 family, which is predominantly found in Gram-positive bacteria and is known to replicate by the rolling-circle mechanism. The copy number of pTX1 was estimated to be about 150 in each cell. Based on the genetic fingerprints and comparison with other plasmids, it is concluded that pTX1 replicates by a rolling circle mechanism which is rarely found for Pseudomonas plasmids.
Keywords
Pseudomonas nitroreducens; cryptic plasmid; rolling circle replication;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Gruss, A.D., Ross, H.F., and Novick, R.P. 1987. Functional analysis of a palindromic sequence required for normal replication of several staphylococcal plasmids. Proc. Natl. Acad. Sci. USA 84, 2165 2169.   DOI   ScienceOn
2 Yen, K.M. and Serdar, C.M. 1988. Genetics of naphthalene catabolism in pseudomonads. Crit. Rev. Microbiol. 15, 247 268.   DOI   ScienceOn
3 Holtwick, R., von Wallbrunn, A., Keweloh, H., and Meinhardt, F. 2001. A novel rolling-circle-replicating plasmid from Pseudomonas putida P8: molecular characterization and use as vector. Microbiology 147, 337 344.   DOI
4 Huang, S.L., Chen, H., Hu, A., Tuan, N.N., and Yu, C.P. 2014. Draft genome sequence of Pseudomonas nitroreducens strain TX1, which degrades nonionic surfactants and estrogen-like alkylphenols. Genome Announc. 2.
5 Bouia, A., Bringel, F., Frey, L., Kammerer, B., Belarbi, A., Guyonvarch, A., and Hubert, J.C. 1989. Structural organization of pLP1, a cryptic plasmid from Lactobacillus plantarum CCM 1904. Plasmid 22, 185-192.   DOI
6 Chae, J.C., Kim, C.K., and Zylstra, G.J. 2005. Characterization of two small cryptic plasmids from Pseudomonas sp. strain S-47. Biochem. Biophys. Res. Commun. 338, 1600 1606.   DOI   ScienceOn
7 Chen, H.J., Guo, G.L., Tseng, D.H., Cheng, C.L., and Huang, S.L. 2006. Growth factors, kinetics and biodegradation mechanism associated with Pseudomonas nitroreducens TX1 grown on octylphenol polyethoxylates. J. Environ. Manage. 80, 279 286.   DOI
8 Chen, H.J., Huang, S.L., and Tseng, D.H. 2004. Aerobic biotransformation of octylphenol polyethoxylate surfactant in soil microcosms. Environ. Technol. 25, 201 210.   DOI
9 Chen, H.J., Tseng, D.H., and Huang, S.L. 2005. Biodegradation of octylphenol polyethoxylate surfactant Triton X-100 by selected microorganisms. Bioresour. Technol. 96, 1483 1491.   DOI
10 Gibson, D.T., Cardini, G.E., Maseles, F.C., and Reino, E. 1970. Oxidative degradation of aromatic hydrocarbons by microorganisms. IV. Incorporation of oxygen-18 into benzene by Pseudomonas putida. Biochemistry 9, 1631 1635.   DOI
11 Kramer, M.G., Espinosa, M., Misra, T.K., and Khan, S.A. 1999. Characterization of a single-strand origin, ssoU, required for broad host range replication of rolling-circle plasmids. Mol. Microbiol. 33, 466 475.   DOI
12 Lin, Y.W., Guo, G.L., Hsieh, H.C., and Huang, S.L. 2010. Growth of Pseudomonas sp. TX1 on a wide range of octylphenol polyethoxylate concentrations and the formation of dicarboxylated metabolites. Bioresour. Technol. 101, 2853 2859.   DOI
13 Qin, Z., Shen, M., and Cohen, S.N. 2003. Identification and characterization of a pSLA2 plasmid locus required for linear DNA replication and circular plasmid stable inheritance in Streptomyces lividans. J. Bacteriol. 185, 6575 6582.   DOI
14 Rehm, B.H.A. 2008. Chapter 11. Pseudomonas plasmids, pp. 293 327. In Thomas, C.M., Haines, A.S., Kosheleva, I.A., and Boronin, A. (eds.), Pseudomonas: model organism, pathogen, cell factory. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany.
15 Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876 4882.   DOI   ScienceOn
16 Tuan, N.N., Hsieh, H.C., Lin, Y.W., and Huang, S.L. 2011. Analysis of bacterial degradation pathways for long-chain alkylphenols involving phenol hydroxylase, alkylphenol monooxygenase and catechol dioxygenase genes. Bioresour. Technol. 102, 4232 4240.   DOI
17 Khan, S.A. 1997. Rolling-circle replication of bacterial plasmids. Microbiol. Mol. Biol. Rev. 61, 442 455.
18 Wilson, K. 2003. UNIT 2.4. Preparation of genomic DNA from bacteria, pp. 208 209. In Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., and Struhl, K. (eds.). Current Protocols in Molecular Biology, John Wiley & Sons, New York, NY, USA.
19 Yasukawa, H., Hase, T., Sakai, A., and Masamune, Y. 1991. Rolling-circle replication of the plasmid pKYM isolated from a Gram-negative bacterium. Proc. Natl. Acad. Sci. USA 88, 10282 10286.   DOI   ScienceOn
20 Ilyina, T.V. and Koonin, E.V. 1992. Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res. 20, 3279 3285.   DOI   ScienceOn
21 Wang, P.Z., Projan, S.J., Henriquez, V., and Novick, R.P. 1993. Origin recognition specificity in pT181 plasmids is determined by a functionally asymmetric palindromic DNA element. EMBO J. 12, 45 52.
22 del Solar, G., Giraldo, R., Ruiz-Echevarria, M.J., Espinosa, M., and Diaz-Orejas, R. 1998. Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 62, 434 464.