Characterization of a Small Cryptic Plasmid from Pseudomonas nitroreducens Strain TX1

국문 초록 (Abstract)

Pseudomonas nitroreducens TX1는 대만의 벼를 재배하는 논의 배수구에서 분리된 세균이다. 이 균주는 알킬페놀 폴리에톡실레이트와 같은 비이온성 계면활성제를 고농도에서도 탄소원으로 이용할 수 있다. 본 연구에서는 TX1 균주에서 분리된 새로운 플라스미드 pTX1의 특성을 조사하였다. 크기는 2,286 bp, GC 함량은 63.3%, 암호된 유전자로는 $Rep_{pTX1}$과 기능이 밝혀지지 않은 ORF1과 ORF2가 동정되었다. $Rep_{pTX1}$은 롤링-서클 기작에 의해 복제되는 그람 양성 세균에서 주로 발견되는 pC194/pUB110 플라스미드 계열에 속하는 DNA 복제 효소임을 알 수 있었다. 또한 세포마다 약 150개의 플라스미드가 존재함을 규명하였다. 플라스미드에 존재하는 유전자 지문과 유사 플라스미드와의 핵산과 아미노산 서열비교를 통해 pTX1은 슈도모나스 세균에서는 흔히 발견되지 않는 롤링-서클 기작에 의해 복제된다는 것을 확인할 수 있었다.

다국어 초록 (Multilingual 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.

참고문헌 (Reference)

• 1 Thompson, J.D., "The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools" 25 : 4876-4882, 1997
• 2 Bouia, A., "Structural organization of pLP1, a cryptic plasmid from Lactobacillus plantarum CCM 1904" 22 : 185-192, 1904
• 3 Yasukawa, H., "Rolling-circle replication of the plasmid pKYM isolated from a Gram-negative bacterium" 88 : 10282-10286, 1991
• 4 Khan, S.A., "Rolling-circle replication of bacterial plasmids" 61 : 442-455, 1997
• 5 del Solar, G., "Replication and control of circular bacterial plasmids" 62 : 434-464, 1998
• 6 Rehm, B.H.A., "Pseudomonas: model organism, pathogen, cell factory" Wiley-VCH Verlag GmbH & Co 293-327, 2008
• 7 Gibson, D.T., "Oxidative degradation of aromatic hydrocarbons by microorganisms. IV. Incorporation of oxygen-18 into benzene by Pseudomonas putida" 9 : 1631-1635, 1970
• 8 Wang, P.Z., "Origin recognition specificity in pT181 plasmids is determined by a functionally asymmetric palindromic DNA element" 12 : 45-52, 1993
• 9 Qin, Z., "Identification and characterization of a pSLA2 plasmid locus required for linear DNA replication and circular plasmid stable inheritance in Streptomyces lividans" 185 : 6575-6582, 2003
• 10 Lin, Y.W., "Growth of Pseudomonas sp. TX1 on a wide range of octylphenol polyethoxylate concentrations and the formation of dicarboxylated metabolites" 101 : 2853-2859, 2010
• 11 Chen, H.J., "Growth factors, kinetics and biodegradation mechanism associated with Pseudomonas nitroreducens TX1 grown on octylphenol polyethoxylates" 80 : 279-286, 2006
• 12 Yen, K.M., "Genetics of naphthalene catabolism in pseudomonads" 15 : 247-268, 1988
• 13 Gruss, A.D., "Functional analysis of a palindromic sequence required for normal replication of several staphylococcal plasmids" 84 : 2165-2169, 1987
• 14 Huang, S.L., "Draft genome sequence of Pseudomonas nitroreducens strain TX1, which degrades nonionic surfactants and estrogen-like alkylphenols" 2-, 2014
• 15 Wilson, K., "Current Protocols in Molecular Biology" John Wiley & Sons 208-209, 2003
• 16 Ilyina, T.V., "Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria" 20 : 3279-3285, 1992
• 17 Chae, J.C., "Characterization of two small cryptic plasmids from Pseudomonas sp. strain S-47" 338 : 1600-1606, 2005
• 18 Kramer, M.G., "Characterization of a single-strand origin, ssoU, required for broad host range replication of rolling-circle plasmids" 33 : 466-475, 1999
• 19 Chen, H.J., "Biodegradation of octylphenol polyethoxylate surfactant Triton X-100 by selected microorganisms" 96 : 1483-1491, 2005
• 20 Tuan, N.N., "Analysis of bacterial degradation pathways for long-chain alkylphenols involving phenol hydroxylase, alkylphenol monooxygenase and catechol dioxygenase genes" 102 : 4232-4240, 2011
• 21 Chen, H.J., "Aerobic biotransformation of octylphenol polyethoxylate surfactant in soil microcosms" 25 : 201-210, 2004
• 22 Holtwick, R., "A novel rolling-circle-replicating plasmid from Pseudomonas putida P8: molecular characterization and use as vector" 147 : 337-344, 2001