Complete Sequence Analysis of Two Methanotroph-specific RepABC-containing Plasmids from Methylocystis Sp. Strain SC2

Overview

Journal Appl Environ Microbiol

Specialties Environmental Health
Microbiology

Date 2012 Apr 17

PMID 22504811

Citations 9

Authors

Bomba Dam

Michael Kube

Somasri Dam

Richard Reinhardt

Werner Liesack

Affiliations

Soon will be listed here.

Abstract

The complete nucleotide sequences of two large, low-copy-number plasmids of 229.6 kb (pBSC2-1) and 143.5 kb (pBSC2-2) were determined during assembly of the whole-genome shotgun sequences of the methane-oxidizing bacterium Methylocystis sp. strain SC2. The physical existence of the two plasmids in strain SC2 was confirmed by pulsed-field gel electrophoresis followed by Southern hybridization. Both plasmids have a conserved replication module of the repABC system and carry genes involved in their faithful maintenance and conjugation. In addition, they contain genes that might be involved in essential metabolic processes. These include several heavy metal resistance genes and copper transport genes in pBSC2-1 and a complete nitrous oxide reductase operon and a pmoC singleton in pBSC2-2, the latter encoding the PmoC subunit of particulate methane monooxygenase.

Citing Articles

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Evolutionary History of Copper Membrane Monooxygenases.

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References

Barkay T, Miller S, Summers A . Bacterial mercury resistance from atoms to ecosystems. FEMS Microbiol Rev. 2003; 27(2-3):355-84. DOI: 10.1016/S0168-6445(03)00046-9. View

Lidstrom M, Wopat A . Plasmids in methanotrophic bacteria: isolation, characterization and DNA hybridization analysis. Arch Microbiol. 1984; 140(1):27-33. DOI: 10.1007/BF00409767. View

Delcher A, Harmon D, Kasif S, White O, Salzberg S . Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999; 27(23):4636-41. PMC: 148753. DOI: 10.1093/nar/27.23.4636. View

Barton B, Harding G, Zuccarelli A . A general method for detecting and sizing large plasmids. Anal Biochem. 1995; 226(2):235-40. DOI: 10.1006/abio.1995.1220. View

Holloway P, McCormick W, Watson R, Chan Y . Identification and analysis of the dissimilatory nitrous oxide reduction genes, nosRZDFY, of Rhizobium meliloti. J Bacteriol. 1996; 178(6):1505-14. PMC: 177832. DOI: 10.1128/jb.178.6.1505-1514.1996. View

Chen Y, Crombie A, Rahman M, Dedysh S, Liesack W, Stott M . Complete genome sequence of the aerobic facultative methanotroph Methylocella silvestris BL2. J Bacteriol. 2010; 192(14):3840-1. PMC: 2897342. DOI: 10.1128/JB.00506-10. View

Richardson D, Felgate H, Watmough N, Thomson A, Baggs E . Mitigating release of the potent greenhouse gas N(2)O from the nitrogen cycle - could enzymic regulation hold the key?. Trends Biotechnol. 2009; 27(7):388-97. DOI: 10.1016/j.tibtech.2009.03.009. View

Pandey D, Gerdes K . Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res. 2005; 33(3):966-76. PMC: 549392. DOI: 10.1093/nar/gki201. View

Gordon D . Viewing and editing assembled sequences using Consed. Curr Protoc Bioinformatics. 2008; Chapter 11:Unit11.2. DOI: 10.1002/0471250953.bi1102s02. View

10.

Lidstrom M, Stirling D . Methylotrophs: genetics and commercial applications. Annu Rev Microbiol. 1990; 44:27-58. DOI: 10.1146/annurev.mi.44.100190.000331. View

11.

Stolyar S, Costello A, Peeples T, Lidstrom M . Role of multiple gene copies in particulate methane monooxygenase activity in the methane-oxidizing bacterium Methylococcus capsulatus Bath. Microbiology (Reading). 1999; 145 ( Pt 5):1235-1244. DOI: 10.1099/13500872-145-5-1235. View

12.

Svenning M, Hestnes A, Wartiainen I, Stein L, Klotz M, Kalyuzhnaya M . Genome sequence of the Arctic methanotroph Methylobacter tundripaludum SV96. J Bacteriol. 2011; 193(22):6418-9. PMC: 3209220. DOI: 10.1128/JB.05380-11. View

13.

Mazur A, Majewska B, Stasiak G, Wielbo J, Skorupska A . repABC-based replication systems of Rhizobium leguminosarum bv. trifolii TA1 plasmids: incompatibility and evolutionary analyses. Plasmid. 2011; 66(2):53-66. DOI: 10.1016/j.plasmid.2011.04.002. View

14.

Dunfield P, Yimga M, Dedysh S, Berger U, Liesack W, Heyer J . Isolation of a Methylocystis strain containing a novel pmoA-like gene. FEMS Microbiol Ecol. 2009; 41(1):17-26. DOI: 10.1111/j.1574-6941.2002.tb00962.x. View

15.

Rasko D, Rosovitz M, Okstad O, Fouts D, Jiang L, Cer R . Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus-group plasmids, including Bacillus anthracis pXO1. J Bacteriol. 2006; 189(1):52-64. PMC: 1797222. DOI: 10.1128/JB.01313-06. View

16.

Baani M, Liesack W . Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2. Proc Natl Acad Sci U S A. 2008; 105(29):10203-8. PMC: 2481331. DOI: 10.1073/pnas.0702643105. View

17.

Dam B, Ghosh W, Das Gupta S . Conjugative Type 4 secretion system of a novel large plasmid from the chemoautotroph Tetrathiobacter kashmirensis and construction of shuttle vectors for Alcaligenaceae. Appl Environ Microbiol. 2009; 75(13):4362-73. PMC: 2704820. DOI: 10.1128/AEM.02521-08. View

18.

Carver T, Berriman M, Tivey A, Patel C, Bohme U, Barrell B . Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics. 2008; 24(23):2672-6. PMC: 2606163. DOI: 10.1093/bioinformatics/btn529. View

19.

Stein L, Klotz M . Nitrifying and denitrifying pathways of methanotrophic bacteria. Biochem Soc Trans. 2011; 39(6):1826-31. DOI: 10.1042/BST20110712. View

20.

Chai Y, Winans S . A small antisense RNA downregulates expression of an essential replicase protein of an Agrobacterium tumefaciens Ti plasmid. Mol Microbiol. 2005; 56(6):1574-85. DOI: 10.1111/j.1365-2958.2005.04636.x. View