title: Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria.
abstract: Magnetotactic bacteria are ubiquitous microorganisms that synthesize intracellular magnetite particles (magnetosomes) by accumulating Fe ions from aquatic environments. Recent molecular studies, including comprehensive proteomic, transcriptomic, and genomic analyses, have considerably improved our hypotheses of the magnetosome-formation mechanism. However, most of these studies have been conducted using pure-cultured bacterial strains of alpha-proteobacteria. Here, we report the whole-genome sequence of Desulfovibrio magneticus strain RS-1, the only isolate of magnetotactic microorganisms classified under delta-proteobacteria. Comparative genomics of the RS-1 and four alpha-proteobacterial strains revealed the presence of three separate gene regions (nuo and mamAB-like gene clusters, and gene region of a cryptic plasmid) conserved in all magnetotactic bacteria. The nuo gene cluster, encoding NADH dehydrogenase (complex I), was also common to the genomes of three iron-reducing bacteria exhibiting uncontrolled extracellular and/or intracellular magnetite synthesis. A cryptic plasmid, pDMC1, encodes three homologous genes that exhibit high similarities with those of other magnetotactic bacterial strains. In addition, the mamAB-like gene cluster, encoding the key components for magnetosome formation such as iron transport and magnetosome alignment, was conserved only in the genomes of magnetotactic bacteria as a similar genomic island-like structure. Our findings suggest the presence of core genetic components for magnetosome biosynthesis; these genes may have been acquired into the magnetotactic bacterial genomes by multiple gene-transfer events during proteobacterial evolution.
authors.affiliation: NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation, Shibuya-ku, Tokyo, Japan.
authors.forename: Hidekazu
authors.initials: H
authors.lastname: Nakazawa
authors.forename: Atsushi
authors.initials: A
authors.lastname: Arakaki
authors.forename: Sachiko
authors.initials: S
authors.lastname: Narita-Yamada
authors.forename: Isao
authors.initials: I
authors.lastname: Yashiro
authors.forename: Koji
authors.initials: K
authors.lastname: Jinno
authors.forename: Natsuko
authors.initials: N
authors.lastname: Aoki
authors.forename: Ai
authors.initials: A
authors.lastname: Tsuruyama
authors.forename: Yoshiko
authors.initials: Y
authors.lastname: Okamura
authors.forename: Satoshi
authors.initials: S
authors.lastname: Tanikawa
authors.forename: Nobuyuki
authors.initials: N
authors.lastname: Fujita
authors.forename: Haruko
authors.initials: H
authors.lastname: Takeyama
authors.forename: Tadashi
authors.initials: T
authors.lastname: Matsunaga
mesh_terms: D003901:Desulfovibrio / Q000235:genetics* / Q000378:metabolism; D004734:Energy Metabolism / Q000235:genetics; D005798:Genes, Bacterial / Q000502:physiology; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D055944:Magnetosomes / Q000235:genetics; D042201:Magnetospirillum / Q000235:genetics* / Q000378:metabolism; D005810:Multigene Family / Q000502:physiology
references.citation: Science. 2006 Jan 13;311(5758):242-5
references.pmid: 16373532
references.citation: Biochim Biophys Acta. 2008 Jul-Aug;1777(7-8):735-9
references.pmid: 18394423
references.citation: Nat Biotechnol. 2004 May;22(5):554-9
references.pmid: 15077118
references.citation: J Bacteriol. 2008 Jan;190(1):377-86
references.pmid: 17965152
references.citation: Appl Environ Microbiol. 2004 Oct;70(10):6230-9
references.pmid: 15466570
references.citation: Science. 2003 Dec 12;302(5652):1967-9
references.pmid: 14671304
references.citation: Appl Biochem Biotechnol. 2000 Spring;84-86:441-6
references.pmid: 10849810
references.citation: Biomaterials. 2007 Dec;28(35):5381-9
references.pmid: 17720242
references.citation: Curr Opin Biotechnol. 2005 Jun;16(3):269-74
references.pmid: 15961027
references.citation: Appl Environ Microbiol. 1994 Oct;60(10):3752-9
references.pmid: 7527204
references.citation: Science. 2002 Jan 4;295(5552):117-9
references.pmid: 11778045
references.citation: J Biol Chem. 1995 Nov 24;270(47):28392-6
references.pmid: 7499342
references.citation: Appl Environ Microbiol. 1995 Sep;61(9):3232-9
references.pmid: 16535116
references.citation: Science. 1993 Feb 5;259(5096):803-6
references.pmid: 17809345
references.citation: Appl Environ Microbiol. 2004 Feb;70(2):1040-50
references.pmid: 14766587
references.citation: Environ Microbiol. 2009 May;11(5):1267-77
references.pmid: 19220405
references.citation: Proteomics. 2006 Oct;6(19):5234-47
references.pmid: 16955514
references.citation: Mol Pathol. 2002 Feb;55(1):55-7
references.pmid: 11836448
references.citation: Appl Environ Microbiol. 2009 Jul;75(14):4835-52
references.pmid: 19465526
references.citation: Appl Environ Microbiol. 1993 Mar;59(3):734-42
references.pmid: 16348888
references.citation: Prog Biophys Mol Biol. 2005 Nov;89(3):292-329
references.pmid: 15950057
references.citation: J Bacteriol. 2007 Jul;189(13):4899-910
references.pmid: 17449609
references.citation: J Biol Chem. 2003 Mar 7;278(10):8745-50
references.pmid: 12496282
references.citation: FEMS Microbiol Lett. 1995 Mar 1;126(3):277-82
references.pmid: 7537237
references.citation: J Bacteriol. 2005 Nov;187(21):7176-84
references.pmid: 16237001
references.citation: DNA Res. 2005;12(3):157-66
references.pmid: 16303747
references.citation: Syst Appl Microbiol. 2006 Jul;29(5):349-57
references.pmid: 16644169
references.citation: J Bacteriol. 2006 Mar;188(6):2275-9
references.pmid: 16513757
references.citation: Microsc Res Tech. 1994 Apr 1;27(5):389-401
references.pmid: 8018991
references.citation: Appl Environ Microbiol. 2001 Oct;67(10):4573-82
references.pmid: 11571158
references.citation: Int J Syst Evol Microbiol. 2002 Jan;52(Pt 1):215-221
references.pmid: 11837306
references.citation: FEBS Lett. 2006 Feb 6;580(3):801-12
references.pmid: 16423350
references.citation: Appl Environ Microbiol. 2006 Sep;72(9):5757-65
references.pmid: 16957191
references.citation: Microbiol Rev. 1981 Jun;45(2):316-54
references.pmid: 7022156
references.citation: Trends Biotechnol. 2007 Apr;25(4):182-8
references.pmid: 17306901
references.citation: Science. 2006 Jan 20;311(5759):371-4
references.pmid: 16424338
references.citation: Nature. 2006 Mar 2;440(7080):110-4
references.pmid: 16299495
references.citation: Nat Rev Microbiol. 2004 Mar;2(3):217-30
references.pmid: 15083157
references.citation: Appl Environ Microbiol. 1993 Aug;59(8):2397-403
references.pmid: 16349008