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Aspergillus oryzae RIB40
Saccharomyces cerevisiae K7
Aeropyrum pernix K1T
Sulfolobus tokodaii strain 7T
Methanocella paludicola SANAET
Pyrococcus horikoshii OT3T
Kitasatospora setae NBRC 14216T
Rhodococcus opacus B4
Rhodococcus erythropolis PR4
Kocuria rhizophila DC2201
Microlunatus phosphovorus NM-1T
Corynebacterium efficiens YS-314T
Streptomyces avermitilis MA-4680T
Caldisericum exile AZM16c01T
Anaerolinea thermophila UNI-1T
Arthrospira platensis NIES-39
Deferribacter desulfuricans SSM1T
Staphylococcus haemolyticus JCSC1435
Staphylococcus aureus MW2
Staphylococcus aureus N315
Brevibacillus brevis NBRC 100599
Tetragenococcus halophilus NBRC 12172
Oscillibacter valericigenes Sjm18-20T
Gemmatimonas aurantiaca T-27T
Acetobacter pasteurianus IFO 3283-32
Acidiphilium multivorum AIU301
Sphingobium japonicum UT26S
Sphingobium sp. SYK-6
Desulfovibrio magneticus RS-1
Salmonella enterica serovar Typhimurium T000240
About this genome
Whole genome sequence of
strain RS-1 revealed common gene clusters in magnetotactic bacteria.
Nakazawa H.,Arakaki A.,Narita-Yamada S.,Yashiro I.,Jinno K.,Aoki N.,Tsuruyama A.,Okamura Y.,Tanikawa S.,Fujita N.,Takeyama H.,Matsunaga T.
Genome Res. 19 (2009) 1801-8
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.
Proteomic analysis of irregular, bullet-shaped magnetosomes in the sulphate-reducing magnetotactic bacterium
Matsunaga T.,Nemoto M.,Arakaki A.,Tanaka M.
Proteomics 9 (2009) 3341-3352
Recent molecular studies on magnetotactic bacteria have identified a number of proteins associated with bacterial magnetites (magnetosomes) and elucidated their importance in magnetite biomineralisation. However, these analyses were limited to magnetotactic bacterial strains belonging to the alpha-subclass of Proteobacteria. We performed a proteomic analysis of magnetosome membrane proteins in Desulfovibrio magneticus strain RS-1, which is phylogenetically classified as a member of the delta-Proteobacteria. In the analysis, the identified proteins were classified based on their putative functions and compared with the proteins from the other magnetotactic bacteria, Magnetospirillum magneticum AMB-1 and M. gryphiswaldense MSR-1. Three magnetosome-specific proteins, MamA (Mms24), MamK, and MamM, were identified in strains RS-1, AMB-1, and MSR-1. Furthermore, genes encoding ten magnetosome membrane proteins, including novel proteins, were assigned to a putative magnetosome island that contains subsets of genes essential for magnetosome formation. The collagen-like protein and putative iron-binding proteins, which are considered to play key roles in magnetite crystal formation, were identified as specific proteins in strain RS-1. Furthermore, genes encoding two homologous proteins of Magnetococcus MC-1 were assigned to a cryptic plasmid of strain RS-1. The newly identified magnetosome membrane proteins might contribute to the formation of the unique irregular, bullet-shaped crystals in this microorganism.
Formation of magnetite by bacteria and its application.
Arakaki A.,Nakazawa H.,Nemoto M.,Mori T.,Matsunaga T.
J R Soc Interface 5 (2008) 977-99
Magnetic particles offer high technological potential since they can be conveniently collected with an external magnetic field. Magnetotactic bacteria synthesize bacterial magnetic particles (BacMPs) with well-controlled size and morphology. BacMPs are individually covered with thin organic membrane, which confers high and even dispersion in aqueous solutions compared with artificial magnetites, making them ideal biotechnological materials. Recent molecular studies including genome sequence, mutagenesis, gene expression and proteome analyses indicated a number of genes and proteins which play important roles for BacMP biomineralization. Some of the genes and proteins identified from these studies have allowed us to express functional proteins efficiently onto BacMPs, through genetic engineering, permitting the preservation of the protein activity, leading to a simple preparation of functional protein-magnetic particle complexes. They were applicable to high-sensitivity immunoassay, drug screening and cell separation. Furthermore, fully automated single nucleotide polymorphism discrimination and DNA recovery systems have been developed to use these functionalized BacMPs. The nano-sized fine magnetic particles offer vast potential in new nano-techniques.
sp. nov., a novel sulfate-reducing bacterium that produces intracellular single-domain-sized magnetite particles.
Sakaguchi T.,Arakaki A.,Matsunaga T.
Int. J. Syst. Evol. Microbiol. 52 (2002) 215-21
A novel type of dissimilatory sulfate-reducing bacterium, designated strain RS-1T, capable of producing intracellular magnetite particles (magnetosomes) was isolated from freshwater sulfide-rich sediments. Phylogenetic analysis based on 16S rDNA sequences revealed that RS-1T is a member of the genus Desulfovibrio. Its closest known relative is Desulfovibrio burkinensis (sequence similarity of 98.7%). Strain RS-1T contains desulfoviridin, c-type cytochromes and, unlike other Desulfovibrio spp., it possesses menaquinone MK-7(H2) instead of MK-6 or MK-6(H2). Strain RS-1T is also unique compared with other members of Desulfovibrio in its ability to synthesize intracellular magnetite particles. A novel species, Desulfovibrio magneticus sp. nov., is proposed for RS-1T (= ATCC 700980T = DSM 13731T), a sulfate-reducing magnetotactic bacterium.
Cadmium recovery by a sulfate-reducing magnetotactic bacterium,
RS-1, using magnetic separation.
Arakaki A.,Takeyama H.,Tanaka T.,Matsunaga T.
Appl. Biochem. Biotechnol. 98-100 (2002) 833-40
Cadmium recovery by a sulfate-reducing magnetotactic bacterium, Desulfovibrio magneticus strain RS-1, was investigated. D. magneticus precipitated >95% of cadmium at an initial concentration of 1.3 ppm in the growth medium. Electron microscopic analysis revealed that D. magneticus formed electron-dense particles on its surface when cultivated in the presence of cadmium ions (Cd2+). Sulfide was also found in the precipitate, and the composition ratio of sulfide/cadmium was 0.7. Sixty percent of viable RS-1 cells was recovered by a simple magnetic separation revealing the removal of 58% cadmium from the culture medium.
Magnetite formation by a sulphate-reducing bacterium.
Sekiguchi T., Burgess JG., Matsunaga T.
Nature 365 (1993) 47-49
BACTERIAL production of magnetite (Fe3O4)1 makes an important contribution to iron biomineralization and rcmanent magnetization of sediments2,3. Accurate magnetostratigraphy, reconstruction of the Earth's past magnetic-field behaviour and extraction of environmental information from the geomagnetic record depend on an understanding of the conditions under which bacterial magnetite is formed. In aquatic sediments, the process is thought to be restricted to a zone between the levels at which nitrate and iron reduction occur4. In sulphate-reducing habitats, deeper in the sediment, the presence of H2S reduces iron oxyhydroxides to iron sulphides5,6. Thus magnetite would not be expected to form under such reducing conditions5,7. We report here the isolation and pure culture of a dissimilatory sulphate-reducing bacterium, designated RS-1, which can synthesize intracellular magnetite particles. RS-1 is a freshwater anaerobe which is also capable of extracellular iron sulphide precipitation. This isolate illustrates the wider meta-bolic diversity of magnetic bacteria and suggests the presence of a novel mechanism of magnetic biomineralization. The discovery of such bacteria may also explain why large quantities of magnetite have been observed in sulphate-rich, oil-bearing, sedimentary deposits8–11. In addition, these results significantly enlarge the environments in which biogenic magnetite may be expected to occur and have important implications regarding the evolution of the ability to synthesize magnetite.
National Institute of Technology and Evaluation
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