Desulfovibrio magneticus RS-1 (= NBRC 104933)
open/close allAbout this Microorganism
Courtesy of Dr. Matsunaga in Tokyo University of Agriculture and Technology
Magnetotactic bacteria make magnetosomes (small membrane-encapsulated magnetites with 30-50nm diameter) in the cells, and swim along the external magnetic field. They are found in both fresh water and seawater sediments, and have various cell shapes such as vibrio, cocci, and spillum. On the other hand, sulfate-reducing bacteria such as those of the genus Desulfovibrio are known to be gram-negative, obligately anaerobic bacteria. They produce hydrogen sulfide by the reduction of sulfate and other oxidized sulfur compounds along with the oxidation of organic compounds, thus playing an important role in the sulfur cycle.
Desulfovibrio magneticus RS-1 (= NBRC 104933) is so far the only magnetotactic bacterium isolated from the group of sulfate-reducing bacteria belonging to delta-proteobacteria, while most of the other characterized magnetotactic bacteria belong to alpha-proteobacteria. It was isolated from the sediment of a waterway near the Kameno river in the Wakayama prefecture.
Genome analysis revealed that the genome of Desulfovibrio magneticus RS-1 consists of a circular chromsome (5,248,049bp) and two circular plasmids (pDMC1: 58,704bp, pDMC2: 8,867bp). Detailed comparison with other sequenced genomes of magnetotactic bacteria, which all belong to alpha-proteobacteria, will elucidate the molecular and evolutionary mechanisms of magnetosome synthesis. The genomic data may also facilitate the utilization of this bacterium in various fields of biotechnology such as the production of industrially useful magnetic materials and the exploitation of the characteristics of sulfate-reducing bacteria in bioremediation.
Project history
2009-08-12 ..... 1
Desulfovibrio magneticus RS-1 database was updated (We changed information of several ORFs)  | List of ORFs updated in annotation
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Summary of the genomic data
| Genomic size | 5,315,620 bp | ||||||||||||||||||||||||||||||||||||||||||||||||||
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| G+C content | 62.67 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
| Number of ORFs assigned | 4,706 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| Percentage of the coding regions | 87.15 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
| Percentage of the intronic regions | 0.00 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
| Number of rRNA genes |
9
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| Number of tRNA genes |
51
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| Number of other features (misc_RNA,misc_feature,repeat) |
1
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General Procedure
The nucleotide sequence of the D. magneticus RS-1 genome was determined by the whole genome shotgun sequencing method as in the case of other organisms analyzed at NITE-DOB.
General Procedure
- DNA shotgun library
DNA shotgun library with inserts of 2-5 kb in pUC118 vector (TAKARA) was constructed. - Cosmid library
A Cosmid library with inserts of 40 kb in the SuperCos-1 cosmid vector was constructed using the SuperCos1 Cosmid Vector Kit (STRATAGENE). - Nucleotide sequencing
Plasmid clones were end-sequenced using dye-terminator chemistry on an ABI PRISM3700 sequencer (ABI).
Cosmid DNA was extracted from E. coli transformants using the Montage BAC96 MiniPrep Kit (Millipore) and end-sequencing was carried out using dye-terminator chemistry on ABI PRISM3700.
Raw sequence data corresponding to approximately 10-fold coverage were assembled using PHRED/PHRAP/CONSED software (http://www.phrap.org). - Gap closing
Cosmid end sequences were mapped onto the assembled sequence.
Cosmid clones that link two contigs were selected and sequenced by primer walking to close gaps.
The sequencing of difficult templates was performed using the CUGA Sequencing Kit (Nippon Genetech). - Validation of the assembled sequence data
From the final nucleotide sequence, PCR primer sequences were generated at appropriate intervals throughout the genome which were then used to amplify the corresponding genomic regions. The restriction enzyme digestion patterns of each of the PCR fragments thus obtained were accordingly compared with those deduced from the sequence data of the regions to validate the correctness of the assembled sequence data.
Genome analysis and annotation
- Putative nontranslated genes were identified using the Rfam and tRNAscan-SE programs, whereas rRNA genes were identified using the BLASTN program.
- For the identification of protein-coding genes, the genome sequence was translated in six frames to generate potential protein products of open reading frames (ORFs) longer than 90 bp, with ATG, GTG and TTG considered as potential initial codons.
- The potential protein sequences were compared with the UniProt databases using the BLASTP program.
- Potential protein sequences that showed significant similarities to known protein sequences in the database were selected.
- The start sites were manually inspected and altered in comparison to the prediction obtained by GLIMMER and GeneHacker.
- These predicted ORFs were further evaluated using the Frameplot program.
- The translated sequences of the predicted protein-coding genes were searched against the nonredundant UniProt database (version 14.0) and the protein signature database, InterPro version 18.0.
- The KEGG database was used for pathway reconstruction.
- Signal peptides in proteins were predicted using SignalP, whereas transmembrane helices were predicted using TMHMM.
