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Desulfovibrio magneticus RS-1 (= NBRC 104933)

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close this sectionAbout 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.

close this sectionProject history

close this date 2009-08-12 ..... 1
2009-08-12 Desulfovibrio magneticus RS-1 database was updated (We changed information of several ORFs)
imageList of ORFs updated in annotation

EC
IDoldnew
DMR_02480-.-.-.- 1.12.7.2
DMR_12950-.-.-.- 1.12.7.2
DMR_12960-.-.-.- 1.12.7.2
DMR_39470-.-.-.- 2.7.7.4
DMR_421703.6.1.34 3.6.3.14
DMR_43510-.-.-.- 1.12.7.2

Product
IDoldnew
DMR_05390 adenylylsulphate reductase alpha subunit adenylylsulfate reductase beta subunit
DMR_05400 adenylylsulphate reductase alpha subunit adenylylsulfate reductase alpha subunit
DMR_40940 MamK protein magnetosome protein MamK
DMR_41020 magnetosome protein MamB magnetosome protein MamM
DMR_41070 putative peptidase putative magnetosome protein MamO
DMR_41090 hypothetical protein hypothetical protein MamP
DMR_41100 hypothetical protein hypothetical protein MamT
DMR_41130 LemA family protein magnetosome protein MamQ

Category
IDoldnew
DMR_024209.98 9.2
DMR_036101.6 1.2
DMR_054201.6 1.2
DMR_128409.2 1.2
DMR_128509.2 1.2
DMR_128609.2 1.2
DMR_128709.2 1.2
DMR_128809.2 1.2
DMR_291601.2 9.2
DMR_336209.1 9.2
DMR_357401.2 9.2
DMR_358401.2 9.2
DMR_410709.1 9.2
DMR_435109.1 1.2

Gene
IDoldnew
DMR_41020 mamB mamM
DMR_41070 mamO
DMR_41090 mamP
DMR_41100 mamT
DMR_41130 mamQ

New ORFs
ID
DMR_01580
DMR_09160
DMR_11850
DMR_31330

close this sectionSummary of the genomic data

MAG
Genomic size 5,315,620 bp
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
5S16S23S
333
Number of tRNA genes 51
AlaArgAsnAspCysGln
551212
GluGlyHisIleLeuLys
231352
MetPheProSerThrTrp
313431
TyrVal
13
Number of other features
(misc_RNA,misc_feature,repeat)
1
ydaO-yuaA
1

close this sectionGeneral 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.

close this sectionRelated links to external databases