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Deferribacter desulfuricans SSM1T (= NBRC 101012T)

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close this sectionAbout this Microorganism


Photo by Dr. Takai in JAMSTEC

Deferribacter desulfuricans SSM1T is thermophilic (optimal temperature 60-65бы) and strictly anaerobic heterotroph capable of using versatile organic compounds. The strain SSM1T has been isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc, JAPAN. Thermophilic microorganisms living on hydrothermal vents are exposed to physically and chemically fluctuating environments. It has also been shown, depending on the hydrothermal vent chimney environment, that Deferribacter-related species are the dominant species in these locations.

The genome of D. desulfuricans SSM1 contains a single circular chromosome of 2,234,389 bp and a megaplasmid (pDF308) of 308,544 bp. Among the 2420 ORFs identified in the D. desulfuricans genome, ~30% of them showed high similarity to those of the species from Deltaproteobacteria, although D. desulfuricans is phylogenetically distant from Deltaproteobacteria. D. desulfuricans especially revealed orthologous relationships to bacteria that possesses sulphur or sulphate-reducing properties. The reconstructed central metabolic pathways from the D. desulfuricans genome showed that various organic acids could be utilize as carbon and energy sources. In addition, numerous genes for chemoreceptors, chemotaxis-like systems and signal transduction machineries encoded in the genome could be linked to the adaptation mechanisms required to survive in variable environments. The genome sequence of D. desulfuricans SSM1 should provide many insights for the better understanding of bacterial life in harsh environments around hydrothermal vents. This is the first complete genome sequence from the phylum Deferribactares.

close this sectionProject history

close this date 2010-03-05 ..... 1
2010-03-05 Release of the Deferribacter desulfuricans SSM1T genomic sequence data
imageWe published the genomic data of Deferribacter desulfuricans SSM1T (= NBRC 101012) including the information of DNA clones distributed from the NBRC.

close this sectionSummary of the genomic data

DD1
Genomic size 2,542,933 bp
G+C content 30.31 %
Number of ORFs assigned 2,420
Percentage of the coding regions 93.16 %
Percentage of the intronic regions 0.00 %
Number of rRNA genes 6
5S16S23S
222
Number of tRNA genes 43
AlaArgAsnAspCysGln
341111
GluGlyHisIleLeuLys
141251
MetPheProSeCSerThr
312143
TrpTyrVal
112
Number of other features
(misc_RNA,misc_feature,repeat)
0

close this sectionGeneral Procedure

The nucleotide sequence of the D. desulfuricans SSM1 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 libraries
    DNA shotgun libraries with inserts of 1.5 and 5 kb in pUC118 vector (TAKARA) was constructed.

  • Fosmid library
    A Fosmid library with inserts of 35 kb in the pCC1FOS fosmid vector was constructed using the CopyControl Fosmid Library Production Kit (Epicentre).

  • Nucleotide sequencing
    Plasmid clones were end-sequenced using dye-terminator chemistry on an ABI PRISM3730 sequencer (ABI).
    Fosmid 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 PRISM3730.
    Raw sequence data corresponding to approximately 15-fold coverage were assembled using PHRED/PHRAP/CONSED suit (http://www.phrap.org).

  • Gap closing
    Gaps between the assembled sequences were closed by primer walking on gap-spanning fosmid closes or with PCR poducts from genomic DNA.


Gene identification and annotation
  • Putative nontranslated genes were identified using the Rfam, tRNAscan-SE programs, whereas rRNA genes were identified using the BLASTN program.

  • For the prediction of protein-coding genes, GLIMMER and GeneMarkS programs were used.

  • The potential protein sequences were further screened with protein databases using the BLASTX program.

  • The start sites were manually inspected and altered in an alignment comparison with the best matches.

  • The translated sequences of the predicted protein-coding genes were searched against the nonredundant database (nr), Uniprot and the protein signature database, Pfam.

  • The KEGG and MetaCyc database was used for pathway reconstruction.

  • Signal peptides in proteins were predicted using SignalP, whereas transmembrane helices were predicted using SOSUI.

  • Cluster of regularly interspaced repeats (CRISPR) were identified using the CRISPRFinder.

close this sectionRelated links to external databases