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Gemmatimonas aurantiaca T-27T (= NBRC 100505T)

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close this sectionAbout this Microorganism


Courtesy of Dr. Hanada in Advanced Industrial Science and Technology (AIST)

Gemmatimonas aurantiaca T-27 (= NBRC 100505) was isolated as a slow growing bacterium from an anaerobic-aerobic sequential batch reactor operated under enhanced biological phosphorous removal (EBPR) conditions for wastewater treatment. The 16S rRNA sequence analysis indicated that the isolate was phylogenetically distant from any known bacterial species. This led to the proposal, for the first time in Japan, of a new valid phylum, Gemmatimonadetes. Members of the phylum Gemmatimonadetes are frequently found by culture-independent surveys in various environments, such as soils and sponges, but only a few isolates were reported to date. Physiological and metabolic features of microbes belonging to this phylum were therefore hardly characterized.

Genome analysis of G. aurantiaca T-27 revealed a circular chromosome consisting of 4,636,964 bp with 64.28% G+C content. 3,935 open reading frames, 48 tRNA genes and single rRNA operon were predicted. Many of the essential genes identified in model organisms such as Escherichia coli and Bacillus subtilis were also found in G. aurantiaca T-27 genome, suggesting that basic cellular systems were not much different from other microbes. Pathway reconstruction suggested that G. aurantiaca T-27 could grow both under aerobic and anaerobic conditions, being consistent with the operating conditions of the anaerobic-aerobic sequential batch reacter which this bacterium was isolated from. Furthermore, G. auratiaca T-27 genome encoded significantly large numbers of signal transduction components, sigma factors and transporters. These genomic features would provide an insight into the life style of G. aurantiaca, and facilitate isolation of not-yet-cultivated Gemmatimonadetes species.

close this sectionProject history

close this date 2012-05-15 ..... 1
2012-05-15 Release of proteome analysis result of Gemmatimonas aurantiaca T-27T
imageWe have analyzed the proteome of Gemmatimonas aurantiaca T-27T by using the following method; 2D-PAGE followed by N-terminal amino acid sequencing.

close this sectionSummary of the genomic data

GA1
Genomic size 4,636,964 bp
G+C content 64.27 %
Number of ORFs assigned 3,935
Percentage of the coding regions 92.14 %
Percentage of the intronic regions 0.00 %
Number of rRNA genes 3
5S16S23S
111
Number of tRNA genes 48
AlaArgAsnAspCysGln
342112
GluGlyHisIleLeuLys
241152
MetPheProSerThrTrp
313531
TyrVal
13
Number of other features
(misc_RNA,misc_feature,repeat)
18
repeat_region
18

close this sectionGeneral Procedure

The nucleotide sequence of the G. aurantiaca T-27T 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 1.5 and 5.0kb in pUC18 vector (TAKARA) was constructed.

  • Fosmid library
    A Fosmid library with inserts of 40 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 end-sequencing was carried out using BaseStation DNA Fragment Analyzer BST-0100 (MJ Research Inc.).
    Raw sequence data corresponding to approximately 15-fold coverage were assembled using PHRED/PHRAP/CONSED software (http://www.phrap.org).

  • Gap closing
    Fosmid end sequences were mapped onto the assembled sequence.
    Fosmid clones that link two contigs were selected and sequenced by primer walking and PCR amplification to close gaps.
    In some cases, Fosmid clones were subcloned by insertion of Entranceposon using Template Generation System II Kit (Finnzymes) and sequenced.

  • Validation of the assembled sequence data
    In construction of final nucleotide sequence, low-quality regions with a Phrap quality score of less than 40 were re-sequenced and verified. Finally, each base of genome was successfully ensured to be sequenced from Phrap quality value more than 40.

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, Glimmer, GeneHacker, GeneMark prediction tools were used and manually inspected.

  • 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