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Kocuria rhizophila DC2201 (= NBRC 103217)

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close this sectionAbout this Microorganism

Photo by Dr.Tamura, NBRC, NITE.

The soil actinomycete Kocuria rhizophila is a coccoid, gram-positive bacterium. It belongs to the family Micrococcaceae in the suborder Micrococcineae, a divergent bacterial group for which only limited amount of genomic information is currently available. The type strain of K. rhizophila (DSM 11926T) was isolated from the rhizosphere of narrowleaf cattail (Typha angustifolia). The genus Kocuria was created from the genus Micrococcus on the basis of the phylogenetic and chemotaxonomic dissection of the genus Micrococcus. Members of the genus Kocuria were isolated from a wide variety of natural sources including mammalian skin, soil, the rhizosphere, fermented foods, clinical specimens, fresh water and marine sediments. K. rhizophila ATCC 9341, formerly Micrococcus luteus, is designated as a quality-control strain in a number of applications, including susceptibility assays for a variety of antibiotics. K. rhizophila DC2201 (= NBRC 103217) was derived from IFO 12708 and characterized as a strain exhibiting tolerance to a wide variety of organic solvents. The small genome size, the ability to grow rapidly and at high cell density, and the robustness of the cells at various growth conditions would be highly advantageous for the development of bacterial bioconversion system which could be used under harsh conditions such as in organic solvents.

Sequencing and annotation of the genome of K. rhizophila DC2201 (NBRC 103217) revealed a single circular chromosome (2,697,540 bp; G+C content of 71.16%) containing 2,357 predicted protein-coding genes. Most of the predicted proteins (87.7%) were orthologous to actinobacterial proteins, and the genome showed fairly good synteny with taxonomically related actinobacterial genomes. On the other hand, the genome seems to encode much smaller numbers of proteins necessary for secondary metabolism (one each of nonribosomal peptide synthetase and type III polyketide synthase), transcriptional regulation and lateral gene transfer, reflecting the small genome size. The presence of probable metabolic pathways for the transformation of phenolic compounds generated from the decomposition of plant materials, and the presence of a large number of genes associated with membrane transport, particularly amino acid transporters and drug efflux pumps, may contribute to the organism's utilization of root exudates as well as the tolerance to various organic compounds.

This work was conducted as a part of the project "Development of a Technological Infrastructure for Industrial Bioprocesses" of the New Energy and Industrial Technology Development Organization (NEDO), Japan.

close this sectionProject history

close this date 2009-05-09 ..... 1
2009-05-09 Kocuria rhizophila DC2201 database was updated (We changed EC number of several ORFs)
imageList of ORFs updated in annotation
KRH_18830 -

close this sectionSummary of the genomic data

Genomic size 2,697,540 bp
G+C content 71.16 %
Number of ORFs assigned 2,356
Percentage of the coding regions 89.01 %
Percentage of the intronic regions 0.00 %
Number of rRNA genes 9
Number of tRNA genes 46
Number of other features

close this sectionGeneral Procedure

The nucleotide sequence of the K. rhizophila DC2201 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 2-3 kb in pUC118 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 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 10-fold coverage were assembled using PHRED/PHARAP/CONSED software (
  • Gap closing Fosmid end sequences were mapped onto the assembled sequence. Fosmid 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).
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 4.4) and the protein signature database, InterPro version 11.0.
  • 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