title: Complete genome sequence of the soil actinomycete Kocuria rhizophila.
abstract: The soil actinomycete Kocuria rhizophila belongs to the suborder Micrococcineae, a divergent bacterial group for which only a limited amount of genomic information is currently available. K. rhizophila is also important in industrial applications; e.g., it is commonly used as a standard quality control strain for antimicrobial susceptibility testing. 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 conservation of 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.
authors.affiliation: NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
authors.forename: Hiromi
authors.initials: H
authors.lastname: Takarada
authors.forename: Mitsuo
authors.initials: M
authors.lastname: Sekine
authors.forename: Hiroki
authors.initials: H
authors.lastname: Kosugi
authors.forename: Yasunori
authors.initials: Y
authors.lastname: Matsuo
authors.forename: Takatomo
authors.initials: T
authors.lastname: Fujisawa
authors.forename: Seiha
authors.initials: S
authors.lastname: Omata
authors.forename: Emi
authors.initials: E
authors.lastname: Kishi
authors.forename: Ai
authors.initials: A
authors.lastname: Shimizu
authors.forename: Naofumi
authors.initials: N
authors.lastname: Tsukatani
authors.forename: Satoshi
authors.initials: S
authors.lastname: Tanikawa
authors.forename: Nobuyuki
authors.initials: N
authors.lastname: Fujita
authors.forename: Shigeaki
authors.initials: S
authors.lastname: Harayama
mesh_terms: D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D016680:Genome, Bacterial; D008835:Micrococcaceae / Q000145:classification / Q000235:genetics*; D008954:Models, Biological; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial