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.

Genome Sequence of the Fleming Strain of Micrococcus luteus , a Simple Free-Living Actinobacterium

“…1). In common with K. rhizophila, there is no evidence of the global GC skew (preference for G on the leading strand) that is commonly observed in many other bacterial genomes, including those of some of its close relatives, including Arthrobacter aurescens and Renibacterium salmoninarum (78,123,137). Of 2,458 predicted genes, 2,403 encode proteins.…”

“…Following automated annotation of the completed genome sequence, a workshop was held in Jerusalem (13 to 18 April 2008), as part of the IMG expert review process, to compare M. luteus with other closely related actinobacteria and illuminate its relationship to Arthrobacter and Kocuria rhizophila (formerly Sarcina lutea) (123), which are two of its closest relatives. Comparative genomic studies were performed in the context of the Integrated Microbial Genomes system (IMG), v.2.2 (73).…”

Persistent Bloodstream Infection with Kocuria rhizophila Related to a Damaged Central Catheter

“…K. rhizophila is also important in industrial applications and is commonly used as a standard quality control strain for antimicrobial susceptibility testing. In 2008, the complete genome sequence of K. rhizophila was determined by Takarada et al (24).…”

Complete Genome Sequence of the Representative γ-Hexachlorocyclohexane-Degrading Bacterium Sphingobium japonicum UT26

“…One S. japonicum UT26 colony was designated UT26S (NBRC 101211), and its complete genome sequence was determined by a whole-genome shotgun sequencing strategy using the Sanger method (10,15,17). The sequences of ca.…”