References

Project:

Kocuria rhizophila DC2201 (= NBRC 103217)

About this genome

*Complete genome sequence of the soil actinomycete Kocuria rhizophila.*
Takarada H.,Sekine M.,Kosugi H.,Matsuo Y.,Fujisawa T.,Omata S.,Kishi E.,Shimizu A.,Tsukatani N.,Tanikawa S.,Fujita N.,Harayama S. J. Bacteriol. 190 (2008) 4139-46 [PMID: 18408034] Abstract
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.

Complete genome sequence of the soil actinomycete Kocuria rhizophila.

Takarada H.,Sekine M.,Kosugi H.,Matsuo Y.,Fujisawa T.,Omata S.,Kishi E.,Shimizu A.,Tsukatani N.,Tanikawa S.,Fujita N.,Harayama S.
J. Bacteriol. 190 (2008) 4139-46 [PMID: 18408034] Abstract

Journal

*The cell structural properties of Kocuria rhizophila* for aliphatic alcohol exposure.**
Fujita K., Hagishita T., Kurita S., Kawakura Y., Kobayashi Y., Matsuyama A., Iwahashi H. Enzyme Microb. Tech. 39 (2006) 511-518 Abstract
Abstract: The Gram-positive bacteria Kocuria rhizophila DC2201 were selected from the screening test in order to identify the strains that failed to cause cytolytic by various organic compounds. K. rhizophila have been shown to be much more susceptible to long-chain alcohols than short-chain alcohols as well as other Gram-positive bacteria and Gram-negative Escherichia coli. However, we found the unique cell structural properties of K. rhizophila for aliphatic alcohol exposure. K. rhizophila exposed to alcohols showed no changes significantly in both cytomorphology and cytoplasmic membrane fluidity even when lethal concentrations were used. Meanwhile, alcohols dramatically altered the individual cell size, intracellular structures, and cytoplasmic membrane fluidity of E. coli. These results provide evidence that K. rhizophila has potentially robust cell structures against organic compounds.
*Reclassification of ATCC 9341 from Micrococcus luteus* to Kocuria rhizophila.**
Tang JS.,Gillevet PM. Int. J. Syst. Evol. Microbiol. 53 (2003) 995-7 [PMID: 12892116] Abstract
Abstract: Strain ATCC 9341, currently known as Micrococcus luteus, has been designated as a quality-control strain in a number of applications. It is also cited as the standard culture in several official methods and manuals, as well as the Code of Federal Regulations. Over the years, it has become apparent that ATCC 9341 does not resemble other M. luteus strains; however, its phenotypic characteristics alone were ambiguous. Recently, a polyphasic study was performed in which molecular data were combined with cytochemical properties and physiological characteristics. The results clearly indicate that ATCC 9341 is a member of the genus Kocuria. Thus, it is proposed to reclassify ATCC 9341 as Kocuria rhizophila and to alert users worldwide of this name change.
Kocuria palustris sp. nov. and Kocuria rhizophila sp. nov., isolated from the rhizoplane of the narrow-leaved cattail (Typha angustifolia).
Kovacs, G., J. Burghardt, S. Pradella, P. Schumann, E. Stackebrandt, and K. Marialigeti. Int. J. Syst. Bacteriol. 49 Pt 1 (1999) 167-73 [PMID: 10028258] Abstract
Abstract: Two Gram-positive, aerobic spherical actinobacteria were isolated from the rhizoplane of narrow-leaved cattail (Typha angustifolia) collected from a floating mat in the Soroksár tributary of the Danube river, Hungary. Sequence comparisons of the 16S rDNA indicated these isolates to be phylogenetic neighbours of members of the genus Kocuria, family Micrococcaceae, in which they represent two novel lineages. The phylogenetic distinctness of the two organisms TA68T and TAGA27T was supported by DNA-DNA similarity values of less than 55% between each other and with the type strains of Kocuria rosea, Kocuria kristinae and Kocuria varians. Chemotaxonomic properties supported the placement of the two isolates in the genus Kocuria. The diagnostic diamino acid of the cell-wall peptidoglycan is lysine, the interpeptide bridge is composed of three alanine residues. Predominant menaquinone was MK-7(H2). The fatty acid pattern represents the straight-chain saturated iso-anteiso type. Main fatty acid was anteiso-C15:0. The phospholipids are diphosphatidylglycerol, phosphatidylglycerol and an unknown component. The DNA base composition of strains TA68T and TAGA27T is 69.4 and 69.6 mol% G+C, respectively. Genotypic, morphological and physiological characteristics are used to describe two new species of Kocuria, for which we propose the names Kocuria palustris, type strain DSM 11925T and Kocuria rhizophila, type strain DSM 11926T.
*Taxonomic dissection of the genus Micrococcus: Kocuria* gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend.**
Stackebrandt E.,Koch C.,Gvozdiak O.,Schumann P. Int. J. Syst. Bacteriol. 45 (1995) 682-92 [PMID: 7547287] Abstract
Abstract: The results of a phylogenetic and chemotaxonomic analysis of the genus Micrococcus indicated that it is significantly heterogeneous. Except for Micrococcus lylae, no species groups phylogenetically with the type species of the genus, Micrococcus luteus. The other members of the genus form three separate phylogenetic lines which on the basis of chemotaxonomic properties can be assigned to four genera. These genera are the genus Kocuria gen. nov. for Micrococcus roseus, Micrococcus varians, and Micrococcus kristinae, described as Kocuria rosea comb. nov., Kocuria varians comb. nov., and Kocuria kristinae comb. nov., respectively; the genus Nesterenkonia gen. nov. for Micrococcus halobius, described as Nesterenkonia halobia comb. nov.; the genus Nesterenkonia gen. nov. for Micrococcus halobius, described as Nesterenkonia halobia comb. nov.; the genus Dermacoccus gen. nov. for Micrococcus nishinomiyaensis, described as Dermacoccus nishinomiyaensis comb. nov.; and the genus Kytocossus gen. nov. for Micrococcus sedentarius, described as Kytococcus sedentarius comb. nov. M. luteus and M. lylae, which are closely related phylogenetically but differ in some chemotaxonomic properties, are the only species that remain in the genus Micrococcus Cohn 1872. An emended description of the genus Micrococcus is given [corrected].