Rhodococcus opacus B4 was isolated as an organic solvent-tolerant bacterium from gasoline-contaminated soil. Members of the genus Rhodococcus are common in many environmental niches from soil to sea water and show remarkable metabolic versatility, including their ability to degrade a wide variety of organic compounds. They are high G+C Gram-positive bacteria classified into the order Actinomycetales, suborder Corynebacterineae, and family Nocardiaceae. R. opacus B4 utilize many aromatic and aliphatic hydrocarbons including benzene, toluene, xylene, ethylbenzene, propylbenzene, n-octane and n-decane as sole sources of carbon and energy. R. opacus B4 is able to retain their metabolic activity in organic solvents and therefore to mediate biosynthesis as a whole-cell catalyst.
Genome analysis of R. opacus B4 genome revealed six replicons composed of one linear chromosome (7,913,450 bp, 67.9% G+C, 7,252 ORF), two linear plasmids pROB01 (558,192 bp, 65.8% G+C, 593 ORF), pROB02 (244,997 bp, 64.2% G+C, 248 ORF), and three circular plasmids pKNR (111,160 bp, 65.0% G+C, 102 ORF), pKNR01 (4,367 bp, 64.5% G+C, 6 ORF) and pKNR02 (2,773 bp, 63.8% G+C, 2 ORF). R. opacus B4 genome showed overall conservation of synteny with sequenced Rhodococcus jostii RHA1 genome which also possesses a linear chromosome. R. opacus B4 chromosome is more similar in its gene arrangement to the circular chromosome Nocardia farcinica than those of Mycobacterium tuberculosis and Corynebacterium glutamicum or the linear chromosome of Streptomyces coelicolor, being consistent with their taxonomic relationships. On the other hand, telomeric sequences of the three linear replicons were conserved with other actinomycete invertorons. The genome encodes extremely abundant catabolic pathways for aromatic compounds including benzene, benzoate, phenol, 4-nitrophenol, 4-hydroxybenzoate, p-cumate, catechol, protocatechuate, and phenylacetate. The genome further encodes genes involved in the degradation of various organic compounds including naphthalene, indene, nicotine, thiocarbamate herbicide (EPTC), and thiocyanate. Genome analysis of R. opacus B4 thus provides important insights into biochemical and genetic bases of the metabolic versatility of Rhodococcus.
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.
|Genomic size||8,834,939 bp|
|G+C content||67.62 %|
|Number of ORFs assigned||8,203|
|Percentage of the coding regions||90.37 %|
|Percentage of the intronic regions||0.00 %|
|Number of rRNA genes||
|Number of tRNA genes||
|Number of other features
The nucleotide sequence of the R. opacus B4 genome was determined by the whole genome shotgun sequencing method as in the case of other organisms analyzed at NITE-DOB.