Abstract
The genus Rhodococcus has proved to be a promising option for the cleanup of polluted sites and application of a microbial biocatalyst. Rhodococcus sp. strain R04, isolated from oil-contaminated soil, can biodegrade polychlorinated biphenyls. Here we report the draft genome sequence of Rhodococcus sp. strain R04, which could be used to predict genes for xenobiotic biodegradation and provide important insights into the applications of this strain.
GENOME ANNOUNCEMENT
The genus Rhodococcus is a very diverse group of bacteria that possess the ability to degrade a large number of organic compounds, including some of the most difficult compounds with respect to recalcitrance and toxicity. Several strains belonging to the genus Rhodococcus have been isolated from various contaminated environments (1, 3, 10, 11, 12), which have proved to be ideal candidates for enhancing the bioremediation of contaminated sites and a wide range of biotransformations, such as steroid modifications, enantioselective synthesis, and the production of amides from nitriles (4, 14).
Rhodococcus sp. strain R04 was isolated from oil-contaminated soil in northern China. Strain R04 was able to biodegrade polychlorinated biphenyls (PCBs) not only via ring cleavage but also through dechlorination (15). In addition, it metabolized phenol, benzoate, and 2-nitropropane when provided as the sole source of carbon and energy and cometabolized pentachlorophenol, dibenzofuran, benzothiophene, and atrazine. It is suggested that strain R04 will potentially be useful in the biotreatment of wastewater and bioremediation of contaminated soils.
The genome sequence of R04 was determined by using the high-throughput Solexa sequencing technology (Illumina GA2x) in Shenzhen, China. Whole-genome shotgun (WGS) sequence data for 825 Mb, giving approximately 92-fold genome coverage, were generated and assembled into 2,548 contigs using SOAPdenovo v.1.04 (7). Furthermore, the contigs were joined into 110 scaffolds (>1 kb in size) using paired-end information. The genome sequence analysis of R04 showed a genome size of 9,125,386 bp, with a mean GC content of 69.62%. Annotation of the open reading frames was performed using Glimmer v.3.0 (2) and by comparison with the corresponding data from the COG, KEGG, Swiss-Prot, TrEMBL, and NR databases. tRNA and rRNA genes were identified by tRNAscan and RNAmmer, respectively (6, 8). There were 9,318 coding sequences (CDSs) with an average length of 826 bp, 99 tRNAs, and 20 rRNAs.
At least 82 genes were found to be potentially involved in xenobiotic metabolism. Among these genes, four extradiol dioxygenase genes (bphC) and two hydrolase genes (bphD) were involved in PCB degradation by R04. In addition, the R04 genome contains at least six ring-hydroxylating dioxygenase genes and 15 cytochrome P450 genes, which enables strain R04 to adapt to catabolize a large number of substrates. Differing from Rhodococcus jostii RHA1 (formerly named by Rhodococcus sp. strain RHA1), whose genome holds two set of polychlorinated biphenyl transformation systems (5), Rhodococcus sp. strain R04 contains only a bph gene cluster consisting of bphA1A2A3A4, bphB, bphC, and bphD (16). In stain R04, ketosteroid-9-α-hydrolase, 3-ketosteroid-δ-dehydrogenase, 3-ketosteroid-1-dehydrogenase, and steroid δ-isomerase are involved in the transformation and metabolism of steroid compounds, and they share 69 to 96% of identity with those of Rhodococcus jostii RHA1, Rhodococcus rhodochrous, and Rhodococcus erythropolis (9, 10, 13). It has been suggested that Rhodococcus sp. R04 is a potential candidate for the industrial production of bioactive steroid compounds.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited into DDBJ/EMBL/GenBank under accession number AFAQ00000000. The version described in this paper is the first version, accession number AFAQ01000000.
Acknowledgments
This research was supported by the National Natural Science Foundation of China (grant 30800030), the Young Science Foundation of Shanxi Province (grant 207021030), and the Natural Science Foundation of Shanxi Province (grant 2007031003).
Footnotes
Published ahead of print on 8 July 2011.
REFERENCES
- 1. Curragh H., et al. 1994. Haloalkane degradation and assimilation by Rhodococcus rhodochrous NCIMB 13064. Microbiology 140:1433–1442 [DOI] [PubMed] [Google Scholar]
- 2. Delcher A. L., Bratke K. A., Powers E. C., Salzberg S. L. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Haroune N., et al. 2004. Metabolism of 2-mercaptobenzothiazole by Rhodococcus rhodochrous. Appl. Environ. Microbiol. 70:6315–6319 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. Kim B. Y., Hyun H. H. 2002. Production of acrylamide using immobilized cells of Rhodococcus rhodochrous M33. Biotechnol. Bioproc. Eng. 7:194–200 [Google Scholar]
- 5. Kitagawa W., et al. 2001. Multiplicity of aromatic ring hydroxylation dioxygenase genes in a strong PCB degrader, Rhodococcus sp. strain RHA1 demonstrated by denaturing gradient gel electrophoresis. Biosci. Biotechnol. Biochem. 65:1907–1911 [DOI] [PubMed] [Google Scholar]
- 6. Lagesen K., et al. 2007. RNAmmer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res. 35:3100–3108 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Li R., et al. 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20:265–272 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Lowe T. M., Eddy S. R. 1997. tRNAscan-SE: a program for improved detection of tRNA genes in genomic sequence. Nucleic Acids Res. 25:955–964 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. McLeod M. P., et al. 2006. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc. Natl. Acad. Sci. U. S. A. 103:15582–15587 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Morii S., et al. 1998. 3-Ketosteroid-delta1-dehydrogenase of Rhodococcus rhodochrous: sequencing of the genomic DNA and hyperexpression, purification, and characterization of the recombinant enzyme. J. Biochem. 124:1026–1032 [DOI] [PubMed] [Google Scholar]
- 11. Prince R. C., Grossman M. J. 2003. Substrate preferences in biodesulfurization of diesel range fuels by Rhodococcus sp. strain ECRD-1. Appl. Environ. Microbiol. 69:5833–5838 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12. Seto M., et al. 1995. A novel transformation of polychlorinated biphenyls by Rhodococcus sp. strain RHA1. Appl. Environ. Microbiol. 61:3353–3358 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. van der Geize R., et al. 2001. Unmarked gene deletion mutagenesis of kstD, encoding 3-ketosteroid delta1-dehydrogenase, in Rhodococcus erythropolis SQ1 using sacB ascounter-selectable marker. FEMS Microbiol. Lett. 205:197–202 [DOI] [PubMed] [Google Scholar]
- 14. Wu Z. L., Li Z. Y. 2003. Highly enantioselective synthesis of α,α-disubstituted malonamic acids through asymmetric hydrolysis of dinitriles with Rhodococcus sp. CGMCC 0497. Chem. Commun. (Camb.) 68:386–387 [DOI] [PubMed] [Google Scholar]
- 15. Yang X. Q., et al. 2007. Characterization and functional analysis of a new gene cluster involved in biphenyl/PCB degradation in Rhodococcus sp. strain R04. J. Appl. Microbiol. 103:2214–2224 [DOI] [PubMed] [Google Scholar]
- 16. Yang X. Q., Sun Y., Qian S. J. 2004. Biodegradation of seven polychlorinated biphenyls by a new isolated aerobic bacterial (Rhodococcus sp. R04). J. Ind. Microbiol. Biotechnol. 31:415–420 [DOI] [PubMed] [Google Scholar]