Abstract
We announce the completion of the genome sequence of a phenol derivative-degrading bacterium, Rhodococcus erythropolis strain CCM2595. This bacterium is interesting in the context of bioremediation for its capability to degrade phenol, catechol, resorcinol, hydroxybenzoate, hydroquinone, p-chlorophenol, p-nitrophenol, pyrimidines, and sterols.
GENOME ANNOUNCEMENT
Members of the genus Rhodococcus possess a wide range of metabolic capabilities applicable for biodegradation of diverse environmental pollutants (1, 2) and for various biotransformations (3, 4). The strain Rhodococcus erythropolis CCM2595 (NCIB8147; JCM3132; ATCC 11048) was isolated from soil. Originally, it was classified as a strain of the species Jensenia canicruria (5). Later, it was reclassified into the species Rhodococcus erythropolis (6). R. erythropolis CCM2595 has been shown to utilize phenol, catechol, resorcinol, hydroxybenzoate, hydroquinone, p-chlorophenol, p-nitrophenol (7), pyrimidines (8), and sterols (9) as carbon sources. In addition to various metabolic activities, some of its characteristics, e.g., resistance to toxic compounds and biofilm formation, have proven useful in the biotechnological industry (10). A host-vector system has been developed for the strain (11), and the methods of genetic manipulation within its chromosome have been established (7). The development of genetic techniques have enabled detailed analysis of the R. erythropolis CCM2595 catRABC gene cluster, which codes for the enzymes of the catechol degradation pathway (12), and construction of recombinant plasmid-carrying R. erythropolis CCM2595 derivatives, which exhibit even more efficient phenol degradation in industrial wastewaters (12). R. erythropolis CCM2595 has also been used for directed biosynthesis of triacylglycerols containing branched-chain fatty acids (13) and ω-phenyl fatty acids (14).
The genome of R. erythropolis CCM2595 was sequenced using 454 GS-FLX technology (15). Whole-genome shotgun sequencing produced 244,559,207 bp of sequencing data in 582,471 reads. The reads were assembled using Newbler 2.5.3 (454 Life Sciences) into 44 contigs with an N50 length of 374,893 bp and an average coverage of 38.3×. All sequencing gaps were closed in Consed 19 (16). The complete genome consists of one circular chromosome (6,281,198 bp) and one circular plasmid (90,223 bp), which is already known as pRECF1 (17). Both replicons have a relatively high GC content of 62.5%.
The complete sequence was searched for putative protein-coding genes using Critica (18), Prodigal (19), and Glimmer (20). Aragorn (21) and tRNAscan (22) were used to localize tRNA and transfer-messenger RNA (tmRNA) genes, and RNAmmer (23) was employed to find rRNA and noncoding RNA (ncRNA) genes. The functions of the predicted protein-coding genes were assigned by the PGAAP pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/). The annotation results were combined and verified within Artemis (24). In total, 5,830 predicted coding regions (CDSs), 12 rRNAs, 53 tRNAs, 1 tmRNA, and 5 ncRNAs were predicted and annotated.
Based on our results, we anticipate that R. erythropolis strain CCM2595 will display rich and complex metabolic capabilities, far beyond the utilization of benzene derivatives or catechol metabolism originally associated with this strain (7, 12).
Nucleotide sequence accession numbers.
The genome sequences were deposited at DDBJ/EMBL/GenBank under the accession numbers CP003761 (chromosome) and CP003762 (plasmid pRECF1).
ACKNOWLEDGMENTS
This project was funded by the Czech Science Foundation (project 13-28283S), the Institute of Molecular Genetics of the ASCR (RVO 68378050), the Czech Ministry of Education, Youth and Sports (AROMAGEN project 2B08062), and the Institute of Microbiology of the ASCR (RVO 61388971).
Footnotes
Citation Strnad H, Patek M, Fousek J, Szokol J, Ulbrich P, Nesvera J, Paces V, Vlcek C. 2014. Genome sequence of Rhodococcus erythropolis strain CCM2595, a phenol derivative-degrading bacterium. Genome Announc. 2(2):e00208-14. doi:10.1128/genomeA.00208-14.
REFERENCES
- 1. Larkin MJ, Kulakov LA, Allen CC. 2005. Biodegradation and Rhodococcus—masters of catabolic versatility. Curr. Opin. Biotechnol. 16:282–290. 10.1016/j.copbio.2005.04.007 [DOI] [PubMed] [Google Scholar]
- 2. Martínková L, Uhnáková B, Pátek M, Nesvera J, Kren V. 2009. Biodegradation potential of the genus Rhodococcus. Environ. Int. 35:162–177. 10.1016/j.envint.2008.07.018 [DOI] [PubMed] [Google Scholar]
- 3. van der Geize R, Dijkhuizen L. 2004. Harnessing the catabolic diversity of rhodococci for environmental and biotechnological applications. Curr. Opin. Microbiol. 7:255–261. 10.1016/j.mib.2004.04.001 [DOI] [PubMed] [Google Scholar]
- 4. Martinkova L, Kren V. 2010. Biotransformations with nitrilases. Curr. Opin. Chem. Biol. 14:130–137. 10.1016/j.cbpa.2009.11.018 [DOI] [PubMed] [Google Scholar]
- 5. Bisset KA, Moore FW. 1950. Jensenia, a new genus of the actinomycetales. J. Gen. Microbiol. 4:280. 10.1099/00221287-4-2-280 [DOI] [PubMed] [Google Scholar]
- 6. Goodfellow M, Alderson G. 1977. The actinomycete-genus Rhodococcus: a home for the “rhodochrous” complex. J. Gen. Microbiol. 100:99–122. 10.1099/00221287-100-1-99 [DOI] [PubMed] [Google Scholar]
- 7. Cejkova A, Masak J, Jirku V, Vesely M, Patek M, Nesvera J. 2005. Potential of Rhodococcus erythropolis as a bioremediation organism. World J. Microbiol. Biotechnol. 21:317–321. 10.1007/s11274-004-2152-1 [DOI] [Google Scholar]
- 8. Soong CL, Ogawa J, Sakuradani E, Shimizu S. 2002. Barbiturase, a novel zinc-containing amidohydrolase involved in oxidative pyrimidine metabolism. J. Biol. Chem. 277:7051–7058. 10.1074/jbc.M110784200 [DOI] [PubMed] [Google Scholar]
- 9. van der Geize R, Hessels GI, van Gerwen R, Vrijbloed JW, van der Meijden P, Dijkhuizen L. 2000. Targeted disruption of the kstD gene encoding a 3-ketosteroid delta(1)-dehydrogenase isoenzyme of Rhodococcus erythropolis strain SQ1. Appl. Environ. Microbiol. 66:2029–2036. 10.1128/AEM.66.5.2029-2036.2000 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Masák J, Cejková A, Jirků V, Kotrba D, Hron P, Siglová M. 2005. Colonization of surfaces by phenolic compounds utilizing microorganisms. Environ. Int. 31:197–200. 10.1016/j.envint.2004.09.015 [DOI] [PubMed] [Google Scholar]
- 11. Veselý M, Pátek M, Nesvera J, Cejková A, Masák J, Jirků V. 2003. Host-vector system for phenol-degrading Rhodococcus erythropolis based on Corynebacterium plasmids. Appl. Microbiol. Biotechnol. 61:523–527. 10.1007/s00253-003-1230-x [DOI] [PubMed] [Google Scholar]
- 12. Veselý M, Knoppová M, Nesvera J, Pátek M. 2007. Analysis of catRABC operon for catechol degradation from phenol-degrading Rhodococcus erythropolis. Appl. Microbiol. Biotechnol. 76:159–168. 10.1007/s00253-007-0997-6 [DOI] [PubMed] [Google Scholar]
- 13. Schreiberová O, Krulikovská T, Sigler K, Cejková A, Rezanka T. 2010. RP-HPLC/MS-APCI analysis of branched chain TAG prepared by precursor-directed biosynthesis with Rhodococcus erythropolis. Lipids 45:743–756. 10.1007/s11745-010-3447-7 [DOI] [PubMed] [Google Scholar]
- 14. Rezanka T, Schreiberová O, Krulikovská T, Masák J, Sigler K. 2010. RP-HPLC/MS-APCI analysis of odd-chain TAGs from Rhodococcus erythropolis including some regioisomers. Chem. Phys. Lipids 163:373–380. 10.1016/j.chemphyslip.2010.01.007 [DOI] [PubMed] [Google Scholar]
- 15. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944–945. 10.1093/bioinformatics/16.10.944 [DOI] [PubMed] [Google Scholar]
- 16. Gordon D, Green P. 2013. Consed: a graphical editor for next-generation sequencing. Bioinformatics 29:2936–2937. 10.1093/bioinformatics/btt515 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17. Knoppová M, Phensaijai M, Veselý M, Zemanová M, Nesvera J, Pátek M. 2007. Plasmid vectors for testing in vivo promoter activities in Corynebacterium glutamicum and Rhodococcus erythropolis. Curr. Microbiol. 55:234–239. 10.1007/s00284-007-0106-1 [DOI] [PubMed] [Google Scholar]
- 18. Badger JH, Olsen GJ. 1999. CRITICA: coding region identification tool invoking comparative analysis. Mol. Biol. Evol. 16:512–524. 10.1093/oxfordjournals.molbev.a026133 [DOI] [PubMed] [Google Scholar]
- 19. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. 10.1186/1471-2105-11-119 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 20. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27:4636–4641. 10.1093/nar/27.23.4636 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 21. Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32:11–16. 10.1093/nar/gkh152 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 22. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955–964. 10.1093/nar/25.5.0955 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 23. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNammer: consistent annotation of ribosomal RNA genes in genomic sequences. Nucleic Acids Res. 35:3100–3108. 10.1093/nar/gkm160 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 24. Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA. 2012. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 28:464–469. 10.1093/bioinformatics/btr703 [DOI] [PMC free article] [PubMed] [Google Scholar]
