Open access
Announcement
20 March 2014

Genome Sequence of Rhodococcus erythropolis Strain CCM2595, a Phenol Derivative-Degrading Bacterium

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).

REFERENCES

1.
Larkin MJ, Kulakov LA, and Allen CC. 2005. Biodegradation and Rhodococcus—masters of catabolic versatility. Curr. Opin. Biotechnol. 16:282–290.
2.
Martínková L, Uhnáková B, Pátek M, Nesvera J, and Kren V. 2009. Biodegradation potential of the genus Rhodococcus. Environ. Int. 35:162–177.
3.
van der Geize R and Dijkhuizen L. 2004. Harnessing the catabolic diversity of rhodococci for environmental and biotechnological applications. Curr. Opin. Microbiol. 7:255–261.
4.
Martinkova L and Kren V. 2010. Biotransformations with nitrilases. Curr. Opin. Chem. Biol. 14:130–137.
5.
Bisset KA and Moore FW. 1950. Jensenia, a new genus of the actinomycetales. J. Gen. Microbiol. 4:280.
6.
Goodfellow M and Alderson G. 1977. The actinomycete-genus Rhodococcus: a home for the “rhodochrous” complex. J. Gen. Microbiol. 100:99–122.
7.
Cejkova A, Masak J, Jirku V, Vesely M, Patek M, and Nesvera J. 2005. Potential of Rhodococcus erythropolis as a bioremediation organism. World J. Microbiol. Biotechnol. 21:317–321.
8.
Soong CL, Ogawa J, Sakuradani E, and Shimizu S. 2002. Barbiturase, a novel zinc-containing amidohydrolase involved in oxidative pyrimidine metabolism. J. Biol. Chem. 277:7051–7058.
9.
van der Geize R, Hessels GI, van Gerwen R, Vrijbloed JW, van der Meijden P, and 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.
Masák J, Cejková A, Jirků V, Kotrba D, Hron P, and Siglová M. 2005. Colonization of surfaces by phenolic compounds utilizing microorganisms. Environ. Int. 31:197–200.
11.
Veselý M, Pátek M, Nesvera J, Cejková A, Masák J, and Jirků V. 2003. Host-vector system for phenol-degrading Rhodococcus erythropolis based on Corynebacterium plasmids. Appl. Microbiol. Biotechnol. 61:523–527.
12.
Veselý M, Knoppová M, Nesvera J, and Pátek M. 2007. Analysis of catRABC operon for catechol degradation from phenol-degrading Rhodococcus erythropolis. Appl. Microbiol. Biotechnol. 76:159–168.
13.
Schreiberová O, Krulikovská T, Sigler K, Cejková A, and Rezanka T. 2010. RP-HPLC/MS-APCI analysis of branched chain TAG prepared by precursor-directed biosynthesis with Rhodococcus erythropolis. Lipids 45:743–756.
14.
Rezanka T, Schreiberová O, Krulikovská T, Masák J, and Sigler K. 2010. RP-HPLC/MS-APCI analysis of odd-chain TAGs from Rhodococcus erythropolis including some regioisomers. Chem. Phys. Lipids 163:373–380.
15.
Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, and Barrell B. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944–945.
16.
Gordon D and Green P. 2013. Consed: a graphical editor for next-generation sequencing. Bioinformatics 29:2936–2937.
17.
Knoppová M, Phensaijai M, Veselý M, Zemanová M, Nesvera J, and Pátek M. 2007. Plasmid vectors for testing in vivo promoter activities in Corynebacterium glutamicum and Rhodococcus erythropolis. Curr. Microbiol. 55:234–239.
18.
Badger JH and Olsen GJ. 1999. CRITICA: coding region identification tool invoking comparative analysis. Mol. Biol. Evol. 16:512–524.
19.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, and Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119.
20.
Delcher AL, Harmon D, Kasif S, White O, and Salzberg SL. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27:4636–4641.
21.
Laslett D and Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32:11–16.
22.
Lowe TM and Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955–964.
23.
Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, and Ussery DW. 2007. RNammer: consistent annotation of ribosomal RNA genes in genomic sequences. Nucleic Acids Res. 35:3100–3108.
24.
Carver T, Harris SR, Berriman M, Parkhill J, and McQuillan JA. 2012. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 28:464–469.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 2Number 21 May 2014
eLocator: 10.1128/genomea.00208-14

History

Received: 21 February 2014
Accepted: 27 February 2014
Published online: 20 March 2014

Contributors

Authors

Hynek Strnad
Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
Miroslav Patek
Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
Jan Fousek
Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
Present address: Jan Fousek, Institute of Experimental Botany AS CR, Prague, Czech Republic.
Juraj Szokol
Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
Pavel Ulbrich
Department of Biochemistry and Microbiology, Institute of Chemical Technology, Prague, Czech Republic
Jan Nesvera
Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
Vaclav Paces
Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
Cestmir Vlcek
Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic

Notes

Address correspondence to Hynek Strnad, [email protected], or Cestmir Vlcek, [email protected].

Metrics & Citations

Metrics

Note:

  • For recently published articles, the TOTAL download count will appear as zero until a new month starts.
  • There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.
  • Citation counts come from the Crossref Cited by service.

Citations

If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. For an editable text file, please select Medlars format which will download as a .txt file. Simply select your manager software from the list below and click Download.

View Options

Figures and Media

Figures

Media

Tables

Share

Share

Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy