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Announcement
24 October 2013

Genome Sequence of Rhodococcus sp. Strain BCP1, a Biodegrader of Alkanes and Chlorinated Compounds

ABSTRACT

Rhodococcus sp. strain BCP1 cometabolizes chlorinated compounds and mineralizes a broad range of alkanes, as it is highly tolerant to them. The high-quality draft genome sequence of Rhodococcus sp. strain BCP1, consisting of 6,231,823 bp, with a G+C content of 70.4%, 5,902 protein-coding genes, and 58 RNA genes, is presented here.

GENOME ANNOUNCEMENT

The Rhodococcus genus comprises Gram-positive, nonsporulating, aerobic bacteria that are widely distributed in the environment (1). Rhodococcus sp. strain BCP1 (formerly Rhodococcus aetherovorans strain BCP1, DSM 44980) was selected from an aerobic butane-utilizing consortium as the prevailing isolate for cometabolizing chloroform, vinyl chloride, and trichloroethylene (2, 3). As BCP1 also catabolizes a wide range of aliphatic, alicyclic, and carboxylated alkanes, it represents a strain of considerable environmental and industrial interest (4).
The genome sequencing of Rhodococcus sp. BCP1 was performed using 454 sequencing technology (Roche GS FLX Titanium). The total numbers of the sequence reads were 668,686 from one shotgun library and 353,744 from one paired-end library (8-kb inserts). All the reads were assembled into 123 contigs using Newbler 2.6, with an N50 length of 237,787 bp and an average genome coverage of 65×. Based on paired-end directional information, the contigs were further ordered into 3 scaffolds, giving a total genome size of 6.2 Mb with a G+C content of 70.4%.
The annotation was performed by using the Rapid Annotations using Subsystems Technology (RAST) server (5). Two scaffolds constituting a total of ~0.2 Mb are likely to be plasmids, as they carry genetic signatures typical of Rhodococcus plasmids.
A total of putative 5,902 open reading frames (ORFs), 8 rRNA genes, and 50 tRNA genes were predicted. RAST annotation indicates that the strains Rhodococcus jostii RHA1 (score, 529) and Rhodococcus opacus B4 (score, 510) are the closest neighbors of strain BCP1. The subsystem categories representing the metabolisms of carbohydrates, amino acids and cofactors, vitamins, prosthetic groups, and pigments are the most abundant, as they account for 623, 565, and 429 proteins, respectively. Four hundred fifteen ORFs are involved in the metabolism of fatty acids, lipids, and isoprenoids, while 135 ORFs participate in the metabolism of aromatic compounds. Seventy-three oxygenases/hydroxylases among the 134 annotated genes are predicted to initiate the oxidation of organic compounds with industrial and environmental relevancy, such as linear alkanes, cyclic ketones, aromatic compounds (e.g., benzoate, catechol, gentisate, salicylate), aminopolycarboxylic acids, nitroalkanes, and phenylalkanoic acids. Twenty-six ORFs encode cytochrome P450 monooxygenases that catalyze regio- and stereospecific oxidation of a large number of substrates (6).

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AVAE00000000. The version described in this paper is version AVAE01000000.

ACKNOWLEDGMENTS

This research was supported by the Italian Ministry of Education and Research through the Flagship (PB05) “Interomics,” HIRMA (RBAP11YS7K), the European “MIMOMICS” projects, and the PAIN project—Regione Autonoma della Sardegna.
M.C. and A.P. are the recipients of postdoctoral and PhD fellowships, respectively, from the University of Bologna (Bo-I).

REFERENCES

1.
Martínková L, Uhnáková B, Pátek M, Nesvera J, and Kren V. 2009. Biodegradation potential of the genus Rhodococcus. Environ. Int. 35:162–177.
2.
Frascari D, Pinelli D, Nocentini M, Fedi S, Pii Y, and Zannoni D. 2006. Chloroform degradation by butane-grown cells of Rhodococcus aetherovorans BCP1. Appl. Microbiol. Biotechnol. 73:421–428.
3.
Cappelletti M, Frascari D, Zannoni D, and Fedi S. 2012. Microbial degradation of chloroform. Appl. Microbiol. Biotechnol. 96:1395–1409.
4.
Cappelletti M, Fedi S, Frascari D, Ohtake H, Turner RJ, and Zannoni D. 2011. Analyses of both the alkB gene transcriptional start site and alkB promoter-inducing properties of Rhodococcus sp. strain BCP1 grown on n-alkanes. Appl. Environ. Microbiol. 77:1619–1627.
5.
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, and Zagnitko O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75.
6.
Urlacher VB and Girhard M. 2012. Cytochrome P450 monooxygenases: an update on perspectives for synthetic application. Trends Biotechnol. 30:26–36.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 1Number 531 October 2013
eLocator: 10.1128/genomea.00657-13

History

Received: 12 August 2013
Accepted: 27 September 2013
Published online: 24 October 2013

Contributors

Authors

M. Cappelletti
Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
P. Di Gennaro
Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
P. D'Ursi
CNR, Institute for Biomedical Technologies, Segrate (MI), Italy
A. Orro
CNR, Institute for Biomedical Technologies, Segrate (MI), Italy
A. Mezzelani
CNR, Institute for Biomedical Technologies, Segrate (MI), Italy
M. Landini
CNR, Institute for Biomedical Technologies, Segrate (MI), Italy
S. Fedi
Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
D. Frascari
Department of Civil, Chemical, Environmental, and Materials Engineering, University of Bologna, Bologna, Italy
A. Presentato
Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
D. Zannoni
Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
L. Milanesi
CNR, Institute for Biomedical Technologies, Segrate (MI), Italy

Notes

Address correspondence to D. Zannoni, [email protected].

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