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. 2011 Jul;193(13):3399–3400. doi: 10.1128/JB.05109-11

Genome Sequence of the Ethene- and Vinyl Chloride-Oxidizing Actinomycete Nocardioides sp. Strain JS614▿

Nicholas V Coleman 1,*, Neil L Wilson 2, Kerrie Barry 3, Thomas S Brettin 4, David C Bruce 5, Alex Copeland 3, Eileen Dalin 6, John C Detter 5, Tijana Glavina del Rio 3, Lynne A Goodwin 5, Nancy M Hammon 3, Shunsheng Han 5, Loren J Hauser 4, Sanjay Israni 3, Edwin Kim 3, Nikolaos Kyrpides 3, Miriam L Land 4, Alla Lapidus 3, Frank W Larimer 4, Susan Lucas 3, Sam Pitluck 3, Paul Richardson 3, Jeremy Schmutz 7, Roxanne Tapia 5, Sue Thompson 5, Hope N Tice 3, Jim C Spain 8, James G Gossett 9, Timothy E Mattes 10
PMCID: PMC3133255  PMID: 21551312

Abstract

Nocardioides sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and energy sources and is of interest for bioremediation and biocatalysis. Sequencing of the complete genome of JS614 provides insight into the genetic basis of alkene oxidation, supports ongoing research into the physiology and biochemistry of growth on ethene and VC, and provides biomarkers to facilitate detection of VC/ethene oxidizers in the environment. This is the first genome sequence from the genus Nocardioides and the first genome of a VC/ethene-oxidizing bacterium.

GENOME ANNOUNCEMENT

Bacteria in the genus Nocardioides (phylum Actinobacteria) are aerobic, nonmotile, Gram-positive rods found in soil. Nocardioides strains can metabolize unusual substrates, including butane (10), jet fuel (14), phenanthrene (13), p-nitrophenol (31), trinitrophenol (25), atrazine (29), ethene (5), and vinyl chloride (VC) (5).

Nocardioides sp. strain JS614 grows on ethene and VC (4) (5) and may be useful for cleaning up VC-contaminated sites (bioremediation); this is of particular interest due to the carcinogenicity and persistence of VC as a pollutant (15, 26). Strain JS614 is distinguished from other VC degraders (5, 7, 11, 30) by its high activity on VC and its unusual physiology (20). Strain JS614 can also grow on propene and butene (27), fluoroethene (28), and nicotine (9) and has been proposed as a biocatalyst for production of chiral epoxides (23).

Genome sequencing of JS614 was performed by the U.S. DOE Joint Genome Institute (JGI) and Oak Ridge and Los Alamos National Laboratories (ORNL and LANL) using a Sanger shotgun sequencing approach (8). Libraries were constructed in pUC18c (29,009 reads), pMCL200 (35,995 reads), and pCC1FOS (989 reads), giving genome coverage of 5.2-fold, 6.14-fold, and 0.6-fold, respectively. Reads were compiled using the JAZZ assembler (1), and gaps were filled by primer walking, PCR, and the Sequence Finishing kit (Amersham). Prediction of protein coding sequences was done via the Glimmer (6) and Critica (2) software programs, with manual confirmation via BLAST against protein databases. Other sequence features were identified using tRNAscan-RE (18), TMHMM (17), and signalP (3).

The complete JS614 genome (5.3 Mb) consists of a single circular 4,985,871-bp chromosome and one 307,814-bp plasmid (pNOCA01). Although the plasmid was annotated as circular, pulsed-field gel electrophoresis experiments indicated that this element is linear (21). The average GC content of the chromosome is 71.65%, while that of the plasmid is 68.01%. The chromosome contains 4,645 putative protein-coding genes, 46 tRNAs, and two rRNA operons. The plasmid contains 256 protein-coding genes. In total, 3,457 genes (69%) had function predictions.

The genome sequence confirms that pNOCA01 carries ethene/VC catabolic genes and coenzyme M biosynthesis genes (16, 19). Like the propene-catabolic genes of Xanthobacter Py2 (NC_009717), the ethene/VC catabolic genes of JS614 have been subject to IS-mediated deletions and duplications. Plasmid pNOCA01 also carries core metabolic genes (encoding cytochrome c oxidase and pyruvate dehydrogenase) and a mercury resistance operon. The putative replication gene (Noca_4704, dnaA homolog) and conjugation coupling gene (Noca_4706, traG homolog) of pNOCA01 have very high similarity to those of the Arthrobacter plasmid pTC1 (22).

A cluster of 10 putative conjugation genes (between Noca_2220 and Noca_2233) similar to those of linear plasmids (24) occurs in the chromosome; this could indicate an integrated plasmid or genomic island. A putative prophage is also present (tape-measure, terminase, and primosome genes; Noca_550, Noca_555, and Noca_570). Other features of interest include a chromate resistance operon (12) and a respiratory nitrate reductase (Noca_1346 to Noca_1349); the latter suggests JS614 could grow anaerobically by denitrification.

Nucleotide sequence accession numbers.

The Nocardioides JS614 sequences have been deposited in GenBank under accession numbers CP000509 and CP000508.

Acknowledgments

This work was performed under the auspices of the U.S. Department of Energy's Office of Science, Biological and Environmental Research Program and by the University of California, Lawrence Livermore National Laboratory, under contract no. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract no. DE-AC03-76SF00098, and Los Alamos National Laboratory under contract no. W-7405-ENG-36.

Footnotes

▿

Published ahead of print on 6 May 2011.

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