Abstract
We report the draft genome sequence of Halomonas sp. strain KM-1, which was isolated in Ikeda City, Osaka, Japan, and which produces the bioplastic poly(3-hydroxybutyrate). The total length of the assembled genome is 4,992,811 bp, and 4,220 coding sequences were predicted within the genome. Genes encoding proteins that are involved in the production and depolymerization of poly(3-hydroxybutyrate) were identified. The identification of these genes might be of use in the production of the bioplastic poly(3-hydroxybutyrate) and its monomer 3-hydroxybutyrate.
GENOME ANNOUNCEMENT
Halomonas sp. strain KM-1 was deposited in the International Patent Organism Depositary (IPOD, AIST, Japan) as FERM BP-10995 (3). Strain KM-1 is a heterotrophic gammaproteobacterium that exhibits a higher level of poly(3-hydroxybutyrate) (PHB) production under aerobic conditions than other species (4). This strain is moderately halophilic and can grow in SOT medium containing NaCl concentrations ranging from 0.1% to 10% (2, 4). Strain KM-1 has attracted much attention in terms of practical bioplastic PHB production using biodiesel waste glycerol without pH adjustment (3). The complete genome sequence of Halomonas elongata (11) and the draft genome sequences of Halomonas sp. strain HAL1 (5), Halomonas sp. strain TD01 (1), Halomonas boliviensis LC1, and Halomonas sp. strain GFAJ-1 (14) have been reported. It was therefore considered desirable to obtain the genomic sequence of a Halomonas strain that produces a higher level of PHB than other strains using glycerol and compare the genes involved in PHB synthesis by high- and low-productivity strains.
The genome of Halomonas sp. strain KM-1 was sequenced using a 454 GS FLX sequencer (6), and the sequence was assembled using the GS de novo assembler Newbler, version 2.0.00.20. The assembled contigs were submitted to the Microbial Genome Annotation Pipeline ver1.060 (MiGAP; http://www.migap.org/index.php/en) annotation server for subsystem classification and functional annotation (12). Protein coding sequences (CDSs) were assigned using the MetaGene annotator with the NCBI RefSeq microbial sequence database (8). MiGAP was employed for gene annotation in preparation for submission to the DDBJ database.
The draft genome sequence of Halomonas sp. strain KM-1 comprises 4,992,811 bases at 41-fold coverage. The assembled genome consists of 173 contigs (>663 bp) with an average contig size of 28,860 bp and a G+C content of 63.9%. The draft genome sequence contains 4,648 CDSs, 56 tRNAs, and one rRNA. Among the CDSs, 4,220 proteins could be assigned to Clusters of Orthologous Groups families (13). The number of proteins with orthologs (bit score of >60) among the 134 reference strains was 3,978. Halomonas elongata and Chromohalobacter salexigens DSM 3043 were identified by MiGAP as the closest neighbors of strain KM-1, in addition to Halomonas sp. strain HAL1 (5).
As expected for an organism that synthesizes PHB and as has been reported for other Halomonas strains (9), the requisite phbA, phbB, and phaC genes, as well as the PHB depolymerase structural gene phaZ, were found in the genome of strain KM-1. The Halomonas sp. strain KM-1 genome also carries multiple genes that are potentially involved in arsenic resistance, as has also been reported for Halomonas sp. strain HAL1 (5) and Halomonas sp. strain GFAJ-1 (14). Halomonas sp. strain KM-1 has two arsenic resistance operons that contain genes encoding the proteins ArsR and ACR3 and the proteins ArsB and ArsC, respectively (7, 10).
The 16S rRNA gene sequence of Halomonas sp. strain KM-1 exhibited a high level of sequence similarity (99.0%) to Halomonas species (3).
Nucleotide sequence accession numbers.
The genome sequence described here has been deposited in the DDBJ database under accession numbers BAEU01000001 to BAEU01000173.
ACKNOWLEDGMENTS
This work was supported by a grant-in-aid for scientific research from the Ministry of the Environment of Japan (K2017, K2161, and K22040), a grant-in-aid for scientific research (C) (23580467), and an AIST research grant.
We are grateful to Shiho Kumata and Akira Kawata for their technical assistance.
REFERENCES
- 1. Cai L, et al. 2011. Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships. Microb. Cell Fact. 10:88. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Hirano M, Imai M, Abe K, Manabe E. 1995. Influence of photosynthetic activity on fatty acid production by Spirulina platensis. J. Mar. Biotechnol. 3:86–88 [Google Scholar]
- 3. Kawata Y, Aiba S. 2010. Poly(3-hydroxybutyrate) production by isolated Halomonas sp. KM-1 using waste glycerol. Biosci. Biotechnol. Biochem. 74:175–177 [DOI] [PubMed] [Google Scholar]
- 4. Kawata Y, Shi LH, Kawasaki K, Shigeri Y. 2012. Taxonomic characterization and metabolic analysis of the Halomonas sp. KM-1, a highly bioplastic poly(3-hydroxybutyrate)-producing bacterium. J. Biosci. Bioeng. 113:456–460 [DOI] [PubMed] [Google Scholar]
- 5. Lin Y, et al. 2012. Draft genome sequence of Halomonas sp. strain HAL1, a moderately halophilic arsenite-oxidizing bacterium isolated from gold-mine soil. J. Bacteriol. 194:199–200 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Margulies M, et al. 2005. Genome sequencing in open microfabricated high-density picolitre reactors. Nature 437:376–380 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Muller D, Lievremont D, Simeonova DD, Hubert JC, Lett MC. 2003. Arsenite oxidase aox genes from a metal-resistant beta-proteobacterium. J. Bacteriol. 185:135–141 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Noguchi H, Taniguchi T, Itoh T. 2008. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res. 15:387–396 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Quillaguamán J, Guzm H, Van-Thuoc D, Hatti-Kaul R. 2010. Synthesis and production of polyhydroxyalkanoates by halophiles: current potential and future prospects. Appl. Microbiol. Biotechnol. 85:1687–1696 [DOI] [PubMed] [Google Scholar]
- 10. Santini JM, vanden Hoven RN. 2004. Molybdenum-containing arsenite oxidase of the chemolithoautotrophic arsenite oxidizer NT-26. J. Bacteriol. 186:1614–1619 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. Schwibbert K, et al. 2011. A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581(T). Environ. Microbiol. 13:1973–1994 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12. Sugawara H, Ohyama A, Mori H, Kurokawa K. 2009. Microbial Genome Annotation Pipeline (MiGAP) for diverse users, poster S001-1-2. 20th International Conference on Genome Informatics (GIW2009), Yokohama, Japan. [Google Scholar]
- 13. Tatusov RL, Galperin MY, Natale DA, Koonin EV. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28:33–36 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14. Wolfe-Simon F, et al. 2011. A bacterium that can grow by using arsenic instead of phosphorus. Science 332:1163–1166 [DOI] [PubMed] [Google Scholar]