Abstract
Members of the carnobacteria have been extensively studied as probiotic cultures in aquacultures and protective cultures in seafood, diary, and meat. We report on the finished genome sequence of Carnobacterium sp. 17-4, which has been isolated from permanently cold seawater. The genetic information reveals a new circular bacteriocin biosynthesis cluster.
GENOME ANNOUNCEMENT
Carnobacteria are ubiquitous lactic acid bacteria, which have been frequently isolated from temperate to polar aquatic environments and food products such as seafood, dairy, and meat (1, 4, 8, 11, 12). Carnobacterium sp. 17-4 was isolated from a seawater sample taken at the Isfjord, Spitsbergen, in autumn 1999 (7). Analysis of the 16S rRNA gene showed that Carnobacterium sp. 17-4 is closely related to the protease-producing arctic isolate Carnobacterium sp. ARCTIC-P35.
The genome sequence of Carnobacterium sp. 17-4 was determined by using a 454 GS-FLX system (Roche 454 Life Science, Mannheim, Germany). Pyrosequencing runs, including two shotgun runs and one paired-end run, resulted in 37-fold coverage. The initial assembly yielded 19 scaffolds containing 69 contigs. PCR-based techniques and Sanger sequencing of the products were used to close the remaining gaps. The manually curated and annotated final sequence of Carnobacterium sp. 17-4 comprises one chromosome of 2,635,294 bp and one plasmid of 50,105 bp. The chromosome (35.25% G+C content) comprises 2,420 predicted protein-encoding genes, 67 tRNA genes, 8 rRNA operons, and 1 single 5S rRNA gene. The plasmid (31.53% G+C content) harbors 54 protein-encoding genes.
Whereas complete genome sequences from many lactic acid bacteria are available, only one draft genome sequence from a member of the genus Carnobacterium (Carnobacterium sp. AT7) has been previously deposited in the databases. Carnobacterium sp. AT7 is a piezophilic strain isolated from the Aleutian trench (9). We used the draft data set of this organism for comparisons. To identify orthologous genes and functions as well as strain-specific gene content, a combination of bidirectional BLAST and a global sequence alignment was employed. Overall, Carnobacterium sp. 17-4 and Carnobacterium sp. AT7 share 1,816 (74.70%) orthologous genes (E value [expect value] < 1e−20; similarity score > 30%). Among the 25.3% species-specific genes of Carnobacterium sp. 17-4, 18.5% belong to the COG categories for transport and metabolism (G, E, F, H, and I) and more precisely to the subcategory carbohydrate transport and metabolism.
Only the replication-associated proteins encoded by the plasmid of Carnobacterium sp. 17-4 shared homologies with putative gene products encoded by a 76,048 bp-contig of Carnobacterium sp. AT7, indicating that this putative plasmid and the plasmid of Carnobacterium sp. 17-4 differ in content and size. In addition to the high number of carbohydrate transport and metabolism genes found on the chromosome, three putative carbohydrate phosphotransferase systems (PTS) are encoded by the plasmid of Carnobacterium sp. 17-4.
A new circular bacteriocin biosynthesis cluster was located in a genomic island of Carnobacterium sp. 17-4. Bacteriocins are antimicrobial peptides that are active against closely related strains. Bacteriocins produced by lactic acid bacteria are generally regarded as safe and possess a high biotechnological potential for various applications such as food preservation and probiotics (1, 2, 3, 5). The genetic organization of the new cluster is similar to that of a reported circular bacteriocin, carnocyclin A, which is produced by Carnobacterium maltaromaticum UAL307 (6, 10). In contrast to the genomic synteny, only little sequence homology was observed.
Nucleotide sequence accession numbers.
The complete genome and plasmid sequences of Carnobacterium sp. 17-4 have been deposited in GenBank under accession numbers CP002563 and CP002564, respectively.
Acknowledgments
We thank Frauke D. Meyer for providing excellent technical assistance and Rüdiger Lehmann for bioinformatics support.
This work was funded by the GenoMikPlus initiative of the German Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung [BMBF]).
Footnotes
Published ahead of print on 6 May 2011.
REFERENCES
- 1. Afzal M. I., et al. 2010. Carnobacterium maltaromaticum: identification, isolation tools, ecology and technological aspects in dairy products. Food Microbiol. 27:573–579 [DOI] [PubMed] [Google Scholar]
- 2. Avonts L., Uytven E. V., Vuyst L. D. 2004. Cell growth and bacteriocin production of probiotic Lactobacillus strains in different media. Int. Dairy J. 14:947–955 [Google Scholar]
- 3. De Vuyst L., Leroy F. 2007. Bacteriocins from lactic acid bacteria: production, purification, and food applications. J. Mol. Microbiol. Biotechnol. 13:194–199 [DOI] [PubMed] [Google Scholar]
- 4. Galkin A., Kulakova L., Ashida H., Sawa Y., Esaki N. 1999. Cold-adapted alanine dehydrogenases from two Antarctic bacterial strains: gene cloning, protein characterization, and comparison with mesophilic and thermophilic counterparts. Appl. Environ. Microbiol. 65:4014–4020 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Gálvez A., Abriouel H., López R. L., Omar N. B. 2007. Bacteriocin-based strategies for food biopreservation. Int. J. Food Microbiol. 120:51–70 [DOI] [PubMed] [Google Scholar]
- 6. Gong X., Martin-Visscher L. A., Nahirney D., Vederas J. C., Duszyk M. 2009. The circular bacteriocin, carnocyclin A, forms anion-selective channels in lipid bilayers. Biochim. Biophys. Acta 1788:1797–1803 [DOI] [PubMed] [Google Scholar]
- 7. Groudieva T., et al. 2004. Diversity and cold-active hydrolytic enzymes of culturable bacteria associated with Arctic sea ice, Spitzbergen. Extremophiles 8:475–488 [DOI] [PubMed] [Google Scholar]
- 8. Holley R. A., Guan T. Y., Peirson M. Y., Yost C. K. 2002. Carnobacterium viridans sp. nov., an alkaliphilic, facultative anaerobe isolated from refrigerated, vacuum-packed bologna sausage. Int. J. Syst. Evol. Microbiol. 52:1881–1885 [DOI] [PubMed] [Google Scholar]
- 9. Lauro F. M., Chastain R. A., Blankenship L. E., Yayanos A. A., Bartlett D. H. 2007. The unique 16S rRNA genes of piezophiles reflect both phylogeny and adaptation. Appl. Environ. Microbiol. 73:838–845 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Martin-Visscher L. A., et al. 2008. Isolation and characterization of carnocyclin A, a novel circular bacteriocin produced by Carnobacterium maltaromaticum UAL307. Appl. Environ. Microbiol. 74:4756–4763 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. Matamoros S., Pilet M. F., Gigout F., Prévost H., Leroi F. 2009. Selection and evaluation of seafood-borne psychrotrophic lactic acid bacteria as inhibitors of pathogenic and spoilage bacteria. Food Microbiol. 26:638–644 [DOI] [PubMed] [Google Scholar]
- 12. Yanagida F., Chen Y. S., Yasaki M. 2007. Isolation and characterization of lactic acid bacteria from lakes. J. Basic Microbiol. 47:184–190 [DOI] [PubMed] [Google Scholar]