Abstract
Lactobacillus helveticus strain H10 was isolated from traditional fermented milk in Tibet, China. We sequenced the whole genome of strain H10 and compared it to the published genome sequence of Lactobacillus helveticus DPC4571.
TEXT
Lactobacillus helveticus has been used as starter culture or adjunct culture in the food and fermentation Industries for a long time (3). Compared to other species, it possesses a high proteolytic activity, which is generally associated with the flavor properties and biological activities of the fermented products (7, 9).
L. helveticus strain H10 was previously isolated from traditional fermented milk in Tibet, China (1). The whole-genome sequencing of strain H10 was performed using Roche 454 (6) and Solexa sequencing technology. A genomic library containing an 8-kb insert was constructed, and 359,874 paired-end reads and 61,235 single-end reads were generated using the GS FLX system (454 Life Science); about 95.50% of the reads were assembled into four large scaffolds, including 167 contigs, having 43.81-fold coverage of the genome. A total of 25,073,857 reads (3-kb library) were generated to reach 866-fold coverage of the genome with an Illumina Solexa genome analyzer IIx (Illumina, San Diego, CA) and mapped to the scaffolds using the Burrows-Wheeler alignment (BWA) tool (4). All the intrascaffold gaps were filled by local assembly of 454 and Solexa reads, and the interscaffold gaps were verified by sequencing of PCR products using an ABI 3730 capillary sequencer. The comparative analysis of the genome was done with the published genome of strain DPC4571 (2).
The complete genome of strain H10 is composed of a single, circular chromosome of 2,145,899 bp and a plasmid of 26,484 bp. The GC contents of the chromosome and the plasmid are both 36.79%. There are 2,049 protein-coding genes, 4 rRNA operons, and 62 tRNA genes in the chromosome and 25 protein-coding genes in the plasmid.
The genomic sequence of strain H10 was a little larger than that of strain DPC4571 (2.08 Mb). Compared to strain DPC4571, most of the functional genes of strain H10 are conserved. There are nearly 300 unique genes present and 130 genes absent in strain H10; many of them encode putative uncharacterized proteins and transposases. Other than that, there are some differences in the transport systems of the two strains, especially among the ABC transporters, which involve the transportation of a wide variety of substrates and may indicate their different environmental adaptations (8).
There are different proteolytic system components in lactic acid bacteria (LAB) (5). From a comparison of the two genomes, we found that there were two proteinase-encoding genes, both of which were annotated as pseudogenes in strain DPC4571 and one of which was a pseudogene in strain H10. Strain DPC4571 possesses three LAB peptide transport systems, the oligopeptide Opp transport system and the di-/tripeptide transport system, Dpp and DtpT (identified as encoded by pseudogenes). In contrast, strain H10 has two peptide transport systems, the Opp and dtpT systems. Twenty-six peptidase-encoding genes were present in each strain; one of these genes was identified as a pseudogene in strain DPC4571, whereas two were identified as pseudogenes in strain H10. This indicates that the proteolytic activity may differ not only between species but also between different strains in L. helveticus.
Nucleotide sequence accession numbers.
The complete genome sequence and annotation information for the chromosome and the one plasmid of Lactobacillus helveticus H10 have been deposited in GenBank under the accession numbers CP002429 and CP002430.
Acknowledgments
This research was supported by the National Natural Science Foundation of China (grant no. 31025019), the Earmarked Fund for Modern Agro-industry Technology Research System (grant no. nycytx-0501), the Prophase Research Program of the 973 Project of China (grant no. 2010CB134502), the National Key Technology R&D Program (grant no. 2009BADC1B01), and the Innovation Team Development of the Ministry of Education of China (grant no. IRT0967).
Footnotes
Published ahead of print on 11 March 2011.
REFERENCES
- 1. Airidengcaicike X. C., et al. 2010. Isolation and identification of cultivable lactic acid bacteria in traditional fermented milk of Tibet in China. Int. J. Dairy Technol. 63:437–444 [Google Scholar]
- 2. Callanan M., et al. 2008. Genome sequence of Lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion. J. Bacteriol. 190:727–735 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Kilpi E. E.-R., Kahala M. M., Steele J. L., Pihlanto A. M., Joutsjoki V. V. 2007. Angiotensin I-converting enzyme inhibitory activity in milk fermented by wild-type and peptidase-deletion derivatives of Lactobacillus helveticus CNRZ32. Int. Dairy J. 17:976–984 [Google Scholar]
- 4. Li H., Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Liu M., Bayianov J. R., Renckens B., Nauta A., Siezen R. J. 2010. The proteolytic system of lactic acid bacteria revisited: a genomic comparison. BMC Genomics 11:36. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Margulies M., et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Meisel H., Bockelmann W. 1999. Bioactive peptides encrypted in milk proteins: proteolytic activation and thropho-functional properties. Antonie Van Leeuwenhoek 76:207–215 [PubMed] [Google Scholar]
- 8. Schroeter J., Klaenhammer T. 2009. Genomics of lactic acid bacteria. FEMS Microbiol. Lett. 292:1–6 [DOI] [PubMed] [Google Scholar]
- 9. Slattery L., O'Callaghan J., Fitzgerald G. F., Beresford T., Ross R. P. 2010. Invited review: Lactobacillus helveticus—a thermophilic dairy starter related to gut bacteria. J. Dairy Sci. 93:4435–4454 [DOI] [PubMed] [Google Scholar]