Jun 27, 2011 - The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences,. 100029 Beijing ...
JOURNAL OF BACTERIOLOGY, Oct. 2011, p. 5596–5597 0021-9193/11/$12.00 doi:10.1128/JB.05670-11 Copyright © 2011, American Society for Microbiology. All Rights Reserved.
Vol. 193, No. 19
Complete Genome Sequence of the Ureolytic Streptococcus salivarius Strain 57.I Jianing Geng,1 Szu-Chuan Huang,2 Shuangli Li,1 Songnian Hu,1 and Yi-Ywan M. Chen2,3* The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100029 Beijing, People’s Republic of China,1 and Department of Microbiology and Immunology2 and Research Center for Pathogenic Bacteria,3 College of Medicine, Chang Gung University, Tao-Yuan, Taiwan Received 27 June 2011/Accepted 18 July 2011
Streptococcus salivarius 57.I is one of the most abundant and highly ureolytic bacteria in the human mouth. It can utilize urea as the sole nitrogen source via the activity of urease. Complete genome sequencing of S. salivarius 57.I revealed a chromosome and a phage which are absent in strain SK126. dromic repeats (CRISPRs) and two potential CRISPRs in the chromosome. The phage DNA is 40,758 bp in length and encodes 55 proteins. Comparative genomic analysis of S. salivarius strains 57.I and SK126 revealed 164 ORFs that are unique in S. salivarius strain 57.I. These genes include the ure operon of 11 genes, encoding all proteins required for assembly of a functional urease (2, 3, 6), the cadDX operon, encoding a system for cadmium and zinc resistance (4), and a cluster of genes encoding sugar transferases involved in extracellular polysaccharide synthesis (Ssal_01171-01174 and Ssal_0117601177), indicating that these two strains are fundamentally different. The complete genome of strain 57.I will allow for comparative genomics to further characterize the polymorphisms of S. salivarius strains and all species within the salivarius group. Nucleotide sequence accession numbers. The complete genome information of S. salivarius strain 57.I was deposited in GenBank under the accession numbers CP002888 and CP002889.
Streptococcus salivarius, a member of the salivarius group of the viridans group streptococci, is one of the early colonizers of the epithelium and a common isolate of the human oral cavity (10). When S. salivarius gains entrance to the bloodstream, it may cause severe systemic infections (13). Although not all S. salivarius strains synthesize urease, the ureolytic activity of S. salivarius strain 57.I is the major alkali generation machinery in the oral cavity that plays an essential role in maintaining oral pH homeostasis and balancing dental plaque ecology (5, 17). Here we report the complete genome and annotation of the ureolytic strain 57.I and compared the genome with that of strain SK126. The complete genome sequence of S. salivarius strain 57.I was determined via a whole-genome shotgun approach employing Roche 454 pyrosequencing on a GS-FLX at 454 Life Sciences. A total of 272,194 high-quality reads were assembled by using Roche’s Newbler assembler with approximately 50⫻ sequence coverage of the entire genome. The order of the contigs was arranged initially based on the gene order of S. salivarius strain SK126 chromosome (ACLO00000000), and the gaps between contigs were then finished by the multiplex PCR and primer walking method. The resulting sequence was edited by the phred/phrap/consed software package (8, 9, 11, 12). The protein-coding genes, tRNAs, and rRNA were predicted by Glimmer 3.0, tRNA-SE, and RNAmmer (7, 14, 15), respectively. The functions of all genes were predicted by searching against the NCBI nonredundant protein database, cluster of orthologous groups (COGs), and InterProScan, and the metabolic pathways were reconstructed by using the Kyoto Encyclopedia of Genes and Genomes (KEGG) (1, 16, 18). The genome has one circular DNA molecule with a GC content of 39.93% and one phage DNA with a 41.24% GC content. The chromosome DNA is 2,138,805 bp in length, carrying 1,942 predicted open reading frames (ORFs), 68 predicted tRNA genes encoding all 20 amino acids, and 6 rRNA operons containing 5S, 16S, and 23S RNA genes. Additionally, there are two clusters of regularly interspaced short palin-
This work was supported in part by the Chang Gung Memorial Hospital (CMRPD10011) and the intramural funding of the Research Center for Pathogenic Bacteria of Chang Gung University. REFERENCES 1. Apweiler, R., et al. 2000. InterPro—an integrated documentation resource for protein families, domains and functional sites. Bioinformatics 16:1145– 1150. 2. Chen, Y. Y., and R. A. Burne. 2003. Identification and characterization of the nickel uptake system for urease biogenesis in Streptococcus salivarius 57.I. J. Bacteriol. 185:6773–6779. 3. Chen, Y. Y., K. A. Clancy, and R. A. Burne. 1996. Streptococcus salivarius urease: genetic and biochemical characterization and expression in a dental plaque streptococcus. Infect. Immun. 64:585–592. 4. Chen, Y. Y., C. W. Feng, C. F. Chiu, and R. A. Burne. 2008. cadDX operon of Streptococcus salivarius 57.I. Appl. Environ. Microbiol. 74:1642–1645. 5. Chen, Y. Y., C. A. Weaver, and R. A. Burne. 2000. Dual functions of Streptococcus salivarius urease. J. Bacteriol. 182:4667–4669. 6. Chen, Y. Y., C. A. Weaver, D. R. Mendelsohn, and R. A. Burne. 1998. Transcriptional regulation of the Streptococcus salivarius 57.I urease operon. J. Bacteriol. 180:5769–5775. 7. Delcher, A. L., K. A. Bratke, E. C. Powers, and S. L. Salzberg. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679. 8. Ewing, B., and P. Green. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186–194. 9. Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175–185.
* Corresponding author. Mailing address: Department of Microbiology and Immunology, College of Medicine, Chang Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan, Tao-Yuan, Taiwan 333. Phone: 886-3-2118800, ext. 3352. Fax: 886-3-2118700. E-mail: mchen@mail .cgu.edu.tw. 5596
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