Complete Genome Sequence of the Serotype k Streptococcus mutans Strain LJ23

Abstract

Streptococcus mutans is the major pathogen of dental caries and occasionally causes infective endocarditis. Here we report the complete genome sequence of serotype k S. mutans strain LJ23, which was recently isolated from the oral cavity of a Japanese patient.

GENOME ANNOUNCEMENT

Streptococcus mutans, a major pathogen of dental caries, is classified into serotypes c, e, f, and k (17). Approximately 70 to 80% of oral isolates are serotype c, while the distribution frequency of serotype k is ∼5% (12). Serotype k strains are not only dental caries pathogens but have been increasingly implicated in infective endocarditis (6, 11). Furthermore, it was recently reported that infection with serotype k strains expressing the collagen-binding protein (CBP) is a potential risk factor for hemorrhagic stroke in mice (10). However, the relationship between serotype and clinical conditions remains unclear. The complete genome sequences of bacteria might help to reveal such relationships, but so far, only the genomes of two S. mutans serotype c strains, NN2025 and UA159, have been fully sequenced (1, 9). Here we describe the first complete genome sequence of a serotype k strain, LJ23, isolated in Japan.

The complete genome sequence of strain LJ23 was determined by a combination of pyrosequencing (143,616,336-bp sequence, 71-fold coverage) and the Sanger method (35,189,307-bp sequence, 17-fold coverage). The pyrosequencing and Sanger reads were assembled using Newbler and Phred/Phrap/Consed, respectively. Gaps between adjacent contigs were closed by sequencing PCR amplicons from genomic DNA. Protein-coding sequences (CDSs) were predicted using a combination of MetaGeneAnnotator (14), GLIMMER (3), and the IMCGE software (In Silico Biology Co., Ltd., Japan). Annotation of CDSs was based on the results of BLASTP searches against the NCBI nonredundant protein database. Insertion sequences (ISs), conjugative transposons, and clustered regularly interspaced short palindromic repeats (CRISPRs) were identified using ISfinder (16), a combination of Mauve (2) and GenomeMatcher (15), and CRISPRFinder (5), respectively. Nontranslated genes were predicted using tRNAscan-SE (8), RNAmmer (7), and Rfam (4).

The genome of S. mutans LJ23 contains a single circular chromosome (2,015,626 bp, 37.05% GC content). The chromosome contains 1,921 CDSs, five rRNA operons, 65 tRNA sequences, 25 noncoding RNAs, 13 ISs, and two CRISPRs.

All-to-all BLASTP analysis with NN2025 and UA159 protein sequences showed that LJ23 possesses 80 strain-specific CDSs. It was previously shown that the distribution of the CBP-encoding cnm gene in clinical isolates was ∼10% and predominant in serotype k or f strains (11, 13), and cnm was found to be an LJ23-specific gene. Approximately half of the strain-specific CDSs were annotated as hypothetical proteins, and 33 CDSs were on mobile elements. Several genes on one mobile element showed high homology with proteins produced by Streptococcus pneumoniae, suggesting that LJ23 may have acquired these CDSs via horizontal gene transfer from this species. Dot plot analysis comparison with the NN2025 and UA159 genome sequences indicated that genome rearrangements occurred between LJ23 and UA159 along the replication axis but not between LJ23 and NN2025. This may be due to the fact that UA159 was isolated in the United States, whereas both LJ23 and NN2025 were isolated in Japan. There remain many questions regarding how the oral environment affects bacterial pathogenicity under different clinical conditions. We believe that genomic analysis of LJ23 could lead to new insights into the mechanisms of pathogenicity of S. mutans.

Nucleotide sequence accession number.

The complete genome sequence of S. mutans LJ23 was deposited in the DDBJ/EMBL/GenBank databases under accession no. AP012336. In addition, genome information for S. mutans LJ23 can be downloaded from our laboratory's website (http://www.tmd.ac.jp/grad/bac/).