Abstract
Streptococcus oralis, a commensal species of the human oral cavity, belongs to the Mitis group of streptococci, which includes one of the major human pathogens as well, S. pneumoniae. We report here the first complete genome sequence of this species. S. oralis Uo5, a high-level penicillin- and multiple-antibiotic-resistant isolate from Hungary, is competent for genetic transformation under laboratory conditions. Comparative and functional genomics of Uo5 will be important in understanding the evolution of pathogenesis among Mitis streptococci and their potential to engage in interspecies gene transfer.
TEXT
The Mitis phylogenetic group of streptococci consists of members of the commensal flora of the upper respiratory tract of humans (1, 2, 9). It includes Streptococcus pneumoniae, one of the major human pathogens and resident in the nasopharynx, and its closest relatives, S. mitis and S. oralis. A detailed in silico comparison of the S. mitis B6 genome with six S. pneumoniae genomes supported the suggestion that S. pneumoniae is a specialized S. mitis clone (3), whereas S. oralis is a well-separated group consisting of many unrelated lineages (1, 2, 9).
Species that belong to the Mitis group are naturally competent for genetic transformation (8). Gene transfer events between different species can be recognized by the mosaic structure of gene sequences such as those for penicillin-binding proteins (PBPs) (4). However, estimations of the extent of interspecies gene transfer on the genomic scale are limited since mainly S. pneumoniae genomes are available (currently 23; http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi), with only one finished S. mitis genome (3).
S. oralis Uo5 (Hu5 [13] or Hu-o5 [7]) has been chosen since it had been specified to be S. oralis by comparative genomic hybridization (7) and multilocus sequence typing (2). It is a high-level penicillin- and multiple-antibiotic-resistant strain isolated in Hungary in the early 1980s (13), a phenotype which is also prevalent among the main S. pneumoniae clone from Hungary, Hu19A−6 (12, 14). Moreover, it is naturally transformable and thus is susceptible to genetic manipulation.
The Uo5 genome was sequenced using a combination of Roche GS-FLX (Roche Diagnostics, Basel, Switzerland) (11) and Solexa (Illumina GA IIx, Illumina, CA) paired-end sequencing technologies. Library preparation, sequencing reaction, and the sequencing run were carried out according to Illumina's instructions. The S. mitis B6 genome was used as a reference genome for the alignment of contigs (3). Gap closures were performed by combinatorial PCR and Sanger sequencing of the PCR products using an ABI 3100 capillary sequencer.
Annotation was performed using the Glimmer (15), tRNAscan-SE (10), and Rfam (6) software programs and software predicting transcriptional terminators (5) and finalized by manual review as described for the S. mitis B6 genome (3). The Uo5 chromosome is 1,958,690 bp in length, which is smaller than the S. pneumoniae and S. mitis B6 genomes, and has a G+C content of 41.14% and a coding percentage of 89.7. There are 1,909 predicted protein coding sequences (CDSs), with an average length of 921 bp, 61 tRNAs, 4 rRNA loci, and another 9 RNA coding genes. Similar to the S. mitis B6 genome, that of Uo5 shows a striking X alignment compared to S. pneumoniae genomes.
Only the main pneumococcal pathogenicity factors are missing in S. oralis Uo5, similar to the case with S. mitis B6 (3). It contains genetic islands and antibiotic resistance determinants that are representatives of the accessory genome of S. pneumoniae and/or other streptococcal species and which are likely to be capable in modulation of the virulence potential. The availability of the first finished S. oralis genome will be helpful for comparative genomics to understand host interaction and pathogenicity within the Mitis group of streptococci.
Nucleotide sequence accession number.
The complete genome sequence has been deposited in the EMBL database under accession no. FR720602.
Acknowledgments
This work was supported by the Bundesministerium für Bildung und Forschung 0313801 l, the Stiftung Rheinland Pfalz für Innovation, 15202-38 62 61/580, and the EU (EuroPathoGenomics LSHB-CT-2005-512061; PREVIS LSHM-CT-2003-503413).
The technical assistance of Sonja Schröck and Michele Memmer is gratefully acknowledged.
Footnotes
Published ahead of print on 1 April 2011.
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