Abstract
Streptococcus parasanguinis, a primary colonizer of the tooth surface, is also an opportunistic pathogen for subacute endocarditis. The complete genome of strain FW213 was determined using the traditional shotgun sequencing approach and further refined by the transcriptomes of cells in early exponential and early stationary growth phases in this study. The transcriptomes also discovered 10 transcripts encoding known hypothetical proteins, one pseudogene, five transcripts matched to the Rfam and additional 87 putative small RNAs within the intergenic regions defined by the GLIMMER analysis. The genome contains five acquired genomic islands (GIs) encoding proteins which potentially contribute to the overall pathogenic capacity and fitness of this microbe. The differential expression of the GIs and various open reading frames outside the GIs at the two growth phases suggested that FW213 possess a range of mechanisms to avoid host immune clearance, to colonize host tissues, to survive within oral biofilms and to overcome various environmental insults. Furthermore, the comparative genome analysis of five S. parasanguinis strains indicates that albeit S. parasanguinis strains are highly conserved, variations in the genome content exist. These variations may reflect differences in pathogenic potential between the strains.
Highlights
Streptococcus parasanguinis is a member of the viridans streptococci that constitute the major population of the oral microbial ecosystem in human
A detailed analysis of pFW213 has been reported previously [29], and will not be discussed in this manuscript. This genome contains 84 hypothetical genes without any matches in the non-redundant protein database; 38 of them are less than 300 bp and are expressed in both the early exponential- and early stationary-phase cultures. As none of these open reading frames (ORFs) matches to the Rfam database [30], these ORFs may encode mini-proteins for various biological processes and regulation in bacteria [31]. 16 transcripts with an average sequence coverage score and a length greater than 100 bp dispersed in the GLIMMER analysis-defined intergenic regions were detected from RNA sequencing (RNA-seq) analysis (Table 1). 10 of these transcripts encode proteins matched to known hypothetical proteins, one is a pseudogene, and the other 5 matched to Rfam database
87 possible small RNA were extracted from intergenic regions by using the integrative computational tool sRNAPredict2 [32] and further confirmed by the transcriptome analysis
Summary
Streptococcus parasanguinis is a member of the viridans streptococci that constitute the major population of the oral microbial ecosystem in human. The oral cavity, S. parasanguinis is one of the early colonizers of the tooth surface. The successful adherence of S. parasanguinis can serve as a substratum for the adherence of additional oral bacteria and subsequently develop into a mature biofilm called dental plaque [1,2]. During oral trauma or surgery, oral streptococci may gain access to the bloodstream and cause transient bacteremia. S. parasanguinis and other viridans streptococci are the common causes of native and prosthetic heart valve endocarditis [3,4]. The ability to evade host immune clearance is critical for the pathogenesis of S. parasanguinis
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