Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains

Abstract

Small RNA (sRNA) genes are expressed in all organisms, primarily as regulators of translation and message stability. We have developed comparative genomic approaches to identify sRNAs that are expressed by Staphylococcus aureus , the most common cause of hospital-acquired infections. This study represents an in-depth analysis of the RNome of a Gram-positive bacterium. A set of sRNAs candidates were identified in silico within intergenic regions, and their expression levels were monitored by using microarrays and confirmed by Northern blot hybridizations. Two sRNAs were also detected directly from purification and RNA sequence determination. In total, at least 12 sRNAs are expressed from the S. aureus genome, five from the core genome and seven from pathogenicity islands that confer virulence and antibiotic resistance. Three sRNAs are present in multiple (two to five) copies. For the sRNAs that are conserved throughout the bacterial phylogeny, their secondary structures were inferred by phylogenetic comparative methods. In vitro binding assays indicate that one sRNA encoded within a pathogenicity island is a trans-encoded antisense RNA regulating the expression of target genes at the posttranscriptional level. Some of these RNAs show large variations of expression among pathogenic strains, suggesting that they are involved in the regulation of staphylococcal virulence.

Proteomic and Transcriptomic Profiling of Staphylococcus aureus Surface LPXTG-proteins: Correlation with agr Genotypes and Adherence Phenotypes

“…aureus produces a plethora of virulence determinants (50), which are regulated by a complex network of two-component regulatory systems, DNA-binding proteins, and small RNAs (3,16,21,30,51,52). This explains why there is no simple approach to assess the presence or absence of each individual pathogenic feature along the successive steps of infection.…”

Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles

“…S. aureus is a human commensal and an opportunistic pathogen that is widely responsible for nosocomial infections. Using NAPP to identify novel ncRNAs could have medical relevance, especially as only few ncRNAs were experimentally confirmed in this species (Pichon and Felden 2005). NAPP performed on strain N315 discerned 189 new ncRNA candidates in the ncRNA-rich clusters (Supplemental Table S6).…”

Genome-wide antisense transcription drives mRNA processing in bacteria

“…In 1993, Novick and coworkers (26) identified the first example of a regulatory RNA (RNAIII) that controls the expression of virulence factors by pairing with the target mRNAs followed by degradation of the RNAIII-mRNA complex by the double-stranded specific RNase III (27). More recently, several studies using computational analysis of intergenic regions, microarray technology, and deep sequencing have allowed the identification of >140 small RNAs, including both trans-and cis-encoded antisense RNAs (10,(28)(29)(30)(31)(32). In this current study, we uncover the existence of an overlapping transcription process covering, in a genome-wide extent, the expressed protein coding genes.…”