A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation

Abstract

Bioinformatic analysis of the intergenic regions of Staphylococcus aureus predicted multiple regulatory regions. From this analysis, we characterized 11 novel noncoding RNAs (RsaA‐K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumulate in the late-exponential phase of growth. All ncRNAs are stable and their expression is Hfq-independent. The transcription of several of them is regulated by the alternative sigma B factor (RsaA, D and F) while the expression of RsaE is agrA-dependent. Six of these ncRNAs are specific to S. aureus, four are conserved in other Staphylococci, and RsaE is also present in Bacillaceae. Transcriptomic and proteomic analysis indicated that RsaE regulates the synthesis of proteins involved in various metabolic pathways. Phylogenetic analysis combined with RNA structure probing, searches for RsaE‐mRNA base pairing, and toeprinting assays indicate that a conserved and unpaired UCCC sequence motif of RsaE binds to target mRNAs and prevents the formation of the ribosomal initiation complex. This study unexpectedly shows that most of the novel ncRNAs carry the conserved C−rich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism.

RsaOG, a new Staphylococcal family of highly transcribed non-coding RNA

“…4 This position is likely a transcriptional start since (i) a 5' RACE performed in the absence of TAP treatment shows a highly reduced level of first strand synthesized cDNA (Fig. 1B) and (ii) a potential -10 and -35 transcription promoter, conserved in other Staphylococcus is present upstream of the identified transcriptional start (Fig.…”

“…2 The ncRNA RsaOG (acronym for RNA S. aureus Orsay G) was initially discovered in a bioinformatics ncRNA screen of the S. aureus genome 3 and confirmed in a second study. 4 Here, we show that it is the founding member of a new trans-acting ncRNA family conserved in all Staphylococcaceae. We define the rsaOG gene boundaries and analyze its RNA sequence alignment, structure and phylogeny.…”

“…Recent and ongoing studies are now changing this view. 3,4 We described here a new Staphylococcal RNA, RsaOG, that is likely involved in trans-acting regulatory functions. The fact that RsaOG is expressed during all growth stages suggests a persistent repression or activation function for this gene (or a fine tuning role involving a second factor).…”

Thermodynamic matchers for the construction of the cuckoo RNA family

“…23 Consistently, Crich loop sequences are a common feature among sRNAs and it was postulated that these motifs generally are signatures of sRNAs that repress the translation of target mRNAs by pairing with the RBS. 24 An example is RNAIII, a sRNA which is predominant in Staphylococcus species. RNAIII harbors a conserved motif, UCCC, in 3 of its hairpin loops.…”

“…25 Moreover, in a comparative study in S. aureus strains, several distinct sRNAs were identified that carry the identical Crich loop motif. 24 The authors hypothesized that these sRNAs are the product of convergent evolution. A similar picture is found in S. meliloti where several representatives of RNA families occur which are either similar to cuckoo HP2 (RFM SmelA003 ), cuckoo HP3 (RFM SmelB008 , RFM SmelC416 , RFM SmelC601 ) or cuckoo HP4 (RFM SmelC023 ) RNAs.…”