SRD: a Staphylococcus regulatory RNA database

Abstract

An overflow of regulatory RNAs (sRNAs) was identified in a wide range of bacteria. We designed and implemented a new resource for the hundreds of sRNAs identified in Staphylococci, with primary focus on the human pathogen Staphylococcus aureus. The "Staphylococcal Regulatory RNA Database" (SRD, http://srd.genouest.org/) compiled all published data in a single interface including genetic locations, sequences and other features. SRD proposes novel and simplified identifiers for Staphylococcal regulatory RNAs (srn) based on the sRNA's genetic location in S. aureus strain N315 which served as a reference. From a set of 894 sequences and after an in-depth cleaning, SRD provides a list of 575 srn exempt of redundant sequences. For each sRNA, their experimental support(s) is provided, allowing the user to individually assess their validity and significance. RNAseq analysis performed on strains N315, NCTC8325, and Newman allowed us to provide further details, upgrade the initial annotation, and identified 159 RNA-seq independent transcribed sRNAs. The lists of 575 and 159 sRNAs sequences were used to predict the number and location of srns in 18 S. aureus strains and 10 other Staphylococci. A comparison of the srn contents within 32 Staphylococcal genomes revealed a poor conservation between species. In addition, sRNA structure predictions obtained with MFold are accessible. A BLAST server and the intaRNA program, which is dedicated to target prediction, were implemented. SRD is the first sRNA database centered on a genus; it is a user-friendly and scalable device with the possibility to submit new sequences that should spread in the literature.

TSS-EMOTE, a refined protocol for a more complete and less biased global mapping of transcription start sites in bacterial pathogens

“…In addition to being downstream of a potential sigma-factor binding site, most TSSs are expected, from a functional point of view, to be immediately upstream of, and on the same strand as, annotated open reading frames (ORFs), although many ncRNAs and pervasive anti-sense transcripts are found in S. aureus [21, 22]. Comparing the detected rTSS positions to the annotated genome gives a median distance to the nearest downstream annotated start codon (i.e.…”

“…Finally, S. aureus TSSs are annotated with the closest predicted non-coding RNA for MW2 strain taken from the staphylococcal regulatory RNA database [22]. We also make use of the work of [4] on the sigma-factor B regulon to flag rTSSs that immediately precede an ORF upregulated by sigma-factor B in S. aureus .…”

Insights into the regulation of small RNA expression: SarA represses the expression of two sRNAs inStaphylococcus aureus

“…This identified a 29 bp sequence sharing 93% identity with sprC 47 (Figure 4). Interestingly, the sequence is located upstream of srn_9340 (22), an sRNA gene identified by RNAseq (45) and recently validated by northern blot under the name S774 (46). As for srn_3610_sprC , the srn_9340 (NCTC 8325: 1863905–1863790) is located in the SaPIn3 (vSaß) PI.…”

“…In addition to TFs, S. aureus expresses about 160 regulatory RNAs (4,21), all recently compiled into a staphylococcal regulatory RNA database (SRD) (22). sRNAs are expressed from both the core and variable accessory genomes, the latter including pathogenicity islands (PIs) and transposons (23).…”

Isobaric Tags for Relative and Absolute Quantitation Proteomics Analysis of Gene Regulation by SprC in Staphylococcus Aureus

“…In S. aureus, about 730 sRNAs have been verified, most of which currently have unknown functional, structural and mechanistic details [3,[5][6][7][8]. Small pathogenicity island RNAs of S. aureus are expressed from genomic pathogenicity islands that present virulence and antimicrobial resistance [9].…”