BSRD: a repository for bacterial small regulatory RNA

Abstract

In bacteria, small regulatory non-coding RNAs (sRNAs) are the most abundant class of post-transcriptional regulators. They are involved in diverse processes including quorum sensing, stress response, virulence and carbon metabolism. Recent developments in high-throughput techniques, such as genomic tiling arrays and RNA-Seq, have allowed efficient detection and characterization of bacterial sRNAs. However, a comprehensive repository to host sRNAs and their annotations is not available. Existing databases suffer from a limited number of bacterial species or sRNAs included. In addition, these databases do not have tools to integrate or analyse high-throughput sequencing data. Here, we have developed BSRD (http://kwanlab.bio.cuhk.edu.hk/BSRD), a comprehensive bacterial sRNAs database, as a repository for published bacterial sRNA sequences with annotations and expression profiles. BSRD contains over nine times more experimentally validated sRNAs than any other available databases. BSRD also provides combinatorial regulatory networks of transcription factors and sRNAs with their common targets. We have built and implemented in BSRD a novel RNA-Seq analysis platform, sRNADeep, to characterize sRNAs in large-scale transcriptome sequencing projects. We will update BSRD regularly.

Absence of YbeY RNase compromises the growth and enhances the virulence plasmid gene expression of Yersinia enterocolitica O:3

“…Due to the fact that the role of non-coding RNA particles in the gene regulation of Yersinia species has been long established (Schiano & Lathem, 2012) and YbeY was implicated into sRNA regulation, the possible role of YbeY in sRNA regulation was investigated. Based on data obtained from the repository for bacterial sRNA (Li et al, 2013) for the serotype O:8 a list of predicted sRNAs was prepared. Subsequently, the sequences of these sRNAs were blasted against the genomic DNA of Y. enterocolitica Y11 and the expression of selected regions was verified using the RNA-seq data.…”

SRD: a Staphylococcus regulatory RNA database

“…Compared with the databases on other prokaryotes sRNAs, SRD is the first sRNA database dedicated to the Staphylococcus genus. SRD assigned a single identifier for the whole genus while other sRNA databases, such as BSRD (Li et al 2013), provide an index per strain. A unique identifier offers a substantial advantage when comparing different strains, as it should avoid the dissemination of multiple redundancies.…”

“…aureus species. While 154 sRNAs were listed for strain N315, mostly based on the work of Beaume et al (2010), there were <60 sequences inventoried by similarity for other Staphylococcal strains (Li et al 2013). All BSRD S. aureus entries are present in our database, and the predictions performed within the genus from a set of 575 srn genes (versus 8248 genes for BSRD), led to a larger set of predicted genes in SRD (Table 4).…”

“…sRNATarbase (Cao et al 2010) was implemented to provide a list of sRNA targets, but is out of date for Staphylococci. Recently, two bacterial sRNA databases were developed: (i) sRNAdb, which focused exclusively on Gram-positive bacteria (Pischimarov et al 2012) but provides only 39 sRNA sequences for S. aureus; (ii) BSRD is a generalist bacterial sRNA database with >700 species included (Li et al 2013). Finally, RNAspace.org is a platform devoted to the prediction, annotation, and analysis of noncoding RNA but does not provide data set (Cros et al 2011).…”

Regulatory RNAs

“…This period of intense discovery has led to the realization of the ubiquitous presence of these short non-coding RNAs throughout bacterial genomes, and of their value as controllers. [4][5][6] Furthermore, regulatory RNAs are involved in important sensing functions and regulatory responses to environmental cues. 7 As these sophisticated regulators are explored and their mechanisms and functions unveiled, Synthetic Biology has continued to arise as a field.…”