Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli

Abstract

BackgroundIn Escherichia coli, approximately 100 regulatory small RNAs (sRNAs) have been identified experimentally and many more have been predicted by various methods. To provide a comprehensive overview of sRNAs, we analysed the low-molecular-weight RNAs (< 200 nt) of E. coli with deep sequencing, because the regulatory RNAs in bacteria are usually 50-200 nt in length.ResultsWe discovered 229 novel candidate sRNAs (≥ 50 nt) with computational or experimental evidence of transcription initiation. Among them, the expression of seven intergenic sRNAs and three cis-antisense sRNAs was detected by northern blot analysis. Interestingly, five novel sRNAs are expressed from prophage regions and we note that these sRNAs have several specific characteristics. Furthermore, we conducted an evolutionary conservation analysis of the candidate sRNAs and summarised the data among closely related bacterial strains.ConclusionsThis comprehensive screen for E. coli sRNAs using a deep sequencing approach has shown that many as-yet-undiscovered sRNAs are potentially encoded in the E. coli genome. We constructed the Escherichia coli Small RNA Browser (ECSBrowser; http://rna.iab.keio.ac.jp/), which integrates the data for previously identified sRNAs and the novel sRNAs found in this study.

Metatranscriptomic Analysis of Microbes in an Oceanfront Deep-Subsurface Hot Spring Reveals Novel Small RNAs and Type-Specific tRNA Degradation

“…(29,51). The developmentally regulated cleavage of tRNAs also has been observed in the bacterium Streptomyces coelicolor (22).…”

“…For example, about 80 sRNAs from Escherichia coli have been registered in RegulonDB (17), and these have been identified with several methods: high-throughput computational searches (2,10,47,69), shotgun cloning (29,60), and tiling array analyses (58,70). In recent years, a new powerful method, next-generation sequencing technology, has been used to discover new sRNAs in the Bacteria, and the results have shown that hundreds of still-undiscovered sRNA genes might exist in the E. coli genome (45,51). It has been reported that the majority of bacterial sRNAs are regulators of gene expression in response to environmental stresses (38) and typically are involved in the modulation of translation efficiency and the stability of mRNA molecules (1).…”

Rho and NusG suppress pervasive antisense transcription in Escherichia coli

“…Antisense transcripts have been identified in diverse bacteria (Georg and Hess 2011), including Bacillus subtilis (Rasmussen et al 2009;Irnov et al 2010;Nicolas et al 2012) and Escherichia coli (Peters et al 2009;Dornenburg et al 2010;Shinhara et al 2011). With the exception of a few well-studied examples (e.g., l OOP [Krinke and Wulff 1987] and E. coli GadY [Opdyke et al 2004]), bacterial antisense transcripts remain largely uncharacterized.…”

Control of Gene Expression at a Bacterial Leader RNA, the agn43 Gene Encoding Outer Membrane Protein Ag43 of Escherichia coli

“…Of course, it is also possible that the terminated leader RNA functions as a small RNA (sRNA), affecting CsrD expression. Indeed, RNAs with a length and sequence consistent with the terminated agn43 leader RNA (named IsrC) were detected at low levels in the cell (40,41). The terminated leader RNA might have defined roles under conditions of nutrient limitation, where termination would take place most frequently.…”