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

Atsuko Shinhara,Motomu Matsui,Kiriko Hiraoka,Akio Kanai,Wataru Nomura,Masaru Tomita,Kenji Nakahigashi,Hirotada Mori,Reiko Hirano

doi:10.1186/1471-2164-12-428

Atsuko Shinhara, Motomu Matsui + Show 7 more

Open Access

https://doi.org/10.1186/1471-2164-12-428

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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.

Highlights

In Escherichia coli, approximately 100 regulatory small RNAs have been identified experimentally and many more have been predicted by various methods
The majority of reads that mapped to annotated regions (Figure 1A [b]) corresponded to rRNAs (73.7%) or tRNAs (12.8%), and the remainder corresponded to coding sequences (CDSs; 4.9%), previously known sRNAs (3.0%), untranslated regions (UTRs; 5.6%) or other regions such as pseudogenes or phantom genes (0.1%)
The reads located on cis-antisense strands of the ribosomal binding sites (RBSs) of known genes, in particular, may be involved in post-transcriptional regulation of mRNAs [2]

Summary

Introduction

In Escherichia coli, approximately 100 regulatory small RNAs (sRNAs) have been identified experimentally and many more have been predicted by various methods. RNA molecules are known to be key genetic regulators in diverse organisms. In bacteria, these regulatory RNAs are generally referred to as small RNAs (sRNAs) because they usually range from 50 to 200 nt in length [1]. It has been reported that the majority of bacterial sRNAs are synthesised under very specific growth conditions and that these RNAs are regulators of gene expression in response to environmental stresses [2,3] such as low iron [4], oxidative stress [5] and elevated glucose-phosphate levels [6]. In Escherichia coli (E. coli), the most exhaustive and diverse searches for sRNAs have been conducted with several methods: high-throughput

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