Identification of microRNA-Size, Small RNAs in Escherichia coli

Abstract

Noncoding small regulatory RNA molecules control gene expression and microRNAs provide one of the best examples in eukaryotes. However, bacterial RNAs of comparable size to eukaryotic microRNAs have received little attention. Here, we demonstrate the existence of microRNA-size, small RNAs (msRNAs) in the model bacterium Escherichia coli. We examined the small RNAs in E. coli using a deep sequencing approach, and analyzed 33.2 million small RNA clone reads after size fractionation. Bioinformatic analysis of the whole set revealed more than 400 individual msRNA species. The cellular contents of selected highly expressed msRNAs were verified by quantitative RT-PCR and northern blotting. Although, the functional significance of these RNAs is unclear, their high abundance suggests that they may play specialized roles in bacteria, analogous to miRNAs in eukaryotes.

Tiny RNAs and their voyage via extracellular vesicles: Secretion of bacterial small RNA and eukaryotic microRNA

“…8,[42][43][44] Their existence in bacteria implies that these kinds of small RNAs are evolutionarily well-conserved from viruses and bacteria to mammals and that research into msRNA-mediated gene regulation may shed light on bacterial genetics.…”

How Our Other Genome Controls Our Epi-Genome

“…In fact, it has previously been suggested that bacteria, such as E. coli and Streptococcus mutans, produce OMVs that contain microRNA-like molecules [33,34]. However, the secondary structures of these 'microRNA-size' RNAs that the authors reported did not resemble those of eukaryotes' microRNAs.…”

Small and Smaller—sRNAs and MicroRNAs in the Regulation of Toxin Gene Expression in Prokaryotic Cells: A Mini-Review

“…Such molecules were found in Streptococcus mutans in 2011 [47] and in E. coli in 2013 [48], although their functions remain to be determined. Another microRNA of bacterial origin has been identified in Mycobacterium marinum , a fish pathogen able to produce a unique mycolactone toxin, mycolactone F [21].…”

“…All the above-presented prokaryotic microRNA-size molecules [20,21,22,47,48,49] have been identified by next generation sequencing (NGS). Such an experimental approach and bioinformatics analysis allowed for extracting large amounts of data and the identification of, e.g., more than 400 [48] or more than 900 [47] individual RNAs of microRNA size (15–26 nt) in a single experiment.…”

“…Such an experimental approach and bioinformatics analysis allowed for extracting large amounts of data and the identification of, e.g., more than 400 [48] or more than 900 [47] individual RNAs of microRNA size (15–26 nt) in a single experiment. Up to now, the cellular abundance of about 30 molecules identified by NGS [20,21,22,47,48,49] was validated experimentally, mainly by qRT-PCR and/or Northern blot techniques. Furthermore, in silico analyses allowed for the prediction and presentation of a total of 24 hairpin-structured precursors for the validated prokaryotic microRNA-size molecules [20,21,22,47,48,49].…”