Regulatory small RNAs from the 3′ regions of bacterial mRNAs

• 3′ regions of bacterial mRNAs are emerging as a rich source of regulatory sRNAs.
• Two major types of sRNA biogenesis from mRNA 3′ regions.
• sRNAs from mRNA 3′ regions act in diverse physiological regulons.
• mRNA 3′ end processing enables mRNA crosstalk in bacteria.
• Many such sRNAs bind Hfq but are also found in organisms without Hfq.

Most studies of small regulatory RNAs in bacteria have focussed on conserved transcripts in intergenic regions. However, several recent developments including single-nucleotide resolution transcriptome profiling by RNA-seq and increased knowledge of the cellular targets of the RNA chaperone Hfq suggest that the bacterial world of functional small RNAs is more diverse. One emerging class are small RNAs that are identical to the 3′ regions of known mRNAs, but are produced either by transcription from internal promoters or by mRNA processing. Using several recently discovered examples of such sRNAs, we discuss their biogenesis and modes of action, and illustrate how they can facilitate mRNA crosstalk in various physiological processes.

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