RNA helicase–regulated processing of the Synechocystis rimO–crhR operon results in differential cistron expression and accumulation of two sRNAs

Abstract

The arrangement of functionally-related genes in operons is a fundamental element of how genetic information is organized in prokaryotes. This organization ensures coordinated gene expression by co-transcription. Often, however, alternative genetic responses to specific stress conditions demand the discoordination of operon expression. During cold temperature stress, accumulation of the gene encoding the sole Asp-Glu-Ala-Asp (DEAD)-box RNA helicase in <i>Synechocystis</i> sp. PCC 6803, <i>crhR</i> (<i>slr0083</i>), increases 15-fold. Here, we show that <i>crhR</i> is expressed from a dicistronic operon with the methylthiotransferase <i>rimO/miaB</i> (<i>slr0082</i>) gene, followed by rapid processing of the operon transcript into two monocistronic mRNAs. This cleavage event is required for and results in destabilization of the <i>rimO</i> transcript. Results from secondary structure modeling and analysis of RNase E cleavage of the <i>rimO-crhR</i> transcript <i>in vitro</i> suggested that CrhR plays a role in enhancing the rate of the processing in an auto-regulatory manner. Moreover, two putative small RNAs are generated from additional processing, degradation, or both of the <i>rimO</i> transcript. These results suggest a role for the bacterial RNA helicase CrhR in RNase E-dependent mRNA processing in <i>Synechocystis</i> and expand the known range of organisms possessing small RNAs derived from processing of mRNA transcripts.