RNA helicase-regulated processing of the operon results in differential cistron expression and accumulation of two sRNAs.

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 sp. PCC 6803, (), increases 15-fold. Here, we show that is expressed from a dicistronic operon with the methylthiotransferase () 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 transcript. Results from secondary structure modeling and analysis of RNase E cleavage of the transcript 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 transcript. These results suggest a role for the bacterial RNA helicase CrhR in RNase E-dependent mRNA processing in and expand the known range of organisms possessing small RNAs derived from processing of mRNA transcripts.