A dual functioning small RNA/Riboswitch controls the expression of the methionine biosynthesis regulator SahR in Desulfovibrio vulgaris Hildenborough

Abstract

ABSTRACTRiboswitches are cis-acting RNA regulatory elements that control expression of a downstream gene(s) by directly binding to a specific metabolite. Here we report a S-adenosylmethionine (SAM)-I riboswitch in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) that plays an additional regulatory role as a trans small noncoding RNA (sRNA) targeting the methionine biosynthesis cycle transcriptional regulator SahR. Sequence and expression analyses indicated that DseA (Desulfovibrio SAM element A) is located upstream of a small hypothetical protein DVU1170 and that the two are co-transcribed. Multiple techniques were used to verify the riboswitch activity of DseA and its activity as a transcriptional terminator in response to SAM. While determining a potential role for DseA in the methionine biosynthesis pathway, a mRNA target encoding SahR was identified. Subsequent electrophoretic mobility shift assays confirmed the ability of DseA to bind the sahR transcript and qRT-PCR analysis of a DseA deletion strain suggested a negative regulatory role. This study presents the first regulatory role for a newly discovered sRNA in Desulfovibrio. Additionally, this study suggests that DseA acts not only as a riboswitch, but also as a trans regulatory molecule.IMPORTANCESulfate-reducing bacteria (SRB) are important contributors to global geochemical cycles while also causing major issues for the petroleum and oil industry due to biocorrosion and souring of oil wells. Despite their significance, gene regulatory networks and pathways remain poorly understood in SRB. Here, we report a trans acting small noncoding RNA that plays a dual role as a SAM sensing riboswitch that controls the expression of a small hypothetical protein. Our findings provide important insights into the regulatory repertoire of sulfate-reducing bacteria.