sRNA41 affects ribosome binding sites within polycistronic mRNAs in Methanosarcina mazei Go1

Several noncoding RNAs potentially involved in nitrogen (N)-regulation have been detected in Methanosarcina mazei, however, targets have been identified only for one of them. Here, we report on the function of sRNA(41), highly expressed under N-sufficiency. Comprising 120 nucleotides, sRNA(41) shows high sequence and structural conservation within draft genomes of numerous Methanosarcina species. In silico target prediction revealed several potential targets, including genes of two homologous operons encoding for acetyl-CoA-decarbonylase/synthase complexes (ACDS) representing highly probable target candidates. A highly conserved single stranded region of sRNA(41) was predicted to mask six independent ribosome binding sites of these two polycistronic mRNAs and was verified in vitro by microscale thermophoresis. Proteome analysis of the respective sRNA(41)-deletion mutant showed increased protein expression of both ACDS complexes in the absence of sRNA(41), whereas no effect on transcript levels was detected, arguing for sRNA(41)-mediated post-transcriptional fine-tuning of ACDS expression. We hypothesize that the physiological advantage of downregulating sRNA(41) under N-limiting conditions is the resulting increase of ACDS protein levels. This provides sufficient amounts of amino acids for nitrogenase synthesis as well as reducing equivalents and energy for N-2-fixation, thus linking the carbon and N-metabolism.