sRNA₄₁ affects ribosome binding sites within polycistronic mRNAs in Methanosarcina mazei Gö1

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 sRNA₄₁ , highly expressed under N-sufficiency. Comprising 120 nucleotides, sRNA₄₁ 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 sRNA₄₁ 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 sRNA₄₁ -deletion mutant showed increased protein expression of both ACDS complexes in the absence of sRNA₄₁ , whereas no effect on transcript levels was detected, arguing for sRNA₄₁ -mediated post-transcriptional fine-tuning of ACDS expression. We hypothesize that the physiological advantage of downregulating sRNA₄₁ 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 N₂ -fixation, thus linking the carbon and N-metabolism.