The Thiamin Pyrophosphate Riboswitch is Affected by Lysine-derived Metabolic Conversion Products in Escherichia coli

Riboswitches are 5′ untranslated regulators that control gene expression by specifically monitoring cellular metabolites. Metabolite binding to the riboswitch triggers the genetic regulation at the transcriptional or translational level. Riboswitches typically exhibit high affinities and strong discrimination against non-cognate metabolites, making them well suited to regulate gene expression. Importantly, despite the well characterized cellular processes ensuring metabolic conversion and recycling in bacteria, there is little information about how these processes influence riboswitch regulation mechanisms. Here, we characterize the regulation mechanisms of the lysine-sensing and thiamin pyrophosphate (TPP)-sensing riboswitches in E. coli. In agreement with previous results, our study indicates that the addition of lysine or TPP to the growth medium significantly reduces the expression of the respective riboswitch-regulated mRNAs. Surprisingly, we find that the addition of lysine also leads to a significant decrease in TPP-regulated mRNAs, suggesting that lysine indirectly affects TPP riboswitches. Using mutant strains from the Keio collection, we observe that the effect of lysine on TPP riboswitches is lost when perturbing the lysine degradation process. These data suggest that lysine degradation products may be used to generate TPP through metabolic conversion. In contrast, our results indicate that TPP does not modulate the regulation of the lysine riboswitch, suggesting that TPP does not indirectly affect the lysine riboswitch genetic control. Together, our results indicate that intracellular changes in lysine concentrations can be detected by TPP riboswitches, thus suggesting that riboswitches may be sensitive to cellular stress that are not directly related to their cognate metabolite.