Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana

摘要

Riboswitches are RNA sensors that afect post-transcriptional processes through their ability to bindto small molecules. Thiamine pyrophosphate (TPP) riboswitch class is the most widespread riboswitchoccurring in all three domains of life. Even though it controls diferent genes involved in the synthesisor transport of thiamine and its phosphorylated derivatives in bacteria, archaea, fungi, and plants, theTPP aptamer has a conserved structure. In this study, we aimed at understanding diferences in thestructural dynamics of TPP riboswitches from Escherichia coli and Arabidopsis thaliana, based on theircrystallographic structures (TPPswec and TPPswat, respectively) and dynamics in aqueous solution,both in apo and holo states. A combination of Molecular Dynamics Simulations and Network Analysisempowered to fnd out slight diferences in the dynamical behavior of TPP riboswitches, althoughrelevant for their dynamics in bacteria and plants species. Our results suggest that distinct interactionsin the microenvironment surrounding nucleotide U36 of TPPswec (and U35 in TPPswat) are related todiferent responses to TPP. The network analysis showed that minor structural diferences in the aptamerenable enhanced intramolecular communication in the presence of TPP in TPPswec, but not in TPPswat.TPP riboswitches of plants present subtler and slower regulation mechanisms than bacteria do.