Abstract
Riboswitches are RNA sensors that affect post-transcriptional processes through their ability to bind to small molecules. Thiamine pyrophosphate (TPP) riboswitch class is the most widespread riboswitch occurring in all three domains of life. Even though it controls different genes involved in the synthesis or transport of thiamine and its phosphorylated derivatives in bacteria, archaea, fungi, and plants, the TPP aptamer has a conserved structure. In this study, we aimed at understanding differences in the structural dynamics of TPP riboswitches from Escherichia coli and Arabidopsis thaliana, based on their crystallographic structures (TPPswec and TPPswat, respectively) and dynamics in aqueous solution, both in apo and holo states. A combination of Molecular Dynamics Simulations and Network Analysis empowered to find out slight differences in the dynamical behavior of TPP riboswitches, although relevant for their dynamics in bacteria and plants species. Our results suggest that distinct interactions in the microenvironment surrounding nucleotide U36 of TPPswec (and U35 in TPPswat) are related to different responses to TPP. The network analysis showed that minor structural differences in the aptamer enable 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.
Highlights
Riboswitches are natural ribonucleic acid (RNA) sensors that affect post-transcriptional processes through their ability to bind to small molecules such as vitamins, amino acids and nucleotides[1,2]
Genes regulated by a given riboswitch are involved in biosynthesis, catabolism, signaling or transport of a metabolite that binds to the riboswitch, creating feedback regulation mechanisms to control its adequate levels[9]
Differences can be found in the J2-4 junction and P2 helix, in which an additional pairing in TPP riboswitch 3D-structures of Escherichia coli (TPPswec) is formed
Summary
Riboswitches are natural ribonucleic acid (RNA) sensors that affect post-transcriptional processes through their ability to bind to small molecules such as vitamins, amino acids and nucleotides[1,2]. The sensory domain is the aptamer, whose sequence and structure are highly conserved It acts as a receptor for particular metabolites, whereas the binding of small molecules are transduced to genetic regulatory signals by the expression platform localized adjacent to the aptamer[10]. This is achieved by a structural rearrangement, resulting in an immediate RNA conformational change that alters mRNA translation. The only riboswitch described in eukaryotes was the TPP riboswitch, since most of the studies have been carried out in prokaryotic organisms[11]. Expression at the translation level[11,12], while the second guides both translation and transcription of 5′ UTR region of the thiC gene[11]
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