Thiamine pyrophosphate riboswitch in some representative plant species: a bioinformatics study

Metabolites regulate their own production by directly interacting with highly conserved regions of mRNA that are capable of forming discrete tertiary structures. Such regions of mRNA are called riboswitches. The thiamine pyrophosphate (TPP) riboswitch is the most common riboswitch in different organisms. The TPP is an essential coenzyme that is synthesized by the coupling of pyrimidine (hydroxymethyl pyrimidine) and thiazole (hydroxyethyl thiazole). The TPP riboswitch was searched across all possible phyla of plant kingdom by using Arabidopsis thaliana, a model organism in which TPP riboswitch is already found. The aptameric domain of the TPP riboswitch is conserved at the sequence as well as structure levels in all chosen plant species. The sequence of the noncoding RNA that acts as a riboswitch and is folded into an appropriate stem-loop hairpin secondary structure with minimum free energy is predicted by several computational tools. Most of the secondary structures are similar but not the same, because of variation in sequence size. The TPP ligand can bind to the 3' untranslated region of the aptameric sequence, between the loops P2, P4, and P5 and the region between J2/3 and J4/5. The sequence of these loop regions in all predicted tertiary structure of the riboswitch in representative plant species--green algae to flowering plants--is the same, and the residues situated in these junctions are directly involved in binding thymine pyrophosphate and are conserved in all the representative species.