Riboswitches are regulatory mRNA elements that, upon binding metabolites, alter the secondary and tertiary structure and influence the regulation of gene expression. Prequeuosine 1 (preQ1) riboswitches are responsible for the regulation of preQ1 biosynthesis and transport. PreQ1 is a precursor molecule of hypermodified guanine nucleotide Q, which is found at wobble sites in tRNA molecules. The aptamer domain of preQ1 riboswitch originating from the bacteria T. tengcongensis recognizes both the preQ1 ligand and modified ligand O6-methyl prequeuosine (m6preQ1). Upon binding of the m6preQ1, the transfer of methyl group from the ligand to a cytosine residue occurs, resulting in specific methylation of RNA and release of preQ1 ligand. Methylation is a widespread post-transcriptional modification that occurs in coding and non-coding RNA that can also affect the regulatory function of riboswitches. The methyltransferase reaction is thought to represent the connection between modern riboswitches and the prebiotic RNA world, where riboswitches have regulated, and ribozymes have catalysed metabolic reactions. Using NMR spectroscopy, we have determined that the addition of methylated and unmethylated ligands induces the folding of the T. tengcongensis preQ1 riboswitch. The methyltransferase reaction of preQ1 riboswitch and m6preQ1 is specific for class I and type 1 preQ1 riboswitches. Identification of riboswitches with methyltransferase activity can serve as starting points for engineering in vitro and in vivo methylation tools.
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