Mechanism of ligand binding signal transduction in a transcriptional riboswitch.

Abstract

Riboswitches are noncoding RNA molecules that regulate gene expression in bacteria. The riboswitch's aptamer domain (AD) senses the cognate ligand and induces a structural change in the expression platform (EP) to signal on/off to the gene expression machinery. Despite extensive studies, the question of how the ligand binding signal is transmitted from the AD to EP resulting in the structural transitions in the EP remains unanswered. We studied the ligand binding signal transduction from AD to EP in the preQ1-sensing transcriptional riboswitch. In the absence of preQ1, both AD and EP individually form stem-loops with no structural overlap between the two stem-loops. The segment between the AD and EP stem loops is rich in adenine. In the presence of preQ1, AD forms a pseudoknot to encapsulate preQ1. We performed coarse-grained molecular dynamics simulations of full-length preQ1 riboswitch in the presence of Mg2+ and preQ1 ligand. In the absence of preQ1 and variation in Mg2+ concentration ([Mg2+]), we observed that AD populates only stem-loop and does not form the pseudoknot required to capture the ligand. Only in the presence of preQ1 AD attains the pseudoknot conformation by wrapping the A-rich region around the pre-existing stem-loop to facilitate ligand binding. The pseudoknot formation at AD allows EP to form the terminator helix and sequester the poly-U through strand invasion. The wrapping of the A-rich region around the AD stem-loop forces the stem-loop at EP to rupture and slide by 10 nucleotides towards 3'-end and form the terminator helix. The propensity of pseudoknot and terminator formation through strand invasion in the presence of preQ1 is enhanced with increment in [Mg2+]. We show that the competition between base-pair formation and helix sliding rate is crucial for the ligand binding signal transduction.