PreQ1 riboswitch

The PreQ1-I riboswitch is a cis-acting element identified in bacteria which regulates expression of genes involved in biosynthesis of the nucleoside queuosine (Q) from GTP.

PreQ1-III riboswitch has an atypically organized pseudoknot that does not appear to incorporate its downstream expression platform at its ribosome binding site (RBS).

[9] The first reported preQ1 riboswitch was located in the leader of the Bacillus subtilis ykvJKLM (queCDEF) operon which encodes four genes necessary for queuosine production.

[8] In this organism, PreQ1 binding to the riboswitch aptamer is thought to induce premature transcription termination within the leader to down-regulate expression of these genes.

[12] The preQ1 ligand is buried in the pseudoknot core and stabilized through intercalation between helical stacks and hydrogen bond interaction with heteroatoms.

[11] In presence of preQ1, the 3’ end of the adenine rich tail domain pairs with the center of P1 hairpin loop to form an H-type pseudoknot.

[13] Translation of protein in prokaryotes is initiated by binding of 30S ribosomal subunit to the Shine-Dalgarno (SD) sequence in mRNA.

[11] The translational riboswitch from bacteria Thermoanaerobacter tengcongensis (Tte) is observed to be transiently closed (pre-docked) in absence of preQ1, whereas in presence of preQ1 a fully docked state is adopted.

Secondary structure of preQ1 class 1 riboswitch from Bacillus subtilis ( Bsu ) obtained from ( PDB : 3FU2 ​) using web-based RNA structure software, viennaRNA web services where P1 and P2 are the stem region, and L1, L2 and L3 are the loop region. These two stems and three loops form H-type pseudoknot in presence of preQ1.
Docking and undocking mechanism of preQ1 riboswitch in presence and absence of ligand preQ1(shown in orange).