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 (pre-queuosine1) is an intermediate in the queuosine pathway, and preQ1 riboswitch, as a type of riboswitch, is an RNA element that binds preQ1. The preQ1 riboswitch is distinguished by its unusually small aptamer, compared to other riboswitches. Its atomic-resolution three-dimensional structure has been determined, with the PDB ID 2L1V.
PreQ1 classification
Three subcategories of the PreQ1 riboswitch exist: preQ1-I, preQ1-II, and preQ1-III. PreQ1-I has a distinctly small aptamer, ranging from 25 to 45 nucleotides long, compared to the structures of PreQ1-II riboswitch and preQ1-III riboswitch. PreQ1-II riboswitch, only found in Lactobacillales, has a larger and more complex consensus sequence and structure than preQ1-I riboswitch, with an average of 58 nucleotides composing its aptamer, which forms as many as five base-paired substructures. PreQ1-III riboswitch has a distinct structure and is also larger in aptamer size than preQ1-I riboswitch, ranging from sizes ranging from 33 to 58 nucleotides. PreQ1-III riboswitch has an atypically organized pseudoknot that does not appear to incorporate its downstream expression platform at its ribosome binding site (RBS).
History
While preQ1 was first discovered as an anticodon sequence of tRNAs from E.coli in 1972, preQ1 riboswitch was not first found until 2004 and recognized even later. 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. 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. Later on, preQ1 riboswitch was identified as a conserved sequence on the 5' UTR of genes in many gram-positive bacteria and was proved to be associated with synthesis of preQ1.
In 2008, a second class of preQ1 riboswitch (PreQ1-II riboswitches) was also found as a representative of the COG4708 RNA motif from Streptococcus pneumoniae R6. Although PreQ1-II riboswitch also works as queuosine biosynthetic intermediate, the structural and molecular recognition characteristics are distinct from preQ1-I riboswitch, indicating that natural aptamers utilizing different structures to bind the same metabolite may be more common than is currently known.
Structure and function
PreQ1 riboswitch has two stems and three loops, and its detailed structure has been shown on the right. The riboswitching action of preQ1 riboswitches in bacteria is regulated by binding of metabolite preQ1 to the aptamer region leading to structural changes in the messenger RNA (mRNA) that governs the downstream genetic regulation. The preQ1 riboswitch structure adopts a compact H-type pseudoknot, which makes it quite different from other purine based riboswitches. The preQ1 ligand is buried in the pseudoknot core and stabilized through intercalation between helical stacks and hydrogen bond interaction with heteroatoms. In absence of preQ1, the P2 tail region is away from the P2 loop region and hence the riboswitch is observed to be in undocked (partially docked) state, whereas on the binding of preQ1 to the riboswitch results the two P2 regions to come closer causing a complete docking of riboswitch. This docking and undocking mechanism of riboswitch with the change in concentration of ligand preQ1 is observed to control the signaling of gene regulation, commonly known as “ON” or “OFF” signaling for gene expression. The docking and undocking mechanism are observed to be affected not only by the ligand, but also with other factors like Mg salt. Like any other riboswitch, the two most common types of gene regulation mediated by preQ1 riboswitch are through transcription attenuation or inhibition of translation initiation. Ligand binding to the transcriptional riboswitch in bacterial causes modification in the structure of riboswitch unit, which leads to hindrance in the activity of RNA polymerase causing attenuation of transcription. Similarly, binding of the ligand to the translational riboswitch causes modification in the secondary structure of riboswitch unit leading to hindrance for ribosome binding and hence inhibiting translational initiation.