Trying on tRNA for Size: RNase P and the T-box Riboswitch as Molecular Rulers

Abstract

Length determination is a fundamental problem in biology and chemistry. Numerous proteins measure distances on linear biopolymers to exert effects with remarkable spatial precision. Recently, ruler-like devices made of noncoding RNAs have been structurally and biochemically characterized. Two prominent examples are the RNase P ribozyme and the T-box riboswitch. Both act as molecular calipers. The two RNAs clamp onto the elbow of tRNA (or pre-tRNA) and make distance measurements orthogonal to each other. Here, we compare and contrast the molecular ruler characteristics of these RNAs. RNase P appears pre-configured to measure a fixed distance on pre-tRNA to ensure the fidelity of its maturation. RNase P is a multiple-turnover ribozyme, and its rigid structure efficiently selects pre-tRNAs, cleaves, and releases them. In contrast, the T-box is flexible and segmented, an architecture that adapts to the intrinsically flexible tRNA. The tripartite T-box inspects the overall shape, anticodon sequence, and aminoacylation status of an incoming tRNA while it folds co-transcriptionally, leading to a singular, conditional genetic switching event. The elucidation of the structures and mechanisms of action of these two RNA molecular rulers may augur the discovery of new RNA measuring devices in noncoding and viral transcriptomes, and inform the design of artificial RNA rulers.

Hierarchical mechanism of amino acid sensing by the T-box riboswitch

“…1a, b ) 13 . Recent structural studies of Stem-I:tRNA complexes have revealed two conserved features of cognate tRNA selection: a sequence-specific interaction between the Specifier sequence and the tRNA anticodon, and a stacking interaction between a double T-loop motif (DTM) and the tRNA elbow that effectively acts as an architectural caliper 14 – 17 of the long side of the tRNA’s “L” shape (Fig. 1c ).…”

An evolving tale of two interacting RNAs—themes and variations of the T‐box riboswitch mechanism

“…3d). This motif is also present in the ribosome L1 stalk and in RNase P where it performs a similar task of recognizing the tRNA elbow (21,(40)(41)(42). Interestingly, bioinformatics and structural modeling analyses of T-box sequences correctly predicted the existence and unusual orientation of this motif, before being experimentally validated by the three crystal structures (43).…”

“…and ) . In addition, a short 2–3‐nt‐long pyrimidine‐rich bulge located between the AG bulge and the Specifier loop acts as a flexible hinge enabling Stem I to act as a tRNA‐measuring caliper . Additional Stem II and Stem IIA/B pseudoknot elements are present 3′ of Stem I in most T‐box riboswitches, such as the tyrS system (Fig.…”

“…The DTM orchestrates the presentation of a conserved base triple that uses its expansive flat surface to stack with the characteristically flat tRNA elbow to provide a platform for tRNA landing during cotranscriptional binding (Fig. g) .…”

Unknown unknowns: essential genes in quest for function

“…In particular, as engineers know, correct distances between objects or catalytic sites must be measured. Molecular rulers are involved in the process (Zhang and Ferré d'Amaré, ). The RulR/YlxR‐RulQ/YlxQ couple (with conserved gene synteny in Firmicutes), with RulQ (MMSYN1_0298) a ruler binding to the widespread RNA structural motif RNA kink turns (K‐turns (Baird et al ., )), bends the helical trajectory of the RNA by 120°, associated to RulR/YlxR, MMSYN1_0299.…”