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Updated: Sep 19, 2025
13:42
RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
31.7K
A pseudouridine synthase shapes tRNA structural dynamics through both catalysis and remodeling
Research Square
|June 5, 2025
Summary
Transfer RNA (tRNA) dynamically samples conformations. The enzyme Pus4/TruB remodels tRNA structure, with pseudouridylation accelerating this process and influencing enzyme activity.
Area of Science:
- Molecular Biology
- Biochemistry
- Structural Biology
Background:
- Transfer RNA (tRNA) is a crucial molecule known for its stable structure.
- tRNA undergoes significant conformational changes when interacting with modification enzymes.
- Pseudouridine modification is a key tRNA alteration impacting its function.
Purpose of the Study:
- To investigate the dynamic structural changes of tRNA upon interaction with the pseudouridine synthase Pus4/TruB.
- To compare the conformational ensembles of unmodified and pseudouridylated tRNA.
- To elucidate the role of Pus4/TruB's catalytic activity in tRNA structural remodeling.
Main Methods:
- Optical binding assays were employed to study molecular interactions.
- Single-molecule Förster Resonance Energy Transfer (smFRET) was used to monitor tRNA structural dynamics.
- The conformational states of tRNA were analyzed before and after interaction with Pus4/TruB.
Main Results:
- Unmodified and pseudouridylated tRNA dynamically sample open and closed conformations.
- Pus4/TruB binding to unmodified tRNA induces additional conformational states.
- Pre-pseudouridylated tRNA adopts the final ensemble faster upon Pus4/TruB binding.
- A catalytically inactive Pus4 mutant exhibits altered binding kinetics and remodeling compared to wild-type.
Conclusions:
- Pus4/TruB catalyzes both a chemical modification and a time-dependent structural remodeling of tRNA.
- Enzyme-induced tRNA structural changes may facilitate subsequent maturation steps.
- tRNA structural dynamics are critical for enzyme recognition and modification processes.
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