Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand
- University of Chicago, United States
- Northwestern University, United States
Abstract
T-box riboswitches are cis-regulatory RNA elements that regulate the expression of proteins involved in amino acid biosynthesis and transport by binding to specific tRNAs and sensing their aminoacylation state. While the T-box modular structural elements that recognize different parts of a tRNA have been identified, the kinetic trajectory describing how these interactions are established temporally remains unclear. Using smFRET, we demonstrate that tRNA binds to the riboswitch in two steps, first anticodon recognition followed by the sensing of the 3' NCCA end, with the second step accompanied by a T-box riboswitch conformational change. Studies on site-specific mutants highlight that specific T-box structural elements drive the two-step binding process in a modular fashion. Our results set up a kinetic framework describing tRNA binding by T-box riboswitches, and propose such binding mechanism is kinetically beneficial for efficient, co-transcriptional recognition of the cognate tRNA ligand.
Data availability
All data generated or analysed during this study are included in the manuscript and supporting files. smFRET trajectories of each data sets included in the manuscript are available in Source Data.
Article and author information
Author details
Funding
Chicago Community Trust
- Jingyi Fei
Chicago Community Trust
- Alfonso Mondragon
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2018, Zhang et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
