Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch
Abstract
Turnip crinkle virus contains a T-shaped, ribosome-binding, translation enhancer (TSS) in its 3'UTR that serves as a hub for interactions throughout the region. The viral RNA-dependent RNA polymerase (RdRp) causes the TSS/surrounding region to undergo a conformational shift postulated to inhibit translation. Using optical tweezers (OT) and steered molecular dynamic simulations (SMD), we found that the unusual stability of pseudoknotted element H4a/Ψ3 required five upstream adenylates, and H4a/Ψ3 was necessary for cooperative association of two other hairpins (H5/H4b) in Mg2+. SMD recapitulated the TSS unfolding order in the absence of Mg2+, showed dependence of the resistance to pulling on the 3D orientation and gave structural insights into the measured contour lengths of the TSS structure elements. Adenylate mutations eliminated one-site RdRp binding to the 3'UTR, suggesting that RdRp binding to the adenylates disrupts H4a/Ψ3, leading to loss of H5/H4b interaction and promoting a conformational switch interrupting translation and promoting replication.
Article and author information
Author details
Funding
National Science Foundation (MCB-1411836)
- My-Tra Le
- Feng Gao
- Megan YL Young
- Xuefeng Yuan
- Anne E Simon
National Institutes of Health (R21AI117882-01)
- My-Tra Le
- Feng Gao
- Anne E Simon
National Cancer Institute (Intramural)
- Wojciech K Kasprzak
- Taejin Kim
- Bruce A Shapiro
National Institutes of Health (T32GM080201)
- Megan YL Young
National Institutes of Health (2T32AI051967-06A1)
- Megan YL Young
- Anne E Simon
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Nahum Sonenberg, McGill University, Canada
Version history
- Received: November 3, 2016
- Accepted: February 7, 2017
- Accepted Manuscript published: February 10, 2017 (version 1)
- Accepted Manuscript updated: February 13, 2017 (version 2)
- Version of Record published: March 3, 2017 (version 3)
Copyright
© 2017, Le 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.
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