Format

Send to

Choose Destination
Elife. 2017 Feb 13;6. pii: e22883. doi: 10.7554/eLife.22883.

Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch.

Author information

1
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States.
2
Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, United States.
3
RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, United States.
4
Department of Materials Science and Engineering, University of Maryland, College Park, United States.

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.

KEYWORDS:

RNA structure; RNA virus; Turnip crinkle virus; biophysics; molecular dynamics; optical tweezers; structural biology

PMID:
28186489
PMCID:
PMC5336357
DOI:
10.7554/eLife.22883
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for eLife Sciences Publications, Ltd Icon for PubMed Central
Loading ...
Support Center