Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch
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 tra...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications Ltd
2017-02-01
|
| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/22883 |
| _version_ | 1811236072392228864 |
|---|---|
| author | My-Tra Le Wojciech K Kasprzak Taejin Kim Feng Gao Megan YL Young Xuefeng Yuan Bruce A Shapiro Joonil Seog Anne E Simon |
| author_facet | My-Tra Le Wojciech K Kasprzak Taejin Kim Feng Gao Megan YL Young Xuefeng Yuan Bruce A Shapiro Joonil Seog Anne E Simon |
| author_sort | My-Tra Le |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T12:02:41Z |
| format | Article |
| id | doaj.art-8c74356cd4e8482fa9a774dd09782c15 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T12:02:41Z |
| publishDate | 2017-02-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-8c74356cd4e8482fa9a774dd09782c152022-12-22T03:33:48ZengeLife Sciences Publications LtdeLife2050-084X2017-02-01610.7554/eLife.22883Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switchMy-Tra Le0Wojciech K Kasprzak1Taejin Kim2Feng Gao3Megan YL Young4Xuefeng Yuan5Bruce A Shapiro6Joonil Seog7Anne E Simon8https://orcid.org/0000-0001-6121-0704Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United StatesBasic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, United StatesRNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, United StatesDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, United StatesDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, United StatesDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, United StatesRNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, United StatesDepartment of Materials Science and Engineering, University of Maryland, College Park, United StatesDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, United StatesTurnip 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.https://elifesciences.org/articles/22883optical tweezersRNA structureTurnip crinkle virusmolecular dynamicsRNA virus |
| spellingShingle | My-Tra Le Wojciech K Kasprzak Taejin Kim Feng Gao Megan YL Young Xuefeng Yuan Bruce A Shapiro Joonil Seog Anne E Simon Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch eLife optical tweezers RNA structure Turnip crinkle virus molecular dynamics RNA virus |
| title | Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch |
| title_full | Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch |
| title_fullStr | Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch |
| title_full_unstemmed | Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch |
| title_short | Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch |
| title_sort | folding behavior of a t shaped ribosome binding translation enhancer implicated in a wide spread conformational switch |
| topic | optical tweezers RNA structure Turnip crinkle virus molecular dynamics RNA virus |
| url | https://elifesciences.org/articles/22883 |
| work_keys_str_mv | AT mytrale foldingbehaviorofatshapedribosomebindingtranslationenhancerimplicatedinawidespreadconformationalswitch AT wojciechkkasprzak foldingbehaviorofatshapedribosomebindingtranslationenhancerimplicatedinawidespreadconformationalswitch AT taejinkim foldingbehaviorofatshapedribosomebindingtranslationenhancerimplicatedinawidespreadconformationalswitch AT fenggao foldingbehaviorofatshapedribosomebindingtranslationenhancerimplicatedinawidespreadconformationalswitch AT meganylyoung foldingbehaviorofatshapedribosomebindingtranslationenhancerimplicatedinawidespreadconformationalswitch AT xuefengyuan foldingbehaviorofatshapedribosomebindingtranslationenhancerimplicatedinawidespreadconformationalswitch AT bruceashapiro foldingbehaviorofatshapedribosomebindingtranslationenhancerimplicatedinawidespreadconformationalswitch AT joonilseog foldingbehaviorofatshapedribosomebindingtranslationenhancerimplicatedinawidespreadconformationalswitch AT anneesimon foldingbehaviorofatshapedribosomebindingtranslationenhancerimplicatedinawidespreadconformationalswitch |