Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for −1 ribosomal frameshifting stimulation

Minus-one ribosomal frameshifting is a translational recoding mechanism widely utilized by many RNA viruses to generate accurate ratios of structural and catalytic proteins. An RNA pseudoknot structure located in the overlapping region of the gag and pro genes of Simian Retrovirus type 1 (SRV-1) sti...

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Main Authors: Zhong, Zhensheng, Yang, Lixia, Zhang, Haiping, Shi, Jiahao, Vandana, J. Jeya, Lam, Do Thuy Uyen Ha, Olsthoorn, René C. L., Lu, Lanyuan, Chen, Gang
Other Authors: School of Biological Sciences
Format: Article
Language:English
Published: 2017
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Online Access:https://hdl.handle.net/10356/83910
http://hdl.handle.net/10220/42835
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spelling sg-ntu-dr.10356-839102023-02-28T17:03:47Z Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for −1 ribosomal frameshifting stimulation Zhong, Zhensheng Yang, Lixia Zhang, Haiping Shi, Jiahao Vandana, J. Jeya Lam, Do Thuy Uyen Ha Olsthoorn, René C. L. Lu, Lanyuan Chen, Gang School of Biological Sciences School of Physical and Mathematical Sciences Biophysical chemistry Molecular conformation Minus-one ribosomal frameshifting is a translational recoding mechanism widely utilized by many RNA viruses to generate accurate ratios of structural and catalytic proteins. An RNA pseudoknot structure located in the overlapping region of the gag and pro genes of Simian Retrovirus type 1 (SRV-1) stimulates frameshifting. However, the experimental characterization of SRV-1 pseudoknot (un)folding dynamics and the effect of the base triple formation is lacking. Here, we report the results of our single-molecule nanomanipulation using optical tweezers and theoretical simulation by steered molecular dynamics. Our results directly reveal that the energetic coupling between loop 2 and stem 1 via minor-groove base triple formation enhances the mechanical stability. The terminal base pair in stem 1 (directly in contact with a translating ribosome at the slippery site) also affects the mechanical stability of the pseudoknot. The −1 frameshifting efficiency is positively correlated with the cooperative one-step unfolding force and inversely correlated with the one-step mechanical unfolding rate at zero force. A significantly improved correlation was observed between −1 frameshifting efficiency and unfolding rate at forces of 15–35 pN, consistent with the fact that the ribosome is a force-generating molecular motor with helicase activity. No correlation was observed between thermal stability and −1 frameshifting efficiency. MOE (Min. of Education, S’pore) Published version 2017-07-12T08:03:14Z 2019-12-06T15:34:25Z 2017-07-12T08:03:14Z 2019-12-06T15:34:25Z 2016 Journal Article Zhong, Z., Yang, L., Zhang, H., Shi, J., Vandana, J. J., Lam, D. T. U. H., et al. (2016). Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for −1 ribosomal frameshifting stimulation. Scientific Reports, 6, 39549-. 2045-2322 https://hdl.handle.net/10356/83910 http://hdl.handle.net/10220/42835 10.1038/srep39549 en Scientific Reports © 2016 The Author(s). This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ 14 p. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic Biophysical chemistry
Molecular conformation
spellingShingle Biophysical chemistry
Molecular conformation
Zhong, Zhensheng
Yang, Lixia
Zhang, Haiping
Shi, Jiahao
Vandana, J. Jeya
Lam, Do Thuy Uyen Ha
Olsthoorn, René C. L.
Lu, Lanyuan
Chen, Gang
Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for −1 ribosomal frameshifting stimulation
description Minus-one ribosomal frameshifting is a translational recoding mechanism widely utilized by many RNA viruses to generate accurate ratios of structural and catalytic proteins. An RNA pseudoknot structure located in the overlapping region of the gag and pro genes of Simian Retrovirus type 1 (SRV-1) stimulates frameshifting. However, the experimental characterization of SRV-1 pseudoknot (un)folding dynamics and the effect of the base triple formation is lacking. Here, we report the results of our single-molecule nanomanipulation using optical tweezers and theoretical simulation by steered molecular dynamics. Our results directly reveal that the energetic coupling between loop 2 and stem 1 via minor-groove base triple formation enhances the mechanical stability. The terminal base pair in stem 1 (directly in contact with a translating ribosome at the slippery site) also affects the mechanical stability of the pseudoknot. The −1 frameshifting efficiency is positively correlated with the cooperative one-step unfolding force and inversely correlated with the one-step mechanical unfolding rate at zero force. A significantly improved correlation was observed between −1 frameshifting efficiency and unfolding rate at forces of 15–35 pN, consistent with the fact that the ribosome is a force-generating molecular motor with helicase activity. No correlation was observed between thermal stability and −1 frameshifting efficiency.
author2 School of Biological Sciences
author_facet School of Biological Sciences
Zhong, Zhensheng
Yang, Lixia
Zhang, Haiping
Shi, Jiahao
Vandana, J. Jeya
Lam, Do Thuy Uyen Ha
Olsthoorn, René C. L.
Lu, Lanyuan
Chen, Gang
format Article
author Zhong, Zhensheng
Yang, Lixia
Zhang, Haiping
Shi, Jiahao
Vandana, J. Jeya
Lam, Do Thuy Uyen Ha
Olsthoorn, René C. L.
Lu, Lanyuan
Chen, Gang
author_sort Zhong, Zhensheng
title Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for −1 ribosomal frameshifting stimulation
title_short Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for −1 ribosomal frameshifting stimulation
title_full Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for −1 ribosomal frameshifting stimulation
title_fullStr Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for −1 ribosomal frameshifting stimulation
title_full_unstemmed Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for −1 ribosomal frameshifting stimulation
title_sort mechanical unfolding kinetics of the srv-1 gag-pro mrna pseudoknot: possible implications for −1 ribosomal frameshifting stimulation
publishDate 2017
url https://hdl.handle.net/10356/83910
http://hdl.handle.net/10220/42835
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