Conformation and mechanical property of rpoS mRNA inhibitory stem studied by optical tweezers and X-ray scattering

Xinyao Hu; Xuanling Li; Lingna Yang; Yilin Zhu; Yunyu Shi; Yinmei Li; Haowei Wang; Qingguo Gong

doi:10.1371/journal.pone.0222938

Conformation and mechanical property of rpoS mRNA inhibitory stem studied by optical tweezers and X-ray scattering

PLoS One. 2019 Sep 26;14(9):e0222938. doi: 10.1371/journal.pone.0222938. eCollection 2019.

Authors

Xinyao Hu¹, Xuanling Li¹, Lingna Yang², Yilin Zhu¹, Yunyu Shi^{1

2}, Yinmei Li¹, Haowei Wang¹, Qingguo Gong^{1

2}

Affiliations

¹ Department of Optics and Optical Engineering, University of Science and Technology of China and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui, P. R. China.
² School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P. R. China.

Abstract

3' downstream inhibitory stem plays a crucial role in locking rpoS mRNA 5' untranslated region in a self-inhibitory state. Here, we used optical tweezers to study the unfolding/refolding of rpoS inhibitory stem in the absence and presence of Mg2+. We found adding Mg2+ decreased the free energy of the RNA junction without re-arranging its secondary structure, through confirming that this RNA formed a canonical RNA three-way junction. We suspected increased free energy might change the relative orientation of different stems of rpoS and confirmed this by small angle X-ray scattering. Such changed conformation may improve Hfq-bridged annealing between sRNA and rpoS RNA inhibitory stem. We established a convenient route to analyze the changes of RNA conformation and folding dynamics by combining optical tweezers with X-ray scattering methods. This route can be easily applied in the studies of other RNA structure and ligand-RNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

3' Untranslated Regions / genetics*
Bacterial Proteins / genetics*
Escherichia coli Proteins / genetics*
Gene Expression Regulation, Bacterial
Magnesium / metabolism
Molecular Imaging / methods*
Nucleic Acid Conformation*
Optical Tweezers
Protein Biosynthesis / genetics
RNA Folding / genetics
Scattering, Small Angle
Sigma Factor / genetics*
X-Ray Diffraction

Substances

3' Untranslated Regions
Bacterial Proteins
Escherichia coli Proteins
Sigma Factor
sigma factor KatF protein, Bacteria
Magnesium

Grants and funding

This work was financially supported by the grants from the National Natural Science Foundation of China (grant 31870759, 61535011, 91540103), the Ministry of science and technology of China (2016YFA0500700) and the Strategic Priority Research Program of the Chinese Academy of Sciences (XDPB10). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.