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


Autoři: Xinyao Hu aff001;  Xuanling Li aff001;  Lingna Yang aff002;  Yilin Zhu aff001;  Yunyu Shi aff001;  Yinmei Li aff001;  Haowei Wang aff001;  Qingguo Gong aff001
Působiště autorů: 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 aff001;  School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P. R. China aff002
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
doi: 10.1371/journal.pone.0222938

Souhrn

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.

Klíčová slova:

DNA transcription – Free energy – RNA structure – RNA annealing – Small-angle scattering – Molecular structure – Magnesium chloride – RNA folding


Zdroje

1. Battesti A, Majdalani N, Gottesman S. The RpoS-Mediated General Stress Response in Escherichia coli. Annu Rev Microbiol. 2011;65:189–213. PubMed PMID: WOS:000299463800012. doi: 10.1146/annurev-micro-090110-102946 21639793

2. Battesti A, Majdalani N, Gottesman S. The RpoS-mediated general stress response in Escherichia coli. Annu Rev Microbiol. 2011;65:189–213. Epub 2011/06/07. doi: 10.1146/annurev-micro-090110-102946 21639793.

3. Weber H, Polen T, Heuveling J, Wendisch VF, Hengge R. Genome-wide analysis of the general stress response network in Escherichia coli: sigma(S)-dependent genes, promoters, and sigma factor selectivity. Journal of Bacteriology. 2005;187(5):1591–603. PubMed PMID: WOS:000227191600006. doi: 10.1128/JB.187.5.1591-1603.2005 15716429

4. Hengge-Aronis R. Stationary phase gene regulation: what makes an Escherichia coli promoter sigma(s)-selective? Current Opinion in Microbiology. 2002;5(6):591–5. PubMed PMID: WOS:000179952800009. 12457703

5. Soper TJ, Woodson SA. The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA. Rna. 2008;14(9):1907–17. Epub 2008/07/29. doi: 10.1261/rna.1110608 18658123; PubMed Central PMCID: PMC2525945.

6. Peng Y, Curtis JE, Fang XY, Woodson SA. Structural model of an mRNA in complex with the bacterial chaperone Hfq. P Natl Acad Sci USA. 2014;111(48):17134–9. PubMed PMID: WOS:000345920800044.

7. Soper TJ, Woodson SA. The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA. Rna-a Publication of the Rna Society. 2008;14(9):1907–17. PubMed PMID: WOS:000258996100021.

8. Lease RA, Woodson SA. Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA. Journal of Molecular Biology. 2004;344(5):1211–23. PubMed PMID: WOS:000225503600005. doi: 10.1016/j.jmb.2004.10.006 15561140

9. Miao ZC, Westhof E. RNA Structure: Advances and Assessment of 3D Structure Prediction. Annu Rev Biophys. 2017;46:483–503. PubMed PMID: WOS:000402908700022. doi: 10.1146/annurev-biophys-070816-034125 28375730

10. Fazal FM, Block SM. Optical tweezers study life under tension. Nature Photonics. 2011;5(6):318–21. PubMed PMID: WOS:000291089000003.

11. Liphardt J, Onoa B, Smith SB, Tinoco I, Bustamante C. Reversible unfolding of single RNA molecules by mechanical force. Science. 2001;292(5517):733–7. PubMed PMID: WOS:000168478300053. doi: 10.1126/science.1058498 11326101

12. Anthony PC, Perez CF, Garcia-Garcia C, Block SM. Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer. P Natl Acad Sci USA. 2012;109(5):1485–9. PubMed PMID: WOS:000299731400035.

13. Ritchie DB, Woodside MT. Probing the structural dynamics of proteins and nucleic acids with optical tweezers. Curr Opin Struc Biol. 2015;34:43–51. PubMed PMID: WOS:000367484400008.

14. Konarev PV, Petoukhov MV, Volkov VV, Svergun DI. ATSAS 2.1, a program package for small-angle scattering data analysis. J Appl Crystallogr. 2006;39:277–86. PubMed PMID: WOS:000235991200021.

15. Konarev PV, Volkov VV, Sokolova AV, Koch MHJ, Svergun DI. PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J Appl Crystallogr. 2003;36:1277–82. PubMed PMID: WOS:000185178600026.

16. Semenyuk AV, Svergun DI. Gnom—a Program Package for Small-Angle Scattering Data-Processing. J Appl Crystallogr. 1991;24:537–40. PubMed PMID: WOS:A1991GL62900015.

17. Svergun DI. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J. 1999;76(6):2879–86. doi: 10.1016/S0006-3495(99)77443-6 PubMed PMID: WOS:000080556700002. 10354416

18. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31(13):3406–15. PubMed PMID: WOS:000183832900029. doi: 10.1093/nar/gkg595 12824337

19. Crooks GE. Path-ensemble averages in systems driven far from equilibrium. Phys Rev E. 2000;61(3):2361–6. PubMed PMID: WOS:000085994000031.

20. Lescoute A, Westhof E. Topology of three-way junctions in folded RNAs. Rna. 2006;12(1):83–93. PubMed PMID: WOS:000234648500009. doi: 10.1261/rna.2208106 16373494

21. Fang XY, Wang JB, O'Carroll IP, Mitchell M, Zuo XB, Wang Y, et al. An Unusual Topological Structure of the HIV-1 Rev Response Element. Cell. 2013;155(3):594–605. PubMed PMID: WOS:000326571800014. doi: 10.1016/j.cell.2013.10.008 24243017

22. Burke JE, Sashital DG, Zuo XB, Wang YX, Butcher SE. Structure of the yeast U2/U6 snRNA complex. Rna. 2012;18(4):673–83. PubMed PMID: WOS:000301954600007. doi: 10.1261/rna.031138.111 22328579

23. Fang XY, Stagno JR, Bhandari YR, Zuo XB, Wang YX. Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures. Curr Opin Struc Biol. 2015;30:147–60. PubMed PMID: WOS:000354588800019.

24. Li H, Aviran S. Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes. Nat Commun. 2018;9. ARTN 606 doi: 10.1038/s41467-018-02923-8 PubMed PMID: WOS:000424641200005. 29426922


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