FMN riboswitch aptamer symmetry facilitates conformational switching through mutually exclusive coaxial stacking configurations

Wilt, Haley M.; Yu, Ping; Tan, Kemin; Wang, Yun-Xing; Stagno, Jason R.

doi:10.1016/j.yjsbx.2020.100035

Title: FMN riboswitch aptamer symmetry facilitates conformational switching through mutually exclusive coaxial stacking configurations

Journal Article · 31 December 2019 · Journal of Structural Biology: X

DOI: https://doi.org/10.1016/j.yjsbx.2020.100035 · OSTI ID:1772122

Wilt, Haley M.; Yu, Ping; Tan, Kemin; Wang, Yun-Xing; Stagno, Jason R.

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Sponsoring Organization:: USDOE

OSTI ID:: 1772122

Journal Information:: Journal of Structural Biology: X, Journal Name: Journal of Structural Biology: X Journal Issue: C Vol. 4; ISSN 2590-1524

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (38)

Riboswitch structure in the ligand-free state: Riboswitch structure in the ligand-free state Liberman, Joseph A.; Wedekind, Joseph E. Wiley Interdisciplinary Reviews: RNA, Vol. 3, Issue 3 https://doi.org/10.1002/wrna.114	journal	September 2011
Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design: Linking aptamer-ligand binding and expression platform folding in riboswitches Aboul-ela, Fareed; Huang, Wei; Abd Elrahman, Maaly Wiley Interdisciplinary Reviews: RNA, Vol. 6, Issue 6 https://doi.org/10.1002/wrna.1300	journal	September 2015
Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria Mandal, Maumita; Boese, Benjamin; Barrick, Jeffrey E. Cell, Vol. 113, Issue 5 https://doi.org/10.1016/S0092-8674(03)00391-X	journal	May 2003
A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes Gelfand, M. Trends in Genetics, Vol. 15, Issue 11 https://doi.org/10.1016/S0168-9525(99)01856-9	journal	November 1999
The purine riboswitch as a model system for exploring RNA biology and chemistry Porter, Ely B.; Marcano-Velázquez, Joan G.; Batey, Robert T. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Vol. 1839, Issue 10 https://doi.org/10.1016/j.bbagrm.2014.02.014	journal	October 2014
The Speed of RNA Transcription and Metabolite Binding Kinetics Operate an FMN Riboswitch Wickiser, J. Kenneth; Winkler, Wade C.; Breaker, Ronald R. Molecular Cell, Vol. 18, Issue 1 https://doi.org/10.1016/j.molcel.2005.02.032	journal	April 2005
Structure and mechanism of purine-binding riboswitches Batey, Robert T. Quarterly Reviews of Biophysics, Vol. 45, Issue 3 https://doi.org/10.1017/S0033583512000078	journal	July 2012
A simple and efficient method to reduce nontemplated nucleotide addition at the 3′ terminus of RNAs transcribed by T7 RNA polymerase Kao, C.; Zheng, M.; RÜDisser, S. RNA, Vol. 5, Issue 9 https://doi.org/10.1017/S1355838299991033	journal	September 1999
Structure–Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch Vicens, Quentin; Mondragón, Estefanía; Reyes, Francis E. ACS Chemical Biology, Vol. 13, Issue 10 https://doi.org/10.1021/acschembio.8b00533	journal	August 2018
Ribozymes and Riboswitches: Modulation of RNA Function by Small Molecules Zhang, Jinwei; Lau, Matthew W.; Ferré-D’Amaré, Adrian R. Biochemistry, Vol. 49, Issue 43 https://doi.org/10.1021/bi1012645	journal	November 2010
Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch Thore, Stéphane; Frick, Christian; Ban, Nenad Journal of the American Chemical Society, Vol. 130, Issue 26 https://doi.org/10.1021/ja801708e	journal	July 2008
Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch Serganov, Alexander; Polonskaia, Anna; Phan, Anh Tuân Nature, Vol. 441, Issue 7097 https://doi.org/10.1038/nature04740	journal	May 2006
Structural insights into amino acid binding and gene control by a lysine riboswitch Serganov, Alexander; Huang, Lili; Patel, Dinshaw J. Nature, Vol. 455, Issue 7217 https://doi.org/10.1038/nature07326	journal	September 2008
Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch Serganov, Alexander; Huang, Lili; Patel, Dinshaw J. Nature, Vol. 458, Issue 7235 https://doi.org/10.1038/nature07642	journal	January 2009
Super-resolution biomolecular crystallography with low-resolution data Schröder, Gunnar F.; Levitt, Michael; Brunger, Axel T. Nature, Vol. 464, Issue 7292 https://doi.org/10.1038/nature08892	journal	April 2010
Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography Stagno, J. R.; Liu, Y.; Bhandari, Y. R. Nature, Vol. 541, Issue 7636 https://doi.org/10.1038/nature20599	journal	November 2016
Riboswitches as antibacterial drug targets Blount, Kenneth F.; Breaker, Ronald R. Nature Biotechnology, Vol. 24, Issue 12 https://doi.org/10.1038/nbt1268	journal	December 2006
Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold Liberman, Joseph A.; Salim, Mohammad; Krucinska, Jolanta Nature Chemical Biology, Vol. 9, Issue 6 https://doi.org/10.1038/nchembio.1231	journal	April 2013
Antibacterial lysine analogs that target lysine riboswitches Blount, Kenneth F.; Wang, Joy Xin; Lim, Jinsoo Nature Chemical Biology, Vol. 3, Issue 1 https://doi.org/10.1038/nchembio842	journal	December 2006
Ribozymes, riboswitches and beyond: regulation of gene expression without proteins Serganov, Alexander; Patel, Dinshaw J. Nature Reviews Genetics, Vol. 8, Issue 10 https://doi.org/10.1038/nrg2172	journal	September 2007
Gene regulation by riboswitches Mandal, Maumita; Breaker, Ronald R. Nature Reviews Molecular Cell Biology, Vol. 5, Issue 6 https://doi.org/10.1038/nrm1403	journal	June 2004
Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions Li, Shuang; Su, Zhaoming; Lehmann, Jean Nature Structural & Molecular Biology, Vol. 26, Issue 12 https://doi.org/10.1038/s41594-019-0326-7	journal	November 2019
An mRNA structure that controls gene expression by binding FMN Winkler, W. C.; Cohen-Chalamish, S.; Breaker, R. R. Proceedings of the National Academy of Sciences, Vol. 99, Issue 25 https://doi.org/10.1073/pnas.212628899	journal	November 2002
Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation Vitreschak, A. G. Nucleic Acids Research, Vol. 30, Issue 14 https://doi.org/10.1093/nar/gkf433	journal	July 2002
Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection Vicens, Quentin; Mondragón, Estefanía; Batey, Robert T. Nucleic Acids Research, Vol. 39, Issue 19 https://doi.org/10.1093/nar/gkr565	journal	July 2011
Riboswitches and the RNA World Breaker, R. R. Cold Spring Harbor Perspectives in Biology, Vol. 4, Issue 2 https://doi.org/10.1101/cshperspect.a003566	journal	November 2010
Riboswitches and Translation Control Breaker, Ronald R. Cold Spring Harbor Perspectives in Biology, Vol. 10, Issue 11 https://doi.org/10.1101/cshperspect.a032797	journal	May 2018
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
Real-time crystallographic studies of the adenine riboswitch using an X-ray free-electron laser Stagno, Jason R.; Bhandari, Yuba R.; Conrad, Chelsie E. The FEBS Journal, Vol. 284, Issue 20 https://doi.org/10.1111/febs.14110	journal	August 2017
Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation Bailor, Maximillian H.; Sun, Xiaoyan; Al-Hashimi, Hashim M. Science, Vol. 327, Issue 5962 https://doi.org/10.1126/science.1181085	journal	January 2010
Long-Range Interactions in Riboswitch Control of Gene Expression Jones, Christopher P.; Ferré-D'Amaré, Adrian R. Annual Review of Biophysics, Vol. 46, Issue 1 https://doi.org/10.1146/annurev-biophys-070816-034042	journal	May 2017
The distributions, mechanisms, and structures of metabolite-binding riboswitches Barrick, Jeffrey E.; Breaker, Ronald R. Genome Biology, Vol. 8, Issue 11 https://doi.org/10.1186/gb-2007-8-11-r239	journal	January 2007
Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism Dussault, Anne-Marie; Dubé, Audrey; Jacques, Frédéric RNA, Vol. 23, Issue 10 https://doi.org/10.1261/rna.061796.117	journal	July 2017
Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis Baird, N. J.; Ferre-D'Amare, A. R. RNA, Vol. 16, Issue 3 https://doi.org/10.1261/rna.1852310	journal	January 2010
Novel Riboswitch Ligand Analogs as Selective Inhibitors of Guanine-Related Metabolic Pathways Mulhbacher, Jérôme; Brouillette, Eric; Allard, Marianne PLoS Pathogens, Vol. 6, Issue 4 https://doi.org/10.1371/journal.ppat.1000865	journal	April 2010

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