Fluoride ion encapsulation by Mg2+ and phosphates in a fluoride riboswitch

Significant advances in our understanding of RNA architecture, folding and recognition have emerged from structure–function studies on riboswitches, non-coding RNAs whose sensing domains bind small ligands and whose adjacent expression platforms contain RNA elements involved in the control of gene regulation. We now report on the ligand-bound structure of the Thermotoga petrophila fluoride riboswitch, which adopts a higher-order RNA architecture stabilized by pseudoknot and long-range reversed Watson–Crick and Hoogsteen A•U pair formation. The bound fluoride ion is encapsulated within the junctional architecture, anchored in place through direct coordination to three Mg2+ ions, which in turn are octahedrally coordinated to water molecules and five inwardly pointing backbone phosphates. Our structure of the fluoride riboswitch in the bound state shows how RNA can form a binding pocket selective for fluoride, while discriminating against larger halide ions. The T. petrophila fluoride riboswitch probably functions in gene regulation through a transcription termination mechanism.

[1]  T. Steitz,et al.  Metals, Motifs, and Recognition in the Crystal Structure of a 5S rRNA Domain , 1997, Cell.

[2]  Evgeny Nudler,et al.  Sensing Small Molecules by Nascent RNA A Mechanism to Control Transcription in Bacteria , 2002, Cell.

[3]  R. Montange,et al.  Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine , 2004, Nature.

[4]  N. Ban,et al.  Structure of the Eukaryotic Thiamine Pyrophosphate Riboswitch with Its Regulatory Ligand , 2006, Science.

[5]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[6]  Randy J Read,et al.  Electronic Reprint Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination , 2022 .

[7]  Eric Westhof,et al.  Halogen bonds in biological molecules. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Yong Xiong,et al.  Structural basis of cooperative ligand binding by the glycine riboswitch. , 2011, Chemistry & biology.

[9]  A. Serganov,et al.  Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. , 2004, Chemistry & biology.

[10]  A. Serganov,et al.  Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch , 2009, Nature.

[11]  Renate Rieder,et al.  Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach , 2007, Nucleic acids research.

[12]  Zasha Weinberg,et al.  Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride , 2012, Science.

[13]  J. Doudna,et al.  A magnesium ion core at the heart of a ribozyme domain , 1997, Nature Structural Biology.

[14]  B. Ganem.  RNA world , 1987, Nature.

[15]  Ronald R. Breaker,et al.  Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression , 2002, Nature.

[16]  E. Nudler,et al.  The riboswitch control of bacterial metabolism. , 2004, Trends in biochemical sciences.

[17]  R. Breaker,et al.  Regulation of bacterial gene expression by riboswitches. , 2005, Annual review of microbiology.

[18]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[19]  Christian F. Perez,et al.  Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer , 2012, Proceedings of the National Academy of Sciences.

[20]  J. Doudna,et al.  Metal ions in ribozyme folding and catalysis. , 2000, Current opinion in chemical biology.

[21]  Zasha Weinberg,et al.  A Glycine-Dependent Riboswitch That Uses Cooperative Binding to Control Gene Expression , 2004, Science.

[22]  A. Serganov,et al.  Preparation and crystallization of riboswitch-ligand complexes. , 2009, Methods in molecular biology.

[23]  A. Serganov,et al.  Ribozymes, riboswitches and beyond: regulation of gene expression without proteins , 2007, Nature Reviews Genetics.

[24]  Catherine A. Wakeman,et al.  Structure and Mechanism of a Metal-Sensing Regulatory RNA , 2007, Cell.

[25]  A. Goldman,et al.  Toward a quantum-mechanical description of metal-assisted phosphoryl transfer in pyrophosphatase , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Thomas R. Schneider,et al.  HKL2MAP: a graphical user interface for macromolecular phasing with SHELX programs , 2004 .

[27]  R. Montange,et al.  Riboswitches: emerging themes in RNA structure and function. , 2008, Annual review of biophysics.

[28]  A. Serganov,et al.  Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch , 2006, Nature.

[29]  Jeffrey E. Barrick,et al.  Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria , 2003, Cell.

[30]  Eduardo A. Groisman,et al.  An RNA Sensor for Intracellular Mg2+ , 2006, Cell.

[31]  A. Serganov,et al.  Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch. , 2010, Molecular cell.