Metabolite Recognition Principles and Molecular Mechanisms Underlying Riboswitch Function

The Dynamic Nature of RNA as Key to Understanding Riboswitch Mechanisms

(2011) Andrea Haller et al.   ACCOUNTS OF CHEMICAL RESEARCH

glmS Riboswitch Binding to the Glucosamine-6-phosphate α-Anomer Shifts the pKatoward Neutrality

(2011) Jared H. Davis et al.   BIOCHEMISTRY

Novel Ligands for a Purine Riboswitch Discovered by RNA-Ligand Docking

(2011) Peter Daldrop et al.   CHEMISTRY & BIOLOGY

Structural Basis of Cooperative Ligand Binding by the Glycine Riboswitch

(2011) Ethan B. Butler et al.   CHEMISTRY & BIOLOGY

Mg2+facilitates leader peptide translation to induce riboswitch-mediated transcription termination

(2011) Guang Zhao et al.   EMBO JOURNAL

Comparison of a PreQ1Riboswitch Aptamer in Metabolite-bound and Free States with Implications for Gene Regulation

(2011) Jermaine L. Jenkins et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Constitutive Regulatory Activity of an Evolutionarily Excluded Riboswitch Variant

(2011) Renaud Tremblay et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Insights into Metalloregulation by M-box Riboswitch RNAs via Structural Analysis of Manganese-Bound Complexes

(2011) Arati Ramesh et al.   JOURNAL OF MOLECULAR BIOLOGY

Differential Analogue Binding by Two Classes of c-di-GMP Riboswitches

(2011) Carly A. Shanahan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural principles of nucleoside selectivity in a 2′-deoxyguanosine riboswitch

(2011) Olga Pikovskaya et al.   Nature Chemical Biology

Molecular insights into the ligand-controlled organization of the SAM-I riboswitch

(2011) Benoit Heppell et al.   Nature Chemical Biology

Conformational capture of the SAM-II riboswitch

(2011) Andrea Haller et al.   Nature Chemical Biology

The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo

(2011) Peter Y Watson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection

(2011) Quentin Vicens et al.   NUCLEIC ACIDS RESEARCH

Single-molecule force spectroscopy of the add adenine riboswitch relates folding to regulatory mechanism

(2011) Krishna Neupane et al.   NUCLEIC ACIDS RESEARCH

Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch

(2011) L. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis of differential ligand recognition by two classes of bis-(3'-5')-cyclic dimeric guanosine monophosphate-binding riboswitches

(2011) K. D. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial aptamers that selectively bind glutamine

(2011) Tyler D. Ames et al.   RNA Biology

Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride

(2011) J. L. Baker et al.   SCIENCE

The Structure of a Tetrahydrofolate-Sensing Riboswitch Reveals Two Ligand Binding Sites in a Single Aptamer

(2011) Jeremiah J. Trausch et al.   STRUCTURE

Comparative Study between Transcriptionally- and Translationally-Acting Adenine Riboswitches Reveals Key Differences in Riboswitch Regulatory Mechanisms

(2011) Jean-François Lemay et al.   PLoS Genetics

Multivector Fluorescence Analysis of thexptGuanine Riboswitch Aptamer Domain and the Conformational Role of Guanine

(2010) Michael D. Brenner et al.   BIOCHEMISTRY

Heterogeneity and Dynamics of the Ligand Recognition Mode in Purine-Sensing Riboswitches

(2010) Niyati Jain et al.   BIOCHEMISTRY

Ribozymes and Riboswitches: Modulation of RNA Function by Small Molecules

(2010) Jinwei Zhang et al.   BIOCHEMISTRY

A Bacterial mRNA Leader that Employs Different Mechanisms to Sense Disparate Intracellular Signals

(2010) Sun-Yang Park et al.   CELL

Analysis of Metal Ion Dependence in glmS Ribozyme Self-Cleavage and Coenzyme Binding

(2010) Kevin Klawuhn et al.   CHEMBIOCHEM

A Eubacterial Riboswitch Class That Senses the Coenzyme Tetrahydrofolate

(2010) Tyler D. Ames et al.   CHEMISTRY & BIOLOGY

Tuning Riboswitch Regulation through Conformational Selection

(2010) Ross C. Wilson et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural Insights into Ligand Recognition by a Sensing Domain of the Cooperative Glycine Riboswitch

(2010) Lili Huang et al.   MOLECULAR CELL

Reengineering orthogonally selective riboswitches

(2010) N. Dixon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Folding of a transcriptionally acting PreQ1 riboswitch

(2010) U. Rieder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-time multidimensional NMR follows RNA folding with second resolution

(2010) M.-K. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Riboswitch-mediated control of gene expression in eukaryotes

(2010) Andreas Wachter   RNA Biology

Structural basis for recognition of S-adenosylhomocysteine by riboswitches

(2010) A. L. Edwards et al.   RNA

Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis

(2010) N. J. Baird et al.   RNA

An Allosteric Self-Splicing Ribozyme Triggered by a Bacterial Second Messenger

(2010) E. R. Lee et al.   SCIENCE

Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain

(2010) Colby D. Stoddard et al.   STRUCTURE

Novel Riboswitch Ligand Analogs as Selective Inhibitors of Guanine-Related Metabolic Pathways

(2010) Jérôme Mulhbacher et al.   PLoS Pathogens

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

(2010) Zasha Weinberg et al.   GENOME BIOLOGY

Design and Antimicrobial Action of Purine Analogues That Bind Guanine Riboswitches

(2009) Jane N. Kim et al.   ACS Chemical Biology

The Structural and Functional Diversity of Metabolite-Binding Riboswitches

(2009) Adam Roth et al.   Annual Review of Biochemistry

A trans-Acting Riboswitch Controls Expression of the Virulence Regulator PrfA in Listeria monocytogenes

(2009) Edmund Loh et al.   CELL

The Structural Basis for Recognition of the PreQ0Metabolite by an Unusually Small Riboswitch Aptamer Domain

(2009) Robert C. Spitale et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Multiple Metal-Binding Cores Are Required for Metalloregulation by M-box Riboswitch RNAs

(2009) Catherine A. Wakeman et al.   JOURNAL OF MOLECULAR BIOLOGY

The Ligand-Free State of the TPP Riboswitch: A Partially Folded RNA Structure

(2009) Mona Ali et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural Insights into Riboswitch Control of the Biosynthesis of Queuosine, a Modified Nucleotide Found in the Anticodon of tRNA

(2009) Mijeong Kang et al.   MOLECULAR CELL

Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch

(2009) Alexander Serganov et al.   NATURE

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase

(2009) Daniel J Klein et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch

(2009) Nadia Kulshina et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural basis of ligand binding by a c-di-GMP riboswitch

(2009) Kathryn D Smith et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Riboswitch structure: an internal residue mimicking the purine ligand

(2009) Vanessa Delfosse et al.   NUCLEIC ACIDS RESEARCH

A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm

(2009) Wei Huang et al.   NUCLEIC ACIDS RESEARCH

A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria

(2009) E. Poiata et al.   RNA

Riboswitches: Emerging Themes in RNA Structure and Function

(2008) Rebecca K. Montange et al.   Annual Review of Biophysics

Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteineThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process.

(2008) Joy Xin Wang et al.   Biochemistry and Cell Biology

RNA dynamics: it is about time

(2008) Hashim M Al-Hashimi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Regulation of magnesium homeostasis in Salmonella: Mg2+ targets the mgtA transcript for degradation by RNase E

(2008) Silvana V. Spinelli et al.   FEMS MICROBIOLOGY LETTERS

Crystal Structure of the Lysine Riboswitch Regulatory mRNA Element

(2008) Andrew D. Garst et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Structural Basis for the Recognition of 2′-Deoxyguanosine by the Purine Riboswitch

(2008) Andrea L. Edwards et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch

(2008) Stéphane Thore et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism

(2008) Elizabeth E. Regulski et al.   MOLECULAR MICROBIOLOGY

Structural insights into amino acid binding and gene control by a lysine riboswitch

(2008) Alexander Serganov et al.   NATURE

Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism

(2008) Changrui Lu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure of the SAM-II riboswitch bound to S-adenosylmethionine

(2008) Sunny D Gilbert et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The UA_handle: a versatile submotif in stable RNA architectures†

(2008) Luc Jaeger et al.   NUCLEIC ACIDS RESEARCH

Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria

(2008) M. M. Meyer et al.   RNA

The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches

(2008) Z. Weinberg et al.   RNA

Ligand-dependent folding of the three-way junction in the purine riboswitch

(2008) C. D Stoddard et al.   RNA

Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers

(2008) W. J. Greenleaf et al.   SCIENCE

Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP

(2008) N. Sudarsan et al.   SCIENCE

Switching the light on plant riboswitches

(2008) Samuel E. Bocobza et al.   TRENDS IN PLANT SCIENCE