The Biochemical Landscape of Riboswitch Ligands

The case of the missing allosteric ribozymes

(2021) Shanker S. S. Panchapakesan et al.   Nature Chemical Biology

Architecture of bacterial respiratory chains

(2021) Ville R. I. Kaila et al.   NATURE REVIEWS MICROBIOLOGY

Widespread bacterial utilization of guanidine as nitrogen source

(2021) Malte Sinn et al.   MOLECULAR MICROBIOLOGY

Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes

(2021) Kenneth I. Brewer et al.   RNA Biology

The potential versatility of RNA catalysis

(2021) Timothy J. Wilson et al.   Wiley Interdisciplinary Reviews-RNA

DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria

(2021) Kenneth I Brewer et al.   BIOINFORMATICS

Riboswitch regulation mechanisms: RNA, metabolites and regulatory proteins

(2020) Anne-Sophie Vézina Bédard et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The czcD (NiCo) Riboswitch Responds to Iron(II)

(2020) Jiansong Xu et al.   BIOCHEMISTRY

Structure and ligand binding of the ADP-binding domain of the NAD+ riboswitch

(2020) Lin Huang et al.   RNA

A bacterial riboswitch class senses xanthine and uric acid to regulate genes associated with purine oxidation

(2020) Diane Yu et al.   RNA

Imaginary Ribozymes

(2020) Ronald R. Breaker   ACS Chemical Biology

Cyclic di-AMP Signaling in Bacteria

(2020) Jörg Stülke et al.   Annual Review of Microbiology

A rare bacterial RNA motif is implicated in the regulation of the purF gene whose encoded enzyme synthesizes phosphoribosylamine

(2020) Sarah Malkowski et al.   RNA

A Second Riboswitch Class for the Enzyme Cofactor NAD+

(2020) Shanker S.S. Panchapakesan et al.   RNA

Biochemical Validation of a Fourth Guanidine Riboswitch Class in Bacteria

(2020) Hubert Salvail et al.   BIOCHEMISTRY

Discovery and characterization of a fourth class of guanidine riboswitches

(2020) Felina Lenkeit et al.   NUCLEIC ACIDS RESEARCH

Re-evaluation of Diadenosine Tetraphosphate (Ap4A) From a Stress Metabolite to Bona Fide Secondary Messenger

(2020) Freya Ferguson et al.   Frontiers in Molecular Biosciences

Alarmones as Vestiges of a Bygone RNA World

(2019) Ricardo Hernández-Morales et al.   JOURNAL OF MOLECULAR EVOLUTION

Genome-wide discovery of structured noncoding RNAs in bacteria

(2019) Shira Stav et al.   BMC MICROBIOLOGY

Guanidine-riboswitch-regulated efflux transporters protect bacteria against ionic liquid toxicity

(2019) Douglas A. Higgins et al.   JOURNAL OF BACTERIOLOGY

A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer

(2019) Ruben M Atilho et al.   eLife

Structure and ligand binding of the glutamine-II riboswitch

(2019) Lin Huang et al.   NUCLEIC ACIDS RESEARCH

Biochemical validation of a second class of tetrahydrofolate riboswitches in bacteria

(2019) Xi Chen et al.   RNA

Evidence that the nadA Motif is a Bacterial Riboswitch for the Ubiquitous Enzyme Cofactor NAD+

(2019) Sarah N Malkowski et al.   RNA

Structural basis for tRNA decoding and aminoacylation sensing by T-box riboregulators

(2019) Robert A. Battaglia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Riboswitches for the alarmone ppGpp expand the collection of RNA-based signaling systems

(2018) Madeline E. Sherlock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SAM-VI RNAs selectively bind S-adenosylmethionine and exhibit similarities to SAM-III riboswitches

(2018) Gayan Mirihana Arachchilage et al.   RNA Biology

Challenges of ligand identification for the second wave of orphan riboswitch candidates

(2018) Etienne B. Greenlee et al.   RNA Biology

Guanidine-sensing riboswitches: How do they work and what do they regulate?

(2018) Robert A. Battaglia et al.   Wiley Interdisciplinary Reviews-RNA

Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria

(2018) Madeline E Sherlock et al.   eLife

Variant Bacterial Riboswitches Associated with Nucleotide Hydrolase Genes Sense Nucleoside Diphosphates

(2018) Madeline E. Sherlock et al.   BIOCHEMISTRY

A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria

(2018) Stephan Klähn et al.   NUCLEIC ACIDS RESEARCH

Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class

(2017) James W. Nelson et al.   MOLECULAR CELL

Iron mediates catalysis of nucleic acid processing enzymes: support for Fe(II) as a cofactor before the great oxidation event

(2017) C. Denise Okafor et al.   NUCLEIC ACIDS RESEARCH

Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions

(2017) Zasha Weinberg et al.   NUCLEIC ACIDS RESEARCH

Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity

(2017) Zasha Weinberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Riboswitch diversity and distribution

(2017) Phillip J. McCown et al.   RNA

The lost language of the RNA World

(2017) James W. Nelson et al.   Science Signaling

The lost language of the RNA World

(2017) James W. Nelson et al.   Science Signaling

Riboswitch-Mediated Gene Regulation: Novel RNA Architectures Dictate Gene Expression Responses

(2016) Anna V. Sherwood et al.   Annual Review of Microbiology

Review: Translational GTPases

(2016) Cristina Maracci et al.   BIOPOLYMERS

Heme Synthesis and Acquisition in Bacterial Pathogens

(2016) Jacob E. Choby et al.   JOURNAL OF MOLECULAR BIOLOGY

Novel genomic island modifies DNA with 7-deazaguanine derivatives

(2016) Jennifer J. Thiaville et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TheyjdFriboswitch candidate regulates gene expression by binding diverse azaaromatic compounds

(2016) Sanshu Li et al.   RNA

Transcription Factors That Defend Bacteria Against Reactive Oxygen Species

(2015) James A. Imlay   Annual Review of Microbiology

Mn 2+ -Sensing Mechanisms of yybP-ykoY Orphan Riboswitches

(2015) Ian R. Price et al.   MOLECULAR CELL

An Ancient Riboswitch Class in Bacteria Regulates Purine Biosynthesis and One-Carbon Metabolism

(2015) Peter B. Kim et al.   MOLECULAR CELL

The Ubiquitous yybP-ykoY Riboswitch Is a Manganese-Responsive Regulatory Element

(2015) Michael Dambach et al.   MOLECULAR CELL

Bacterial Riboswitches Cooperatively Bind Ni 2+ or Co 2+ Ions and Control Expression of Heavy Metal Transporters

(2015) Kazuhiro Furukawa et al.   MOLECULAR CELL

Control of bacterial exoelectrogenesis by c-AMP-GMP

(2015) James W. Nelson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GEMM-I riboswitches fromGeobactersense the bacterial second messenger cyclic AMP-GMP

(2015) Colleen A. Kellenberger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Queuine Micronutrient: Charting a Course from Microbe to Man

(2015) Claire Fergus et al.   Nutrients

Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch

(2015) Aiming Ren et al.   Cell Reports

The Pho regulon: a huge regulatory network in bacteria

(2015) Fernando Santos-Beneit   Frontiers in Microbiology

Biosynthesis and physiology of coenzyme Q in bacteria

(2014) Laurent Aussel et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Themes and variations in riboswitch structure and function

(2014) Alla Peselis et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The T box riboswitch: A novel regulatory RNA that utilizes tRNA as its ligand

(2014) Tina M. Henkin   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Structural, Functional, and Taxonomic Diversity of Three PreQ1 Riboswitch Classes

(2014) Phillip J. McCown et al.   CHEMISTRY & BIOLOGY

Cyclic-AMP and bacterial cyclic-AMP receptor proteins revisited: adaptation for different ecological niches

(2014) Jeffrey Green et al.   CURRENT OPINION IN MICROBIOLOGY

Bacterial group I introns: mobile RNA catalysts

(2014) Georg Hausner et al.   Mobile DNA

A Decade of Riboswitches

(2013) Alexander Serganov et al.   CELL

Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA

(2013) Jinwei Zhang et al.   NATURE

Riboswitches in eubacteria sense the second messenger c-di-AMP

(2013) James W Nelson et al.   Nature Chemical Biology

B12 cofactors directly stabilize an mRNA regulatory switch

(2012) James E. Johnson Jr et al.   NATURE

The ydaO motif is an ATP-sensing riboswitch in Bacillus subtilis

(2012) Peter Y Watson et al.   Nature Chemical Biology

RNA Folding and Catalysis Mediated by Iron (II)

(2012) Shreyas S. Athavale et al.   PLoS One

An ABC-Type Cobalt Transport System Is Essential for Growth of Sinorhizobium melilotiat Trace Metal Concentrations

(2011) J. Cheng et al.   JOURNAL OF BACTERIOLOGY

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

Prospects for Riboswitch Discovery and Analysis

(2011) Ronald R. Breaker   MOLECULAR CELL

Ribosome-associated GTPases: The role of RNA for GTPase activation

(2011) Nina Clementi et al.   RNA Biology

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

A Rearrangement of the Guanosine-Binding Site Establishes an Extended Network of Functional Interactions in theTetrahymenaGroup I Ribozyme Active Site

(2010) Marcello Forconi et al.   BIOCHEMISTRY

A Eubacterial Riboswitch Class That Senses the Coenzyme Tetrahydrofolate

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

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

(2010) E. R. Lee et al.   SCIENCE

Riboswitches: Structures and Mechanisms

(2010) A. D. Garst et al.   Cold Spring Harbor Perspectives in Biology

Riboswitches and the RNA World

(2010) R. R. Breaker   Cold Spring Harbor Perspectives in Biology

The Structural and Functional Diversity of Metabolite-Binding Riboswitches

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

The Deazapurine Biosynthetic Pathway Revealed: In Vitro Enzymatic Synthesis of PreQ0from Guanosine 5′-Triphosphate in Four Steps

(2009) Reid M. McCarty et al.   BIOCHEMISTRY

Riboswitches: from ancient gene-control systems to modern drug targets

(2009) Ronald R Breaker   Future Microbiology

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

(2009) Bryson D Bennett et al.   Nature Chemical Biology

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

An embarrassment of riches: the enzymology of RNA modification

(2008) Dirk Iwata-Reuyl   CURRENT OPINION IN CHEMICAL BIOLOGY

Structure of the transcriptional regulator LmrR and its mechanism of multidrug recognition

(2008) Pramod Kumar Madoori et al.   EMBO JOURNAL

Riboswitches that Sense S-adenosylhomocysteine and Activate Genes Involved in Coenzyme Recycling

(2008) Joy Xin Wang et al.   MOLECULAR CELL

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

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

Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria

(2008) M. M. Meyer et al.   RNA

Riboswitch effectors as protein enzyme cofactors

(2008) J. C. Cochrane et al.   RNA

Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP

(2008) N. Sudarsan et al.   SCIENCE