Ronald Breaker

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Organization: Yale University

Department: Department of Molecular, Cellular and Developmental Biology

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References

Biochemical Validation of a Second Guanidine Riboswitch Class in Bacteria

Co-reporter:Madeline E. Sherlock;Sarah N. Malkowski;Ronald R. Breaker

Biochemistry January 17, 2017 Volume 56(Issue 2) pp:352-358

Publication Date(Web):December 21, 2016

DOI:10.1021/acs.biochem.6b01270

Recently, it was determined that representatives of the riboswitch candidates called ykkC and ykkC-III directly bind free guanidine. Guanidine-binding ykkC motif RNAs, now renamed guanidine-I riboswitches, were demonstrated to commonly regulate the expression of genes encoding guanidine carboxylases, as well as others encoding guanidine efflux proteins such as EmrE and SugE. Likewise, genes encoding similar efflux proteins are associated with ykkC-III motif RNAs, which have now been renamed guanidine-III riboswitches. Prior to the validation of guanidine as the ligand for these newly established riboswitch classes, another RNA motif was discovered by comparative genomic analysis and termed mini-ykkC because of its small size and gene associations similar to those of the original ykkC motif. It was hypothesized that these distinct RNA structures might respond to the same ligand. However, the small size and repetitive nature of mini-ykkC RNAs suggested that it might respond to ligand via the action of a protein factor. Herein, we demonstrate that, despite its extremely simple architecture, mini-ykkC motif RNAs constitute a distinct class of guanidine-sensing RNAs, called guanidine-II riboswitches. Surprisingly, each of the two stem–loop structures that comprise the mini-ykkC motif appears to directly bind free guanidine in a cooperative manner. These findings reveal that bacteria make extensive use of diverse guanidine-responsive riboswitches to overcome the toxic effects of this compound.

The Biology of Free Guanidine As Revealed by Riboswitches

Co-reporter:Ronald R. Breaker, Ruben M. Atilho, Sarah N. Malkowski, James W. Nelson, and Madeline E. Sherlock

Biochemistry 2017 Volume 56(Issue 2) pp:

Publication Date(Web):January 6, 2017

DOI:10.1021/acs.biochem.6b01269

The lost language of the RNA World

Co-reporter:James W. Nelson;Ronald R. Breaker

Science Signaling 2017 Volume 10(Issue 483) pp:

Publication Date(Web):13 Jun 2017

DOI:10.1126/scisignal.aam8812

RNA-derived signaling molecules in modern cells may represent evolutionary vestiges of a time when all cellular functions were performed by RNAs.

Biochemical Validation of a Third Guanidine Riboswitch Class in Bacteria

Co-reporter:Madeline E. SherlockRonald R. Breaker

Biochemistry 2017 Volume 56(Issue 2) pp:

Publication Date(Web):December 21, 2016

DOI:10.1021/acs.biochem.6b01271

Recently, it was determined that representatives of the riboswitch candidates called ykkC and mini-ykkC directly bind free guanidine. These riboswitches regulate the expression of genes whose protein products are implicated in overcoming the toxic effects of this ligand. Thus, the relevant ykkC motif and mini-ykkC motif RNAs have been classified as guanidine-I and guanidine-II riboswitch RNAs, respectively. Moreover, we had previously noted that a third candidate riboswitch class, called ykkC-III, was associated with a distribution of genes similar to those of the other two motifs. Therefore, it was predicted that ykkC-III motif RNAs would sense and respond to the same ligand. In this report, we present biochemical data supporting the hypothesis that ykkC-III RNAs represent a third class of guanidine-sensing RNAs called guanidine-III riboswitches. Members of the guanidine-III riboswitch class bind their ligand with an affinity similar to that observed for members of the other two classes. Notably, there are some sequence similarities between guanidine-II and guanidine-III riboswitches. However, the characteristics of ligand discrimination by guanidine-III RNAs are different from those of the other guanidine-binding motifs, suggesting that the binding pockets have distinct features among the three riboswitch classes.

Small Molecule Fluoride Toxicity Agonists

Co-reporter:James W. Nelson, Mark S. Plummer, Kenneth F. Blount, Tyler D. Ames, Ronald R. Breaker

Chemistry & Biology 2015 Volume 22(Issue 4) pp:527-534

Publication Date(Web):23 April 2015

DOI:10.1016/j.chembiol.2015.03.016

•A riboswitch was used to report increased fluoride levels inside bacteria•Molecules that trigger riboswitch reporter activity were isolated via HTS•Improved hit compounds enhance fluoride toxicity in bacteriaFluoride is a ubiquitous anion that inhibits a wide variety of metabolic processes. Here, we report the identification of a series of compounds that enhance fluoride toxicity in Escherichia coli and Streptococcus mutans. These molecules were isolated by using a high-throughput screen (HTS) for compounds that increase intracellular fluoride levels as determined via a fluoride riboswitch reporter fusion construct. A series of derivatives were synthesized to examine structure-activity relationships, leading to the identification of compounds with improved activity. Thus, we demonstrate that small molecule fluoride toxicity agonists can be identified by HTS from existing chemical libraries by exploiting a natural fluoride riboswitch. In addition, our findings suggest that some molecules might be further optimized to function as binary antibacterial agents when combined with fluoride.

Control of bacterial exoelectrogenesis by c-AMP-GMP

Co-reporter:Narasimhan Sudarsan;Christina E. Lünse;Shira Stav;Grace E. Phillips;Ronald R. Breaker;James W. Nelson;Phillip J. McCown

PNAS 2015 Volume 112 (Issue 17 ) pp:5389-5394

Publication Date(Web):2015-04-28

DOI:10.1073/pnas.1419264112

Major changes in bacterial physiology including biofilm and spore formation involve signaling by the cyclic dinucleotides c-di-GMP and c-di-AMP. Recently, another second messenger dinucleotide, c-AMP-GMP, was found to control chemotaxis and colonization by Vibrio cholerae. We have identified a superregulon of genes controlled by c-AMP-GMP in numerous Deltaproteobacteria, including Geobacter species that use extracellular insoluble metal oxides as terminal electron acceptors. This exoelectrogenic process has been studied for its possible utility in energy production and bioremediation. Many genes involved in adhesion, pilin formation, and others that are important for exoelectrogenesis are controlled by members of a variant riboswitch class that selectively bind c-AMP-GMP. These RNAs constitute, to our knowledge, the first known specific receptors for c-AMP-GMP and reveal that this molecule is used by many bacteria to control specialized physiological processes.

The Expanding View of RNA and DNA Function

Co-reporter:Ronald R. Breaker, Gerald F. Joyce

Chemistry & Biology 2014 Volume 21(Issue 9) pp:1059-1065

Publication Date(Web):18 September 2014

DOI:10.1016/j.chembiol.2014.07.008

RNA and DNA are simple linear polymers consisting of only four major types of subunits, and yet these molecules carry out a remarkable diversity of functions in cells and in the laboratory. Each newly discovered function of natural or engineered nucleic acids enforces the view that prior assessments of nucleic acid function were far too narrow and that many more exciting findings are yet to come. This Perspective highlights just a few of the numerous discoveries over the past 20 years pertaining to nucleic acid function, focusing on those that have been of particular interest to chemical biologists. History suggests that there will continue to be many opportunities to engage chemical biologists in the discovery, creation, and manipulation of nucleic acid function in the years to come.

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

Co-reporter:Phillip J. McCown, Jonathan J. Liang, Zasha Weinberg, Ronald R. Breaker

Chemistry & Biology 2014 Volume 21(Issue 7) pp:880-889

Publication Date(Web):17 July 2014

DOI:10.1016/j.chembiol.2014.05.015

•Additional variant types of class I and II preQ1 riboswitches have been discovered•A third riboswitch class that senses preQ1 has been discovered and validated•Our findings expand the bacterial lineages that exploit preQ1-sensing riboswitchesPreviously, two riboswitch classes have been identified that sense and respond to the hypermodified nucleobase called prequeuosine1 (preQ1). The enormous expansion of available genomic DNA sequence data creates new opportunities to identify additional representatives of the known riboswitch classes and to discover novel classes. We conducted bioinformatics searches on microbial genomic DNA data sets to discover numerous additional examples belonging to the two previously known riboswitch classes for preQ1 (classes preQ1-I and preQ1-II), including some structural variants that further restrict ligand specificity. Additionally, we discovered a third preQ1-binding riboswitch class (preQ1-III) that is structurally distinct from previously known classes. These findings demonstrate that numerous organisms monitor the concentrations of this modified nucleobase by exploiting one or more riboswitch classes for this widespread compound.Figure optionsDownload full-size imageDownload high-quality image (372 K)Download as PowerPoint slide

Gramicidin D enhances the antibacterial activity of fluoride

Co-reporter:James W. Nelson, Zhiyuan Zhou, Ronald R. Breaker

Bioorganic & Medicinal Chemistry Letters 2014 Volume 24(Issue 13) pp:2969-2971

Publication Date(Web):1 July 2014

DOI:10.1016/j.bmcl.2014.03.061

Fluoride is a toxic anion found in many natural environments. One of the major bacterial defenses against fluoride is the cell envelope, which limits passage of the membrane-impermeant fluoride anion. Accordingly, compounds that enhance the permeability of bacterial membranes to fluoride should also enhance fluoride toxicity. In this study, we demonstrate that the pore-forming antibiotic gramicidin D increases fluoride uptake in Bacillus subtilis and that the antibacterial activity of this compound is potentiated by fluoride. Polymyxin B, another membrane-targeting antibiotic with a different mechanism of action, shows no such improvement. These results, along with previous findings, indicate that certain compounds that destabilize bacterial cell envelopes can enhance the toxicity of fluoride.

Small, Highly Active DNAs That Hydrolyze DNA

Co-reporter:Hongzhou Gu ; Kazuhiro Furukawa ; Zasha Weinberg ; Daniel F. Berenson ;Ronald R. Breaker

Journal of the American Chemical Society 2013 Volume 135(Issue 24) pp:9121-9129

Publication Date(Web):May 16, 2013

DOI:10.1021/ja403585e

DNA phosphoester bonds are exceedingly resistant to hydrolysis in the absence of chemical or enzymatic catalysts. This property is particularly important for organisms with large genomes, as resistance to hydrolytic degradation permits the long-term storage of genetic information. Here we report the creation and analysis of two classes of engineered deoxyribozymes that selectively and rapidly hydrolyze DNA. Members of class I deoxyribozymes carry a catalytic core composed of only 15 conserved nucleotides and attain an observed rate constant (kobs) of ∼1 min–1 when incubated near neutral pH in the presence of Zn2+. Natural DNA sequences conforming to the class I consensus sequence and structure were found that undergo hydrolysis under selection conditions (2 mM Zn2+, pH 7), which demonstrates that the inherent structure of certain DNA regions might promote catalytic reactions, leading to genomic instability.

Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins

Co-reporter:Kathryn D. Smith;Ronald R. Breaker;Patricia B. Gordon;Jared H. Davis;Sanshu Li;Scott A. Strobel

PNAS 2013 Volume 110 (Issue 47 ) pp:19018-19023

Publication Date(Web):2013-11-19

DOI:10.1073/pnas.1310439110

Fluorine is an abundant element and is toxic to organisms from bacteria to humans, but the mechanisms by which eukaryotes resist fluoride toxicity are unknown. The Escherichia coli gene crcB was recently shown to be regulated by a fluoride-responsive riboswitch, implicating it in fluoride response. There are >8,000 crcB homologs across all domains of life, indicating that it has an important role in biology. Here we demonstrate that eukaryotic homologs [renamed FEX (fluoride exporter)] function in fluoride export. FEX KOs in three eukaryotic model organisms, Neurospora crassa, Saccharomyces cerevisiae, and Candida albicans, are highly sensitized to fluoride (>200-fold) but not to other halides. Some of these KO strains are unable to grow in fluoride concentrations found in tap water. Using the radioactive isotope of fluoride, 18F, we developed an assay to measure the intracellular fluoride concentration and show that the FEX deletion strains accumulate fluoride in excess of the external concentration, providing direct evidence of FEX function in fluoride efflux. In addition, they are more sensitive to lower pH in the presence of fluoride. These results demonstrate that eukaryotic FEX genes encode a previously unrecognized class of fluoride exporter necessary for survival in standard environmental conditions.

Engineered Allosteric Ribozymes That Sense the Bacterial Second Messenger Cyclic Diguanosyl 5′-Monophosphate

Co-reporter:Hongzhou Gu, Kazuhiro Furukawa, and Ronald R. Breaker

Analytical Chemistry 2012 Volume 84(Issue 11) pp:4935

Publication Date(Web):April 23, 2012

DOI:10.1021/ac300415k

A series of allosteric ribozymes that respond to the bacterial second messenger cyclic diguanosyl-5′-monophosphate (c-di-GMP) have been created by using in vitro selection. An RNA library was generated by using random-sequence bridges to join a hammerhead self-cleaving ribozyme to an aptamer from a natural c-di-GMP riboswitch. Specific bridge sequences, called communication modules, emerged through two in vitro selection efforts that either activate or inhibit ribozyme self-cleavage upon ligand binding to the aptamer. Representative RNAs were found that exhibit EC50 (half-maximal effective concentration) values for c-di-GMP as low as 90 nM and IC50 (half-maximal inhibitory concentration) values as low as 180 nM. The allosteric RNAs display molecular recognition characteristics that mimic the high discriminatory ability of the natural aptamer. Some engineered RNAs operate with ribozyme rate constants approaching that of the parent hammerhead ribozyme. By use of these allosteric ribozymes, cytoplasmic concentrations of c-di-GMP in three mutant strains of Escherichia coli were quantitatively estimated from cell lysates. Our findings demonstrate that engineered c-di-GMP-sensing ribozymes can be used as convenient tools to monitor c-di-GMP levels from complex biological or chemical samples. Moreover, these ribozymes could be employed in high-throughput screens to identify compounds that trigger c-di-GMP riboswitch function.

Identification of Ligand Analogues that Control c-di-GMP Riboswitches

Co-reporter:Kazuhiro Furukawa, Hongzhou Gu, Narasimhan Sudarsan, Yoshihiro Hayakawa, Mamoru Hyodo, and Ronald R. Breaker

ACS Chemical Biology 2012 Volume 7(Issue 8) pp:1436

Publication Date(Web):May 30, 2012

DOI:10.1021/cb300138n

Riboswitches for the bacterial second messenger c-di-GMP control the expression of genes involved in numerous cellular processes such as virulence, competence, biofilm formation, and flagella synthesis. Therefore, the two known c-di-GMP riboswitch classes represent promising targets for developing novel modulators of bacterial physiology. Here, we examine the binding characteristics of circular and linear c-di-GMP analogues for representatives of both class I and II c-di-GMP riboswitches derived from the pathogenic bacterium Vibrio choleae (class I) and Clostridium difficile (class II). Some compounds exhibit values for apparent dissociation constant (KD) below 1 μM and associate with riboswitch RNAs during transcription with a speed that is sufficient to influence riboswitch function. These findings are consistent with the published structural models for these riboswitches and suggest that large modifications at various positions on the ligand can be made to create novel compounds that target c-di-GMP riboswitches. Moreover, we demonstrate the potential of an engineered allosteric ribozyme for the rapid screening of chemical libraries for compounds that bind c-di-GMP riboswitches.

Fluoride enhances the activity of fungicides that destabilize cell membranes

Co-reporter:Sanshu Li, Ronald R. Breaker

Bioorganic & Medicinal Chemistry Letters 2012 Volume 22(Issue 9) pp:3317-3322

Publication Date(Web):1 May 2012

DOI:10.1016/j.bmcl.2012.03.006

Fluoride has long been known to inhibit bacterial and fungal cell growth most likely by blocking the functions of key metabolic enzymes. In this study, we demonstrate that antifungal compounds that disrupt cell membrane integrity exhibit improved ability to inhibit cell growth when used with millimolar concentrations of fluoride. Specifically, antifungal compounds of the polyene class and an antifungal peptide exhibit synergy with fluoride to inhibit the growth of various fungal species, including Candida albicans. Our results demonstrate that certain compounds can be found that increase the cellular uptake of fluoride, and provide new opportunities for creating antimicrobial compounds whose functions are enhanced when combined with otherwise sub-inhibitory concentrations of small ions.

Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride

Co-reporter:Jenny L. Baker;Ronald R. Breaker;Adam Roth;Zasha Weinberg;Narasimhan Sudarsan;Randy B. Stockbridge

Science 2012 Volume 335(Issue 6065) pp:233-235

Publication Date(Web):13 Jan 2012

DOI:10.1126/science.1215063

A Eubacterial Riboswitch Class That Senses the Coenzyme Tetrahydrofolate

Co-reporter:Tyler D. Ames, Dmitry A. Rodionov, Zasha Weinberg, Ronald R. Breaker

Chemistry & Biology 2010 Volume 17(Issue 7) pp:681-685

Publication Date(Web):30 July 2010

DOI:10.1016/j.chembiol.2010.05.020

Comparative sequence analyses of bacterial genomes are revealing many structured RNA motifs that function as metabolite-binding riboswitches. We have identified an RNA motif frequently positioned in the 5′ UTRs of folate transport and biosynthesis genes in Firmicute genomes. Biochemical experiments confirm that representatives of this new-found RNA class selectively bind derivatives of the vitamin folate, including di- and tetrahydrofolate coenzymes. In addition, representatives of this aptamer class occasionally reside upstream of RNA structures that are predicted to control translation initiation in response to ligand binding. These findings expand the number of coenzymes that are directly sensed by RNA and reveal possible riboswitch-controlled regulons that respond to changes in single-carbon metabolism.Graphical AbstractFigure optionsDownload full-size imageDownload high-quality image (318 K)Download as PowerPoint slide

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

Co-reporter:Zasha Weinberg;Joy X Wang;Jarrod Bogue;Jingying Yang;Keith Corbino

Genome Biology 2010 Volume 11( Issue 3) pp:

Publication Date(Web):2010 March

DOI:10.1186/gb-2010-11-3-r31

Structured noncoding RNAs perform many functions that are essential for protein synthesis, RNA processing, and gene regulation. Structured RNAs can be detected by comparative genomics, in which homologous sequences are identified and inspected for mutations that conserve RNA secondary structure.By applying a comparative genomics-based approach to genome and metagenome sequences from bacteria and archaea, we identified 104 candidate structured RNAs and inferred putative functions for many of these. Twelve candidate metabolite-binding RNAs were identified, three of which were validated, including one reported herein that binds the coenzyme S-adenosylmethionine. Newly identified cis-regulatory RNAs are implicated in photosynthesis or nitrogen regulation in cyanobacteria, purine and one-carbon metabolism, stomach infection by Helicobacter, and many other physiological processes. A candidate riboswitch termed crcB is represented in both bacteria and archaea. Another RNA motif may control gene expression from 3'-untranslated regions of mRNAs, which is unusual for bacteria. Many noncoding RNAs that likely act in trans are also revealed, and several of the noncoding RNA candidates are found mostly or exclusively in metagenome DNA sequences.This work greatly expands the variety of highly structured noncoding RNAs known to exist in bacteria and archaea and provides a starting point for biochemical and genetic studies needed to validate their biologic functions. Given the sustained rate of RNA discovery over several similar projects, we expect that far more structured RNAs remain to be discovered from bacterial and archaeal organisms.

Co-reporter:Elaine R. Lee;Jenny L. Baker;Zasha Weinberg;Narasimhan Sudarsan;Ronald R. Breaker

Science 2010 Volume 329(Issue 5993) pp:

Publication Date(Web):

DOI:10.1126/science.1190713

Riboswitch Revealed

Short regulatory regions—riboswitches—are found in the messenger RNAs of many bacteria, plants, and fungi. They bind to small-molecule metabolites and, through switching between alternate RNA secondary structures, regulate the expression of the linked RNA. Lee et al. (p. 845) have identified a c-di-GMP (cyclic di-guanosyl-5′-monophosphate)–binding riboswitch in the bacterium Clostridium difficile that regulates the splicing of a group I self-splicing ribozyme. Binding of c-di-GMP to the riboswitch favors a conformation of the ribozyme that promotes splicing in the presence of guanosine triphosphate (as is typical for this class of ribozymes). Concomitantly, splicing promotes the formation of a ribosome binding site, thereby stimulating protein production from the downstream pathogenesis-related gene. This regulatory region may thus constitute a two-input gene-control system that reads the concentration of both GTP and c-di-GMP. Thus, not all group I self-splicing ribozymes represent selfish genetic elements.

Design and Antimicrobial Action of Purine Analogues That Bind Guanine Riboswitches

Co-reporter:Jane N. Kim, Kenneth F. Blount, Izabela Puskarz, Jinsoo Lim, Kristian H. Link and Ronald R. Breaker

ACS Chemical Biology 2009 Volume 4(Issue 11) pp:915

Publication Date(Web):September 9, 2009

DOI:10.1021/cb900146k

Riboswitches are structured RNA domains that can bind directly to specific ligands and regulate gene expression. These RNA elements are located most commonly within the noncoding regions of bacterial mRNAs, although representatives of one riboswitch class have been discovered in organisms from all three domains of life. In several Gram-positive species of bacteria, riboswitches that selectively recognize guanine regulate the expression of genes involved in purine biosynthesis and transport. Because these genes are involved in fundamental metabolic pathways in certain bacterial pathogens, guanine-binding riboswitches may be targets for the development of novel antibacterial compounds. To explore this possibility, the atomic-resolution structure of a guanine riboswitch aptamer from Bacillus subtilis was used to guide the design of several riboswitch-compatible guanine analogues. The ability of these compounds to be bound by the riboswitch and repress bacterial growth was examined. Many of these rationally designed compounds are bound by a guanine riboswitch aptamer in vitro with affinities comparable to that of the natural ligand, and several also inhibit bacterial growth. We found that one of these antimicrobial guanine analogues (6-N-hydroxylaminopurine, or G7) represses expression of a reporter gene controlled by a guanine riboswitch in B. subtilis, suggesting it may inhibit bacterial growth by triggering guanine riboswitch action. These studies demonstrate the utility of a three-dimensional structure model of a natural aptamer to design ligand analogues that target riboswitches. This approach also could be implemented to design antibacterial compounds that specifically target other riboswitch classes.

Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches

Co-reporter:K H Link and R R Breaker

Gene Therapy 2009 16(10) pp:1189-1201

Publication Date(Web):July 9, 2009

DOI:10.1038/gt.2009.81

In the last two decades, remarkable advances have been made in the development of technologies used to engineer new aptamers and ribozymes. This has encouraged interest among researchers who seek to create new types of gene-control systems that can be made to respond specifically to small-molecule signals. Validation of the fact that RNA molecules can exhibit the characteristics needed to serve as precision genetic switches has come from the discovery of numerous classes of natural ligand-sensing RNAs called riboswitches. Although a great deal of progress has been made toward engineering useful designer riboswitches, considerable advances are needed before the performance characteristics of these RNAs match those of protein systems that have been co-opted to regulate gene expression. In this review, we will evaluate the potential for engineered RNAs to regulate gene expression and lay out possible paths to designer riboswitches based on currently available technologies. Furthermore, we will discuss some technical advances that would empower RNA engineers who seek to make routine the production of designer riboswitches that can function in eukaryotes.

Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis

Co-reporter:Zasha Weinberg, Jonathan Perreault, Michelle M. Meyer & Ronald R. Breaker

Nature 2009 462(7273) pp:656

Publication Date(Web):2009-12-03

DOI:10.1038/nature08586

Existing DNA sequence databases carry only a tiny fraction of the total amount of DNA sequence space from bacterial species. Bioinformatics searches of genomic DNA from bacteria commonly identify new noncoding RNAs (ncRNAs) such as riboswitches. Here, an updated computational pipeline is used to discover ncRNAs that rival the known large ribozymes in size and structural complexity; other such RNAs probably remain to be discovered.

Co-reporter:N. Sudarsan;E. R. Lee;Z. Weinberg;R. H. Moy;K. H. Link;J. N. Kim;R. R. Breaker

Science 2008 Volume 321(Issue 5887) pp:

Publication Date(Web):

DOI:10.1126/science.1159519

Abstract

Cyclic di-guanosine monophosphate (di-GMP) is a circular RNA dinucleotide that functions as a second messenger in diverse species of bacteria to trigger wide-ranging physiological changes, including cell differentiation, conversion between motile and biofilm lifestyles, and virulence gene expression. However, the mechanisms by which cyclic di-GMP regulates gene expression have remained a mystery. We found that cyclic di-GMP in many bacterial species is sensed by a riboswitch class in messenger RNA that controls the expression of genes involved in numerous fundamental cellular processes. A variety of cyclic di-GMP regulons are revealed, including some riboswitches associated with virulence gene expression, pilus formation, and flagellum biosynthesis. In addition, sequences matching the consensus for cyclic di-GMP riboswitches are present in the genome of a bacteriophage.

The distributions, mechanisms, and structures of metabolite-binding riboswitches

Co-reporter:Jeffrey E Barrick;Ronald R Breaker

Genome Biology 2007 Volume 8( Issue 11) pp:

Publication Date(Web):2007 November

DOI:10.1186/gb-2007-8-11-r239

Riboswitches are noncoding RNA structures that appropriately regulate genes in response to changing cellular conditions. The expression of many proteins involved in fundamental metabolic processes is controlled by riboswitches that sense relevant small molecule ligands. Metabolite-binding riboswitches that recognize adenosylcobalamin (AdoCbl), thiamin pyrophosphate (TPP), lysine, glycine, flavin mononucleotide (FMN), guanine, adenine, glucosamine-6-phosphate (GlcN6P), 7-aminoethyl 7-deazaguanine (preQ1), and S-adenosylmethionine (SAM) have been reported.We have used covariance model searches to identify examples of ten widespread riboswitch classes in the genomes of organisms from all three domains of life. This data set rigorously defines the phylogenetic distributions of these riboswitch classes and reveals how their gene control mechanisms vary across different microbial groups. By examining the expanded aptamer sequence alignments resulting from these searches, we have also re-evaluated and refined their consensus secondary structures. Updated riboswitch structure models highlight additional RNA structure motifs, including an unusual double T-loop arrangement common to AdoCbl and FMN riboswitch aptamers, and incorporate new, sometimes noncanonical, base-base interactions predicted by a mutual information analysis.Riboswitches are vital components of many genomes. The additional riboswitch variants and updated aptamer structure models reported here will improve future efforts to annotate these widespread regulatory RNAs in genomic sequences and inform ongoing structural biology efforts. There remain significant questions about what physiological and evolutionary forces influence the distributions and mechanisms of riboswitches and about what forms of regulation substitute for riboswitches that appear to be missing in certain lineages.

Guanine riboswitch variants from Mesoplasma florum selectively recognize 2′-deoxyguanosine

Co-reporter:Jane N. Kim;Adam Roth;Ronald R. Breaker

PNAS 2007 104 (41 ) pp:16092-16097

Publication Date(Web):2007-10-09

DOI:10.1073/pnas.0705884104

Several mRNA aptamers have been identified in Mesoplasma florum that have sequence and structural features resembling those of guanine and adenine riboswitches. Two features distinguish these RNAs from established purine-sensing riboswitches. All possess shortened hairpin-loop sequences expected to alter tertiary contacts known to be critical for aptamer folding. The RNAs also carry nucleotide changes in the core of each aptamer that otherwise is strictly conserved in guanine and adenine riboswitches. Some aptamers retain the ability to selectively bind guanine or adenine despite these mutations. However, one variant type exhibits selective and high-affinity binding of 2′-deoxyguanosine, which is consistent with its occurrence in the 5′ untranslated region of an operon containing ribonucleotide reductase genes. The identification of riboswitch variants that bind nucleosides and reject nucleobases reveals that natural metabolite-sensing RNA motifs can accrue mutations that expand the diversity of ligand detection in bacteria.

Control of alternative RNA splicing and gene expression by eukaryotic riboswitches

Co-reporter:Ming T. Cheah, Andreas Wachter, Narasimhan Sudarsan & Ronald R. Breaker

Nature 2007 447(7143) pp:497

Publication Date(Web):2007-04-29

DOI:10.1038/nature05769

Bacteria make extensive use of riboswitches1, 2 to sense metabolites and control gene expression, and typically do so by modulating premature transcription termination or translation initiation. The most widespread riboswitch class known in bacteria responds to the coenzyme thiamine pyrophosphate (TPP)3, 4, which is a derivative of vitamin B1. Representatives of this class have also been identified5, 6 in fungi and plants, where they are predicted5, 7 to control messenger RNA splicing or processing. We examined three TPP riboswitches in the filamentous fungus Neurospora crassa, and found that one activates and two repress gene expression by controlling mRNA splicing. A detailed mechanism involving riboswitch-mediated base-pairing changes and alternative splicing control was elucidated for precursor NMT1 mRNAs, which code for a protein involved in TPP metabolism. These results demonstrate that eukaryotic cells employ metabolite-binding RNAs to regulate RNA splicing events that are important for the control of key biochemical processes.

Riboswitches as antibacterial drug targets

Co-reporter:

Nature Biotechnology 2006 24(12) pp:1558-1564

Publication Date(Web):11 December 2006

DOI:10.1038/nbt1268

New validated cellular targets are needed to reinvigorate antibacterial drug discovery. This need could potentially be filled by riboswitches—messenger RNA (mRNA) structures that regulate gene expression in bacteria. Riboswitches are unique among RNAs that serve as drug targets in that they have evolved to form structured and highly selective receptors for small drug-like metabolites. In most cases, metabolite binding to the receptor represses the expression of the gene(s) encoded by the mRNA. If a new metabolite analog were designed that binds to the receptor, the gene(s) regulated by that riboswitch could be repressed, with a potentially lethal effect to the bacteria. Recent work suggests that certain antibacterial compounds discovered decades ago function at least in part by targeting riboswitches. Herein we will summarize the experiments validating riboswitches as drug targets, describe the existing technology for riboswitch drug discovery and discuss the challenges that may face riboswitch drug discoverers.

Tandem Riboswitch Architectures Exhibit Complex Gene Control Functions

Co-reporter:Narasimhan Sudarsan;Ming C. Hammond;Kirsten F. Block;Rüdiger Welz;Jeffrey E. Barrick;Adam Roth;Ronald R. Breaker

Science 2006 Vol 314(5797) pp:300-304

Publication Date(Web):13 Oct 2006

DOI:10.1126/science.1130716

Abstract

Riboswitches are structured RNAs typically located in the 5′ untranslated regions of bacterial mRNAs that bind metabolites and control gene expression. Most riboswitches sense one metabolite and function as simple genetic switches. However, we found that the 5′ region of the Bacillus clausii metE messenger RNA includes two riboswitches that respond to S-adenosylmethionine and coenzyme B₁₂. This tandem arrangement yields a composite gene control system that functions as a two-input Boolean NOR logic gate. These findings and the discovery of additional tandem riboswitch architectures reveal how simple RNA elements can be assembled to make sophisticated genetic decisions without involving protein factors.

Identification of a large noncoding RNA in extremophilic eubacteria

Co-reporter:Elena Puerta-Fernandez;Adam Roth;Ronald R. Breaker;Jeffrey E. Barrick

PNAS 2006 Volume 103 (Issue 51 ) pp:19490-19495

Publication Date(Web):2006-12-19

DOI:10.1073/pnas.0607493103

We have discovered a large and highly conserved RNA motif that typically resides in a noncoding section of a multigene messenger RNA in extremophilic Gram-positive eubacteria. RNAs of this class adopt an ornate secondary structure, are large compared with most other noncoding RNAs, and have been identified only in certain extremophilic bacteria. These ornate, large, extremophilic (OLE) RNAs have a length of ≈610 nucleotides, and the 35 representatives examined exhibit extraordinary conservation of nucleotide sequence and base pairing. Structural probing of the OLE RNA from Bacillus halodurans corroborates a complex secondary structure model predicted from comparative sequence analysis. The patterns of structural conservation, and its unique phylogenetic distribution, suggest that OLE RNA carries out a complex and critical function only in certain extremophilic bacteria.

Molecular-Recognition Characteristics of SAM-Binding Riboswitches

Co-reporter:Jinsoo Lim Dr.;Wade C. Winkler Dr.;Shingo Nakamura Dr.;Valerie Scott;Ronald R. Breaker

Angewandte Chemie 2006 Volume 118(Issue 6) pp:

Publication Date(Web):28 DEC 2005

DOI:10.1002/ange.200503198

Eine Serie von Analoga des S-Adenosylmethionins (SAM) wurde verwendet, um die molekulare Erkennung eines genetischen RNA-Elements, eines Riboschalters, zu untersuchen. Nach biochemischen Tests ist der Riboschalter der SAM-I-Klasse hoch selektiv für SAM und unterscheidet sich in seinem Erkennungsmuster deutlich von Riboschaltern der SAM-II-Klasse.

Molecular-Recognition Characteristics of SAM-Binding Riboswitches

Co-reporter:Jinsoo Lim, Wade C. Winkler, Shingo Nakamura, Valerie Scott,Ronald R. Breaker

Angewandte Chemie International Edition 2006 45(6) pp:964-968

Publication Date(Web):

DOI:10.1002/anie.200503198

Characteristics of Ligand Recognition by a glmS Self-Cleaving Ribozyme

Co-reporter:Jinsoo Lim Dr.;Beth C. Grove;Adam Roth Dr.;Ronald R. Breaker

Angewandte Chemie International Edition 2006 Volume 45(Issue 40) pp:

Publication Date(Web):20 SEP 2006

DOI:10.1002/anie.200602534

A tweak here, a tweak there: A series of analogues of glucosamine-6-phosphate (GlcN6P, see picture) was used to examine the molecular-recognition characteristics of a glmS ribozyme that is activated by this ligand. Although several functional groups on the ligand are critical for binding, there are opportunities to create new analogues that fully trigger ribozyme action.

Gene regulation by riboswitches

Co-reporter:Maumita Mandal & Ronald R. Breaker

Nature Reviews Molecular Cell Biology 2004 5(6) pp:451

Publication Date(Web):

DOI:10.1038/nrm1403

Riboswitches are complex folded RNA domains that serve as receptors for specific metabolites. These domains are found in the non-coding portions of various mRNAs, where they control gene expression by harnessing allosteric structural changes that are brought about by metabolite binding. New findings indicate that riboswitches are robust genetic elements that are involved in regulating fundamental metabolic processes in many organisms.

A Glycine-Dependent Riboswitch That Uses Cooperative Binding to Control Gene Expression

Co-reporter:Maumita Mandal;Mark Lee;Jeffrey E. Barrick;Zasha Weinberg;Gail Mitchell Emilsson;Walter L. Ruzzo;Ronald R. Breaker

Science 2004 Vol 306(5694) pp:275-279

Publication Date(Web):08 Oct 2004

DOI:10.1126/science.1100829

Abstract

We identified a previously unknown riboswitch class in bacteria that is selectively triggered by glycine. A representative of these glycine-sensing RNAs from Bacillus subtilis operates as a rare genetic on switch for the gcvT operon, which codes for proteins that form the glycine cleavage system. Most glycine riboswitches integrate two ligand-binding domains that function cooperatively to more closely approximate a two-state genetic switch. This advanced form of riboswitch may have evolved to ensure that excess glycine is efficiently used to provide carbon flux through the citric acid cycle and maintain adequate amounts of the amino acid for protein synthesis. Thus, riboswitches perform key regulatory roles and exhibit complex performance characteristics that previously had been observed only with protein factors.

New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control

Co-reporter:Jeffrey E. Barrick;Keith A. Corbino;Wade C. Winkler;Ali Nahvi;Maumita Mandal;Jennifer Collins;Mark Lee;Adam Roth;Narasimhan Sudarsan;Inbal Jona;J. Kenneth Wickiser;Ronald R. Breaker

PNAS 2004 101 (17 ) pp:6421-6426

Publication Date(Web):2004-04-27

DOI:10.1073/pnas.0308014101

The expression of certain genes involved in fundamental metabolism is regulated by metabolite-binding “riboswitch” elements embedded within their corresponding mRNAs. We have identified at least six additional elements within the Bacillus subtilis genome that exhibit characteristics of riboswitch function (glmS, gcvT, ydaO/yuaA, ykkC/yxkD, ykoK, and yybP/ykoY). These motifs exhibit extensive sequence and secondary-structure conservation among many bacterial species and occur upstream of related genes. The element located upstream of the glmS gene in Gram-positive organisms functions as a metabolite-dependent ribozyme that responds to glucosamine-6-phosphate. Other motifs form complex folded structures when transcribed as RNA molecules and carry intrinsic terminator structures. These findings indicate that riboswitches serve as a major genetic regulatory mechanism for the control of metabolic genes in many microbial species.

Adenine riboswitches and gene activation by disruption of a transcription terminator

Co-reporter:

Nature Structural and Molecular Biology 2004 11(1) pp:29-35

Publication Date(Web):29 December 2003

DOI:10.1038/nsmb710

A class of riboswitches that recognizes guanine and discriminates against other purine analogs was recently identified. RNAs that carry the consensus sequence and structural features of guanine riboswitches are located in the 5' untranslated region (UTR) of numerous prokaryotic genes, where they control the expression of proteins involved in purine salvage and biosynthesis. We report that three representatives of this riboswitch class bind adenine with values for apparent dissociation constant (apparent K d) that are several orders of magnitude lower than those for binding guanine. Because preference for adenine is attributable to a single nucleotide substitution, the RNA most likely recognizes its ligand by forming a Watson-Crick base pair. In addition, the adenine riboswitch associated with the ydhL gene of Bacillus subtilis functions as a genetic 'on' switch, wherein adenine binding causes a structural rearrangement that precludes formation of an intrinsic transcription terminator stem.

Control of gene expression by a natural metabolite-responsive ribozyme

Co-reporter:Wade C. Winkler, Ali Nahvi, Adam Roth, Jennifer A. Collins and Ronald R. Breaker

Nature 2004 428(6980) pp:281

Publication Date(Web):

DOI:10.1038/nature02362

An mRNA structure that controls gene expression by binding S-adenosylmethionine

Co-reporter:

Nature Structural and Molecular Biology 2003 10(9) pp:701-707

Publication Date(Web):10 August 2003

DOI:10.1038/nsb967

Riboswitches are metabolite-binding RNA structures that serve as genetic control elements for certain messenger RNAs. These RNA switches have been identified in all three kingdoms of life and are typically responsible for the control of genes whose protein products are involved in the biosynthesis, transport or utilization of the target metabolite. Herein, we report that a highly conserved RNA domain found in bacteria serves as a riboswitch that responds to the coenzyme S-adenosylmethionine (SAM) with remarkably high affinity and specificity. SAM riboswitches undergo structural reorganization upon introduction of SAM, and these allosteric changes regulate the expression of 26 genes in Bacillus subtilis. This and related findings indicate that direct interaction between small metabolites and allosteric mRNAs is an important and widespread form of genetic regulation in bacteria.

Genetic Control by Metabolite-Binding Riboswitches

Co-reporter:Wade C. Winkler Dr.;Ronald R. Breaker

ChemBioChem 2003 Volume 4(Issue 10) pp:

Publication Date(Web):26 SEP 2003

DOI:10.1002/cbic.200300685

Metabolite-sensing mRNAs: Riboswitches are highly structured RNA domains that typically reside in the 5′-untranslated regions of certain bacterial mRNAs. These RNA domains serve as ligand-dependent genetic switches that provide a means by which RNA can control gene expression without the need for protein factors. Distinct classes of riboswitches are responsive to seven different metabolites and guide the maintenance of fundamental biochemical processes. One example is the regulation of the E. coli thiM mRNA by thiamine pyrophosphate (TPP; see representation).

An mRNA structure that controls gene expression by binding FMN

Co-reporter:Wade C. Winkler;Smadar Cohen-Chalamish;Ronald R. Breaker;

Proceedings of the National Academy of Sciences 2002 99(25) pp:15908-15913

Publication Date(Web):November 27, 2002

DOI:10.1073/pnas.212628899

The RFN element is a highly conserved domain that is found frequently in the 5′-untranslated regions of prokaryotic mRNAs that encode for flavin mononucleotide (FMN) biosynthesis and transport proteins. We report that this domain serves as the receptor for a metabolite-dependent riboswitch that directly binds FMN in the absence of proteins. Our results also indicate that in Bacillus subtilis, the riboswitch most likely controls gene expression by causing premature transcription termination of the ribDEAHT operon and precluding access to the ribosome-binding site of ypaA mRNA. Sequence and structural analyses indicate that the RFN element is a natural FMN-binding aptamer, the allosteric character of which is harnessed to control gene expression.

Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression

Co-reporter:Wade Winkler, Ali Nahvi and Ronald R. Breaker

Nature 2002 419(6910) pp:952

Publication Date(Web):

DOI:10.1038/nature01145

Although proteins fulfil most of the requirements that biology has for structural and functional components such as enzymes and receptors, RNA can also serve in these capacities. For example, RNA has sufficient structural plasticity to form ribozyme1, 2 and receptor3, 4 elements that exhibit considerable enzymatic power and binding specificity. Moreover, these activities can be combined to create allosteric ribozymes5, 6 that are modulated by effector molecules. It has also been proposed7, 8, 9, 10, 11, 12 that certain messenger RNAs might use allosteric mechanisms to mediate regulatory responses depending on specific metabolites. We report here that mRNAs encoding enzymes involved in thiamine (vitamin B1) biosynthesis in Escherichia coli can bind thiamine or its pyrophosphate derivative without the need for protein cofactors. The mRNA–effector complex adopts a distinct structure that sequesters the ribosome-binding site and leads to a reduction in gene expression. This metabolite-sensing regulatory system provides an example of a ‘riboswitch’ whose evolutionary origin might pre-date the emergence of proteins.

Structural diversity of self-cleaving ribozymes

Co-reporter:Jin Tang;Ronald R. Breaker

PNAS 2000 Volume 97 (Issue 11 ) pp:5784-5789

Publication Date(Web):2000-05-23

DOI:10.1073/pnas.97.11.5784

In vitro selection was used to isolate Mg2+-dependent self-cleaving ribozymes from random sequence. Characterization of representative clones revealed the emergence of at least 12 classes of ribozymes that adopt distinct secondary structure motifs. Only one class corresponds to a previously known structural motif, that of the naturally occurring hammerhead ribozyme. Each ribozyme promotes self-cleavage via an internal phosphoester transfer reaction involving the adjacent 2′-hydroxyl group with a chemical rate enhancement of between 103- and 106-fold greater than the corresponding uncatalyzed rate. These findings indicate that RNA can form a multitude of secondary and tertiary structures that promote cleavage by internal phosphoester transfer. Upon further in vitro selection, a class I ribozyme that adopts an “X motif” structure dominates over all other ribozymes in the population. Thus, self-cleaving RNAs isolated by in vitro selection from random-sequence populations can rival the catalytic efficiency of natural ribozymes.

Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP

Co-reporter:

Nature Structural and Molecular Biology 1999 6(11) pp:1062 - 1071

Publication Date(Web):

DOI:10.1038/14947

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

Co-reporter:Joy Xin Wang, Elaine R. Lee, Dianali Rivera Morales, Jinsoo Lim, Ronald R. Breaker

Molecular Cell (28 March 2008) Volume 29(Issue 6) pp:691-702

Publication Date(Web):28 March 2008

DOI:10.1016/j.molcel.2008.01.012

We have identified a highly conserved RNA motif that occurs upstream of genes involved in S-adenosyl-L-methionine (SAM) recycling in many Gram-positive and Gram-negative species of bacteria. The phylogenetic distribution and the conserved structural features of representatives of this motif are indicative of riboswitch function. Riboswitches are widespread metabolite-sensing gene control elements that are typically found in the 5′ untranslated regions (UTRs) of bacterial mRNAs. We experimentally verified that examples of this RNA motif specifically recognize S-adenosylhomocysteine (SAH) in protein-free in vitro assays, and confirmed that these RNAs strongly discriminate against SAM and other closely related analogs. A representative SAH motif was found to activate expression of a downstream gene in vivo when the metabolite is bound. These observations confirm that SAH motif RNAs are distinct ligand-binding aptamers for a riboswitch class that selectively binds SAH and controls genes essential for recycling expended SAM coenzymes.

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

Co-reporter:Peter B. Kim, James W. Nelson, Ronald R. Breaker

Molecular Cell (22 January 2015) Volume 57(Issue 2) pp:317-328

Publication Date(Web):22 January 2015

DOI:10.1016/j.molcel.2015.01.001

•A widespread riboswitch class directly binds the purine derivatives ZMP and ZTP•ZTP riboswitches can be used to report 10f-THF deficiency•ZTP riboswitches regulate the response to 10f-THF deficiencyOver 30 years ago, ZTP (5-aminoimidazole-4-carboxamide riboside 5′-triphosphate), a modified purine biosynthetic intermediate, was proposed to signal 10-formyl-tetrahydrofolate (10f-THF) deficiency in bacteria. However, the mechanisms by which this putative alarmone or its precursor ZMP (5-aminoimidazole-4-carboxamide ribonucleotide, also known as AICAR) brings about any metabolic changes remain unexplained. Herein, we report the existence of a widespread riboswitch class that is most commonly associated with genes related to de novo purine biosynthesis and one-carbon metabolism. Biochemical data confirm that members of this riboswitch class selectively bind ZMP and ZTP with nanomolar affinity while strongly rejecting numerous natural analogs. Indeed, increases in the ZMP/ZTP pool, caused by folate stress in bacterial cells, trigger changes in the expression of a reporter gene fused to representative ZTP riboswitches in vivo. The wide distribution of this riboswitch class suggests that ZMP/ZTP signaling is important for species in numerous bacterial lineages.Download high-res image (394KB)Download full-size image

Bacterial Riboswitches Cooperatively Bind Ni2+ or Co2+ Ions and Control Expression of Heavy Metal Transporters

Co-reporter:Kazuhiro Furukawa, Arati Ramesh, Zhiyuan Zhou, Zasha Weinberg, ... Ronald R. Breaker

Molecular Cell (19 March 2015) Volume 57(Issue 6) pp:1088-1098

Publication Date(Web):19 March 2015

DOI:10.1016/j.molcel.2015.02.009

•NiCo RNA is the first conserved riboswitch class that responds to transition metals•NiCo selectively recognizes cobalt or nickel, binding with positive cooperativity•NiCo riboswitches control metal homeostasis by regulating metal transport proteinsBacteria regularly encounter widely varying metal concentrations in their surrounding environment. As metals become depleted or, conversely, accrue to toxicity, microbes will activate cellular responses that act to maintain metal homeostasis. A suite of metal-sensing regulatory (“metalloregulatory”) proteins orchestrate these responses by allosterically coupling the selective binding of target metals to the activity of DNA-binding domains. However, we report here the discovery, validation, and structural details of a widespread class of riboswitch RNAs, whose members selectively and tightly bind the low-abundance transition metals, Ni2+ and Co2+. These riboswitches bind metal cooperatively, and with affinities in the low micromolar range. The structure of a Co2+-bound RNA reveals a network of molecular contacts that explains how it achieves cooperative binding between adjacent sites. These findings reveal that bacteria have evolved to utilize highly selective metalloregulatory riboswitches, in addition to metalloregulatory proteins, for detecting and responding to toxic levels of heavy metals.Download high-res image (195KB)Download full-size image

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

Co-reporter:James W. Nelson, Ruben M. Atilho, Madeline E. Sherlock, Randy B. Stockbridge, Ronald R. Breaker

Molecular Cell (19 January 2017) Volume 65(Issue 2) pp:220-230

Publication Date(Web):19 January 2017

DOI:10.1016/j.molcel.2016.11.019

•Bacteria naturally produce, sense, and respond to guanidine•Most ykkC RNA motif representatives are aptamer domains of guanidine riboswitches•Riboswitches control guanidine carboxylase genes previously declared urea carboxylases•Many annotated EmrE and SugE multidrug efflux pumps are likely guanidine transportersThe guanidyl moiety is a component of fundamental metabolites, including the amino acid arginine, the energy carrier creatine, and the nucleobase guanine. Curiously, reports regarding the importance of free guanidine in biology are sparse, and no biological receptors that specifically recognize this compound have been previously identified. We report that many members of the ykkC motif RNA, the longest unresolved riboswitch candidate, naturally sense and respond to guanidine. This RNA is found throughout much of the bacterial domain of life, where it commonly controls the expression of proteins annotated as urea carboxylases and multidrug efflux pumps. Our analyses reveal that these proteins likely function as guanidine carboxylases and guanidine transporters, respectively. Furthermore, we demonstrate that bacteria are capable of endogenously producing guanidine. These and related findings demonstrate that free guanidine is a biologically relevant compound, and several gene families that can alleviate guanidine toxicity exist.Download high-res image (200KB)Download full-size image

Prospects for Riboswitch Discovery and Analysis

Co-reporter:Ronald R. Breaker

Molecular Cell (16 September 2011) Volume 43(Issue 6) pp:867-879

Publication Date(Web):16 September 2011

DOI:10.1016/j.molcel.2011.08.024

An expanding number of metabolite-binding riboswitch classes are being discovered in the noncoding portions of bacterial genomes. Findings over the last decade indicate that bacteria commonly use these RNA genetic elements as regulators of metabolic pathways and as mediators of changes in cell physiology. Some riboswitches are surprisingly complex, and they rival protein factors in their structural and functional sophistication. Each new riboswitch discovery expands our knowledge of the biochemical capabilities of RNA, and some give rise to new questions that require additional study to be addressed. Some of the greatest prospects for riboswitch research and some of the more interesting mysteries are discussed in this review.

RNA Switches Out in the Cold

Co-reporter:Ronald R. Breaker

Molecular Cell (15 January 2010) Volume 37(Issue 1) pp:1-2

Publication Date(Web):15 January 2010

DOI:10.1016/j.molcel.2009.12.032

In this issue of Molecular Cell, Giuliodori et al. (2010) describe a cold-induced genetic switch made of RNA. Could thermo-sensing RNAs be among the most common types of RNA genetic switches?