Featured Publications
Discovering riboswitches: the past and the future
Kavita K, Breaker RR. Discovering riboswitches: the past and the future. Trends In Biochemical Sciences 2022, 48: 119-141. PMID: 36150954, PMCID: PMC10043782, DOI: 10.1016/j.tibs.2022.08.009.Peer-Reviewed Original ResearchNa+ riboswitches regulate genes for diverse physiological processes in bacteria
White N, Sadeeshkumar H, Sun A, Sudarsan N, Breaker RR. Na+ riboswitches regulate genes for diverse physiological processes in bacteria. Nature Chemical Biology 2022, 18: 878-885. PMID: 35879547, PMCID: PMC9337991, DOI: 10.1038/s41589-022-01086-4.Peer-Reviewed Original ResearchConceptsOsmotic stressGene expressionDiverse physiological processesMetal ion transportersGene expression changesExpression of genesRiboswitch classesBacterial proteinsIon transportersExpression changesPhysiological processesATP productionLow mM rangeGenesProteinExpressionBacteriaTranscriptionDissociation constantsOrganismsBiologyMM rangeTransportersMotifStress
2024
Prospects for Riboswitches in Drug Development
Mohsen M, Breaker R. Prospects for Riboswitches in Drug Development. Methods And Principles In Medicinal Chemistry 2024, 203-226. DOI: 10.1002/9783527840458.ch8.Peer-Reviewed Original ResearchUntranslated regions of messenger RNAsRegions of messenger RNAsModulate gene expressionBacterial physiologyEngineered riboswitchesSynthetic switchesRNA structureRiboswitch functionRiboswitchUntranslated regionSmall moleculesDrug developmentGene expressionDrug-like small moleculesHuman gene therapy applicationsMessenger RNARNAGene therapy applicationsAntibiotic agentsTargeting ligandsTherapy applicationsProteinMoleculesDrug
2023
8-oxoguanine riboswitches in bacteria detect and respond to oxidative DNA damage
Dhakal S, Kavita K, Panchapakesan S, Roth A, Breaker R. 8-oxoguanine riboswitches in bacteria detect and respond to oxidative DNA damage. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2307854120. PMID: 37748066, PMCID: PMC10556655, DOI: 10.1073/pnas.2307854120.Peer-Reviewed Original ResearchConceptsAptamer domainGene expressionLigand specificityOxidative damageLigand-binding pocketRiboswitch classesFamilies of bacteriaRare variantsRiboswitch aptamerCertain oxidative stressesExposure of cellsOxidative DNA damageRiboswitchGene associationsRNA aptamersDNA damageNucleotide poolBacteriaTarget ligandsOxidative stressMutationsNumerous alterationsPurine derivativesExpressionVariantsRiboswitches
Salvail H, Breaker R. Riboswitches. Current Biology 2023, 33: r343-r348. PMID: 37160088, PMCID: PMC11207198, DOI: 10.1016/j.cub.2023.03.069.Peer-Reviewed Original ResearchExploiting natural riboswitches for aptamer engineering and validation
Mohsen M, Midy M, Balaji A, Breaker R. Exploiting natural riboswitches for aptamer engineering and validation. Nucleic Acids Research 2023, 51: 966-981. PMID: 36617976, PMCID: PMC9881172, DOI: 10.1093/nar/gkac1218.Peer-Reviewed Original ResearchConceptsNatural riboswitchesRiboswitch aptamerReporter gene expressionSecondary structure featuresRNA poolExpression platformVivo functionGene expressionSurvival mechanismRNA sequencesStructural featuresRiboswitchAptamer selectionSmall moleculesSequenceAptamerCellsGuanineTest tubeFuture effortsSelectionSelection strategyExpressionPoolAptamer engineering
2022
Lithium-sensing riboswitch classes regulate expression of bacterial cation transporter genes
White N, Sadeeshkumar H, Sun A, Sudarsan N, Breaker R. Lithium-sensing riboswitch classes regulate expression of bacterial cation transporter genes. Scientific Reports 2022, 12: 19145. PMID: 36352003, PMCID: PMC9646797, DOI: 10.1038/s41598-022-20695-6.Peer-Reviewed Original Research
2018
Large Noncoding RNAs in Bacteria
Harris K, Breaker R. Large Noncoding RNAs in Bacteria. 2018, 515-526. DOI: 10.1128/9781683670247.ch30.Peer-Reviewed Original ResearchNcRNA classesSelfish genetic elementsLarge noncoding RNAsGenetic information processingProtein-coding regionsGroup II intronsSelf-splicing ribozymesStructured ncRNAsPrecursor tRNAsRNA splicingCellular processesDNA genomeNoncoding RNAsGenetic elementsGene expressionExon flanksPeptide bond formationRNA cleavagePhysiological adaptationsBind ionsRibozyme structureEssential roleRibozymeIntriguing possibilityBacteria
2009
Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches
Link K, Breaker R. Engineering ligand-responsive gene-control elements: lessons learned from natural riboswitches. Gene Therapy 2009, 16: 1189-1201. PMID: 19587710, PMCID: PMC5325117, DOI: 10.1038/gt.2009.81.Peer-Reviewed Original Research
2008
Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP
Sudarsan N, Lee E, Weinberg Z, Moy R, Kim J, Link K, Breaker R. Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP. Science 2008, 321: 411-413. PMID: 18635805, PMCID: PMC5304454, DOI: 10.1126/science.1159519.Peer-Reviewed Original ResearchConceptsCyclic di-GMPVirulence gene expressionGene expressionSecond messenger cyclic di-GMPNumerous fundamental cellular processesCyclic di-guanosine monophosphateFundamental cellular processesExpression of genesGMP riboswitchRiboswitch classesFlagellum biosynthesisBiofilm lifestyleCellular processesDiverse speciesPilus formationSecond messengerCell differentiationRiboswitchBacterial speciesMessenger RNARNA dinucleotideSpeciesExpressionPhysiological changesRegulonGene Regulation by Riboswitches
Breaker R. Gene Regulation by Riboswitches. The FASEB Journal 2008, 22: 97.3-97.3. DOI: 10.1096/fasebj.22.1_supplement.97.3.Peer-Reviewed Original ResearchGene expressionRiboswitch classesS-adenosylmethionineUntranslated regionWidespread riboswitch classesS-adenosylhomocysteineControl gene expressionDiversity of mechanismsGene regulationAlternative splicingModern organismsBacterial mRNAsUncharacterized mechanismRiboswitchRNA elementsMolecular switchFunctional potentialAptamer structureRNADiversityExpressionMRNAEukaryotesSplicingGenesRiboswitches as new antibiotics targets
Blount K, Breaker R. Riboswitches as new antibiotics targets. The FASEB Journal 2008, 22: 264.3-264.3. DOI: 10.1096/fasebj.22.1_supplement.264.3.Peer-Reviewed Original ResearchDrug targetsAntibacterial drug discoveryNew antibiotic targetsNew cellular targetsDrug discoveryAntibiotic targetsRiboswitchGene expressionRNA structureCellular targetsDrug discoverersAntibacterial compoundsGenesLethal effectsBacteriaExpressionMetabolite analogsReceptorsTargetDiscoveryRNABindsSelective receptorsMRNARecent work
2006
Genetic control by riboswitches and ribozymes
Breaker R. Genetic control by riboswitches and ribozymes. The FASEB Journal 2006, 20: a455-a456. DOI: 10.1096/fasebj.20.4.a455-d.Peer-Reviewed Original ResearchGenetic switchGene expressionAptamer domainBacterial speciesCertain messenger RNAsControl gene expressionMessenger RNA stabilityNon-coding regionsComplex genetic elementsSelf-cleaving ribozymesRiboswitch classesReceptor-ligand interactionsTranscription elongationTranslation initiationRNA stabilityRNA transcriptionRiboswitchAllosteric changesGenetic controlGenetic elementsRNA structureMessenger RNATarget metabolitesRNARecent findingsRiboswitches: Natural Metabolite‐binding RNAs Controlling Gene Expression
Roth A, Welz R, Breaker R. Riboswitches: Natural Metabolite‐binding RNAs Controlling Gene Expression. 2006, 191-207. DOI: 10.1002/3527608192.ch8.Peer-Reviewed Original Research