Featured Publications
Na+ 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
The discovery of novel noncoding RNAs in 50 bacterial genomes
Narunsky A, Higgs G, Torres B, Yu D, de Andrade G, Kavita K, Breaker R. The discovery of novel noncoding RNAs in 50 bacterial genomes. Nucleic Acids Research 2024, 52: 5152-5165. PMID: 38647067, PMCID: PMC11109978, DOI: 10.1093/nar/gkae248.Peer-Reviewed Original ResearchBacterial genomesDomains of lifeIntergenic regionNcRNA classesGC-rich intergenic regionsBacterial domain of lifeIndividual bacterial genomesStructured noncoding RNAsNovel noncoding RNAsProtein coding genesNoncoding RNAsNcRNA motifsRiboswitch candidatesBacterial domainRiboswitch classesCoding genesGene regulationCellular processesCytidine nucleotidesBacterial speciesGenomeComputational pipelineNcRNAsDiverse functionsGenes
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 derivativesExpressionVariantsA conserved uORF in the ilvBNC mRNA of Corynebacterium species regulates ilv operon expression
Narunsky A, Kavita K, Panchapakesan S, Fris M, Breaker R. A conserved uORF in the ilvBNC mRNA of Corynebacterium species regulates ilv operon expression. Microbial Genomics 2023, 9: mgen001019. PMID: 37233150, PMCID: PMC10272879, DOI: 10.1099/mgen.0.001019.Peer-Reviewed Original ResearchConceptsBranched-chain amino acidsRNA motifsUpstream open reading framesTranscription attenuation mechanismStructured noncoding RNAsOpen reading frameRiboswitch classesTranscription attenuationProtein translationNoncoding RNAsOperon expressionGenetic approachesReading frameStart codonUORF translationStop codonBacterial speciesHost cellsGenesUORFsAmino acidsMotifCodonCommon mechanismCorynebacterium species
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
2019
Genome‐wide Discovery of Rare Riboswitches in Bacteria
Arachchilage G, Atilho R, Stav S, Higgs G, Breaker R. Genome‐wide Discovery of Rare Riboswitches in Bacteria. The FASEB Journal 2019, 33: 778.8-778.8. DOI: 10.1096/fasebj.2019.33.1_supplement.778.8.Peer-Reviewed Original ResearchRiboswitch candidatesBacterial genomesGC-rich intergenic regionsDifferent bacterial genomesGenome-wide discoverySequenced bacterial genomesNascent RNA transcriptsRiboswitch classesThiamin biosynthesisRiboswitch aptamerStructured ncRNAsNcRNA classesIntergenic regionHydroxymethylpyrimidine pyrophosphateRiboswitchBioinformatics pipelineRNA transcriptsTranscription processComputational pipelinePhysiological pathwaysConformational changesNcRNAsGenomeFASEB JournalHoward Hughes Medical Institute
2018
High Throughput Validation of Orphan Riboswitch Candidates
Arachchilage G, Sherlock M, White N, Panchapakesan S, Breaker R. High Throughput Validation of Orphan Riboswitch Candidates. The FASEB Journal 2018, 32: lb18-lb18. DOI: 10.1096/fasebj.2018.32.1_supplement.lb18.Peer-Reviewed Original ResearchRiboswitch candidatesRiboswitch classesIntergenic regionCognate ligandsS-adenosylmethionineLong intergenic regionCis-acting genesDiscovery of riboswitchesExperimental Biology 2018 MeetingImportant biological pathwaysHigh-throughput validationHigh-throughput strategyS-adenosylhomocysteineComparative genomicsRecent bioinformaticsBacterial mRNAsLine probingRNA elementsRiboswitchGenetic validationReporter assaysBiological pathwaysComputational approachThroughput strategyFASEB Journal
2010
Bacterial Riboswitch Discovery and Analysis
Ames T, Breaker R. Bacterial Riboswitch Discovery and Analysis. 2010, 433-454. DOI: 10.1002/9780470664001.ch20.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 structureRNADiversityExpressionMRNAEukaryotesSplicingGenes
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 findings