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
Improved methods for genetic manipulation of the alkaliphile Halalkalibacterium halodurans
Wencker F, Lyon S, Breaker R. Improved methods for genetic manipulation of the alkaliphile Halalkalibacterium halodurans. Frontiers In Microbiology 2024, 15: 1465811. PMID: 39360312, PMCID: PMC11445130, DOI: 10.3389/fmicb.2024.1465811.Peer-Reviewed Original ResearchThe 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 functionsGenesGenetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation
Soares L, King C, Fernando C, Roth A, Breaker R. Genetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2318008121. PMID: 38306478, PMCID: PMC10861870, DOI: 10.1073/pnas.2318008121.Peer-Reviewed Original ResearchConceptsMotif RNAsGenetic disruptionSecondary structure modelKnock-out strainTrans-acting factorsNoncoding RNAsCell differentiation processAbundant RNATransfer RNANcRNA classesRibosomal RNASpore formationMotif genesCellular processesBacterial speciesCellular functionsBioinformatics analysisExpression analysisMotifRNAGenesBiochemical mechanismsNcRNAsDifferentiation processStructural probes
2023
A 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 speciesScreening for small molecule inhibitors of SAH nucleosidase using an SAH riboswitch
Sadeeshkumar H, Balaji A, Sutherland A, Mootien S, Anthony K, Breaker R. Screening for small molecule inhibitors of SAH nucleosidase using an SAH riboswitch. Analytical Biochemistry 2023, 666: 115047. PMID: 36682579, PMCID: PMC11149561, DOI: 10.1016/j.ab.2023.115047.Peer-Reviewed Original ResearchConceptsHigh-throughput screenAutoinducer-2Reporter geneBacterial processesEssential bacterial processesGram-negative bacterial cellsQuorum sensing signalsΒ-galactosidase reporter geneSmall molecule inhibitorsAntibiotic drug discoveryNatural riboswitchesAntimicrobial drug developmentRNA elementsPhysiological signalingRiboswitchBacterial cellsMolecule inhibitorsS-adenosylmethionineEscherichia coliCritical functionsNew targetsGenesDrug discoverySmall moleculesPromising target
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
2010
Riboswitches That Sense Cyclic Di‐GMP
Lee E, Sudarsan N, Breaker R. Riboswitches That Sense Cyclic Di‐GMP. 2010, 215-229. DOI: 10.1128/9781555816667.ch15.Peer-Reviewed Original ResearchGMP riboswitchSecond messengerUntranslated regionCyclic di-GMPHigh sequence conservationAssociation of genesSecond messenger signalingSecondary structure elementsEntire regulonDifferent genetic backgroundsTranscription elongationSequence conservationRNA functionTranslation initiationLine probingDifferent environmental conditionsRiboswitchRegulatory ligandsProtein productsNew hostGenesMessenger RNAGenetic backgroundGreat diversityEnvironmental conditions
2008
Gene 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
Riboswitches as Genetic Control Elements
Nahvi A, Breaker R. Riboswitches as Genetic Control Elements. 2006, 89-106. DOI: 10.1007/978-0-387-47257-7_6.Peer-Reviewed Original ResearchGene control mechanismsCertain messenger RNAsGenetic control elementsGene expression systemRNA stabilityExpression platformRNA elementsExpression systemRiboswitchRNA structureLigand bindingMRNA transcriptionMessenger RNATarget metabolitesControl elementsTranscriptionControl mechanismsGenesRNABacteriaBindingExpressionTranslationMetabolitesAptamer