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 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
Evidence that OLE RNA is a component of a major stress‐responsive ribonucleoprotein particle in extremophilic bacteria
Breaker R, Harris K, Lyon S, Wencker F, Fernando C. Evidence that OLE RNA is a component of a major stress‐responsive ribonucleoprotein particle in extremophilic bacteria. Molecular Microbiology 2023, 120: 324-340. PMID: 37469248, DOI: 10.1111/mmi.15129.Peer-Reviewed Original ResearchConceptsOLE RNAPrecise biochemical functionFundamental cellular processesCell growthTOR complexesProtein partnersRibonucleoprotein complexesCellular processesRNP complexesBiochemical functionsGram-positive bacteriaNoncoding RNAsRibonucleoprotein particleExtremophilic bacteriaBacterial speciesGenetic disruptionStress conditionsDiverse pathwaysRNAMetabolic adaptationCell membraneExtreme environmentsCarbon sourceBacteriaComplexes
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
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 changesRegulon
1997
Rational design of allosteric ribozymes
Tang J, Breaker R. Rational design of allosteric ribozymes. Cell Chemical Biology 1997, 4: 453-459. PMID: 9224568, DOI: 10.1016/s1074-5521(97)90197-6.Peer-Reviewed Original ResearchConceptsAllosteric regulationAllosteric ribozymesEffector moleculesProtein enzymesActive siteCatalytic ratePresence of dATPSelf-cleaving ribozymesSmall effector moleculesPresence of ATPSmall molecule receptorRational design strategyCellular processesEnzyme active siteAptamer domainAllosteric controlAllosteric enzymeCatalytic RNARNA aptamersConformational changesLigand moleculesMetabolic pathwaysCatalytic activityAllosteric hammerheadCatalytic features