Featured Publications
Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex
Yang Y, Harris KA, Widner DL, Breaker RR. Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2020393118. PMID: 33619097, PMCID: PMC7936274, DOI: 10.1073/pnas.2020393118.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBacillusBacterial ProteinsBase SequenceBinding SitesCloning, MolecularCrystallography, X-RayEscherichia coliGene ExpressionGene Expression Regulation, BacterialGenetic VectorsMolecular Docking SimulationNucleic Acid ConformationProtein BindingProtein Conformation, alpha-HelicalProtein Conformation, beta-StrandProtein Interaction Domains and MotifsRecombinant ProteinsRibonucleoproteinsRNA, BacterialRNA, UntranslatedConceptsOLE RNARNP complexesBiological functionsBacterial noncoding RNAsRNA-binding surfaceProtein-RNA interfacesHigh-resolution structuresUnique structural elementsKOW motifProtein partnersHigh conservationRibonucleoprotein complexesRNA classesRNA interactionsNoncoding RNAsBacterial responseOapBRNA targetsRNA fragmentsAtomic detailRNAProtein BMolecular contactsProtein AStructural features
2024
Bioinformatic prediction of proteins relevant to functions of the bacterial OLE ribonucleoprotein complex
Fernando C, Breaker R. Bioinformatic prediction of proteins relevant to functions of the bacterial OLE ribonucleoprotein complex. MSphere 2024, 9: e00159-24. PMID: 38771028, PMCID: PMC11332333, DOI: 10.1128/msphere.00159-24.Peer-Reviewed Original ResearchOLE RNANoncoding RNA classesRNP complexesRNA classesSequence conservationProtein partnersBiochemical functionsDiverse stress conditionsProtein binding partnersEmergence of proteinsPhylogenetic profilesRibonucleoprotein complexSpore formationBacterial speciesCellular stressExtremophilic bacteriaProtein componentsRibonucleoproteinGenetic disruptionRNATransport proteinsRelevant to functionBioinformatics predictionGram-positivePrimitive organismsDisruption of the bacterial OLE RNP complex impairs growth on alternative carbon sources
Lyon S, Wencker F, Fernando C, Harris K, Breaker R. Disruption of the bacterial OLE RNP complex impairs growth on alternative carbon sources. PNAS Nexus 2024, 3: pgae075. PMID: 38415217, PMCID: PMC10898510, DOI: 10.1093/pnasnexus/pgae075.Peer-Reviewed Original ResearchRNP complexesMinimal mediumWild-type cellsAlternative carbon sourcesUnfavorable growth conditionsOLE RNASuppressor selectionDiverse stressesCarbon/energy sourceProtein secretionCarbon sourceGenetic disruptionCellular adaptationNoncoding RNAsFunctional linkRNAGrowth conditionsRibonucleoproteinImpaired growthPhosphate homeostasisFundamental processesHomeostasisShort-chain alcoholsElevated MgCarbon/energy
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
2022
Ornate, large, extremophilic (OLE) RNA forms a kink turn necessary for OapC protein recognition and RNA function
Lyon S, Harris K, Odzer N, Wilkins S, Breaker R. Ornate, large, extremophilic (OLE) RNA forms a kink turn necessary for OapC protein recognition and RNA function. Journal Of Biological Chemistry 2022, 298: 102674. PMID: 36336078, PMCID: PMC9723947, DOI: 10.1016/j.jbc.2022.102674.Peer-Reviewed Original ResearchConceptsOLE RNARNP complexesRNA-protein binding assaysPrecise biochemical functionRNA structural motifsInability of cellsNatural binding sitesRibonucleoprotein complexesRNA functionBiochemical functionsExhibit phenotypesBacterial proteinsK-turnKink turnBacillus haloduransDisruptive mutationsSame proteinBacterial speciesProtein recognitionAnaerobic bacterial speciesFunctional roleSecondary structureRNAProteinOapB
2010
The large, noncoding OLE RNA is associated with membrane biochemistry
Block K, Wallace J, Puerta‐Fernandez E, Breaker R. The large, noncoding OLE RNA is associated with membrane biochemistry. The FASEB Journal 2010, 24: 493.2-493.2. DOI: 10.1096/fasebj.24.1_supplement.493.2.Peer-Reviewed Original ResearchOLE RNAB. haloduransMembrane biochemistryMembrane-spanning proteinsHigh-throughput sequencingEnergy-generating pathwaysEscherichia coli cellsGel shift assaysNorthern blot analysisRNA fluorescenceSpecific ribonucleoproteinGram-positive bacteriaShift assaysColi cellsUnknown functionProbable binding siteSitu hybridizationBlot analysisBinding sitesHaloduransHoward Hughes Medical InstituteRNAProteinBiochemistryCells