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
2021
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
1999
Mapping RNA−Protein Interactions in Ribonuclease P from Escherichia coli Using Electron Paramagnetic Resonance Spectroscopy †
Gopalan V, Kühne H, Biswas R, Li H, Brudvig G, Altman S. Mapping RNA−Protein Interactions in Ribonuclease P from Escherichia coli Using Electron Paramagnetic Resonance Spectroscopy †. Biochemistry 1999, 38: 1705-1714. PMID: 10026248, DOI: 10.1021/bi9807106.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBacterial ProteinsBinding SitesComputer SimulationElectron Spin Resonance SpectroscopyEndoribonucleasesEscherichia coliEscherichia coli ProteinsModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedProtein FoldingRibonuclease PRibonucleoproteinsRNA, BacterialRNA, CatalyticSpin LabelsStructure-Activity RelationshipConceptsM1 RNAC5 proteinRibonuclease PCysteine residuesEscherichia coliRNA-protein interfaceCatalytic RNA subunitNative cysteine residuesSulfhydryl-specific reagentsCatalytic ribonucleoproteinRNA subunitHoloenzyme complexRNP complexesProtein cofactorsMutant derivativesDeletion derivativesRNASpin labelsProteinSpectroscopy-based approachRibonucleoproteinResiduesPosition 16Coli
1989
[32] Immunoprecipitation of ribonucleoproteins using autoantibodies
Steitz J. [32] Immunoprecipitation of ribonucleoproteins using autoantibodies. Methods In Enzymology 1989, 180: 468-481. PMID: 2693908, DOI: 10.1016/0076-6879(89)80118-1.Peer-Reviewed Original ResearchConceptsSmall ribonucleoproteinImmunoprecipitation procedureTissue culture cellsRNP complexesRNA degradationLaemmli gelsRibonucleoproteinCulture cellsImmunoprecipitationWestern blottingProteinMouse ascitesRNAsCell culture supernatantsCulture supernatantsPhosphoproteinMonoclonal antibodiesRNAImmunoprecipitatesTissueRibonuclease levelsHigh backgroundMouse monoclonal autoantibodyBlottingMonoclonal autoantibodies
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