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 organismsGenetic 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 probesDisruption 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