2025
The extracytoplasmic sigma factor σX supports biofilm formation and increases biocontrol efficacy in Bacillus velezensis 118
Cai Y, Tao H, Gaballa A, Pi H, Helmann J. The extracytoplasmic sigma factor σX supports biofilm formation and increases biocontrol efficacy in Bacillus velezensis 118. Scientific Reports 2025, 15: 5315. PMID: 39939707, PMCID: PMC11822112, DOI: 10.1038/s41598-025-89284-7.Peer-Reviewed Original ResearchConceptsPlant growth-promoting rhizobacteriaBiocontrol efficacyBiocontrol activityIncrease biocontrol efficacyReduced biocontrol efficacyEffect of Bacillus sppFusarium wilt of bananaWilt of bananaGrowth-promoting rhizobacteriaColonize plant rootsExtracytoplasmic functionBiocontrol agentsBiofilm formationEnhancing crop productivityPlant rootsPromoting rhizobacteriaBiocontrolLipopeptide productionFusarium wiltRoot colonizationSoil isolatesReduced biofilm formationSigX mutantSwarming motilityCrop production
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
2018
Maturing Mycobacterium smegmatis peptidoglycan requires non-canonical crosslinks to maintain shape
Baranowski C, Welsh M, Sham L, Eskandarian H, Lim H, Kieser K, Wagner J, McKinney J, Fantner G, Ioerger T, Walker S, Bernhardt T, Rubin E, Rego E. Maturing Mycobacterium smegmatis peptidoglycan requires non-canonical crosslinks to maintain shape. ELife 2018, 7: e37516. PMID: 30324906, PMCID: PMC6231781, DOI: 10.7554/elife.37516.Peer-Reviewed Original ResearchConceptsPenicillin-binding proteinsAsymmetric polar growthRod-shaped bacteriaPolar growthPolar elongationShape maintenanceCell wallGenetic relationshipsDrug targetsUnusual crosslinksD-transpeptidasesSingle cellsPeptidoglycanCellsCrosslinksProteinMycobacteriaBacteriaPathogensTypes of crosslinksElongationGrowthMaintenanceTargetAntagonism of Two Plant-Growth Promoting Bacillus velezensis Isolates Against Ralstonia solanacearum and Fusarium oxysporum
Cao Y, Pi H, Chandrangsu P, Li Y, Wang Y, Zhou H, Xiong H, Helmann J, Cai Y. Antagonism of Two Plant-Growth Promoting Bacillus velezensis Isolates Against Ralstonia solanacearum and Fusarium oxysporum. Scientific Reports 2018, 8: 4360. PMID: 29531357, PMCID: PMC5847583, DOI: 10.1038/s41598-018-22782-z.Peer-Reviewed Original ResearchConceptsPlant growthRalstonia solanacearumBacillus velezensisFusarium oxysporumPathogen F. oxysporumStrong antagonistic activityRhizosphere colonizationSpore-forming bacilliBiocontrol agentsR. solanacearumB. velezensisCell motilityBiological processesF. oxysporumGreenhouse conditionsSolanacearumBiofilm formationOxysporumLP productionAntagonistic activityLipopeptide compoundsIturinRhizobacteriaPrimary rolePGPR
2011
The β Subunit Loop That Couples Catalysis and Rotation in ATP Synthase Has a Critical Length*
Mnatsakanyan N, Kemboi SK, Salas J, Weber J. The β Subunit Loop That Couples Catalysis and Rotation in ATP Synthase Has a Critical Length*. Journal Of Biological Chemistry 2011, 286: 29788-29796. PMID: 21705326, PMCID: PMC3191020, DOI: 10.1074/jbc.m111.254730.Peer-Reviewed Original ResearchImproved genetic transformation methods for the model alkaliphile Bacillus halodurans C‐125
Wallace J, Breaker R. Improved genetic transformation methods for the model alkaliphile Bacillus halodurans C‐125. Letters In Applied Microbiology 2011, 52: 430-432. PMID: 21362000, PMCID: PMC5315388, DOI: 10.1111/j.1472-765x.2011.03017.x.Peer-Reviewed Original Research
2010
Ecology of Speciation in the Genus Bacillus
Connor N, Sikorski J, Rooney A, Kopac S, Koeppel A, Burger A, Cole S, Perry E, Krizanc D, Field N, Slaton M, Cohan F. Ecology of Speciation in the Genus Bacillus. Applied And Environmental Microbiology 2010, 76: 1349-1358. PMID: 20048064, PMCID: PMC2832372, DOI: 10.1128/aem.01988-09.Peer-Reviewed Original ResearchConceptsEcotype SimulationSoil textureEvolutionary historyEcology of speciationClade's evolutionary historyB. subtilisDNA sequence diversityPutative ecotypesEcological divergenceDivergent lineagesMicrobial ecologistsEcological changesEcological diversityEcological differencesEcological dimensionsEcotype differencesSequence diversityTemperature adaptationGenus BacillusSolar exposureCladeEcotypesEnvironmental parametersBacterial populationsTaxa
2009
Tertiary architecture of the Oceanobacillus iheyensis group II intron
Toor N, Keating KS, Fedorova O, Rajashankar K, Wang J, Pyle AM. Tertiary architecture of the Oceanobacillus iheyensis group II intron. RNA 2009, 16: 57-69. PMID: 19952115, PMCID: PMC2802037, DOI: 10.1261/rna.1844010.Peer-Reviewed Original ResearchConceptsGroup II intronsPotential evolutionary relationshipsGroup II intron structureGroup IIC intronIntron structureEvolutionary relationshipsEukaryotic spliceosomeInteraction networksRNA moleculesIntronsTertiary structural organizationGenetic studiesRibose zipperRNA foldingTertiary interactionsLarge ribozymesInteraction nodesStructural organizationTertiary architectureEukaryotesSpliceosomeGene therapyGenomeZipperFoldingATP Synthase with Its γ Subunit Reduced to the N-terminal Helix Can Still Catalyze ATP Synthesis*
Mnatsakanyan N, Hook JA, Quisenberry L, Weber J. ATP Synthase with Its γ Subunit Reduced to the N-terminal Helix Can Still Catalyze ATP Synthesis*. Journal Of Biological Chemistry 2009, 284: 26519-26525. PMID: 19636076, PMCID: PMC2785340, DOI: 10.1074/jbc.m109.030528.Peer-Reviewed Original ResearchThe Role of the βDELSEED-loop of ATP Synthase*
Mnatsakanyan N, Krishnakumar AM, Suzuki T, Weber J. The Role of the βDELSEED-loop of ATP Synthase*. Journal Of Biological Chemistry 2009, 284: 11336-11345. PMID: 19246448, PMCID: PMC2670139, DOI: 10.1074/jbc.m900374200.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAmino Acid SequenceATP Synthetase ComplexesBacillusBinding SitesCell MembraneEscherichia coliMitochondrial Proton-Translocating ATPasesMolecular ConformationMolecular Sequence DataMutationNucleotidesPhosphorylationProtein Structure, TertiarySequence Homology, Amino AcidConceptsWild-type enzymeATP synthaseDELSEED-loopDeletion mutantsATP hydrolysisUnique rotational mechanismTransmembrane proton gradientHelix motifRate-limiting catalytic stepTerminal domainFunctional analysisMutantsBeta subunitMembrane vesiclesATP synthesisProton gradientAmino acidsLow abundanceCatalytic stepMechanochemical couplingCatalytic siteSynthaseChemical energyEnzymeMembrane preparations
2008
Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics
Koeppel A, Perry E, Sikorski J, Krizanc D, Warner A, Ward D, Rooney A, Brambilla E, Connor N, Ratcliff R, Nevo E, Cohan F. Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 2504-2509. PMID: 18272490, PMCID: PMC2268166, DOI: 10.1073/pnas.0712205105.Peer-Reviewed Original ResearchConceptsBacterial systematicsNatural communitiesSequence-based approachesEvolution CanyonBacterial domainEcotype SimulationSuch ecotypesMicrobial ecologyDistinct lineagesMultiple ecotypesEvolutionary dynamicsBacterial diversityDifferent solar exposureTraditional speciesBacterial populationsBacterial ecologyEcotypesBacterial cellsEcologyDistinct rolesSystematicsFundamental unitDiverse setCladeLineages
2007
Mass spectrometric analysis of lipopeptides from Bacillus strains isolated from diverse geographical locations
Price N, Rooney A, Swezey J, Perry E, Cohan F. Mass spectrometric analysis of lipopeptides from Bacillus strains isolated from diverse geographical locations. FEMS Microbiology Letters 2007, 271: 83-89. PMID: 17419767, DOI: 10.1111/j.1574-6968.2007.00702.x.Peer-Reviewed Original Research
2003
Trimeric Subunit Stoichiometry of the Glutamate Transporters from Bacillus caldotenax and Bacillus stearothermophilus †
Yernool D, Boudker O, Folta-Stogniew E, Gouaux E. Trimeric Subunit Stoichiometry of the Glutamate Transporters from Bacillus caldotenax and Bacillus stearothermophilus †. Biochemistry 2003, 42: 12981-12988. PMID: 14596613, DOI: 10.1021/bi030161q.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAmino Acid Transport System X-AGBacillusChromatography, GelCross-Linking ReagentsElectrophoresis, Polyacrylamide GelGenetic VectorsGeobacillus stearothermophilusGlutaralLasersLiposomesMolecular Sequence DataMolecular WeightProtein SubunitsProtein TransportScattering, RadiationSpectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationSpectrophotometry, UltravioletConceptsSubunit stoichiometryBacillus caldotenaxMembrane proteinsPolytopic integral membrane proteinPrimary structureAmino acid sequence relationshipsGlutamate transportersBacillus stearothermophilusKingdoms of lifeIntegral membrane proteinsNeutral amino acid transporterTrimeric quaternary structureNative molecular massDetergent-solubilized stateAmino acid transportersSize exclusion chromatographyB. caldotenaxEukaryotic organismsHigh-affinity glutamate transportersEukaryotic transportersQuaternary organizationAqueous solutionNutrient uptakeLife formsDetergent micelles
1975
TROPICAL ULCERS
ARIYAN S, KRIZEK T. TROPICAL ULCERS. Plastic & Reconstructive Surgery 1975, 55: 324-329. PMID: 1118492, DOI: 10.1097/00006534-197555030-00009.Peer-Reviewed Original Research
1974
Cistron specificity of 30S ribosomes heterologously reconstituted with components from Escherichia coli and Bacillus stearothermophilus.
Goldberg M, Steitz J. Cistron specificity of 30S ribosomes heterologously reconstituted with components from Escherichia coli and Bacillus stearothermophilus. Biochemistry 1974, 13: 2123-9. PMID: 4597073, DOI: 10.1021/bi00707a020.Peer-Reviewed Original Research
1973
Discriminatory Ribosome Rebinding of Isolated Regions of Protein Synthesis Initiation from the Ribonucleic Acid of Bacteriophage R17
Steitz J. Discriminatory Ribosome Rebinding of Isolated Regions of Protein Synthesis Initiation from the Ribonucleic Acid of Bacteriophage R17. Proceedings Of The National Academy Of Sciences Of The United States Of America 1973, 70: 2605-2609. PMID: 4582190, PMCID: PMC427065, DOI: 10.1073/pnas.70.9.2605.Peer-Reviewed Original ResearchConceptsR17 RNARibosome-binding siteProtein synthesis initiationEscherichia coli ribosomesPolypeptide chain initiationCoat protein regionRibosome bindingBacterial ribosomeRNA moleculesInitiator regionRibosome protectionSynthesis initiationMRNA moleculesInitiator codonColi ribosomesRibosomesNative RNABacteriophage R17Bacillus stearothermophilusRNAMessenger RNARibonucleic acidR17Replicase regionFragmentsSpecific recognition of non-initiator regions in RNA bacteriophage messengers by ribosomes of Bacillus stearothermophilus
Steitz J. Specific recognition of non-initiator regions in RNA bacteriophage messengers by ribosomes of Bacillus stearothermophilus. Journal Of Molecular Biology 1973, 73: 1-16. PMID: 4570382, DOI: 10.1016/0022-2836(73)90155-1.Peer-Reviewed Original ResearchBacillusBase SequenceBinding SitesCentrifugation, Density GradientChromatography, Thin LayerColiphagesDipeptidesEscherichia coliGenetic CodeNucleotidesPeptide Chain Initiation, TranslationalPeptide Initiation FactorsRibonucleasesRibosomesRNA, MessengerRNA, TransferRNA, ViralSpecies SpecificityTemperatureViral ProteinsThe effect of growth temperatures on the in vivo ribose methylation of Bacillus stearothermophilus transfer RNA
Agris P, Koh H, Söll D. The effect of growth temperatures on the in vivo ribose methylation of Bacillus stearothermophilus transfer RNA. Archives Of Biochemistry And Biophysics 1973, 154: 277-282. PMID: 4689778, DOI: 10.1016/0003-9861(73)90058-1.Peer-Reviewed Original Research
1971
Temperature dependence of the aminoacylation of tRNA by bacillus stearothermophilus aminoacyl‐tRNA synthetases
Johnson L, Söll D. Temperature dependence of the aminoacylation of tRNA by bacillus stearothermophilus aminoacyl‐tRNA synthetases. Biopolymers 1971, 10: 2209-2221. PMID: 4940767, DOI: 10.1002/bip.360101114.Peer-Reviewed Original ResearchConceptsSpecific transfer RNAsTRNA-IleTransfer RNAThermal denaturation profilesB. stearothermophilusAminoacyl-tRNA synthetasesDenaturation profilesAminoacylation of tRNAAmino acid acceptor activityTRNA-ValAcceptor activityTRNATertiary structureMycoplasma spBacillus stearothermophilusEscherichia coliAminoacylation reactionStearothermophilusAminoacylationRNASpeciesIleSynthetasesNucleaseSynthetase preparations
1969
Mechanism of protein biosynthesis.
Lengyel P, Söll D. Mechanism of protein biosynthesis. Microbiology And Molecular Biology Reviews 1969, 33: 264-301. PMID: 4896351, PMCID: PMC378322, DOI: 10.1128/br.33.2.264-301.1969.Peer-Reviewed Original Research
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