2016
RNA secondary structures regulate three steps of Rho-dependent transcription termination within a bacterial mRNA leader
Kriner MA, Groisman EA. RNA secondary structures regulate three steps of Rho-dependent transcription termination within a bacterial mRNA leader. Nucleic Acids Research 2016, 45: 631-642. PMID: 28123036, PMCID: PMC5314796, DOI: 10.1093/nar/gkw889.Peer-Reviewed Original Research
2012
Inhibition of Bacterial Virulence: Drug‐Like Molecules Targeting the Salmonella enterica PhoP Response Regulator
Tang YT, Gao R, Havranek JJ, Groisman EA, Stock AM, Marshall GR. Inhibition of Bacterial Virulence: Drug‐Like Molecules Targeting the Salmonella enterica PhoP Response Regulator. Chemical Biology & Drug Design 2012, 79: 1007-1017. PMID: 22339993, PMCID: PMC3445336, DOI: 10.1111/j.1747-0285.2012.01362.x.Peer-Reviewed Original ResearchConceptsTwo-component signal transductionResponse regulatorPhoP response regulatorHistidine kinaseBacterial virulenceGene expressionSensor histidine kinaseVirulence gene regulationSignal transduction systemSignal transduction pathwaysExpression of genesTCST systemsStructure-based virtual screeningGene regulationSignal transductionTranscription factorsTransduction pathwaysTransduction systemVirtual screeningBiophysical assaysAntibacterial developmentMode of actionExternal signalsRegulatorRegulatory systemIntrinsic Negative Feedback Governs Activation Surge in Two-Component Regulatory Systems
Yeo WS, Zwir I, Huang HV, Shin D, Kato A, Groisman EA. Intrinsic Negative Feedback Governs Activation Surge in Two-Component Regulatory Systems. Molecular Cell 2012, 45: 409-421. PMID: 22325356, PMCID: PMC3713471, DOI: 10.1016/j.molcel.2011.12.027.Peer-Reviewed Original Research
2010
Defining the Plasticity of Transcription Factor Binding Sites by Deconstructing DNA Consensus Sequences: The PhoP-Binding Sites among Gamma/Enterobacteria
Harari O, Park SY, Huang H, Groisman EA, Zwir I. Defining the Plasticity of Transcription Factor Binding Sites by Deconstructing DNA Consensus Sequences: The PhoP-Binding Sites among Gamma/Enterobacteria. PLOS Computational Biology 2010, 6: e1000862. PMID: 20661307, PMCID: PMC2908699, DOI: 10.1371/journal.pcbi.1000862.Peer-Reviewed Original ResearchMeSH KeywordsArtificial IntelligenceBacterial ProteinsBase SequenceBinding SitesChromatin ImmunoprecipitationCluster AnalysisComputational BiologyConsensus SequenceDNA, BacterialEnterobacteriaceaeEvolution, MolecularGene Expression ProfilingGenome, BacterialModels, GeneticMolecular Sequence DataNucleic Acid ConformationOligonucleotide Array Sequence AnalysisPattern Recognition, AutomatedSequence AlignmentTranscription FactorsConceptsGene expressionSite sequenceKey cis-regulatory elementsExpression of dozensGenome-wide analysisCis-regulatory elementsTranscription Factor Binding SitesDifferential gene expressionSpecific DNA sequencesDNA consensus sequencePhoP proteinAncestral geneTarget promotersDistant speciesHigh conservationTranscriptional regulatorsInter-species differencesChromatin immunoprecipitationRelated speciesRNA polymeraseDNA sequencesTarget genesRegulatory proteinsMolecular basisConsensus sequence
2009
Identifying promoter features of co-regulated genes with similar network motifs
Harari O, del Val C, Romero-Zaliz R, Shin D, Huang H, Groisman EA, Zwir I. Identifying promoter features of co-regulated genes with similar network motifs. BMC Bioinformatics 2009, 10: s1. PMID: 19426448, PMCID: PMC2681069, DOI: 10.1186/1471-2105-10-s4-s1.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBinding SitesComputational BiologyDNA-Directed RNA PolymerasesEscherichia coliGene Expression Regulation, BacterialGene Regulatory NetworksGenome, BacterialMolecular Sequence DataPromoter Regions, GeneticRegulatory Sequences, Nucleic AcidSalmonella typhiTranscription FactorsConceptsTranscriptional regulatorsPromoter featuresNetwork motifsTranscription factorsTarget genesRegulatory proteinsPhoP/PhoQ regulatory systemExpression patternsGene expressionCo-regulated genesGroup of genesGene regulatory networksDifferential gene expressionCis-acting elementsDifferent expression patternsCharacteristic expression patternsSalmonella enterica serovar TyphimuriumProteobacterial genomesPhoP proteinEnterica serovar TyphimuriumRegulatory networksRNA polymeraseRegulatory regionsRepression siteMultiple promoters
2008
Overcoming H-NS-mediated Transcriptional Silencing of Horizontally Acquired Genes by the PhoP and SlyA Proteins in Salmonella enterica *
Perez JC, Latifi T, Groisman EA. Overcoming H-NS-mediated Transcriptional Silencing of Horizontally Acquired Genes by the PhoP and SlyA Proteins in Salmonella enterica *. Journal Of Biological Chemistry 2008, 283: 10773-10783. PMID: 18270203, PMCID: PMC2447644, DOI: 10.1074/jbc.m709843200.Peer-Reviewed Original ResearchConceptsHistone-like nucleoid structuring proteinPagC geneSlyA proteinRNA polymeraseRNA polymerase recruitmentH-NS repressionNucleoid structuring proteinHorizontal gene transferDifferent regulatory proteinsSalmonella entericaPolymerase recruitmentTranscriptional silencingNew traitsForeign DNAGene transcriptionRegulatory proteinsUgtLRespective promotersTranscriptionPhoPRecipient organismGenesPagC promoterGene transferProtein
2005
Transcriptional Regulation of the 4-Amino-4-deoxy-L-arabinose Biosynthetic Genes in Yersinia pestis *
Winfield MD, Latifi T, Groisman EA. Transcriptional Regulation of the 4-Amino-4-deoxy-L-arabinose Biosynthetic Genes in Yersinia pestis *. Journal Of Biological Chemistry 2005, 280: 14765-14772. PMID: 15710615, DOI: 10.1074/jbc.m413900200.Peer-Reviewed Original ResearchMeSH KeywordsAmino SugarsBacterial ProteinsBase SequenceBinding SitesCell ProliferationDeoxyribonuclease IDNA PrimersGene DeletionGene Expression Regulation, BacterialIronLipid AMagnesiumModels, BiologicalMolecular Sequence DataPlasmidsPolymyxin BPromoter Regions, GeneticSalmonella entericaSingle-Strand Specific DNA and RNA EndonucleasesTranscription FactorsTranscription, GeneticYersinia pestisConceptsPmrD proteinBiosynthetic genesPhoP/PhoQ systemTwo-component regulatory systemTranscription of PmrADisparate regulatory pathwaysYersinia pestisRelated bacterial speciesPmrA/PmrBSalmonella enterica serovar TyphimuriumPmrA proteinPhoP proteinGram-negative bacteriaTranscriptional regulationUgd geneMembrane remodelingEnterica serovar TyphimuriumRegulatory pathwaysCationic antimicrobial peptidesDistinct binding sitesBacterial membranesBacterial speciesDifferent promotersGenesPmrB protein
2004
Signal-dependent Binding of the Response Regulators PhoP and PmrA to Their Target Promoters in Vivo *
Shin D, Groisman EA. Signal-dependent Binding of the Response Regulators PhoP and PmrA to Their Target Promoters in Vivo *. Journal Of Biological Chemistry 2004, 280: 4089-4094. PMID: 15569664, DOI: 10.1074/jbc.m412741200.Peer-Reviewed Original ResearchConceptsResponse regulator PhoPPmrA proteinPhoP proteinRegulator PhoPTranscription of PhoPWild-type strainTarget promotersPromoter occupancyChromatin immunoprecipitationPromotes phosphorylationRegulatory regionsTarget genesPhoPValine residueLow Mg2GenesPhosphorylationPromoterProteinAsp 52TranscriptionSalmonella entericaVivoImmunoprecipitationMg2Transcriptional Control of the Antimicrobial Peptide Resistance ugtL Gene by the Salmonella PhoP and SlyA Regulatory Proteins*
Shi Y, Latifi T, Cromie MJ, Groisman EA. Transcriptional Control of the Antimicrobial Peptide Resistance ugtL Gene by the Salmonella PhoP and SlyA Regulatory Proteins*. Journal Of Biological Chemistry 2004, 279: 38618-38625. PMID: 15208313, DOI: 10.1074/jbc.m406149200.Peer-Reviewed Original ResearchMeSH KeywordsAntimicrobial Cationic PeptidesBacterial ProteinsBase SequenceBeta-GalactosidaseBinding SitesBlotting, SouthernDeoxyribonuclease IGene Expression Regulation, BacterialMagaininsMagnesiumMembrane ProteinsModels, BiologicalMolecular Sequence DataMutationPeptidesPlasmidsPolymyxin BPromoter Regions, GeneticProtein BindingSalmonellaSingle-Strand Specific DNA and RNA EndonucleasesTranscription FactorsTranscription, GeneticTranscriptional ActivationXenopus ProteinsConceptsPhoP proteinSlyA mutantSlyA proteinPhoP/PhoQTranscription start siteAntimicrobial peptidesTwo-component systemMagainin 2Transcriptional activatorAbility of SalmonellaTranscriptional controlStart siteMaster regulatorRegulatory proteinsTranscriptionVirulence attenuationAntimicrobial peptide magainin 2PhoPGenesProteinPromoterMutantsSlyA.PhoQPeptides
2003
Signal-dependent Requirement for the Co-activator Protein RcsA in Transcription of the RcsB-regulated ugd Gene*
Mouslim C, Latifi T, Groisman EA. Signal-dependent Requirement for the Co-activator Protein RcsA in Transcription of the RcsB-regulated ugd Gene*. Journal Of Biological Chemistry 2003, 278: 50588-50595. PMID: 14514676, DOI: 10.1074/jbc.m309433200.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsBase SequenceBeta-GalactosidaseBinding SitesChromosomesDeoxyribonuclease IEscherichia coli ProteinsGene DeletionIronMagnesiumModels, BiologicalModels, GeneticMolecular Sequence DataMutationPeriplasmic ProteinsPlasmidsPromoter Regions, GeneticSalmonellaSequence Homology, Amino AcidSingle-Strand Specific DNA and RNA EndonucleasesTemperatureTranscription FactorsTranscription, GeneticConceptsUgd genePmrA/PmrB systemTwo-component systems PhoP/PhoQS1 mapping experimentsPhoP/PhoQPmrA/PmrBUDP-glucose dehydrogenasePhoP proteinPhosphorelay systemIndependent transcriptionVariety of signalsPmrA mutantMembrane proteinsSame promoterCps operonRcsBGene expressionRcsATranscriptionGenesMapping experimentsCps transcriptionPhoPPromoterLow Mg2Closing the loop: The PmrA/PmrB two-component system negatively controls expression of its posttranscriptional activator PmrD
Kato A, Latifi T, Groisman EA. Closing the loop: The PmrA/PmrB two-component system negatively controls expression of its posttranscriptional activator PmrD. Proceedings Of The National Academy Of Sciences Of The United States Of America 2003, 100: 4706-4711. PMID: 12676988, PMCID: PMC153620, DOI: 10.1073/pnas.0836837100.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceArtificial Gene FusionBacterial ProteinsBase SequenceBinding SitesDNA, BacterialFeedbackGene Expression Regulation, BacterialGenes, BacterialModels, GeneticMolecular Sequence DataMutationPlasmidsPromoter Regions, GeneticProtein BindingSalmonella typhimuriumTranscription FactorsConceptsPmrA proteinTwo-component systemResponse regulator PmrAAppropriate cellular responsesPmrA/PmrBPhoQ proteinPhoP proteinRegulatory circuitsPosttranscriptional levelPromoter upstreamNegative regulationCellular responsesPmrB proteinCellular levelProteinPmrASalmonella entericaGenesMultiple signalsPmrDFeedback loopSingular exampleExpressionPhoPFundamental questionsMg2+ Sensing by the Mg2+ Sensor PhoQ of Salmonella enterica
Chamnongpol S, Cromie M, Groisman EA. Mg2+ Sensing by the Mg2+ Sensor PhoQ of Salmonella enterica. Journal Of Molecular Biology 2003, 325: 795-807. PMID: 12507481, DOI: 10.1016/s0022-2836(02)01268-8.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAmino Acid SubstitutionBacterial ProteinsBase SequenceBinding SitesConserved SequenceDNA, BacterialMagnesiumMolecular Sequence DataMutagenesis, Site-DirectedPhosphorylationProtein Structure, TertiaryRecombinant ProteinsSalmonella entericaSequence Homology, Amino AcidTranscription, GeneticConceptsTranscription of PhoPPhoQ proteinSensor PhoQPeriplasmic domainTwo-component regulatory systemResponse regulator PhoPExpression of phoPPhoP/PhoQWild-type responseWild-type abilityAmino acid residuesGram-negative speciesRegulator PhoPGene transcriptionPhoPAcid residuesTranscriptionHistidine residuesPhoQGenesAcetyl phosphateRegulatory systemProteinMutantsSalmonella enterica
2000
A Signal Transduction System that Responds to Extracellular Iron
Wösten M, Kox L, Chamnongpol S, Soncini F, Groisman E. A Signal Transduction System that Responds to Extracellular Iron. Cell 2000, 103: 113-125. PMID: 11051552, DOI: 10.1016/s0092-8674(00)00092-1.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsBinding SitesCarrier ProteinsDrug Resistance, MicrobialExtracellular SpaceGene Expression Regulation, BacterialIronIron-Binding ProteinsPhenotypePolymyxinsProtein Structure, TertiarySalmonella entericaSignal TransductionTranscription FactorsTranscription, GeneticTransferrin-Binding ProteinsConceptsSignal transduction systemTransduction systemTranscription of PmrAWild-type resistancePmrA/PmrBPeriplasmic domainPmrA mutantIron transporterFerritin light chainIron binding proteinAntibiotic polymyxinBinding proteinPmrB proteinIron homeostasisNovel pathwayExtracellular ironIron toxicityProteinVariety of oxidantsLight chainMutantsTranscriptionGenesOrganismsFerric iron
1997
Characterization of the Bacterial Sensor Protein PhoQ EVIDENCE FOR DISTINCT BINDING SITES FOR Mg2+ AND Ca2+ *
Véscovi E, Ayala Y, Di E, Groisman E. Characterization of the Bacterial Sensor Protein PhoQ EVIDENCE FOR DISTINCT BINDING SITES FOR Mg2+ AND Ca2+ *. Journal Of Biological Chemistry 1997, 272: 1440-1443. PMID: 8999810, DOI: 10.1074/jbc.272.3.1440.Peer-Reviewed Original ResearchConceptsTranscription of PhoPPhoQ proteinDistinct binding sitesTwo-component regulatory systemGram-negative bacterium Salmonella typhimuriumPhoP/PhoQSingle amino acid substitutionBacterium Salmonella typhimuriumTryptophan intrinsic fluorescenceBinding sitesAmino acid substitutionsPeriplasmic domainAcid polypeptide