2021
Low Cytoplasmic Magnesium Increases the Specificity of the Lon and ClpAP Proteases
Yeom J, Groisman EA. Low Cytoplasmic Magnesium Increases the Specificity of the Lon and ClpAP Proteases. Journal Of Bacteriology 2021, 203: 10.1128/jb.00143-21. PMID: 33941609, PMCID: PMC8223949, DOI: 10.1128/jb.00143-21.Peer-Reviewed Original ResearchConceptsBacterium Salmonella enterica serovar TyphimuriumCytoplasmic MgSalmonella enterica serovar TyphimuriumLon substratesClpAP proteaseEnterica serovar TyphimuriumAntibiotic persistenceEnteric bacteriaSerovar TyphimuriumSpectrum of substratesPhoP proteinProtease LonAcetyl coenzyme ATranscriptional regulatorsProtein bindsPhoP boxRegulatory proteinsProtease specificityPromoter regionCritical regulatorProtein synthesisLiving cellsLonPhoPEscherichia coli
2020
Salmonella expresses foreign genes during infection by degrading their silencer
Choi J, Groisman EA. Salmonella expresses foreign genes during infection by degrading their silencer. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 8074-8082. PMID: 32209674, PMCID: PMC7149492, DOI: 10.1073/pnas.1912808117.Peer-Reviewed Original ResearchConceptsForeign genesH-NSForeign DNAHeat-stable nucleoid-structuring (H-NS) proteinH-NS bindingNucleoid structuring proteinGram-negative bacterial speciesFacultative intracellular pathogenPhoP proteinLon proteaseProtease LonRegulatory sequencesVirulence regulatorGene silencingIntramacrophage survivalStructuring proteinBacterial speciesGenesInside macrophagesIntracellular pathogensSerovar TyphimuriumUncovered mechanismProteinVirulence genesDNA
2014
Bacterial Nucleoid-Associated Protein Uncouples Transcription Levels from Transcription Timing
Zwir I, Yeo WS, Shin D, Latifi T, Huang H, Groisman EA. Bacterial Nucleoid-Associated Protein Uncouples Transcription Levels from Transcription Timing. MBio 2014, 5: 10.1128/mbio.01485-14. PMID: 25293763, PMCID: PMC4196223, DOI: 10.1128/mbio.01485-14.Peer-Reviewed Original ResearchConceptsTranscription timingPhoP proteinAncestral geneExpression timingTranscriptional regulatorsGene ancestryTranscription factorsTranscription levelsHistone-like nucleoid structuring proteinHigher mRNA levelsExpression behaviorH-NS proteinNucleoid structuring proteinBacterium Salmonella enterica serovar TyphimuriumExpression of genesSalmonella enterica serovar TyphimuriumH-NSLatter genesEnterica serovar TyphimuriumMRNA levelsCorresponding promotersTarget genesDevelopmental pathwaysEarly genesGenes
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
Activated by Different Signals, the PhoP/PhoQ Two-Component System Differentially Regulates Metal Uptake
Choi E, Groisman EA, Shin D. Activated by Different Signals, the PhoP/PhoQ Two-Component System Differentially Regulates Metal Uptake. Journal Of Bacteriology 2009, 191: 7174-7181. PMID: 19801407, PMCID: PMC2786564, DOI: 10.1128/jb.00958-09.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesBacterial ProteinsBiological TransportBlotting, WesternCation Transport ProteinsGene Expression Regulation, BacterialHydrogen-Ion ConcentrationMagnesiumMembrane Transport ProteinsMetalsPhosphorylationReverse Transcriptase Polymerase Chain ReactionSalmonella typhimuriumConceptsPhoP/PhoQ systemPhoP/PhoQTwo-component systemTwo-component regulatory systemMgtA genePhoP proteinVirulence functionsMgtA transcriptionSalmonella genesLeader regionTransporter geneBiological consequencesGenesRegulatory systemAntimicrobial peptidesDistinct setsPhoQTranscriptionMetal uptakeSalmonella entericaMultiple signalsProteinExpressionPhoPMgtAIdentifying 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 promotersEvolution of a Bacterial Regulon Controlling Virulence and Mg2+ Homeostasis
Perez JC, Shin D, Zwir I, Latifi T, Hadley TJ, Groisman EA. Evolution of a Bacterial Regulon Controlling Virulence and Mg2+ Homeostasis. PLOS Genetics 2009, 5: e1000428. PMID: 19300486, PMCID: PMC2650801, DOI: 10.1371/journal.pgen.1000428.Peer-Reviewed Original ResearchConceptsRegulatory proteinsSpecies-specific traitsHorizontal gene transferDifferent gene setsSpecies-specific targetsPhoP proteinTranscriptional rewiringPhoP regulonRelated organismsPhoPQ operonGene setsVariable membersCell envelopeProtein activityRegulonBacterial speciesGene transferSpeciesProteinPhoPFamily EnterobacteriaceaeGenesVirulenceHomeostasisWidespread effectsTranscription factor function and promoter architecture govern the evolution of bacterial regulons
Perez JC, Groisman EA. Transcription factor function and promoter architecture govern the evolution of bacterial regulons. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 4319-4324. PMID: 19251636, PMCID: PMC2649204, DOI: 10.1073/pnas.0810343106.Peer-Reviewed Original ResearchConceptsRegulatory circuitsBacterial regulonsPhoP proteinRegulatory protein PhoPBacterial transcription factorsTranscription factor functionCis-regulatory elementsGene regulatory circuitsHorizontal gene transferPathogen Salmonella entericaPromoter architectureEvolutionary changeRelated organismsVirulence regulatorTranscription factorsRegulonPhenotypic differencesFactor functionGene transferYersinia pestisSalmonella entericaCore membersProteinEukaryotesPhoP
2008
The PhoQ/PhoP Regulatory Network of Salmonella enterica
Kato A, Groisman EA. The PhoQ/PhoP Regulatory Network of Salmonella enterica. Advances In Experimental Medicine And Biology 2008, 631: 7-21. PMID: 18792679, DOI: 10.1007/978-0-387-78885-2_2.Peer-Reviewed Original ResearchConceptsTwo-component regulatory systemPathogen Salmonella enterica serovar TyphimuriumEnteric pathogen Salmonella enterica serovar TyphimuriumDistinct expression levelsPhoQ/PhoPTwo-component systemSalmonella enterica serovar TyphimuriumBacterial cell surfacePhoQ proteinPhoP proteinResponse regulatorTranscriptional cascadeConnector proteinEnterica serovar TyphimuriumPromoter structureRegulatory networksTranscription factorsSalmonella genesRegulatory architectureSalmonella lifestyleMajor regulatorExpression propertiesCell surfaceModifies expressionRegulatory system
2007
[18] Gene Promoter Scan Methodology for Identifying and Classifying Coregulated Promoters
Zwir I, Harari O, Groisman EA. [18] Gene Promoter Scan Methodology for Identifying and Classifying Coregulated Promoters. Methods In Enzymology 2007, 422: 361-385. PMID: 17628149, PMCID: PMC3755887, DOI: 10.1016/s0076-6879(06)22018-4.Peer-Reviewed Original ResearchConceptsCoregulated promotersTwo-component regulatory systemCis-acting regulatory elementsDistinct regulatory networksSingle transcription factorPhoP/PhoQPhoP proteinGenomic approachesCoregulated genesPhoP regulonRegulatory networksRegulatory interactionsTranscription factorsRegulatory featuresGene transcriptionRegulatory elementsPostgenomic eraNovel memberDifferential expressionGenesEscherichia coliRegulatory systemSalmonella entericaPromoterMultiple mechanisms
2005
Analysis of differentially-regulated genes within a regulatory network by GPS genome navigation
Zwir I, Huang H, Groisman EA. Analysis of differentially-regulated genes within a regulatory network by GPS genome navigation. Bioinformatics 2005, 21: 4073-4083. PMID: 16159917, DOI: 10.1093/bioinformatics/bti672.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsArtificial IntelligenceCluster AnalysisComputational BiologyDatabases, GeneticEscherichia coliEscherichia coli ProteinsGene Expression RegulationGene Expression Regulation, BacterialGenomeGenomicsPromoter Regions, GeneticResponse ElementsSalmonella entericaSoftwareTranscription, GeneticConceptsPhoP proteinRegulatory featuresGene expressionEnteric bacteria Escherichia coliCis-regulatory featuresCo-regulated promotersPost-genomic eraTranscription initiationRegulatory networksRegulatory interactionsGene transcriptionNovel memberExpression patternsBacteria Escherichia coliGenesEscherichia coliSalmonella entericaMultiple mechanismsProteinFundamental mechanismsExpressionRegulonTranscriptionPromoterReduced datasetThe PhoP/PhoQ system controls the intramacrophage type three secretion system of Salmonella enterica
Bijlsma JJ, Groisman EA. The PhoP/PhoQ system controls the intramacrophage type three secretion system of Salmonella enterica. Molecular Microbiology 2005, 57: 85-96. PMID: 15948951, DOI: 10.1111/j.1365-2958.2005.04668.x.Peer-Reviewed Original ResearchConceptsSPI-2 pathogenicity islandPhoP/PhoQ systemType three secretion systemThree secretion systemPhoP proteinSecretion systemSsa genesPathogenicity islandTwo-component regulatory systemResponse regulator SsrBPhoP/PhoQRegulatory systemTwo-component systemSalmonella entericaEukaryotic cellsChromatin immunoprecipitationCentral roleDifferent regulatory systemsSalmonella virulenceUntranslated regionDistinct signalsPhoPGenesEffectorsProteinTranscriptional 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 proteinDissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica
Zwir I, Shin D, Kato A, Nishino K, Latifi T, Solomon F, Hare JM, Huang H, Groisman EA. Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica. Proceedings Of The National Academy Of Sciences Of The United States Of America 2005, 102: 2862-2867. PMID: 15703297, PMCID: PMC548500, DOI: 10.1073/pnas.0408238102.Peer-Reviewed Original ResearchConceptsRegulatory networksEnteric bacteria Escherichia coliDistinct regulatory networksEscherichia coliPhoP/PhoQTwo-component systemSalmonella entericaCoregulated promotersPhoP proteinGenomic approachesPhoP regulonPromoter featuresRegulatory featuresGene transcriptionGene expressionBacteria Escherichia coliRegulatory systemGenesMultiple mechanismsColiResistance determinantsEntericaRegulonPhoQTranscription
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 questionsControl of the Salmonella ugd gene by three two‐component regulatory systems
Mouslim C, Groisman EA. Control of the Salmonella ugd gene by three two‐component regulatory systems. Molecular Microbiology 2003, 47: 335-344. PMID: 12519186, DOI: 10.1046/j.1365-2958.2003.03318.x.Peer-Reviewed Original Research
2000
Acetyl phosphate-dependent activation of a mutant PhoP response regulator that functions independently of its cognate sensor kinase11Edited by M. Gottesman
Chamnongpol S, Groisman E. Acetyl phosphate-dependent activation of a mutant PhoP response regulator that functions independently of its cognate sensor kinase11Edited by M. Gottesman. Journal Of Molecular Biology 2000, 300: 291-305. PMID: 10873466, DOI: 10.1006/jmbi.2000.3848.Peer-Reviewed Original ResearchMeSH KeywordsAllelesAmino Acid SubstitutionBacterial ProteinsEnvironmentGene Expression Regulation, BacterialGenes, BacterialGenes, RegulatorMagnesiumMembrane ProteinsMethyl-Accepting Chemotaxis ProteinsModels, MolecularMutationOperonOrganophosphatesPhosphorylationProtein BindingProtein BiosynthesisProtein Structure, TertiaryRecombinant Fusion ProteinsSalmonella entericaTrans-ActivatorsTranscription, GeneticConceptsTranscription of PhoPResponse regulatorAcetyl phosphateResponse regulator receiver domainSites of phosphorylationVirulence gene expressionPhoP response regulatorTwo-component systemPhoQ proteinPhoP proteinReceiver domainSensor kinaseTranscriptional repressionCognate sensorMutant proteinsM. GottesmanPhosphorylated stateAspartate residueGene expressionPhoPTranscriptionPhosphate donorRegulatorProteinSalmonella enterica