2020
Horizontally acquired regulatory gene activates ancestral regulatory system to promote Salmonella virulence
Choi J, Groisman EA. Horizontally acquired regulatory gene activates ancestral regulatory system to promote Salmonella virulence. Nucleic Acids Research 2020, 48: 10832-10847. PMID: 33045730, PMCID: PMC7641745, DOI: 10.1093/nar/gkaa813.Peer-Reviewed Original ResearchConceptsPhoP/PhoQAncestral regulatorNucleoid structuring protein H-NSProtein H-NSS. bongoriSalmonella enterica serovar TyphimuriumAncestral genomesH-NSTarget promotersEnterica serovar TyphimuriumRegulatory genesBacterial virulenceSalmonella virulencePromoter regionSsrBOpposite regulationGenesS. typhimuriumPhoQRegulatory systemSerovar TyphimuriumVirulenceTranscriptionPromoterRegulator
2012
An Allele of an Ancestral Transcription Factor Dependent on a Horizontally Acquired Gene Product
Chen HD, Jewett MW, Groisman EA. An Allele of an Ancestral Transcription Factor Dependent on a Horizontally Acquired Gene Product. PLOS Genetics 2012, 8: e1003060. PMID: 23300460, PMCID: PMC3531487, DOI: 10.1371/journal.pgen.1003060.Peer-Reviewed Original ResearchConceptsPolymyxin B resistanceGene productsTranscription of PmrAGene regulatory circuitsB resistanceSingle amino acid differenceAmino acid differencesPmrA proteinAncestral genomesAncestral genePmrD proteinRegulatory circuitsB alleleHorizontal transferGene expressionPhenotypic differencesAcid differencesGenesBiochemical propertiesBiofilm formationPmrAAllelesSalmonella entericaS. entericaProteinThe promoter architectural landscape of the Salmonella PhoP regulon
Zwir I, Latifi T, Perez JC, Huang H, Groisman EA. The promoter architectural landscape of the Salmonella PhoP regulon. Molecular Microbiology 2012, 84: 463-485. PMID: 22435712, PMCID: PMC3335776, DOI: 10.1111/j.1365-2958.2012.08036.x.Peer-Reviewed Original ResearchConceptsPromoter architectureDistinct promoter architecturesPathogen Salmonella enterica serovar TyphimuriumGene expression behaviorSalmonella enterica serovar TyphimuriumEnterica serovar TyphimuriumPhoP regulonPromoter featuresBiochemical functionsPhoPExpression behaviorPhysiological roleBacterial activatorsGenesSerovar TyphimuriumPromoterRegulonDifferent mechanismsTranscriptionVirulenceActivatorAncestryExpressionLarge numberLimited number
2010
Positive Autoregulation Shapes Response Timing and Intensity in Two-component Signal Transduction Systems
Mitrophanov AY, Hadley TJ, Groisman EA. Positive Autoregulation Shapes Response Timing and Intensity in Two-component Signal Transduction Systems. Journal Of Molecular Biology 2010, 401: 671-680. PMID: 20600106, PMCID: PMC2942797, DOI: 10.1016/j.jmb.2010.06.051.Peer-Reviewed Original ResearchAn antisense RNA that governs the expression kinetics of a multifunctional virulence gene
Lee EJ, Groisman EA. An antisense RNA that governs the expression kinetics of a multifunctional virulence gene. Molecular Microbiology 2010, 76: 1020-1033. PMID: 20398218, PMCID: PMC2909850, DOI: 10.1111/j.1365-2958.2010.07161.x.Peer-Reviewed Original ResearchConceptsAntisense RNAGenome-wide transcriptome analysisRegulatory protein PhoPLong antisense RNAProtein levelsAntisense transcriptionMgtC proteinTranscriptome analysisRNase EAntisense transcriptsPolycistronic messageRNase IIISalmonella virulenceBacterial speciesPhysiological roleExpression kineticsTranscriptionRNAVirulence genesApparent roleVirulencePhoPSalmonella entericaMgtCAmgRS
2009
Promoter and Riboswitch Control of the Mg2+ Transporter MgtA from Salmonella enterica
Cromie MJ, Groisman EA. Promoter and Riboswitch Control of the Mg2+ Transporter MgtA from Salmonella enterica. Journal Of Bacteriology 2009, 192: 604-607. PMID: 19897653, PMCID: PMC2805325, DOI: 10.1128/jb.01239-09.Peer-Reviewed Original ResearchIdentifying 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 promotersTranscription 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
RstA-Promoted Expression of the Ferrous Iron Transporter FeoB under Iron-Replete Conditions Enhances Fur Activity in Salmonella enterica
Jeon J, Kim H, Yun J, Ryu S, Groisman EA, Shin D. RstA-Promoted Expression of the Ferrous Iron Transporter FeoB under Iron-Replete Conditions Enhances Fur Activity in Salmonella enterica. Journal Of Bacteriology 2008, 190: 7326-7334. PMID: 18790861, PMCID: PMC2576650, DOI: 10.1128/jb.00903-08.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsBlotting, WesternElectrophoretic Mobility Shift AssayGene ExpressionGene Expression ProfilingGene Expression Regulation, BacterialIronIron DeficienciesOligonucleotide Array Sequence AnalysisOperonPromoter Regions, GeneticProtein BindingRepressor ProteinsReverse Transcriptase Polymerase Chain ReactionSalmonella entericaTranscription, GeneticConceptsFerrous iron transporter FeoBFur proteinIron-replete conditionsFur activityTarget genesIron-responsive genesWild-type levelsFerrous iron uptakeFeoAB operonFur geneTranscriptional activationIron acquisitionExpression experimentsRegulatory pathwaysTranscription levelsIron uptakeGenesPrimary regulatorRstAProteinFeOBRepressionSalmonella entericaPromoterExpression
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 ResearchMeSH KeywordsAlgorithmsEscherichia coliEscherichia coli ProteinsGenome, BacterialGenomicsModels, GeneticPromoter Regions, GeneticSalmonellaTranscription, GeneticConceptsCoregulated 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
2006
A Positive Feedback Loop Promotes Transcription Surge That Jump-Starts Salmonella Virulence Circuit
Shin D, Lee EJ, Huang H, Groisman EA. A Positive Feedback Loop Promotes Transcription Surge That Jump-Starts Salmonella Virulence Circuit. Science 2006, 314: 1607-1609. PMID: 17158330, DOI: 10.1126/science.1134930.Peer-Reviewed Original ResearchAn RNA Sensor for Intracellular Mg2+
Cromie MJ, Shi Y, Latifi T, Groisman EA. An RNA Sensor for Intracellular Mg2+. Cell 2006, 125: 71-84. PMID: 16615891, DOI: 10.1016/j.cell.2006.01.043.Peer-Reviewed Original ResearchMeSH Keywords5' Untranslated RegionsAdenosine TriphosphatasesBacterial ProteinsBiosensing TechniquesConserved SequenceCytoplasmGene Expression Regulation, BacterialMagnesiumMembrane Transport ProteinsModels, GeneticMutationNucleic Acid ConformationOpen Reading FramesPhylogenyPromoter Regions, GeneticRegulatory Sequences, Nucleic AcidRibonucleasesRNA, BacterialRNA, MessengerTerminator Regions, GeneticTranscription, GeneticConceptsMost RNA moleculesDifferent cellular compartmentsStem-loop structureOnly protein componentSalmonella enterica serovar TyphimuriumDifferent stem-loop structuresTransporter MgtAMgtA geneEnterica serovar TyphimuriumMgtA transcriptionRNA polymeraseCellular compartmentsGene transcriptionRNA moleculesTranscription systemUntranslated regionProtein componentsTranscriptionRNA sensorsEnzymatic propertiesSerovar TyphimuriumMgtACytoplasmicDisparate stepsSingular exampleThe PmrA/PmrB and RcsC/YojN/RcsB systems control expression of the Salmonella O‐antigen chain length determinant
Delgado MA, Mouslim C, Groisman EA. The PmrA/PmrB and RcsC/YojN/RcsB systems control expression of the Salmonella O‐antigen chain length determinant. Molecular Microbiology 2006, 60: 39-50. PMID: 16556219, DOI: 10.1111/j.1365-2958.2006.05069.x.Peer-Reviewed Original ResearchConceptsPmrA/PmrBO-antigen subunitSame start siteHydrophobic lipid ASDS/PAGE gelsChain length determinantTwo-component systemSalmonella enterica serovar TyphimuriumO-antigenGram-negative bacteriaNull mutantsEnterica serovar TyphimuriumStart siteRcsB mutantDifferent environmental conditionsCell envelopeRegulatory proteinsLPS genesOutermost componentCore oligosaccharideSerovar TyphimuriumGenesEnvironmental conditionsPAGE gelsRcsB
2005
Virulence and drug resistance roles of multidrug efflux systems of Salmonella enterica serovar Typhimurium
Nishino K, Latifi T, Groisman EA. Virulence and drug resistance roles of multidrug efflux systems of Salmonella enterica serovar Typhimurium. Molecular Microbiology 2005, 59: 126-141. PMID: 16359323, DOI: 10.1111/j.1365-2958.2005.04940.x.Peer-Reviewed Original ResearchConceptsDrug efflux systemsEfflux systemSalmonella virulenceEscherichia coli homologueToxic compound extrusionResponse regulator PhoPATP-binding cassette (ABC) superfamiliesPhoP/PhoQOuter membrane componentsAmino acid sequenceDrug resistance rolesTwo-component systemSalmonella enterica serovar TyphimuriumGram-negative speciesMultidrug efflux systemsSame operonEnterica serovar TyphimuriumRegulator PhoPCompound extrusionAcid sequenceMajor facilitatorEfflux system genesPromoter regionVirulence phenotypesMajor regulatorAnalysis 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 entericaVivoImmunoprecipitationMg2Connecting two-component regulatory systems by a protein that protects a response regulator from dephosphorylation by its cognate sensor
Kato A, Groisman EA. Connecting two-component regulatory systems by a protein that protects a response regulator from dephosphorylation by its cognate sensor. Genes & Development 2004, 18: 2302-2313. PMID: 15371344, PMCID: PMC517523, DOI: 10.1101/gad.1230804.Peer-Reviewed Original ResearchMeSH KeywordsAllelesBacterial ProteinsBase SequenceGene Expression Regulation, BacterialMagnesiumMolecular Sequence DataPhosphorylationPromoter Regions, GeneticProtein Processing, Post-TranslationalProtein Structure, TertiarySalmonella entericaSignal TransductionTranscription FactorsTranscription, GeneticConceptsTwo-component systemResponse regulatorPhosphorylated formTwo-component regulatory systemTranscription of PmrAResponse regulator PmrAPhoP/PhoQPmrA/PmrBPmrA proteinTarget promotersCognate sensorProtein bindsSignal transductionCellular responsesDephosphorylationRegulatory systemPmrAProteinTranscriptionMultiple signalsRegulatorHigh affinityPmrA.Fundamental questionsPhoP