2012
Intramolecular arrangement of sensor and regulator overcomes relaxed specificity in hybrid two-component systems
Townsend GE, Raghavan V, Zwir I, Groisman EA. Intramolecular arrangement of sensor and regulator overcomes relaxed specificity in hybrid two-component systems. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 110: e161-e169. PMID: 23256153, PMCID: PMC3545799, DOI: 10.1073/pnas.1212102110.Peer-Reviewed Original ResearchConceptsTwo-component regulatory systemResponse regulatorSensor kinasePhosphotransfer specificityRelaxed specificityTwo-component systemHuman gut symbiont Bacteroides thetaiotaomicronGut symbiont Bacteroides thetaiotaomicronRR pairsCognate response regulatorCognate protein partnersRegulatory systemProtein partnersTransduce signalsCellular processesSignal transductionSingle polypeptidePhosphoryl transferNoncognate proteinsBacteroides thetaiotaomicronSpecific interactionsRegulatorIntramolecular arrangementTransductionKinase
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
Short-Term Signatures of Evolutionary Change in the Salmonella enterica Serovar Typhimurium 14028 Genome
Jarvik T, Smillie C, Groisman EA, Ochman H. Short-Term Signatures of Evolutionary Change in the Salmonella enterica Serovar Typhimurium 14028 Genome. Journal Of Bacteriology 2009, 192: 560-567. PMID: 19897643, PMCID: PMC2805332, DOI: 10.1128/jb.01233-09.Peer-Reviewed Original ResearchMeSH KeywordsEvolution, MolecularGenome, BacterialModels, GeneticMolecular Sequence DataSalmonella typhimuriumConceptsComplete genomic sequenceGenomic sequencesSalmonella enterica serovar TyphimuriumTyphoid-like diseaseEnterica serovar TyphimuriumEvolutionary changeSequence evolutionGram-negative pathogensS. typhimuriumSerovar TyphimuriumComplete inventoryGenetic alterationsAvirulent strainsS. entericaPathogenic organismsSequenceLaboratory passageS. typhimurium strainTyphimuriumGenomeStrainsTyphimurium strainsLT2 strainOrganismsProgenitors
2007
A connector of two-component regulatory systems promotes signal amplification and persistence of expression
Kato A, Mitrophanov AY, Groisman EA. A connector of two-component regulatory systems promotes signal amplification and persistence of expression. Proceedings Of The National Academy Of Sciences Of The United States Of America 2007, 104: 12063-12068. PMID: 17615238, PMCID: PMC1924540, DOI: 10.1073/pnas.0704462104.Peer-Reviewed Original ResearchConceptsTwo-component regulatory systemBacterial signal transductionRegulatory systemPersistence of expressionSignal transductionGene transcriptionRegulatory architectureSmall proteinsSalmonella entericaPathwayFunctional characteristicsPmrDExpressionFunctional propertiesPhoP.AmplificationTranscriptionSignal amplificationTransductionGenesDominant formOrganismsProteinPersistenceEnterica[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
2006
An 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 example
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 entericaVivoImmunoprecipitationMg2
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 questions
1995
Transcriptional autoregulation of the Salmonella typhimurium phoPQ operon
Soncini FC, Véscovi EG, Groisman EA. Transcriptional autoregulation of the Salmonella typhimurium phoPQ operon. Journal Of Bacteriology 1995, 177: 4364-4371. PMID: 7543474, PMCID: PMC177185, DOI: 10.1128/jb.177.15.4364-4371.1995.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsBase SequenceCloning, MolecularDNA Transposable ElementsGene Expression Regulation, BacterialHomeostasisLac OperonModels, GeneticMolecular Sequence DataMutationNucleic Acid ConformationOperonPromoter Regions, GeneticRNA, BacterialRNA, MessengerSalmonella typhimuriumTranscription FactorsTranscription, GeneticConceptsPhoPQ operonTranscriptional fusionsTranscriptional autoregulationPhoP-PhoQTwo-component regulatory systemAbsence of PhoPTranscriptional regulator PhoPExpression of phoPPhospho-PhoPPhoQ proteinPhoP proteinRegulator PhoPEnvironmental signalsDifferent transcriptsIndependent promotersPosttranscriptional mechanismsOperonPhoPPhoQGenesRegulatory systemBasal levelsProtein levelsProteinPromoter