2023
Dietary sugars silence the master regulator of carbohydrate utilization in human gut Bacteroides species
Pearce V, Groisman E, Townsend G. Dietary sugars silence the master regulator of carbohydrate utilization in human gut Bacteroides species. Gut Microbes 2023, 15: 2221484. PMID: 37358144, PMCID: PMC10294740, DOI: 10.1080/19490976.2023.2221484.Peer-Reviewed Original ResearchConceptsMaster regulatorMicrobial populationsOrthologous transcription factorsMammalian gut microbiotaMicrobial gene expressionHuman gut symbiontHuman gut BacteroidesDistinct microbial populationsIntestinal Bacteroides speciesGut symbiontsCarbohydrate utilizationMRNA leaderTranscription factorsHost dietGut BacteroidesNutrient availabilityGene expressionMolecular pathwaysUnknown mechanismDietary sugarsBacteroides speciesFuture therapeutic interventionsRegulatorSimple sugarsPathogenic outcomes
2020
The phosphorelay BarA/SirA activates the non-cognate regulator RcsB in Salmonella enterica
Salvail H, Groisman EA. The phosphorelay BarA/SirA activates the non-cognate regulator RcsB in Salmonella enterica. PLOS Genetics 2020, 16: e1008722. PMID: 32392214, PMCID: PMC7241856, DOI: 10.1371/journal.pgen.1008722.Peer-Reviewed Original ResearchConceptsBarA/SirACell wall perturbationSet of genesBacterium Salmonella enterica serovar TyphimuriumOuter-membrane stressSalmonella enterica serovar TyphimuriumPhosphorelay proteinsPhosphorelay systemLuria-Bertani mediumEnterica serovar TyphimuriumRcsBEnvironmental stressGene transcriptionGene expressionWall perturbationDifferent regulatorsSpectrum of environmentsPhosphorelaySerovar TyphimuriumRegulatorRcsCProteinTranscriptionSalmonella entericaGenes
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. entericaProteinInhibition 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 systemRiboswitch control of Rho-dependent transcription termination
Hollands K, Proshkin S, Sklyarova S, Epshtein V, Mironov A, Nudler E, Groisman EA. Riboswitch control of Rho-dependent transcription termination. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 5376-5381. PMID: 22431636, PMCID: PMC3325659, DOI: 10.1073/pnas.1112211109.Peer-Reviewed Original ResearchConceptsRho-dependent transcription terminationTranscription terminationRiboswitch ligandsGene expressionControl gene expressionRho-specific inhibitorIntrinsic transcription terminationATPase activityActivity of RhoSalmonella enterica serovar TyphimuriumRiboswitch actionRiboswitch controlTranscription machineryProtein effectorsGene regulationRho ATPase activityEnterica serovar TyphimuriumTranslation initiationThird general mechanismRiboswitchTranscriptionEscherichia coliRNA sensorsWidespread modeSerovar Typhimurium
2011
Genome-wide detection of novel regulatory RNAs in E. coli
Raghavan R, Groisman EA, Ochman H. Genome-wide detection of novel regulatory RNAs in E. coli. Genome Research 2011, 21: 1487-1497. PMID: 21665928, PMCID: PMC3166833, DOI: 10.1101/gr.119370.110.Peer-Reviewed Original ResearchConceptsSmall RNAsLeader sequenceIntergenic regionRegulatory elementsRegulatory RNAsNew small RNAsStable RNA secondary structureNovel regulatory RNAsProtein-coding transcriptsNovel small RNAsGenome-wide detectionNoncoding regulatory RNAsE. coliRNA secondary structureProtein HfqPhylogenetic conservationBacterial genomesEvolutionary analysisPresence of hundredsSequencing approachGene expressionCompensatory mutationsEnteric speciesSecondary structureEscherichia coli
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
Response Acceleration in Post-translationally Regulated Genetic Circuits
Mitrophanov AY, Groisman EA. Response Acceleration in Post-translationally Regulated Genetic Circuits. Journal Of Molecular Biology 2009, 396: 1398-1409. PMID: 19932119, PMCID: PMC2861412, DOI: 10.1016/j.jmb.2009.11.043.Peer-Reviewed Original ResearchConceptsRegulatory proteinsTwo-component system familyBacterial signal transductionGenetic regulatory circuitsTwo-component systemSteady-state output levelGenetic circuitsRegulatory circuitsSignal transductionSensor proteinsTranscription factorsGene expressionLiving cellsPhosphorylation levelsProteinSpecific signalsKinetic propertiesSuch modificationsCellsTransductionPhosphorylationRegulatorMechanismPrevalent formExpressionIdentifying 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 promotersControl of Salmonella pathogenicity island-2 gene expression
Fass E, Groisman EA. Control of Salmonella pathogenicity island-2 gene expression. Current Opinion In Microbiology 2009, 12: 199-204. PMID: 19264535, PMCID: PMC2805070, DOI: 10.1016/j.mib.2009.01.004.Peer-Reviewed Original ResearchConceptsSPI-2 genesTwo-component systems PhoP/PhoQOmpR/EnvZType III secretion systemDifferent pathogenicity islandsSalmonella pathogenicity island 2PhoP/PhoQPathogenicity island 2H-NSEffector proteinsProtein IHFSecretion systemGene expressionRobust silencingIsland 2Pathogenicity islandHost cellsGenesExpressionEnvZSlyASsrBPhoQTranscriptionSilencing
2007
The intricate world of riboswitches
Coppins RL, Hall KB, Groisman EA. The intricate world of riboswitches. Current Opinion In Microbiology 2007, 10: 176-181. PMID: 17383225, PMCID: PMC1894890, DOI: 10.1016/j.mib.2007.03.006.Peer-Reviewed Original Research
2006
Acid pH activation of the PmrA/PmrB two‐component regulatory system of Salmonella enterica
Perez JC, Groisman EA. Acid pH activation of the PmrA/PmrB two‐component regulatory system of Salmonella enterica. Molecular Microbiology 2006, 63: 283-293. PMID: 17229213, PMCID: PMC1804205, DOI: 10.1111/j.1365-2958.2006.05512.x.Peer-Reviewed Original ResearchConceptsGlutamic acid residuesPmrA/PmrB systemAcid residuesTwo-component regulatory systemPathogen Salmonella enterica serovar TyphimuriumResponse regulator PmrATranscription of genesPmrA/PmrBSalmonella enterica serovar TyphimuriumPmrA proteinPolymyxin B resistancePeriplasmic domainWild-type SalmonellaEnterica serovar TyphimuriumGene productsGene expressionAnimal hostsRegulatory systemB resistanceSerovar TyphimuriumTranscriptionSalmonella entericaCellular changesGenesPH activation
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 datasetDissecting 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
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 Mg2
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
1998
The ins and outs of virulence gene expression: Mg2+ as a regulatory signal
Groisman E. The ins and outs of virulence gene expression: Mg2+ as a regulatory signal. BioEssays 1998, 20: 96-101. PMID: 9504051, DOI: 10.1002/(sici)1521-1878(199801)20:1<96::aid-bies13>3.0.co;2-3.Peer-Reviewed Original ResearchConceptsSignal transduction systemTransduction systemCellular locationPhoP/PhoQ systemPathogen Salmonella enterica serovar TyphimuriumIntracellular pathogen Salmonella enterica serovar TyphimuriumTranscription of genesPhoP/PhoQVirulence gene expressionFacultative intracellular pathogen Salmonella enterica serovar TyphimuriumSalmonella enterica serovar TyphimuriumDifferent cell typesRegulatory hierarchyEnterica serovar TyphimuriumRegulatory signalsExtracellular environmentGene expressionHost cellsHost cuesCell typesMultiple environmentsSerovar TyphimuriumPrecise tissuePhoQTranscription