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
A Master Regulator of Bacteroides thetaiotaomicron Gut Colonization Controls Carbohydrate Utilization and an Alternative Protein Synthesis Factor
Townsend GE, Han W, Schwalm ND, Hong X, Bencivenga-Barry NA, Goodman AL, Groisman EA. A Master Regulator of Bacteroides thetaiotaomicron Gut Colonization Controls Carbohydrate Utilization and an Alternative Protein Synthesis Factor. MBio 2020, 11: 10.1128/mbio.03221-19. PMID: 31992627, PMCID: PMC6989115, DOI: 10.1128/mbio.03221-19.Peer-Reviewed Original ResearchPutative translation factorProtein synthesis factorsTranslation factorsMammalian gutDietary fiber utilizationTranscriptional regulatorsBeneficial microbesSpecialized translation factorHundreds of genesMajor transcriptional regulatorGut colonizationCarbohydrate utilizationSynthesis factorsHuman gut microbiotaGlobal regulonGenetic repertoireTranscription factorsMaster regulatorDNA sequencesDerive nutrientsColonization defectUtilization of carbohydratesCellular metabolismComplex polysaccharidesGenes
2016
Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron
Schwalm ND, Townsend GE, Groisman EA. Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron. MBio 2016, 7: 10.1128/mbio.01342-16. PMID: 27729509, PMCID: PMC5061871, DOI: 10.1128/mbio.01342-16.Peer-Reviewed Original ResearchConceptsMammalian gut microbiotaPolysaccharide utilization genesUtilization genesHost dietGut symbiont Bacteroides thetaiotaomicronComplex polysaccharidesBacteroides thetaiotaomicronPleiotropic transcriptional regulatorDomains of lifeSubset of organismsRegulatory paradigmCritical nutrient sourceTranscriptional activatorTranscriptional regulatorsTranscriptional repressorCentral metabolismGenomic analysisMammalian gutMammalian hostsRegulatory architectureGut BacteroidesPolymeric fructanGut microbiotaGut bacteriumPolysaccharide breakdown
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
2013
The Biology of the PmrA/PmrB Two-Component System: The Major Regulator of Lipopolysaccharide Modifications
Chen HD, Groisman EA. The Biology of the PmrA/PmrB Two-Component System: The Major Regulator of Lipopolysaccharide Modifications. Annual Review Of Microbiology 2013, 67: 83-112. PMID: 23799815, PMCID: PMC8381567, DOI: 10.1146/annurev-micro-092412-155751.Peer-Reviewed Original ResearchConceptsPmrA/PmrBTwo-component systemPmrA/PmrB systemMajor regulatorEnteric pathogen Salmonella entericaGene expression outputPathogen Salmonella entericaTranscriptional regulatorsExpression outputEcological nichesOuter membraneRelated bacteriaLPS modificationsExtent bacteriaLipopolysaccharide modificationDifferential survivalRegulatorHost immune systemNegative bacteriaSalmonella entericaBacteriaBiologyPmrBQuantitative differencesImmune system
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
1993
Molecular, functional, and evolutionary analysis of sequences specific to Salmonella.
Groisman EA, Sturmoski MA, Solomon FR, Lin R, Ochman H. Molecular, functional, and evolutionary analysis of sequences specific to Salmonella. Proceedings Of The National Academy Of Sciences Of The United States Of America 1993, 90: 1033-1037. PMID: 8430070, PMCID: PMC45805, DOI: 10.1073/pnas.90.3.1033.Peer-Reviewed Original ResearchConceptsAtypical base compositionIndependent evolutionary eventsPhenotypic characteristicsOpen reading frameLac gene fusionsWild-type parentLysR familyEvolutionary eventsDeletion strainEvolutionary analysisTranscriptional regulatorsReading frameSalmonella genomeNucleotide sequenceBase compositionHorizontal transferDNA fragmentsGene fusionsBacterial speciesEnteric bacteriaStructural similaritySpeciesVirulenceSequenceUnprecedented array
1989
Salmonella typhimurium phoP virulence gene is a transcriptional regulator.
Groisman EA, Chiao E, Lipps CJ, Heffron F. Salmonella typhimurium phoP virulence gene is a transcriptional regulator. Proceedings Of The National Academy Of Sciences Of The United States Of America 1989, 86: 7077-7081. PMID: 2674945, PMCID: PMC297997, DOI: 10.1073/pnas.86.18.7077.Peer-Reviewed Original ResearchConceptsExpression of lociAmino acid sequenceDifferent environmental stimuliFacultative intracellular pathogenGram-negative speciesTranscriptional regulatorsYeast SaccharomycesExtensive homologyDNA sequencesGene productsAcid sequenceHost phagocytic cellsPhosphate availabilityEnvironmental stimuliIntracellular pathogensPhoP genePhoP mutationVirulence genesPhoPGenesLociSequenceSalmonella typhimuriumPhagocytic cellsPhoB