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
Evolution 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 effects
2008
Evolution and Dynamics of Regulatory Architectures Controlling Polymyxin B Resistance in Enteric Bacteria
Mitrophanov AY, Jewett MW, Hadley TJ, Groisman EA. Evolution and Dynamics of Regulatory Architectures Controlling Polymyxin B Resistance in Enteric Bacteria. PLOS Genetics 2008, 4: e1000233. PMID: 18949034, PMCID: PMC2565834, DOI: 10.1371/journal.pgen.1000233.Peer-Reviewed Original ResearchConceptsRegulatory architectureComplex genetic networksDirect transcriptional controlEnteric bacteriaPolymyxin B resistanceEvolutionary historyTranscriptional controlGenetic networksRegulatory proteinsRegulatory pathwaysCellular responsesStructural modulesIndirect regulationRapid activationB resistanceExpression levelsMRNA expression levelsAntibiotic polymyxin BRegulation circuitBacteriaInducible resistanceFunctional propertiesProteinSystem postTransitional stage
1999
The selC‐associated SHI‐2 pathogenicity island of Shigella flexneri
Moss J, Cardozo T, Zychlinsky A, Groisman E. The selC‐associated SHI‐2 pathogenicity island of Shigella flexneri. Molecular Microbiology 1999, 33: 74-83. PMID: 10411725, DOI: 10.1046/j.1365-2958.1999.01449.x.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsChromosome MappingChromosomes, BacterialCloning, MolecularColicinsDNA Transposable ElementsDNA, BacterialEnterobacteriaceaeEscherichia coliGenes, BacterialHydroxamic AcidsIntegrasesOperonSequence AlignmentSequence Homology, Nucleic AcidShigella flexneriSpecies SpecificityTransposasesVirulenceConceptsPathogenicity islandSHI-2Different pathogenicity islandsChromosomal gene clusterRelated non-pathogenic speciesMultiple mobile genetic elementsMobile genetic elementsNon-pathogenic speciesSite of integrationTRNA genesSelC locusTRNA locusGene clusterNovel proteinGenetic elementsKb downstreamSiderophore systemStressful environmentsEscherichia coliVirulence factorsEnterohaemorrhagic E. coliE. coliUropathogenic Escherichia coliSalmonella entericaGenes
1995
The evolution off invasion by enteric bacteria
Ochman H, Groisman EA. The evolution off invasion by enteric bacteria. Canadian Journal Of Microbiology 1995, 41: 555-561. PMID: 7641138, DOI: 10.1139/m95-074.Peer-Reviewed Original ResearchMeSH KeywordsAntigens, BacterialEnterobacteriaceaeGenes, BacterialMultigene FamilyPhylogenyVirulenceConceptsPhylogenetic distributionGenomic locationPlant pathogensDivergent pathogensSecretory pathwayVirulence proteinsGene complexHost rangeHost cellsSimilar machineryEnteric bacteriaPathogensProteinDisease pathologyEnteric pathogensMachineryBacteriaPathwayShigella sppSppAnalogous structuresSequenceInvasionCellsComplexes
1993
Molecular genetic analysis of a locus required for resistance to antimicrobial peptides in Salmonella typhimurium.
Parra‐Lopez C, Baer MT, Groisman EA. Molecular genetic analysis of a locus required for resistance to antimicrobial peptides in Salmonella typhimurium. The EMBO Journal 1993, 12: 4053-4062. PMID: 8223423, PMCID: PMC413698, DOI: 10.1002/j.1460-2075.1993.tb06089.x.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAmino Acid SequenceAnti-Bacterial AgentsATP-Binding Cassette TransportersBase SequenceBiological TransportCloning, MolecularDrug Resistance, MicrobialEnterobacteriaceaeGenes, BacterialMelittenModels, BiologicalMolecular Sequence DataOperonPeptidesProtaminesSalmonella typhimuriumSequence Analysis, DNASequence Homology, Amino AcidConceptsUptake of oligopeptidesSet of genesOpen reading frameMolecular genetic analysisMammalian mdrYeast STE6Wild-type plasmidOperon structurePeriplasmic componentPeptide pheromoneNovel transporterReading frameKb segmentSalmonella typhimuriumGenetic analysisKb mRNASmall cationic peptidesSuccessful pathogenAntimicrobial peptide melittinSequence analysisCassette familyEnteric bacteriaPeptide transportAntimicrobial peptidesCancer cells
1988
Isolation, characterization, and cloning of a plasmid-borne gene encoding a phosphotransferase that confers high-level amikacin resistance in enteric bacilli
Gaynes R, Groisman E, Nelson E, Casadaban M, Lerner S. Isolation, characterization, and cloning of a plasmid-borne gene encoding a phosphotransferase that confers high-level amikacin resistance in enteric bacilli. Antimicrobial Agents And Chemotherapy 1988, 32: 1379-1384. PMID: 2848443, PMCID: PMC175872, DOI: 10.1128/aac.32.9.1379.Peer-Reviewed Original Research
1987
Cloning of genes from members of the family Enterobacteriaceae with mini-Mu bacteriophage containing plasmid replicons
Groisman EA, Casadaban MJ. Cloning of genes from members of the family Enterobacteriaceae with mini-Mu bacteriophage containing plasmid replicons. Journal Of Bacteriology 1987, 169: 687-693. PMID: 3542967, PMCID: PMC211834, DOI: 10.1128/jb.169.2.687-693.1987.Peer-Reviewed Original ResearchConceptsSensitive recipient strainFamily EnterobacteriaceaeHigh phage titersC. freundiiProteus mirabilisPlasmid repliconsCitrobacter freundiiS. typhimuriumDrug-resistant transductantsSpecific mutationsMu derivativesE. coliSalmonella typhimuriumEnterobacteriaceaeFreundiiRecipient strainPhage titerTyphimuriumEscherichia coli bacteriophageInfectionTiters