2023
Advancing evolution: Bacteria break down gene silencer to express horizontally acquired genes
Groisman E, Choi J. Advancing evolution: Bacteria break down gene silencer to express horizontally acquired genes. BioEssays 2023, 45: e2300062. PMID: 37533411, PMCID: PMC10530229, DOI: 10.1002/bies.202300062.Peer-Reviewed Original ResearchConceptsH-NSAT-rich DNAHeat-stable nucleoid-structuring (H-NS) proteinConserved amino acid sequencesNucleoid structuring proteinHorizontal gene transferAmino acid sequenceSalmonella enterica serovar TyphimuriumBacterial evolutionLon proteaseProtease LonDiverse bacteriaEnterica serovar TyphimuriumRNA polymeraseAlternative promotersAcid sequenceStructuring proteinGene silencersGenesCleavage siteEnteric bacteriaEscherichia coliGene transferCommensal Escherichia coliSerovar Typhimurium
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
DNA supercoiling differences in bacteria result from disparate DNA gyrase activation by polyamines
Duprey A, Groisman EA. DNA supercoiling differences in bacteria result from disparate DNA gyrase activation by polyamines. PLOS Genetics 2020, 16: e1009085. PMID: 33125364, PMCID: PMC7598504, DOI: 10.1371/journal.pgen.1009085.Peer-Reviewed Original ResearchConceptsE. coli enzymeDNA supercoilingColi enzymeDNA supercoiling resultsGlobal DNA supercoilingDNA gyraseSignal transduction pathwaysAmino acid identityDNA gyrase activityE. coliSpecies Escherichia coliSalmonella enterica serovar TyphimuriumEnterica serovar TyphimuriumAcid identityTransduction pathwaysPrecursor putrescineGyrase activitySupercoilingHigh extracellular Mg2DNA gyrasesPolyamines spermidineEscherichia coliTopoisomerase ISerovar TyphimuriumDisparate activation
2012
The Impact of Differential Regulation on Bacterial Speciation
Groisman E. The Impact of Differential Regulation on Bacterial Speciation. 2012, 109-114. DOI: 10.1128/9781555818470.ch15.Peer-Reviewed Original ResearchBacterial speciesGene regulatory strategiesRelated bacterial speciesResistance proteinAmino acid sequenceEukaryotic speciesRelated speciesBacterial speciationRelated organismsIndividual speciesRegulatory proteinsAcid sequenceBacterial behaviorEnteric speciesGenetic differencesGenetic scenariosDifferential regulationResistance genesEscherichia coliSpeciesEconomic importanceProteinSalmonella entericaFamily EnterobacteriaceaeOrganismsRiboswitch 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
Ancestral Genes Can Control the Ability of Horizontally Acquired Loci to Confer New Traits
Chen HD, Jewett MW, Groisman EA. Ancestral Genes Can Control the Ability of Horizontally Acquired Loci to Confer New Traits. PLOS Genetics 2011, 7: e1002184. PMID: 21811415, PMCID: PMC3140997, DOI: 10.1371/journal.pgen.1002184.Peer-Reviewed Original ResearchMeSH KeywordsAnti-Bacterial AgentsBacterial ProteinsDNA, BacterialDrug Resistance, BacterialEscherichia coliEscherichia coli ProteinsGene Expression Regulation, BacterialGene Transfer, HorizontalKineticsMagnesiumMolecular Sequence DataPhosphorylationPolymyxin BReverse Transcriptase Polymerase Chain ReactionSalmonella typhimuriumSequence Analysis, DNATranscription FactorsTransformation, BacterialConceptsGene productsPmrD proteinPmrA/PmrB systemSpecies-specific traitsPmrA/PmrBE. coliHigh phosphatase activityBacterium Escherichia coliTwo-component systemPmrA proteinPolymyxin B resistanceAncestral locusAncestral proteinAncestral geneAncestral pathwayNew traitsBiochemical activityDifferent speciesGenesPmrB proteinEscherichia coliPhosphatase activityB resistanceProteinSalmonella entericaGenome-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
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 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
The PhoP/PhoQ two-component system stabilizes the alternative sigma factor RpoS in Salmonella enterica
Tu X, Latifi T, Bougdour A, Gottesman S, Groisman EA. The PhoP/PhoQ two-component system stabilizes the alternative sigma factor RpoS in Salmonella enterica. Proceedings Of The National Academy Of Sciences Of The United States Of America 2006, 103: 13503-13508. PMID: 16938894, PMCID: PMC1557385, DOI: 10.1073/pnas.0606026103.Peer-Reviewed Original ResearchConceptsSigma factor RpoSPhoP/PhoQTwo-component systemAlternative sigma factor RpoSTwo-component regulatory system PhoP/PhoQPhoP/PhoQ.Stress response genesSalmonella enterica serovar TyphimuriumRpoS stabilityClpXP proteaseTranscriptional activatorEnterica serovar TyphimuriumRegulatory circuitsRpoS mutantResponse genesRegulatory proteinsProtein turnoverRpoSBacterial speciesEscherichia coliPhoP geneGenesSerovar TyphimuriumE. coliPhoQ
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
2004
Phenotypic differences between Salmonella and Escherichia coli resulting from the disparate regulation of homologous genes
Winfield MD, Groisman EA. Phenotypic differences between Salmonella and Escherichia coli resulting from the disparate regulation of homologous genes. Proceedings Of The National Academy Of Sciences Of The United States Of America 2004, 101: 17162-17167. PMID: 15569938, PMCID: PMC534605, DOI: 10.1073/pnas.0406038101.Peer-Reviewed Original ResearchConceptsPmrD proteinPolymyxin B resistanceHomologous genesB resistancePhenotypic differencesDifferential regulationRange of nichesSpecies-specific genesPmrA/PmrBE. coliE. coli KTwo-component systemEnterica serovar TyphimuriumGene transcriptionS. enterica serovar TyphimuriumEcological consequencesColi KLPS modificationsNatural isolatesPathogenicity islandE. coli strainsGenesMolecular analysisEscherichia coliSerovar Typhimurium
2002
Fe(III)‐mediated cellular toxicity
Chamnongpol S, Dodson W, Cromie MJ, Harris ZL, Groisman EA. Fe(III)‐mediated cellular toxicity. Molecular Microbiology 2002, 45: 711-719. PMID: 12139617, DOI: 10.1046/j.1365-2958.2002.03041.x.Peer-Reviewed Original ResearchConceptsIsogenic wild-type strainSignal transduction systemWild-type strainGram-negative speciesPmrA mutantOuter membraneIron-mediated toxicityTransduction systemMicrobicidal activityBacterial survivalMajor regulatorCell deathPmrA geneIron homeostasisMutantsEscherichia coliSalmonella mutantsDeleterious metalsCellular toxicitySalmonella entericaExcellent biocatalystAnaerobic conditionsGenesRegulatorSpecies
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 entericaGenesThe SPI-3 Pathogenicity Island ofSalmonella enterica
Blanc-Potard A, Solomon F, Kayser J, Groisman E. The SPI-3 Pathogenicity Island ofSalmonella enterica. Journal Of Bacteriology 1999, 181: 998-1004. PMID: 9922266, PMCID: PMC93469, DOI: 10.1128/jb.181.3.998-1004.1999.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesAdhesins, Escherichia coliAmino Acid SequenceBacterial ProteinsBase CompositionCarrier ProteinsCation Transport ProteinsChromosomes, BacterialDNA PrimersDNA-Binding ProteinsEscherichia coliEvolution, MolecularMolecular Sequence DataMultigene FamilyOpen Reading FramesOperonPhylogenyPolymerase Chain ReactionRNA, BacterialRNA, TransferSalmonella entericaSequence AlignmentTranscription FactorsTranscription, GeneticVibrio choleraeVirulenceConceptsOpen reading framePathogenicity islandReading framePathogen-specific virulence genesSubspecies of SalmonellaFour-gene clusterMolecular genetic structureSalmonella enterica serovar TyphimuriumGenetic structureTranscriptional unitsChromosomal clustersEnterica serovar TyphimuriumTRNA locusSequence similaritySalmonella genomeRegulatory proteinsEnteropathogenic Escherichia coliSPI-3Escherichia coliSerovar TyphimuriumInsertion sequenceVibrio choleraeVirulence genesMultistep processSubspecies
1998
Seeking the genetic basis of phenotypic differences among bacterial species
Ochman H, Groisman E. Seeking the genetic basis of phenotypic differences among bacterial species. 1998, 221-235. DOI: 10.1007/978-3-0348-8948-3_12.Peer-Reviewed Original ResearchEnteric bacteria Escherichia coliBacterial speciesSpecies-specific genesSpecies-specific charactersGene complementSole carbon sourceDNA regionsPhenotypic charactersGenetic basisAllelic variationBacteria Escherichia coliPhenotypic differencesEscherichia coliSpeciesSalmonella entericaCarbon sourceGenesMicrobesCertain compoundsColiObserved differencesPhysiologySequenceEntericaCharacter
1997
The Salmonella selC locus contains a pathogenicity island mediating intramacrophage survival
Blanc‐Potard A, Groisman E. The Salmonella selC locus contains a pathogenicity island mediating intramacrophage survival. The EMBO Journal 1997, 16: 5376-5385. PMID: 9311997, PMCID: PMC1170169, DOI: 10.1093/emboj/16.17.5376.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesAnimalsBacterial ProteinsBase SequenceCarrier ProteinsCation Transport ProteinsCulture MediaEscherichia coliEscherichia coli ProteinsFemaleGenes, BacterialMacrophagesMagnesiumMembrane Transport ProteinsMiceMice, Inbred BALB CMolecular Sequence DataMultigene FamilyMutationOperonPhenotypeRecombination, GeneticRNA, TransferSalmonella Infections, AnimalSalmonella typhimuriumConceptsPathogenicity islandSelC locusIntramacrophage survivalSalmonella typhimurium chromosomePhoP/PhoQKb DNA segmentVirulence genesNon-pathogenic bacterial speciesTwo-component systemSite of integrationChromosomal clustersTRNA locusVirulence functionsDNA segmentsSalmonella virulenceHomologous regionsMajor regulatorBacterial speciesLociEnteric bacteriaEscherichia coliGenesBenign strainsLow Mg2Virulence
1994
A Salmonella protein that is required for resistance to antimicrobial peptides and transport of potassium.
Parra‐Lopez C, Lin R, Aspedon A, Groisman EA. A Salmonella protein that is required for resistance to antimicrobial peptides and transport of potassium. The EMBO Journal 1994, 13: 3964-3972. PMID: 8076592, PMCID: PMC395316, DOI: 10.1002/j.1460-2075.1994.tb06712.x.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBase SequenceBiological TransportCarrier ProteinsCloning, MolecularDrug Resistance, MicrobialMelittenMembrane ProteinsMolecular Sequence DataNADPeptidesPotassiumProtaminesReceptor, trkARecombinant ProteinsRestriction MappingSalmonella typhimuriumSequence Analysis, DNASequence Homology, Amino AcidConceptsE. coli proteinsAntimicrobial peptidesMolecular genetic analysisAntimicrobial peptide protaminePutative transportersTransport of peptidesColi proteinsSingle mutantsSalmonella proteinsSame resistance pathwaysSAP mutantsHost defense moleculesGenetic analysisDefense moleculesLoci participateChannel proteinsExhibit hypersensitivityEfflux proteinsUptake systemResistance pathwaysMutantsEscherichia coliProteinTransport of potassiumHost tissuesThe origin and evolution of species differences in Escherichia coli and Salmonella typhimurium
Ochman H, Groisman EA. The origin and evolution of species differences in Escherichia coli and Salmonella typhimurium. EXS 1994, 69: 479-493. PMID: 7994120, DOI: 10.1007/978-3-0348-7527-1_27.Peer-Reviewed Original ResearchConceptsSpecies-specific sequencesSalmonella chromosomeEscherichia coliCodon usage patternsOpen reading frameHost epithelial cellsCommon ancestorMap positionPhenotypic charactersReading frameBase compositionHorizontal transferSalmonella typhimuriumMutant strainGenetic differencesEnteric speciesBacterial speciesGenomePoint mutationsPhenotypic characteristicsSpeciesCorresponding regionChromosomesSpecies differencesEpithelial cells
1992
Horizontal transfer of a phosphatase gene as evidence for mosaic structure of the Salmonella genome.
Groisman EA, Saier MH, Ochman H. Horizontal transfer of a phosphatase gene as evidence for mosaic structure of the Salmonella genome. The EMBO Journal 1992, 11: 1309-1316. PMID: 1339343, PMCID: PMC556579, DOI: 10.1002/j.1460-2075.1992.tb05175.x.Peer-Reviewed Original ResearchMeSH KeywordsAcid PhosphataseAmino Acid SequenceBase CompositionBase SequenceChromosomes, BacterialCloning, MolecularCodonDNAEscherichia coliGenes, BacterialGenome, BacterialMolecular Sequence DataMosaicismPhylogenyPlasmidsRestriction MappingSalmonella typhimuriumSequence Homology, Nucleic AcidTransfectionConceptsBase compositionPhoN geneNon-specific acid phosphatase activityAtypical base compositionSpacing of genesOverall base compositionNon-specific acid phosphataseCodon usage patternsGram-negative speciesChromosome sizeBacterial genomesPhosphatase geneKb regionSalmonella chromosomeSalmonella genomeGenetic basisHorizontal transferAcid phosphatase activityTrinucleotide frequenciesHigh similarityGenomeGenesEscherichia coliPhosphatase activityOriT region