2024
Chaperone Hsp70 helps Salmonella survive infection-relevant stress by reducing protein synthesis
Chan C, Groisman E. Chaperone Hsp70 helps Salmonella survive infection-relevant stress by reducing protein synthesis. PLOS Biology 2024, 22: e3002560. PMID: 38574172, PMCID: PMC10994381, DOI: 10.1371/journal.pbio.3002560.Peer-Reviewed Original ResearchMeSH KeywordsBacteriaEscherichia coliEscherichia coli ProteinsHSP70 Heat-Shock ProteinsMagnesiumMolecular ChaperonesProtein FoldingSalmonellaConceptsRibosome associationProtein synthesisProtein homeostasisS. typhimuriumProtein folding capacityPreventing protein aggregationC-terminal amino acidsDomains of lifeProtein synthesis in vitroInhibit protein synthesisFolding capacityHsp70 chaperonesJ-domainSynthesis in vitroProtein foldingReduction of protein synthesisChaperone Hsp70DnaKRibosomeProtein aggregationChaperoneAmino acidsProteinStarvationHSP70
2022
Degradation of gene silencer is essential for expression of foreign genes and bacterial colonization of the mammalian gut
Choi J, Schmukler M, Groisman EA. Degradation of gene silencer is essential for expression of foreign genes and bacterial colonization of the mammalian gut. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2210239119. PMID: 36161931, PMCID: PMC9546599, DOI: 10.1073/pnas.2210239119.Peer-Reviewed Original ResearchConceptsH-NSForeign genesHeat-stable nucleoid-structuring (H-NS) proteinWild-type H-NSNucleoid-associated proteinsH-NS proteinsNucleoid structuring proteinHorizontal gene transferBacterial evolutionLon proteaseSilences expressionCorresponding genesForeign DNAMammalian gutMammalian hostsStructuring proteinGene silencersGenesMurine gutEnteric bacteriaGene transferBiofilm formationProteinGeneral mechanismColonization
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 ResearchMeSH KeywordsDNA GyraseDNA Topoisomerases, Type IDNA, SuperhelicalEscherichia coliMagnesiumPutrescineSalmonella typhimuriumSpermidineConceptsE. 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 activationFEDS: a Novel Fluorescence-Based High-Throughput Method for Measuring DNA Supercoiling In Vivo
Duprey A, Groisman EA. FEDS: a Novel Fluorescence-Based High-Throughput Method for Measuring DNA Supercoiling In Vivo. MBio 2020, 11: 10.1128/mbio.01053-20. PMID: 32723920, PMCID: PMC7387798, DOI: 10.1128/mbio.01053-20.Peer-Reviewed Original ResearchConceptsDNA supercoilingFluorescent proteinDNA supercoiling resultsBacterial DNA supercoilingSingle-cell heterogeneityGreen fluorescent proteinRed fluorescent proteinCellular physiologyDNA processesHigh-throughput methodConstitutive promoterNovel regulatorNucleotide sequenceGenetic informationRegulatory loopHigh-throughput measurementsSupercoilingForms of lifeGenesSingle cellsTranscriptionPromoterProteinChemical supportNovel fluorescence
2018
Reduction in adaptor amounts establishes degradation hierarchy among protease substrates
Yeom J, Gao X, Groisman EA. Reduction in adaptor amounts establishes degradation hierarchy among protease substrates. Proceedings Of The National Academy Of Sciences Of The United States Of America 2018, 115: e4483-e4492. PMID: 29686082, PMCID: PMC5948988, DOI: 10.1073/pnas.1722246115.Peer-Reviewed Original ResearchConceptsRegulatory protein PhoPATP-dependent proteaseCritical cellular processesExpression of genesCellular processesAntibiotic persistersCytoplasmic MgProtease substratesUvrYDifferential stabilityProteasePhoPPhysiological conditionsGenesAdaptorAbundanceUnfoldaseFtsATranscriptionSubunitsSubstrateProteolysisVirulenceProteinBindsProtein synthesis controls phosphate homeostasis
Pontes MH, Groisman EA. Protein synthesis controls phosphate homeostasis. Genes & Development 2018, 32: 79-92. PMID: 29437726, PMCID: PMC5828397, DOI: 10.1101/gad.309245.117.Peer-Reviewed Original ResearchConceptsPi starvation responsesStarvation responseProtein synthesisPi transporter genesProtein synthesis controlATP consumptionPi starvationRegulatory connectionsPi homeostasisTransporter geneExtracellular milieuCytoplasmic MgCytoplasmic PiSerovar TyphimuriumPharmacological inhibitionATP levelsRibosomesCytoplasmic magnesiumBacteriumHomeostasisSynthesis controlPhoBSaccharomycesTranscriptionYeast
2017
ATP-Dependent Persister Formation in Escherichia coli
Shan Y, Gandt A, Rowe S, Deisinger J, Conlon B, Lewis K, Zgurskaya H, Groisman E. ATP-Dependent Persister Formation in Escherichia coli. MBio 2017, 8: e02267-16. PMID: 28174313, PMCID: PMC5296605, DOI: 10.1128/mbio.02267-16.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateDrug ToleranceEscherichia coliGene Expression Regulation, BacterialMicrobial ViabilityConceptsChronic infectionFluorescence-activated cell sortingDrug toleranceATP levelsPersister formationDrug-tolerant persistersFluoroquinolone treatmentStress-induced activationSubpopulation of cellsLevels of ATPDormant variantsAntibiotic-tolerant cellsCellular ATP levelsBactericidal antibioticsDim cellsInfectionActivationPersister cellsAntibioticsCell sortingTreatmentSubpopulationsCellsActive toxinToxin activation
2016
Reducing Ribosome Biosynthesis Promotes Translation during Low Mg2+ Stress
Pontes MH, Yeom J, Groisman EA. Reducing Ribosome Biosynthesis Promotes Translation during Low Mg2+ Stress. Molecular Cell 2016, 64: 480-492. PMID: 27746019, PMCID: PMC5500012, DOI: 10.1016/j.molcel.2016.05.008.Peer-Reviewed Original ResearchConceptsSynthesis of ribosomesAmino acid abundanceExpression of proteinsPromotes TranslationAvailability of ATPRibosomal componentsRegulatory circuitsTranslational arrestCytosolic MgRRNA geneProtein synthesisRibosomesATP levelsLevels of ATPATP amountATPDivalent cationsMutantsTranscriptionNegative chargeGenesLow Mg2TranslationProteinAbundance
2015
When Too Much ATP Is Bad for Protein Synthesis
Pontes MH, Sevostyanova A, Groisman EA. When Too Much ATP Is Bad for Protein Synthesis. Journal Of Molecular Biology 2015, 427: 2586-2594. PMID: 26150063, PMCID: PMC4531837, DOI: 10.1016/j.jmb.2015.06.021.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateEnergy MetabolismEscherichia coliHumansMagnesiumProtein BiosynthesisRibosomesTranscription, GeneticConceptsProtein synthesisStructure of ribosomesEnergy-dependent activitiesATP levelsRibosome productionCellular processesTranslation initiationCytoplasmic membraneEssential enzymeCellular ATPEnergy currencyLiving cellsATPCellsDivalent cationsCrucial roleTriphosphateRibosomesAminoacylationOrganismsNon-physiological increaseCofactorEnzymeBiochemistryCommon divalent cations
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
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
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
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
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
2003
Role of Nonhost Environments in the Lifestyles of Salmonella and Escherichia coli
Winfield MD, Groisman EA. Role of Nonhost Environments in the Lifestyles of Salmonella and Escherichia coli. Applied And Environmental Microbiology 2003, 69: 3687-3694. PMID: 12839733, PMCID: PMC165204, DOI: 10.1128/aem.69.7.3687-3694.2003.Peer-Reviewed Original Research
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