2015
Species-Specific Dynamic Responses of Gut Bacteria to a Mammalian Glycan
Raghavan V, Groisman EA. Species-Specific Dynamic Responses of Gut Bacteria to a Mammalian Glycan. Journal Of Bacteriology 2015, 197: 1538-1548. PMID: 25691527, PMCID: PMC4403648, DOI: 10.1128/jb.00010-15.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBacteroidesChondroitin SulfatesGastrointestinal TractGene Expression ProfilingGene Expression Regulation, BacterialMammalsConceptsUtilization genesRelated speciesBacterial speciesBacteroides speciesPolysaccharide utilization genesCase of genesGut bacteriaGut bacterial speciesOrthologous genesCommunity compositionExpression dynamicsMammalian glycansSole carbon sourceRelated microbesBacterial communitiesMicrobial speciesMammalian intestineSame geneStable coexistenceGut microbial compositionDifferential regulationExpression behaviorGenesMicrobial compositionSustained activation
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
2008
RstA-Promoted Expression of the Ferrous Iron Transporter FeoB under Iron-Replete Conditions Enhances Fur Activity in Salmonella enterica
Jeon J, Kim H, Yun J, Ryu S, Groisman EA, Shin D. RstA-Promoted Expression of the Ferrous Iron Transporter FeoB under Iron-Replete Conditions Enhances Fur Activity in Salmonella enterica. Journal Of Bacteriology 2008, 190: 7326-7334. PMID: 18790861, PMCID: PMC2576650, DOI: 10.1128/jb.00903-08.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsBlotting, WesternElectrophoretic Mobility Shift AssayGene ExpressionGene Expression ProfilingGene Expression Regulation, BacterialIronIron DeficienciesOligonucleotide Array Sequence AnalysisOperonPromoter Regions, GeneticProtein BindingRepressor ProteinsReverse Transcriptase Polymerase Chain ReactionSalmonella entericaTranscription, GeneticConceptsFerrous iron transporter FeoBFur proteinIron-replete conditionsFur activityTarget genesIron-responsive genesWild-type levelsFerrous iron uptakeFeoAB operonFur geneTranscriptional activationIron acquisitionExpression experimentsRegulatory pathwaysTranscription levelsIron uptakeGenesPrimary regulatorRstAProteinFeOBRepressionSalmonella entericaPromoterExpression