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
2004
Signal-dependent Binding of the Response Regulators PhoP and PmrA to Their Target Promoters in Vivo *
Shin D, Groisman EA. Signal-dependent Binding of the Response Regulators PhoP and PmrA to Their Target Promoters in Vivo *. Journal Of Biological Chemistry 2004, 280: 4089-4094. PMID: 15569664, DOI: 10.1074/jbc.m412741200.Peer-Reviewed Original ResearchConceptsResponse regulator PhoPPmrA proteinPhoP proteinRegulator PhoPTranscription of PhoPWild-type strainTarget promotersPromoter occupancyChromatin immunoprecipitationPromotes phosphorylationRegulatory regionsTarget genesPhoPValine residueLow Mg2GenesPhosphorylationPromoterProteinAsp 52TranscriptionSalmonella entericaVivoImmunoprecipitationMg2
1986
crp genes of Shigella flexneri, Salmonella typhimurium, and Escherichia coli
Cossart P, Groisman EA, Serre MC, Casadaban MJ, Gicquel-Sanzey B. crp genes of Shigella flexneri, Salmonella typhimurium, and Escherichia coli. Journal Of Bacteriology 1986, 167: 639-646. PMID: 3525518, PMCID: PMC212937, DOI: 10.1128/jb.167.2.639-646.1986.Peer-Reviewed Original ResearchConceptsE. coli crp geneNucleotide sequenceCatabolite gene activator proteinCRP geneGene activator proteinCrp gene productCorresponding amino acid sequencesE. coli CRPComplete nucleotide sequenceAmino acid divergenceEscherichia coli KAmino acid sequenceBase pair changesAmino acid differencesSalmonella typhimurium LT2S. typhimuriumRegulatory genesCodon usageActivator proteinRegulatory regionsGene productsAcid sequenceColi KPair changesAcid differences