title: Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in gamma-proteobacteria.
abstract: Comparative approach is a powerful tool for analysis of gene regulation in bacterial genomes. Here we apply it to analysis of regulation of the multidrug resistance transport (MDRT) systems in enterobacteria Escherichia coli, Salmonella typhi, Klebsiella pneumoniae and Yersinia pestis. Comparison of nucleotide sequences upstream of MDRT genes was performed in order to predict new regulatory sites (operators) and identify candidate regulons. Since the regulatory sites diverge slower than the non-coding regions in general, they are visible as strongly conserved islands. This analysis resulted in description of a regulatory network for known and hypothetical MDRT systems and porins. New candidate members of the MarA regulon were detected. Putative binding sites for EmrR and AcrR were suggested. A new hypothetical MarX regulon was described that includes some multidrug transporters and porins.
authors.affiliation: State Scientific Center GosNIIGenetika, Moscow, Russia.
authors.forename: D A
authors.initials: DA
authors.lastname: Rodionov
authors.forename: M S
authors.initials: MS
authors.lastname: Gelfand
authors.forename: A A
authors.initials: AA
authors.lastname: Mironov
authors.forename: A B
authors.initials: AB
authors.lastname: Rakhmaninova
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D017124:Conserved Sequence; D004268:DNA-Binding Proteins / Q000235:genetics; D004352:Drug Resistance, Microbial; D018432:Drug Resistance, Multiple; D004926:Escherichia coli / Q000235:genetics; D029968:Escherichia coli Proteins; D020563:Gammaproteobacteria / Q000187:drug effects / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D014644:Genetic Variation; D016680:Genome, Bacterial; D007711:Klebsiella pneumoniae / Q000235:genetics; D008969:Molecular Sequence Data; D018085:Regulon; D012097:Repressor Proteins / Q000235:genetics; D012485:Salmonella typhi / Q000235:genetics; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D015534:Trans-Activators / Q000235:genetics; D015010:Yersinia pestis / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C080002:MarA protein, E coli; C080004:MarR protein, E coli; D012097:Repressor Proteins; D015534:Trans-Activators