title: Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks.
abstract: Bacterial response to nitric oxide (NO) is of major importance since NO is an obligatory intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides metabolism in bacteria is diverse and involves FNR-like transcription factors HcpR, DNR, and NnrR; two-component systems NarXL and NarQP; NO-responsive activator NorR; and nitrite-sensitive repressor NsrR. Using comparative genomics approaches, we predict DNA-binding motifs for these transcriptional factors and describe corresponding regulons in available bacterial genomes. Within the FNR family of regulators, we observed a correlation of two specificity-determining amino acids and contacting bases in corresponding DNA recognition motif. Highly conserved regulon HcpR for the hybrid cluster protein and some other redox enzymes is present in diverse anaerobic bacteria, including Clostridia, Thermotogales, and delta-proteobacteria. NnrR and DNR control denitrification in alpha- and beta-proteobacteria, respectively. Sigma-54-dependent NorR regulon found in some gamma- and beta-proteobacteria contains various enzymes involved in the NO detoxification. Repressor NsrR, which was previously known to control only nitrite reductase operon in Nitrosomonas spp., appears to be the master regulator of the nitric oxides' metabolism, not only in most gamma- and beta-proteobacteria (including well-studied species such as Escherichia coli), but also in gram-positive Bacillus and Streptomyces species. Positional analysis and comparison of regulatory regions of NO detoxification genes allows us to propose the candidate NsrR-binding motif. The most conserved member of the predicted NsrR regulon is the NO-detoxifying flavohemoglobin Hmp. In enterobacteria, the regulon also includes two nitrite-responsive loci, nipAB (hcp-hcr) and nipC (dnrN), thus confirming the identity of the effector, i.e. nitrite. The proposed NsrR regulons in Neisseria and some other species are extended to include denitrification genes. As the result, we demonstrate considerable interconnection between various nitrogen-oxides-responsive regulatory systems for the denitrification and NO detoxification genes and evolutionary plasticity of this transcriptional network.
authors.affiliation: Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia. rodionov@iitp.ru
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Rodionov
authors.forename: Inna L
authors.initials: IL
authors.lastname: Dubchak
authors.forename: Adam P
authors.initials: AP
authors.lastname: Arkin
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Alm
authors.forename: Mikhail S
authors.initials: MS
authors.lastname: Gelfand
mesh_terms: D020816:Amino Acid Motifs; D001419:Bacteria / Q000378:metabolism*; D001426:Bacterial Proteins / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D023281:Genomics / Q000379:methods*; D008954:Models, Biological; D005810:Multigene Family; D009573:Nitrites; D009589:Nitrogen Oxides / Q000737:chemistry*; D010084:Oxidation-Reduction; D010802:Phylogeny; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D009573:Nitrites; D009589:Nitrogen Oxides