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 FNRlike 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 NsrRbinding 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.

Microbial Sensor Systems for Dihydrogen, Nitric Oxide, and Carbon Monoxide

“…NsrR, another primary NO sensor, is encoded in the genomes of many proteobacteria, bacilli, and some actinobacteria [35]. Responsiveness of NsrR-controlled genes towards NO was verified experimentally in E. coli, two Neisseria species, and Bacillus subtilis [42].…”

“…Genes for NorR orthologs are present in the genomes of several denitrifying and nondenitrifying b-and c-proteobacteria [35]. The protein has been studied on the biochemical and the physiological level in R. eutropha and the ammonifier E. coli.…”

“…Flavorubredoxins are soluble NO reductases widely distributed among proteobacteria and Firmicutes that are unrelated to respiratory NO reductases, but are of similar physiological importance for detoxification of NO [36]. In other bacteria, predicted targets of norR include genes for flavohemoglobin and hybrid cluster protein [35], both of which have been implicated in defense against NO. It is interesting to note that NorR and all of its target genes are usually located in direct vicinity.…”

“…For example, each of them may control expression of genes for flavohemoglobin, flavorubredoxin, and hybrid cluster protein Hcp in different species. Nevertheless NorR and NsrR may fulfill different physiological roles, because several b-and c-proteobacterial genomes contain genes for both of them [35].…”

“…Based on the sequence of the recognition helix in the DNA-binding domain, NO-sensing CAP domain proteins fall into at least three different subgroups termed DNR, NnrR, and HcpR [35]. While DNR proteins are found in b-and c-proteobacteria, NnrR proteins can be attributed to a-proteobacteria.…”