Dissimilatory metabolism of nitrogen oxides in bacteria: Comparative reconstruction of transcriptional networks

Dmitry A. Rodionov, Inna L. Dubchak, Adam P. Arkin, Eric J. Alm, Mikhail S. Gelfand

Research output: Contribution to journalArticlepeer-review

170 Citations (Scopus)

Abstract

Bacterial response to nitric oxide (NiO) is of major importance since MO is an obligatory intermediate of the nitrogen cycie, Transcriptiona! reguSation of the dissimuatory nitric osddes metabolism in bacteria is diverse and involves F&SR[ike transcription factors HcpR, D&8R, and NnrR; two-component systems MarXL and torQP; MQ~responsive activator fcSorR,- and nitrite-sensitive represser MsrR. Using comparative genomics approaches, we predict DMA-binding motifs for these transcriptions! factors and describe corresponding regisSons in available bacteriaf genomes. Within the FNR family of regulators, we observed a correlation of two specificity-determining amino acids and contacting bases in corresponding DNiA recognition motif. Highay conserved reguaors HcpR for the hybrid cluster protean arsd some other redox enzymes is present in diverse anaerobic bacteria, anciyding Gostridaa, ihermotogafes, and defta-proteobacteria. NnrR and DHK corstro! dersatrafacatior in aipha- and beta-proteobacteria, respectively. Sigma-S4-deperdent MorR regyion foynd in some gamma- and beta-proteobacteria contains various enzymes involved in the ?>JO detoxification. Repressor NisrR, which was previoissiy known to contra! oniy nitrate redyctase operon in Nitrosomonas spp., appears to be the master regulator of the nitric oxides' metaboiism, rsot only irs most gamma- arsd beta-proteobacteria (irtcluding wel!-stydied species such as Escherichia colt}, but aiso in Gram-positive BadSlus and Sfreptomyces species. Positional analysis and comparison of reguiaiory regions of MO detoxification genes allows us to propose the candidate fJsrRbinding motif. The most conserved member of the predicted NlsrR regyion is the hiO-detoxifying faavohemogiobin Hmp. in enterobacteria, the reguion aiso includes two nitrite-responsive ioci, nip AB (hcp-hcr) and nipC (dnrN), thus confirming the identity of the effector, i.e. nitrite. The proposed terR regulons in Neissertei and some other species are extended to include denitdfkation genes. As the result, we demonstrate considerabie interconnection between various rfitrogera-oxides-resporssive reguiatory systems for the denitrification and MO detosssfscatiors genes and evolutionary plasticity of this transcriptions! network. Copyright:

Original languageEnglish
Pages (from-to)415-431
Number of pages17
JournalPLoS Computational Biology
Volume1
Issue number5
DOIs
Publication statusPublished - 2005
Externally publishedYes

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