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PMID: 16261196 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks.

PLoS computational biology ·Vol. 1 ·No. 5 ·2005-10-00 ·Pages e55

Rodionov DA, Dubchak IL, Arkin AP, Alm EJ, Gelfand MS

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.

MeSH Terms
Amino Acid Motifs Bacteria/metabolism Bacterial Proteins/chemistry Computational Biology/methods Escherichia coli/metabolism Escherichia coli Proteins/metabolism Gene Expression Regulation, Bacterial Genomics/methods Models, Biological Multigene Family Nitrites Nitrogen Oxides/chemistry Oxidation-Reduction Phylogeny Transcription, Genetic
Chemicals
Bacterial Proteins Escherichia coli Proteins Nitrites Nitrogen Oxides
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Rodionov Dmitry A
Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia. [email protected]
Dubchak Inna L
Arkin Adam P
Alm Eric J
Gelfand Mikhail S
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Article Info
Journal
PLoS computational biology
Abbr.
PLoS Comput Biol
ISSN
1553-7358
DOI
10.1371/journal.pcbi.0010055
Email
[email protected]
Published
2005-10-00
Epub
2005-00-28
Pages
e55
Language
English
Region
United States
NLM ID
101238922
PMCID
PMC1274295
Subset
IM
External Links
PubMed source DOI: 10.1371/journal.pcbi.0010055 PMC Full Text View journal details
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