Characterization of a member of the NnrR regulon in Rhodobacter sphaeroides 2.4.3 encoding a haem–copper protein The GenBank accession number for nnrS is U62403.

Bartnikas, Thomas B.; Wang, Yousheng; Bobo, Tanya; Veselov, A.V.; Scholes, Charles P.; Shapleigh, James P.

doi:10.1099/00221287-148-3-825

Cited by 41 publications

(43 citation statements)

References 38 publications

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“…The conserved NnrR recognition motif with consensus ctTTGcgnnnncgCAAag was identified upstream of most denitrification genes (Table S3). The same candidate NnrR sites have been previously identified in R. sphaeroides by a comparison of the nir, nor, and nnrS upstream regions and then confirmed for the latter gene by site-directed mutagenesis [36].…”

Section: Dnr and Nnrr Core Regulonsmentioning

confidence: 82%

“…Importantly, both these candidate sites are highly conserved in multiple alignments of dnrN and hmp upstream regions from related enterobacteria ( Figures S2 and S3). Search in the S. oneidensis genome identified the same DNA motif upstream of hcp-hcr, SO4302 (dnrN), and SO2805 (nnrS), the latter encoding a hypothetical heme-copper-containing membrane protein [36]. The hmp gene is absent in this genome ( Figure 6).…”

Section: Nsrr: Recognition Motifs and Core Regulonmentioning

confidence: 99%

“…The only exception seems to be R. capsulatus E1F1, whose genome contains an nsrR ortholog close to the hcp gene within the nitrate assimilation nas gene cluster [17]. However, in denitrifying species, including R. sphaeroides and B. japonicum, the FNR-like transcriptional factor NnrR activates expression of nitrite and NO reductases and of the nnrS gene [36][37][38]. Orthologs of nnrR were identified in six a-proteobacteria, all of which also possess the nir and nor genes involved in denitrification ( Figure 5).…”

Section: Dnr and Nnrr Core Regulonsmentioning

confidence: 99%

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Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks

Rodionov¹,

Dubchak²,

Arkin³

et al. 2005

PLoS Comp Biol

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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.

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Section: Dnr and Nnrr Core Regulonsmentioning

confidence: 82%

Section: Nsrr: Recognition Motifs and Core Regulonmentioning

confidence: 99%

Section: Dnr and Nnrr Core Regulonsmentioning

confidence: 99%

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Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks

Rodionov¹,

Dubchak²,

Arkin³

et al. 2005

PLoS Comp Biol

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“…R. sphaeroides 2.4.3 and 2.4.1 are the wild-type denitrifying and partially denitrifying strains, respectively. R213 and R125 are FnrL-and NnrR-deficient strains of 2.4.3, respectively (5,38). PC12 is a Cyt cЈ-deficient mutant of 2.4.3.…”

Section: Methodsmentioning

confidence: 99%

Regulation and Function of Cytochrome c ′ in Rhodobacter sphaeroides 2.4.3

et al. 2005

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“…Moreover, sequence analysis of the nirK, norC, and nosR promoters reveals that each contains a putative NnrA binding site. Indeed, since NnrA is homologous to NnrR of R. sphaeroides, it is expected to recognize similar sites on DNA close to the TTGCG(N) 4 CACAA sequence found upstream of nnrS in R. sphaeroides (2). Similar sites are found in B. melitensis promoters nirK (AGGCGTGAA CACAA, at 198 nucleotides [nt] upstream of ATG), norC (TTGCCTATTCGCAA, at 129 nt upstream of ATG), and nosR (TTGCGTCATAT CAA, at 221 nt upstream of ATG) but not in the narK promoter, which also suggests that NnrA modulates transcription from the nirK, norC, and nosR promoters in B. melitensis.…”

mentioning

confidence: 99%

NnrA Is Required for Full Virulence and Regulates Several Brucella melitensis Denitrification Genes

et al. 2006

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We identified two regulators of denitrification genes in Brucella melitensis 16M: NarR, which regulates the nitrate reductase (nar) operon, and NnrA, which is involved in the expression of the last three reductases of the denitrification pathway (nirK, norB, and nosZ). NnrA is required for virulence in mice and for intracellular resistance to nitric oxide.Brucella species are facultative intracellular pathogens that infect animals and occasionally humans (10). Recently, analysis of the complete Brucella melitensis sequence suggested the presence of an anaerobic electron transfer system and the enzymes allowing the reduction of nitrate into dinitrogen gas (nitrate, nitrite, NO [1] and nitrous oxide reductases) (3). These reactions are collectively named denitrification (17) and could allow Brucella to grow under low-oxygen conditions by respiration of nitrate (11).Since the replicative compartment of Brucella suis is characterized by low oxygen tension, it was postulated that, during the infectious process, Brucella could use denitrification to survive using nitrogen oxides as terminal electron acceptors (6). Another potential role of this system is limiting the production of reactive nitrogen intermediates by the host during infection. Indeed, Brucella abortus was shown to counteract the effect of NO after 24 h of infection in activated macrophages (14).When analyzing the B. melitensis genome, we observed that three predicted coding sequences for Crp/Fnr regulators (narR, nnrA, and nnrB) are located near the genes putatively involved in denitrification (Fig. 1). NarR belongs to the NarR subfamily of the Dnr cluster, while NnrA and NnrB belong to the NnrR cluster, according to the Korner classification (7). Three other Crp/ Fnr genes are predicted from the genomic sequence (5); two of them belong to the A cluster while the last belongs to the FnrN family (7). The B. melitensis genome contains the narKGHJI, nirKV, norEFCBQD, and nosRZDFYSLX gene clusters that are coding for a respiratory membrane-bound nitrate reductase (Nar, with the nitrite extrusion protein NarK), a copper nitrite reductase (Nir), a NO reductase (Nor), and a nitrous oxide reductase (Nos), respectively. The narR gene is found next to genes encoding the nitrate reductase, nnrA is next to genes encoding the nitrite and NO reductases, and nnrB is located downstream of genes encoding the nitrous oxide reductase. Furthermore, the regulators encoded by narR, nnrA, and nnrB genes are homologous to regulators involved in denitrification in other bacteria. Indeed, NarR from B. melitensis is homologous to the Paracoccus pantotrophus NarR, a regulator of the nitrate reductase genes (16). NnrB and NnrA belong to the NnrR family, comprising the NnrR regulator from Rhodobacter sphaeroides 2.4.3, which controls the expression of the nitrite and NO reductases (12).As a starting hypothesis, we postulated that the genomic colocalization between the denitrification genes and narR, nnrA, and nnrB could indicate that these Crp/Fnr regulators are involved in the tran...

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Characterization of a member of the NnrR regulon in Rhodobacter sphaeroides 2.4.3 encoding a haem–copper protein The GenBank accession number for nnrS is U62403.

Cited by 41 publications

References 38 publications

Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks

Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks

Regulation and Function of Cytochrome c ′ in Rhodobacter sphaeroides 2.4.3

NnrA Is Required for Full Virulence and Regulates Several Brucella melitensis Denitrification Genes

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