Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium

Abstract

Sulfate-reducing bacteria (SRB) are sensitive to low concentrations of nitrite, and nitrite has been used to control SRB-related biofouling in oil fields. Desulfovibrio vulgaris Hildenborough, a model SRB, carries a cytochrome c-type nitrite reductase (nrfHA) that confers resistance to low concentrations of nitrite. The regulation of this nitrite reductase has not been directly examined to date. In this study, we show that DVU0621 (NrfR), a sigma54-dependent two-component system response regulator, is the positive regulator for this operon. NrfR activates the expression of the nrfHA operon in response to nitrite stress. We also show that nrfR is needed for fitness at low cell densities in the presence of nitrite because inactivation of nrfR affects the rate of nitrite reduction. We also predict and validate the binding sites for NrfR upstream of the nrfHA operon using purified NrfR in gel shift assays. We discuss possible roles for NrfR in regulating nitrate reductase genes in nitrate-utilizing Desulfovibrio spp. IMPORTANCEThe NrfA nitrite reductase is prevalent across several bacterial phyla and required for dissimilatory nitrite reduction. However, regulation of the nrfA gene has been studied in only a few nitrate-utilizing bacteria. Here, we show that in D. vulgaris, a bacterium that does not respire nitrate, the expression of nrfHA is induced by NrfR upon nitrite stress. This is the first report of regulation of nrfA by a sigma54-dependent two-component system. Our study increases our knowledge of nitrite stress responses and possibly of the regulation of nitrate reduction in SRB. Sulfate-reducing bacteria (SRB) are important members of syntrophic anaerobic microbial communities. While SRB are useful in remediation of contaminated groundwater by reduction of toxic heavy metals (1), they are also a major problem in offshore oil industries, where they cause biofouling due to corrosive sulfide production (2). Additions of nitrate and nitrite have been used to control SRB growth and the resulting biofouling sulfide (3, 4). Nitrite is more effective for inhibition of SRB than nitrate (3), and most SRB are sensitive to low concentrations of nitrite (5, 6). Nitrite is toxic because it inhibits sulfite reduction by competing for the sulfite reductase enzyme (7,8). Also, the reaction of nitrite with sulfide to form polysulfide results in the release of reactive nitrogen species (9).The sensitivity to nitrite varies among SRB. Some SRB, such as Desulfovibrio alaskensis G20, lack any means for reducing the nitrite and are highly sensitive to small amounts of nitrite (10, 11). However, other SRB can reduce nitrite via a cytochrome c-type nitrite reductase, NrfA, and are able to tolerate low millimolar amounts of nitrite (7, 12). NrfA-carrying SRB also can utilize nitrite as the sole terminal electron acceptor (TEA), provided the nitrite is at subinhibitory concentrations (12-14). Some nitritereducing SRB also have the ability to utilize nitrate as the TEA via dissimilatory nitrate/nitrite reduction (15).NrfA is ...

The Porphyromonas gingivalis Hybrid Cluster Protein Hcp Is Required for Growth with Nitrite and Survival with Host Cells

“…The nrfAH nitrite reductase system has been shown to be upregulated in response to low or intermediate levels of nitrite in an anaerobic environment in E. coli and Desulfovibrio spp. (20,25). However, in our RNA-seq studies we did not see any change in the P. gingivalis homologues of nrfAH (PG1820 and PG1821) in response to nitrite.…”

“…This is a large periplasmic complex that utilizes nitrite as an electron sink, reducing it to ammonia to create a membrane potential (20)(21)(22). The nrf operon has been shown to play a role in protection against nitrosative stress in other Gramnegative anaerobic and microaerophilic bacteria (23)(24)(25). However, its function and role in nitrosative stress defense in P. gingivalis have not been investigated.…”

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

“…The genomes of L. pratensis DSM100886 (subdivision 6), G. fermentans DSM14018 (subdivision 8) and H. foetida TMBS4 (subdivision 8) harboured genes encoding for a dissimilatory nitrite reductase (nrfHA) that catalyses the reduction of nitrite to ammonia, in contrast to NirK or NirS that catalyse the conversion of nitrite to nitric oxide. This respiratory nitrite ammonification is not only described to contribute to energy conservation but also plays a major role in detoxification as it mediates the nitrosative stress response caused, e.g., by the presence of nitric oxide, nitrite or hydroxylamine (e.g., Zumft, 1997;Kern et al, 2011;Rajeev et al, 2015). Homologues for norBC (also termed cNOR) and norZ (also termed qNOR) were detected in the putative nitrate/nitrite-reducing strains (L. pratensis DSM100886, G. fermentans DSM14018, H. foetida TMBS4 and T. aquaticum MP-01), but also in subdivisions 1 and 3 strains that did not harbour any dissimilatory nitrate/nitrite reductases (Supporting Information Table S6).…”

A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport

“…D. vulgaris was grown at 32 °C in 15 ml centrifuge tubes in an anaerobic chamber (Coy Laboratories, Grasslake, MI) in an atmosphere of 85% N 2 /10% CO 2 /5% H 2 . WT and GZ0407 (Tn5::DVU3193) were grown from freezer stocks in 10 ml LS4D (Rajeev et al ., ) supplemented with 0.1% yeast extract overnight. For the mutant, G418 (400 μg/ml) was added to the medium throughout the experiment.…”