[Show abstract][Hide abstract] ABSTRACT: Many denitrifying organisms contain the norEF gene cluster which codes for two proteins that are thought to be involved in denitrification because they are expressed during the reduction of nitrite and nitric oxide. The products of both genes are predicted to be membrane associated and the norE product is a member of the cytochrome c oxidase subunit III family. The specific role of norEF is unknown, however. The denitrification phenotypes of Rhodobacter sphaeroides strains with and without norEF genes were studied, and it was found that loss of norEF slowed the rate of denitrification from nitrate and resulted in accumulation of micromolar concentrations of nitric oxide during denitrification from nitrite. norEF appears to have no direct role in the reduction of nitric oxide, however, since deletion of norEF in wild type 2.4.3 had essentially no influence on the kinetics of potential nitric oxide reduction (Vmax and Ks) as measured by monitoring the depletion of a bolus of nitric oxide injected to anoxic cultures without any other electron acceptors. However, norEF deficient cells that had undergone a more chronic exposure to micromolar concentrations of nitric oxide showed a ∼50 % reduction in Vmax but no change in apparent Ks. These results can explain the occurrence of norEF in the 2.4.3 strain of R. sphaeroides, which can reduce nitrate to nitrous oxide, and their absence in strains such as 2.4.1 which likely use nitric oxide reductase to mitigate stress due to episodic exposure to nitric oxide from exogenous sources.
Journal of bacteriology 04/2014; · 2.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We used metatranscriptomics to study the gene transcription patterns of microbial plankton (0.2 - 64 μm) at a mesohaline station in Chesapeake Bay under transitions from oxic to anoxic waters in spring, and anoxic to oxic waters in autumn. Samples were collected from surface [i.e. above pycnocline] waters (3m) and waters beneath the pycnocline (16 - 22 m) in both 2010 and 2011. Metatranscriptome profiles based on function and potential phylogeny were different between 2010 and 2011, and strongly variable in 2011. This difference in variability corresponded with a highly variable ratio of eukaryotic to bacterial sequences (0.3 - 5.5), reflecting transient algal blooms in 2011 that were absent in 2010. The similarity between metatranscriptomes changed at a lower rate during the transition from oxic to anoxic waters than after the return to oxic conditions. Transcripts related to photosynthesis and low-affinity cytochrome oxidases were significantly higher in shallow than in deep waters, while in deep water genes involved in anaerobic metabolism, particularly sulfate reduction, succinyl to propionyl CoA conversion, and menaquinone synthesis were enriched relative to shallow waters. Expected transitions in metabolism between oxic and anoxic deep waters were reflected in elevated anaerobic respiratory reductases and utilization of propenediol and acetoin. The percentage of archaeal transcripts increased in both years in late summer (0.1 - 4.4 % of all transcripts in 2010 and from 0.1 to 6.2 % in 2011). Denitrification-related genes were expressed in a predicted pattern during the oxic-anoxic transition. Overall, our data suggest that Chesapeake Bay microbial assemblages express gene suites differently in shallow and deep waters, and that differences in deep waters reflect variable redox states.
Applied and Environmental Microbiology 10/2013; · 3.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Reactive nitrogen species (RNS), in particular nitric oxide (NO), are toxic to bacteria, and bacteria have mechanisms to allow growth despite this stress. Understanding how bacteria interact with NO is essential to understanding bacterial physiology in many habitats, including pathogenesis; however, many targets of NO and enzymes involved in NO resistance remain uncharacterized. We performed for the first time a metabolomic screen on NO-treated and -untreated bacteria to broadly define the effects of NO on bacterial physiology, as well as to identify the function of NnrS, a previously uncharacterized enzyme involved in defense against NO. We found many known and novel targets of NO. We also found that iron-sulfur cluster enzymes were preferentially inhibited in a strain lacking NnrS due to the formation of iron-NO complexes. We then demonstrate that NnrS is particularly important for resistance to nitrosative stress under anaerobic conditions. Our data thus reveal the breadth of the toxic effects of NO on metabolism and identify the function of an important enzyme for alleviating this stress.
Journal of bacteriology 08/2013; · 2.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Thauera species are members of the betaproteobacteria and are most noted for their ability to metabolize aromatic compounds under anoxic conditions. Here, we announce the draft genome sequences of five Thauera strains in an effort to provide further genetic information as a resource for understanding the ecological function of this environmentally important genus.
[Show abstract][Hide abstract] ABSTRACT: The metabolically versatile purple bacterium Rhodobacter sphaeroides 2.4.3 is a denitrifier whose genome contains two periplasmic nitrate reductase-encoding gene clusters. This work demonstrates nonredundant physiological roles for these two enzymes. One cluster is expressed aerobically and repressed under low oxygen while the second is maximally expressed under low oxygen. Insertional inactivation of the aerobically expressed nitrate reductase eliminated aerobic nitrate reduction, but cells of this strain could still respire nitrate anaerobically. In contrast, when the anaerobic nitrate reductase was absent, aerobic nitrate reduction was detectable, but anaerobic nitrate reduction was impaired. The aerobic nitrate reductase was expressed but not utilized in liquid culture but was utilized during growth on solid medium. Growth on a variety of carbon sources, with the exception of malate, the most oxidized substrate used, resulted in nitrite production on solid medium. This is consistent with a role for the aerobic nitrate reductase in redox homeostasis. These results show that one of the nitrate reductases is specific for respiration and denitrification while the other likely plays a role in redox homeostasis during aerobic growth.
Journal of bacteriology 09/2011; 193(23):6483-9. · 2.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Denitrification is generally considered to occur under micro-oxic or anoxic conditions. With this in mind, the physiological function and regulation of several steps in the denitrification of model α-proteobacteria are compared in the present review. Expression of the periplasmic nitrate reductase is quite variable, with this enzyme being maximally expressed under oxic conditions in some bacteria, but under micro-oxic conditions in others. Expression of nitrite and NO reductases in most denitrifiers is more tightly controlled, with expression only occurring under micro-oxic conditions. A possible exception to this may be Roseobacter denitrificans, but the physiological role of these enzymes under oxic conditions is uncertain.
Biochemical Society Transactions 01/2011; 39(1):179-83. · 2.59 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: R. sphaeroides strain 2.4.3, when lacking the cbb(3) oxidase, is unable to transition from aerobic respiration to denitrification using cellular respiration as a means of reducing oxygen levels. This is due to an inability to express nirK, the gene encoding nitrite reductase. Under certain photosynthetic conditions this strain can transition from aerobic to nitrate respiration, demonstrating that nirK expression can occur in the absence of a functional cbb(3) oxidase. If oxygen levels are reduced under non-photosynthetic conditions using low-oxygen gas mixes, nitrite reductase activity is detected at wild-type levels in the strain lacking the oxidase. In addition, co-culture experiments show that incubation of the cbb(3) deficient strain 2.4.3 with R. sphaeroides 2.4.1, which is nirK deficient but has the high-affinity cbb(3) oxidase, restores denitrification in sealed-vessel experiments. Taken together these results indicate that high end-point O(2) levels are the reason why the strain lacking the cbb(3) oxidase cannot transition from aerobic respiration to denitrification under certain conditions. The protein probably being affected by these O(2) levels is the transcriptional regulator NnrR.
[Show abstract][Hide abstract] ABSTRACT: Analysis of the Rhodobacter sphaeroides 2.4.3 genome revealed four previously unidentified sequences similar to the binding site of the transcriptional regulator NnrR. Expression studies demonstrated that three of these sequences are within the promoters of genes, designated paz, norEF, and cdgA, in the NnrR regulon, while the status of the fourth sequence, within the tat operon promoter, remains uncertain. nnrV, under control of a previously identified NnrR site, was also identified. paz encodes a pseudoazurin that is a donor of electrons to nitrite reductase. paz inactivation did not decrease nitrite reductase activity, but loss of pseudoazurin and cytochrome c(2) together reduced nitrite reduction. Inactivation of norEF reduced nitrite and nitric oxide reductase activity and increased the sensitivity to nitrite in a taxis assay. This suggests that loss of norEF increases NO production as a result of decreased nitric oxide reductase activity. 2.4.3 is the only strain of R. sphaeroides with norEF, even though all four of the strains whose genomes have been sequenced have the norCBQD operon and nnrR. norEF was shown to provide resistance to nitrite when it was mobilized into R. sphaeroides strain 2.4.1 containing nirK. Inactivation of the other identified genes did not reveal any detectable denitrification-related phenotype. The distribution of members of the NnrR regulon in R. sphaeroides revealed patterns of coselection of structural genes with the ancillary genes identified here. The strong coselection of these genes indicates their functional importance under real-world conditions, even though inactivation of the majority of them does not impact denitrification under laboratory conditions.
Journal of bacteriology 12/2009; 192(4):903-11. · 2.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Cytochrome c' is a heme protein from a denitrifying variant of Rhodobacter sphaeroides which may serve to store and transport metabolic NO while protecting against NO toxicity. Its heme site bears resemblance through its 5-coordinate NO-binding capability to the regulatory site in soluble guanylate cyclase. A conserved arginine (Arg-127) abuts the 5-coordinate NO-heme binding site, and the alanine mutant R127A provided insight into the role of the Arg-127 in establishing the electronic structure of the heme-NO complex and in modifying the heme-centered redox potential and NO-binding affinity. By comparison to R127A, the wild-type Arg-127 was determined to increase the heme redox potential, diminish the NO-binding affinity, perturb and diminish the 14NO hyperfine coupling determined by ENDOR (electron nuclear double resonance), and increase the maximal electronic g-value. The larger isotropic NO hyperfine and the smaller maximal g-value of the R127A mutant together predicted that the Fe-N-O bond angle in the mutant is larger than that of the Arg-127-containing wild-type protein. Deuterium ENDOR provided evidence for exchangeable H/D consistent with hydrogen bonding of Arg-127, but not Ala-127, to the O of the NO. Proton ENDOR features previously assigned to Phe-14 on the distal side of the heme were unperturbed by the proximal side R127A mutation, implying the localized nature of that mutational perturbation at the proximal, NO-binding side of the heme. From this work two functions of positively charged Arg-127 emerged: the first was to maintain the KD of the cytochrome c' in the 1 microM range, and the second was to provide a redox potential that enhances the stability of the ferrous heme.
[Show abstract][Hide abstract] ABSTRACT: The ability of Agrobacetrium tumefaciens to perform balanced transitions from aerobic to anaerobic respiration was studied by monitoring oxygen depletion, transcription of nirK and norB, and the concentrations of nitrite, nitric oxide (NO) and nitrous oxide in stirred batch cultures with different initial oxygen, nitrate or nitrite concentrations. Nitrate concentrations (0.2-2 mM) did not affect oxygen depletion, nor the oxygen concentration at which denitrification was initiated (1-2 microM). Nitrite (0.2-2 mM), on the other hand, retarded the oxygen depletion as it reached approximately 20 microM, and caused initiation of active denitrification as oxygen concentrations reached 10-17 microM. Unbalanced transitions occurred in treatments with high cell densities (i.e. with rapid transition from oxic to anoxic conditions), seen as NO accumulation to muM concentrations and impeded nitrous oxide production. This phenomenon was most severe in nitrite treatments, and reduced the cells' ability to respire oxygen during subsequent oxic conditions. Transcripts of norB were only detectable during the period with active denitrification. In contrast, nirK transcripts were detected at low levels both before and after this period. The results demonstrate that the transition from aerobic to anaerobic metabolism is a regulatory challenge, with implications for survival and emission of trace gases from denitrifying bacteria.
[Show abstract][Hide abstract] ABSTRACT: Agrobacterium tumefaciens can grow anaerobically via denitrification. To learn more about how cells regulate production of nitrite and nitric oxide, experiments were carried out to identify proteins involved in regulating expression and activity of nitrite and nitric oxide reductase. Transcription of NnrR, required for expression of these two reductases, was found to be under control of FnrN. Insertional inactivation of the response regulator actR significantly reduced nirK expression and Nir activity but not nnrR expression. Purified ActR bound to the nirK promoter but not the nor or nnrR promoter. A putative ActR binding site was identified in the nirK promoter region using mutational analysis and an in vitro binding assay. A nirK promoter containing mutations preventing the binding of ActR showed delayed expression but eventually reached about 65% of the activity of an equivalent wild-type promoter lacZ fusion. Truncation of the nirK promoter revealed that truncation up to and within the ActR binding site reduced expression, but fragments lacking the ActR binding site and retaining the NnrR binding site showed expression as high as or higher than the full-length fragment. Additional experiments revealed that expression of paz, encoding the copper protein pseudoazurin, was highly reduced in the actR or fnrN mutants and that ActR binds to the paz promoter. Inactivation of paz reduced Nir activity by 55%. These results help explain why Nir activity is very low in the actR mutant even though a nirK promoter with mutations in the ActR binding site showed significant expression.
Journal of bacteriology 02/2008; 190(1):78-86. · 2.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Nitrate reduction can be either a dissimilatory or assimilatory process. Nitrate reduction to nitrogen gas via a series of
nitrogen oxide intermediates is a dissimilatory process termed denitrification. Denitrification is common among the purple
photosynthetic bacteria. While some reduce nitrate to nitrogen gas many are missing components of the denitrification pathway.
In the complete denitrifiers, denitrification can be used as an alternative form of respiration when oxygen levels are low.
Denitrification can also be used as a mechanism to dispose of excess reducing equivalents. In partial denitrifiers, it is
unlikely that denitrification serves a respiratory function. In these bacteria it is likely that the enzymes that are present
are used for redox balancing, or to mitigate the toxicity of certain nitrogen oxide intermediates.
Available genome sequences demonstrate that closely related bacteria can have different denitrification capacities. For example,
analysis of three strains of Rhodobacter sphaeroides revealed that one is a complete denitrifier, while one of the other strains has two of the four nitrogen oxide reductases
enzymes, and the other strain has only one. This suggests that denitrification is selectively modified to best fit each bacterium’s
environmental niche and the entire pathway does not have to be present for dissimilatory nitrogen oxide reduction to be beneficial.
Optimal expression of the nitrogen oxide reductases requires the presence of nitrogen oxides and low oxygen. Nitrate along
with nitric oxide and nitrous oxide, two of the denitrification intermediates, are effector molecules. Denitrification has
also been shown to be under control of the global Reg/Prr regulatory system. This may coordinate expression of denitrification
with other energy conservation and redox dissipation processes.
Some photosynthetic bacteria can also reduce nitrate to ammonia, which is then used for assimilatory purposes. As with denitrification,
the capacity for nitrate assimilation does not follow any obvious phylogenetic pattern. The genes for nitrate assimilation
are expressed when ammonia and other forms of fixed nitrogen are limiting and nitrate is available.
[Show abstract][Hide abstract] ABSTRACT: Rhizobium sullae strain HCNT1 contains a nitric oxide-producing nitrite reductase of unknown function due to the absence of a complementary nitric oxide reductase. HCNT1 had the ability to grow on selenite concentrations as high as 50 mM, and during growth, selenite was reduced to the less toxic elemental selenium. An HCNT1 mutant lacking nitrite reductase grew poorly in the presence of 5 mM selenite, was unable to grow in the presence of 25 or 50 mM selenite and also showed no evidence of selenite reduction. A naturally occurring nitrite reductase-deficient R. sullae strain, CC1335, also showed little growth on the higher concentrations of selenite. Mobilization of a plasmid containing the HCNT1 gene encoding nitrite reductase into CC1335 increased its resistance to selenite. To confirm that this ability to grow in the presence of high concentrations of selenite correlated with nitrite reductase activity, a new nitrite reductase-containing strain was isolated from the same location where HCNT1 was isolated. This strain was also resistant to high concentrations of selenite. Inactivation of the gene encoding nitrite reductase in this strain increased selenite sensitivity. These data suggest that the nitrite reductase of R. sullae provides resistance to selenite and offers an explanation for the radically truncated denitrification found uniquely in this bacterium.
[Show abstract][Hide abstract] ABSTRACT: With limited reductant and nitrite under anaerobic conditions, copper-containing nitrite reductase (NiR) of Rhodobacter sphaeroides yielded endogenous NO and the Cu(I)NO derivative of NiR. (14)N- and (15)N-nitrite substrates gave rise to characteristic (14)NO and (15)NO EPR hyperfine features indicating NO involvement, and enrichment of NiR with (63)Cu isotope caused an EPR line shape change showing copper involvement. A markedly similar Cu(I)NONiR complex was made by anaerobically adding a little endogenous NO gas to reduced protein and immediately freezing. The Cu(I)NONiR signal accounted for 60-90% of the integrated EPR intensity formerly associated with the Type 2 catalytic copper. Analysis of NO and Cu hyperfine couplings and comparison to couplings of inorganic Cu(I)NO model systems indicated approximately 50% spin on the N of NO and approximately 17% spin on Cu. ENDOR revealed weak nitrogen hyperfine coupling to one or more likely histidine ligands of copper. Although previous crystallography of the conservative I289V mutant had shown no structural change beyond the 289 position, this mutation, which eliminates the Cdelta1 methyl of I289, caused the Cu(I)NONiR EPR spectrum to change and proton ENDOR features to be significantly altered. The proton hyperfine coupling that was significantly altered was consistent with a dipolar interaction between the Cdelta1 protons of I289 and electron spin on the NO, where the NO would be located 3.0-3.7 A from these protons. Such a distance positions the NO of Cu(I)NO as an axial ligand to Type 2 Cu(I).
Journal of the American Chemical Society 11/2006; 128(40):13102-11. · 11.44 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The role of cytochrome c(2), encoded by cycA, and cytochrome c(Y), encoded by cycY, in electron transfer to the nitrite reductase of Rhodobacter sphaeroides 2.4.3 was investigated using both in vivo and in vitro approaches. Both cycA and cycY were isolated, sequenced and insertionally inactivated in strain 2.4.3. Deletion of either gene alone had no apparent effect on the ability of R. sphaeroides to reduce nitrite. In a cycA-cycY double mutant, nitrite reduction was largely inhibited. However, the expression of the nitrite reductase gene nirK from a heterologous promoter substantially restored nitrite reductase activity in the double mutant. Using purified protein, a turnover number of 5 s(-1) was observed for the oxidation of cytochrome c(2) by nitrite reductase. In contrast, oxidation of c(Y) only resulted in a turnover of approximately 0.1 s(-1). The turnover experiments indicate that c(2) is a major electron donor to nitrite reductase but c(Y) is probably not. Taken together, these results suggest that there is likely an unidentified electron donor, in addition to c(2), that transfers electrons to nitrite reductase, and that the decreased nitrite reductase activity observed in the cycA-cycY double mutant probably results from a change in nirK expression.
[Show abstract][Hide abstract] ABSTRACT: The five-coordinate NO-bound heme in cytochrome c' from an overexpressing variant of denitrifying R. sphaeroides 2.4.3 was investigated by proton, nitrogen, and deuterium Q-band ENDOR (electron nuclear double resonance). ENDOR was a direct probe of the unpaired electron density on the nitrogen of NO and, as measured across the EPR line shape, showed a hyperfine coupling range from 36 to 44 MHz for 14NO and 51 to 63 MHz for 15NO. The smallest NO coupling occurred at an electronic g-tensor axis perpendicular to the FeNO plane, and the largest hyperfine coupling occurred in the FeNO plane where the highest nitrogen valence spin density is located. The isotropic component of the NO hyperfine coupling indicated that the electron spin on the NO is not simply in a pi orbital having only 2p character but is in an orbital having 2s and 2p character in a 1:2 ratio. ENDOR frequencies from heme meso-protons, assigned with reference to porphyrin models, were determined to result from an anisotropic hyperfine tensor. This tensor indicated the orientation of the heme with respect to the FeNO plane and showed that the FeNO plane bisects the heme N-Fe-N 90 degrees angle. ENDOR provided additional structural information through dipolar couplings, as follows: (1) to the nearest proton of the Phe14 ring, approximately 3.1 A away from the heme iron, where Phe14 is positioned to occlude binding of NO as a 6th (distal) ligand; (2) to exchangeable deuterons assigned to Arg127 which may H-bond with the proximal NO ligand.
Journal of the American Chemical Society 05/2006; 128(15):5021-32. · 11.44 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A series of experiments was undertaken to learn more about the impact on other bacteria of nitric oxide (NO) produced during denitrification. The denitrifier Rhodobacter sphaeroides 2.4.3 was chosen as a denitrifier for these experiments. To learn more about NO production by this bacterium, NO levels during denitrification were measured by using differential mass spectrometry. This revealed that NO levels produced during nitrate respiration by this bacterium were in the low muM range. This concentration of NO is higher than that previously measured in denitrifiers, including Achromobacter cycloclastes and Paracoccus denitrificans. Therefore, both 2.4.3 and A. cycloclastes were used in this work to compare the effects of various NO levels on nondenitrifying bacteria. By use of bacterial overlays, it was found that the NO generated by A. cycloclastes and 2.4.3 cells during denitrification inhibited the growth of both Bacillus subtilis and R. sphaeroides 2.4.1 but that R. sphaeroides 2.4.3 caused larger zones of inhibition in the overlays than A. cycloclastes. Both R. sphaeroides 2.4.3 and A. cycloclastes induced the expression of the NO stress response gene hmp in B. subtilis. Taken together, these results indicate that there is variability in the NO concentrations produced by denitrifiers, but, irrespective of the NO levels produced, microbes in the surrounding environment were responsive to the NO produced during denitrification.
Applied and Environmental Microbiology 04/2006; 72(3):2200-5. · 3.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Most denitrifying bacteria reduce nitrate to the inert gases nitrous oxide or nitrogen. A remarkable exception to this is Rhizobium sullae strain HCNT1, which catalyses only a single step in the denitrification pathway, the reduction of nitrite to the reactive molecule nitric oxide. Further study demonstrated that HCNT1 does not encode the genes for NO reductase. Prolonged incubation of HCNT1 under anoxic conditions revealed that the cells had reduced culturability but not viability when nitrite was present. This may indicate an adaptation to anoxic conditions to provide resistance to environmental stresses. A closely related strain of R. sullae, strain CC1335, which is unable to denitrify, was found to lose culturability but not viability irrespective of the presence of nitrite. When the gene for nitrite reductase was mobilized into CC1335, this increased culturability with or without nitrite. These results indicate that the presence of nitrite reductase can influence the long-term survival of R. sullae strains and may provide an explanation as to why HCNT1 possesses this unusual truncation of its denitrification electron transport chain.
Biochemical Society Transactions 03/2006; 34(Pt 1):130-2. · 3.24 Impact Factor