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1.
Nat Commun ; 15(1): 1911, 2024 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-38429292

RESUMO

When the supply of inorganic carbon is limiting, photosynthetic cyanobacteria excrete nitrite, a toxic intermediate in the ammonia assimilation pathway from nitrate. It has been hypothesized that the excreted nitrite represents excess nitrogen that cannot be further assimilated due to the missing carbon, but the underlying molecular mechanisms are unclear. Here, we identified a protein that interacts with nitrite reductase, regulates nitrogen metabolism and promotes nitrite excretion. The protein, which we named NirP1, is encoded by an unannotated gene that is upregulated under low carbon conditions and controlled by transcription factor NtcA, a central regulator of nitrogen homeostasis. Ectopic overexpression of nirP1 in Synechocystis sp. PCC 6803 resulted in a chlorotic phenotype, delayed growth, severe changes in amino acid pools, and nitrite excretion. Coimmunoprecipitation experiments indicated that NirP1 interacts with nitrite reductase, a central enzyme in the assimilation of ammonia from nitrate/nitrite. Our results reveal that NirP1 is widely conserved in cyanobacteria and plays a crucial role in the coordination of C/N primary metabolism by targeting nitrite reductase.


Assuntos
Nitritos , Synechocystis , Nitritos/metabolismo , Nitratos/metabolismo , Nitrito Redutases/genética , Nitrito Redutases/metabolismo , Amônia/metabolismo , Proteínas de Bactérias/metabolismo , Regulação Bacteriana da Expressão Gênica , Synechocystis/genética , Synechocystis/metabolismo , Nitrogênio/metabolismo , Carbono/metabolismo , Nitrato Redutase/genética , Nitrato Redutase/metabolismo
2.
mSystems ; 9(3): e0096723, 2024 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-38323850

RESUMO

The biological route of nitrate reduction has important implications for the bioavailability of nitrogen within ecosystems. Nitrate reduction via nitrite, either to ammonium (ammonification) or to nitrous oxide or dinitrogen (denitrification), determines whether nitrogen is retained within the system or lost as a gas. The acidophilic sulfate-reducing bacterium (aSRB) Acididesulfobacillus acetoxydans can perform dissimilatory nitrate reduction to ammonium (DNRA). While encoding a Nar-type nitrate reductase, A. acetoxydans lacks recognized nitrite reductase genes. In this study, A. acetoxydans was cultivated under conditions conducive to DNRA. During cultivations, we monitored the production of potential nitrogen intermediates (nitrate, nitrite, nitric oxide, hydroxylamine, and ammonium). Resting cell experiments were performed with nitrate, nitrite, and hydroxylamine to confirm their reduction to ammonium, and formed intermediates were tracked. To identify the enzymes involved in DNRA, comparative transcriptomics and proteomics were performed with A. acetoxydans growing under nitrate- and sulfate-reducing conditions. Nitrite is likely reduced to ammonia by the previously undescribed nitrite reductase activity of the NADH-linked sulfite reductase AsrABC, or by a putatively ferredoxin-dependent homolog of the nitrite reductase NirA (DEACI_1836), or both. We identified enzymes and intermediates not previously associated with DNRA and nitrosative stress in aSRB. This increases our knowledge about the metabolism of this type of bacteria and helps the interpretation of (meta)genome data from various ecosystems on their DNRA potential and the nitrogen cycle.IMPORTANCENitrogen is crucial to any ecosystem, and its bioavailability depends on microbial nitrogen-transforming reactions. Over the recent years, various new nitrogen-transforming reactions and pathways have been identified, expanding our view on the nitrogen cycle and metabolic versatility. In this study, we elucidate a novel mechanism employed by Acididesulfobacillus acetoxydans, an acidophilic sulfate-reducing bacterium, to reduce nitrate to ammonium. This finding underscores the diverse physiological nature of dissimilatory reduction to ammonium (DNRA). A. acetoxydans was isolated from acid mine drainage, an extremely acidic environment where nitrogen metabolism is poorly studied. Our findings will contribute to understanding DNRA potential and variations in extremely acidic environments.


Assuntos
Compostos de Amônio , Nitratos , Nitratos/metabolismo , Compostos de Amônio/metabolismo , Nitritos/metabolismo , Ecossistema , Desnitrificação , Bactérias/metabolismo , Hidroxilamina , Nitrito Redutases/metabolismo , Nitrogênio , Hidroxilaminas , Sulfatos
3.
J Hazard Mater ; 465: 133365, 2024 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-38163407

RESUMO

The molecular mechanisms underlying high and low cadmium (Cd) accumulation in hot pepper cultivars remain unclear. In this study, comparative transcriptome analysis of root between high-Cd (J) and low-Cd (Z) cultivars was conducted under hydroponic cultivation with 0 and 0.4 mg/L Cd, respectively. The results showed that J enhanced the root uptake of Cd by elevating the expression of Nramp5 and counteracting Cd toxicity by increasing the expression of genes, such as NIR1, GLN1, and IAA9. Z reduced Cd accumulation by enhancing the cell wall lignin synthesis genes PAL, COMT, 4CL, LAC, and POD and the Cd transporters ABC, MTP1, and DTX1. Elevated expression of genes related to sulfur metabolism was observed in Z, potentially contributing to its ability to detoxify Cd. To investigate the function of CaCOMT1, an Arabidopsis thaliana overexpression line (OE-CaCOMT1) was constructed. The results revealed that OE-CaCOMT1 drastically increased the lignin content by 38-42% and reduced the translocation of Cd to the aboveground parts by 32%. This study provides comprehensive insights into the mechanisms underlying Cd accumulation in hot pepper cultivars using transcriptome analysis. Moreover, this study elucidates the critical function of CaCOMT1, providing a theoretical foundation for the production of low-Cd vegetables for food safety.


Assuntos
Proteínas de Arabidopsis , Arabidopsis , Capsicum , Poluentes do Solo , Cádmio/metabolismo , Capsicum/genética , Capsicum/metabolismo , Arabidopsis/metabolismo , Lignina/metabolismo , Raízes de Plantas/metabolismo , Perfilação da Expressão Gênica , Poluentes do Solo/metabolismo , Nitrito Redutases/metabolismo , Proteínas de Arabidopsis/genética
4.
Sci Total Environ ; 918: 170273, 2024 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-38280590

RESUMO

The increased use of disinfection since the pandemic has led to increased effective chlorine concentration in municipal wastewater. Whereas, the specific impacts of active chlorine on nitrogen and phosphorus removal, the mediating communities, and the related metabolic activities in wastewater treatment plants (WWTPs) lack systematic investigation. We systematically analyzed the influences of chlorine disinfection on nitrogen and phosphorus removal activities using activated sludge from five full-scale WWTPs. Results showed that at an active chlorine concentration of 1.0 mg/g-SS, the nitrogen and phosphorus removal systems were not significantly affected. Major effects were observed at 5.0 mg/g-SS, where the nitrogen and phosphorus removal efficiency decreased by 38.9 % and 44.1 %, respectively. At an active chlorine concentration of 10.0 mg/g-SS, the nitrification, denitrification, phosphorus release and uptake activities decreased by 15.1 %, 69.5-95.9 %, 49.6 % and 100 %, respectively. The proportion of dead cells increased by 6.1 folds. Reverse transcriptional quantitative polymerase chain reaction (RT-qPCR) analysis showed remarkable inhibitions on transcriptions of the nitrite oxidoreductase gene (nxrB), the nitrite reductase genes (nirS and nirK), and the nitrite reductase genes (narG). The nitrogen and phosphorus removal activities completely disappeared with an active chlorine concentration of 25.0 mg/g-SS. Results also showed distinct sensitivities of different functional bacteria in the activated sludge. Even different species within the same functional group differ in their susceptibility. This study provides a reference for the understanding of the threshold active chlorine concentration values which may potentially affect biological nitrogen and phosphorus removal in full-scale WWTPs, which are expected to be beneficial for decision-making in WWTPs to counteract the potential impacts of increased active chlorine concentrations in the influent wastewater.


Assuntos
Águas Residuárias , Purificação da Água , Esgotos/microbiologia , Cloro , Nitrogênio/metabolismo , Fósforo/metabolismo , Desinfecção , Nitrificação , Nitrito Redutases/metabolismo , Desnitrificação , Reatores Biológicos , Eliminação de Resíduos Líquidos/métodos
5.
J Am Heart Assoc ; 13(2): e031085, 2024 Jan 16.
Artigo em Inglês | MEDLINE | ID: mdl-38214271

RESUMO

BACKGROUND: Skeletal muscles are postulated to be a potent regulator of systemic nitric oxide homeostasis. In this study, we aimed to evaluate the impact of physical training on the heart and skeletal muscle nitric oxide bioavailability (judged on the basis of intramuscular nitrite and nitrate) in rats. METHODS AND RESULTS: Rats were trained on a treadmill for 8 weeks, performing mainly endurance running sessions with some sprinting runs. Muscle nitrite (NO2-) and nitrate (NO3-) concentrations were measured using a high-performance liquid chromatography-based method, while amino acids, pyruvate, lactate, and reduced and oxidized glutathione were determined using a liquid chromatography coupled with tandem mass spectrometry technique. The content of muscle nitrite reductases (electron transport chain proteins, myoglobin, and xanthine oxidase) was assessed by western immunoblotting. We found that 8 weeks of endurance training decreased basal NO2- in the locomotory muscles and in the heart, without changes in the basal NO3-. In the slow-twitch oxidative soleus muscle, the decrease in NO2- was already present after the first week of training, and the content of nitrite reductases remained unchanged throughout the entire period of training, except for the electron transport chain protein content, which increased no sooner than after 8 weeks of training. CONCLUSIONS: Muscle NO2- level, opposed to NO3-, decreases in the time course of training. This effect is rapid and already visible in the slow-oxidative soleus after the first week of training. The underlying mechanisms of training-induced muscle NO2- decrease may involve an increase in the oxidative stress, as well as metabolite changes related to an increased muscle anaerobic glycolytic activity contributing to (1) direct chemical reduction of NO2- or (2) activation of muscle nitrite reductases.


Assuntos
Nitratos , Condicionamento Físico Animal , Ratos , Animais , Nitratos/metabolismo , Nitritos , Óxido Nítrico/metabolismo , Dióxido de Nitrogênio/metabolismo , Músculo Esquelético/metabolismo , Exercício Físico , Nitrito Redutases/metabolismo
6.
Nucleic Acids Res ; 52(1): 186-203, 2024 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-38000372

RESUMO

The ubiquitous bacterial second messenger cyclic diguanylate (c-di-GMP) coordinates diverse cellular processes through its downstream receptors. However, whether c-di-GMP participates in regulating nitrate assimilation is unclear. Here, we found that NasT, an antiterminator involved in nitrate assimilation in Pseudomonas putida, specifically bound c-di-GMP. NasT was essential for expressing the nirBD operon encoding nitrite reductase during nitrate assimilation. High-level c-di-GMP inhibited the binding of NasT to the leading RNA of nirBD operon (NalA), thus attenuating the antitermination function of NasT, resulting in decreased nirBD expression and nitrite reductase activity, which in turn led to increased nitrite accumulation in cells and its export. Molecular docking and point mutation assays revealed five residues in NasT (R70, Q72, D123, K127 and R140) involved in c-di-GMP-binding, of which R140 was essential for both c-di-GMP-binding and NalA-binding. Three diguanylate cyclases (c-di-GMP synthetases) were found to interact with NasT and inhibited nirBD expression, including WspR, PP_2557, and PP_4405. Besides, the c-di-GMP-binding ability of NasT was conserved in the other three representative Pseudomonas species, including P. aeruginosa, P. fluorescens and P. syringae. Our findings provide new insights into nitrate assimilation regulation by revealing the mechanism by which c-di-GMP inhibits nitrate assimilation via NasT.


Assuntos
Proteínas de Bactérias , GMP Cíclico , Nitratos , Pseudomonas putida , Proteínas de Bactérias/metabolismo , GMP Cíclico/metabolismo , Regulação Bacteriana da Expressão Gênica , Simulação de Acoplamento Molecular , Nitratos/metabolismo , Nitrito Redutases/genética , Nitrito Redutases/metabolismo , Pseudomonas aeruginosa/genética , Pseudomonas putida/genética , Pseudomonas putida/metabolismo
7.
Nat Commun ; 14(1): 8249, 2023 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-38086813

RESUMO

Nitrate ammonification is important for soil nitrogen retention. However, the ecology of ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screen 1 million genomes for nrfA and onr, encoding ammonifier nitrite reductases. About 40% of ammonifier assemblies carry at least one denitrification gene and show higher potential for nitrous oxide production than consumption. We then use a phylogeny-based approach to recruit gene fragments of nrfA, onr and denitrification nitrite reductase genes (nirK, nirS) in 1861 global terrestrial metagenomes. nrfA outnumbers the nearly negligible onr counts in all biomes, but denitrification genes dominate, except in tundra. Random forest modelling teases apart the influence of the soil C/N on nrfA-ammonifier vs denitrifier abundance, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and identifies factors ultimately controlling the fate of soil nitrate.


Assuntos
Bactérias , Nitratos , Nitratos/farmacologia , Bactérias/genética , Nitrito Redutases/genética , Nitrito Redutases/farmacologia , Solo , Ecossistema , Nitrogênio/farmacologia , Desnitrificação , Microbiologia do Solo
8.
Environ Sci Pollut Res Int ; 30(55): 117637-117653, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-37870669

RESUMO

The possibility of using the non-nitrogen-fixing cyanobacterium (Chroococcus sp.) for the reduction of soil nitrate contamination was tested through Petri dish experiments. The application of 0.03, 0.05 and 0.08 mg/cm2 Chroococcus sp. efficiently removed NO3--N from the soil through assimilation of nitrate nutrient and promotion of soil denitrification. At the optimal application dose of 0.05 mg/cm2, 44.06%, 36.89% and 36.17% of NO3--N were removed at initial NO3--N concentrations of 60, 90 and 120 mg/kg, respectively. The polysaccharides released by Chroococcus sp. acted as carbon sources for bacterial denitrification and facilitated the reduction of soil salinity, which significantly (p < 0.05) stimulated the growth of denitrifying bacteria (Hyphomicrobium denitrificans and Hyphomicrobium sp.) as well as significantly (p < 0.05) elevated the activities of nitrate reductase and nitrite reductase by 1.07-1.23 and 1.15-1.22 times, respectively. The application of Chroococcus sp. promoted the dominance of Nocardioides maradonensis in soil microbial community, which resulted in elevated phosphatase activity and increased available phosphorus content. The application of Chroococcus sp. positively regulated the growth of soil bacteria belonging to the genera Chitinophaga, Prevotella and Tumebacillus, which may contribute to increased soil fertility through the production of beneficial enzymes such as invertase, urease and catalase. To date, this is the first study verifying the remediation effect of non-nitrogen-fixing cyanobacteria on nitrate-contaminated soil.


Assuntos
Cianobactérias , Nitratos , Cianobactérias/metabolismo , Nitrato Redutase/metabolismo , Nitrito Redutases/metabolismo , Solo , Desnitrificação
9.
Molecules ; 28(15)2023 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-37570788

RESUMO

Molybdenum-containing enzymes of the xanthine oxidase (XO) family are well known to catalyse oxygen atom transfer reactions, with the great majority of the characterised enzymes catalysing the insertion of an oxygen atom into the substrate. Although some family members are known to catalyse the "reverse" reaction, the capability to abstract an oxygen atom from the substrate molecule is not generally recognised for these enzymes. Hence, it was with surprise and scepticism that the "molybdenum community" noticed the reports on the mammalian XO capability to catalyse the oxygen atom abstraction of nitrite to form nitric oxide (NO). The lack of precedent for a molybdenum- (or tungsten) containing nitrite reductase on the nitrogen biogeochemical cycle contributed also to the scepticism. It took several kinetic, spectroscopic and mechanistic studies on enzymes of the XO family and also of sulfite oxidase and DMSO reductase families to finally have wide recognition of the molybdoenzymes' ability to form NO from nitrite. Herein, integrated in a collection of "personal views" edited by Professor Ralf Mendel, is an overview of my personal journey on the XO and aldehyde oxidase-catalysed nitrite reduction to NO. The main research findings and the path followed to establish XO and AO as competent nitrite reductases are reviewed. The evidence suggesting that these enzymes are probable players of the mammalian NO metabolism is also discussed.


Assuntos
Óxido Nítrico , Nitritos , Animais , Mamíferos/metabolismo , Molibdênio/química , Óxido Nítrico/metabolismo , Nitrito Redutases/química , Nitritos/química , Oxirredução , Oxigênio/metabolismo , Xantina Oxidase/metabolismo
10.
Biomolecules ; 13(8)2023 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-37627281

RESUMO

The copper-containing nitrite reductase from Neisseria gonorrhoeae has been shown to play a critical role in the infection mechanism of this microorganism by producing NO and abolishing epithelial exfoliation. This enzyme is a trimer with a type 1 copper center per subunit and a type 2 copper center in the subunits interface, with the latter being the catalytic site. The two centers were characterized for the first time by EPR and CD spectroscopy, showing that the type 1 copper center has a high rhombicity due to its lower symmetry and more tetragonal structure, while the type 2 copper center has the usual properties, but with a smaller hyperfine coupling constant (A// = 10.5 mT). The thermostability of the enzyme was analyzed by differential scanning calorimetry, which shows a single endothermic transition in the thermogram, with a maximum at 94 °C, while the CD spectra in the visible region indicate the presence of the type 1 copper center up to 80 °C. The reoxidation of the N. gonorrhoeae copper-containing nitrite reductase in the presence of nitrite were analyzed by visible spectroscopy and showed a pH dependence, being higher at pH 5.5-6.0. The high thermostability of this enzyme may be important to maintaining a high activity in the extracellular space and to making it less susceptible to denaturation and proteolysis, contributing to the proliferation of N. gonorrhoeae.


Assuntos
Cobre , Neisseria gonorrhoeae , Nitrito Redutases , Nitritos
11.
FEMS Microbiol Lett ; 3702023 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-37573143

RESUMO

The soybean endosymbiont Bradyrhizobium diazoefficiens harbours the complete denitrification pathway that is catalysed by a periplasmic nitrate reductase (Nap), a copper (Cu)-containing nitrite reductase (NirK), a c-type nitric oxide reductase (cNor), and a nitrous oxide reductase (Nos), encoded by the napEDABC, nirK, norCBQD, and nosRZDFYLX genes, respectively. Induction of denitrification genes requires low oxygen and nitric oxide, both signals integrated into a complex regulatory network comprised by two interconnected cascades, FixLJ-FixK2-NnrR and RegSR-NifA. Copper is a cofactor of NirK and Nos, but it has also a role in denitrification gene expression and protein synthesis. In fact, Cu limitation triggers a substantial down-regulation of nirK, norCBQD, and nosRZDFYLX gene expression under denitrifying conditions. Bradyrhizobium diazoefficiens genome possesses a gene predicted to encode a Cu-responsive repressor of the CsoR family, which is located adjacent to copA, a gene encoding a putative Cu+-ATPase transporter. To investigate the role of CsoR in the control of denitrification gene expression in response to Cu, a csoR deletion mutant was constructed in this work. Mutation of csoR did not affect the capacity of B. diazoefficiens to grow under denitrifying conditions. However, by using qRT-PCR analyses, we showed that nirK and norCBQD expression was much lower in the csoR mutant compared to wild-type levels under Cu-limiting denitrifying conditions. On the contrary, copA expression was significantly increased in the csoR mutant. The results obtained suggest that CsoR acts as a repressor of copA. Under Cu limitation, CsoR has also an indirect role in the expression of nirK and norCBQD genes.


Assuntos
Bradyrhizobium , Cobre , Cobre/metabolismo , Desnitrificação , Nitrito Redutases/genética , Nitrito Redutases/metabolismo , Nitratos/metabolismo , Bradyrhizobium/genética , Bradyrhizobium/metabolismo , Regulação Bacteriana da Expressão Gênica , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo
12.
Dalton Trans ; 52(32): 11254-11264, 2023 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-37526523

RESUMO

Copper nitrite reductase mimetics were synthesized using three new tridentate ligands sharing the same N,N,N motif of coordination. The ligands were based on L-proline modifications, attaching a pyridine and a triazole to the pyrrolidine ring, and differ by a pendant group (R = phenyl, n-butyl and n-propan-1-ol). All complexes coordinate nitrite, as evidenced by cyclic voltammetry, UV-Vis, FTIR and electron paramagnetic resonance (EPR) spectroscopies. The coordination mode of nitrite was assigned by FTIR and EPR as κ2O chelate mode. Upon acidification, EPR experiments indicated a shift from chelate to monodentate κO mode, and 15N NMR experiments of a Zn2+ analogue, suggested that the related Cu(II) nitrous acid complex may be reasonably stable in solution, but in equilibrium with free HONO under non catalytic conditions. Reduction of nitrite to NO was performed both chemically and electrocatalytically, observing the highest catalytic activities for the complex with n-propan-1-ol as pendant group. These results support the hypothesis that a hydrogen bond moiety in the secondary coordination sphere may aid the protonation step.


Assuntos
Cobre , Nitritos , Nitritos/química , Cobre/química , Ligantes , Biomimética , Nitrito Redutases/química , Espectroscopia de Ressonância de Spin Eletrônica , Catálise , Oxirredução , Cristalografia por Raios X
13.
Environ Microbiol ; 25(11): 2338-2350, 2023 11.
Artigo em Inglês | MEDLINE | ID: mdl-37395163

RESUMO

Copper plays a critical role in controlling greenhouse gas emissions as it is a key component of the particulate methane monooxygenase and nitrous oxide reductase. Some methanotrophs excrete methanobactin (MB) that has an extremely high copper affinity. As a result, MB may limit the ability of other microbes to gather copper, thereby decreasing their activity as well as impacting microbial community composition. Here, we show using forest soil microcosms that multiple forms of MB; MB from Methylosinus trichosporium OB3b (MB-OB3b) and MB from Methylocystis sp. strain SB2 (MB-SB2) increased nitrous oxide (N2 O) production as well caused significant shifts in microbial community composition. Such effects, however, were mediated by the amount of copper in the soils, with low-copper soil microcosms showing the strongest response to MB. Furthermore, MB-SB2 had a stronger effect, likely due to its higher affinity for copper. The presence of either form of MB also inhibited nitrite reduction and generally increased the presence of genes encoding for the iron-containing nitrite reductase (nirS) over the copper-dependent nitrite reductase (nirK). These data indicate the methanotrophic-mediated production of MB can significantly impact multiple steps of denitrification, as well as have broad effects on microbial community composition of forest soils.


Assuntos
Methylocystaceae , Methylosinus trichosporium , Cobre , Óxido Nitroso , Methylocystaceae/genética , Methylosinus trichosporium/genética , Nitrito Redutases , Solo
14.
FEMS Microbiol Lett ; 3702023 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-37460131

RESUMO

Dissimilatory nitrate reduction to ammonia (DNRA) is a central pathway in the biogeochemical nitrogen cycle, allowing for the utilization of nitrate or nitrite as terminal electron acceptors. In contrast to the competing denitrification to N2, a major part of the essential nutrient nitrogen in DNRA is retained within the ecosystem and made available as ammonium to serve as a nitrogen source for other organisms. The second step of DNRA is mediated by the pentahaem cytochrome c nitrite reductase NrfA that catalyzes the six-electron reduction of nitrite to ammonium and is widely distributed among bacteria. A recent crystal structure of an NrfA ortholog from Geobacter lovleyi was the first characterized representative of a novel subclass of NrfA enzymes that lacked the canonical Ca2+ ion close to the active site haem 1. Here, we report the structural and functional characterization of NrfA from the closely related G. metallireducens. We established the recombinant production of catalytically active NrfA with its unique, lysine-coordinated active site haem heterologously in Escherichia coli and determined its three-dimensional structure by X-ray crystallography to 1.9 Å resolution. The structure confirmed GmNrfA as a further calcium-independent NrfA protein, and it also shows an altered active site that contained an unprecedented aspartate residue, D80, close to the substrate-binding site. This residue formed part of a loop that also caused a changed arrangement of the conserved substrate/product channel relative to other NrfA proteins and rendered the protein insensitive to the inhibitor sulphate. To elucidate the relevance of D80, we produced and studied the variants D80A and D80N that showed significantly reduced catalytic activity.


Assuntos
Compostos de Amônio , Nitritos , Nitritos/metabolismo , Nitratos/metabolismo , Domínio Catalítico , Ecossistema , Compostos de Amônio/metabolismo , Amônia , Escherichia coli/genética , Escherichia coli/metabolismo , Heme , Nitrogênio , Nitrito Redutases/genética , Nitrito Redutases/metabolismo
15.
Appl Environ Microbiol ; 89(8): e0080023, 2023 08 30.
Artigo em Inglês | MEDLINE | ID: mdl-37470485

RESUMO

Bacteria specialized in anaerobic ammonium oxidation (anammox) are widespread in many anoxic habitats and form an important functional guild in the global nitrogen cycle by consuming bio-available nitrogen for energy rather than biomass production. Due to their slow growth rates, cultivation-independent approaches have been used to decipher their diversity across environments. However, their full diversity has not been well recognized. Here, we report a new family of putative anammox bacteria, "Candidatus Subterrananammoxibiaceae," existing in the globally distributed terrestrial and marine subsurface (groundwater and sediments of estuary, deep-sea, and hadal trenches). We recovered a high-quality metagenome-assembled genome of this family, tentatively named "Candidatus Subterrananammoxibius californiae," from a California groundwater site. The "Ca. Subterrananammoxibius californiae" genome not only contains genes for all essential components of anammox metabolism (e.g., hydrazine synthase, hydrazine oxidoreductase, nitrite reductase, and nitrite oxidoreductase) but also has the capacity for urea hydrolysis. In an Arctic ridge sediment core where redox zonation is well resolved, "Ca. Subterrananammoxibiaceae" is confined within the nitrate-ammonium transition zone where the anammox rate maximum occurs, providing environmental proof of the anammox activity of this new family. Phylogenetic analysis of nitrite oxidoreductase suggests that a horizontal transfer facilitated the spreading of the nitrite oxidation capacity between anammox bacteria (in the Planctomycetota phylum) and nitrite-oxidizing bacteria from Nitrospirota and Nitrospinota. By recognizing this new anammox family, we propose that all lineages within the "Ca. Brocadiales" order have anammox capacity. IMPORTANCE Microorganisms called anammox bacteria are efficient in removing bioavailable nitrogen from many natural and human-made environments. They exist in almost every anoxic habitat where both ammonium and nitrate/nitrite are present. However, only a few anammox bacteria have been cultured in laboratory settings, and their full phylogenetic diversity has not been recognized. Here, we present a new bacterial family whose members are present across both the terrestrial and marine subsurface. By reconstructing a high-quality genome from the groundwater environment, we demonstrate that this family has all critical enzymes of anammox metabolism and, notably, also urea utilization. This bacterium family in marine sediments is also preferably present in the niche where the anammox process occurs. These findings suggest that this novel family, named "Candidatus Subterrananammoxibiaceae," is an overlooked group of anammox bacteria, which should have impacts on nitrogen cycling in a range of environments.


Assuntos
Compostos de Amônio , Nitritos , Humanos , Nitritos/metabolismo , Nitratos/metabolismo , Oxidação Anaeróbia da Amônia , Filogenia , Sedimentos Geológicos/microbiologia , Bactérias , Compostos de Amônio/metabolismo , Oxirredutases/metabolismo , Nitrito Redutases/genética , Oxirredução , Nitrogênio/metabolismo , Anaerobiose , RNA Ribossômico 16S/genética
16.
FEMS Microbiol Lett ; 3702023 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-37422443

RESUMO

As the association of denitrification with global warming and nitrogen removal from ecosystems has gained attention in recent decades, numerous studies have examined denitrification rates and the distribution of denitrifiers across different environments. In this minireview, reported studies focused on coastal saline environments, including estuaries, mangroves, and hypersaline ecosystems, have been analysed to identify the relationship between denitrification and saline gradients. The analyses of the literature and databases stated the direct effect of salinity on the distribution patterns of denitrifiers. However, few works do not support this hypothesis thus making this topic controversial. The specific mechanisms by which salinity influences denitrifier distribution are not fully understood. Nevertheless, several physical and chemical environmental parameters, in addition to salinity, have been shown to play a role in structuring the denitrifying microbial communities. The prevalence of nirS or nirK denitrifiers in ecosystems is a subject of debate in this work. In general terms, in mesohaline environments, the predominant nitrite reductase is NirS type and, NirK is found predominantly in hypersaline environments. Moreover, the approaches used by different researchers are quite different, resulting in a huge amount of unrelated information, making it difficult to establish comparative analysis. The main techniques used to analyse the distribution of denitrifying populations along salt gradients have been also discussed.


Assuntos
Desnitrificação , Microbiota , Sedimentos Geológicos , Estuários , Nitrito Redutases
17.
J Am Chem Soc ; 145(30): 16718-16725, 2023 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-37478476

RESUMO

l-Alanosine is a diazeniumdiolate (N-nitrosohydroxylamine) antibiotic that inhibits MTAP-deficient tumor cells by blocking de novo adenine biosynthesis. Previous work revealed the early steps in the biosynthesis of l-alanosine. In the present study, we used genome mining to discover two new l-alanosine-producing strains that lack the aspartate-nitrosuccinate pathway genes found in the original l-alanosine producer. Instead, nitrate is reduced with a unique set of nitrate-nitrite reductases. These enzymes are typically used as part of the nitrogen cycle for denitrification or assimilation, and our report here shows how enzymes from the nitrogen cycle can be repurposed for the biosynthesis of specialized metabolites. The widespread distribution of nitric-oxide-producing reductases also indicates a potential for the discovery of new nitric-oxide-derived natural products.


Assuntos
Nitratos , Óxido Nítrico , Oxirredutases/genética , Nitrito Redutases , Nitrato Redutases
18.
Chemosphere ; 335: 139080, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37263510

RESUMO

Important functions of constructed wetland related to biogeochemical processes are mediated by soil microbes and low-temperature damage is the main limiting factor for microbes in winter. However, the response thresholds for active microbial community and enzyme activities to continuous decreases in temperature remain unclear. In this study, total 90 soil samples were collected every week over a 6-week period to track the dynamics of four enzymes involved in cycles of C, N, P and active bacterial community as field soil temperature decreased continuously from 6.62 °C to 0.55 °C. Enzyme activity changed suddenly when the temperature decreased to 4.83 °C, the nitrite reductase activity reduced by 36.2%, while alkaline phosphatase activity is increased by 396%. The cellulase and urease were only marginally influenced by cold stress. Decreased nitrite reductase activities corresponded with loss of nir-type denitrifiers important for nitrite reduction. For cold stress, N-related bacteria were sensitive species. Whereas increased alkaline phosphatase activity may be due to the fact that P-related bacteria were opportunistic species. Key functional taxa connected with degradation of cellulose promoted species coexistence and microbial network stability. The lower and upper temperature thresholds for community change were 4.85 °C and 6.30 °C, respectively. Collectively, these results revealed that microbial taxa involved in C, N and P cycling respond differently to continuous decreases in temperature and higher than 4.85 °C is an ideal environment to prevent loss of microbial diversity and functions in winter, providing a scientific reference for the targeted isolation and cultivation of key microbial taxa in rhizosphere soil and adjusting temperature range to improve the purification capacity of wetlands during low temperature periods.


Assuntos
Microbiota , Áreas Alagadas , Temperatura , Fosfatase Alcalina/metabolismo , Bactérias/metabolismo , Solo/química , Nitrito Redutases/metabolismo , Microbiologia do Solo
19.
Int J Mol Sci ; 24(7)2023 Mar 31.
Artigo em Inglês | MEDLINE | ID: mdl-37047528

RESUMO

Nitrobindins (Nbs) are all-ß-barrel heme proteins spanning from bacteria to Homo sapiens. They inactivate reactive nitrogen species by sequestering NO, converting NO to HNO2, and promoting peroxynitrite isomerization to NO3-. Here, the nitrite reductase activity of Nb(II) from Mycobacterium tuberculosis (Mt-Nb(II)), Arabidopsis thaliana (At-Nb(II)), Danio rerio (Dr-Nb(II)), and Homo sapiens (Hs-Nb(II)) is reported. This activity is crucial for the in vivo production of NO, and thus for the regulation of blood pressure, being of the utmost importance for the blood supply to poorly oxygenated tissues, such as the eye retina. At pH 7.3 and 20.0 °C, the values of the second-order rate constants (i.e., kon) for the reduction of NO2- to NO and the concomitant formation of nitrosylated Mt-Nb(II), At-Nb(II), Dr-Nb(II), and Hs-Nb(II) (Nb(II)-NO) were 7.6 M-1 s-1, 9.3 M-1 s-1, 1.4 × 101 M-1 s-1, and 5.8 M-1 s-1, respectively. The values of kon increased linearly with decreasing pH, thus indicating that the NO2--based conversion of Nb(II) to Nb(II)-NO requires the involvement of one proton. These results represent the first evidence for the NO2 reductase activity of Nbs(II), strongly supporting the view that Nbs are involved in NO metabolism. Interestingly, the nitrite reductase reactivity of all-ß-barrel Nbs and of all-α-helical globins (e.g., myoglobin) was very similar despite the very different three-dimensional fold; however, differences between all-α-helical globins and all-ß-barrel Nbs suggest that nitrite reductase activity appears to be controlled by distal steric barriers, even though a more complex regulatory mechanism can be also envisaged.


Assuntos
Arabidopsis , Dióxido de Nitrogênio , Humanos , Heme/metabolismo , Globinas/metabolismo , Nitrito Redutases/metabolismo , Mioglobina/metabolismo , Arabidopsis/metabolismo , Oxirredução , Cinética , Nitritos/metabolismo
20.
BMC Genomics ; 24(1): 104, 2023 Mar 09.
Artigo em Inglês | MEDLINE | ID: mdl-36894890

RESUMO

Lelliottia amnigena PTJIIT1005 is a bacterium that utilizes nitrate as the sole nitrogen source and can remediate nitrate from media. The annotation was done related to nitrogen metabolic genes using the PATRIC, RAST tools, and PGAP from the genome sequence of this bacterium. Multiple sequence alignments and phylogenetic analysis of respiratory nitrate reductase, assimilatory nitrate reductase, nitrite reductase, glutamine synthetase, hydroxylamine reductase, nitric oxide reductase genes from PTJIIT1005 were done to find out sequence identities with the most similar species. The identification of operon arrangement in bacteria was also identified. The PATRIC KEGG feature mapped the N-metabolic pathway to identify the chemical process, and the 3D structure of representative enzymes was also elucidated. The putative protein 3D structure was analyzed using I-TASSER software. It gave good quality protein models of all nitrogen metabolism genes and showed good sequence identity with reference templates, approximately 81-99%, except for two genes; assimilatory nitrate reductase and nitrite reductase. This study suggested that PTJIIT1005 can remove N-nitrate from water because of having N-assimilation and denitrification genes.


Assuntos
Nitratos , Nitrogênio , Nitratos/metabolismo , Nitrogênio/metabolismo , Filogenia , Nitrato Redutase/genética , Nitrato Redutase/metabolismo , Nitrito Redutases/genética , Nitrito Redutases/metabolismo , Bactérias/metabolismo
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