The enzymes of oxalate metabolism: unexpected structures and mechanisms

Role of oxalic acid in fungal and bacterial metabolism and its biotechnological potential

Oxalic acid and oxalates are secondary metabolites secreted to the surrounding environment by fungi, bacteria, and plants. Oxalates are linked to a variety of processes in soil, e.g. nutrient availability, weathering of minerals, or precipitation of metal oxalates. Oxalates are also mentioned among low-molecular weight compounds involved indirectly in the degradation of the lignocellulose complex by fungi, which are considered to be the most effective degraders of wood. The active regulation of the oxalic acid concentration is linked with enzymatic activities; hence, the biochemistry of microbial biosynthesis and degradation of oxalic acid has also been presented. The potential of microorganisms for oxalotrophy and the ability of microbial enzymes to degrade oxalates are important factors that can be used in the prevention of kidney stone, as a diagnostic tool for determination of oxalic acid content, as an antifungal factor against plant pathogenic fungi, or even in efforts to improve the quality of edible plants. The potential role of fungi and their interaction with bacteria in the oxalate-carbonate pathway are regarded as an effective way for the transfer of atmospheric carbon dioxide into calcium carbonate as a carbon reservoir.

Zn2+ regulates human oxalate metabolism by manipulating oxalate decarboxylase to treat calcium oxalate stones

A high concentration of oxalate is associated with an increased risk of kidney calcium oxalate (CaOx) stones, and the degradation of exogenous oxalate mostly depends on oxalate-degrading enzymes from the intestinal microbiome. We found that zinc gluconate supplement to patients with CaOx kidney stones could significantly improve the abundance of oxalate metabolizing bacteria in humans through clinical experiments on patients also subjected to antibiotic treatment. The analysis of clinical samples revealed that an imbalance of Lactobacillus and oxalate decarboxylase (OxDC) was involved in the formation of CaOx kidney stones. Then, we identified that Zn²⁺ could be used as an external factor to improve the activity of OxDC and promote Lactobacillus in the intestinal flora, and this treatment achieved a therapeutic effect on rats with stones aggravated by antibiotics. Finally, by analyzing the three-dimensional structure of OxDC and completing in vitro experiments, we propose a model of the Zn²⁺-induced reduction of CaOx kidney stone symptoms in rats by increasing the metabolism of oxalate through the positive effects of Zn²⁺ on Lactobacillus and OxDC.

Molecular characterization and in silico analysis of oxalate decarboxylase of Pseudomonas sp. OXDC12

Oxalate decarboxylase (OxDC) is a Mn-dependent hexameric enzyme that is highly important in management of calcium oxalate mediated nephrolithiasis. The present study reported the production and purification of OxDC from Pseudomonas sp. OXDC12 up to 45.3-fold with an overall yield of 7%. The purified OxDC displayed a single band of approximately 40 kDa on SDS-PAGE and 240 kDa on Native-PAGE suggesting it to be a hexameric enzyme. The purified OxDC displayed an optimum activity at 26 °C and pH 4.5 in the presence of substrate sodium oxalate (30 mg/mL) with a K_m and V_max value of 43.9 mM and 8.9 µmol/min, respectively and an activation energy of 52.49 kJ/mol. The enzyme activity was significantly enhanced by adding o-phenylenediamine to the reaction mixture. OxDC exhibited a very low 17 haemolytic activity which suggested a relatively safer therapeutic aspect of the tested OxDC. The structure prediction studies of the OxDC revealed a tertiary structure with α/β chains that formed the β barrel structure, typical of all cupin domains. The Ramachandran plot produced by PROCHECK shows that 90.5% of the residues are in the most favoured region and hence the OxDC model produced was a good one. Docking studies revealed the binding of the metal ions and ligands to cluster of three histidine residues in the N terminal domain that formed the active site pocket of the enzyme. It was suggested that the histidine coordinated Mn2+ ion was critical for substrate recognition and binding and was also directly involved in OxDC catalyses.highlightsOxalate decarboxylase (OxDC) was successfully purified from Pseudomonas sp. OXDC12 up-to 45.3-fold.The K_m and V_max values of the purified OxDC were calculated as 43.9 mM and 8.9 µmol/min, respectively.Genre analysis and structure prediction studies revealed the presence of β barrel structure typical of all cupin domains. The model exhibited a bi-cupin domain that forms the dimer of the homo-hexameric OxDC.Docking experiments revealed that the cluster of three HIS residues in the N terminal domain of the tested enzyme formed the active site pocket for binding of Mn as well as the ligands.Communicated by Ramaswamy H. Sarma.

Oxalic acid degradation in wood-rotting fungi. Searching for a new source of oxalate oxidase

Oxalate oxidase (EC 1.2.3.4) is an oxalate-decomposing enzyme predominantly found in plants but also described in basidiomycete fungi. In this study, we investigated 23 fungi to determine their capability of oxalic acid degradation. After analyzing their secretomes for the products of the oxalic acid-degrading enzyme activity, three groups were distinguished among the fungi studied. The first group comprised nine fungi classified as oxalate oxidase producers, as their secretome pattern revealed an increase in the hydrogen peroxide concentration, no formic acid, and a reduction in the oxalic acid content. The second group of fungi comprised eight fungi described as oxalate decarboxylase producers characterized by an increase in the formic acid level associated with a decrease in the oxalate content in their secretomes. In the secretomes of the third group of six fungi, no increase in formic acid or hydrogen peroxide contents was observed but a decline in the oxalate level was found. The intracellular activity of OXO in the mycelia of Schizophyllum commune, Trametes hirsuta, Gloeophyllum trabeum, Abortiporus biennis, Cerrena unicolor, Ceriosporopsis mediosetigera, Trametes sanguinea, Ceriporiopsis subvermispora, and Laetiporus sulphureus was confirmed by a spectrophotometric assay.

A conserved oxalyl-coenzyme A decarboxylase in oxalate catabolism

The ability to biosynthesize oxalic acid can provide beneficial functions to plants; however, uncontrolled or prolonged exposure to this strong organic acid results in multiple physiological problems. Such problems include a disruption of membrane integrity, mitochondrial function, metal chelation, and free radical formation. Recent work suggests that a CoA-dependent pathway of oxalate catabolism plays a critical role in regulating tissue oxalate concentrations in plants. Although this CoA-dependent pathway of oxalate catabolism is important, large gaps in our knowledge of the enzymes catalyzing each step remain. Evidence that an oxalyl-CoA decarboxylase (OXC) catalyzes the second step in this pathway, accelerating the conversion of oxalyl-CoA to formyl-CoA, has been reported. Induction studies revealed that OXC gene expression was upregulated in response to an exogenous oxalate supply. Phylogenetic analysis indicates that OXCs are conserved across plant species. Evolutionarily the plant OXCs can be separated into dicot and monocot classes. Multiple sequence alignments and molecular modeling suggest that OXCs have similar functionality with three conserved domains, the N-terminal PYR domain, the middle R domain, and the C-terminal PP domain. Further study of this CoA-dependent pathway of oxalate degradation would benefit efforts to develop new strategies to improve the nutrition quality of crops.

Tomato Oxalyl-CoA Synthetase Degrades Oxalate and Affects Fruit Quality

Acyl activating enzyme 3 (AAE3) encodes oxalyl-CoA synthetase involved in oxalate degradation. In this study, we investigated the role of AAE3 (SlAAE3) in the fruit quality of tomato (Solanum lycopersicum). The purified recombinant SlAAE3 protein from Escherichia coli exhibited a high activity toward oxalate, with a K _m of 223.8 ± 20.03 μm and V _max of 7.908 ± 0.606 μmol mg^-1 protein min^-1. Transient expression of SlAAE3-green fluorescent protein (GFP) fusion proteins suggests that SlAAE3 is a soluble protein without specific subcellular localization. The expression of SlAAE3 is both tissue- and development-dependent, and increased during fruit ripping. The Slaae3 knockout mutants had improved fruit quality as evidenced by the increased sugar-acid ratio and mineral nutrient content. To find the mechanism by which SlAAE3 affects fruit quality, transcriptome, and metabolome were employed on SlAAE3 over-expressed line and wide type fruits. The transcriptomic and metabolic profiles indicated that SlAAE3 in fruits mainly functions at 20 days post-anthesis (20 DPA) and mature green (MG) stages, resulting in up-regulation of amino acid derivatives, nucleotides, and derivatives, but down-regulation of lipid compounds. However, differentially expressed genes (DEGs) were mainly enriched at redox pathways. Taken together, both in vivo and in vitro results suggest that SlAAE3-encoded protein acts as an oxalyl-CoA synthetase, which also participates in redox metabolism. These data provide a further understanding of the mechanism by which SlAAE3 participates in tomato fruit quality.

High and low oxalate content in spinach: an investigation of accumulation patterns

BACKGROUND

Oxalic acid is a common antinutrient in the human diet, found in large quantities in spinach. However, spinach is highly regarded by vegetable producers because of its nutritional content and economic value. One of the primary purposes of spinach-breeding programs is to improve the nutritional value of spinach by adjusting oxalate accumulation. Knowledge of the biosynthetic patterns of oxalic acid, and its different forms, is important for a better understanding of this process.

RESULTS

We found three biosynthetic patterns of accumulation and concentration of oxalates. Two of them are related to the maximum type and one is related to the minimum type. We also developed a general model of variations in these compounds in the genotypes that were studied.

CONCLUSION

This study introduced a unique type of spinach with high oxalate accumulation, which could be particularly suitable for consumption. This had the highest ratio of insoluble oxalate to soluble oxalate. It also accumulated more ascorbic acid (AA) than other types. Our findings in this study also indicate a small role for AA as a precursor to oxalate production in spinach, possibly confirming the significant role of glyoxylate as the most critical precursor in this plant. © 2021 Society of Chemical Industry.

The identification and characterization of an oxalyl-CoA synthetase from grass pea (Lathyrus sativus L.)

Oxalic acid is a small metabolite that can be found in many plants in which it serves as protection from herbivores, a chelator of metal ions, a regulator of calcium...

Thermally stable manganese(III) peroxido complexes with hindered N3 tripodal ligands: Structures and their physicochemical properties

Mononuclear manganese(III) peroxido complexes are candidates for the reaction intermediates in manganese containing proteins, such as manganese superoxide dismutase (Mn-SOD) etc. In this study, manganese(III) peroxido complexes [Mn(O₂)(L3)] and [Mn(O₂)(L10)] ligated by anionic N3 type ligands with sterically hindered substituents, hydrotris(3-tertiary butyl-5-isopropyl-1-pyrazolyl)borate (L3^-) and hydrotris(3-adamantyl-5-isopropyl-1-pyrazolyl)borate (L10^-), respectively, were structurally characterized. These complexes are the first examples of structurally characterized five-coordinate manganese(III) peroxido complexes. Their characteristic ν(OO) and ν(MnO) stretchings were determined by using H₂¹⁸O₂ for the first time. Theoretical calculations were performed to obtain further insight into their structural parameters. The decomposed products were obtained as [{Mn^III(μ-O)(L3)}₂Mn^IV] and [Mn^III(OH){L10(O)}] from [Mn(O₂)(L3)] and [Mn(O₂)(L10)], respectively.

Bioinspired mononuclear Mn complexes for O2 activation and biologically relevant reactions

A general interest in harnessing the oxidizing power of dioxygen (O₂) continues to motivate research efforts on bioinspired and biomimetic complexes to better understand how metalloenzymes mediate these reactions. The ubiquity of Fe- and Cu-based enzymes attracts significant attention and has resulted in many noteworthy developments for abiotic systems interested in direct O₂ reduction and small molecule activation. However, despite the existence of Mn-based metalloenzymes with important O₂-dependent activity, there has been comparatively less focus on the development of these analogues relative to Fe- and Cu-systems. In this Perspective, we summarize important contributions to the development of bioinspired mononuclear Mn complexes for O₂ activation and studies on their reactivity, emphasizing important design parameters in the primary and secondary coordination spheres and outlining mechanistic trends.

Bacillus subtilis HSY21 can reduce soybean root rot and inhibit the expression of genes related to the pathogenicity of Fusarium oxysporum

Soybean root rot occurs globally and seriously affects soybean production. To avoid the many disadvantages of chemical fungicides, the addition of Bacillus is gradually becoming an alternative strategy to tackle soybean root rot. However, the molecular mechanism of phytopathogenic fungi in this process by Bacillus inhibition is rarely reported. In this study, we isolated a strain of B. subtilis HSY21 from soybean rhizosphere soil, which had an inhibition rate of 81.30 ± 0.15% (P < 0.05) against Fusarium oxysporum. The control effects of this strain against soybean root rot under greenhouse and field conditions were 63.83% and 57.07% (P < 0.05), respectively. RNA-seq analysis of F. oxysporum after treatment with strain HSY21 revealed 1445 downregulated genes and 1561 upregulated genes. Among them, genes involved in mycelial growth, metabolism regulation, and disease-related enzymes were mostly downregulated. The activities of cellulase, β-glucosidase, α-amylase, and pectin-methyl- galacturonase as well as levels of oxalic acid and ergosterol in F. oxysporum were significantly decreased after HSY21 treatment. These results demonstrated that B. subtilis HSY21 could effectively control F. oxysporum by inhibiting its growth and the expression of pathogenic genes, thus indicating that this strain may be an ideal candidate for the prevention and control of soybean root rot.

An Arabidopsis Oxalyl-CoA Decarboxylase, AtOXC, Is Important for Oxalate Catabolism in Plants

Considering the widespread occurrence of oxalate in nature and its broad impact on a host of organisms, it is surprising that so little is known about the turnover of this important acid. In plants, oxalate oxidase is the most well-studied enzyme capable of degrading oxalate, but not all plants possess this activity. Recently, acyl-activating enzyme 3 (AAE3), encoding an oxalyl-CoA synthetase, was identified in Arabidopsis. This enzyme has been proposed to catalyze the first step in an alternative pathway of oxalate degradation. Since this initial discovery, this enzyme and proposed pathway have been found to be important to other plants and yeast as well. In this study, we identify, in Arabidopsis, an oxalyl-CoA decarboxylase (AtOXC) that is capable of catalyzing the second step in this proposed pathway of oxalate catabolism. This enzyme breaks down oxalyl-CoA, the product of AtAAE3, into formyl-CoA and CO₂. AtOXC:GFP localization suggested that this enzyme functions within the cytosol of the cell. An Atoxc knock-down mutant showed a reduction in the ability to degrade oxalate into CO₂. This reduction in AtOXC activity resulted in an increase in the accumulation of oxalate and the enzyme substrate, oxalyl-CoA. Size exclusion studies suggest that the enzyme functions as a dimer. Computer modeling of the AtOXC enzyme structure identified amino acids of predicted importance in co-factor binding and catalysis. Overall, these results suggest that AtOXC catalyzes the second step in this alternative pathway of oxalate catabolism.

Wild Soybean Oxalyl-CoA Synthetase Degrades Oxalate and Affects the Tolerance to Cadmium and Aluminum Stresses

Acyl activating enzyme 3 (AAE3) was identified as being involved in the acetylation pathway of oxalate degradation, which regulates the responses to biotic and abiotic stresses in various higher plants. Here, we investigated the role of Glycine sojaAAE3 (GsAAE3) in Cadmium (Cd) and Aluminum (Al) tolerances. The recombinant GsAAE3 protein showed high activity toward oxalate, with a Km of 105.10 ± 12.30 μM and Vmax of 12.64 ± 0.34 μmol min-1 mg-1 protein, suggesting that it functions as an oxalyl-CoA synthetase. The expression of a GsAAE3-green fluorescent protein (GFP) fusion protein in tobacco leaves did not reveal a specific subcellular localization pattern of GsAAE3. An analysis of the GsAAE3 expression pattern revealed an increase in GsAAE3 expression in response to Cd and Al stresses, and it is mainly expressed in root tips. Furthermore, oxalate accumulation induced by Cd and Al contributes to the inhibition of root growth in wild soybean. Importantly, GsAAE3 overexpression increases Cd and Al tolerances in A. thaliana and soybean hairy roots, which is associated with a decrease in oxalate accumulation. Taken together, our data provide evidence that the GsAAE3-encoded protein plays an important role in coping with Cd and Al stresses.

Calcium oxalate crystal deposition in the kidney: identification, causes and consequences

Calcium oxalate (CaOx) crystal deposition within the tubules is often a perplexing finding on renal biopsy of both native and transplanted kidneys. Understanding the underlying causes may help diagnosis and future management. The most frequent cause of CaOx crystal deposition within the kidney is hyperoxaluria. When this is seen in native kidney biopsy, primary hyperoxaluria must be considered and investigated further with biochemical and genetic tests. Secondary hyperoxaluria, for example due to enteric hyperoxaluria following bariatric surgery, ingested ethylene glycol or vitamin C overdose may also cause CaOx deposition in native kidneys. CaOx deposition is a frequent finding in renal transplant biopsy, often as a consequence of acute tubular necrosis and is associated with poorer long-term graft outcomes. CaOx crystal deposition in the renal transplant may also be secondary to any of the causes associated with this phenotype in the native kidney. The pathophysiology underlying CaOx deposition is complex but this histological phenotype may indicate serious underlying pathology and should always warrant further investigation.

Abundance, Functional, and Evolutionary Analysis of Oxalyl-Coenzyme A Decarboxylase in Human Microbiota

Oxalic acid and its oxalate salts have been linked to kidney stones and other health problems and about 80% kidney stones are made up of calcium oxalate. Oxalyl coenzyme A decarboxylase (OXC) is a key enzyme in the catabolism of oxalate. In this study, we performed bioinformatic and biochemical analysis of OXC. First, we mined the OXC sequences from a public protein database and collected 1396 putative OXC sequences. These sequences were widely spread and mainly distributed in Actinobacteria, Alphaproteobacteria, Gammaproteobacteria, and Betaproteobacteria and classified into seven clusters. The phylogenetic relationship and evolutionary rate of the 7 clusters showed that OXC are highly conserved. Second, the abundance of the different clusters of OXC was explored in 380 human microbiome datasets, which showed that OXCs in Cluster 1 were relatively high in the gut while OXCs in Clusters 2-4 were relatively enriched in the vagina. Third, we measured the activity of one OXC from Mycobacterium mageritense (OXCmm) in Cluster 3, in which there was no experimentally characterized enzymes. Mutation analysis showed that OXCmm shared the same active sites with the OXC from Oxalobacter formigenes. Taken together, this analysis provides a better insight into the distribution and catalysis of OXC and further potential alternative application of OXC active bacteria as probiotics in the management of kidney stone disease.

Oxalate oxidase from Abortiporus biennis - protein localisation and gene sequence analysis

We have described for the first time the localisation of oxalate oxidase (OXO, EC 1.2.3.4) in Abortiporus biennis cells, using histochemical and immunochemical methods coupled with transmission electron microscopy. Rabbit anti-oxalate oxidase immunoglobulins with anti-rabbit secondary antibody conjugated with 10-nm gold particles were used. Moreover, the formation of electron dense precipitation of reaction of diaminobenzidine (DAB) with horseradish peroxidase (HRP) for histochemical localisation of the enzyme was found. OXO was localised close to the membranous structures of the cell membranes, in membranous vesicles located close to the outer cell membrane, and vacuolar membranes surrounding vacuoles. The positive immunoreaction to OXO was also intense in cell wall areas. Moreover, we proved that gene coding for OXO was expressed in the same cultures. Corresponding mRNA was isolated, full length cDNA was synthesized, cloned and sequenced. Two copies of cupin domains were found in the sequence of amino-acids conserved domain coding for the cupin enzyme. Comparison of the genomic DNA and cDNA sequences has revealed the presence of seventeen introns in the gene. The isoelectric point of the protein was estimated at pH 4.5 and several possible N-glycosylation sites were predicted.

Manganese in Plants: From Acquisition to Subcellular Allocation

Manganese (Mn) is an important micronutrient for plant growth and development and sustains metabolic roles within different plant cell compartments. The metal is an essential cofactor for the oxygen-evolving complex (OEC) of the photosynthetic machinery, catalyzing the water-splitting reaction in photosystem II (PSII). Despite the importance of Mn for photosynthesis and other processes, the physiological relevance of Mn uptake and compartmentation in plants has been underrated. The subcellular Mn homeostasis to maintain compartmented Mn-dependent metabolic processes like glycosylation, ROS scavenging, and photosynthesis is mediated by a multitude of transport proteins from diverse gene families. However, Mn homeostasis may be disturbed under suboptimal or excessive Mn availability. Mn deficiency is a serious, widespread plant nutritional disorder in dry, well-aerated and calcareous soils, as well as in soils containing high amounts of organic matter, where bio-availability of Mn can decrease far below the level that is required for normal plant growth. By contrast, Mn toxicity occurs on poorly drained and acidic soils in which high amounts of Mn are rendered available. Consequently, plants have evolved mechanisms to tightly regulate Mn uptake, trafficking, and storage. This review provides a comprehensive overview, with a focus on recent advances, on the multiple functions of transporters involved in Mn homeostasis, as well as their regulatory mechanisms in the plant's response to different conditions of Mn availability.

Effects of different operating parameters on hydrogen production by Parageobacillus thermoglucosidasius DSM 6285

Hydrogen gas represents a promising alternative energy source to dwindling fossil fuel reserves, as it carries the highest energy per unit mass and its combustion results in the release of water vapour as only byproduct. The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius is able to produce hydrogen via the water–gas shift reaction catalyzed by a carbon monoxide dehydrogenase–hydrogenase enzyme complex. Here we have evaluated the effects of several operating parameters on hydrogen production, including different growth temperatures, pre-culture ages and inoculum sizes, as well as different pHs and concentrations of nickel and iron in the fermentation medium. All of the tested parameters were observed to have a substantive effect on both hydrogen yield and (specific) production rates. A final experiment incorporating the best scenario for each tested parameter showed a marked increase in the H₂ production rate compared to each individual parameter. The optimised parameters serve as a strong basis for improved hydrogen production with a view of commercialisation of this process.

Biochemical properties and oxalate-degrading activity of oxalate decarboxylase from bacillus subtilis at neutral pH

Oxalate decarboxylase (OxDC) from Bacillus subtilis is a Mn-dependent hexameric enzyme that converts oxalate to carbon dioxide and formate. OxDC has greatly attracted the interest of the scientific community, mainly due to its biotechnological and medical applications in particular for the treatment of hyperoxaluria, a group of pathologic conditions caused by oxalate accumulation. The enzyme has an acidic optimum pH, but most of its applications involve processes occurring at neutral pH. Nevertheless, a detailed biochemical characterization of the enzyme at neutral pH is lacking. Here, we compared the structural-functional properties at acidic and neutral pH of wild-type OxDC and of a mutant form, called OxDC-DSSN, bearing four amino acid substitutions in the lid (Ser161-to-Asp, Glu162-to-Ser, Asn163-toSer, and Ser164-to-Asn) that improve the oxalate oxidase activity and almost abolish the decarboxylase activity. We found that both enzymatic forms do not undergo major structural changes as a function of pH, although OxDC-DSSN displays an increased tendency to aggregation, which is counteracted by the presence of an active-site ligand. Notably, OxDC and OxDC-DSSN at pH 7.2 retain 7 and 15% activity, respectively, which is sufficient to degrade oxalate in a cellular model of primary hyperoxaluria type I, a rare inherited disease caused by excessive endogenous oxalate production. The significance of the data in the light of the possible use of OxDC as biological drug is discussed. © 2019 IUBMB Life, 1-11, 2019.

Expression Analysis of Oxalate Metabolic Pathway Genes Reveals Oxalate Regulation Patterns in Spinach

Spinach (Spinacia oleracea L.) is one of most important leafy vegetables because of its high nutritional value and high oxalate content, which can be toxic with negative effects on human nutrition. Ammonium and nitrate can effectively regulate oxalate accumulation, although the mechanisms underlying the oxalate biosynthesis and regulation are still undetermined in plants. In the present study, we identified 25 putative genes that are involved in the oxalate biosynthetic and degradation pathway, before analyzing the oxalate content and the expression levels of the corresponding proteins under normal growth conditions, with or without ammonium and nitrate treatments, using high and low oxalate-accumulated spinach genotypes. The two cultivars exhibited different profiles of total oxalate and soluble oxalate accumulation. The high oxalate concentrations in spinach were as a result of the high transcription levels of the genes that are involved in oxalate biosynthesis under normal growth conditions, such as SoGLO2, SoGLO3, three SoOXACs, SoMLS, SoMDH1, SoMDH2, and SoMDH4. The results revealed that the ammonium and nitrate were able to control the oxalate content in leaves, possibly because of the different transcription levels of the genes. The oxalate content is regulated by complex regulatory mechanisms and is varied in the different varieties of spinach. The results from this research may be used to assist the investigation of the mechanism of oxalate regulation and breeding for reduced oxalate content in spinach.

Rapid start-up of a bioelectrochemical system under alkaline and saline conditions for efficient oxalate removal

This study examined a new approach for starting up a bioelectrochemical system (BES) for oxalate removal from an alkaline (pH > 12) and saline (NaCl 25 g/L) liquor. An oxalotrophic biofilm pre-grown aerobically onto granular graphite carriers was used directly as both the microbial inoculum and the BES anode. At anode potential of +200 mV (Ag/AgCl) the biofilm readily switched from using oxygen to graphite as sole electron acceptor for oxalate oxidation. BES performance was characterised at various hydraulic retention times (HRTs, 3-24 h), anode potentials (-600 to +200 mV vs. Ag/AgCl) and influent oxalate (25 mM) to acetate (0-30 mM) ratios. Maximum current density recorded was 363 A/m³ at 3 h HRT with a high coulombic efficiency (CE) of 70%. The biofilm could concurrently degrade acetate and oxalate (CE 80%) without apparent preference towards acetate. Pyro-sequencing analysis revealed that known oxalate degraders Oxalobacteraceae became abundant signifying their role in this novel bioprocess.

Bioelectrochemical oxidation of organics by alkali-halotolerant anodophilic biofilm under nitrogen-deficient, alkaline and saline conditions

This work aimed to study the feasibility of using bioelectrochemical systems (BES) for organics removal under alkaline-saline and nitrogen (N) deficient conditions. Two BES inoculated with activated sludge were examined for organics (oxalate, acetate, formate) oxidation under alkaline-saline (pH 9.5, 25g/L NaCl) and N deficient conditions. One reactor (R1) received ammonium chloride as an N-source, while the other (R2) without. The reactors were initially loaded with only oxalate (25mM), but start-up was achieved only when acetate was added as co-substrate (5mM). Maximum current were R1: 908A/m³ (organic removal rate (ORR) 4.61kgCOD/m³·d) and R2: 540A/m³ (ORR 2.06kgCOD/m³·d). Formate was utilised by both anodic biofilms, but the inefficient oxalate removal was likely due to the paucity of microorganisms that catalyse decarboxylation of oxalate into formate. Further development of this promising technology for the treatment of alkaline-saline wastewater is warranted.

Biological functions controlled by manganese redox changes in mononuclear Mn-dependent enzymes

Remarkably few enzymes are known to employ a mononuclear manganese ion that undergoes changes in redox state during catalysis. Many questions remain to be answered about the role of substrate binding and/or protein environment in modulating the redox properties of enzyme-bound Mn(II), the nature of the dioxygen species involved in the catalytic mechanism, and how these enzymes acquire Mn(II) given that many other metal ions in the cell form more stable protein complexes. Here, we summarize current knowledge concerning the structure and mechanism of five mononuclear manganese-dependent enzymes: superoxide dismutase, oxalate oxidase (OxOx), oxalate decarboxylase (OxDC), homoprotocatechuate 3,4-dioxygenase, and lipoxygenase (LOX). Spectroscopic measurements and/or computational studies suggest that Mn(III)/Mn(II) are the catalytically active oxidation states of the metal, and the importance of 'second-shell' hydrogen bonding interactions with metal ligands has been demonstrated for a number of examples. The ability of these enzymes to modulate the redox properties of the Mn(III)/Mn(II) couple, thereby allowing them to generate substrate-based radicals, appears essential for accessing diverse chemistries of fundamental importance to organisms in all branches of life.

Hydrogen peroxide inhibition of bicupin oxalate oxidase

Oxalate oxidase is a manganese containing enzyme that catalyzes the oxidation of oxalate to carbon dioxide in a reaction that is coupled with the reduction of oxygen to hydrogen peroxide. Oxalate oxidase from Ceriporiopsis subvermispora (CsOxOx) is the first fungal and bicupin enzyme identified that catalyzes this reaction. Potential applications of oxalate oxidase for use in pancreatic cancer treatment, to prevent scaling in paper pulping, and in biofuel cells have highlighted the need to understand the extent of the hydrogen peroxide inhibition of the CsOxOx catalyzed oxidation of oxalate. We apply a membrane inlet mass spectrometry (MIMS) assay to directly measure initial rates of carbon dioxide formation and oxygen consumption in the presence and absence of hydrogen peroxide. This work demonstrates that hydrogen peroxide is both a reversible noncompetitive inhibitor of the CsOxOx catalyzed oxidation of oxalate and an irreversible inactivator. The build-up of the turnover-generated hydrogen peroxide product leads to the inactivation of the enzyme. The introduction of catalase to reaction mixtures protects the enzyme from inactivation allowing reactions to proceed to completion. Circular dichroism spectra indicate that no changes in global protein structure take place in the presence of hydrogen peroxide. Additionally, we show that the CsOxOx catalyzed reaction with the three carbon substrate mesoxalate consumes oxygen which is in contrast to previous proposals that it catalyzed a non-oxidative decarboxylation with this substrate.

Effect of pH and Temperature on <I>Bacillus subtilis</I> FNCC 0059 Oxalate Decarboxylase Activity

BACKGROUND AND OBJECTIVE

Bacillus subtilis is a bacterium that can produce the oxalate decarboxylase (ODC) enzyme. This enzyme decomposes oxalate. ODC enzyme activity is influenced by temperature and pH. This study was conducted to determine the optimum pH and temperature for ODC enzyme activity in B. subtilis FNCC 0059.

MATERIALS AND METHODS

B. subtilis was cultivated in oxalate medium at different incubation temperatures for 24 h. The tested temperatures were 25, 29, 33, 37, 41 and 45°C. In separate experiments, cultures were grown in oxalate medium at varying pH from 4-8.5. The cell growth assay and enzyme activity were performed and all the experiments were done with 3 replicates. Data were analyzed using one-way analysis of variance.

RESULTS

The optimum temperature of 37°C could produce maximum ODC enzyme activity (0.041 U mL-1) enzyme activity increased to the point of the optimum pH and then decreased 5.6% when the pH was increased 0.5 from the optimum. Maximum ODC enzyme activity (0.0413 U mL-1) was achieved at pH 5.5.

CONCLUSION

Temperature and the pH of the medium affected ODC enzyme activity. Optimum medium condition of B. subtilis was reached at 37°C and pH 5.5.

Oxygen activation by mononuclear Mn, Co, and Ni centers in biology and synthetic complexes

The active sites of metalloenzymes that catalyze O₂-dependent reactions generally contain iron or copper ions. However, several enzymes are capable of activating O₂ at manganese or nickel centers instead, and a handful of dioxygenases exhibit activity when substituted with cobalt. This minireview summarizes the catalytic properties of oxygenases and oxidases with mononuclear Mn, Co, or Ni active sites, including oxalate-degrading oxidases, catechol dioxygenases, and quercetin dioxygenase. In addition, recent developments in the O₂ reactivity of synthetic Mn, Co, or Ni complexes are described, with an emphasis on the nature of reactive intermediates featuring superoxo-, peroxo-, or oxo-ligands. Collectively, the biochemical and synthetic studies discussed herein reveal the possibilities and limitations of O₂ activation at these three "overlooked" metals.

Production of superoxide from photosystem II-light harvesting complex II supercomplex in STN8 kinase knock-out rice mutants under photoinhibitory illumination

When phosphorylation of Photosystem (PS) II core proteins is blocked in STN8 knock-out mutants of rice (Oryza sativa) under photoinhibitory illumination, the mobilization of PSII supercomplex is prevented. We have previously proposed that more superoxide (O2(-)) is produced from PSII in the mutant (Nath et al., 2013, Plant J. 76, 675-686). Here, we clarify the type and site for the generation of reactive oxygen species (ROS). Using both histochemical and fluorescence probes, we observed that, compared with wild-type (WT) leaves, levels of ROS, including O2(-) and hydrogen peroxide (H2O2), were increased when leaves from mutant plants were illuminated with excess light. However, singlet oxygen production was not enhanced under such conditions. When superoxide dismutase was inhibited, O2(-) production was increased, indicating that it is the initial event prior to H2O2 production. In thylakoids isolated from WT leaves, kinase was active in the presence of ATP, and spectrophotometric analysis of nitrobluetetrazolium absorbance for O2(-) confirmed that PSII-driven superoxide production was greater in the mutant thylakoids than in the WT. This contrast in levels of PSII-driven superoxide production between the mutants and the WT plants was confirmed by conducting protein oxidation assays of PSII particles from osstn8 leaves under strong illumination. Those assays also demonstrated that PSII-LHCII supercomplex proteins were oxidized more in the mutant, thereby implying that PSII particles incur greater damage even though D1 degradation during PSII-supercomplex mobilization is partially blocked in the mutant. These results suggest that O2(-) is the major form of ROS produced in the mutant, and that the damaged PSII in the supercomplex is the primary source of O2(-).

Substrate Binding Mode and Molecular Basis of a Specificity Switch in Oxalate Decarboxylase

Oxalate decarboxylase (OxDC) catalyzes the conversion of oxalate into formate and carbon dioxide in a remarkable reaction that requires manganese and dioxygen. Previous studies have shown that replacing an active-site loop segment Ser¹⁶¹-Glu¹⁶²-Asn¹⁶³-Ser¹⁶⁴ in the N-terminal domain of OxDC with the cognate residues Asp¹⁶¹-Ala¹⁶²-Ser-¹⁶³-Asn¹⁶⁴ of an evolutionarily related, Mn-dependent oxalate oxidase gives a chimeric variant (DASN) that exhibits significantly increased oxidase activity. The mechanistic basis for this change in activity has now been investigated using membrane inlet mass spectrometry (MIMS) and isotope effect (IE) measurements. Quantitative analysis of the reaction stoichiometry as a function of oxalate concentration, as determined by MIMS, suggests that the increased oxidase activity of the DASN OxDC variant is associated with only a small fraction of the enzyme molecules in solution. In addition, IE measurements show that C–C bond cleavage in the DASN OxDC variant proceeds via the same mechanism as in the wild-type enzyme, even though the Glu¹⁶² side chain is absent. Thus, replacement of the loop residues does not modulate the chemistry of the enzyme-bound Mn(II) ion. Taken together, these results raise the possibility that the observed oxidase activity of the DASN OxDC variant arises from an increased level of access of the solvent to the active site during catalysis, implying that the functional role of Glu¹⁶² is to control loop conformation. A 2.6 Å resolution X-ray crystal structure of a complex between oxalate and the Co(II)-substituted ΔE162 OxDC variant, in which Glu¹⁶² has been deleted from the active site loop, reveals the likely mode by which the substrate coordinates the catalytically active Mn ion prior to C–C bond cleavage. The “end-on” conformation of oxalate observed in the structure is consistent with the previously published V/K IE data and provides an empty coordination site for the dioxygen ligand that is thought to mediate the formation of Mn(III) for catalysis upon substrate binding.

Formation, Characterization, and O-O Bond Activation of a Peroxomanganese(III) Complex Supported by a Cross-Clamped Cyclam Ligand

Although there have been reports describing the nucleophilic reactivity of peroxomanganese(III) intermediates, as well as their conversion to high-valent oxo-bridged dimers, it remains a challenge to activate peroxomanganese(III) species for conversion to high-valent, mononuclear manganese complexes. Herein, we report the generation, characterization, and activation of a peroxomanganese(III) adduct supported by the cross-clamped, macrocyclic Me2EBC ligand (4,11-dimethyl-1,4,8,11-tetraazabicyclo[6.6.2]hexadecane). This ligand is known to support high-valent, mononuclear Mn(IV) species with well-defined spectroscopic properties, which provides an opportunity to identify mononuclear Mn(IV) products from O-O bond activation of the corresponding Mn(III)-peroxo adduct. The peroxomanganese(III) intermediate, [Mn(III)(O2)(Me2EBC)](+), was prepared at low-temperature by the addition of KO2 to [Mn(II)(Cl)2(Me2EBC)] in CH2Cl2, and this complex was characterized by electronic absorption, electron paramagnetic resonance (EPR), and Mn K-edge X-ray absorption (XAS) spectroscopies. The electronic structure of the [Mn(III)(O2)(Me2EBC)](+) intermediate was examined by density functional theory (DFT) and time-dependent (TD) DFT calculations. Detailed spectroscopic investigations of the decay products of [Mn(III)(O2)(Me2EBC)](+) revealed the presence of mononuclear Mn(III)-hydroxo species or a mixture of mononuclear Mn(IV) and Mn(III)-hydroxo species. The nature of the observed decay products depended on the amount of KO2 used to generate [Mn(III)(O2)(Me2EBC)](+). The Mn(III)-hydroxo product was characterized by Mn K-edge XAS, and shifts in the pre-edge transition energies and intensities relative to [Mn(III)(O2)(Me2EBC)](+) provide a marker for differences in covalency between peroxo and nonperoxo ligands. To the best of our knowledge, this work represents the first observation of a mononuclear Mn(IV) center upon decay of a nonporphyrinoid Mn(III)-peroxo center.

An Oxalyl-CoA Dependent Pathway of Oxalate Catabolism Plays a Role in Regulating Calcium Oxalate Crystal Accumulation and Defending against Oxalate-Secreting Phytopathogens in Medicago truncatula

Considering the widespread occurrence of oxalate in nature and its broad impact on a host of organisms, it is surprising that so little is known about the turnover of this important acid. In plants, oxalate oxidase is the most well studied enzyme capable of degrading oxalate, but not all plants possess this activity. Recently, an Acyl Activating Enzyme 3 (AAE3), encoding an oxalyl-CoA synthetase, was identified in Arabidopsis. AAE3 has been proposed to catalyze the first step in an alternative pathway of oxalate degradation. Whether this enzyme and proposed pathway is important to other plants is unknown. Here, we identify the Medicago truncatula AAE3 (MtAAE3) and show that it encodes an oxalyl-CoA synthetase activity exhibiting high activity against oxalate with a Km = 81 ± 9 μM and Vmax = 19 ± 0.9 μmoles min-1mg protein-1. GFP-MtAAE3 localization suggested that this enzyme functions within the cytosol of the cell. Mtaae3 knock-down line showed a reduction in its ability to degrade oxalate into CO2. This reduction in the capacity to degrade oxalate resulted in the accumulation of druse crystals of calcium oxalate in the Mtaae3 knock-down line and an increased susceptibility to oxalate-secreting phytopathogens such as Sclerotinia sclerotiorum. Taken together, these results suggest that AAE3 dependent turnover of oxalate is important to different plants and functions in the regulation of tissue calcium oxalate crystal accumulation and in defense against oxalate-secreting phytopathogens.

Diversity and ecology of oxalotrophic bacteria

Oxalate is present in environments as diverse as soils or gastrointestinal tracts. This organic acid can be found as free acid or forming metal salts (e.g. calcium, magnesium). Oxalotrophy, the ability to use oxalate as carbon and energy sources, is mainly the result of bacterial catabolism, which can be either aerobic or anaerobic. Although some oxalotrophic bacterial strains are commonly used as probiotics, little is known about the diversity and ecology of this functional group. This review aims at exploring the taxonomic distribution and the phylogenetic diversity of oxalotrophic bacteria across biomes. In silico analyses were conducted using the two key enzymes involved in oxalotrophy: formyl-coenzyme A (CoA) transferase (EC 2.8.3.16) and oxalyl-CoA decarboxylase (EC 4.1.1.8), encoded by the frc and oxc genes, respectively. Our analyses revealed that oxalate-degrading bacteria are restricted to three phyla, namely Actinobacteria, Firmicutes and Proteobacteria and originated from terrestrial, aquatic and clinical environments. Diversity analyses at the protein level suggest that total Oxc diversity is more constrained than Frc diversity and that bacterial oxalotrophic diversity is not yet fully described. Finally, the contribution of oxalotrophic bacteria to ecosystem functioning as well as to the carbon cycle is discussed.

Intrinsic Carbon-Carbon Bond Reactivity at the Manganese Center of Oxalate Decarboxylase from Density Functional Theory

The detailed manganese-dependent chemistry employed by oxalate decarboxylase (OxDC) to catalyze the nonoxidative decarboxylation of oxalic acid remains poorly understood. For example, enzyme activity requires the presence of dioxygen even though this compound is not a formal substrate in the reaction. We now report density functional theory (DFT) calculations upon a series of hypothetical OxDC active site model structures. Our results suggest that the function of the metal ion may be to position dioxygen and oxalate such that electrons can be shuttled directly between these species, thereby removing the need for the existence of Mn(III) as an intermediate in the mechanism. These calculations also indicate that the intrinsic, gas-phase reactivity of the Bacillus subtilis oxalate decarboxylase active center is to oxidize oxalate. Since this reactivity is not observed for OxDC, our DFT results suggest that protein environment modulates the intrinsic metallocenter reactivity, presumably by affecting the electronic distribution at the manganese center during catalysis.

Oxalate-degrading microorganisms or oxalate-degrading enzymes: which is the future therapy for enzymatic dissolution of calcium-oxalate uroliths in recurrent stone disease?

Renal urolithiasis is a pathological condition common to a multitude of genetic, physiological and nutritional disorders, ranging from general hyperoxaluria to obesity. The concept of quickly dissolving renal uroliths via chemolysis, especially calcium-oxalate kidney stones, has long been a clinical goal, but yet to be achieved. Over the past 25 years, there has been a serious effort to examine the prospects of using plant and microbial oxalate-degrading enzymes known to catabolize oxalic acid and oxalate salts. While evidence is emerging that bacterial probiotics can reduce recurrent calcium-oxalate kidney stone disease by lowering systemic hyperoxaluria, the possible use of free oxalate-degrading enzyme therapy remains a challenge with several hurdles to overcome before reaching clinical practice.

Detection of hydrogen peroxide in Photosystem II (PSII) using catalytic amperometric biosensor

Hydrogen peroxide (H2O2) is known to be generated in Photosystem II (PSII) via enzymatic and non-enzymatic pathways. Detection of H2O2 by different spectroscopic techniques has been explored, however its sensitive detection has always been a challenge in photosynthetic research. During the recent past, fluorescence probes such as Amplex Red (AR) has been used but is known to either lack specificity or limitation with respect to the minimum detection limit of H2O2. We have employed an electrochemical biosensor for real time monitoring of H2O2 generation at the level of sub-cellular organelles. The electrochemical biosensor comprises of counter electrode and working electrodes. The counter electrode is a platinum plate, while the working electrode is a mediator based catalytic amperometric biosensor device developed by the coating of a carbon electrode with osmium-horseradish peroxidase which acts as H2O2 detection sensor. In the current study, generation and kinetic behavior of H2O2 in PSII membranes have been studied under light illumination. Electrochemical detection of H2O2 using the catalytic amperometric biosensor device is claimed to serve as a promising technique for detection of H2O2 in photosynthetic cells and subcellular structures including PSII or thylakoid membranes. It can also provide a precise information on qualitative determination of H2O2 and thus can be widely used in photosynthetic research.

Immobilization of Bacillus subtilis oxalate decarboxylase on a Zn-IMAC resin

Oxalate decarboxylase, a bicupin enzyme coordinating two essential manganese ions per subunit, catalyzes the decomposition of oxalate into carbon dioxide and formate in the presence of oxygen. Current efforts to elucidate its catalytic mechanism are focused on EPR studies of the Mn. We report on a new immobilization strategy linking the enzyme's N-terminal His₆-tag to a Zn-loaded immobilized metal affinity resin. Activity is lowered somewhat due to the expected crowding effect. High-field EPR spectra of free and immobilized enzyme show that the resin affects the coordination environment of the active site Mn ions only minimally. The immobilized preparation was used to study the effect of varying pH on the same sample. Repeated freeze-thaw cycles lead to break down of the resin beads and some enzyme loss from the sample. However, the EPR signal increases due to higher packing efficiency on the sample column.

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Immobilization of Oxalate decarboxylase on Zn-IMAC resin.

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Overall K_M is unaffected after immobilization.

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Immobilized enzyme exhibits lower overall activity due to crowding on the resin.

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High-field EPR confirms minimal perturbations of manganese sites due to immobilization.

Glyphosate, pathways to modern diseases III: Manganese, neurological diseases, and associated pathologies

Manganese (Mn) is an often overlooked but important nutrient, required in small amounts for multiple essential functions in the body. A recent study on cows fed genetically modified Roundup(®)-Ready feed revealed a severe depletion of serum Mn. Glyphosate, the active ingredient in Roundup(®), has also been shown to severely deplete Mn levels in plants. Here, we investigate the impact of Mn on physiology, and its association with gut dysbiosis as well as neuropathologies such as autism, Alzheimer's disease (AD), depression, anxiety syndrome, Parkinson's disease (PD), and prion diseases. Glutamate overexpression in the brain in association with autism, AD, and other neurological diseases can be explained by Mn deficiency. Mn superoxide dismutase protects mitochondria from oxidative damage, and mitochondrial dysfunction is a key feature of autism and Alzheimer's. Chondroitin sulfate synthesis depends on Mn, and its deficiency leads to osteoporosis and osteomalacia. Lactobacillus, depleted in autism, depend critically on Mn for antioxidant protection. Lactobacillus probiotics can treat anxiety, which is a comorbidity of autism and chronic fatigue syndrome. Reduced gut Lactobacillus leads to overgrowth of the pathogen, Salmonella, which is resistant to glyphosate toxicity, and Mn plays a role here as well. Sperm motility depends on Mn, and this may partially explain increased rates of infertility and birth defects. We further reason that, under conditions of adequate Mn in the diet, glyphosate, through its disruption of bile acid homeostasis, ironically promotes toxic accumulation of Mn in the brainstem, leading to conditions such as PD and prion diseases.

Facile C(sp(2))-C(sp(2)) bond cleavage in oxalic acid-derived radicals

Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. Many questions remain about the catalytic mechanism of OxDC although it has been proposed that the reaction proceeds via substrate-based radical intermediates. Using coupled cluster theory combined with implicit solvation models we have examined the effects of radical formation on the structure and reactivity of oxalic acid-derived radicals in aqueous solution. Our results show that the calculated solution-phase free-energy barrier for C-C bond cleavage to form CO2 is decreased from 34.2 kcal/mol for oxalic acid to only 9.3 kcal/mol and a maximum of 3.5 kcal/mol for the cationic and neutral oxalic acid-derived radicals, respectively. These studies also show that the C-C σ bonding orbital of the radical cation contains only a single electron, giving rise to an elongated C-C bond distance of 1.7 Å; a similar lengthening of the C-C bond is not observed for the neutral radical. This study provides new chemical insights into the structure and stability of plausible intermediates in the catalytic mechanism of OxDC, and suggests that removal of an electron to form a radical (with or without the concomitant loss of a proton) may be a general strategy for cleaving the unreactive C-C bonds between adjacent sp(2)-hybridized carbon atoms.

Observation of superoxide production during catalysis of Bacillus subtilis oxalate decarboxylase at pH 4

This contribution describes the trapping of the hydroperoxyl radical at a pH of 4 during turnover of wild-type oxalate decarboxylase and its T165V mutant using the spin-trap BMPO. Radicals were detected and identified by a combination of EPR and mass spectrometry. Superoxide, or its conjugate acid, the hydroperoxyl radical, is expected as an intermediate in the decarboxylation and oxidation reactions of the oxalate monoanion, both of which are promoted by oxalate decarboxylase. Another intermediate, the carbon dioxide radical anion was also observed. The quantitative yields of superoxide trapping are similar in the wild type and the mutant while it is significantly different for the trapping of the carbon dioxide radical anion. This suggests that the two radicals are released from different sites of the protein.

Bio-inspired design of electrocatalysts for oxalate oxidation: a combined experimental and computational study of Mn–N–C catalysts

A novel non-PGM MnAAPyr catalyst that shows electrochemical activity towards the oxidation of oxalic acid comparable to Pt.