Oxalate-Degrading Enzyme Recombined Lactic Acid Bacteria Strains Reduce Hyperoxaluria

Optimizing antigen preparation for oxalyl-CoA decarboxylase enzyme diagnostic kit and ELISA system cutoff determination

The prevalence of kidney stone disease is increasing globally, with calcium oxalate stones being the most common type. Oxalyl-CoA decarboxylase (OXC), an enzyme produced by the gut bacterium Oxalobacter formigenes, plays a crucial role in oxalate metabolism. Deficiencies in OXC activity can lead to the accumulation of oxalate, contributing to kidney stone formation. This study aimed to develop a reliable diagnostic assay for OXC by optimizing antigen production and establishing a cutoff value for an enzyme-linked immunosorbent assay (ELISA). We cloned, expressed, and purified recombinant OXC protein in Escherichia coli BL21(DE3), and generated specific polyclonal antibodies in rabbits. The ELISA system was optimized and validated using serum samples from 40 healthy individuals and 6 patients with oxalate-related disorders. The cutoff value was determined using the formula (M + 2SD), where (M) is the mean and (SD) is the standard deviation of the healthy sample results. The calculated cutoff value of 0.656750 effectively distinguished between healthy and affected individuals, with a sensitivity of 97.5% and a specificity of 83.3%. These findings provide a valuable tool for the early detection and management of oxalate-related disorders, with significant implications for clinical practice.

Engineered microorganisms: A new direction in kidney stone prevention and treatment

Numerous studies have shown that intestinal and urinary tract flora are closely related to the formation of kidney stones. The removal of probiotics represented by lactic acid bacteria and the colonization of pathogenic bacteria can directly or indirectly promote the occurrence of kidney stones. However, currently existing natural probiotics have limitations. Synthetic biology is an emerging discipline in which cells or living organisms are genetically designed and modified to have biological functions that meet human needs, or even create new biological systems, and has now become a research hotspot in various fields. Using synthetic biology approaches of microbial engineering and biological redesign to enable probiotic bacteria to acquire new phenotypes or heterologous protein expression capabilities is an important part of synthetic biology research. Synthetic biology modification of microorganisms in the gut and urinary tract can effectively inhibit the development of kidney stones by a range of means, including direct degradation of metabolites that promote stone production or indirect regulation of flora homeostasis. This article reviews the research status of engineered microorganisms in the prevention and treatment of kidney stones, to provide a new and effective idea for the prevention and treatment of kidney stones.

Recent Advances of Oxalate Decarboxylase: Biochemical Characteristics, Catalysis Mechanisms, and Gene Expression and Regulation

Oxalate decarboxylase (OXDC) is a typical Mn2+/Mn3+ dependent metal enzyme and splits oxalate to formate and CO2 without any organic cofactors. Fungi and bacteria are the main organisms expressing the OXDC gene, but with a significantly different mechanism of gene expression and regulation. Many articles reported its potential applications in the clinical treatment of hyperoxaluria, low-oxalate food processing, degradation of oxalate salt deposits, oxalate acid diagnostics, biocontrol, biodemulsifier, and electrochemical oxidation. However, some questions still remain to be clarified about the role of substrate binding and/or protein environment in modulating the redox properties of enzyme-bound Mn(II)/Mn(III), the nature of dioxygen involved in the catalytic mechanism, and how OXDC acquires Mn(II) /Mn(III). This review mainly summarizes its biochemical and structure characteristics, gene expression and regulation, and catalysis mechanism. We also deep-mined oxalate decarboxylase gene data from National Center for Biotechnology Information to give some insights to explore new OXDC with diverse biochemical properties.

Detection of oxalyl-CoA decarboxylase (oxc) and formyl-CoA transferase (frc) genes in novel probiotic isolates capable of oxalate degradation in vitro

Oxalate degradation is one of lactic acid bacteria's desirable activities. It is achieved by two enzymes, formyl coenzyme A transferase (frc) and oxalyl coenzyme A decarboxylase (oxc). The current study aimed to screen 15 locally isolated lactic acid bacteria to select those with the highest oxalate degradation ability. It also aimed to amplify the genes involved in degradation. MRS broth supplemented with 20 mM sodium oxalate was used to culture the tested isolates for 72 h. This was followed by an enzymatic assay to detect remaining oxalate. All isolates showed oxalate degradation activity to variable degrees. Five isolates demonstrated high oxalate degradation, 78 to 88%. To investigate the oxalate-degradation potential of the selected isolates, they have been further tested for the presence of genes that encode for enzymes involved in oxalate catabolism, formyl coenzyme A transferase (frc) and oxalyl coenzyme A decarboxylase (oxc). Three strains showed bands with the specific OXC and FRC forward and reverse primers designated as (SA-5, 9 and 37). Species-level identification revealed Loigolactobacillus bifermentans, Lacticaseibacillus paracasei, and Lactiplantibacillus plantarum. Preliminary results revealed that the tested probiotic strains harbored both oxc and frc whose products are putatively involved in oxalate catabolism. The probiotic potential of the selected strains was evaluated, and they showed high survival rates to both simulated gastric and intestinal fluids and variable degrees of antagonism against the tested Gram-positive and negative pathogens and were sensitive to clarithromycin but resistant to both metronidazole and ceftazidime. Finally, these strains could be exploited as an innovative approach to establish oxalate homeostasis in humans and prevent kidney stone formation.

Oxalate Homeostasis in Non-Stone-Forming Chronic Kidney Disease: A Review of Key Findings and Perspectives

Chronic kidney disease (CKD) is a significant global public health concern associated with high morbidity and mortality rates. The maintenance of oxalate homeostasis plays a critical role in preserving kidney health, particularly in the context of CKD. Although the relationship between oxalate and kidney stone formation has been extensively investigated, our understanding of oxalate homeostasis in non-stone-forming CKD remains limited. This review aims to present an updated analysis of the existing literature, focusing on the intricate mechanisms involved in oxalate homeostasis in patients with CKD. Furthermore, it explores the key factors that influence oxalate accumulation and discusses the potential role of oxalate in CKD progression and prognosis. The review also emphasizes the significance of the gut-kidney axis in CKD oxalate homeostasis and provides an overview of current therapeutic strategies, as well as potential future approaches. By consolidating important findings and perspectives, this review offers a comprehensive understanding of the present knowledge in this field and identifies promising avenues for further research.

Metabolic changes in kidney stone disease

Kidney stone disease (KSD) is one of the earliest medical diseases known, but the mechanism of its formation and metabolic changes remain unclear. The formation of kidney stones is a extensive and complicated process, which is regulated by metabolic changes in various substances. In this manuscript, we summarized the progress of research on metabolic changes in kidney stone disease and discuss the valuable role of some new potential targets. We reviewed the influence of metabolism of some common substances on stone formation, such as the regulation of oxalate, the release of reactive oxygen species (ROS), macrophage polarization, the levels of hormones, and the alternation of other substances. New insights into changes in substance metabolism changes in kidney stone disease, as well as emerging research techniques, will provide new directions in the treatment of stones. Reviewing the great progress that has been made in this field will help to improve the understanding by urologists, nephrologists, and health care providers of the metabolic changes in kidney stone disease, and contribute to explore new metabolic targets for clinical therapy.

Oxalate decarboxylase uses electron hole hopping for catalysis

The hexameric low-pH stress response enzyme oxalate decarboxylase catalyzes the decarboxylation of the oxalate mono-anion in the soil bacterium Bacillus subtilis. A single protein subunit contains two Mn-binding cupin domains, and catalysis depends on Mn(III) at the N-terminal site. The present study suggests a mechanistic function for the C-terminal Mn as an electron hole donor for the N-terminal Mn. The resulting spatial separation of the radical intermediates directs the chemistry toward decarboxylation of the substrate. A π-stacked tryptophan pair (W96/W274) links two neighboring protein subunits together, thus reducing the Mn-to-Mn distance from 25.9 Å (intrasubunit) to 21.5 Å (intersubunit). Here, we used theoretical analysis of electron hole-hopping paths through redox-active sites in the enzyme combined with site-directed mutagenesis and X-ray crystallography to demonstrate that this tryptophan pair supports effective electron hole hopping between the C-terminal Mn of one subunit and the N-terminal Mn of the other subunit through two short hops of ∼8.5 Å. Replacement of W96, W274, or both with phenylalanine led to a large reduction in catalytic efficiency, whereas replacement with tyrosine led to recovery of most of this activity. W96F and W96Y mutants share the wildtype tertiary structure. Two additional hole-hopping networks were identified leading from the Mn ions to the protein surface, potentially protecting the enzyme from high Mn oxidation states during turnover. Our findings strongly suggest that multistep hole-hopping transport between the two Mn ions is required for enzymatic function, adding to the growing examples of proteins that employ aromatic residues as hopping stations.

Antioxidant and Cytotoxic Effects and Identification of Ophiocordyceps sinensis Bioactive Proteins Using Shotgun Proteomic Analysis

RESEARCH BACKGROUND

Ophiocordyceps sinensis, a highly valued medicinal fungus, is close to extinction due to overexploitation. Successful cultivation of O. sinensis fruiting body (OCS02®) shows that the cultivar has a promising nutritional value and numerous bioactive compounds. Antioxidant and antiproliferative properties and biologically active proteins of the OCS02® are investigated for possible development into nutraceuticals.

EXPERIMENTAL APPROACH

The chemical composition of the OCS02® cold water extract was determined, and the antioxidant activities were examined using ferric reducing, DPPH• and O2 •- scavenging assays. Tetrazolium dye (MTT) cytotoxic assay was performed to assess the antiproliferative activity of the extract. Bioactive proteins in the active fraction of the extract were identified using liquid chromatography (LC) and tandem-mass spectrometry (MS/MS).

RESULTS AND CONCLUSIONS

The OCS02® extract exhibited strong O2 •- scavenging (expressed as Trolox equivalents (18.4±1.1) mol/g) and potent cytotoxic activities against adenocarcinomic human alveolar basal epithelial (A549) cells (IC50=(58.2±6.8) µg/mL). High molecular mass polysaccharides, proteins and protein-polysaccharide complexes could have contributed to the antioxidant and cytotoxic selectivity of the OCS02®. LC-MS/MS analysis identified several potential cytotoxic proteases and an oxalate decarboxylase protein which may exhibit protection effects on kidneys.

NOVELTY AND SCIENTIFIC CONTRIBUTIONS

The findings demonstrate the potential of OCS02® to be developed into functional food due to its promising superoxide anion radical scavenging capacity, cytotoxic effect and presence of biopharmaceutically active proteins.

Subsequent urinary stone events are predicted by the magnitude of urinary oxalate excretion in enteric hyperoxaluria

 

Data directly demonstrating the relationship between urinary oxalate (UOx) excretion and stone events in those with enteric hyperoxaluria (EH) are limited. Therefore, we assessed the relationship between UOx excretion and risk of kidney stone events in a retrospective population-based EH cohort. In all, 297 patients from Olmsted County, Minnesota were identified with EH based upon having a 24-h UOx ≥40 mg/24 h preceded by a diagnosis or procedure associated with malabsorption. Diagnostic codes and urologic procedures consistent with kidney stones during follow-up after baseline UOx were considered a new stone event. Logistic regression and accelerated failure time modeling were performed as a function of UOx excretion to predict the probability of new stone event and the annual rate of stone events, respectively, with adjustment for urine calcium and citrate. Mean ± standard deviation age was 51.4 ± 11.4 years and 68% were female. Median (interquartile range) UOx was 55.4 (46.6-73.0) mg/24 h and 81 patients had one or more stone event during a median follow-up time of 4.9 (2.8-7.8) years. Higher UOx was associated with a higher probability of developing a stone event (P < 0.01) and predicted an increased annual risk of kidney stones (P = 0.001). Estimates derived from these analyses suggest that a 20% decrease in UOx is associated with 25% reduction in the annual odds of a future stone event. Thus, these data demonstrate an association between baseline UOx and stone events in EH patients and highlight the potential benefit of strategies to reduce UOx in this patient group.

BACKGROUND

Data directly demonstrating the relationship between urinary oxalate (UOx) excretion and stone events in those with enteric hyperoxaluria (EH) are limited.

METHODS

We assessed the relationship between UOx excretion and risk of kidney stone events in a retrospective population-based EH cohort. In all, 297 patients from Olmsted County, Minnesota were identified with EH based upon having a 24-h UOx ≥40 mg/24 h preceded by a diagnosis or procedure associated with malabsorption. Diagnostic codes and urologic procedures consistent with kidney stones during follow-up after baseline UOx were considered a new stone event. Logistic regression and accelerated failure time modeling were performed as a function of UOx excretion to predict the probability of new stone event and the annual rate of stone events, respectively, with adjustment for urine calcium and citrate.

RESULTS

Mean ± SD age was 51.4 ± 11.4 years and 68% were female. Median (interquartile range) UOx was 55.4 (46.6-73.0) mg/24 h and 81 patients had ≥1 stone event during a median follow-up time of 4.9 (2.8-7.8) years. Higher UOx was associated with a higher probability of developing a stone event (P < 0.01) and predicted an increased annual risk of kidney stones (P = 0.001). Estimates derived from these analyses suggest that a 20% decrease in UOx is associated with 25% reduction in the annual odds of a future stone event.

CONCLUSIONS

These data demonstrate an association between baseline UOx and stone events in EH patients and highlight the potential benefit of strategies to reduce UOx in this patient group.

Grey mould control by oxalate degradation using non-antifungal Pseudomonas abietaniphila strain ODB36

Grey mould is an important necrotrophic fungal pathogen that causes huge economic losses in agriculture. Many types of bacteria are used for biological control of grey mould via competition for space or nutrients and/or the production of antifungal metabolites. Oxalate is a key component of virulent necrotic fungal pathogens. In this study, we isolated non-antifungal oxalate-degrading bacteria (ODB) from the surfaces of oxalate-rich spinach and strawberries to investigate their ability to control necrotic fungal pathogens such as grey mould. A total of 36 bacteria grown on oxalate minimal (OM) agar plates were tested for oxalate-degrading activity. Five isolates exhibiting the highest oxalate degradation activity were subjected to molecular identification using 16S rRNA gene sequencing. Two isolates exhibiting non-antifungal activity were subjected to disease suppression assays using Arabidopsis–Botrytis systems. The isolate Pseudomonas abietaniphila ODB36, which exhibited significant plant protective ability, was finally selected for further investigation. Based on whole-genome information, the pseudomonad oxalate degrading (podA) gene, which encodes formyl-CoA transferase, was analysed. The podA⁻ mutant did not inhibit Botrytis infection and oxalate toxicity; the defects were recovered by podA complementation. Purified PodA–His converted oxalate to formate and eliminated oxalate toxicity. These results indicate that P. abietaniphila ODB36 and PodA enzyme are associated with various aspects of grey mould disease inhibitory effects.

Analytical procedures and methods validation for oxalate content estimation

Increased urinary oxalate is considered a major risk factor in the formation of calcium oxalate kidney stones. Gut microbiota may reduce the risk of stone formation. Anyway, the first step for any research about monitoring of oxalate content (both in vitro and in vivo) is a determination of its concentration, while there are different methods reported in the literature for oxalate content determination. In this research, the main reported methods including titration with two titrators (potassium permanganate, and NaOH) as well as enzymatic method (oxalate assay kit) are presented and compared for the measurement of oxalate in both inoculated and non-inoculated media.

Evaluation of Oxalobacter formigenes DSM 4420 biodegradation activity for high oxalate media content: An in vitro model

Oxalate is a common component of many foods typically present as a salt of oxalic acid, which will be excreted in the urine. Hyperoxaluria is known to be a considerable risk factor for urolithiasis, and formation of oxalate kidney stone. Oxalate degradation by the probiotic anaerobic bacterium Oxalobacter formigenes DSM 4420 has high yield and efficiency both in the human colon helping to prevent hyperoxaluria and disorders such as the development of kidney stones and as a novel approach in reducing the high concentration of foodstuff oxalate content such as tea, coffee, and nuts. For determining the effective factors to enhance high concentration oxalate biodegradation activity of Oxalobacter formigenes DSM 4420 Plackett-Burman screening design was applied to evaluate the impact of 10 process variables. After determining the main factors by screening design, a response surface methodology was used to find suitable treatment combination for oxalate biodegradation by this probiotic. A second-order quadratic model estimated that the highest biodegradation of 60.2% was achieved in presence of 1.35 (g/L) inulin, 36.56 (g/L) glucose, 26 (mmol/L) ammonium oxalate, and pH 6. In other word, the optimum point showed that in the above condition the high concentration of ammonium oxalate content of 26 mmoL/L will reach to 9.95 mmoL/L. Reconfirmation experiment showed the validity of predicted optimum conditions. A surface model using the RSM and optimizing this model using the GA technique, resulted in a useful method of finding an optimal set of process parameters.

Molecular basis of primary hyperoxaluria: clues to innovative treatments

Primary hyperoxalurias (PHs) are rare inherited disorders of liver glyoxylate metabolism, characterized by the abnormal production of endogenous oxalate, a metabolic end-product that is eliminated by urine. The main symptoms are related to the precipitation of calcium oxalate crystals in the urinary tract with progressive renal damage and, in the most severe form named Primary Hyperoxaluria Type I (PH1), to systemic oxalosis. The therapies currently available for PH are either poorly effective, because they address the symptoms and not the causes of the disease, or highly invasive. In the last years, advances in our understanding of the molecular bases of PH have paved the way for the development of new therapeutic strategies. They include (i) substrate-reduction therapies based on small-molecule inhibitors or the RNA interference technology, (ii) gene therapy, (iii) enzyme administration approaches, (iv) colonization with oxalate-degrading intestinal microorganisms, and, in PH1, (v) design of pharmacological chaperones. This paper reviews the basic principles of these new therapeutic strategies and what is currently known about their application to PH.

Structural Characterization and Repair Mechanism of Gracilaria lemaneiformis Sulfated Polysaccharides of Different Molecular Weights on Damaged Renal Epithelial Cells

Natural Gracilaria lemaneiformis sulfated polysaccharide (GLP0, molecular weight = 622 kDa) was degraded by H2O2 to obtain seven degraded fragments, namely, GLP1, GLP2, GLP3, GLP4, GLP5, GLP6, and GLP7, with molecular weights of 106, 49.6, 10.5, 6.14, 5.06, 3.71, and 2.42 kDa, respectively. FT-IR and NMR results indicated that H2O2 degradation does not change the structure of GLP polysaccharides, whereas the content of the characteristic -OSO3H group (13.46% ± 0.10%) slightly increased than that of the natural polysaccharide (13.07%) after degradation. The repair effects of the polysaccharide fractions on oxalate-induced damaged human kidney proximal tubular epithelial cells (HK-2) were compared. When 60 μg/mL of each polysaccharide was used to repair the damaged HK-2 cells, cell viability increased and the cell morphology was restored, as determined by HE staining. The amount of lactate dehydrogenase released decreased from 16.64% in the injured group to 7.55%-13.87% in the repair groups. The SOD activity increased, and the amount of MDA released decreased. Moreover, the mitochondrial membrane potential evidently increased. All polysaccharide fractions inhibited S phase arrest through the decreased percentage of cells in the S phase and the increased percentage of cells in the G2/M phase. These results reveal that all GLP fractions exhibited repair effect on oxalate-induced damaged HK-2 cells. The repair ability is closely correlated with the molecular weight of the fractions. GLP2 with molecular weight of about 49.6 kDa exhibited the strongest repair effect, and GLP with higher or lower molecular weight than 49.6 kDa showed decreased repair ability. Our results can provide references for inhibiting the formation of kidney stones and developing original anti-stone polysaccharide drugs.