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

Deciphering the mineral code of urinary stones: A first look at zinc isotopes

Zinc (Zn) is an essential element for all living organisms, and Zn isotopes play a key role in studying the formation of disease. Despite extensive studies on Zn isotopes in healthy and diseased human tissues, the role of Zn isotopes in urinary stones remains unexplored. This study investigates Zn isotopes in 37 urinary stones using multi-collector inductively coupled plasma mass spectrometry. The δ66Zn values of urinary stones range from -0.15‰ to 0.47‰, with a mean value of 0.11‰. Carbonate apatite (CA) stones exhibit lighter Zn isotopic compositions (δ66Zn = -0.15‰ ∼ -0.03‰) compared to calcium oxalate (CO) stones (δ66Zn = -0.11‰ ∼ 0.47‰). The variation in Zn isotopic compositions between CO and CA stones may result from urinary pH differences during stone formation. At higher urinary pH, CA stones are enriched in lighter Zn isotopes compared to CO stones. Urinary stones are enriched in lighter Zn isotopes compared to blood and urine. This study identifies two steps influencing Zn isotope variations during kidney transport. The first step involves kidney filtration and reabsorption, enriching heavy Zn isotope in the urine. The second step is the deposition process of urinary stones, where light isotopes, due to their lower bond energy, are more prone to breaking. This kinetic fractionation effect leads to an enrichment of light Zn isotope in urinary stones. Overall, this study offers preliminary insights into the geochemical mechanisms that influence the Zn isotopic composition in urinary stones.

Enzymatic and structural properties of a novel oxalate decarboxylase BsOxdC from Bacillus safensis and its potential pH-dependent catalytic mechanism

Oxalate decarboxylase converts oxalate to formate and CO2 without requiring organic cofactors, making it biotechnologically relevant for applications in food, agriculture, and diagnostics. Its activity is highly dependent on pH; however, the pH-dependent catalytic mechanism remains poorly understood. This study identified a novel oxalate decarboxylase, BsOxdC, from Bacillus safensis and investigated its catalytic properties through heterologous expression and enzymatic assays. The purified BsOxdC efficiently degrades oxalate at an optimum temperature of 50 °C and a pH of 4.0, achieving a Vmax of 8.54 μmol/(min·mg). The apparent values of kcat, Km, and kcat/Km were 85.35 s-1, 4.67 μM, and 18.28 μM/s, respectively. The predicted structure of BsOxdC features two conserved cupin barrel folds at the N-terminal and C-terminal. Additionally, the docking model of the oxalate-BsOxdC complex is more stable than those of the formate-BsOxdC or acetate-BsOxdC complexes due to its lowest binding energy. In the open conformation of BsOxdC, the carboxyl group of the catalytic residue E181, located in the active loop S180E181N182S183T184, points away from both the oxalate and the active-site Mn ion. Simulations suggest that S180 and E181 interact with the substrate via ionic bonds and/or water bridges only at low pH (4.0), not at pH 8.0. Additionally, THR184 forms more molecular interactions with oxalate at pH 4.0 than at pH 8.0.

Association between the composite dietary antioxidant index and the prevalence and recurrence of kidney stones: results of a nationwide survey

Aim

This study aims to evaluate the relationship between the Composite Dietary Antioxidant Index (CDAI) and the prevalence and recurrence of kidney stones.

Methods

Data from the National Health and Nutrition Examination Survey (NHANES) collected between 2007 and 2014 were used in this cross-sectional analysis. The CDAI was derived by standardizing the intake of dietary antioxidants from 24 h dietary recalls. The study assessed the prevalence and recurrence of kidney stones based on questionnaire responses. The association between the CDAI and both the prevalence and recurrence of kidney stones was investigated using multivariable logistic regression. Subgroup analyses and interaction tests further evaluated the robustness of this relationship.

Results

The study included 20,743 participants, and the reported incidence and recurrence rates of kidney stones were 9.09 and 2.90%, respectively. After stratifying the CDAI into tertiles, an inverse trend was observed in both kidney stones' prevalence and recurrence probabilities with increasing CDAI levels. Adjusting for confounding factors, individuals in the top tertile had a 23% lower prevalence of kidney stones (OR = 0.77, 95% CI: 0.66, 0.90, p = 0.0011) and a 39% lower recurrence rate (OR = 0.61, 95% CI: 0.47, 0.80, p = 0.0003) than those in the bottom tertile. In addition, interaction tests showed that age, gender, body mass index, hypertension, and diabetes did not significantly affect the relationship between CDAI levels and kidney stone prevalence and recurrence rates.

Conclusion

Our study suggests that increased levels of CDAI are associated with reduced incidence and recurrence rates of kidney stones. Therefore, increasing the intake of dietary antioxidants may be an effective strategy for preventing kidney stones and their recurrence.

Mechanism of oxalate decarboxylase Oxd_S12 from Bacillus velezensis BvZ45-1 in defence against cotton verticillium wilt

Verticillium wilt, a soilborne vascular disease caused by Verticillium dahliae, strongly affects cotton yield and quality. In this study, an isolated rhizosphere bacterium, designated Bacillus velezensis BvZ45-1, exhibited >46% biocontrol efficacy against cotton verticillium wilt under greenhouse and field conditions. Moreover, through crude protein extraction and mass spectrometry analyses, we found many antifungal compounds present in the crude protein extract of BvZ45-1. The purified oxalate decarboxylase Odx_S12 from BvZ45-1 inhibited the growth of V. dahliae Vd080 by reducing the spore yield, causing mycelia to rupture, spore morphology changes, cell membrane rupture, and cell death. Subsequently, overexpression of Odx_S12 in Arabidopsis significantly improved plant resistance to V. dahliae. Through studies of the resistance mechanism of Odx_S12, V. dahliae was shown to produce oxalic acid (OA), which has a toxic effect on Arabidopsis leaves. Odx_S12 overexpression reduced Arabidopsis OA content, enhanced tolerance to OA, and improved resistance to verticillium wilt. Transcriptomics and quantitative real-time PCR analysis revealed that Odx_S12 promoted a reactive oxygen species burst and a salicylic acid- and abscisic acid-mediated defence response in Arabidopsis. In summary, this study not only identified B. velezensis BvZ45-1 as an efficient biological control agent, but also identified the resistance gene Odx_S12 as a candidate for cotton breeding against verticillium wilt.

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.

Navigating the Evolving Landscape of Primary Hyperoxaluria: Traditional Management Defied by the Rise of Novel Molecular Drugs

Primary hyperoxalurias (PHs) are inherited metabolic disorders marked by enzymatic cascade disruption, leading to excessive oxalate production that is subsequently excreted in the urine. Calcium oxalate deposition in the renal tubules and interstitium triggers renal injury, precipitating systemic oxalate build-up and subsequent secondary organ impairment. Recent explorations of novel therapeutic strategies have challenged and necessitated the reassessment of established management frameworks. The execution of diverse clinical trials across various medication classes has provided new insights and knowledge. With the evolution of PH treatments reaching a new milestone, prompt and accurate diagnosis is increasingly critical. Developing early, effective management and treatment plans is essential to improve the long-term quality of life for PH patients.

Glyoxal in Foods: Formation, Metabolism, Health Hazards, and Its Control Strategies

Glyoxal is a highly reactive aldehyde widely present in common diet and environment and inevitably generated through various metabolic pathways in vivo. Glyoxal is easily produced in diets high in carbohydrates and fats via the Maillard reaction, carbohydrate autoxidation, and lipid peroxidation, etc. This leads to dietary intake being a major source of exogenous exposure. Exposure to glyoxal has been positively associated with a number of metabolic diseases, such as diabetes mellitus, atherosclerosis, and Alzheimer's disease. It has been demonstrated that polyphenols, probiotics, hydrocolloids, and amino acids can reduce the content of glyoxal in foods via different mechanisms, thus reducing the risk of exogenous exposure to glyoxal and alleviating carbonyl stresses in the human body. This review discussed the formation and metabolism of glyoxal, its health hazards, and the strategies to reduce such health hazards. Future investigation of glyoxal from different perspectives is also discussed.

Carboxylated Pocoa polysaccharides inhibited oxidative damage and inflammation of HK-2 cells induced by calcium oxalate nanoparticles

The inhibitory effects of Chinese medicine Pocoa (PCPs) with different carboxyl group (-COOH) contents on oxidative damage and inflammatory response of renal epithelial cells and the influence of -COOH content in polysaccharides were investigated. HK-2 cell damage model was established by nanocalcium oxalate crystals (nanoCOM), and then PCPs with -COOH contents of 2.56% (PCP0), 7.48% (PCP1), 12.07% (PCP2), and 17.18% (PCP3) were used to protect the cells. PCPs could inhibit the damage of nanoCOM to HK-2 cells, increase cell viability, restore cytoskeleton and morphology, and improve lysosomal integrity. PCPs can reduce the oxidative stress response of nanoCOM to cells, inhibit the opening of mPTP and cell necrotic apoptosis, reduce the level of Ca2+ ions in cells, the production of ATP and MDA, and increase SOD expression. PCPs can also reduce the cellular inflammatory response caused by oxidative damage, and reduce the expression of nitric oxide (NO), inflammatory factors TNF-α, IL-6, IL-1β and MCP-1, as well as the content of inflammasome NLRP3. After protection, PCPs can inhibit the endocytosis of nanoCOM crystals by cells. With the increase in -COOH content in PCPs, its ability to inhibit nanoCOM cell damage, reduce oxidative stress, reduce inflammatory response, and inhibit crystal endocytosis increases, that is, PCP3 with the highest -COOH content, shows the best biological activity. Inhibiting cell damage and inflammation and reducing a large amount of endocytosis of crystals by cells are beneficial to inhibit the formation of kidney stones.