Expression of heterologous oxalate decarboxylase in HEK293 cells confers protection against oxalate induced oxidative stress as a therapeutic approach for calcium oxalate stone disease

Decarboxylase mediated oxalic acid metabolism is important to antioxidation and detoxification rather than pathogenicity in Magnaporthe oryzae

Oxalic acid (OA), an essential pathogenic factor, has been identified in several plant pathogens, and researchers are currently pursuing studies on interference with OA metabolism as a treatment for related diseases. However, the metabolic route in Magnaporthe oryzae remains unknown. In this study, we describe D-erythroascorbic acid-mediated OA synthesis and its metabolic and clearance pathways in rice blast fungus. By knocking out the D-arabino-1,4-lactone oxidase gene (Moalo1), one-third of oxalic acid remained in M. oryzae, indicating a main pathway for oxalic acid production. M. oryzae OxdC (MoOxdC) is an oxalate decarboxylase that appears to play a role in relieving oxalic acid toxicity. Loss of Mooxdc does not affect mycelial growth, conidiophore development, or appressorium formation in M. oryzae; however, the antioxidant and pathogenic abilities of the mutant were enhanced. This is owing to Mooxdc deletion upregulated a series of OA metabolic genes, including the oxalate oxidase gene (Mooxo) and Moalo1, as well as both OA transporter genes. Simultaneously, as feedback to the tricarboxylic acid (TCA) cycle, the decrease of formic acid in ΔMooxdc leads to the reduction of acetyl-CoA content, and two genes involved in the β-oxidation of fatty acids were also upregulated, which enhanced the fatty acid metabolism of the ΔMooxdc. Overall, this work reveals the role of OA in M. oryzae. We found that OA metabolism was mainly involved in the growth and development of M. oryzae, OA as a byproduct of D-erythroascorbic acid after removing H2O2, the OA-associated pathway ensures the TCA process and ATP supply.

GOLPH3 promotes calcium oxalate-induced renal injury and fibrosis through Golgi stress-mediated apoptosis and inflammatory responses

A common urological disorder, calcium oxalate (CaOx) stones are the most common form of kidney stones. Deposition of CaOx crystals leads to tubular damage, interstitial fibrosis, and chronic kidney disease. Understanding the intrinsic mechanisms of kidney stone formation is essential for the prevention of kidney stones and the development of new therapeutic agents. The Golgi apparatus is a key organelle in the secretory pathway of eukaryotic cells, which plays an important role in the sorting, modification, and transport of proteins within the cell, and has been reported to be involved in several diseases, including prostate tumors, gastrointestinal tumors, sepsis, and so on. GOLPH3 is also known as GPP34, GMx33, or MIDAS. It is a glycoprotein that regulates traffic between the trans-Golgi network and the cell membrane. However, its role in renal injury caused by CaOx crystal deposition is still unclear. Results from immunohistochemistry, qRT-PCR, western blot, and public database single nucleotide RNA-seq showed that GOLPH3 was significantly upregulated in kidney stone patients and animal kidneys. Significant inhibition of Golgi stress, apoptosis, and renal fibrosis by GOLPH3 inhibition with siRNA in CaOx-stimulated HK-2 cells. The PI3K\AKT\mTOR signaling pathway was inhibited by GOLPH3 knockdown, which may be associated with reduced inflammatory response and apoptosis, as well as restoration of Golgi morphology and function. In conclusion, GOLPH3 plays a critical role in CaOx-induced kidney injury by promoting Golgi stress and increasing inflammatory responses, apoptosis, and renal fibrosis, suggesting that GOLPH3 is a potential therapeutic target for kidney stones.

Mitochondrial dysfunction and NLRP3 inflammasome: key players in kidney stone formation

The mitochondrion serves as a critical intracellular organelle, engaging in essential roles in the regulation of energy production, oxidative stress management, calcium homeostasis, and apoptosis. One such disease that has been particularly associated with these functions is kidney stone disease (KSD), specifically calcium oxalate (CaOx). It is underpinned by oxidative stress and tissue inflammation. Recent studies have shed light on the vital involvement of mitochondrial dysfunction, the nucleotide-binding domain and leucine-rich repeat containing protein 3 (NLRP3) inflammasome, endoplasmic reticulum stress and subsequent cell death in CaOx crystal retention and aggregation. These processes are pivotal in the pathogenesis of kidney stone formation. This review focuses on the pivotal roles of mitochondria in renal cell functions and provides an overview of the intricate interconnectedness between mitochondrial dysfunction and NLRP3 inflammasome activation in the context of KSD. It is essential to recognise the utmost significance of gaining a comprehensive understanding of the mechanisms that safeguard mitochondrial function and regulate the NLRP3 inflammasome. Such knowledge carries significant scientific implications and opens up promising avenues for the development of innovative strategies to prevent the formation of kidney stones.

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.

Therapeutic effects of probiotics and herbal medications on oxalate nephrolithiasis: a mini systematic review

Background and Objectives

The majority of all kidney stone cases are oxalate urolithiasis with a high risk of recurrence. Beside its widespread occurrence, kidney stones are characterized by severe complications and high treatment costs. Probiotics and herbal medications could be forthcoming therapeutic interventions in the management of oxalate kidney stones.

Materials and Methods

The PubMed/MEDLINE database was searched for keywords "Oxalobacter formigenes" AND "Oxalate" OR "oxalate degradation" AND "Lactobacillus" OR "Bifidobacterium" OR "recombinant Lactobacillus" OR "Bacillus subtilis", and "urolithiasis" AND "herbal extract". The search returned 253 results, 38 of which were included in the review.

Results

Most of the oxalate-degrading probiotics belong to the Oxalobacter formigenes, Lactobacillus, Bifidobacterium, and Bacillus genus with a minimum dosage of 107 CFU in the form of capsules, sachets, and lyophilized powder. Oxalate concentration in media was 5-50mM with an incubation time ranging from 24h to 14 days. The majority of the studies suggested that probiotic supplementation might be useful for reducing urinary excretion of oxalate and urea and alleviation of stone formation. Different herbal extracts were used on murine models of nephrolithiasis (induced by 0.5-3% ethylene glycol) with reduction of renal inflammation and urinary parameters, and calcium oxalate crystals.

Conclusion

Several strains of probiotics and herbal extracts confer protective effects against kidney stone/nephrolithiasis, indicating their promising nature for being considered as elements of preventive / adjuvant therapeutic strategies.

Overexpression of sirtuin 1 attenuates calcium oxalate-induced kidney injury by promoting macrophage polarization

Sirtuin 1 (SIRT1) protein is involved in macrophage differentiation, while NOTCH signaling affects inflammation and macrophage polarization. Inflammation and macrophage infiltration are typical processes that accompany kidney stone formation. However, the role and mechanism of SIRT1 in renal tubular epithelial cell injury caused by calcium oxalate (CaOx) deposition and the relationship between SIRT1 and the NOTCH signaling pathway in this urological disorder are unclear. This study investigated whether SIRT1 promotes macrophage polarization to inhibit CaOx crystal deposition and reduce renal tubular epithelial cell injury. Public single-cell sequencing data, RT-qPCR, immunostaining approaches, and Western blotting showed decreased SIRT1 expression in macrophages treated with CaOx or exposed to kidney stones. Macrophages overexpressing SIRT1 differentiated towards the anti-inflammatory M2 phenotype, significantly inhibiting apoptosis and alleviating injury in the kidneys of mice with hyperoxaluria. Conversely, decreased SIRT1 expression in CaOx-treated macrophages triggered Notch signaling pathway activation, promoting macrophage polarization towards the pro-inflammatory M1 phenotype. Our results suggest that SIRT1 promotes macrophage polarization towards the M2 phenotype by repressing the NOTCH signaling pathway, which reduces CaOx crystal deposition, apoptosis, and damage in the kidney. Therefore, we propose SIRT1 as a potential target for preventing disease progression in patients with kidney stones.

Mitochondria-derived vesicles and their potential roles in kidney stone disease

Recent evidence has shown significant roles of mitochondria-derived vesicles (MDVs) in mitochondrial quality control (MQC) system. Under mild stress condition, MDVs are formed to carry the malfunctioned mitochondrial components, such as mitochondrial DNA (mtDNA), peptides, proteins and lipids, to be eliminated to restore normal mitochondrial structure and functions. Under severe oxidative stress condition, mitochondrial dynamics (fission/fusion) and mitophagy are predominantly activated to rescue mitochondrial structure and functions. Additionally, MDVs generation can be also triggered as the major MQC machinery to cope with unhealthy mitochondria when mitophagy is unsuccessful for eliminating the damaged mitochondria or mitochondrial fission/fusion fail to recover the mitochondrial structure and functions. This review summarizes the current knowledge on MDVs and discuss their roles in physiologic and pathophysiologic conditions. In addition, the potential clinical relevance of MDVs in therapeutics and diagnostics of kidney stone disease (KSD) are emphasized.

LncRNA LINC01197 inhibited the formation of calcium oxalate-induced kidney stones by regulating miR-516b-5p/SIRT3/FOXO1 signaling pathway

Long non-coding RNA (lncRNA) plays a key role in the regulation of calcium oxalate (CaOx) crystals-induced kidney stone formation and deposition. The purpose of this study is to study the effect of lncRNA LINC01197 on CaOx-induced kidney stone formation and the underlying mechanism. Crystal cell adhesion in HK-2 cells was evaluated by analyzing Ca2+ concentration. Apoptosis was detected by flow cytometry. The RT-qPCR and western blot were used to detect the mRNA and protein expression. Patients with kidneys stones showed down-regulated LINC01197 and SIRT3 expression, and up-regulated miR-516b-5p expression. LINC01197 knockdown promoted CaOx-induced cell adherence and cell apoptosis, increased Bax, decreased Bcl-2 expression. Luciferase reporter assay showed that SIRT3 expression was promoted by LINC01197 competing binds to miR-516b-5p. In addition, LINC01197 expression was promoted by SIRT3/FOXO1 overexpression, and could be reversed by FOXO1 knockdown. In conclusion, the present study revealed that lncRNA LINC01197 inhibited CaOx-induced kidney stones formation by regulating the miR-516b-5p/SIRT3/FOXO1 signaling pathway.

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.

Advantages of Herbal Over Allopathic Medicine in the Management of Kidney and Urinary Stones Disease

Kidney and urinary stone disease (Nephrolithiasis and urolithiasis) are the condition where urinary stones or calculi are formed in the urinary tract. The problem of urinary stones is very ancient; these stones are found in all parts of the urinary tract, kidney, ureters, and the urinary bladder and may vary considerably in size. It is a common disease estimated to occur in approximately 12% of the population, with a recurrence rate of 70-81% in males and 47-60% in females. The treatment of kidney and urinary stone diseases such as a western (allopathy) medicine and surgery is now in trends. However, most people preferred plant-based (herbal) therapy because of the overuse of allopathic drugs, which results in a higher incidence rate of adverse or severe side effects. Therefore, people every year turn to herbal therapy because they believe plant-based medicine is free from undesirable side effects, although herbal medicines are generally considered to be safe and effective. In the present article, an attempt has been made to emphasize an herbal therapy is better than allopathic therapy for the management of the kidney and urinary stone disease.

Oxidative stress and endoplasmic stress in calcium oxalate stone disease: the chicken or the egg?

Crystal modulators play a significant role in the formation of calcium oxalate stone disease. When renal cells are subjected to oxalate stress, the loss in cell integrity leads to exposure of multiple proteins that assist and/or inhibit crystal attachment and retention. Contact between oxalate and calcium oxalate with urothelium proves fatal to cells as a result of reactive oxygen species generation and onset of oxidative stress. Hence, as a therapeutic strategy it was hypothesised that supplementation of antioxidants would suffice. On the contrary to popular belief, the detection of oxalate induced endoplasmic reticulum mediated apoptosis proved the ineffectiveness of antioxidant therapy alone. Thus, the inadequacy of antioxidant supplementation in oxalate stress invoked the presence of an alternative pathway for the induction of kidney fibrosis in hyperoxaluric rats. In addition to settling this query, the link between oxidative stress and ER stress is not well understood, especially in urolithiasis.

SIRT3 inhibited the formation of calcium oxalate-induced kidney stones through regulating NRF2/HO-1 signaling pathway

Oxidative stress is important for the calcium oxalate (CaOx)-induced kidney stone formation. Sirtuin 3 (SIRT3) plays an essential role in the amelioration of oxidative damages. This study aims to explore the effect of SIRT3 on the formation of CaOx-induced kidney stones and the underlying mechanism. SIRT3 expression in renal tissues was detected by immunohistochemistry. Apoptosis in renal tissues was examined by TUNEL staining. Crystal-cell adherence and cell apoptosis in HK-2 cells were assessed by analyzing Ca²⁺ concentration and by the flow cytometry analysis, respectively. Protein expression of SIRT3, nuclear factor erythroid 2-related factor (NRF2), heme oxygenase-1 (HO-1), and Bax in renal tissues or HK-2 cells was examined by Western blot analysis. Renal pathological changes and the adhesion of CaOx crystals in the kidneys were examined by hematoxylin-eosin and von Kossa staining, respectively. Human kidneys with stones showed enhanced renal apoptosis, downregulated SIRT3 expression, and upregulated NRF2/HO-1 expression, compared with the controls. Furthermore, SIRT3 overexpression inhibited the CaOx-induced promotion of crystal-cell adherence and cell apoptosis in human proximal tubular cell line HK-2 cells, which was reversed by the NRF2 knockdown. Moreover, our in vivo assay further confirmed that SIRT3 overexpression alleviated the glyoxylate administration-induced renal damage, renal apoptosis, and crystals deposition in the kidneys from the stone model mice, which was also associated with its activation of the NRF2/HO-1 pathway. Our findings support the notion that overexpression of SIRT3 may inhibit the formation of CaOx-induced kidney stones, at least in part, through regulating the NRF2/HO-1 signaling pathway.

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.

Manipulation of oxalate metabolism in plants for improving food quality and productivity

Oxalic acid is a naturally occurring metabolite in plants and a common constituent of all plant-derived human diets. Oxalic acid has diverse unrelated roles in plant metabolism, including pH regulation in association with nitrogen metabolism, metal ion homeostasis and calcium storage. In plants, oxalic acid is also a pathogenesis factor and is secreted by various fungi during host infection. Unlike those of plants, fungi and bacteria, the human genome does not contain any oxalate-degrading genes, and therefore, the consumption of large amounts of plant-derived oxalate is considered detrimental to human health. In this review, we discuss recent biotechnological approaches that have been used to reduce the oxalate content of plant tissues.

Long noncoding RNA LINC00339 promotes renal tubular epithelial pyroptosis by regulating the miR-22-3p/NLRP3 axis in calcium oxalate-induced kidney stone

This study aims to investigate the role of long noncoding RNA (lncRNA) long intergenic nonprotein coding RNA 339 (LINC00339) in regulating renal tubular epithelial pyroptosis in kidney stones and to explore the underlying mechanism. The human renal proximal tubular epithelial (HK-2) cells were treated with calcium oxalate monohydrate (COM) for 72 hours to establish the cell model of renal tubular injury. Relative expression of LINC00339 and miR-22-3p was measured by real-time quantitative reverse transcription polymerase chain reaction. Expression of pyroptosis-related molecules was measured by Western blot analysis (NLRP3, ASC, and cleaved caspase-1 p10) and enzyme-linked immunosorbent assay (interleukin-1β [IL-1β] and IL-18). Pyroptosis was also determined by lactate dehydrogenase release and active caspase-1-propidium iodide double staining. Luciferase reporter assays were performed to verify whether miR-22-3p could bind to LINC00339 or NLRP3. We observed increased LINC00339, decreased miR-22-3p, NLRP3 inflammasome activation, and enhanced cell pyroptosis in COM-treated HK-2 cells. Furthermore, overexpression of both LINC00339 and NLRP3 activated NLRP3 inflammasome and promoted pyroptosis in COM-treated HK-2 cells, whereas miR-22-3p mimic and NLRP3 knockdown exerted the opposite effects. Mechanically, LINC00339 functioned as a competitive endogenous RNA by sponging miR-22-3p to facilitate NLRP3 expression. In conclusion, lncRNA LINC00339 promotes cell pyroptosis by sponging miR-22-3p to regulate NLRP3 expression in COM-treated HK-2 cells.

Chromosomal integration of heterologous oxalate decarboxylase in Lactobacillus plantarum WCFS1 using mobile genetic element Ll.LtrB

Lactobacillus plantarum WCFS1 (L. plantarum WCFS1) is commonly used as a potential cell factory because of its 'generally recognized as safe' status. The plasmid instability and the presence of antibiotic selection marker complicate the application of genetically modified L. plantarum in human clinical trials. In the present study, we aimed to integrate oxalate decarboxylase (oxdC) gene of Bacillus subtilis origin by targeted chromosomal mutation in L. plantarum using mobile genetic element Ll.LtrB as a therapeutic tool against calcium oxalate stone disease. oxdC expression cassette was constructed and integrated into a targeted gene, thymidylate synthase (thyA) in the L. plantarum genome. The dependence on external thymidine for growth and survival was established by live dead population assay and SEM (scanning electron microscopy) analysis. The western blotting assay showed the secretion of 44 kDa OxdC protein in the culture supernatant of L. plantarum ∆thyA:OxdC. The biologically contained recombinant strain significantly reduced the oxalate concentration by 53% and exhibited a loss of viability when introduced to environmental samples. Biologically contained L. plantarum secreting OxdC constructed using group II intron has the ability to degrade oxalate present in the extracellular environment and could be used as a therapeutic tool for the calcium oxalate stone disease.

Downregulated Expression of Solute Carrier Family 26 Member 6 in NRK-52E Cells Attenuates Oxalate-Induced Intracellular Oxidative Stress

Solute carrier family 26 member 6 (Slc26a6), which is mainly expressed in the intestines and kidneys, is a multifunctional anion transporter that is crucial in the transport of oxalate anions. This study is aimed at investigating the effect of Slc26a6 expression on oxalate-induced cell oxidation and crystal formation. Lentivirus transfection was used to upregulate or downregulate Slc26a6 expression in NRK cells. Cell viability and apoptosis, reactive oxygen species (ROS) and malondialdehyde (MDA) generation, and superoxide dismutase (SOD) activity were measured. Crystal adhesion and the cell ultrastructure were observed using light and transmission electron microscopy (TEM). Three groups of rats, normal control, lentivirus-vector, and lentivirus-small interfering RNA (lv-siRNA) groups, were used, and after lentivirus transfection, they were fed 1% ethylene glycol (EG) and 0.5% ammonium chloride (NH₄Cl) for 2 weeks. Dihydroethidium (DHE), terminal deoxynucleotidyl transferase (TdT) deoxyuridine dUTP nick-end labeling (TUNEL), and von Kossa staining were performed, and nuclear factor κB (NFκB) and osteopontin (OPN) expression were measured. In the vitro study, compared to the control group, downregulated Slc26a6 NRK cells showed alleviation of the cell viability decrease, cell apoptosis rate, ROS generation, and SOD activity decrease after oxalate treatment. Crystal adhesion and vesicles were significantly less after oxalate exposure than in the untreated controls. Rats infected with lentivirus-siRNA exhibited attenuated SOD generation, cell apoptosis, and crystal formation in the kidneys. Increased phosphorylation of NFκB and OPN was involved in the pathological process. In conclusion, the results of the present study indicate that reducing the expression of Slc26a6 in the kidney may be a potential strategy for preventing stone formation.