Metal ion availability and homeostasis as drivers of metabolic evolution and enzyme function

Fabrication of imine-based COFs with different linker lengths for HRP and GOx immobilization and colorimetric detection of glucose and H2O2

Covalent organic frameworks (COFs) have emerged as excellent candidates for enzyme immobilization due to their high surface tunability, diverse structures, inherent porosity, and metal-free characteristics. However, reports on optimizing the efficiency of immobilized enzymes in COFs by controlling linker length are scarce. In this work, horseradish peroxidase (HRP) and glucose oxidase (GOx), are co-immobilized on three imine-based COFs with different linker lengths using a one-pot method, resulting in HRP&GOX@COF (COF = LZU1, TbBD, TbDI). The immobilization of HRP and GOX using these three COF materials led to a slight decrease in enzyme activity compared to the free enzymes; however, a significant improvement in the stability of the immobilized enzymes was achieved. Besides, the experimental results demonstrate that all three materials HRP&GOX@COF (COF = LZU1, TbBD, TbDI) exhibit good colorimetric detection, stability, and recyclability for glucose and hydrogen peroxide (H2O2), using 2,2'-biazobis (3-ethylbenzothiazole-6-sulfonic acid) diammonium salt (ABTS) as a chromogenic agent. Notably, HRP&GOX@LZU1, which has the shortest linker, shows the highest enzyme loading efficiency (45.3 %) and the most effective colorimetric detection, with detection limits of 0.265 mM for glucose and 0.100 mM for H2O2. This work highlights the importance of linker length in designing COFs for enzyme immobilization and colorimetric recognition of H2O2 and glucose.

From nutrient bioavailability to disease resistance: The comprehensive benefits of chelated minerals in aquaculture

The integration of chelated minerals into aquaculture diets represents a significant advancement in enhancing the health and productivity of aquatic species. These minerals improve nutrient bioavailability, boost immune responses, and increase disease resistance in fish and shrimp, effectively addressing key challenges in aquaculture sustainability. This review highlights the benefits of chelated minerals, including their role in improving feed efficiency, promoting resilience against infections, and mitigating heavy metal toxicity. Key findings indicate that chelated minerals enhance nutrient absorption, which is crucial for optimizing growth and overall health. Furthermore, they strengthen immune responses, thereby increasing resilience to diseases in aquaculture environments. Additionally, these minerals boost antioxidant capacity, helping to alleviate oxidative stress caused by environmental factors and pathogens. The review emphasizes the need for further research to optimize the use of chelated minerals, focusing on mechanisms of action, species-specific responses, and long-term impacts on ecosystems. Successful implementation will require collaboration among researchers, nutritionists, and practitioners to develop evidence-based guidelines for their responsible use. In conclusion, the incorporation of chelated minerals into aquaculture diets has the potential to revolutionize practices and significantly improve the welfare of aquatic species.

Characterization of a Na+-stimulated acidic hyaluronate lyase from Microbulbifer sp. ALW1 and the antioxidant activity of its hydrolysates

Hyaluronic acid (HA) is a natural polymer that can be degraded by hyaluronate lyase into oligomers with diverse biological activities. In this study, a novel hyaluronate lyase (named HCLase6) of polysaccharide lyase family 6 from Microbulbifer sp. ALW1 was cloned and characterized. Optimal temperature and pH for HCLase6 was determined to be 40 ℃ and 5.0, respectively. It displayed good stability at temperature up to 45 ℃ and in the pH range of 4.0-9.0. In addition, HCLase6 demonstrated good tolerance to detergents of Tween 20, Tween 80 and SDS, and was halophilic and halotolerant to Na+. Molecular dynamics simulations indicated that the presence of Na+ increased the flexibility of the loop region adjacent to the active pocket of HCLase6, altered the surface hydrophobicity and electrostatic potential, and strengthened the motion correlation between amino acid residues. Notably, the enzymatic products of HA oligosaccharides (O-HA) produced by HCLase6 showed significantly enhanced free radical scavenging activities and iron reducing power. They also exhibited the antioxidant activity in human keratinocytes cells after exposure to PM SRM 1648a. This study provides the knowledge of the enzymatic properties of HCLase6 and a reference for its industrial application.

Origin of the RNA World in Cold Hadean Geothermal Fields Enriched in Zinc and Potassium: Abiogenesis as a Positive Fallout from the Moon-Forming Impact?

The ubiquitous, evolutionarily oldest RNAs and proteins exclusively use rather rare zinc as transition metal cofactor and potassium as alkali metal cofactor, which implies their abundance in the habitats of the first organisms. Intriguingly, lunar rocks contain a hundred times less zinc and ten times less potassium than the Earth's crust; the Moon is also depleted in other moderately volatile elements (MVEs). Current theories of impact formation of the Moon attribute this depletion to the MVEs still being in a gaseous state when the hot post-impact disk contracted and separated from the nascent Moon. The MVEs then fell out onto juvenile Earth's protocrust; zinc, as the most volatile metal, precipitated last, just after potassium. According to our calculations, the top layer of the protocrust must have contained up to 1019 kg of metallic zinc, a powerful reductant. The venting of hot geothermal fluids through this MVE-fallout layer, rich in metallic zinc and radioactive potassium, both capable of reducing carbon dioxide and dinitrogen, must have yielded a plethora of organic molecules released with the geothermal vapor. In the pools of vapor condensate, the RNA-like molecules may have emerged through a pre-Darwinian selection for low-volatile, associative, mineral-affine, radiation-resistant, nitrogen-rich, and polymerizable molecules.

Identification of biomarkers in Alzheimer's disease and COVID-19 by bioinformatics combining single-cell data analysis and machine learning algorithms

BACKGROUND

Since its emergence in 2019, COVID-19 has become a global epidemic. Several studies have suggested a link between Alzheimer's disease (AD) and COVID-19. However, there is little research into the mechanisms underlying these phenomena. Therefore, we conducted this study to identify key genes in COVID-19 associated with AD, and evaluate their correlation with immune cells characteristics and metabolic pathways.

METHODS

Transcriptome analyses were used to identify common biomolecular markers of AD and COVID-19. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were performed on gene chip datasets (GSE213313, GSE5281, and GSE63060) from AD and COVID-19 patients to identify genes associated with both conditions. Gene ontology (GO) enrichment analysis identified common molecular mechanisms. The core genes were identified using machine learning. Subsequently, we evaluated the relationship between these core genes and immune cells and metabolic pathways. Finally, our findings were validated through single-cell analysis.

RESULTS

The study identified 484 common differentially expressed genes (DEGs) by taking the intersection of genes between AD and COVID-19. The black module, containing 132 genes, showed the highest association between the two diseases according to WGCNA. GO enrichment analysis revealed that these genes mainly affect inflammation, cytokines, immune-related functions, and signaling pathways related to metal ions. Additionally, a machine learning approach identified eight core genes. We identified links between these genes and immune cells and also found a association between EIF3H and oxidative phosphorylation.

CONCLUSION

This study identifies shared genes, pathways, immune alterations, and metabolic changes potentially contributing to the pathogenesis of both COVID-19 and AD.

Predicting substrates for orphan solute carrier proteins using multi-omics datasets

Solute carriers (SLC) are integral membrane proteins responsible for transporting a wide variety of metabolites, signaling molecules and drugs across cellular membranes. Despite key roles in metabolism, signaling and pharmacology, around one third of SLC proteins are 'orphans' whose substrates are unknown. Experimental determination of SLC substrates is technically challenging, given the wide range of possible physiological candidates. Here, we develop a predictive algorithm to identify correlations between SLC expression levels and intracellular metabolite concentrations by leveraging existing cancer multi-omics datasets. Our predictions recovered known SLC-substrate pairs with high sensitivity and specificity compared to simulated random pairs. CRISPR-Cas9 dependency screen data and metabolic pathway adjacency data further improved the performance of our algorithm. In parallel, we combined drug sensitivity data with SLC expression profiles to predict new SLC-drug interactions. Together, we provide a novel bioinformatic pipeline to predict new substrate predictions for SLCs, offering new opportunities to de-orphanise SLCs with important implications for understanding their roles in health and disease.

The ability of pentose pathways to form all essential metabolites provides clues to the origins of metabolism

The structure of the early metabolic network is unknown. Here, we report that when considered together, pentose utilization pathways form all life-essential precursors. We speculate that the chemistry preserved in pentose metabolism could therefore have been a central structural element in early metabolism.

Assembly and biological functions of metal-biomolecule network nanoparticles formed by metal-phosphonate coordination

Metal-organic networks have attracted widespread interest owing to their hybrid physicochemical properties. Natural biomolecules represent attractive building blocks for these materials because of their inherent biological function and high biocompatibility; however, assembling them into coordination network materials, especially nanoparticles (NPs), is challenging. Herein, we exploit the coordination between metal ions and phosphonate groups, which are present in many biomolecules, to form metal-biomolecule network (MBN) NPs in aqueous solution at room temperature. Various phosphonate-containing biomolecules, including plant phytate, DNA, and proteins, were used to assemble MBN NPs with tunable physicochemical properties (e.g., size). In addition to excellent biocompatibility and high cargo-loading efficiency (>95%), these two-component MBN NPs have various biological functionalities, including endosomal escape, immune regulation, and molecular recognition, thus offering advantages over nonbiomolecular-based coordination materials. This work expands our understanding of metal-organic chemistry with the emerging class of metal-biomolecule systems and provides a pathway for incorporating biofunctionalities into advanced coordination materials for diverse fields.

Biomolecular Condensation of Trypsin Prevents Autolysis and Promotes Ca2+-Mediated Activation of Esterase Activity

The presence of Ca2+ ions is known to facilitate the activity of trypsin-like serine proteases via structural stabilization against thermal denaturation and autolysis. Herein, we report a new and hidden regulatory role of Ca2+ in the catalytic pathways of trypsin and α-chymotrypsin under physiological conditions. We discovered that macromolecular crowding promotes spontaneous homotypic condensation of trypsin via liquid-liquid phase separation to yield membraneless condensates over a broad range of concentrations, pH, and temperature, which are stabilized by multivalent hydrophobic interactions. Interestingly, we found that Ca2+ binding in the calcium binding loop reversibly regulates the condensation of trypsin and α-chymotrypsin. Spontaneous condensation effectively prevents autolysis of trypsin and preserves its native-like esterase activity for a prolonged period of time. It has also been found that phase-separated trypsin responds to Ca2+-dependent activation of its esterase activity even after 14 days of storage while free trypsin failed to do so. The present study highlights an important physiological aspect by which cells can spatiotemporally regulate the biocatalytic efficacy of trypsin-like serine proteases via Ca2+-signaling.

Unveiling the role of inorganic nanoparticles in Earth's biochemical evolution through electron transfer dynamics

This article explores the intricate interplay between inorganic nanoparticles and Earth's biochemical history, with a focus on their electron transfer properties. It reveals how iron oxide and sulfide nanoparticles, as examples of inorganic nanoparticles, exhibit oxidoreductase activity similar to proteins. Termed "life fossil oxidoreductases," these inorganic enzymes influence redox reactions, detoxification processes, and nutrient cycling in early Earth environments. By emphasizing the structural configuration of nanoparticles and their electron conformation, including oxygen defects and metal vacancies, especially electron hopping, the article provides a foundation for understanding inorganic enzyme mechanisms. This approach, rooted in physics, underscores that life's origin and evolution are governed by electron transfer principles within the framework of chemical equilibrium. Today, these nanoparticles serve as vital biocatalysts in natural ecosystems, participating in critical reactions for ecosystem health. The research highlights their enduring impact on Earth's history, shaping ecosystems and interacting with protein metal centers through shared electron transfer dynamics, offering insights into early life processes and adaptations.

Activation of Coq6p, a FAD Monooxygenase Involved in Coenzyme Q Biosynthesis, by Adrenodoxin Reductase/Ferredoxin

Adrenodoxin reductase (AdxR) plays a pivotal role in electron transfer, shuttling electrons between NADPH and iron/sulfur adrenodoxin proteins in mitochondria. This electron transport system is essential for P450 enzymes involved in various endogenous biomolecules biosynthesis. Here, we present an in-depth examination of the kinetics governing the reduction of human AdxR by NADH or NADPH. Our results highlight the efficiency of human AdxR when utilizing NADPH as a flavin reducing agent. Nevertheless, akin to related flavoenzymes such as cytochrome P450 reductase, we observe that low NADPH concentrations hinder flavin reduction due to intricate equilibrium reactions between the enzyme and its substrate/product. Remarkably, the presence of MgCl2 suppresses this complex kinetic behavior by decreasing NADPH binding to oxidized AdxR, effectively transforming AdxR into a classical Michaelis-Menten enzyme. We propose that the addition of MgCl2 may be adapted for studying the reductive half-reactions of other flavoenzymes with NADPH. Furthermore, in vitro experiments provide evidence that the reduction of the yeast flavin monooxygenase Coq6p relies on an electron transfer chain comprising NADPH-AdxR-Yah1p-Coq6p, where Yah1p shuttles electrons between AdxR and Coq6p. This discovery explains the previous in vivo observation that Yah1p and the AdxR homolog, Arh1p, are required for the biosynthesis of coenzyme Q in yeast.

An ancient bacterial zinc acquisition system identified from a cyanobacterial exoproteome

Bacteria have developed fine-tuned responses to cope with potential zinc limitation. The Zur protein is a key player in coordinating this response in most species. Comparative proteomics conducted on the cyanobacterium Anabaena highlighted the more abundant proteins in a zur mutant compared to the wild type. Experimental evidence showed that the exoprotein ZepA mediates zinc uptake. Genomic context of the zepA gene and protein structure prediction provided additional insights on the regulation and putative function of ZepA homologs. Phylogenetic analysis suggests that ZepA represents a primordial system for zinc acquisition that has been conserved for billions of years in a handful of species from distant bacterial lineages. Furthermore, these results show that Zur may have been one of the first regulators of the FUR family to evolve, consistent with the scarcity of zinc in the ecosystems of the Archean eon.

A PD-L1-targeting Regulator for Metabolic Reprogramming to Enhance Glutamine Inhibition-Mediated Synergistic Antitumor Metabolic and Immune Therapy

Inhibition of glutamine metabolism in tumor cells can cause metabolic compensation-mediated glycolysis enhancement and PD-L1 upregulation-induced immune evasion, significantly limiting the therapeutic efficacy of glutamine inhibitors. Here, inspired by the specific binding of receptor and ligand, a PD-L1-targeting metabolism and immune regulator (PMIR) are constructed by decorating the glutaminase inhibitor (BPTES)-loading zeolitic imidazolate framework (ZIF) with PD-L1-targeting peptides for regulating the metabolism within the tumor microenvironment (TME) to improve immunotherapy. At tumor sites, PMIR inhibits glutamine metabolism of tumor cells for elevating glutamine levels within the TME to improve the function of immune cells. Ingeniously, the accompanying PD-L1 upregulation on tumor cells causes self-amplifying accumulation of PMIR through PD-L1 targeting, while also blocking PD-L1, which has the effects of converting enemies into friends. Meanwhile, PMIR exactly offsets the compensatory glycolysis, while disrupting the redox homeostasis in tumor cells via the cooperation of components of the ZIF and BPTES. These together cause immunogenic cell death of tumor cells and relieve PD-L1-mediated immune evasion, further reshaping the immunosuppressive TME and evoking robust immune responses to effectively suppress bilateral tumor progression and metastasis. This work proposes a rational strategy to surmount the obstacles in glutamine inhibition for boosting existing clinical treatments.

Calcium carbonate-actuated ion homeostasis perturbator for oxidative damage-augmented Ca2+/Mg2+ interference therapy

Ion homeostasis distortion through exogenous overload or underload of intracellular ion species has become an arresting therapeutic approach against malignant tumor. Nevertheless, treatment outcomes of such ion interference are always compromised by the intrinsic ion homeostasis maintenance systems in cancer cells. Herein, an ion homeostasis perturbator (CTC) is facilely designed by co-encapsulation of carvacrol (CAR) and meso-tetra-(4-carboxyphenyl)porphine (TCPP) into pH-sensitive nano-CaCO3, aiming to disrupt the self-defense mechanism during the process of ion imbalance. Upon the endocytosis of CTC into tumor cells, lysosomal acidity can render the decomposition of CaCO3, resulting in the instant Ca2+ overload and CO2 generation in cytoplasm. Simultaneously, CaCO3 disintegration triggers the release of CAR and TCPP, which are devoted to TRPM7 inhibition and sonosensitization, respectively. The malfunction of TRPM7 can impede the influx of Mg2+ and allow unrestricted influx of Ca2+ based on the antagonism relationship between Mg2+ and Ca2+, leading to an aggravated Ca2+/Mg2+ dyshomeostasis through ion channel deactivation. In another aspect, US-triggered cavitation can be significantly enhanced by the presence of inert CO2 microbubbles, further amplifying the generation of reactive oxygen species. Such oxidative damage-augmented Ca2+/Mg2+ interference therapy effectively impairs the mitochondrial function of tumor, which may provide useful insights in cancer therapy.

Membrane transporters in cell physiology, cancer metabolism and drug response

By controlling the passage of small molecules across lipid bilayers, membrane transporters influence not only the uptake and efflux of nutrients, but also the metabolic state of the cell. With more than 450 members, the Solute Carriers (SLCs) are the largest transporter super-family, clustering into families with different substrate specificities and regulatory properties. Cells of different types are, therefore, able to tailor their transporter expression signatures depending on their metabolic requirements, and the physiological importance of these proteins is illustrated by their mis-regulation in a number of disease states. In cancer, transporter expression is heterogeneous, and the SLC family has been shown to facilitate the accumulation of biomass, influence redox homeostasis, and also mediate metabolic crosstalk with other cell types within the tumour microenvironment. This Review explores the roles of membrane transporters in physiological and malignant settings, and how these roles can affect drug response, through either indirect modulation of sensitivity or the direct transport of small-molecule therapeutic compounds into cells.

Protection Mechanism of Metal Ion Pre-Stress on Lactobacillus acidophilus CICC 6074 under Acid Tolerance

The prerequisite for the probiotic effect of lactic acid bacteria is that they could survive the acid stress environment of production and application. In this experiment, the mechanism for the effect of different metal ion pre-stress on the acid-tolerant survival of Lactobacillus was investigated. Scanning electron microscopy, Fourier infrared spectroscopy, and flow cytometry were used to analyze the condition of bacteria after acid treatment, which revealed that different metal ion pre-stress could improve the survival ability of Lactobacillus acidophilus CICC 6074 under low acid conditions by improving cell morphology, mitigating cell membrane damage, and regulating surface protein expression. Furthermore, Tandem Mass Tags (TMT) proteomic analysis revealed that Mn2+ pre-stress showed relatively more superior protective effects on acid tolerance in L. acidophilus CICC 6074 through activation of DNA replication, RNA synthesis, S-layer protein secretion, H+-ATPase enzyme activity, etc. This study will provide new ideas and a theoretical basis for the development and application of lactic acid bacteria.

Prebiotic Synthesis of Aspartate Using Life's Metabolism as a Guide

A protometabolic approach to the origins of life assumes that the conserved biochemistry of metabolism has direct continuity with prebiotic chemistry. One of the most important amino acids in modern biology is aspartic acid, serving as a nodal metabolite for the synthesis of many other essential biomolecules. Aspartate's prebiotic synthesis is complicated by the instability of its precursor, oxaloacetate. In this paper, we show that the use of the biologically relevant cofactor pyridoxamine, supported by metal ion catalysis, is sufficiently fast to offset oxaloacetate's degradation. Cu²⁺-catalysed transamination of oxaloacetate by pyridoxamine achieves around a 5% yield within 1 h, and can operate across a broad range of pH, temperature, and pressure. In addition, the synthesis of the downstream product β-alanine may also take place in the same reaction system at very low yields, directly mimicking an archaeal synthesis route. Amino group transfer supported by pyridoxal is shown to take place from aspartate to alanine, but the reverse reaction (alanine to aspartate) shows a poor yield. Overall, our results show that the nodal metabolite aspartate and related amino acids can indeed be synthesised via protometabolic pathways that foreshadow modern metabolism in the presence of the simple cofactor pyridoxamine and metal ions.

Peroxidase-Mimicking DNAzymes as Receptors for Label-Free Discriminating Heavy Metal Ions by Chemiluminescence Sensor Arrays

Receptors are crucial to the analytical performance of sensor arrays. Different from the previous receptors in sensor arrays, herein, peroxidase-mimicking DNAzymes were innovatively used as receptors to develop a label-free chemiluminescence sensor array for discriminating various heavy metal ions in complex samples. The peroxidase-mimicking DNAzymes are composed of functional oligonucleotides and hemin, including G-triplex-hemin DNAzyme (G3-DNAzyme), G-quadruplex-hemin DNAzyme (G4-DNAzyme), and the dimer of G-quadruplex-hemin DNAzyme (dG4-DNAzyme). Circular dichroism (CD) spectroscopy demonstrated that different metal ions diversely affect the conformation of G-quadruplex and G-triplex, resulting in a change in the activity of peroxidase-mimicking DNAzyme. Thus, the unique fingerprints formed to easily discriminate seven kinds of heavy metal ions by principal component analysis (PCA) within 20 min. The discrimination of unknown metal ions in tap water further confirmed its ability for discriminating multiple heavy metal ions. Moreover, it will not bring water pollution due to the good biocompatibility of DNA. Therefore, it not only merely offers a label-free, rapid, environment-friendly, and cheap (1.49 $) sensor assay for discriminating metal ions but also comes up with an innovative way for developing sensor arrays.