Search Results (40)

The investigation of the structure–function relationship in hypoxanthine-guanine phosphoribosyltransferases (HGPRT) is a direction that is relevant for the development of drugs and approaches of enzymatic synthesis of modified nucleosides and nucleotides. This research paper is dedicated to the investigation of binding of sulphonate molecules, such as HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) in the active sites of HGPRT and similar proteins. We report the crystal structure of HGPRT from Escherichia coli (EcoHGPRT) in a complex with HEPES. In the obtained X-ray structure, a HEPES molecule binds to the active site in a position that mimics one of the HGPRT substrates, namely phosphoribosylpyrophosphate (PRPP). Enzymological study has shown that HEPES is an inhibitor of EcoHGPRT, along with two structurally similar molecules, namely MES and PIPES. Comparison of the observed EcoHGPRT/HEPES complex to other reported structures in the context of inhibition study results provides an opportunity to explore the variety of binding modes of HEPES and similar molecules and to discuss the structure–function relationship in this enzyme and similar proteins. Full article

Cyclic nucleotide signaling pathways play essential roles in the physiology of the nematode Caenorhabditis elegans, influencing processes such as reproduction, environmental sensing, and cellular homeostasis. The intracellular levels of cAMP and cGMP are tightly regulated by their synthesis by adenylyl and guanylyl cyclases and their degradation catalyzed by 3′,5′-cyclic nucleotide phosphodiesterases (PDEs). Mammals possess eleven PDE families (PDE1 through PDE11), whereas nematode genomes contain six PDE genes orthologous to six of the mammalian PDE families. Despite their evolutionary conservation, the signaling pathways, regulatory mechanisms, and enzymatic properties of nematode PDEs remain incompletely understood. This review synthesizes current knowledge on the regulation of cyclic nucleotide levels in C. elegans, highlighting how dysregulation of nematode PDEs affects a wide range of physiological and behavioral processes, including sensory transduction, development, and locomotion. Full article

Hyaluronic acid (HA) is a linear heteropolysaccharide that naturally occurs in vertebrates. Thanks to its unique physico-chemical properties, it is involved in many key processes in living organisms. These biological activities provide the basis for its broad applications in cosmetics, medicine, and the food industry. The molecular weight of HA might vary significantly, as it can be less than 10 kDa or reach more than 6000 kDa. There is a strong correlation between variations in its molecular weight and bioactivities, as well as with various pathological processes. Consequently, monodispersity is a crucial requirement for HA production, together with purity and safety. Common industrial approaches, such as extraction from animal sources and microbial fermentation, have limits in fulfilling these requests. Research and protein engineering with hyaluronic acid synthases can provide a strong tool for the production of monodisperse HA. One-pot multi-enzyme reactions that include in situ nucleotide phosphate regeneration systems might represent the future of HA production. In this review, we explore the current knowledge about HA, its production, hyaluronic synthases, the most recent stage of in vitro enzymatic synthesis research, and one-pot approaches. Full article

Termitomyces, a rare edible fungus with both nutritional and medicinal value, has garnered significant attention for its antioxidant properties. This study aims to elucidate the effects of various nutritional components on the antioxidant activity of Termitomyces. Through assays including FRAP, DPPH, ABTS, and •OH scavenging activity, strain XNQL025, which exhibits high antioxidant activity, was identified. Subsequent optimization of culture medium components using single-factor experiments and response surface methodology revealed that aspartic acid (Asp) significantly enhances the antioxidant capacity of this strain. Transcriptomic analysis showed that Asp activates key pathways, including glycolysis/gluconeogenesis, propanoate metabolism, amino sugar and nucleotide sugar metabolism, valine–leucine–isoleucine biosynthesis, and tryptophan metabolism, along with modulating the peroxisome and mitogen-activated protein kinase (MAPK) signaling pathways. These regulatory actions promote the synthesis of antioxidant compounds and establish a multi-layered antioxidant defense system comprising enzymatic (catalase) and non-enzymatic (leucine/chitooligosaccharides) components. The synergistic interaction between these systems significantly strengthens the antioxidant defense capacity of Termitomyces. This study is the first to elucidate the molecular network by which Asp enhances the antioxidant activity of Termitomyces, thereby providing a foundation for its development as a natural antioxidant. Full article

Dictyostelium is a unique model used to study the complex and interactive cyclic nucleotide signaling pathways that regulate multicellular development. Dictyostelium grow as individual single cells, but in the absence of nutrients, they initiate a multicellular developmental program. Central to this is secreted cAMP, a primary GPCR-response signal. Activated cAMP receptors at the cell surface direct a number of downstream signaling pathways, including synthesis of the intracellular second messengers cAMP and cGMP. These, in turn, activate a series of downstream targets that direct chemotaxis within extracellular cAMP gradients, multicellular aggregation, and, ultimately, cell-specific gene expression, morphogenesis, and cytodifferentiation. Extracellular cAMP and intracellular cAMP and cGMP exhibit rapid fluctuations in concentrations and are, thus, subject to exquisite regulation by both synthesis and degradation. The Dictyostelium genome encodes seven phosphodiesterases (PDEs) that degrade cyclic nucleotides to nucleotide 5’-monophosphates. Each PDE has a distinct structure, substrate specificity, regulatory input, cellular localization, and developmentally regulated expression pattern. The intra- or extra-cellular localizations and enzymatic specificities for cAMP or cGMP are essential for degradative precision at different developmental stages. We discuss the diverse PDEs, the nucleotide cyclases, and the target proteins for cAMP and cGMP in Dictyostelium. We further outline the major molecular, cellular, and developmental events regulated by cyclic nucleotide signaling, with emphasis on the input of each PDE and consequence of loss-of-function mutations. Finally, we relate the structures and functions of the Dictyostelium PDEs with those of humans and in the context of potential therapeutic understandings. Full article

Nucleoside-5′-triphosphates (5′-NTPs) are essential building blocks of nucleic acids in nature and play an important role in molecular biology, diagnostics, and mRNA therapeutic synthesis. Chemical synthesis has long been the standard method for producing modified 5′-NTPs. However, chemical routes face limitations, including low regio- and stereoselectivity, along with the need for protection/deprotection cycles, resulting in low yields, high costs, and lengthy processes. In contrast, enzymatic synthesis methods offer significant advantages, such as improved regio- and stereoselectivity and the use of mild reaction conditions, which often leads to higher product yields in “one-pot” reactions. Despite the extensive review of chemical synthesis routes for 5′-NTPs, there has not yet been any comprehensive analysis of enzymatic approaches. Initially, this review provides a brief overview of the enzymes involved in nucleotide metabolism, introducing valuable biocatalysts for 5’-NTP synthesis. Furthermore, the available enzymatic methods for efficient 5′-NTP synthesis using purified enzymes and starting from either nucleobases or nucleosides are examined, highlighting their respective advantages and disadvantages. Special attention is also given to the importance of ATP regeneration systems for 5′-NTP synthesis. We aim to demonstrate the remarkable potential of enzymatic in vitro cascade reactions, promoting their broader application in both basic research and industry. Full article

Tetrahydrofolate (THF), the biologically active form of folate, serves as a crucial carrier of one-carbon units essential for synthesizing cellular components such as amino acids and purine nucleotides in vivo. It also acts as an important precursor for the production of pharmaceuticals, including folinate and L-5-methyltetrahydrofolate (L-5-MTHF). In this study, we developed an efficient enzyme cascade system for the production tetrahydrofolate from folate, incorporating NADPH recycling, and explored its application in the synthesis of L-5-MTHF, a derivative of tetrahydrofolate. To achieve this, we first screened dihydrofolate reductases (DHFRs) from various organisms, identifying SmDHFR from Serratia marcescens as the enzyme with the highest catalytic activity. We then conducted a comparative analysis of formate dehydrogenases (FDHs) from different sources, successfully establishing an NADPH recycling system. To further enhance biocatalytic efficiency, we optimized key reaction parameters, including temperature, pH, enzyme ratio, and substrate concentration. To address the challenge of pH mismatch in dual-enzyme reactions, we employed an enzymatic microenvironment regulation strategy. This involved covalently conjugating SmDHFR with a superfolder green fluorescent protein mutant carrying 30 surface negative charges (−30sfGFP), using the SpyCatcher/SpyTag system. This modification resulted in a 2.16-fold increase in tetrahydrofolate production, achieving a final yield of 4223.4 µM. Finally, we extended the application of this tetrahydrofolate synthesis system to establish an enzyme cascade for L-5-MTHF production with NADH recycling. By incorporating methylenetetrahydrofolate reductase (MTHFR), we successfully produced 389.8 μM of L-5-MTHF from folate and formaldehyde. This work provides a novel and efficient pathway for the biosynthesis of L-5-MTHF and highlights the potential of enzyme cascade systems in the production of tetrahydrofolate-derived compounds. Full article

Nuclease P1 (NP1) is critical for producing 5′-nucleotides, which are essential flavor enhancers in the food industry. Traditional use of free NP1 is hampered by poor reusability, high costs, and potential residual enzyme protein contamination, compromising product quality. This study introduces a novel immobilization technique using a cross-linking approach with food-grade ion exchange resin AER1 to create NP1@AER1-GA. This method achieves an enzyme activity of 51,015 U/g, with a notable immobilization yield of 67.7%. The immobilized NP1@AER1-GA exhibits significantly enhanced stability and catalytic efficiency while ensuring industrial compatibility and maintaining stringent safety standards. Under optimized conditions, NP1@AER1-GA demonstrates exceptional performance in 5′-nucleotide production, retaining approximately 85% of its initial activity after 10 cycles of reuse. This breakthrough not only boosts the efficiency and sustainability of nucleotide synthesis but also offers a scalable solution for industrial applications, promoting sustainable manufacturing practices within the food industry. By addressing key challenges associated with traditional enzymatic methods, this immobilization technique sets a new benchmark for biocatalyst design in the food processing industry. Full article

Dihydroorotase (DHOase; EC 3.5.2.3) is a zinc-dependent metalloenzyme that plays a key role in the de novo pyrimidine biosynthesis pathway, catalyzing the reversible cyclization of N-carbamoyl aspartate to dihydroorotate. This reaction is essential for the production of uridine monophosphate, the precursor of all pyrimidine nucleotides required for DNA and RNA synthesis. Despite its conserved enzymatic function, DHOase exhibits significant structural diversity across species, particularly in its oligomeric states, gene fusion patterns, and active site architecture. A crucial structural feature of DHOase is its flexible active site loop, which undergoes dynamic conformational changes during catalysis. Previously, the loop-in conformation was associated with substrate binding, whereas the loop-out conformation was linked to product release and non-substrate ligand binding. However, recent crystallographic studies challenge this paradigm, revealing that certain non-substrate ligands and inhibitors, including malate, 5-fluoroorotate, plumbagin, 5-aminouracil, and 5-fluorouracil, interact with DHOase via a loop-in binding mechanism rather than the previously assumed loop-out mode. These findings necessitate a reassessment of the catalytic mechanism of DHOase and underscore the active site loop as a potential target for drug development. This review revisits the structural and biochemical mechanisms of DHOase, with a focus on recent crystallographic insights that redefine the loop-in binding mode for ligand interaction. By leveraging the unique conformational dynamics of the active site loop, novel inhibitors may be developed to selectively target pyrimidine biosynthesis in cancer cells and microbial pathogens. These insights emphasize the crucial role of structural biology in therapeutic design and highlight DHOase as a promising drug target. Full article

The notion of RNA-based therapeutics has gained wide attractions in both academic and commercial institutions. RNA is a polymer of nucleic acids that has been proven to be impressively versatile, dating to its hypothesized RNA World origins, evidenced by its enzymatic roles in facilitating DNA replication, mRNA decay, and protein synthesis. This is underscored through the activities of riboswitches, spliceosomes, ribosomes, and telomerases. Given its broad range of interactions within the cell, RNA can be targeted by a therapeutic or modified as a pharmacologic scaffold for diseases such as nucleotide repeat disorders, infectious diseases, and cancer. RNA therapeutic techniques that have been researched include, but are not limited to, CRISPR/Cas gene editing, anti-sense oligonucleotides (ASOs), siRNA, small molecule treatments, and RNA aptamers. The knowledge gleaned from studying RNA-centric mechanisms will inevitably improve the design of RNA-based therapeutics. Building on this understanding, we explore the physiological diversity of RNA functions, examine specific dysfunctions, such as splicing errors and viral interactions, and discuss their therapeutic implications. Full article

Nucleosides, nucleotides, and their analogues are an important class of molecules that are used as substrates in research of enzymes and nucleic acid, or as antiviral and antineoplastic agents. Nucleoside phosphorylation is usually achieved with chemical methods; however, enzymatic phosphorylation is a viable alternative. Here, we present a chemoenzymatic synthesis of modified cytidine monophosphates, where a chemical synthesis of novel N⁴-modified cytidines is followed by an enzymatic phosphorylation of the nucleosides by nucleoside kinases. To enlarge the substrate scope, multiple mutant variants of Drosophila melanogaster deoxynucleoside kinase (DmdNK) (EC:2.7.1.145) and Bacillus subtilis deoxycytidine kinase (BsdCK) (EC:2.7.1.74) have been created and tested. It has been determined that certain point mutations in the active sites of the kinases alter their substrate specificities noticeably and allow phosphorylation of compounds that had been otherwise not phosphorylated by the wild-type DmdNK or BsdCK. Full article

The rhizosphere is a dynamic and highly interactive habitat where diverse microbial communities are established, and it plays crucial roles in plant health and disease dynamics. In this study, microbial communities and functional profiles in the rhizosphere of both asymptomatic and symptomatic apple trees were investigated through amplicon sequencing and shotgun metagenomics. The research was conducted at a location in the municipality of Cuauhtemoc, Chihuahua State, Mexico, and a total of 22 samples were collected, comprising 12 for amplicon sequencing and 10 for shotgun metagenomic sequencing. Symptomatic trees were identified based on reddish branches and internal necrosis in the trunk and root, while asymptomatic trees exhibited a healthy physiology. The findings showed that the dominant bacterial phyla included Proteobacteria, Actinobacteria, and Bacteroidetes, with prevalent genera such as Streptomyces, Pseudomonas, and Rhodanobacter. The fungal communities featured Ascomycota, Mortierellomycota, and Basidiomycota, which were dominated by Fusarium, Penicillium, and Mortierella. In the fungal communities, Mortierellomycota, notably abundant in asymptomatic trees, holds potential as a biocontrol agent, as seen in other studies on the suppression of Fusarium wilt disease. The application of shotgun metagenomic sequencing revealed significant differences in alpha and beta diversities in bacterial communities, suggesting a health-dependent change in species composition and abundance. Functional profile analysis highlighted enzymatic activities associated with lipid synthesis/degradation, amino acid biosynthesis, carbohydrate metabolism, and nucleotide synthesis, which have been documented to participate in symbiotic relationships between plants. These insights not only contribute to understanding the dynamics of rhizosphere microbial activity but also provide valuable perspectives on the potential application of microbial communities for tree health and implications for the management of apple orchards. Full article

Enzymatic oligonucleotide synthesis is used for the development of functional oligonucleotides selected by in vitro selection. Expanding available sugar modifications for in vitro selection helps the functional oligonucleotides to be used as therapeutics reagents. We previously developed a KOD DNA polymerase mutant, KOD DGLNK, that enzymatically synthesized fully-LNA- or 2′-O-methyl-modified oligonucleotides. Here, we report a further expansion of the available 2′-O-alkyl-modified nucleotide for enzymatic synthesis by KOD DGLNK. We chemically synthesized five 2′-O-alkyl-5-methyluridine triphosphates and incorporated them into the oligonucleotides. We also enzymatically synthesized a 2′-O-alkyl-modified oligonucleotide with a random region (oligonucleotide libraries). The 2′-O-alkyl-modified oligonucleotide libraries showed high nuclease resistance and a wide range of hydrophobicity. Our synthesized 2′-O-alkyl-modified oligonucleotide libraries provide novel possibilities that can promote the development of functional molecules for therapeutic use. Full article

Enzymatic glycosylation is a versatile and sustainable biotechnological approach that plays a pivotal role in the production of bioactive compounds. This process involves the enzymatic transfer of sugar moieties onto various acceptor molecules, such as small molecules, peptides, or proteins, resulting in the synthesis of glycosides. These glycosides often exhibit enhanced bioactivity, improved solubility, and enhanced stability, making them valuable in pharmaceuticals, nutraceuticals, and the food industry. This review explores the diverse enzymatic glycosylation strategies employed in the synthesis of bioactive compounds. It highlights the enzymatic catalysts involved, including glycosyltransferases, glycosidases, glycophosphorylases, and glycosynthases. It considers the advantages and disadvantages of these biocatalysts in the stereoselective and regioselective synthesis of different types of glycosylated molecules, phenolic and aliphatic alcohols, oligosaccharides, polysaccharides, glycoderivatives, glycopeptides, and glycoproteins with a clear focus on food and pharmaceutical chemistry. Furthermore, the review outlines various sources of sugar donors, activated glycosides, and sugar nucleotides, as well as the utilization of engineered enzymes and microorganisms for glycosylation reactions. The advantages of enzymatic glycosylation, including its high regioselectivity, stereoselectivity, and sustainability, are emphasized. Therefore, these approaches combining the use of different catalytic systems, the improvement of tools such as immobilization technology or chemical or genetic modification to improve the glycosylation process, could be useful tools in continuous biotechnological advancements. Full article

Enzymes are essential catalysts for various chemical reactions in biological systems and often rely on metal ions or cofactors to stabilize their structure or perform functions. Improving enzyme performance has always been an important direction of protein engineering. In recent years, various artificial small molecules have been successfully used in enzyme engineering. The types of enzymatic reactions and metabolic pathways in cells can be expanded by the incorporation of these artificial small molecules either as cofactors or as building blocks of proteins and nucleic acids, which greatly promotes the development and application of biotechnology. In this review, we summarized research on artificial small molecules including biological metal cluster mimics, coenzyme analogs (mNADs), designer cofactors, non-natural nucleotides (XNAs), and non-natural amino acids (nnAAs), focusing on their design, synthesis, and applications as well as the current challenges in synthetic biology. Full article