Search Results (132)

Enzymes are highly selective and efficient biological catalysts that play a critical role in modern industrial biocatalysis. Their ability to operate under mild conditions and reduce environmental impact makes them ideal alternatives to conventional chemical catalysts. This review provides a comprehensive overview of advances in enzyme-based catalysis, focusing on enzyme classification, engineering strategies, and industrial applications. The six major enzyme classes—hydrolases, oxidoreductases, transferases, lyases, isomerases, and ligases—are discussed in the context of their catalytic roles across sectors such as pharmaceuticals, food processing, textiles, biofuels, and environmental remediation. Recent developments in protein engineering, including directed evolution, rational design, and computational modeling, have significantly enhanced enzyme performance, stability, and substrate specificity. Emerging tools such as machine learning and synthetic biology are accelerating the discovery and optimization of novel enzymes. Progress in enzyme immobilization techniques and reactor design has further improved process scalability, reusability, and operational robustness. Enzyme sourcing has expanded from traditional microbial and plant origins to extremophiles, metagenomic libraries, and recombinant systems. These advances support the integration of enzymes into green chemistry and circular economy frameworks. Despite challenges such as enzyme deactivation and cost barriers, innovative solutions continue to emerge. Enzymes are increasingly enabling cleaner, safer, and more efficient production pathways across industries, supporting the global shift toward sustainable and circular manufacturing. Full article

Oxygenic and anoxygenic photosynthesis have long been considered defining traits of cyanobacteria. However, whether the important cyanobacterial genus Synechococcus is capable of anoxygenic photosynthesis remains unconfirmed. Here, we report that Synechococcus sp. PCC 7002 is capable of anoxygenic photosynthesis when sulfide (H₂S) is supplied as the sole electron donor. Combining the targeted deletion of the sulfide: quinone oxidoreductase gene (Δsqr) with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) mediated the inhibition of photosystem II. We demonstrated that SQR-mediated H₂S oxidation sustains light-dependent CO₂ fixation in the absence of O₂ evolution. Our genome-wide transcriptomic profiling further revealed that polysulfide (H₂S_n) and hydrogen peroxide (H₂O₂) function as distinct signaling molecules in oxygenic and anoxygenic photosynthesis, modulating central carbon and energy metabolism. In central carbon metabolism, H₂S_n markedly upregulates the expression of key genes, including psbA, petC, rbcL, and rbcS, whereas H₂O₂ downregulates these genes. Within energy metabolism, both molecules converge on oxidative phosphorylation by upregulating genes encoding NADH dehydrogenase and ATP synthase. Furthermore, H₂Sₙ treatment uniquely induces sulfur-assimilation and ROS-detoxifying enzymes, conferring a markedly higher tolerance than H₂O₂. These findings provide direct evidence of anoxygenic photosynthesis in the genus Synechococcus and uncover a dual regulatory network that allows Synechococcus sp. PCC 7002 to balance redox homeostasis under fluctuating oxic/anoxic conditions. Full article

Molecular diversity is a key component of overall biodiversity, playing a vital role in evolution. It results from the adaptation of organisms to various habitats, which impacts their survival. The Amaryllidoideae subfamily is a significant group of monocotyledonous plants known for producing an exclusive and still-expanding group of molecules with diverse biological activities. Galanthamine (Gal), the most renowned metabolite from Amaryllidoideae subfamily, has been marketed for the palliative treatment of Alzheimer’s disease since 2001 due to its ability to inhibit the acetylcholinesterase enzyme. Due to the high cost and low yield of its synthesis, pharmaceutical companies extract this drug from Amaryllidoideae plants, such as Narcissus pseudonarcissus cv. Carlton in Europe and Lycoris radiata in China. The aim of this study was to describe the alkaloid profile of fifteen different species of Narcissus L. (commonly known as daffodils) collected in Spain using gas chromatography coupled with mass spectrometry. Fifty-one alkaloids were identified and quantified within these species through our private library of Amaryllidaceae alkaloids (AA) built over the last four decades, while thirty structures remained not identified in thirteen of these species. The highest concentration of these nitrogenate metabolites was quantified in N. confusus, 541 μg Gal·100 mg⁻¹ DW, which also exhibited a notably high concentration of Gal, 301 μg Gal·100 mg⁻¹ DW, which represents about 55% of the alkaloids identified in this species. The species N. bujei was also found to contain a significant quantity of this compound, amounting to 103.2 μg Gal·100 mg⁻¹ DW. The plant N. assoanus harbored a total of seven unidentified compounds, indicating that this species could be a potentially important source of novel alkaloids. In conclusion, this study facilitates a direct comparison of alkaloid profiles for fifteen Narcissus plant species. This serves as a valuable tool for identifying possible new sources of galanthamine, as well as other novel medicinal alkaloids. Finally, this work presents the first alkaloid profile of the species N. minor and N. nevadensis. Full article

Breakthrough advances in artificial intelligence (AI) are propelling de novo protein design past the boundaries of natural evolution, making it possible to engineer proteins with entirely novel structures and functions. Benefiting from iterative improvements in machine learning algorithms, AI-driven de novo strategies have overcome traditional reliance on natural templates. These approaches autonomously optimize catalytic sites and overall stability, significantly enhancing enzyme performance and applicability. Generative models, including large language models and diffusion models, can rapidly produce novel protein structures with specialized functions, offering innovative technological paths for biomolecule development. This review systematically discusses recent key developments and representative examples of AI applications in enzyme engineering and design. We highlight a fundamental shift from traditional “structure-based function analysis” to a new paradigm of “function-driven structural innovation.” Furthermore, we comprehensively evaluate current challenges in AI-driven protein engineering and suggest promising future directions. Full article

Zearalenone (ZEN), a mycotoxin produced by Fusarium species, widely contaminates grains and feed, posing a serious threat to animal and human health. Traditional physical and chemical detoxification methods face challenges, including low efficiency, high costs, and nutrient loss. In contrast, enzymatic biodegradation has emerged as a research hotspot due to its high efficiency, specificity, and environmental friendliness. Lactone hydrolase can specifically hydrolyze the lactone ring of ZEN, converting it into a low-toxicity or non-toxic degradation product, thereby demonstrating significant potential for application in ensuring the safety of food, feed, and agricultural products. In recent years, with advancements in enzyme engineering and various biological technologies, remarkable progress has been made in ZEN-degrading enzyme research. Novel and highly efficient enzyme genes have been discovered through gene mining, while directed evolution and rational design have improved catalytic efficiency and stability. Additionally, immobilization techniques and formulation optimization have enhanced industrial applicability. This review, based on practical application needs, establishes a comprehensive evaluation system integrating enzyme characteristics, modification technologies, and process applicability, aiming to provide actionable theoretical guidance for the large-scale application of biological detoxification technologies. Full article

Enzymatic CO₂ fixation offers great potential for the sustainable synthesis of value-added compounds. Malic enzyme (ME) catalyzes the reverse carboxylation of pyruvate to malate, enabling direct CO₂ conversion into C₄ compounds with broad biosynthetic applications. However, the reverse carboxylation activity of wild-type ME is insufficient, and conventional enzyme engineering strategies remain limited by the complexity of identifying distal functional sites. Here, we present a Structure–Sequence–SCANNER (3S) co-evolution strategy that integrates protein structural analysis, sequence conservation profiling, and co-evolutionary network analysis to enable systematic identification of functionally relevant hotspot residues. Using this approach, we engineered Escherichia coli ME (EcME) variants with enhanced CO₂ fixation activities. In total, 106 single-point variants were constructed and screened. Among these, variants A464S and D97E exhibited significantly improved reverse carboxylation activities, with 1.7-fold and 1.6-fold increases in catalytic activity and 1.5-fold and 1.8-fold improvements in catalytic efficiency (k_cat/K_m), respectively, compared to wild-type EcME. Their catalytic efficiencies (k_cat/K_m) improved by 1.5-fold and 1.8-fold, increasing from 80 mM⁻¹·min⁻¹ for the wild-type enzyme to 120 and 130 mM⁻¹·min⁻¹, respectively. Mechanistic analyses revealed that A464S introduces a stabilizing hydrogen bond with N462, enhancing NADPH binding, while D97E forms a new salt bridge network with K513, resulting in contraction of the substrate pocket entrance and increased pyruvate affinity. These findings demonstrate the effectiveness of the 3S strategy in reprogramming enzyme functions and highlight its potential for constructing efficient artificial CO₂ fixation systems. Full article

Microorganisms exhibit remarkable diversity, making their comprehensive characterization essential for understanding ecosystem functioning and safeguarding human health. However, traditional culture-based methods entail inherent limitations for resolving microbial heterogeneity, isolating slow-growing microorganisms, and accessing uncultivated microbes. Conversely, droplet-based microfluidics enables a high-throughput and precise platform for single-bacterium manipulation by physically isolating individual cells within microdroplets. This technology presents a transformative approach to overcoming the constraints of conventional techniques. This review outlines the fundamental principles, recent research advances, and key application domains of droplet-based microfluidics, with a particular focus on innovations in single-bacterium encapsulation, sorting, cultivation, and functional analysis. Applications such as antibiotic susceptibility testing, enzyme-directed evolution screening, microbial interaction studies, and the cultivation of novel bacterial species are discussed, underscoring the technology’s broad potential in microbiological research and biotechnology. Full article

Silicon has a striking similarity to carbon and is found in plant cells. However, there is no specific role that has been assigned to silicon in the life cycle of plants. The amount of silicon in plant cells is species specific and can reach levels comparable to macronutrients. Silicon is used extensively in artificial intelligence, nanotechnology, and the digital revolution, and thus can serve as an informational molecule such as nucleic acids. The diverse potential of silicon to bond with different chemical species is analogous to carbon; thus, it can serve as a structural candidate similar to proteins. The discovery of large amounts of silicon on Mars and the moon, along with the recent development of enzyme that can incorporate silicon into organic molecules, has propelled the theory of creating silicon-based life. The bacterial cytochrome has been modified through directed evolution such that it could cleave silicon–carbon bonds in organo-silicon compounds. This consolidates the idea of utilizing silicon in biomolecules. In this article, the potential of silicon-based life forms has been hypothesized, along with the reasoning that autotrophic virus-like particles could be used to investigate such potential. Such investigations in the field of synthetic biology and astrobiology will have corollary benefits for Earth in the areas of medicine, sustainable agriculture, and environmental sustainability. Full article

The shikimate pathway is the fundamental metabolic route for aromatic amino acid biosynthesis in bacteria, plants, and fungi, but is absent in mammals. This review explores how multi-enzyme synergy and allosteric regulation coordinate metabolic flux through this pathway by focusing on three key enzymes: 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase, chorismate mutase, and tryptophan synthase. We examine the structural diversity and distribution of these enzymes across evolutionary domains, highlighting conserved catalytic mechanisms alongside species-specific regulatory adaptations. The review covers directed evolution strategies that have transformed naturally regulated enzymes into standalone biocatalysts with enhanced activity and expanded substrate scope, enabling synthesis of non-canonical amino acids and complex organic molecules. Industrial applications demonstrate the pathway’s potential for sustainable production of pharmaceuticals, polymer precursors, and specialty chemicals through engineered microbial platforms. Additionally, we discuss the therapeutic potential of inhibitors targeting pathogenic organisms, particularly their mechanisms of action and antimicrobial efficacy. This comprehensive review establishes the shikimate pathway as a paradigmatic system where understanding allosteric networks enables the rational design of biocatalytic platforms, providing blueprints for biotechnological innovation and demonstrating how evolutionary constraints can be overcome through protein engineering to create superior industrial biocatalysts. Full article

Peroxidases are essential enzymes that catalyze redox reactions, with wide-ranging biological implications. Among these, an enhanced ascorbate peroxidase (APEX) has emerged as a valuable tool for studying intricate intracellular events with spatiotemporal precision, particularly in protein–protein, protein–RNA, and protein–DNA interaction networks in living cells. This review discusses APEX’s structural and functional attributes, its evolution through genetic engineering, and its transformative applications in high-resolution mapping used for proteomic and transcriptomic studies. Furthermore, it highlights recent advancements in substrate innovation and addresses current challenges and future directions in leveraging APEX for cutting-edge biological research. Full article

Enzymes and biosurfactants, often referred to as “green chemicals,” play pivotal roles in enhancing the washing performance of bio-based detergents—a growing trend driven by environmentally conscious consumers. However, the widespread adoption of such bio-based detergents faces challenges, including high costs, limited efficiency, and the need for ongoing innovations. Bacillus species have long been universally acknowledged and exploited for industrial applications, and Bacillus spp. are largely differentiated from other microorganisms for their enzymatic applications, particularly in detergent production. Recent developments in bio-surfactant production by Bacillus sp. support the adoption of green detergents, and these bacterial biosurfactants are a promising source for detergent manufacturing. This article provides an overview of the current understanding of promising Bacillus species and their potential to advance and accelerate the production of bio-based detergents. Full article

Chinese lacquer, a historically significant bio-based coating, has garnered increasing attention in sustainable materials research due to its outstanding corrosion resistance, thermal stability, and environmental friendliness. Its curing process relies on the laccase-catalyzed oxidation and polymerization of urushiol to form a dense lacquer film. However, the stringent temperature and humidity requirements (20–30 °C, 70–80% humidity) and a curing period that can extend over several weeks severely constrain its industrial application. Recent studies have significantly enhanced the curing efficiency through strategies such as pre-polymerization control, metal ion catalysis (e.g., Cu²⁺ reducing drying time to just one day), and nanomaterial modification (e.g., nano-Al₂O₃ increasing film hardness to 6H). Nevertheless, challenges remain, including the sensitivity of laccase activity to environmental fluctuations, the trade-off between accelerated curing and film performance, and issues related to toxic pigments and VOC emissions. Future developments should integrate enzyme engineering (e.g., directed evolution to broaden laccase tolerance), intelligent catalytic systems (e.g., photo-enzyme synergy), and green technologies (e.g., UV curing), complemented by multiscale modeling and circular design strategies, to drive the innovative applications of Chinese lacquer in high-end fields such as aerospace sealing and cultural heritage preservation. Full article

In this review, we trace the evolution of liquid chromatography from the pioneering work of Tennikova and Svec to the current monolithic polymethacrylate supports for performing liquid chromatography with biological macromolecules and nanoparticles, which offer rapid, high-throughput separations. By using interconnected channels with a tailored channel diameter, monoliths minimize the diffusion limitations typical of particle-based systems. Radial flow designs and optimized channel architectures enable the direct loading of complex biological fluids, reducing the need for sample preparation and optimizing the purification of large biomolecules and nanoparticles such as proteins, nucleic acids, extracellular vesicles, and viruses. Recent work has integrated monoliths into immunoaffinity and enzyme reactor platforms, streamlining analytical workflows and preparative applications in vaccine production and gene therapy. The ongoing advances in monolithic materials, channel geometry, and continuous processing hold promise for even greater efficiency and scalability in future applications. Full article

As fossil fuel depletion and environmental pollution become increasingly severe, biodiesel has emerged as a promising renewable alternative to conventional diesel due to its biodegradability, low sulfur emissions, and high combustion efficiency. This paper provides a comprehensive review of the evolution of biodiesel feedstocks, major production technologies, and key factors influencing production efficiency and fuel quality. It traces the development of feedstocks from first-generation edible oils, second-generation non-edible oils and waste fats, to third-generation microalgal oils and fourth-generation biofuels based on synthetic biology, with a comparative analysis of their respective advantages and limitations. Various production technologies such as transesterification, direct esterification, supercritical alcohol methods, and enzyme-catalyzed transesterification are examined in terms of reaction mechanisms, process conditions, and applicability. The effects of critical process parameters including the alcohol-to-oil molar ratio, reaction time, and temperature on biodiesel yield and quality are discussed in detail. Particular attention is given to the role of catalysts, including both homogeneous and heterogeneous types, in enhancing conversion efficiency. In addition, life cycle assessment (LCA) is briefly considered to evaluate the environmental impact and sustainability of biodiesel production. This review serves as a valuable reference for improving biodiesel production technologies, advancing sustainable feedstock development, and promoting the commercial application of biodiesel. Full article

The Schrödinger equation, Heisenberg’s uncertainty principles, and the Boltzmann constant represent transformative scientific achievements, the impacts of which extend far beyond their original domain of physics. As we celebrate the centenary of these fundamental quantum mechanical formulations, this review examines their evolution from abstract mathematical concepts to essential tools in contemporary drug discovery and development. While these principles describe the behavior of subatomic particles and molecules at the quantum level, they have profound implications for understanding biological processes such as enzyme catalysis, receptor–ligand interactions, and drug–target binding. Quantum tunneling, a direct consequence of these principles, explains how some reactions occur despite classical energy barriers, enabling novel therapeutic approaches for previously untreatable diseases. This understanding of quantum mechanics from 100 years ago is now creating innovative approaches to drug discovery with diverse prospects, as explored in this review. However, the fact that the quantum phenomenon can be described but never understood places us in a conundrum with both philosophical and ethical implications; a prospective and inconclusive discussion of these aspects is added to ensure the incompleteness of the paradigm remains unshifted. Full article