As a class of enzymes widely distributed in nature, peroxidases are involved in important life processes such as innate immunity and epidemic prevention of organisms, anti-oxidative stress of plant microorganisms, fungal lignin degradation, plant cell wall metabolism and wound healing. With the rapid development of DNA sequencing, gene editing, recombinant protein expression and high-throughput screening technologies, more and more peroxidases have been discovered, characterized and recombinantly expressed. These peroxidases, characterized by their species diversity, abundant quantity, and excellent catalytic performance, have attracted extensive attention in many fields of application research. In recent years, remarkable progress has been made in the recombinant expression of peroxidases, further promoting their development in the field of applied research. Additionally, as we deepen our understanding of the catalytic properties of peroxidases, new opportunities have emerged for their application in the field of biosynthesis. Their high catalytic activity allows for rapid oxidation reactions under mild conditions and enables the construction of multi-enzyme cascade systems in conjunction with other enzymes, thereby facilitating the efficient synthesis of complex compounds. This paper provides a brief overview of peroxidases from the perspective of systematic evolutionary classification and function. It systematically reviews recent progress in the recombinant expression of peroxidases in Escherichia coli, yeast, and fungi, as well as their application achievements in environmental remediation and compound detection. The focus is on the latest research advances in the application of peroxidases for the biosynthesis of high-value-added compounds. The paper also discusses the current issues in this field, such as substrate and product non-specificity and the cytotoxicity of the cofactor H₂O₂. Peroxidases have enormous potential for applications in medical diagnostics, environmental protection, and biosynthesis. However, current technologies and applications still face several challenges, such as the stability and activity of peroxidases in complex environments, high production costs of enzyme preparations, and poor specificity. In the future, by integrating the latest advances in protein engineering, synthetic biology, and immobilization technology, these challenges can be effectively solved, promoting the widespread application of peroxidases across various fields.

Production of chemicals using renewable bioresources and green biomanufacturing processes is highly important for sustainable bioeconomy. Diols are important bulk chemicals widely used in the production of polymers, cosmetics, fuels, food, and pharmaceutical industries due to their versatile functional properties. Currently, most of diols are produced mainly from fossil resources via energy-cost chemical approaches. The development of biosynthetic routes for the production of diols from renewable resources such as biomass and C₁ has garnered significant attention due to its potential in reducing the utilization of fossil resources and carbon dioxide emissions. Although biological production of 1,3-propanediol, 1,3-butanediol and 1,4-butanediol has been commercialized, the biosynthesis of other major diols remains challenging due to the absence of efficient natural biosynthetic pathways and low efficiency of the recombinant microbes. Recent development of metabolic engineering and synthetic biology enables the production of non-natural chemicals via artificial metabolic pathways and novel biological parts, significantly expanding the boundary of biomanufacturing. This review comprehensively explores recent advances in the microbial synthesis of diols, emphasizing the development of new pathways and engineering strategies for the biosynthesis of C₂ to C₅ diols. Especially, we focus on the innovative approaches include constructing non-natural synthetic pathways to achieve the biosynthesis of non-natural diols, or using alternative carbon sources such as lignocellulose through specific metabolic pathways to synthesize diols. Furthermore, this review also discusses the primary challenges and future perspectives in transforming these biosynthetic processes toward industrial applications. Key challenges involve the accessibility of low-cost and sustainable raw materials, the complexities in scaling up these processes, the development of extraction techniques that cater to specific downstream requirements, and the economic assessment of these processes to ensure profitability and sustainability. These advancements are essential for the economic and environmental viability of producing diols from renewable resources, thereby facilitating the transition to more sustainable industrial practices globally.

Phosphinothricin (PPT) is one of the top three herbicides, known for its broad spectrum, high herbicidal activity, and non-selectivity, with a highly optimistic market prospect. However, PPT exists in two enantiomers (D-PPT and L-PPT), with the herbicidal activity primarily stemming from L-PPT. Therefore, efficient synthesis of L-PPT with high optical purity is crucial. Pesticide manufacturing enterprises have attempted to develop chemical synthesis methods for L-PPT using approaches such as racemic compound splitting, asymmetric synthesis, natural amino acid chiral source method, and chiral auxiliary induction. However, due to challenges such as low stereo-selectivity, low product yield, and high production costs, large-scale production has not been achieved. Under the guidance of Academician Yin-Chu Shen, the “Father of Biopesticides in China”, our research group has conducted scientific research and industrial practice on the biosynthesis of L-PPT for over 20 years. In cooperation with multiple enterprises, we have developed more than ten process routes and technologies. Among them, five routes (racemic mixture derivatization-resolution route, racemic PPT-chiral separation route, generic compound cyanation followed by hydrolysis route, de novo synthesis from common chemicals route, and synthesis of homoserine followed by chemical synthesis) are discussed in detail in this review. Each route’s reconstruction, establishment of bioinorganic amine technology, creation of biocatalysts, high-density fermentation for enzyme production, product separation and purification, and reaction equipment are included. Notably, we developed the BioHPP^®, a biomanufacturing technology for the synthesis of highly optically pure L-PPT. Based on this technology, a ten-thousand-ton digital and intelligent production line for L-PPT was established. Utilizing smart sensors and actuators, real-time data collection, transmission, analysis, and feedback adjustment were achieved at over a thousand control points. This led to fully automated parameter collection and control, increasing production efficiency by 50% and reducing labor intensity by more than 70%, thereby realizing the bio-intelligent manufacturing of ten thousand tons of L-PPT. Based on the long-term accumulation of our research efforts, we summarize and analyze the mainstream production processes of D,L-PPT, detailing on the principles and methods of biomanufacturing technology and synthetic biology to construct the key synthesis system for L-PPT. We also compare the characteristics and key points of industrialization implementation of these routes in terms of substrate synthesis and selection, types of biocatalysts, use of amino donors, and separation and purification. It can be foreseeable that, with the aid of synthetic biology technology, an increasing number of high-optical-purity chiral pesticides will be produced on a large scale through biomanufacturing in the future.

Hydrogenases catalyze the reversible conversion of hydrogen gas into protons and electrons which is promising for industrial application. However, free hydrogenases face challenges such as oxygen sensitivity and low electron transfer rates. This review summarized the immobilization of hydrogenases by carbon materials, metals, semiconductors, polymers and metal-organic-frameworks (MOFs). Carbon materials provide the advantages of low cost and large specific surface areas, while they tend to agglomerate. Hydrogenases are immobilizated on carbon materials through adsorption, usually involving electrostatic interactions and hydrophobic interactions, and are used in bioelectrocatalysis, biofuel cells and bioreactors. Metals and semiconductors, known for high conductivity and excellent reactive activity, are expensive and less stable. Through adsorption involving electrostatic interaction and hydrophobic interaction, immobilization of hydrogenases on metals and semiconductors are normally applied in bioelectrocatalysis, biofuel cells and photoelectrocatalysis. Polymers have good biocompatibility and mechanical strength but low conductivity. Immobilization of hydrogenases on polymers can improve the stability and oxygen tolerance of hydrogenases. Immobilization on polymers is realized through adsorption and entrapment, involving hydrogen bonds, hydrophobic interactions and π-π interactions, and is often used in bioelectrocatalysis and photoelectrocatalysis. MOFs are designable and have high specific surface areas, which provide wide choices for hydrogenases immobilization. However, MOFs tend to collapse in harsh conditions. Immobilization on MOFs through adsorption and entrapment involves coordinate bonds, hydrophobic interaction, and π-π interaction. Furthermore, the prospect of immobilization of hydrogenases by novel hybrid materials was proposed which can expand the applications of immobilized hydrogenases. Immobilization of hydrogenases facilitates the stability of hydrogenases, which can be applied in efficient production and application of hydrogen, as well as biological asymmetric hydrogenation for chiral medicine preparation. Immobilization of hydrogenases provide alternative options for transforming energy structures, realizing green manufacturing and solving environmental problems.

1,3-Propanediol (PDO) is an important chemical extensively used in material science and the cosmetics industry. The biomanufacturing of PDO offers numerous advantages, such as the renewability of raw materials and environmental friendliness. Among various microorganisms, Clostridium pasteurianum emerges as an ideal choice for industrial PDO production due to its safety, non-pathogenic nature, rapid glycerol metabolism, fast growth rate, independence from expensive culture medium components, and its inherent efficient metabolic pathway for PDO production. This review begins by introducing the current state and challenges of PDO biomanufacturing, followed by an in-depth discussion of the methods for producing PDO using C. pasteurianum. Special attention is paid to the glycerol metabolism mechanism, strategies for glycerol fermentation, and the design of the fermentation process. Notably, our research group has identified C. pasteurianum mutant strains and developed robust processes that have largely addressed the organism’s traditional sensitivities to environmental conditions, especially regarding iron concentration and impurities of raw glycerol. In an electricity-aided fermentation process, PDO concentration as high as 120.6 g/L was achieved, with a productivity of 4.8 g/(L·h) and a yield reaching the theoretical maximum. We further discuss the natural limitations of genetic engineering in C. pasteurianum, exploring strategies based on rational genomic modification and directed evolution. Finally, the development of efficient downstream processing technologies is emphasized as crucial for realizing the cost-effective microbial production of PDO from renewable resources, since the industrial application of PDO requires a very high purity (>99.9%). The discussion on PDO downstream processing mainly focuses on evaporation, distillation, and extraction-based purification techniques. Through a comprehensive coverage of metabolic engineering, strain evolution, fermentation optimization, and product separation technologies, this review discusses about the characteristics and advantages of PDO production from C. pasteurianum, highlighting key considerations for advancing this microorganism as a new industrial chassis.

Huge challenges, such as food security, energy security, climate change, dual-carbon target, and so on, motivate human society to seek disruptive and innovative solutions. In vitro biotransformation (ivBT), bridging the gap between whole-cell-based fermentation and enzyme-based biocatalysis, is an emerging biomanufacturing platform designed for the production of biocommodities (e.g., synthetic starch, healthy sweeteners, organic acids, etc.) and bioenergy. In ivBT, in vitro synthetic enzymatic biosystem (ivSEB) is its high-efficiency biocatalyst. Based on the Chinese philosophy that “Tao is simple”, ivSEB is the in vitro reconstruction of artificial (non-natural) enzymatic pathways with a number of natural enzymes, artificial enzymes, and/or (biomimetic or natural) coenzymes, and/or artificial membrane, without living cell’s constraints, such as cell duplication, bioenergetics, basic metabolisms, regulation, and so on. ivBT enables it to surpass the limitations of whole-cell fermentation and has multiple advantages, such as theoretical product yield, at least 10-time volumetric productivity, tolerance to toxic substrate/product, and so on. This review defines the concept of ivBT, presents its design principles, distinguishes it from other seemingly-like concepts, such as cell-free protein synthesis and cascade enzyme biocatalysis, introduces several representative examples, and discusses its challenges and opportunities. The development of ivBT is based on the linear strategy of “Design-Build-GoNG-Optimization”, leading to super-biomanufacturing machines that can meet national needs, such as food security and new energy system. To address food security, we propose two out-of-the-box solutions: (1) in vitro biotransformation of cellulose to starch, possibly increasing the starch supply by a factor of 10; (2) artificial starch synthesis from CO₂ by combining ivBT and chemical catalysis. Furthermore, the revolutionary production of starch could open a door to the starch-based carbohydrate economy, wherein starch is a high-density hydrogen carrier, more than 2.5 times that of compressed hydrogen, and an ultra-high electricity storage compound, more than 10 times of lithium-ion battery. In a word, ivBT featuring ultra-high energy efficiency and potentially-low-cost production could become a third industrial biomanufacturing platform and help solve huge challenges.

Biomanufacturing is a green production that applies such bio-organisms as plants, animals, microorganisms, enzymes as well as in vitro synthetic enzymatic biosystems, to process and/or synthesize numerous value-added compounds, which would change the world′s future of industrial manufacturing in the energy, agricultural, chemical, and pharmaceutical industries. The competition of biomanufacturing is a key part of the battlefield of science and technology. Here we attempt to apply the ancient Chinese philosophy to provide enlightenment to the future development of industrial biomanufacturing. The ancient Chinese philosophy of “Tao-Fa-Shu-Qi” encompasses four key elements: “Tao is a way or direction, Fa is rules, Shu is techniques, and Qi is tools for accomplishing goals”. First, we define and explain the “Tao and Fa” of industrial biomanufacturing analyzes. Second, we analyze the limits and restriction set by Fa. Third, we expound this philosophy of “Tao and Fa” and how it guides way or choice of biomanufacturing type for the desired products. Based on “Tao-Fa-Shu-Qi”, we also present some predictions that a few hot products cannot be manufactured economically by seemingly-promising new techniques based on the limits and restriction of Fa. We take Amyris, a pioneering American company in synthetic biology as an example to analyze and discuss the important roles of “Tao and Fa” in the selection of biomanufactured products, far more important than “Shu and Qi”. Amyris’ failure was destined at its beginning because it went a wrong way (Tao) and ignored basic laws (Fa), although it exhibited advanced abilities of technologies and tools (“Shu and Qi”). Also, we briefly discuss opportunities and challenges of ensuring food security of China by using two disruptive technologies-making synthetic starch from lignocellulosic biomass and carbon dioxide catalyzed by in vitro synthetic enzymatic biosystems. In a word, the ancient Chinese philosophy “the way is simple, from top to down, the way guides techniques and tools” would provide top-level design methodology, identify the future research and development priorities in industrial biomanufacturing, and help effectively solve the major challenges, such as food security, dual carbon goals, and sustainable development.

Chiral amino acids represent a crucial class of chiral building blocks with significant value in food, medicine, chemical industry, and agriculture. The market scale of pharmaceuticals, pesticides, food, and chemical industries relying on chiral amino acids is substantial and has been attracting increasing attention. The pursuit of efficient, environmentally friendly, and cost-effective synthesis of chiral amino acids has long been a goal for scientists. Commonly used preparation methods for chiral amino acids fall into four following categories: protein hydrolysis, fermentation, chemical synthesis, and enzyme-catalyzed synthesis. Among these, enzyme-catalyzed synthesis has demonstrated great potential due to its mild reaction conditions, high stereo-selectivity, simplicity of steps, and wide application range. In recent years, with the rapid development of bioinformatics, protein engineering, and computational biology, there has been an increasing number of high-performance enzyme preparations developed, leading to a steady increase in the diversity of enzymes and the gradual diversification of catalyzed reactions, further promoting the wide application of enzyme-catalyzed synthesis of chiral amino acids. The enzyme-catalyzed synthesis of chiral amino acids can be categorized into three groups: asymmetric synthesis, deracemization synthesis, and kinetic resolution. Kinetic resolution, due to its theoretical yield of only 50% and low atom economy, is not suitable for industrial applications. In contrast, asymmetric synthesis and deracemization synthesis with theoretical yield of 100% find wider industrial application. This article reviews the application of enzymatic asymmetric synthesis and deracemization synthesis in the synthesis of chiral amino acids. It includes the development and modification of key enzyme such as amino acid dehydrogenase, transaminase, ammonia lyase, aldolase, amino acid oxidase, and amino acid deaminase, as well as their application in the synthesis of high-value chiral amino acids such as phosphinothricin, tert-leucine, and intermediate of sitagliptin. Additionally, it summarizes the main challenges faced in the field of enzymatic synthesis of chiral amino acids, such as the lack of key enzyme components, and low enantioselectivity, narrow substrate spectra, low catalytic activity, poor stability, limited reaction conditions of wild-type enzymes. Finally, it looks ahead to the application of cutting-edge technologies such as automated experimental devices, machine learning, and artificial intelligence in the field of enzyme modification, as well as the development of more efficient and environmentally friendly catalytic processes through reactor design and reaction process control. These endeavors collectively aim to facilitate the broader industrial application of enzymatic synthesis for chiral amino acids.

Chitin, a linear homo-polysaccharides composed of N-acetylglucosamine (GlcNAc) through β-1,4-glycosidic bonds, is the richest nitrogen containing biomass resource on earth, with an annual production of 10 billion tonnes. Chitin is widely distributed in nature, mainly found in the shells of shrimps and crabs, the exoskeletons of insects, and the cell walls of fungi. Due to its abundance and renewablity, especially the presence of the valuable nitrogen element, chitin receives widespread attention. However, the abundant hydrogen bonds in the structure of chitin and its huge molecular weight make it highly crystalline and insoluble in water, which leads to challenges in its degradation and high-value utilization. Thus, chitin resource is often discarded as wastes or buried, leading to serious environment issues and wasted resources. Conversion of abundant chitin resources into high value-added chemicals has both environmental and economic significance. Nowadays, the utilization of chitin resources is mainly done by efficient, low-cost chemical method, but causing huge environmental pollution. Compared with chemical method, the biological method shows great potential in the context of green and sustainable development due to the advantages of environmentally friendly process and mild reaction conditions. In this review, the sources and classifications, catalytic mechanisms and properties of key enzymes for chitin degradation are introduced. Secondly, the current status of chitin biodegradation to monosaccharides (GlcNAc and glucosamine) and oligosaccharides (N-acetyl chitooligosaccharides and chitooligosaccharides), and further bio-converted into nitrogen-containing chemicals are reviewed. Although many studies on enzymes involved in chitin degradation and conversion have been carried out with certain achievements, the diversity and complexity of these enzymes, coupled with the low activity and secretory nature and other factors, have hindered the real industrial chitin degradation and conversion. Consequently, the challenges in biodegradation and high-value conversion process of chitin such as low activity of enzyme, poor efficiency and high cost are highlighted. Finally, the important role of rapidly developing synthetic biology technologies in chitin utilization is envisaged, which will aid the efficient bio-refining of chitinous resources.

Hydrogenases are the most important enzymes in biological hydrogen production and hydrogen energy utilization. They are widely distributed, oxygen-sensitive, multiunit complexed metal enzymes. In vitro synthetic enzymatic biosystems (ivSEB) is a type of in vitro biotransformation (ivBT) technology, which is an emerging biomanufacturing powerhouse that combines microbial fermentation with enzymatic biocatalysis, allowing for novel and efficient hydrogen production, also breaking the Thauer limit and achieving a yield of hydrogen close to the theoretical value of chemistry (1 mole of glucose to produce 12 moles of hydrogen in maximum). It represents the future direction of biological hydrogen production. However, the recombinant expression of hydrogenase is the main bottleneck limiting the wide application of ivSEB for hydrogen production technology. Hydrogenases are widely distributed in all life domains, but are oxygen-sensitive and mostly consist of metalloproteins with multi-subunits, bearing [Fe] only, [NiFe] or [FeFe] dinuclear core in their catalytic center. Oxygen not only inhibits the activity of hydrogenase, but also affects the transcription of the enzyme-encoding gene and post-translational process of the enzymes. As a result, the levels of recombinant hydrogenase are usually low and the enzymatic activities are also incomparable to the native enzymes, often leading to high production costs due to the strict anaerobic purification procedures. In order to meet the requirements of industrial hydrogen production, hydrogenases must possess excellent catalytic properties, such as a high catalytic turnover number, great thermal stability, and the ability to tolerate trace amounts of oxygen. This review summarizes the studies on the structural and catalytic characterizations of hydrogenases, including their classification, oxygen resistance mechanisms, and progress in recombinant expression. Additionally, the evolution of natural electron transfer chains and the design of artificial routes, which can improve hydrogen production efficiency and reduce costs, are briefly discussed. The review also discussed the progress in the studies on the mechanisms of hydrogenases’ tolerance toward oxygen, the strategies for microbial expression of recombinant hydrogenases as well as the optimization of the artificial electron transfer chains adapted for the production of hydrogen using ivSEB, in expectations of promoting the applications of hydrogenases involved ivSEB, from renewable energy storage, anaerobic artificial respiration, to clean hydrogenation or dehydrogenation in biocatalysis.