Lignin is a major component of lignocellulose, accounting for 15%-30% on a dry weight basis, with an annual yield estimated to be 20 billion tonnes. Lignin is a heterogenous aromatic polymer of phenylpropanoids linked by various C—C and C—O bonds. It is an integral component of the secondary cell wall from terrestrial plants, providing plants with rigidness and fending off microbial pathogens. The abundance and renewability of lignin has recently attracted ample interest in valorizing this readily available polymer. However, the complex nature of lignin presents a significant challenge for lignin breakdown and utilization, and at present the majority of lignin is simply burned as a fuel. Among the different methods, biological utilization of lignin has emerged as a highly attractive approach, since it proceeds under mild conditions and is generally considered environmentally friendly, especially considering that environmental sustainability is trending worldwide. This review comprises three major sections. First, we will summarize key enzymes that nature has created to break down lignin, including laccase, manganese peroxidase, lignin peroxidase, dye-decolorizing peroxidase, and versatile peroxidase etc. Relevant enzymes and their catalytic mechanisms will also be briefly discussed. Second, we will review key reactions in priming and processing lignin derived aromatics before they enter microbial metabolic pathways: O-demethylation, hydroxylation, decarboxylation, and ring opening, as well as representative enzymes involved and their catalytic mechanisms. Finally, we will present engineering efforts toward biological valorization of lignin and lignin derived aromatics, which is largely driven by synthetic biology approaches. Biological valorization of lignin is undoubtedly a field full of potential, however its realization still faces several major hurdles, such as low conversion efficiency and long processing time. Nevertheless, as synthetic biology is developing rapidly, harnessing the power of genetic and metabolic engineering to improve the efficiency of lignin breakdown and utilization, microbial tolerance to toxic aromatics, and redox balance will certainly be a promising path forward, paving the way for industrial application in the near future.

Increasing petroleum consumption and growing environmental concerns necessitate the sustainable production of chemicals and fuels from renewable resources. By utilizing renewable resources as raw materials and engineered microorganisms as the core tools, the bio-manufacturing of bio-based materials has become a hot research topic due to its green and low-carbon advantages. ω-Amino acids are a type of non-natural amino acids with amino and carboxyl groups located at the ends of the straight carbon chain. Self-cyclization of ω-amino acids produce lactams, which are the key monomers for the synthesis of polyamide materials, commonly known as nylon. Polyamide materials have wide applications and a huge global market over seven million tons per year. Nowadays, polyamide materials and their monomers are primarily produced through petrochemical routes with non-renewable resources. The research on biosynthesis of these materials and monomers is still in the early stages, but significant progress has been made in recent years. This review article systematically introduces the recent advances in the biosynthesis of ω-amino acids and lactams. To achieve the bio-manufacturing of bio-based polyamide materials, researchers have designed artificial biosynthetic pathways for ω-amino acids from renewable carbon sources such as glucose. The key enzymes for the cyclization of ω-amino acids to form lactams have been identified. By assembling the biosynthetic pathway in microbial chassis such as Escherichia coli and Corynebacterium glutamicum, production of ω-amino acids and lactams have been achieved. Furthermore, the metabolic flux was fine-tuned by regulating and optimizing the expression of key genes to improve the biosynthesis of ω-amino acids and lactams. Besides, biosensors of lactams have been developed to transfer the intracellular concentrations of lactams into easily detectable signals such as fluorescence. Such biosensors have been successfully used for high-throughput screening of ω-amino acid cyclization enzymes and dynamic regulation of biosynthetic pathway. These effects have resulted in the successful biosynthesis of C₄-C₆ ω-amino acids and lactams. Particularly, using glucose as a raw material, the production of valerolactam by fed-batch fermentation exceeded 70 g/L, with a productivity of about 1 g/(L·h), which approaches the level required for industrialization and commercialization. Finally, the review article discusses the current challenges faced in the biosynthesis of ω-amino acids and lactams, including the low yield of biosynthetic pathways, rate-limitations posed by key cyclization enzymes, and insufficient utilization of non-food carbon sources such as one-carbon compounds.

One-carbon compounds are liquid or gaseous substances that can be naturally occurring or produced in industrial processes, offering the advantages of being abundant, cost-effective, and sustainable to produce. They are anticipated to serve as fundamental raw materials for the next phase of bio-manufacturing, encompassing easily transportable and storable liquid methanol, formic acid, and gaseous CO₂, CO, and CH₄. China is currently focusing on reducing carbon emissions and aims to progressively achieve the targets of carbon peak and carbon neutrality through diverse approaches. Amidst the flourishing landscape of bio-manufacturing, microorganisms are being genetically manipulated using synthetic biology techniques to efficiently harness one-carbon compounds for the creation of high-value products like lipids and single-cell protein. This initiative aims to reduce dependence on imported food and fossil resources, serving as a strategic measure to alleviate food and energy crises. This review presents a comprehensive overview of the most recent advancements in converting one-carbon compounds into valuable oils and single-cell proteins through the utilization of metabolic pathways, chassis genetic modification, and other methodologies involving methylotrophic microorganisms, acetogenic bacteria, yeast, and other microorganisms. It discusses pertinent studies on enhancing molecularly engineered strains through the fermentation process using one-carbon compounds and includes research cases focusing on the production of ultra-long-chain fatty acids. Furthermore, it collates industrial instances related to the conversion of one-carbon compounds from research institutions or companies. Lastly, by addressing the constraints in metabolic pathway design and genetic tools for utilizing one-carbon compound strains, as well as the energy conversion challenges between acetogenic bacteria and lipids-producing microorganisms, it offers foresight into the future opportunities and obstacles encountered in the bio-manufacturing of lipids and single-cell proteins. It suggests advancing inter-disciplinary, efficient systematic integration for fermentation within complex systemic bio-manufacturing processes, driving exploration on the biological conversion of one-carbon compounds, proposing novel solutions to current theoretical and practical challenges, and providing guidance for practical applications and industrial advancements.

Biomimetic compartmentalization immobilization of multi-enzyme system is a frontier for in vitro synthetic biology, focusing on the spatial and temporal separation of reactions. Compared with simple co-immobilization, biomimetic compartmentalization immobilization can form substrate channels and promote the transmission of intermediates for sequential or coupling reaction. By controlling the relative positions of the enzymes on carriers, this method improves system stability, productivity, as well as purity of product. In this review, we summarized the recent advances of carriers for biomimetic compartmentalization immobilization of multi-enzyme systems, including metal-organic frameworks (MOFs), polymer vesicles and polymer capsules. Metal-organic frameworks (MOFs) are porous coordination materials which are composed of metal ions as nodes and organic linkers. MOFs possess unique characteristics including high porosity, large specific surface area and tunable structure, which are suitable for multi-enzyme systems. The strategies involving the hierarchically porous MOFs, MOF-on-MOF and multi-MOF combinations construct compartmentalized environments for efficient catalytic reactions in vitro. Polymer vesicles are hollow nanostructures composed of amphiphilic block copolymers. The membrane structure of polymer vesicles, similar to the natural phospholipid bilayers, has good mechanical stability and biocompatibility for protecting enzyme molecules, and provides unique microenvironment for sequential reactions. Multiple small vesicles were encapsulated into the larger vesicles to form a “vesicle-in-vesicle” by mimicking the structure of cellular organelles. Polymer capsules with a core-shell spherical nanostructure are formed by the templating method, and have structural stability and excellent shape controllability. Multilayered core-shell structures created by layer-by-layer self-assembly are applied for compartmentalized immobilization of multi-enzyme. In the future, the integration of microfluidic technologies with biomimetic compartmentalization immobilization of multi-enzyme is expected to provide highly efficient and stable multi-enzyme catalytic systems for in vitro synthetic biology and green biomanufacturing.

In order to achieve carbon neutrality and green economy, people use biorefinery technology to transform and utilize CO₂. Microbial electrosynthesis (MES) is an emerging technology that converts CO₂ into chemicals by electrically driven biocatalysts. Currently, the low efficiency of microbial carbon sequestration, an incomplete understanding of electron transfer mechanisms, low synthesis rate, and poor applicability of reactor components have been the limiting factors for the large-scale application of MES. In this paper, the mechanisms of electron supply in the MES system, including through electrodes and electron donors such as H₂, formic acid, CO, and other molecules, are systematically reviewed based on how cathodic microorganisms obtain electrons. It is an effective method to improve electron transport efficiency by modifying conductive nanowires of electroactive microorganisms and optimizing the expression of microbially associated hydrogenase, formate dehydrogenase and CO dehydrogenase using synthetic biology techniques. Additionally, cathode modification aimed at improving electron transfer rates between microbes and electrodes, enhancing the biocompatibility, and providing more reducing power can facilitate the generation of value-added products. In addition to enhancing the electron transfer efficiency of the cathode, the construction of a reactor with high efficiency of gas-liquid-solid mass transfer and electron transfer, the reduction of anode potential for water electrolysis, and the regulation of microbial activity are also important strategies to enhance MES performance. In the future, it is necessary to further elucidate the mechanism of microbial electron transport and strengthen the performance of MES by means of synthetic biological communities, and by designing a more efficient electrode interface that balances electron transfer rate, substrate mass transfer and biocompatibility. In terms of the scaling-up of reaction devices, electron transfer and gas mass transfer can be improved through the combination of various methods, and integrating product separation processes can promote the further development of the technology and provide new ideas for the realization of the “Carbon Peak and Carbon Neutrality” goal.

Advances in science and technology are creating huge benefits and value for society. The digitalization of the world has brought great changes to human being’s daily life. Meanwhile, the increasing degree of digitalization has led to an unprecedented explosion of data, resulting in increasingly severe information storage challenges. According to the current developing trend, the global data volume is expected to reach 175 zettabytes by 2025. With the rapid growth of global data volume and the exponential growth of total data, the existing storage methods will no longer be able to meet the storage needs brought by the digitalization of the world and then there is an urgent need to develop information storage methods with better storage performance, higher storage efficiency and more durable storage media. Nature has offered a powerful solution by using DNA molecules as carriers of information, where genetic information has been transferred stably more than a million years. DNA storage has many advantages over traditional storage media, including high storage density, potentially low maintenance costs, and ease of synthesis and chemical modification, which make it an ideal alternative for information storage. The current process of storing data in DNA includes six main steps: encoding, writing, preservation, retrieval, reading, and decoding. Among them, the writing of data is the basic for realizing the storage of data in DNA, concluding writing data in DNA sequence and in DNA structure. In this review, we first introduce strategies for in vivo data writing in DNA storage systems, which primarily involve writing data into DNA sequences and DNA structures. This is followed by an overview of the development of in vivo writing techniques in DNA storage systems. Finally, we discuss the challenges faced by DNA storage systems in terms of high writing costs and slow writing speeds, and prospects for large-scale synthesis of high-purity DNA and improved biocatalysts.

Synthetic biology offers boundless possibilities and revolutionary changes to material fields. One remarkable outcome of interdisciplinary integration of synthetic biology and material science is the development of environmentally friendly polyhydroxyalkanoates (PHAs), which serve as ideal alternatives to petroleum-based plastics. PHAs are a family of linear biopolyesters synthesized by various microorganisms as their intracellular storage materials for energy and carbon sources. With at least 150 various monomers, PHAs exhibit diverse structures, material properties, and applications, collectively known as “PHAomics”. When reprograming microbial genomes via synthetic biology and metabolic engineering, in combination with the feeding of special precursors, tailor-made PHAs with defined structures and varied properties can be synthesized. PHAs has been extensively studied in both academia and industry in the last few decades, leading to the commercialization of some PHAs. Next generation industrial biotechnology (NGIB) based on halophilic Halomonas spp. as chassis has been developed to overcome the limitations of current industrial biotechnology. NGIB offers a long lasting, open and continuous, energy and freshwater-saving bioprocess using low-cost mixed substrates and allows morphology engineering for simplified downstream processing. NGIB facilitates low-cost production of various PHAs in large scale. This review introduces PHAomics and summarizes the diverse properties of PHAs produced via NGIB. It primarily focuses on the composition, structure, and material properties of PHAs, as well as their extensive applications in biodegradable plastics, medical implants, medicine, drug delivery carriers, energy sources, and potential smart materials. Additionally, it covers the strategies and tools for strain engineering and their achievements in the tailor-made biosynthesis of PHA using reprogrammed Pseudomonas spp. and Halomonas spp. Finally, this review discusses strategies on how to further reduce the production cost and improve material properties of PHAs. This review summarizes the progresses on the low-cost customized synthesis of PHA biomaterials by synthetic biology, demonstrating the integration of biology and chemistry.

Natural product is an important source of small-molecule drugs and probes, but its synthesis is challenging and has attracted lasting attention in the field of organic chemistry. With the continuous advancement of chromatographic techniques for separation and spectroscopic methods for structural analysis, the pace of discovering tiny bioactive natural products is accelerating, concomitantly leading to an increase in the diversity and complexity of the newly identified structures. However, to meet the demand of the quantity for the study of their structure-activity relationships, target identification, in vivo activity evaluation, etc., growing challenges in the requirement for the synthetic efficiency, economy, and scalability of natural products are emerging. Synthetic practices in a chemoenzymatic way have provided multi-dimensional visions for natural product research, which emerged as a hot research topic in recent years. On the one hand, enzymatic catalysis has provided highly efficient and selective synthetic methodologies that would complement traditional synthetic methods. On the other hand, the introduction of enzyme-catalyzed reactions would bring a new mode of strategic design for synthesis, enabling the rapid and diverse synthesis of natural products with high efficiency. In this context, how to integrate the enzyme-catalyzed reactions into the synthesis of natural products is the key to a successful chemoenzymatic synthesis. We herein summarized three roles played by the applications of enzyme-catalyzed reactions in the current practices of chemoenzymatic synthesis of natural products. ①The involvement of biocatalysis would introduce a chiral center or a key functional group into the starting material, or supply complex synthetic precursors (e.g., polysubstituted (hetero)aromatics, chiral pools, etc.) via in vitro enzyme-catalyzed reactions or fermentation, hence advancing the starting line of synthesis; ②Late-stage enzyme-catalyzed chemo-, regio-, and stereoselective modifications of substrates with heavily substituted functional groups or inert positions of complex skeletons; ③The strategic application of enzymatic catalysis as a key carbon-carbon bond-forming step in the construction of the skeleton of natural product. Finally, we have also discussed the current challenges and future trends of the chemoenzymatic synthesis of natural products in three facets, including the design of synthetic strategy, the development of synthetic methods, as well as persons involved in the research. Thus, the integration of interdisciplinary methods and technologies, including chemical synthesis and biocatalysis, would invigorate the synthesis of natural products.

The extensive consumption of fossil oil and the rapid accumulation of greenhouse gas emissions have caused long-term changes in the global climate and environment, sparking widespread interest in society for CO₂ bioconversion technologies as a means to address energy transition and climate change. As a new-generation biorefinery platform based on synthetic biology, the synthetic phototrophic community comprises closely cooperating phototrophic and heterotrophic microorganisms. This community is capable of efficiently converting light energy directly into biomass and a variety of chemicals through mutualistic metabolic division of labor among community members. Synthetic phototrophic community is one of the potential ways to achieve sustainable carbon-negative biomanufacturing, and has attracted widespread attention attributed to its advantages in applicability and robustness. In recent years, with the rapid development of systems biology and synthetic biotechnology, a variety of research efforts have been applied to the design and optimization of synthetic phototrophic communities, achieving stable progress and promoting the understanding of phototrophic community production. In this review, we briefly introduced an overview of the advances and current status of synthetic phototrophic community, including mutualistic mechanisms related to element, energy, and information flow. Subsequently, the unique advantages of phototrophic community were outlined. Meanwhile, recent systems biology approaches of phototrophic community were summarized, such as integrative analysis of multi-omics data, genome-scale metabolic modelling, flux balance analysis and community performance predictive algorithms. We also focused on the design and optimization strategies, such as chassis upgrading, immobilization/compartmentalization techniques, and enhanced internal multilayer regulation of synthetic phototrophic community, as well as the progress of their applications in various fields. Furthermore, we analyzed and discussed the constraints and challenges for the further deployment of synthetic phototrophic community on a larger scale, ranging from photosynthetic carbon production rate, intermediate organic matter selection, external predator invasion, to light distribution under high density cultivation. Finally, the future research strategies and engineering directions of synthetic phototrophic community encompassing semiconductor biohybrids, fine regulation of interspecies interaction and multi-omics community model construction were proposed. We conclude by providing a perspective on the future application scenarios of synthetic phototrophic communities in biochemistry, biomedicine, bioremediation and bioagriculture.

DNA-Encoded Library (DEL) technology, as an emerging means of small molecule drug screening, has become an important and indispensable technology platform for new drug discovery and development. The technology incorporates many advantages from combinatorial chemistry, molecular biology, and chemical bioinformatics, which greatly improve the efficiency of compound library synthesis and screening. Meanwhile, driven by the development of nucleic acid-compatible chemical reactions and high-throughput sequencing technology, DEL technology has made remarkable progress and gradually become a fast, economical, and efficient high-throughput screening platform, and has been more and more widely used in seedling compounds screening by universities, research institutes, and large pharmaceutical companies. The success of a DEL screening relies heavily on the chemical space and structural diversity of the compound libraries, both of which are directly affected by the number of chemical reactions compatible with nucleic acids. Therefore, developing the on-DNA chemical reactions to continuously enrich the chemical toolbox for DEL synthesis and thus enhance the structural diversity and drug potential of the molecules in the libraries has been the focus in this field. In recent years, the number of on-DNA chemical reactions has increased significantly, greatly broadening the scope of chemical reactions available for DEL construction. Meanwhile, a series of novel reaction methods, such as photocatalysis, electrocatalysis, and biosynthesis, have also emerged in the application of on-DNA chemical reactions and further expanded the field that on-DNA chemical reactions can reach. In this paper, we systematically review the metal-catalyzed on-DNA chemical reactions in recent years, including C(sp²)—C(sp²) bond-formation reactions, C(sp³)—C(sp³) bond-formation reactions, C(sp²)—C(sp³) bond-formation reactions, and C(sp²)—X bond-formation reactions; the synthesis of on-DNA privileged heterocycles with single-ring, fused-ring, and spirocyclic rings by using target-oriented synthetic and diversity-oriented synthetic strategies; the research progress of photocatalytic and enzyme-catalyzed on-DNA chemical reactions. However, the current developments in on-DNA reactions also have limitations, such as compatibility with nucleic acids and substrate suitability. In the future, it is important to exploit more robust on-DNA reactions that can proceed under mild conditions, new types of on-DNA reactions, and the combination of high-throughput screening and computer-assisted on-DNA reactions.