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    Research advances in biosynthesis of natural product drugs within the past decade
    FENG Jin, PAN Haixue, TANG Gongli
    Synthetic Biology Journal    2024, 5 (3): 408-446.   DOI: 10.12211/2096-8280.2023-092
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    Natural products have long been considered as an important source for potential drugs. In history, natural products and their structural analogs have contributed substantially to the treatment of various diseases, especially cancers and infectious diseases. After a long history of applications, people have gradually begun to explore active ingredients in natural products that truly exert therapeutic effects, and discovered a series of functional compounds, such as morphine, quinine, ephedrine, etc. Over the past two hundred years, the discovery and research of natural products has undergone tremendous changes, from traditional identification and isolation methods to multidisciplinary approaches in the modern genomic era. Strategies for discovering natural products and tools for their prediction have been developed continuously. Although many novel and active natural products have been mined and discovered in the past two decades, considering the huge reserve of natural products in nature, a large number of genes or gene clusters encoding key enzymes for the biosynthesis of natural products have not yet been characterized, and both terrestrial and marine natural product resources are to be explored. Compared with traditional chemically synthesized molecules, natural products possess diverse skeletons for structural complexity, which have shown remarkable advantages in the discovery of new drugs. While there are still many challenges in discovering new drugs from natural products, such as the effective mining of molecules with new structural features, identification and isolation of functional natural products with trace abundance, derivatization of natural product analogs for exploring connections between their structures and activities, and the complete synthesis of complicated active natural products at large scales, etc., the emergence of novel analytical technologies and mining strategies is expected to substantially renovate natural product discovery. This review comments on the natural product drugs and semisynthetic drugs derived from natural products approved by the U.S. Food and Drug Administration within the past decade from January 2014 to October 2023, and provides an overview on the research progress on the biosynthesis of these natural products and their precursors. In addition, important progress in the biosynthesis of some drugs approved by FDA before is also briefly summarized. An in-depth understanding of the biosynthetic pathways and mechanisms underlying their efficacy is expected to provide valuable insights for the discovery and research of more new drugs in the future.

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    Research progress in synthesis of astaxanthin by microbial fermentation
    ZHOU Qiang, ZHOU Dawei, SUN Jingxiang, WANG Jingnan, JIANG Wankui, ZHANG Wenming, JIANG Yujia, XIN Fengxue, JIANG Min
    Synthetic Biology Journal    2024, 5 (1): 126-143.   DOI: 10.12211/2096-8280.2023-065
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    Astaxanthin is a value-added terpene with strong antioxidant activity as well as other physiological functions, such as anti-cancer, enhancing immunity, eye protection, and cardio-cerebrovascular protection. Natural astaxanthin mainly comes from algae and aquatic crustaceans such as lobster shell. Astaxanthin presents with stereoisomerism and geometric isomerism, which have different biological activities and applications. Currently, astaxanthin in the market is obtained primarily through natural extraction from Haematococcus pluvialis or Xanthophyllomyces dendrorhous and chemical synthesis as well. While H. pluvialis has a long growth cycle and high light demand, leading to low biomass productivity and extraction rate for high production cost of astaxanthin, X. dendrorhous has a low astaxanthin yield and is easy to degenerate, making them challenging for the large-scale commercial production. The chemical synthesis of astaxanthin involves multiple reactions with complicated processes, producing mixed isomers and various byproducts, which consequently compromises its antioxidant capacity. Moreover, the assimilation and utilization of chemically synthesized astaxanthin in vivo is poor compared to its natural product, making it not suitable for being used by human being. With the continuous development of synthetic biology, microbial fermentation has been developed as an effective way for the commercial production of astaxanthin to better meet consumer demand. At present, astaxanthin-producing microorganisms include bacteria, fungi, and algae. This review introduces astaxanthin's structure, properties, production methods, and processes for its extraction and purification, with an emphasis on natural and engineered biosynthetic pathways. The latest progress in the production of astaxanthin by different microorganisms such as H. pluvialis, Yarrowia lipolytica and Escherichia coli is summarized, along with strategies for increasing astaxanthin production through genetic engineering and fermentation process optimization. Future metabolic engineering strategies are proposed, such as over-expression of astaxanthin synthesis genes, promoters with higher substitution intensity, subcellular localization, metabolic pathway optimization, etc, to increase astaxanthin yield for wide usage in food, medical, cosmetic and feed industries.

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    Research progress on bio-degradation and valuable bio-conversion of chitinous resources
    ZHANG Alei, WEI Guoguang, ZHANG Chi, CHEN Lei, ZHOU Xi, LIU Wei, CHEN Kequan
    Synthetic Biology Journal    2024, 5 (6): 1279-1299.   DOI: 10.12211/2096-8280.2024-041
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    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.

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    Advances in synthesis and mining strategies for functional peptides
    TANG Chuan′gen, WANG Jing, ZHANG Shuo, ZHANG Haoning, KANG Zhen
    Synthetic Biology Journal    2025, 6 (2): 461-478.   DOI: 10.12211/2096-8280.2024-067
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    Functional peptides are short chain peptides composed of 2 to 50 amino acids, and their biological activities are closely related to their amino acid sequences, chain length, and structural architectures. Functional peptides can play a regulatory role in a variety of physiological processes by specifically recognizing and binding to target molecules in vivo. Due to their rapid action, strong specificity, less side effect and toxicity, functional peptides have shown great application potentials in many fields such as biomedicine, food science and cosmetics. For example, in the field of biomedicine, functional peptides can be used as the basic material of antimicrobe, anticancer, immune regulation and other therapeutic factors. In the food industry, they are used as natural supplements to enhance nutritional value for health benefit. In the field of cosmetics, functional peptides are widely used for the anti-aging, moisturizing, and repairing of the skin. In this paper, we discuss the ways of obtaining functional peptides, mainly including protein hydrolysis, chemical synthesis, and biosynthesis (e.g., through microbial recombinant expression technology), and compare their advantages and disadvantages and respective application scenarios. In terms of strategies for mining functional peptides, we review the latest research progress including phage surface display, machine learning algorithm, molecular docking and artificial intelligence. These techniques show significant potentials in the screening and design of functional peptides. In recent years, the rapid development of synthetic biology and the wide applications of bioinformatics and artificial intelligence have provided new ideas and strategies for the discovery and optimization of functional peptides, making it possible to screen functional peptides through machine learning and high throughput. Looking forward to the future, the research of functional peptides will face new challenges and opportunities. Improving the synthesis process for high efficiency, improving the stability of functional peptides through structural modifications, and using computer-aided optimization and artificial intelligence to design multifunctional peptides will become important research directions. At the same time, strengthening the safety and efficacy assessment of functional peptides can further enhance the applications of functional peptides.

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    Advancements in the study of probiotics for adjunctive prevention and treatment of malignancies
    ZHU Xinyue, CHEN Tiantian, SHAO Hengxuan, TANG Manyu, HUA Wei, CHENG Yanling
    Synthetic Biology Journal    2025, 6 (4): 899-919.   DOI: 10.12211/2096-8280.2025-004
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    Cancer continues to pose a significant global public health challenge, as its incidence and mortality rates persistently rise. Conventional cancer treatments, which include chemotherapy, radiotherapy, and surgery, often involves severe side effects and potential drug resistance. This comprehensive review examines the pivotal role of probiotics in cancer prevention, treatment, and management, elucidating their underlying mechanisms and clinical applications. Probiotics, defined as beneficial microorganisms that colonize the human gastrointestinal tract and other mucosal surfaces, have emerged as potential adjuncts in the prevention and treatment of cancer. The mechanisms of action include modulating the tumor microenvironment (TME), enhancing immune responses, and inhibiting carcinogenesis. In cancer prevention, probiotics can modulate the gut microbiota to inhibit carcinogen generation. For example, specific strains of Lactobacillus and Bifidobacterium have been shown to decrease the activity of enzymes involved in carcinogen production, such as β-glucuronidase and nitroreductase. Moreover, Probiotics and their metabolites, such as short-chain fatty acids (SCFAs) and indole compounds, play an antitumor role by regulating the tumor microenvironment such as regulating cancer-related gene expression, the PI3K-AKT signaling pathway, and the tryptophan-indole metabolic pathway. In the context of adjuvant therapy for malignant tumors, probiotics have shown inhibitory effects on various cancers in the digestive and reproductive systems. They can modulate the intestinal microenvironment, influence tumor cell proliferation and apoptosis, and ultimately suppress tumor growth. Additionally, probiotics can alleviate the adverse effects of cancer therapies. For example, they can mitigate chemotherapy-induced diarrhea and radiation-induced mucositis, and promote postoperative recovery by enhancing gut barrier function and reducing inflammation. This review offers a comprehensive and systematic synthesis of research on the role of probiotics in the prevention and adjuvant treatment of malignant tumors. It delves into their potential mechanisms of action and explores their clinical applications, aiming to establish a solid theoretical foundation and practical guidance for the integrated management of cancer. Looking ahead, the integration of synthetic biology with probiotics holds significant potential for cancer therapy. Advances in synthetic biology have enabled the enhancement of the anti-tumor efficacy of probiotics through genetic engineering. Engineered strains, such as Escherichia coli Nissle 1917 and attenuated Salmonella typhimurium VNP20009, have shown potential in tumor-targeted therapy. When combined with emerging technologies such as nanotechnology and photodynamic therapy, the application of probiotics in cancer treatment is expected to become more precise and effective. However, the safety and efficacy of engineered probiotics require further validation, particularly regarding the potential risks associated with long-term use. Future research should concentrate on personalized probiotic applications, the development of engineered strains, and their synergistic effects with other therapeutic modalities to advance this field. In conclusion, probiotics hold significant promise as adjuncts in cancer prevention and treatment, with the potential to modulate the TME, enhance immune responses, and alleviate treatment-related side effects. Further research is necessary to fully elucidate their mechanisms of action and optimize their clinical application, thereby facilitating their integration into comprehensive cancer care strategies. {L-End}

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    Green biomanufacturing of ceramide sphingolipids
    LU Jinchang, WU Yaokang, LV Xueqin, LIU Long, CHEN Jian, LIU Yanfeng
    Synthetic Biology Journal    2025, 6 (2): 422-444.   DOI: 10.12211/2096-8280.2024-059
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    Ceramide, a fundamental bioactive molecule found ubiquitously in eukaryotic organisms, exerts profound regulatory effect on cellular physiology, encompassing critical roles in signaling cascades, cellular proliferation, differentiation, and apoptosis, as well as immunomodulation. In dermatology, ceramides play an indispensable role as constituents of the stratum corneum, the outermost layer of the skin, where they are crucial for maintaining the integrity of the epidermal barrier, regulating moisture retention, combating oxidative stress linked to aging, and exhibiting notable antimicrobial and anti-inflammatory properties. The multifaceted biological functions of ceramides underscore their extensive applications in various industries, including cosmetics, biomedicine, functional food, and animal nutrition, highlighting their significant market potential and therapeutic value. The chemical synthesis of ceramides poses substantial challenges due to the intricate stereochemistry involved, necessitating precise control over synthetic pathways. As a result, current commercial sources predominantly rely on semi-synthetic methods that integrate traditional natural extraction techniques with biochemical transformations of sphingolipid precursors to achieve targeted ceramide structures. Recent advancements in synthetic biology have explored microbial systems for the production of sphingolipids, including ceramides, offering promising avenues for scalable and sustainable synthesis. However, optimizing de novo synthesis pathways and their efficiency in microbial cell factories remains a primary research focus. Strategies aimed at enhancing ceramide yield and purity through metabolic engineering and pathway optimization are pivotal for advancing industrial applications. This paper provides a systematic review of the physiological effectiveness and function of ceramides, encompassing their physiological roles and various applications. It begins with an overview of ceramide extraction methods, including both natural extraction techniques and chemical synthesis approaches for ceramides and their precursor compounds. Subsequently, the review addresses the sphingolipid synthesis pathways and their associated key enzymes, detailing strategies for pathway regulation and optimization, as well as the aspects of product transport, storage, and secretion. Additionally, it explores the identification and expression of key enzymes. The paper concludes by examining future directions in the field, such as addressing aggregation toxicity in ceramide synthesis, enhancing transport and secretion mechanisms, advancing digital modifications of catalytic elements, and expanding gene regulatory target exploration. By synthesizing current knowledge and highlighting avenues for innovation, this review aims to catalyze further research effort toward achieving efficient ceramide production. Ultimately, optimizing ceramide synthesis has the potential to unlock its full potential in various sectors, contributing to its advancement in skincare, therapeutics, and functional materials. The integration of microbial systems is particularly promising for expanding production capabilities while addressing sustainability concerns in ceramide manufacturing. Continued advancements in synthetic biology and biotechnology are expected to revolutionize the landscape of ceramide applications, paving the way for enhanced therapeutic interventions and novel industrial applications in the future.

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    Biological degradation and utilization of lignin
    LIU Kuanqing, ZHANG Yi-Heng P.Job
    Synthetic Biology Journal    2024, 5 (6): 1264-1278.   DOI: 10.12211/2096-8280.2023-062
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    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.

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    Research progress of the CRISPR-Cas system in the detecting pathogen nucleic acids
    DU Yao, GAO Hongdan, LIU Jiakun, LIU Xiaorong, XING Zhihao, ZHANG Tao, MA Dongli
    Synthetic Biology Journal    2024, 5 (1): 202-216.   DOI: 10.12211/2096-8280.2022-068
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    The CRISPR-Cas system consists of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins, which has become the focus of molecular diagnosis because it recognizes and cleaves specific DNA or RNA sequences. Using Cas proteins (Cas12, Cas13, Cas14, Cas3, etc.) combined with signal amplification and transformation techniques (fluorescence, potentiometric, colorimetric, lateral flow assay, etc.), researchers have developed many diagnostic platforms with high sensitivity, good specificity, and low cost, which provide a new tool for detecting pathogen nucleic acids. This review presents the biological mechanism and classification of the CRISPR-Cas system, and also summarizes existing technologies for detecting pathogenic nucleic acids based on the trans-cleavage activity of Cas proteins, commenting their properties, functions and application scenarios, with future applications prospected based on the functional characteristics of the CRISPR-Cas system, which is expected to become an ideal detection platform for other multiple targets.

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    Research progress in the biosynthesis of salidroside
    HUANG Shuhan, MA He, LUO Yunzi
    Synthetic Biology Journal    2025, 6 (2): 391-407.   DOI: 10.12211/2096-8280.2024-076
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    Salidroside, a natural product known for its anti-hypoxia, anti-oxidation, anti-inflammatory, anti-aging, and anti-tumor properties, is extensively utilized in the food, cosmetics and pharmaceutical industries. Traditionally, salidroside has been obtained through the extraction from the rhizomes and tubers of Rhodiola species, including water extraction, two-phase aqueous extraction, supercritical CO2 extraction and microwave assisted extraction. However, its low natural abundance (with the salidroside content in rhizomes and tubers of Rhodiola species ranging from 0.5% to 0.8%), coupled with escalating demand, has led to a progressive depletion of these plant resources. Given the broad application potential of salidroside, the rapid growth of market demand, and the increasing scarcity of natural resources, there is an urgent need to develop innovative synthetic approaches for this valuable compound. Chemical synthesis of salidroside is characterized by its efficiency and rapid processing time. However, the use of strong acids, bases, and catalysts with heavy metal ions in the synthesis process poses challenges for the separation of salidroside with environmental risks. In recent years, with the advancements in synthetic biology, the construction of microbial cell factories for the biosynthesis of salidroside has become a viable strategy for addressing the current supply-demand imbalance and resource scarcity associated with the natural biosynthetic pathway of salidroside. To enhance the production of salidroside biosynthesis, two major strategies can be employed. First, metabolic engineering approaches can be used to overexpress key genes in the synthesis pathways while knocking out or downregulating the expression of genes related to the bypass routes, thereby increasing precursor accumulation and enhancing the metabolic flux. Second, enzyme engineering can be applied to improve the catalytic efficiency and regioselectivity of natural glycosyltransferases, which often exhibit low activity and poor selectivity. Sequence alignment techniques can be used to identify and screen potential glycosyltransferases from various biological genomes. Additionally, protein engineering combined with computational approaches can be utilized to optimize these enzymes to meet specific requirements, ultimately improving the production of salidroside. In this comprehensive review, we systematically assess the pharmacological activities of salidroside, the plant biosynthetic pathway, the mining and screening of the enzymes, and the biosynthetic advancements in Escherichia coli and Saccharomyces cerevisiae. Additionally, we discuss the separation and purification methods of salidroside and its application potential as a synthetic intermediate in the preparation of other compounds, such as hydroxysalidroside, verbascoside and echinacoside. This review aims to enhance the understanding of the biosynthetic pathway of salidroside, thereby promoting a greener and more efficient biosynthetic approach to salidroside production.

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    Research progress in biosensors based on bacterial two-component systems
    ZHAO Jingyu, ZHANG Jian, QI Qingsheng, WANG Qian
    Synthetic Biology Journal    2024, 5 (1): 38-52.   DOI: 10.12211/2096-8280.2023-016
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    Two-component systems (TCSs) in bacteria, are capable of sensing and making responses to physical, chemical, and biological stimuli within and outside the cells, and subsequently induce a wide range of cellular processes through the role played by the regulatory component and the response component in combination, which is a ubiquitous signal transduction pathway. At present, an growing number of synthetic biologists have devoted their effort to using the specific and irreplaceable properties of TCSs to design biosensors with the aim of applying in optogenetics, materials science, engineering of gut microbiome, biorefining and soil improvement, and the like. The purpose of this review is to focus on the most recent research advances in the development of biosensors based on TCSs and their potential applications. At the same time, topics of great importance are discussed on how to use novel engineering methods with synthetic biology to improve the reliability and robustness of the performance of the biosensors, such as genetic remodeling, DNA-binding domain swapping, tuning of the detection threshold and isolation of phosphorylation crosstalk as well as on how to customize the signal characteristics of TCSs to meet particular needs according to the requirements of specific applications. It would be possible in the future for scientists to combine these methods with gene synthesis on a large scale and high-throughput screening in order to speed up and give synthetic biologists a hand in the discovery of TCSs with numerous uncharacterized signal inputs and the development of genetically encoded novel biosensors that may be capable of responding to a broad range of stimuli. This allows for extending the applications of the biosensors in different fields.

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    Applications of machine learning in the reconstruction and curation of genome-scale metabolic models
    WU Ke, LUO Jiahao, LI Feiran
    Synthetic Biology Journal    2025, 6 (3): 566-584.   DOI: 10.12211/2096-8280.2024-090
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    Since the publication of the first genome-scale metabolic model (GEM) in 1999, GEMs have become an essential tool for analyzing metabolism. The models integrate genes, metabolites, and reactions for combining stoichiometric matrices with constraint-based optimization to systematically describe and simulate metabolic processes in organisms. The development of automated pipelines for reconstructing GEMs has expanded their applicability to organisms from all kingdoms of life. Additionally, GEMs can integrate kinetic parameters, thermodynamic parameters, multi-omics data and multi-cellular processes to reconstruct more accurate models, thereby improving prediction accuracy. However, the reconstruction of GEMs remains heavily dependent on pre-existing knowledge, inherently limiting their scope to currently available information. This dependency restricts our ability to fully unravel the complexity and dynamic nature of metabolism. Recent advances in machine learning have demonstrated extraordinary capabilities for biological tasks such as protein structure prediction, disease identification and GEM reconstruction with functional annotation and large-scale data integration, showcasing its power in identifying patterns and uncovering hidden relationships within biological systems. Machine learning provides a promising pathway to overcome the limitations of GEMs by expanding their applicability to areas previously constrained by data availability and complexity. This review summarizes the traditional reconstruction methods of GEMs and their applications in integrating multi-dimensional data to build multi-constraint and multi-process models. The review also focuses on key applications of machine learning in gene function annotation, pathway analysis, gap-filling prediction in the reconstruction of GEMs. Additionally, the potential of machine learning in predicting kinetic, thermodynamic, and other key biochemical parameters in the reconstruction of multi-constraint and multi-process models is discussed. By combining GEMs with machine learning innovations, researchers can improve model accuracy, enhance scalability, and gain new insights into previously elusive metabolic mechanisms, bridging gaps in metabolic knowledge, and underscoring its importance as a cornerstone for future development in systems biology and biotechnology.

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    Advances in applications of deep learning for predicting sequence-based protein interactions
    ZHU Jingyong, LI Junxiang, LI Xuhui, ZHANG Jin, WU Wenjing
    Synthetic Biology Journal    2024, 5 (1): 88-106.   DOI: 10.12211/2096-8280.2023-074
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    Protein-protein interactions play a crucial role in biological processes such as cell signal transduction, gene expression and metabolic regulation, and thus their identification is essential for understanding these complex biological processes. Predicting protein-protein interactions is a hot topic of great significance, which can provide assistances in areas such as drug discovery and protein function research and design as well. In recent years, with the development of artificial intelligence, machine learning technologies have been applied gradually to the prediction of protein-protein interactions, which has shown good potentials. However, when processing a large amount of protein information, traditional machine learning methods are difficult to mine the intrinsic patterns and potential features, and deep learning techniques are needed. Compared with the three-dimensional structure of proteins, sequence information is easier to obtain, and the development of high-throughput sequencing technology provides abundant protein sequence information, which greatly facilitates the development of sequence-based deep learning technologies. Sequence-based deep learning models predict protein-protein interactions by learning intrinsic patterns and features from protein sequence information, which greatly improves prediction efficiency and accuracy. In this review, we focus on progress of deep learning in predicting sequence-based protein interactions, categorize, which is summarized according to the algorithmic framework and timeline, briefly describing the construction methods of datasets and the evaluation metrics of the models, discussing in detail the sequence encoding methods and common algorithmic architectures, and demonstrating the computational models based on various types of algorithms and their features and advantages. Finally, we analyze current challenges in predicting protein-protein interactions using deep learning methods, and discuss possible solutions. With the development of deep learning technology, the efficiency of predicting protein-protein interactions has increased dramatically. As a result, there is a need to develop models with stronger generalization and more robust prediction capabilities to aid the prediction of protein-protein interactions in the future.

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    Biosynthesis of flavonoids and their applications in cosmetics
    WEI Lingzhen, WANG Jia, SUN Xinxiao, YUAN Qipeng, SHEN Xiaolin
    Synthetic Biology Journal    2025, 6 (2): 373-390.   DOI: 10.12211/2096-8280.2024-058
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    Flavonoids are natural ingredients commonly used in cosmetics, mainly for their antioxidant and anti-inflammatory effects, but they also present a variety of other biological activities such as antimicrobial, whitening, and anti-ultraviolet. Therefore, flavonoids have a huge application potential waiting to be explored. In this review, firstly, the numerous biological properties of flavonoids used in cosmetics, as well as examples of their applications in cosmetics are presented, with their biosynthetic pathways addressed. Then, recent advances in biosynthesis of typical flavonoids (e.g., phloretin, naringenin, apigenin, luteolin, chrysin, rutin, and anthocyanins) are reviewed and discussed, with a focus on the novel synthetic biology and metabolic engineering strategies to improve the productivity and yield of biosynthesized flavonoids, including the enhancement of precursor supply, characterization and modification of key enzymes, regulation of gene expression, and optimization of fermentation processes. With the continuous innovation of synthetic biology technology, there has been an increase in the efficiency of flavonoid biosynthesis and a significant reduction in production cost, which contributes substantially to the widespread use of flavonoids in cosmetics. However, the prevalence of poor solubility and low stability of flavonoids limits their applications in cosmetics. To address this issue, we outline the research process of two main strategies: nanocarrier technology and moiety modification. The application of these research results opens up new possibilities for the use of flavonoids in cosmetics. At the end, we discuss two major challenges in high-yield synthesis of complex flavonoids: the difficulty of key enzyme modification and the imbalance of metabolic flux. We also look forward to AI-assisted synthetic biology to address these challenges and drive the yield improvement and industrialization of flavonoid biosynthesis, providing biotechnological power for the development and innovation of the cosmetics industry.

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    Research advances on paclitaxel biosynthesis
    LIU Xiaonan, LI Jing, ZHU Xiaoxi, XU Zishuo, QI Jian, JIANG Huifeng
    Synthetic Biology Journal    2024, 5 (3): 527-547.   DOI: 10.12211/2096-8280.2023-085
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    Paclitaxel (Taxol) is a natural broad-spectrum anticancer drug, which is well-known for its potent anticancer activity. Its production mainly relies on the extraction and purification from the rare Taxus plant, followed by chemical semi-synthesis. The limited natural resource for paclitaxel imposes a significant constraint on its production capacity. In recent years, with the complete decoding of the Taxus genome and the rapid development of synthetic biology, constructing recombinant cells through synthetic biology techniques has emerged as an effective method to address this challenge. Since paclitaxel biosynthesis involves more than 20 steps of complicated enzymatic reactions and about half of them are P450 enzyme-mediated hydroxylation reactions, the complete elucidation of its biosynthetic pathway remains elusive. Meanwhile, the production of paclitaxel by engineered microbes is still at the initial stage, and there are numerous by-products, which seriously compromise the efficient synthesis of paclitaxel. Therefore, this article reviews research progress related to paclitaxel synthesis pathways, Taxus omics analyses, construction of chassis cells, synthesis of key precursors, modifications of crucial enzymes, and catalytic mechanisms underlying paclitaxel biosynthesis. Special attention is given to the recent breakthrough in elucidating the formation of oxetane ring and the discovery of Taxane 1-β- and 9-α-hydroxylases. Recent advances in the study of the catalytic mechanism of Taxadiene-5-α-hydroxylase and significant progress in engineering tobacco and yeast chassis will also be commented. Furthermore, challenges and future prospects involved in the paclitaxel synthetic biology research are discussed, such as the issues of low enzyme catalytic efficiency, significant product promiscuity, unknown specific reaction sequences, and the biosynthesis of critical paclitaxel intermediates, aiming to enhance the understandings of paclitaxel biosynthetic pathways and catalytic mechanisms for greener and more efficient production of paclitaxel.

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    Chemoenzymatic synthesis of natural products: evolution of synthetic methodology and strategy
    ZHANG Shouqi, WANG Tao, KONG Yao, ZOU Jiasheng, LIU Yuanning, XU Zhengren
    Synthetic Biology Journal    2024, 5 (5): 913-940.   DOI: 10.12211/2096-8280.2024-028
    Abstract2723)   HTML156)    PDF(pc) (5090KB)(2618)       Save

    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.

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    Synthetic biology ushers cosmetic industry into the “bio-cosmetics” era
    ZHANG Lu’ou, XU Li, HU Xiaoxu, YANG Ying
    Synthetic Biology Journal    2025, 6 (2): 479-491.   DOI: 10.12211/2096-8280.2024-056
    Abstract2554)   HTML196)    PDF(pc) (1267KB)(2534)       Save

    The field of synthetic biology has been profoundly transformed over the past two decades due to major advances in biotechnology. Notable instances of this seismic shift can be seen in DNA sequencing, where the cost for human whole genome sequencing (WGS) has dropped by ten million-fold in the past 20 years from nearly 3 billion USD in 2003 to less than 300 USD currently. For perspective, in the field of computer technology the effects of “Moore’s Law” has drove computation cost down by a thousand-fold in the past 20 years. Significant advances in technologies underpinning synthetic biology in recent years are transforming many major industries, and one remarkable example of synthetic biology driven transformation is the cosmetics and skincare industry. Historically, changes in skincare have been driven by changes in raw materials: from ancient plant-based concoctions to industrial-era chemicals in the twentieth century, and later to the concept of “cosmeceuticals” emerged in the U.S., integrating pharmaceutical benefits into cosmetics to meet the growing demand for anti-aging skincare products. Today, there’s an increasing demand for more potent cosmetics, alongside a growing voice for environmentally sustainable production. Traditional skincare product development often involves reformulating existing ingredients, which faces limitations in efficacy. Additionally, the reliance on chemical synthesis or natural extraction methods for production poses additional environmental cost due to the use of chemical reagents and significant energy consumption. Rapid advances in biotechnology enables us to overcome such efficacy and environmental limitations through direct synthesis of biomaterials that are safer and more cost-effective than their industrial chemical counterparts. Synthetic biology tools such as AI-assisted protein design and strain engineering are enabling the production of much more potent biomaterials at industrial scales, thus providing more effective and sustainable bioactive ingredients for skincare. For example, previously expensive and hard-to-obtain compounds such as hyaluronic acid, ceramides, and collagen are now produced at a fraction of the cost compared to the previous decade. In recent years, synthesized collagen has shown that it can be designed to be humanized to minimize adverse human immune reactions, thus greatly reducing allergy and other health risks of the end product. The incorporation of biomaterials that were once exclusive to expensive therapeutics into consumer skincare product is rapidly transforming the cosmetics industry by narrowing the gap between medical-grade treatment and consumer-grade anti-aging. This trend marks a significant leap toward more effective, safer, and environmentally sustainable cosmetics products. Ultimately, the advent of synthetic biology-based cosmetics is ushering in the transitioning from traditional industrial chemical-based cosmetics to a new era of “bio-cosmetics”.

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    A review on enzyme-catalyzed synthesis of chiral amino acids
    WANG Ziyuan, YANG Lirong, WU Jianping, ZHENG Wenlong
    Synthetic Biology Journal    2024, 5 (6): 1319-1349.   DOI: 10.12211/2096-8280.2024-015
    Abstract1452)   HTML72)    PDF(pc) (7957KB)(2520)       Save

    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.

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    Synthetic genetic circuit engineering: principles, advances and prospects
    GAO Ge, BIAN Qi, WANG Baojun
    Synthetic Biology Journal    2025, 6 (1): 45-64.   DOI: 10.12211/2096-8280.2023-096
    Abstract2498)   HTML237)    PDF(pc) (3184KB)(2471)       Save

    Synthetic genetic circuits are engineered gene networks comprised of redesigned genetic parts for interacting to perform customized functions in cells. With the rapid development of synthetic biology, synthetic genetic circuits have shown significant application potentials in many fields such as biomanufacturing, healthcare and environmental monitoring. However, the efforts to scale up genetic circuits are hindered by the limited number of orthogonal parts, the difficulty of functionally composing large-scale circuits, and the poor predictability of circuit behaviors. A longstanding goal of synthetic biology research is to engineer complex synthetic biological circuits, using modular genetic parts, as we do with electronic circuits. Synthetic biologists have developed various genetic toolboxes and functional assembly methods over the past few decades. Here we present an overview of the latest advances, challenges, and future prospects in genetic circuit engineering from four aspects corresponding to the four key engineering principles for circuit design, i.e. orthogonality, standardization, modularity, and automation. Firstly, the design and construction of orthogonal genetic part libraries are discussed in both prokaryotes and eukaryotes at the levels of DNA replication, transcription, and translation, respectively. Standardized characterization methods and the design of modular genetic parts are subsequently summarized. Furthermore, progress in developing modular genetic circuits are presented, providing new concepts and ways for engineering increasingly large and complex circuits. Finally, how to achieve automated design and building of genetic circuits are addressed from the advances in software, hardware and artificial intelligence, respectively, with an aim to replacing the presently time-consuming manual trial-and-error mode with the iterative "design-build-test-learn" cycle for improved efficiency and predictability of circuit design. The integration of these fundamental principles and the latest advances in information technology such as artificial intelligence and lab automation will accelerate the paradigm shift in genetic circuit engineering and synthetic biology research, making it feasible for designing synthetic lives to meet various customized needs.

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    Progress in biomanufacturing of lipids and single cell protein from one-carbon compounds
    ZHAO Liang, LI Zhenshuai, FU Liping, LYU Ming, WANG Shi’an, ZHANG Quan, LIU Licheng, LI Fuli, LIU Ziyong
    Synthetic Biology Journal    2024, 5 (6): 1300-1318.   DOI: 10.12211/2096-8280.2024-013
    Abstract1364)   HTML95)    PDF(pc) (1899KB)(2453)       Save

    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.

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    The enlightenment of the Chinese philosophy “Tao-Fa-Shu-Qi” to industrial biomanufacturing
    ZHANG Yi-Heng P. Job
    Synthetic Biology Journal    2024, 5 (6): 1231-1241.   DOI: 10.12211/2096-8280.2023-066
    Abstract2301)   HTML275)    PDF(pc) (1617KB)(2434)       Save

    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.

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