With the rapid growth of consumption in cosmetics, demand for their raw materials is expanding correspondingly, which not only drive the efficacy and product competitiveness but are also crucial for ensuring safety. Synthetic biology, an emerging interdisciplinary field based on engineering principles, leverages gene editing, computer simulation, and bioengineering technologies to design, modify, and even resynthesize organisms through rational strategies. Saccharomyces cerevisiae, an important microbial platform, is increasingly used in the production of cosmetic raw materials. Constructing S. cerevisiae cell factories for the heterologous biosynthesis of cosmetic ingredients presents an eco-friendly and sustainable alternative to traditional plant extraction and chemical synthesis, addressing both environmental concern and resource limitation. In this article, we review the development of gene editing technology and its key role in constructing biosynthetic pathways for the production of cosmetic raw materials with S. cerevisiae. We also summarize the application of metabolic engineering strategies such as multi-copy gene integration, compartmentalization, transporter engineering, and multicellular system in the optimization of S. cerevisiae cell factories. Moreover, we present the latest progress in the biosynthesis of different cosmetic active ingredients with S. cerevisiae cell factories, such as terpenes, vitamins, polyphenols, proteins and amino acids. While the potential and advantages of using S. cerevisiae for large-scale production of cosmetic raw materials are significant, a series of challenges remain, including incomplete biosynthetic pathway analysis, low biosynthesis yield, and low yield with the separation and purification. Looking ahead, the integration of artificial intelligence, machine learning, and other advanced technologies is expected to establish more efficient gene editing tools for the optimization of yeast cell factories and the biosynthesis of cosmetic raw materials, providing technical support and practical guidance for the sustainable development of the cosmetics industry.

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.

Monoterpenoids constitute a significant subclass of terpenoids, known for their volatility and strong aromatic properties. These compounds are extensively employed across multiple sectors, including pharmaceuticals, foods, flavors, cosmetics, agriculture, and energy, due to their diverse pharmacological and biological activities. Currently, monoterpenoids are primarily sourced from plant extracts or chemical synthesis. However, low yield and high cost associated with plant extracts as well as low purity and high energy consumption with chemical synthesis cannot address the growing demand. As a result, the heterologous synthesis of monoterpenoids using microorganisms presents an alternative pathway that is efficient, sustainable, and eco-friendly. Yeasts show promise as hosts for monoterpenoid biosynthesis due to their fast growth, inherent mevalonate (MVA) pathway, and robust post-translational modification systems. Currently, the industrial production of the artemisinin precursor artemisinic acid and the sesquiterpene farnesene has been achieved using Saccharomyces cerevisiae. Advances in synthetic biology have enabled the construction of microbial cell factories for monoterpenoid synthesis. However, challenges remain in scaling up production due to limited precursor availability and monoterpene cytotoxicity. This review first introduces the foundational pathways of monoterpenoid biosynthesis in yeast, followed by discussion on engineering strategies and advancements in yeast-mediated monoterpenoid synthesis, which include enhancing the supply and utilization of acetyl coenzyme A and geranyl pyrophosphate (GPP), regulating and modifying key enzymes such as GPP synthase and monoterpene synthase, optimizing subcellular organelle localization and compartmentalization of MVA pathway genes and monoterpenoid synthases, and implementing exocytosis and tolerance engineering to mitigate monoterpene cytotoxicity. Future directions and strategies to overcome bottlenecks in microbial synthesis are explored to guide research in yeast synthesis of monoterpenoids.

L-arginine is an alkaline amino acid that has been used as a neutralizer, moisturizer, and antioxidant in skin care products. In addition, L-arginine is also widely used in feed, medicine, and food industries. The wide range of applications for L-arginine has garnered significant attention for its robust production. L-arginine can be produced through protein hydrolysis and microbial fermentation. However, protein hydrolysis has drawbacks, including complicated operation, high purification cost, low recovery efficiency, and environmental pollution. In contrast, the microbial fermentation can use renewable and cheap feedstock. Besides, the process is performed under mild conditions, and thus is more environmentally friendly. At present, engineered microorganisms such as Corynebacterium glutamicum and Escherichia coli are major producers of L-arginine, and design and construction of microbial strains is the robust production of L-arginine through microbial fermentation. Random mutagenesis and screening strategies are used to develop L-arginine producing microbial strains, which are random with uncertainties, resulting in a low-efficiency for the breeding. With the development of synthetic biotechnology, development of L-arginine producing strains is empowered by the rational design of artificial synthetic pathways and regulatory machineries, taking advantages of advanced genome editing technologies. This paper reviews the progress in the studies of the synthetic pathways and regulatory mechanisms of L-arginine production that have been discovered in different microorganisms. Synthetic biology-guided metabolic engineering strategies for improving L-arginine production in C. glutamicum and E. coli are summarized. Besides, the application of the biosensor-based high-throughput screening strategy for selecting L-arginine producing strains is introduced. Finally, potential strategies to enhancing L-arginine production and the possibility of using new carbon resources such as non-food biomass and one-carbon feedstock for L-arginine production are discussed. It is envisioned that synthetic biology-guided strain engineering will further enhance the production of L-arginine, particularly using non-food feedstock in the near future.

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.

Biomanufacturing is one of the strategic emerging industries in China during the “14th Five-Year Plan” period. The author once proposed “Tao-Fa-Shu-Qi” for the industrial biomanufacturing and provided its philosophical guideline. Focusing on the “Fa” of biological manufacturing and further analyzing the concept of “Fa as rules” in biomanufacturing, the author first proposed the concept of “Price to Cost-of-raw-materials Ratio” (PC value), which is the ratio of product market price to cost with raw materials. Biomanufactured products can be categorized by PC value into high-value products, value-added products, biocommodity, and products for public good. The PC value is a key indicator for evaluating the technological capability and economic viability of biomanufactured products. It is simple, transparent, and publicly accessible, offering a new approach for categorizing biomanufactured products. This indicator aids in guiding new technologies towards pathways of efficiency enhancement and cost reduction, forecasting future manufacturing costs and market prices for bioproducts, and assessing the industrialization potential of emerging biotechnologies. This article focuses on the biomanufacturing of fructose syrup, fructose solution, crystalline fructose, allulose, myo-inositol, and tagatose as examples, analyzing pathways for developing new technologies and predicting their economic feasibility. The calculation and analysis of the PC value could provide a new methodological tool for the top-level strategic design of the future development of emerging biomanufacturing industries, and could effectively facilitate the high-quality development of the bioeconomy.

Non-renewable resources, such as petrochemicals, have made great contributions to modern civilization. However, the extensive use of fossil fuels, which have been buried for hundreds of millions of years, has led to a substantial increase in carbon imbalance. The imbalance leads to severe ecological and environmental problems. Industrial biomanufacturing, often referred to as a “sunshine economy”, represents a novel sustainable production paradigm, utilizing renewable resources in a carbon-cycling mode. This paper discusses several ways in which biomanufacturing can support China’s “carbon peaking and carbon neutrality” goals from the perspectives of manufacturing feedstock, production mode and product usage. Biomanufacturing can reduce carbon emissions through feedstock substitution, technology iteration and product replacement. Utilization of straw biomass, producing non-food proteins and establishing a biobased industry landscape are important approaches for reducing carbon emissions in biomanufacturing. Efficient biomanufacturing of food and natural products can substantially improve production efficiency, conserve significant land resources, and thus provide land resources for “carbon replacement”. Optimizing agricultural products through biotechnology advancements and innovative product development is a crucial way to reduce pollution but also enhance the carbon sink capacity of the agricultural sector.

Glucoraphanin (GRA), a secondary metabolite of plants, is a glucosinolate (GSL) derived from methionine. It is relatively stable in nature, and both GRA and its degradation product sulforaphane (SFN) play important roles in anticancer, neuroprotection, and other broad biological functions and health-benefits, and in particular, SFN has been reported as the best natural product for anticancer. In this article, we review the physicochemical properties, sources, biological functions, synthetic pathways, current production status of GRA, and discuss the potential strategy for the efficient biological synthesis of GRA in the future. The synthesis pathway of GRA involves three stages: side chain elongation, core structure information, and side chain modification. GRA can be converted into SFN and other active compounds by plant myrosinase (MYR) and intestinal microorganisms. Brassicaceae crops such as broccoli have high levels of GRA, and are currently the main source of GRA. However, the cultivation cycle of GRA-rich plants is long, and its extraction yield is low. Therefore, the development of economical and renewable new resources of GRA will greatly advance its applications. With the elucidation of the biosynthesis and regulation pathways of GRA, its genetic engineering-assisted efficient biological synthesis shows great potential, suggesting that the possibility for developing strategies with the manipulation of multiple genes for regulated expression at different dimensions to synthesize GRA more efficiently compared to the current mainstream strategy through manipulating single genes. This review focuses on the genetic engineering-assisted efficient biosynthesis of GRA in Brassicaceae crops, systematically outlining potential genes for engineering at each stage of GRA synthesis and highlights chassis crop species from the perspective of enrichment organs, aiming to providing ideas and strategies for the future regulation of GRA biosynthesis in plants through transgenic technology and molecular breeding for large-scale sustainable production of GRA.

The CRISPR-Cas gene editing technology has revolutionized the fields of biology, medicine, agronomy, etc. due to its simplicity and efficiency. Laboratory-developed tools, such as the widely recognized CRISPR-Cas9, have played a pivotal role in addressing a multitude of genetic diseases. By harnessing the targeted nucleic acid capabilities of the CRISPR-Cas system, researchers have successfully integrated various functionalities into Cas proteins, including fluorescent markers, transcriptional regulatory proteins, and base editing components. This has unlocked new possibilities, including chromosome imaging, transcriptional regulation, and precise base editing. Currently, Cas nucleases with large molecular weights, often exceeding 1000 amino acids, are commonly used. However, adeno-associated virus (AAV) vectors, which are extensively employed in gene therapy, have limited capacity to accommodate additional functional components beyond the coding sequences of CRISPR nucleases and guide RNAs (gRNAs). This limitation severely constrains their utilization in gene therapy and other applications. As a result, a significant focus of research has been placed on the miniaturization of CRISPR tools, making them compact enough to align with current delivery methods. Compact Cas protein variants within CRISPR-Cas systems hold the potential to create and deliver genome editing and regulatory tools into human cells using AAV. Hence, the development of miniaturized CRISPR-Cas systems presents a crucial avenue for addressing this technical challenge. This article provides a comprehensive review of research progress in miniaturizing key proteins within two classes of Cas systems: Cas9 and Cas12 for targeting DNA, and Cas13 for targeting RNA. This review encompasses the screening of novel Cas proteins, the reduction of protein structural domains, and the modification of guide RNAs, all with the intention of presenting innovative ideas for the further advancement of compact, precise gene editing, and regulatory tools. The miniaturization of CRISPR-Cas systems is a critical step toward unlocking their full potential in various fields, including biomedicine, agriculture, and basic research. As researchers continue to explore and refine these compact gene editing and regulatory tools, we can expect significant advancement in understanding and manipulating genetic information. This ongoing progress promises to have a profound impact on the future of science and technology. At present, the limitations of the miniaturized CRISPR-Cas system are mainly with the size of protein molecular weight and the efficiency and specificity of gene editing. If we can solve these problems and obtain a smaller structure in future research, not only can we optimize the transmission of the system in the body, but also develop high-efficiency and low-damage treatment methods for clinic applications.

The inquiry into the essence of organisms has long been a thriving topic in biology and philosophy. Hypothesises are commonly employed in biological research to understand lives. These hypothesises can be grouped into two categories: ① the machine hypothesis, likening the components and organizational structure of organisms to the operation of machines, and ② the autopoietic hypothesis, likening organisms to complex systems with purposeful and unique attributes. Both play an epistemic role in various fields of biology, serving as theoretical hypotheses, heuristic tools, and means of scientific communication. The machine hypothesis, for instance, has been influential in areas such as molecular biology and systems biology, where organisms are viewed as intricate machines made up of interacting components. The autopoietic hypothesis, on the other hand, has been more prominent in theoretical biology and philosophy of biology, highlighting the self-organizing and self-producing nature of living systems. The development of synthetic biology, which aims to redesigning and constructing biological systems from scratch, has challenged the traditional dichotomy between natural and artificial entities. Both the machine and autopoietic hypothesises are reflected in the advancement of synthetic biology, as researchers attempt to engineer living systems using principles and methods adapted from various disciplines, including engineering, computer science, and materials science. While the hypothesises serve epistemic purposes, their usage also raises some controversies, particularly in the context of synthetic biology. The conflation of ontology and epistemology, where hypothesises are mistaken for literal descriptions of reality, can lead to ethical concerns. For example, the machine hypothesis may suggest that organisms are merely complicated machines to be manipulated, potentially diminishing their intrinsic value and ethical status. This article examines the origin and clarification of these two hypothesises, their applications in synthetic biology, and addresses the potential confusions and ethical implications arising from their usage. It advocates for a cautious approach to the usage of the epistemological hypothesis, considering both its epistemic impact and ethical consequence. As synthetic biology continues to advance, it is crucial to maintain a critical and nuanced understanding of hypothesises employed, recognizing their heuristic value while also acknowledging their limitations and potential pitfalls. The discussion of hypothesises for organism origins in the context of synthetic biology highlights the importance of interdisciplinary collaboration and dialogue between scientists, philosophers, and ethicists. By examining the philosophical and ethical issues of hypothesises, we can better navigate the complex and rapidly evolving landscape of synthetic biology, ensuring that our scientific endeavors are guided by a deep appreciation for the intricate and multifaceted nature of lives.