Synthetic biology, as a science transforming life science in the 21st century, is interdisciplinary in nature, breaking boundaries, emphasizing human roles, and shaping our way of living through technology, presenting common challenges in the Anthropocene era we live in. As a technology of the Anthropocene, synthetic biology blurs the line between nature and artificiality, merging the two and demonstrating the profound impact of technology on life itself. Synthetic life not only obscures the boundary between nature and artificiality but also transcends traditional disciplinary divisions, becoming a research object across various fields, thereby promoting interdisciplinary collaboration and integration. In this process, the openness of synthetic life and the generative nature of synthetic biology determine its future-oriented characteristics, altering the direction of technological research in the Anthropocene. Finally, the “big questions” and “small questions” that the philosophy of technology concerns about are unified in synthetic biology. Synthetic biology encompasses both general issues and its specific developments and applications. In summary, philosophical reflections on synthetic biology as a technological platform in the Anthropocene contribute to a deeper understanding of synthetic biology within a new theoretical framework.

DNA information storage is a new technology that uses DNA molecules as data carriers. It encodes information for synthesizing DNA with a specific sequence and reads out data through sequencing technology. Compared with traditional magnetic, optical, and electronic storage media, DNA storage has significant advantages in data density, retention duration, energy efficiency, and security, since it is not easily affected by electromagnetic interference. With the rapid increase in the total amount of global data, DNA storage has gradually become a research hotspot with its efficient storage capacity, low maintenance cost, and unique chemical property for synthesizing easily. However, DNA storage technology is still in its early stages of development and there are still many technical bottlenecks to be addressed. For example, an important advantage of DNA storage is its ultra-high storage density and long-term stability. However, achieving these goals require overcoming many technical challenges, such as reducing the error rate for synthesis and improving the encoding efficiency. Understanding existing key technologies, such as DNA encoding, error correction, random access, and DNA information encryption, can help identify and address those shortcomings, thereby promoting further technological innovation and development in DNA storage. Encoding strategy is one of the core aspects of DNA storage technology, directly determining data storage efficiency, reading accuracy, and error correction capability. To achieve efficient and stable DNA information storage, it is essential to develop more advanced encoding algorithms to enhance storage density, reduce synthesis and sequencing error rates, and ensure data accuracy and integrity. Moreover, the information security of DNA storage is becoming increasingly important, particularly in terms of data and privacy protection. As a potential data carrier, DNA storage needs to address challenges related to data encryption, information security, and tamper-proof to ensure data confidentiality and integrity. Therefore, integrating modern cryptographic techniques with DNA storage to establish a secure and reliable information storage system has become a key research focus in this field. This article first introduces the basic process of DNA storage, and then reviews the key technologies involved in DNA information storage, especially the research progress of encoding strategies, error correction technology, random access and DNA information encryption. In addition, the current development status and main challenges of DNA storage technology are also discussed. For example, the scale of DNA data storage in the laboratory is small, and the operation time for synthesis is long. Moreover, most DNA storage steps rely on experimenters, making it difficult to automate the information storage and reading process. With the advancement of synthetic biology and encoding and decoding methods, we believe that these bottlenecks will be solved in the near future, and promote the transformation of technology from laboratory research to practical applications.

Protein engineering performs specific designs and modifications on proteins through directed evolution, semi-rational or rational design, computer-assisted design, and so on. The engineered proteins, with improved properties, have significant applications in food, medicine, fuel, and material industries. For the chemical and pharmaceutical industry, engineered enzymes can serve as efficient biocatalysts for the synthesis of active pharmaceutical ingredients (API) and their intermediates, aligning with the concepts and principles of green chemistry and manufacturing. For the biopharmaceutical industry, the engineering of peptide or protein modifying enzymes can boost the efficiency in preparing drug candidates, while engineered diagnostic enzymes can make detection more accurate and sensitive. Moreover, protein engineering can improve the bioactivities of biological drugs such as therapeutic enzymes and antibodies, increase stability, and mitigate immunogenic response for their safety and efficacy. Here, we review the tremendous progress in protein engineering, elucidate its importance in the research and development of chemically derived drugs and biologics, and provide examples of its applications. These examples encompass the discovery of enzymes or antibodies, the process of protein engineering, and the subsequent economic advantages. We aim to showcase the practical implementation of protein engineering in the pharmaceutical industry and facilitate technology transfer, thereby fostering seamless integration between research, development, and industrial production. Furthermore, we discuss challenges such as cost-effectiveness and market changes in the synthesis of API, and multi-target optimization, long cycle and high risk in the discovery and development of biopharmaceuticals. Finally, we look forward to the prospects of protein engineering in pharmaceutical industry. In the future, automated pipelines consisting artificial intelligence and self-driving laboratories will accelerate the design-build-test-learn cycle, leading to rapid progress in molecular design and discovery.

Arbutins are a kind of natural glycoside compounds found widely in nature. α-arbutin, one of its isomers, has received increasing market attention due to its efficient and safe whitening effect and other excellent pharmacological effects. Studies have revealed that the production methods of α-arbutin mainly fall into three categories: plant extraction, chemical synthesis, and biosynthesis. For the plant extraction, raw materials are widely available, and the process is simple, but the yield fails to meet the requirement for large scale production and applications. The chemical synthesis has a higher yield but with harsh reaction conditions, and thus is not environmentally friendly. Through research has found that the biosynthesis of α-arbutin has higher yield, safer environment, more competitive cost and other advantages compared with the natural extraction and chemical synthesis as well, making it the mainstream production method. This article discusses the advantages and disadvantages of different synthetic methods and studies on the seven enzymes commonly used in the biosynthesis of α-arbutin including α-amylase, sucrose phosphorylase, cyclodextrin glycosyltransferase, α-glucosylase, dextransucrase, amylosucrase, and sucrose isomerase. These enzymes use different sugar donors and catalyze the transglycosylation reaction with hydroquinone as the receptor substrate to synthesize α-arbutin. Additionally, we provide a comprehensive review on research progress in the whole-cell catalysis and microbial fermentation to produce α-arbutin, and potentials for its industrial production are assessed. Furthermore, we highlight challenges that exist in the biosynthesis of α-arbutin, such as the oxidation of hydroquinone during synthesis that increases cell toxicity and reduces the yield, the low utilization rate of glucose and the generation of other glycoside products, and the poor performance of experimental strains, and corresponding solutions are proposed. Finally, future directions for α-arbutin synthesis are prospected, with the aim of providing new ideas for achieving more efficient and lower-cost production of α-arbutin and enhancing its applications in the fields of cosmetics and medicines.

Optogenetics represents an advanced technology that facilitates precise control of gene expression and neuronal activity in living cells through light. Introduced by neuroscientist K. Deisseroth in 2005, this methodology has transformed neuroscience research, empowering researchers to modulate excitable tissues and neural circuits with exceptional spatiotemporal accuracy. Optogenetics necessitates the expression of light-sensitive proteins, including channelrhodopsins, halorhodopsins, and various microbial opsins, within specific cells. Employing viral vectors and tissue-specific promoters, these proteins ensure targeted expression. Exposure to designated wavelengths of light permits these proteins to activate or inhibit cellular activity, thereby modulating neuronal behavior. The implementation of optogenetics has significantly enhanced comprehension of learning, memory, and neural plasticity. This technology enables the examination of the molecular dynamics associated with synaptic plasticity, long-term potentiation (LTP), and long-term depression (LTD), which are pivotal for memory. Real-time manipulating of specific neuronal populations can elucidate the intricate neural circuits involved in these phenomena. Additionally, optogenetics has facilitated the exploration of potential therapeutic approaches for neurological conditions such as Alzheimer’s disease by meticulously controlling memory-associated circuits. The utility of optogenetics transcends fundamental research, yielding promising prospects in addiction to studies and motor function enhancement. By modulating distinct neural circuits, it is possible to alter addiction-related behaviors and augment motor functions. Furthermore, the amalgamation of optogenetics with cutting-edge technologies like artificial intelligence and deep learning is anticipated to refine stimulation protocols, resulting in more precise and efficacious experimental outcomes. Notwithstanding its transformative capacity, the clinical application of optogenetics encounters significant obstacles, including the requisites for safe and effective gene delivery systems and the formulation of light-sensitive proteins with optimal characteristics for applications in human beings. Future investigations should concentrate on surmounting these hurdles while expanding the applications of optogenetics in neuroscience and related fields. The integration of optogenetics with multidisciplinary approaches is poised to unveil new realms in brain research, yielding profound insights into mechanisms governing memory, learning, and neural plasticity.

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.

During gene transcription, RNA polymerase initiates the process by recognizing the promoter sequence, and terminates it upon recognizing the terminator sequence located at the 3′-UTR, leading to dissociation of the transcription complex. Therefore, promoters and terminators within the transcription unit play the role of initiating and terminating transcription, respectively. For downstream transcription units, in addition to the direct effect of terminating transcript read-through, the dissociation of the RNA polymerase from the terminator may affect the binding of the promoter to RNA polymerase in the subsequent transcription unit, thus indirectly altering the expression of the downstream transcription unit. This interplay between terminators and promoters across transcription units remains poorly understood, therefore, elucidating the impact of terminators on the transcriptional strength of downstream transcription units is of great significance for the precise regulation of gene expression and the development of efficient terminators. In this study, a library containing 405 different combinatorial elements (terminator-spacer-promoter) was constructed by combining nine terminators, five spacer sequences, and nine promoters using one-pot assembly technology. All combinations in the library were sequenced and analyzed in terms of fluorescence intensity based on the FlowSeq technology to establish the correlations between combinatorial sequences and downstream gene expression. The results showed that combinations of weak terminators, short spacers, and strong terminators were more favorable to enhance the expression of downstream genes, while combinations of strong terminators, long spacers, and weak terminators reduced the expression of downstream genes. Quantitative analysis of transcription revealed that weak terminators not only enhanced downstream leakage transcription (21~70-fold enhancement), but also facilitated downstream promoters to re-recruit RNA polymerase for re-promoted transcription (2~3-fold enhancement). This study has elucidated the effect and mechanism of terminators on the regulation of gene expression in the downstream transcription units, providing a design framework for the construction of gene circuits using terminators.

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.

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