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    Significant research progress in synthetic biology
    Mingzhu DING, Bingzhi LI, Ying WANG, Zexiong XIE, Duo LIU, Yingjin YUAN
    Synthetic Biology Journal    2020, 1 (1): 7-28.   DOI: 10.12211/2096-8280.2020-057
    Abstract6634)   HTML1229)    PDF(pc) (3953KB)(8034)       Save

    As an emerging, interdisciplinary field, synthetic biology has made great advances in many directions due to wide acceptance of its core principles and rapid progress in DNA synthesis. In this paper, recent development in gene circuits, genome design and synthesis, cell factories, and synthetic microbial consortia is reviewed. The complexity of artificial gene circuits that can be designed and constructed is gradually increasing with more refined control. Synthetic genomes are routinely assembled, expanding from prokaryotes (Mycoplasma to Escherichia coli) to eukaryotes (Saccharomyces cerevisiae), and improved capacity in genome design promotes the research of biological evolution. Metabolic pathways of ever-increasing lengths are constructed based on modularization and orthogonality principles to produce molecules of complex structures, and fundamental rewiring of cellular metabolism is performed for enhanced robustness and compatibility. The design and construction of synthetic microbial consortia have been expanded from two-species systems to multi-species systems, so that more sophisticated functions can be achieved. At the end of this paper, new research directions resulted from the interdisciplinary integration of synthetic biology and other disciplines are discussed.

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    Microbial promoter engineering strategies in synthetic biology
    Huimin YU, Yukun ZHENG, Yan DU, Miaomiao WANG, Youxiang LIANG
    Synthetic Biology Journal    2021, 2 (4): 598-611.   DOI: 10.12211/2096-8280.2020-092
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    Synthetic biology is of vital importance to the green biomanufacturing industry and sustainable development strategies of our country. Promoter is the core-component of synthetic biology, playing a significant role in highly efficient and fine-tuning expression and regulation of target genes at the transcriptional level. Herein we summarized and discussed the key progress and future frontiers of microbial promoter engineering, particularly for prokaryotic microorganisms. Firstly, we introduced the basic DNA sequence characteristics of promoters and the regular mechanism for promoter recognition and transcription-initiation by RNA polymerase sigma factors. Inducible mechanisms for both negative and positive regulation were particularly highlighted with the typical lac operator of Escherichia coli as an example. Then, effective strategies for obtaining improved-promoters were summarized, which were roughly divided into two categories: endogenous promoter mutation and heterologous promoter replacement. For the endogenous promoter mutation, the following strategies, e.g. point mutation toward sigma factor consensus sequence, coupling optimization of -35 and -10 regions with RBS sequence, random mutation or saturation mutagenesis of UP element or spacer sequences accompanying with promoter library construction and high-throughput screening were emphasized. For the heterologous promoter replacement, strategies such as substituting the native promoter into stronger ones from other microorganisms, introducing phage-source chimeric promoters, tuning the constitutive promoter into inducible pattern and integrating positive regulator(s), were mainly discussed. We further sorted out the representative inducers for inducible promoters reported so far, including both chemical molecules and physical signals. Progress in constitutive promoters of non-model and model microbial organisms were simply summarized as well. Next, arising from the breakthrough development of dynamic metabolic regulation and artificial intelligence (AI), we proposed that the innovative research on identification and evolution of new and unique promoters with dynamic-response features and AI de novo design for promoters with novel/superior functions will be the new frontiers of promoter engineering. Finally, we analyzed the challenging scientific issues in the microbial promoter engineering, from the viewpoint of both basic research and large-scale applications; and further discussed the research priority coupling with the vigorous development of synthetic biology.

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    Advances of CRISPR gene editing in microbial synthetic biology
    Yang LI, Xiaolin SHEN, Xinxiao SUN, Qipeng YUAN, Yajun YAN, Jia WANG
    Synthetic Biology Journal    2021, 2 (1): 106-120.   DOI: 10.12211/2096-8280.2020-039
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    With the increase of global consumption on fossil resources for energy products and chemicals and their consequent impact on environment, construction of microbial cell factories for efficient production of biofuels and bio-based chemicals from renewable sources has gained much attention. Pathway engineering of the hosts, such as over-expression of key genes, disruption of competing pathways and integration of heterologous pathways, plays significant role in fulfilling such a purpose. Successful implementation of these pathway engineering strategies requires efficient and accurate gene editing tools. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) systems are a powerful gene editing strategy that was found in prokaryotic organisms such as archaea and bacteria, which provide adaptive immunity against foreign elements. When host cells are infected by viruses, a small sequence of the viral genome is integrated into the CRISPR locus to immunize the host cells, and this small sequence is transcribed into small RNA guide that directs the cleavage of the viral DNA by the Cas nuclease. Inspired by the natural talent, many modified CRISPR systems have been developed to modify genes and genomes, including knock-in, knock-down, large deletions, indels, replacements and chromosomal rearrangements. In this review, we briefly comment on the technical basis and advances in CRISPR-related genome editing tools applied for constructing microbial cell factories, with a focus on the CRISPR-based tools for metabolic engineering of the model organisms E. coli and S. cerevisiae. Furthermore, we highlight major challenges in developing CRISPR tools for multiplex genome editing and sophisticated expression regulation. Finally, we propose future perspectives on the application of CRISPR-based technologies for constructing microbial ecosystems toward high production of desired chemicals. We intend to provide insights and ideas for developing CRISPR-related genome editing tools to better serve the construction of efficient microbial cell factories.

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    From chemical synthesis to biosynthesis: trends toward total synthesis of natural products
    Faguang ZHANG, Ge QU, Zhoutong SUN, Jun′an MA
    Synthetic Biology Journal    2021, 2 (5): 674-696.   DOI: 10.12211/2096-8280.2021-039
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    The complexity and diversity of natural products have made them a rich source for drug and agrochemical discovery. To overcome the supplying limitation of natural resources, tremendous effort has been made by the academic and industrial communities during the past two centuries for the total artificial synthesis of natural products. In this regard, total chemical synthesis has achieved significant progress, and numerous highly complex natural products have been synthesized through different chemical processes. Despite these great achievements in total chemical synthesis, there are still many challenges including expensive chemical reagents, harsh reaction conditions, difficult control on stereoselectivity, long synthetic route, and low product yield. Notably, the development of synthetic biology has allowed more and more natural products to be produced through biological cell factories, which provides a new and complementary strategy for the synthesis of natural products at a large scale. This review critically comments on the representative advances in total chemical synthesis of natural products (Section 1), and then highlight major progress and trends in the biosynthesis of pharmaceutically important natural products (Sections 2 and 3). In Section 2.1, we selected the production of penicillin, erythromycin, and avermectin as examples to analyze the modification and optimization of natural product biosynthetic pathways. The discovery and utilization of secondary metabolites from microorganisms has been a continuous driving force in the field of natural products. Notably, significant progress has been made in the total biosynthesis of natural products from secondary metabolism via the genetic manipulation of microbial cells. In Section 2.2, we selected Vitamin B12 and Tropane alkaloids as examples to demonstrate the use of heterologous expression and biological production for natural product synthesis. In recent years, on the basis of analyzing the structure of natural products in animals, plants, and microorganisms, great advances have emerged in exploring their biochemical reaction mechanisms and synthetic routes. More importantly, expressing and regulating the relative genes in heterologous microbial cells have enabled the complete biosynthesis of many natural products. Furthermore, in Section 3, human insulin, artemisinin, saframycin, azaphilone, kainic acid, and podophyllotoxin were selected as examples to showcase the power of merging chemical and biological processes for the total synthesis of natural products. Although there are still many challenges in the total synthesis of new and complex natural products, biosynthesis will ultimately play a significant role in the construction of natural molecules and their relative analogues. By taking advantage of the merits with organic chemistry, synthetic biology, and artificial intelligence, the development of highly efficient and automatic biosynthesis could be a trend in this field.

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    Application of dynamic regulation strategies in metabolic engineering
    Zheng Yu, Xiaolin SHEN, Xinxiao Sun, Jia Wang, Qipeng Yuan
    Synthetic Biology Journal    2020, 1 (4): 440-453.   DOI: 10.12211/2096-8280.2020-029
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    As a sustainable biochemical reactor, microbial cell factories are widely used in the production of value-added compounds such as natural products, pharmaceuticals and nutraceuticals. In order to make microbial cell factories produce target compounds with high titer, productivity and yield, metabolic engineering strategies are employed to rationally modify and regulate their metabolism. However, knockout and overexpression of genes inevitably bring stresses such as redox imbalance and toxic intermediate accumulation. While dynamic control strategy has been proven as a promising tool to address these challenges by balancing carbon flux and energy generation and dissipation for cell growth and generation of target compounds. As a result, many dynamic regulation elements and gene circuits have been developed and widely used in metabolic engineering so far. In this review, we summarize four types of attractive dynamic regulation systems based on metabolite-response, quorum sensing-response, environmental parameter-response and protein level regulation, with a focus on the construction method of various regulatory elements and their applications in metabolic engineering. In addition, challenges faced by different dynamic control strategies in industrial applications are analyzed. At the same time, we prospect the application potentials of some strategies such as high-throughput screening, protein engineering, computer simulation and mathematical model analysis coupled with gene control elements in solving the problems of narrow response threshold and limited control range of dynamic regulation tools. With the further development of synthetic biology and metabolic engineering, we believe that dynamic control strategy will be widely used for the construction of microbial cell factories in the near future.

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    Recent progress of synthetic biology applications in microbial pharmaceuticals research
    Cong RAO, Xuan YUN, Yi YU, Zixin DENG
    Synthetic Biology Journal    2020, 1 (1): 92-102.   DOI: 10.12211/2096-8280.2020-036
    Abstract3843)   HTML447)    PDF(pc) (1980KB)(3649)       Save

    Microbial natural products are a major source in the innovation of novel pharmaceuticals, including anti-bacterial, anti-tumor, and immunosuppressive agents for clinical use. Currently, the development of microbial drugs is facing significant challenges due to the growing prevalence of multidrug-resistant bacteria, the continuous emergence of new pathogens and viruses, and the increasing difficulties in the discovery of natural products with new scaffolds. Synthetic biology is an emerging interdisciplinary research area leading to great breakthrough in the field of biomedical sciences in the 21st century, which provides new methods and ideas for drug discovery and development. The application of synthetic biology could unlock the potential of natural product mining, design new biosynthetic routes, and generate much more “unnatural” natural products and structural analogs. This review summarizes the technical innovations of synthetic biology in the field of microbial pharmaceuticals, and its applications in the mining, biosynthesis, and new scaffold generation of aminoglycoside antibiotics, nucleotide antibiotics, ribosomally synthesized and posttranslationally modified peptides, terpenoids, and polyketides in the last five years.

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    Advances in synthetic biomanufacturing
    Yuanyuan ZHANG, Yan ZENG, Qinhong WANG
    Synthetic Biology Journal    2021, 2 (2): 145-160.   DOI: 10.12211/2096-8280.2020-052
    Abstract3435)   HTML524)    PDF(pc) (2003KB)(3532)       Save

    Synthetic biomanufacturing is a paradigm for material processing and synthesis via synthetic biology. It is expected to completely transform the traditional production mode for medicines, chemicals, food, energy, materials and agriculture in the future, trigger new industrial revolution, lead to new economic growth and reshape carbon-based civilization. In particular, the COVID-19 global spread that has accelerated the reshaping process of the world's economic and social development. In the foreseeable future, human life and production patterns will undergo profound changes in medicines and healthcare, food and agriculture, energy and materials, etc., during which demands for new technologies will promote evolution in the field of biotechnology, and the biomanufacturing industry in the post COVID-19 era is facing unprecedented opportunities for revitalization and new challenges. According to the analysis of the research report from the Ministry of Economy, Trade and Industry of Japan, engineered biological cells and their combination with information & artificial intelligence technologies will become the main driving force for the "post-fourth industrial revolution".Synthetic biomanufacturing has the characteristics of cleanliness, efficiency and renewableness that can reduce the impact of industrial economy on the ecological environment. Here, in this review, we summarize the progress of synthetic biomanufacturing with respect to bulk fermentation products, fine and pharmaceutical chemicals, renewable chemicals and bio-based polymeric materials, natural products, foods and the utilization of C1 raw materials. The technological progress, status and potential of industrial applications of many important bio-based products via synthetic biomanufacturing are analyzed and discussed. The development of synthetic biomanufacturing shows great potentials for building up the ecological route of industrial economy and addressing current issues of economic sustainability in terms of limited substrate, high cost, and poor viability, and to form whole new industry chain with sustainable growth. In the future, with the development of synthetic biology, and the integration of new technologies such as artificial intelligence and big data, more and more bio-based products can be produced via synthetic biomanufacturing. The formation of bioeconomy can be promoted, and the sustainable development of human society will be better served.

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    Computational design and directed evolution strategies for optimizing protein stability
    Qingyun RUAN, Xin HUANG, Zijun MENG, Shu QUAN
    Synthetic Biology Journal    2023, 4 (1): 5-29.   DOI: 10.12211/2096-8280.2022-038
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    Most natural proteins tend to be marginally stable, which allows them to gain flexibility for biological functions. However, marginal stability is often associated with protein misfolding and aggregation under stress conditions, presenting a challenge for protein research and applications such as proteins as biocatalysts and therapeutic agents. In addition, protein instability has been increasingly recognized as one of the major factors causing human diseases. For example, the formation of toxic protein aggregates is the hallmark of many neurodegenerative diseases, including Alzheimer's and Parkinson's diseases. Therefore, optimizing protein folding and maintaining protein homeostasis in cells are long-standing goals for the scientific community. Confronting these challenges, various methods have been developed to stabilize proteins. In this review, we classify and summarize various techniques for engineering protein stability, with a focus on strategies for optimizing protein sequences or cellular folding environments. We first outline the principles of protein folding, and describe factors that affect protein stability. Then, we describe two main approaches for protein stability engineering, namely, computational design and directed evolution. Computational design can be further classified into structure-based, phylogeny-based, folding energy calculation-based and artificial intelligence-assisted methods. We present the principles of several methods under each category, and also introduce easily accessible web-based tools. For directed evolution approaches, we focus on library-based, high-throughput screening or selection techniques, including cellular or cell-free display and stability biosensors, which link protein stability to easily detectable phenotypes. We not only introduce the applications of these techniques in protein sequence optimization, but also highlight their roles in identifying novel folding factors, including molecular chaperones, chemical chaperones, and inhibitors of protein aggregation. Moreover, we demonstrate the applications of protein stability engineering in biomedicine and pharmacotherapeutics, including identifying small molecules to stabilize disease-related, aggregation-prone proteins, obtaining conformation-fixed and stable antigens for vaccine development, and targeting protein stability as a means to control protein homeostasis. Finally, we look forward to the trends and prospects of protein stabilization technologies, and believe that protein stability engineering will lead to a better understanding of protein folding processes to facilitate the development of precision medicine. {L-End}

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    Recent development of directed evolution in protein engineering
    Yanping QI, Jin ZHU, Kai ZHANG, Tong LIU, Yajie WANG
    Synthetic Biology Journal    2022, 3 (6): 1081-1108.   DOI: 10.12211/2096-8280.2022-025
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    Directed evolution aims to accelerate the natural evolution process in vitro or in vivo through iterative cycles of genetic diversification and screening or selection. It has been one of the most solid and widely used tools in protein engineering. This review outlines the representative methods developed in the past 10 years that increase the throughput of directed evolution, including in vitro and in vivo gene diversification methods, high-throughput selection and screening methods, continuous evolution strategies, automation-assisted evolution strategies, and AI-assisted protein engineering. To illustrate the significant applications of directed evolution in protein engineering, this review subsequently discusses some remarkable cases to show how directed evolution was used to improve various properties of enzymes, such as the tolerance to elevated temperature or organic solvent, the activities on non-native substrates, and chemo-, regio-, stereo-, and enantio-selectivities. In addition, directed evolution has also been widely used to expand the biocatalytic repertories by engineering enzymes with abiotic activities. In addition to the native enzymes, directed evolution has also been used to engineer de novo designed enzymes and artificial metalloenzymes with activities comparable to or exceeding the ones of the native enzymes. Finally, this review has pointed out that further improving the efficiency and effectiveness of directed evolution remains challenging. Some advanced continuous evolution and high throughput screening strategies have been succesfully demonstrated in improving the throughput of directed evolutions extensively, but they have been limited to engineering certain protein targets. To resolve those issues, continuously improved computational modeling tools and machine learning strategies can assist us to create a smaller but more accurate library to enhance the probabilities of discovering variants with improved properties. Additionally, laboratorial automation platforms coupled with advanced screening and selection techniques also have great potential to extensively explore the protein fitness landscape by evolving multiple targets continuously in a high throughput manner.

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    Recent advances in plant synthetic biology
    Bo ZHANG, Yongshuo MA, Yi SHANG, Sanwen HUANG
    Synthetic Biology Journal    2020, 1 (2): 121-140.   DOI: 10.12211/2096-8280.2020-016
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    Synthetic biology is a new interdisciplinary field that combines engineering and biology. With an initial focus on microbial systems, it is now increasingly developed for plants. Plant synthetic biology has been applied to design crops for improved yield and nutritional value. It is also possible to transform plants into living factories for producing high-value natural products. In this review, we first summarize the definition of plant synthetic biology and introduce emerging technologies, including DNA synthesis and assembly, genome editing, genetic transformation targeting nucleus and plastid, and chromosome engineering. We then discuss recent applications in biosensor design, yield and nutrition improvement, and natural product and protein biosynthesis. We conclude with the current challenges and future perspective of this field. We envision plant synthetic biology will revolutionize crop breeding.

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    DNA information storage: bridging biological and digital world
    Mingzhe HAN, Weigang CHEN, Lifu SONG, Bingzhi LI, Yingjin YUAN
    Synthetic Biology Journal    2021, 2 (3): 309-322.   DOI: 10.12211/2096-8280.2021-001
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    The external preservation of information enables reliable inheritance of human thoughts, playing important roles in the progress of human civilization. Starting from tying knots in ropes to storing data in magnetic and optical media, these technologies have documented and will continue to record the splendid civilization. However, driven by the global digitalization, the global data volume is growing rapidly and challenging the storage capability of existing storage technologies. DNA, as the natural carrier of genetic information, is believed to be a potential candidate to deal with the data storage challenge due to the revealed high density, long-term duration and low maintaining cost features. In this review, we first describe the fundamental principles and technical processes of DNA information storage. The pivotal position of DNA information storage bridging the biological and digital world is also pointed out. Then, according to the different characteristics of data writing and reading, we categorize these technologies into three storage modes, termed as "DNA hard drive", "DNA compact disc" and "DNA tape", by analogy with the popular storage media correspondingly. "DNA hard drive" mode shows the potential in the volume enlargement of the existing information storage system using oligonucleotide pools. "DNA compact disc" mode provides direct in vivo processing on DNA data storage enabling massive data distribution at low cost. "DNA tape" mode provides intracellular information recoding solutions, which may promote the future developments of cellular computing and communication. The up-to-date progress of these three modes is also summarized. We then discuss the main obstacles and potential technical routes towards practical applications of DNA information storage. We envision a cheaper, faster DNA information storage technology, and its appropriate integration with information storage systems in the future. Finally, we conclude that DNA information storage is a cutting-edge interdisciplinary technology and hope this review can bring more focus and research efforts from various fields to DNA information storage.

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    Scalable mining of proteins for biocatalysis via synthetic biology
    Jianzhi ZHANG, Lihao FU, Ting TANG, Songya ZHANG, Jing ZHU, Tuo LI, Zining WANG, Tong SI
    Synthetic Biology Journal    2020, 1 (3): 319-336.   DOI: 10.12211/2096-8280.2020-028
    Abstract2903)   HTML267)    PDF(pc) (2526KB)(3243)       Save

    Biomanufacturing provides a sustainable alternative to traditional petrochemical processes in producing chemicals, drugs, and functional materials. Enzymes are cores for creating catalytic biosystems with diverse functions. Due to the lack of predictive models for enzyme functions, however, rational design is still challenging. On the other hand, next-generation sequencing reveals millions of diverse natural enzymes, of which only a tiny fraction have been experimentally characterized. Synthetic biology applies engineering principles to study, engineer, and create biological systems. Through standardization and modularization, synthetic biology enables large-scale prototyping of enzyme sequences, which not only helps to identify efficient biocatalytic parts, but also accelerates quantitative understanding of sequence-structure-function relationship. Here we review recent advances in scalable mining of enzymes via synthetic biology. We firstly introduce computational tools for functional clustering and prioritization of promising sequences from enormous genome/protein databases, followed by experimental approaches for high-throughput cloning, expression, and characterization of selected candidates. We then discuss the applications of such tools in systematic studies of enzyme (super) families. We conclude with future perspectives in creating integrated synthetic biology foundries to accelerate enzyme mining.

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    Research advances in synthetic microbial communities
    Zepeng QU, Moxian CHEN, Zhaohui CAO, Wenlong ZUO, Ye CHEN, Lei DAI
    Synthetic Biology Journal    2020, 1 (6): 621-634.   DOI: 10.12211/2096-8280.2020-012
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    Synthetic microbial communities are an emerging research field at the intersection of synthetic biology and microbiome. A synthetic microbial community is created artificially by co-culturing of multiple species under a well-defined condition. Synthetic communities that retain the key features of their natural counterparts can act as a model system to study the ecology and function of microbial communities in a controlled way. This review covers important topics and research progress in synthetic microbial communities. We start with a summary of ecological factors that shape the structure of microbial communities, including interactions among microbes, host metabolism and immunity and environmental conditions. We then discuss the methods and experimental techniques in design-build-test-learn (DBTL) cycle, used to study synthetic microbial communities. In addition, we review the potential applications of synthetic microbiome in human health, agriculture, industrial production and environmental remediation. Finally, we summarize key scientific questions for future studies of synthetic microbial communities,including how to construct a controllable and stable microbial interaction network, how to characterize and manage the spatial structure of microbial communities, and how to accurately shape the function of microbial communities.

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    Artificial intelligence-assisted protein engineering
    Jiahao BIAN, Guangyu YANG
    Synthetic Biology Journal    2022, 3 (3): 429-444.   DOI: 10.12211/2096-8280.2021-032
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    Protein engineering is one of the important research fields of synthetic biology. However, de novo design of protein functions based on rational design is still challenging, because of the limited understanding on biological fundamentals such as protein folding and the natural evolution mechanism of enzymes. Directed evolution is capable of optimizing protein functions effectively by mimicking the principle of natural evolution in the laboratory without relying on structure and mechanism information. However, directed evolution is highly dependent on high-throughput screening methods, which also limits its applications on proteins which lack high-throughput screening methods. In recent years, artificial intelligence has been developed very rapidly for integrating into multidisciplinary fields. In synthetic biology, artificial intelligence-assisted protein engineering has become an efficient strategy for protein engineering besides rational design and directed evolution, which has shown unique advantages in predicting the structure, function, solubility of proteins and enzymes. Artificial intelligence models can learn the internal properties and relationships from given sequence-function data sets to make predictions on properties for virtual sequences. In this article, we review the application of artificial intelligence-assisted protein engineering. With the basic and process of the strategy introduced, three key points that affect the performance of the predictive model are analyzed: data, molecular descriptors and artificial intelligence algorithms. In order to provide useful tools for researchers who want to take advantage of this strategy, we summarize the main public database, diverse toolkits and web servers of the common molecular descriptors and artificial intelligence algorithms. We also comment on the functions, applications and websites of several artificial intelligence-assisted protein engineering platforms, through which a complete prediction task including protein sequences representation, feature analysis, model construction and output can be completed easily. Finally, we analyze some challenges that need to be solved in the artificial intelligence-assisted protein engineering, such as the lack of high-quality data, deviation in data sets and lacking of the universal models. However, with the development of automated gene annotations, ultra-high-throughput screening technologies and artificial intelligence algorithms, sufficient high-quality data and appropriate algorithms will be developed, which can enhance the performance of artificial intelligence-assisted protein engineering and thus facilitate the development of synthetic biology techniques.

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    Applications and prospects of genome mining in the discovery of natural products
    Qian YANG, Botao CHENG, Zhijun TANG, Wen LIU
    Synthetic Biology Journal    2021, 2 (5): 697-715.   DOI: 10.12211/2096-8280.2021-012
    Abstract3010)   HTML300)    PDF(pc) (6343KB)(3057)       Save

    Natural products have been an abundant source of leader compounds for new drugs, but traditional isolation and analysis technologies to obtain novel natural products cannot satisfy the requirement for drug discovery. Genomic data have been utilized for identifying potential drug targets, or exploring biosynthesis pathways for natural products that were neglected before. Genome sequencing has unveiled a plethora of undeveloped chemical diversity in microorganisms and plants. From genome sequences, a large amount of information is available, from functional enzymes to conserved patterns/signatures, even potential structures and features that can be interpreted to hunt for new biocatalysts. With the advent of the genomic era, the computational mining of genomes has become an important part in the discovery of novel natural products as drug leads. Meanwhile, the development of high-throughput sequencing and the establishment of DNA database, genome mining methods and tools have contributed to the discovery and characterization of these natural products. In spite of the diversity of natural products, the biosynthetic rules and thus the biosynthetic machineries for many of these compounds are often remarkably conserved, which is highlighted in the high amino acid sequence similarity of the core biosynthetic enzymes, such as polyketides synthases (PKS), non-ribosomally peptides synthetases (NRPS), and many others. Besides, most of natural products are considered to be produced by the host to kill or limit the growth of competitors through the inhibition or inactivation of essential housekeeping enzymes. Therefore, accumulating knowledge on the self-resistance mechanisms, for instance, mining for SRE (self-resistance enzyme), have promoted research on natural products. Moreover, a phylogeny-guided mining approach provides a method to quickly screen a large number of microbial genomes or metagenomes to detect new biosynthetic gene clusters of interest, and many web tools and databases have been developed and utilized by researchers to mine for key enzymes. This paper reviews recent advances in the genome mining tools, databases and approaches, with a focus on the ways of mining biosynthetic gene clusters (BGCs) of natural products, from classical genome mining to resistance-based and phylogeny-guided mining, and also include a short overview on status and perspective in the discovery of novel natural products.

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    The past and present of vitamin E
    Tian MA, Zixin DENG, Tiangang LIU
    Synthetic Biology Journal    2020, 1 (2): 174-186.   DOI: 10.12211/2096-8280.2020-022
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    Vitamin E, as one of the most important antioxidants in biological systems, has a variety of biological functions. For example, it can maintain normal metabolism and improve the fertility and immunity of humans and animals. It occupies an important position in the fields of medicine and feed. It is a basic supplemental product for people in China and also one of the three major vitamin products with big production volume and sale in the international market. Since it was developed in 1938, the synthesis technology of vitamin E has experienced a history of more than 80 years. With technological innovations, a relatively stable market has gradually formed for vitamin E. Here, we summarized the development of vitamin E synthesis technology, including extraction from natural resources and synthesis with chemical, biological and biochemical routes. The technologies of chemical and biochemical synthesis as the most competitive processes are introduced in details. The history of vitamin E is reviewed and the future development of vitamin E is prospected.

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    Advances and applications of phage synthetic biology
    Shengjian YUAN, Yingfei MA
    Synthetic Biology Journal    2020, 1 (6): 635-655.   DOI: 10.12211/2096-8280.2020-027
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    Bacteriophage (phage) are viruses that specifically infect bacterial and archaea. Phage is the most diverse and abundant biological entity on the planet. For more than a century, phage is one of the most important model organisms in the molecular biological research. Many important discoveries upon phage research have enabled us to understand the mechanisms of genetic materials in biological activities, and many phage-derived enzymes are greatly useful in the molecular biological research. Phage has also been recognized as natural antimicrobial agents for treating the bacterial infections. In particular, nowadays, the concern related to the emergence of bacteria resistance to multiple antibiotics is increasing. However, the challenges in phage therapy, such as narrow host range and bacterial resistance, limited the application of phage therapy in treating the diseases of antibiotic-resistant bacterial infections. Novel strategies are needed to be developed to overcome the hurdles associated with phage therapy. Synthetic biology aims to design and reprogram new biological systems according to the known principles. Because of their relatively small genome size (5—735 kb), fast growth rate, ease of genetic manipulation, and simple structure, phages have become the most important biological system for synthetic biology research. In this review, we discuss the advances of synthetic biology facing the major challenges of natural phages in basic and application research. For example, synthetic biology has been applied to enhance the infection efficiency of phages, improve the phage biosafety, alter the phage host ranges, adjust the bacterial communities, and knock out the specific bacterial genes. We also present some examples to show the methods that were widely used for phage engineering to obtain phages with new functions. In addition, phage display and phage-assisted continuous evolution have also become powerful tools in synthetic biology. In short, the development of synthetic biology will inspire scientists to design modular phages as multifunctional biological agents for clearance of multi-drug resistant bacteria, detection of the pathogen, regulation of bacterial diversity, and drug delivery.

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    Establishing carbon dioxide-based third-generation biorefinery for a sustainable low-carbon economy
    Shuobo SHI, Qiongyu MENG, Weibo QIAO, Huimin ZHAO
    Synthetic Biology Journal    2020, 1 (1): 44-59.   DOI: 10.12211/2096-8280.2020-015
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    Due to the sharply increased greenhouse gas (GHG) emissions, there is an urgent need to transit from the traditional ‘take-make-dispose’ economy to a sustainable economy with ecological balances through circular green technologies such as biorefineries. Based on the source of the feedstocks, existing biorefineries can be classified into three types: starch-based first-generation biorefinery, cellulosic biomass-based second-generation biorefinery, and carbon dioxide (CO2)-based third-generation biorefinery. Compared to the first- and second-generation biorefineries, the third-generation biorefinery will not only significantly reduce the GHG emissions but also have no issues on food and water security. However, one of the major challenges in establishing the third-generation biorefinery is the design and engineering of microbial cell factories capable of efficiently utilizing CO2 for the production of chemicals, fuels, and materials. In the past decades, a variety of CO2 fixation pathways have been discovered in naturally occurring CO2 fixation microorganisms (autotrophs) such as microalgae, cyanobacteria, and acetogens, and significant progress has been made in engineering these autotrophs to extend the product portfolio or improve the carbon fixation efficiencies. Recently, some of these CO2 fixation pathways were successfully incorporated into heterotrophic microorganisms commonly used as microbial cell factories such as Escherichia coli and Pichia pastoris. In this review, we will first introduce both the naturally occurring and artificially designed CO2 fixation pathways, and then discuss the application of synthetic biology strategies and tools for engineering autotrophs and heterotrophs to convert CO2 into a variety of industrially important compounds. Finally, we will briefly comment on the prospects of CO2-based biorefinery and the relevant scientific opportunities and challenges.

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    Analysis of global patents for the trend of synthetic biology inventions
    Daming CHEN, Guangming ZHOU, Xiao LIU, Yuelei FAN, Yue WANG, Kaiyun MAO, Xuebo ZHANG, Yan XIONG
    Synthetic Biology Journal    2020, 1 (3): 372-384.   DOI: 10.12211/2096-8280.2020-035
    Abstract2646)   HTML291)    PDF(pc) (2356KB)(2768)       Save

    Synthetic biology is an emerging interdisciplinary field which combines the principles of engineering and biology, aiming at the (re-) design, modification and fabrication of new and existing biological systems. The techniques developed by synthetic biology are revolutionizing biotechnology and the pharmaceutical industry. From the perspective of patent analysis, this article reviews the technological history of synthetic biology and its applications. The development of synthetic biology techniques can be divided into four stages. 1) The first stage before 2005, is represented by the application of gene regulatory circuits in the field of metabolic engineering, and large-scale production of artemisinin precursor in E.coli was achieved. 2) During the second stage from 2005 to 2011, basic research on improving engineered natural and artificial cells was developed rapidly, however the number of patent applications did not increase significantly, but new tools and methods continued to accumulate, reflecting the early development characteristics of "engineering biology". 3) In the third stage from 2011 to 2015, with the development of novel genome editing, as well as the incorporation of those fundamentals into synthetic biology tools, patent application was doubled. 4) At the fourth stage since 2015, the design-build-test (DBT) cycle of synthetic biology has been extended to the design-build-test-learn (DBTL) cycle, therefore enabling broader convergence and interoperability of semiconductor synthetic biology, engineering biology and other emerging frontiers. After going through the above four development stages, a number of synthetic biology companies have grown up, and many traditional pharmaceutical companies have also invested in the field of synthetic biology for drug development, generating a variety of patents related to gene synthesis, gene therapy, cell therapy, biological materials, genome editing, et al. Through the analysis of representative synthetic biology enterprises' product development and their corresponding patent layout, we highlight the main technical modules and application fields of synthetic biology technologies. Based on the systematic analysis of these key technologies and patents, we develope a break-up and comprehensive analysis framework to clarify the characteristics of synthetic biology for competitive landscapes and predict their technological trends. Especially, we developed a synthetic biology knowledge map to systematically present a landscape for synthetic biology development. By translating patent information into competitive intelligence, this study also investigated the impact of synthetic biology applications on various aspects of industry and society. Finally, this article summarizes and speculates the development of synthetic biology, including the development of enabling technology platforms and tools, definition and use of standard essential patents (SEPs), and relationship between intellectual property management and product accessment.

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    Advances in design, construction and applications of Bacillus subtilis chassis cells
    Lu LIN, Xueqin LV, Yanfeng LIU, Guocheng DU, Jian CHEN, Long LIU
    Synthetic Biology Journal    2020, 1 (2): 247-265.   DOI: 10.12211/2096-8280.2020-030
    Abstract2445)   HTML227)    PDF(pc) (2797KB)(2730)       Save

    As a model industrial host and an important generally recognized as safe microorganism, Bacillus subtilis has been used for a wide range of applications such as the industrial production of enzymes and nutraceuticals. In recent years, with the elucidation of the genetic regulation mechanism of B. subtilis, various research strategies and technologies have been designed and developed with this chassis, including gene editing, gene circuits, spatial biomolecular scaffold and cell-free expression systems. In this review, we start with systematic summaries on the construction of B. subtilis chassis based on gene editing systems and endogenous regulatory mechanisms. Then applications of B. subtilis cell factories are discussed for producing N-acetylglucosamine, menaquinone-7, riboflavin, hyaluronic acid and β-cyclodextrin glycosyltransferase. Finally, prospects for the design, construction and applications of engineered B. subtilis strains are commented, with an emphasis on improving genome editing efficiency, expanding responsive metabolite spectrum for genetic circuits, and rewiring the whole genome.

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