Synthetic Biology Journal

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2020, 1(1): 0-0.

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Significant research progress in synthetic biology

Mingzhu DING, Bingzhi LI, Ying WANG, Zexiong XIE, Duo LIU, Yingjin YUAN

2020, 1(1): 7-28. doi:10.12211/2096-8280.2020-057

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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.

The application of biological reverse engineering in synthetic biology

Xinmao CHEN, Qi OUYANG

2020, 1(1): 29-43. doi:10.12211/2096-8280.2020-063

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Aiming to purposefully and rationally design and construct predictable man-made life systems with pre-defined functions under the guidance of engineering principles, synthetic biology is an advanced interdisciplinary science by combining a broad range of methodologies from various disciplines, such as traditional biology, bioengineering, systems biology, mathematics, physics, chemistry, and information science. With the booming development for nearly two decades, great progress has been made in synthetic biology. However, there are a number of factors that should be taken into account for rationally designing complex systems, such as robustness and bifurcation. Because of the consistency between the research idea of biological reverse engineering and the design process of synthetic biology, we are enlightened to resolve these problems in rationally designing genetic circuits with compley pre-defined functions with the help of reverse engineering In this review, based on the accumulated experience of our research group in reverse engineering, we started with engineering principles and design difficulties in synthetic biology, and then summarized the current methods of applying reverse engineering in synthetic biology, including network enumeration, sub-network combinations, the method from Boolean network model to continuous model. In addition, we proved the efficiency of combining reverse engineering with synthetic biology to rationally design biological complex regulation networks. Finally, we concluded with the analysis of bottlenecks for the application of reverse engineering in synthetic biology.

Establishing carbon dioxide-based third-generation biorefinery for a sustainable low-carbon economy

Shuobo SHI, Qiongyu MENG, Weibo QIAO, Huimin ZHAO

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.

Microbial utilization of carbon dioxide to synthesize fuels and chemicals——third-generation biorefineries

Kai WANG, Zihe LIU, Biqiang CHEN, Meng WANG, Yang ZHANG, Haoran BI, Yali ZHOU, Yiying HUO, Tianwei TAN

2020, 1(1): 60-70. doi:10.12211/2096-8280.2020-058

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Concerns about oil depletion and global climate change caused by greenhouse gas emissions have stimulated interests in renewable alternatives to fossil fuels. Extensive research and exploration have been conducted to convert renewable feedstock and atmospheric carbon dioxide into fuels and chemicals using microbial cell factories. In this article, we discuss the latest developments in the use of synthetic biology technologies to promote microbial utilization of carbon dioxide to synthesize fuels and chemicals (third-generation biorefineries). After summarizing the key enzymes and energy utilization profiles of the six carbon dioxide fixation pathways that have been found in nature, we review the application of carbon dioxide as a raw material for microbes (including microorganisms and photoelectric coupled microbes). Then, we discuss the major opportunities and barriers in carbon dioxide fixation and energy capture. Finally, we summarize the factors that should be considered for the selection of ideal microorganisms and the currently attractive host microorganisms for carbon dioxide utilization.

Research progress in bioproduction of aliphatic diamines by synthetic biotechnology

Xin WANG, Jing WANG, Kequan CHEN, Pingkai OUYANG

2020, 1(1): 71-83. doi:10.12211/2096-8280.2020-054

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As a rapidly developing interdiscipline, synthetic biology has provided powerful tools for the development of the efficient microbial cell factories to promote the industrial preparation of bio-based products. As important monomers, diamines have been widely used in the synthesis of polymeric materials such as polyester, polyurethane, polyamide, etc. The aliphatic diamines with 3—5 carbon atoms, including 1,3-propanediamine, 1,4-butanediamine, and 1,5-pentanediamine are considered to be promising alternatives to traditional fossil-fuel-based diamines. In this review, the current status of the art of the biosynthesis of the aliphatic diamines with 3—5 carbon atoms by engineered Escherichia?coli or Corynebacterium glutamicum are discussed. Several synthetic biology strategies, such as the design and construction of biosynthetic pathways, the design and reconstruction of key structural elements, the mining and optimization of regulatory elements, the optimization of cofactor regulation modules or mass transport modules, and their system integration were focused on due to their application in the improvement of cell production capacity. Furthermore, the utilization of non-food biomass and the recycling of CO₂generated during the diamine production process to improve the atom economy of diamine synthesis are also reviewed. Finally, the optimization of diamine producers by using synthetic biotechnology to promote the industrial production of bio-based diamines is prospected.

Synthetic biology and food manufacturing

Yanfeng LIU, Jingwen ZHOU, Long LIU, Jian CHEN

2020, 1(1): 84-91. doi:10.12211/2096-8280.2020-005

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As global environmental pollution intensifies, climate continues to change, and population continues to grow, how to ensure safe, nutritious and sustained food supply faces huge challenges. These challenges put forward new requirements for the future food supply and function. Using synthetic biology technologies to create cell factories applicable in the food industry to convert renewable raw materials into important food components, functional food additives and nutritional chemicals is an important way to solve the problems facing the food industry. This article first introduces the importance of synthetic biology to the innovation and breakthroughs in the field of food manufacturing. Secondly, taking artificial food, plant natural products and human milk oligosaccharide, three typical food products from biological manufacturing, as examples, the current tasks and challenges of food synthetic biology are discussed. Finally, the development trends of synthetic biology and food manufacturing in China are summarized and prospected. By strengthening the development and application of food synthetic biology and the related food biotechnologies and being the first to achieve their industrialization, researchers will be able to seize the frontiers of science and technology and industrial highlands globally and benefit mankind.

Recent progress of synthetic biology applications in microbial pharmaceuticals research

Cong RAO, Xuan YUN, Yi YU, Zixin DENG

2020, 1(1): 92-102. doi:10.12211/2096-8280.2020-036

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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.

Progress in the study of genetic code expansion related methods, principles and applications

Xian FU, Tao LIN, Fan ZHANG, Huiming ZHANG, Wenwei ZHANG, Huanming YANG, Shida ZHU, Xun XU, Yue SHEN

2020, 1(1): 103-119. doi:10.12211/2096-8280.2020-007

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All life on the earth uses a set of 20 amino acids to synthesize proteins according to the highly conservative codon table, and these limited kinds of amino acids serve as the building blocks for the natural protein synthesis. During the long-term evolution, nature is able to expand the structure and function of cellular proteins via changing the sequence order of amino acids. However, the evolution process is random and lack of controllability. Manipulating the structure and function of target proteins can also be realized by incorporating an expanded set of building blocks with new chemical and physical properties. Genetic code expansion for synthesis of proteins containing unnatural amino acids at any designed position can be achieved via the manipulation of the cellular components responsible for the translation step of the central dogma, which could endow target proteins with new and expanded properties. This review will be focused on the introduction of principles, strategies, techniques to engineer and rewire translational machinery and chassis underpinning genetic code expansion technology. Furthermore, emerging applications in the field of protein function regulation, innovative biomedicine and biocontainment relying on this technology will also be discussed.

Most lifes on the earth use a set of 20 naturally occurring amino acids as the building blocks for protein synthesis, according to the highly conserved codon table. Natural evolution modulates the structure and function of cellular proteins via random mutations among the limited, canonical collection of basic units. Instead, an expanded set of unnatural amino acids with new chemical and physical properties can be incorporated into proteins by synthetic biologists with molecular precision. Genetic code expansion for proteins can be achieved by engineering the translation step of the central dogma. This review will first introduce the principles, strategies, and techniques underpinning genetic code expansion technology, which targets the translational machinery in model chassis. Furthermore, related, emerging applications including protein function regulation, innovative biomedicine, and enhanced biocontainment will be discussed. We conclude with future perspectives.

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