Engineering microbial consortia through synthetic biology approach / 生物工程学报

There are a large number of natural microbial communities in nature. Different populations inside the consortia expand the performance boundary of a single microbial population through communication and division of labor, reducing the overall metabolic burden and increasing the environmental adaptability. Based on engineering principles, synthetic biology designs or modifies basic functional components, gene circuits, and chassis cells to purposefully reprogram the operational processes of the living cells, achieving rich and controllable biological functions. Introducing this engineering design principle to obtain structurally well-defined synthetic microbial communities can provide ideas for theoretical studies and shed light on versatile applications. This review discussed recent progresses on synthetic microbial consortia with regard to design principles, construction methods and applications, and prospected future perspectives.

Advances on the microbial synthesis of plant-derived diterpenoids / 生物工程学报

Natural plant-derived diterpenoids are a class of compounds with diverse structures and functions. These compounds are widely used in pharmaceuticals, cosmetics and food additives industries because of their pharmacological properties such as anticancer, anti-inflammatory and antibacterial activities. In recent years, with the gradual discovery of functional genes in the biosynthetic pathway of plant-derived diterpenoids and the development of synthetic biotechnology, great efforts have been made to construct a variety of diterpenoid microbial cell factories through metabolic engineering and synthetic biology, resulting in gram-level production of many compounds. This article summarizes the construction of plant-derived diterpenoid microbial cell factories through synthetic biotechnology, followed by introducing the metabolic engineering strategies applied to improve plant-derived diterpenoids production, with the aim to provide a reference for the construction of high-yield plant-derived diterpenoid microbial cell factories and the industrial production of diterpenoids.

Fermentative production of tetraacetyl phytosphingosine: a review / 生物工程学报

Tetraacetyl phytosphingosine (TAPS) is an excellent raw material for natural skin care products. Its deacetylation leads to the production of phytosphingosine, which can be further used for synthesizing the moisturizing skin care product ceramide. For this reason, TAPS is widely used in the skin care oriented cosmetics industry. The unconventional yeast Wickerhamomyces ciferrii is the only known microorganism that can naturally secrete TAPS, and it has become the host for the industrial production of TAPS. This review firstly introduces the discovery, functions of TAPS, and the metabolic pathway for TAPS biosynthesis is further introduced. Subsequently, the strategies for increasing the TAPS yield of W. ciferrii, including haploid screening, mutagenesis breeding and metabolic engineering, are summarized. In addition, the prospects of TAPS biomanufacturing by W. ciferrii are discussed in light of the current progresses, challenges, and trends in this field. Finally, guidelines for engineering W. ciferrii cell factory using synthetic biology tools for TAPS production are also presented.

Preface for special issue on chemical bioproduction / 生物工程学报

Engineering efficient enzymes or microbial cell factories should help to establish green bio-manufacturing process for chemical overproduction. The rapid advances and development in synthetic biology, systems biology and enzymatic engineering accerleate the establishing feasbile bioprocess for chemical biosynthesis, including expanding the chemical kingdom and improving the productivity. To consolidate the latest advances in chemical biosynthesis and promote green bio-manufaturing, we organized a special issue on chemical bioproduction that including review or original research papers about enzymatic biosynthesis, cell factory, one-carbon based biorefinery and feasible strategies. These papers comprehensively discussed the latest advaces, the challenges as well as the possible solutions in chemical biomanufacturing.

Adaptive evolution of microorganisms based on industrial environmental perturbations / 生物工程学报

The development of synthetic biology has greatly promoted the construction of microbial cell factories, providing an important strategy for green and efficient chemical production. However, the bottleneck of poor tolerance to harsh industrial environments has become the key factor hampering the productivity of microbial cells. Adaptive evolution is an important method to domesticate microorganisms for a certain period by applying targeted selection pressure to obtain desired phenotypic or physiological properties that are adapted to a specific environment. Recently, with the development of technologies such as microfluidics, biosensors, and omics analysis, adaptive evolution has laid the foundation for efficient productivity of microbial cell factories. Herein, we discuss the key technologies of adaptive evolution and their important applications in improvement of environmental tolerance and production efficiency of microbial cell factories. Moreover, we looked forward to the prospects of adaptive evolution to realize industrial production by microbial cell factories.

Design and applications of synthetic electroactive microbial consortia / 生物工程学报

Synthetic electroactive microbial consortia, which include exoelectrogenic and electrotrophic communities, catalyze the exchange of chemical and electrical energy in cascade metabolic reactions among different microbial strains. In comparison to a single strain, a community-based organisation that assigns tasks to multiple strains enables a broader feedstock spectrum, faster bi-directional electron transfer, and greater robustness. Therefore, the electroactive microbial consortia held great promise for a variety of applications such as bioelectricity and biohydrogen production, wastewater treatment, bioremediation, carbon and nitrogen fixation, and synthesis of biofuels, inorganic nanomaterials, and polymers. This review firstly summarized the mechanisms of biotic-abiotic interfacial electron transfer as well as biotic-biotic interspecific electron transfer in synthetic electroactive microbial consortia. This was followed by introducing the network of substance and energy metabolism in a synthetic electroactive microbial consortia designed by using the "division-of-labor" principle. Then, the strategies for engineering synthetic electroactive microbial consortiums were explored, which included intercellular communications optimization and ecological niche optimization. We further discussed the specific applications of synthetic electroactive microbial consortia. For instance, the synthetic exoelectrogenic communities were applied to biomass generation power technology, biophotovoltaics for the generation of renewable energy and the fixation of CO2. Moreover, the synthetic electrotrophic communities were applied to light-driven N2 fixation. Finally, this review prospected future research of the synthetic electroactive microbial consortia.

Biomanufacturing driven by engineered organisms (2022) / 生物工程学报

This article summarizes the reviews and original research papers published in Chinese Journaol of Biotechnology in the area of biomanufacturing driven by engineered organisms in the year of 2022. The enabling technologies including DNA sequencing, DNA synthesis, and DNA editing as well as regulation of gene expression and in silico cell modeling were highlighted. This was followed by discussing the biomanufacturing of biocatalytics products, amino acids and its derivatives, organic acids, natural products, antibiotics and active peptides, functional polysaccharides, and functional proteins. Lastly, the technologies for utilizing C1 compounds and biomass as well as synthetic microbial consortia were discussed. The aim of this article was to help the readers to gain insights into this rapidly developing field from the journal point of view.

Design and implementation of the course on Synthetic Biology based on the concept of general education / 生物工程学报

As an emerging branch of biology, Synthetic Biology has seen rapid development with great potential in theoretical research and application. With a lot of brand-new concepts and research methods, it brings challenges to university teachers, and little experience is available in China on the teaching of Synthetic Biology. In this study, we discussed the general education-based development and application of the course on Synthetic Biology (a discipline in "liberal arts" in Zhejiang University) from the background, design, implementation, outcome, and problems of the course, hoping to provide a reference for the optimization of the course and the design of similar courses in other universities in China.

Cultivation of college students' innovative and entrepreneurial thinking and ability based on Synthetic Biology and iGEM / 生物工程学报

Synthetic Biology is one of the most promising fields of modern Biology and a frontier interdisciplinary subject in the 21st century. With the rapid development of synthetic biology, the International Genetically Engineered Machine (iGEM) competition has emerged. The iGEM competition, based on the subject foundation of Synthetic Biology, intends to solve the biological problems in our daily life by applying modern biological technology. In recent years, with the continuous increase of participating teams, the iGEM competition has received extensive attention and achieved great progress. On the basis of the development of Synthetic Biology, we analyzed the 2018-2020 award-winning projects of the iGEM competition and illustrated the role and significance of the iGEM competition in cultivating college students' innovative thinking and ability with the participation experience of the iGEM team of Southwest Jiaotong University as an example.

Production of carboxylic acids by metabolically engineered Yarrowia lipolytica: a review / 生物工程学报

Yarrowia lipolytica is a non-conventional yeast with unique physiological and metabolic characteristics. It is suitable for production of various products due to its natural ability to utilize a variety of inexpensive carbon sources, excellent tolerance to low pH, and strong ability to secrete metabolites. Currently, Y. lipolytica has been demonstrated to produce a wide range of carboxylic acids with high efficiency. This article summarized the progress in engineering Y. lipolytica to produce various carboxylic acids by using metabolic engineering and synthetic biology approaches. The current bottlenecks and solutions for high-level production of carboxylic acids by engineered Y. lipolytica were also discussed, with the aim to provide useful information for relevant studies in this field.

Advances in synthetic biology of CO2 fixation by heterotrophic microorganisms / 生物工程学报

Human activities increase the concentration of atmospheric carbon dioxide (CO2), which leads to global climate warming. Microbial CO2 fixation is a promising green approach for carbon neutral. In contrast to autotrophic microorganisms, heterotrophic microorganisms are characterized by fast growth and ease of genetic modification, but the efficiency of CO2 fixation is still limited. In the past decade, synthetic biology-based enhancement of heterotrophic CO2 fixation has drawn wide attention, including the optimization of energy supply, modification of carboxylation pathway, and heterotrophic microorganisms-based indirect CO2 fixation. This review focuses on the research progress in CO2 fixation by heterotrophic microorganisms, which is expected to serve as a reference for peaking CO2 emission and achieving carbon neutral by microbial CO2 fixation.

Advances in the biosynthesis of tetrapyrrole compounds / 生物工程学报

Tetrapyrrole compounds are a class of compounds with important functions. They exist in living organisms and have been widely used in agriculture, food, medicine, and other fields. The cumbersome process and high cost of chemical synthesis, as well as the shortcomings of unstable quality of animal and plant extraction methods, greatly hampered the industrial production and applications of tetrapyrrole compounds. In recent years, the rapid development of synthetic biology has provided new tools for microorganisms to efficiently synthesize tetrapyrrole compounds from renewable biomass resources. This article summarizes various strategies for the biosynthesis of tetrapyrrole compounds, discusses methods to improve its biosynthesis efficiency and future prospects, with the aim to facilitate the research on biosynthesis of tetrapyrrole compounds.

Construction and application of microbial cell factories for unnatural amino acids / 生物工程学报

Unnatural amino acids are widely used in medicine, pesticide, material, and other industries and the green and efficient synthesis has attracted a lot of attention. In recent years, with the rapid development of synthetic biology, microbial cell factories have become a promising means for biosynthesis of unnatural amino acids. This study reviewed the construction and application of microbial cell factories for unnatural amino acid, including the synthetic pathway reconstruction, design/modification of key enzymes and their coordinated regulation with precursors, blocking of competitive alternative pathways, and construction of cofactor circulation systems. Meanwhile, on the basis of the new principles for designing the microbial cell factories, new biosynthetic pathways adapted to cells and the production environment, as well as new biomanufacturing system established based on cell adaptive evolution and intelligent fermentation regulation, we looked forward to the further construction and application of microbial cell factories for industrial bio-production.

Using OMICS technologies to analyze the mechanisms of synthetic microbial co-culture systems: a review / 生物工程学报

In recent years, the interaction mechanisms underpinning the synthetic microbial co-culture systems have gained increasing attention due to their potentials in various biotechnological applications. Exploration of the inter-species mechanisms underpinning the synthetic microbial co-culture system could contribute to a better understanding of the theoretical basis to further optimize the existing co-culture systems, and design new synthetic co-culture system for large-scale application. OMICS technologies such as genomics, transcriptomics, proteomics, and metabolomics could analyze the biological processes in a high throughput manner. Multi-omics analysis could achieve a "global view" of various members in the microbial co-culture systems, which presents opportunities in understanding synthetic microbial consortia better. This article summarizes recent advances in understanding the mechanisms of synthetic microbial co-culture systems using omics technologies, from the aspects of metabolic network, energy metabolism, signal transduction, membrane transport, stress response, community stability and structural rationality. All these findings could provide important theoretical basis for future application of the microbial co-culture systems with the aids of emerging biotechnologies such as synthetic biology and genome editing.

Microbial synthesis of monoterpenoids: a review / 生物工程学报

Monoterpenoids that belong to the terpenoids family are usually volatile and have strong aroma. Some monoterpenoids also have antioxidant, antibacterial and anti-inflammatory activities, which make them important raw materials for medicine, food and cosmetics industry. In recent years, the heterologous synthesis of monoterpenoids by microorganisms has attracted extensive attention. However, its large-scale application is greatly hampered by the low yield and high production cost. Nowadays, the rapid development of synthetic biology provides new approaches for enhancing the production of monoterpenoids by microorganisms. Different kinds of recombinant strains can be obtained via engineering of microbial cells to produce a variety of monoterpenoids with different properties. This paper summarized the latest strategies and progress in the application of synthetic biology to produce monoterpenoids by microorganisms, including the design and modification of biosynthetic pathway, as well as the design and optimization of high-yield monoterpenoids producing chassis cells.

Therapeutic cell engineering: designing programmable synthetic genetic circuits in mammalian cells

Cell therapy approaches that employ engineered mammalian cells for on-demand production of therapeutic agents in the patient's body are moving beyond proof-of-concept in translational medicine. The therapeutic cells can be customized to sense user-defined signals, process them, and respond in a programmable and predictable way. In this paper, we introduce the available tools and strategies employed to design therapeutic cells. Then, various approaches to control cell behaviors, including open-loop and closed-loop systems, are discussed. We also highlight therapeutic applications of engineered cells for early diagnosis and treatment of various diseases in the clinic and in experimental disease models. Finally, we consider emerging technologies such as digital devices and their potential for incorporation into future cell-based therapies.

Development of the iGEM high school track / 生物工程学报

The international genetically engineered machine (iGEM) competition is a global top college academic competition in synthetic biology. The iGEM competition has exhibited extensive international influence and attracted teams from more than 40 countries and regions around the world to participate in. The annual iGEM outputs have attracted the attention of top academic journals or international media such as Science, Nature, Scientific American, The Economist, British Broadcasting Corporation (BBC), etc. High school teams participated in iGEM since 2011, and the number of high school teams has increased year by year. High school participants are increasingly becoming one of the most important forces to promote the development of iGEM and synthetic biology. IGEM competition has also become an important platform to foster the core literacy of high school students. This paper summarized the track rules, topic selection tendency and awards of high school teams based on data of 2017 to 2021 iGEM competition. In addition, we analyzed the significance of iGEM competition on fostering of high school students' core literacy and discussed the development trend of global high school teams, with the aim to provide a reference for high school team building in the future.

Kinetic and toxicological effects of synthesized palladium(II) complex on snake venom (Bungarus sindanus) acetylcholinesterase

The venom of the krait (Bungarus sindanus), an Elapidae snake, is highly toxic to humans and contains a great amount of acetylcholinesterase (AChE). The enzyme AChE provokes the hydrolysis of substrate acetylcholine (ACh) in the nervous system and terminates nerve impulse. Different inhibitors inactivate AChE and lead to ACh accumulation and disrupted neurotransmission. Methods: The present study was designed to evaluate the effect of palladium(II) complex as antivenom against krait venom AChE using kinetics methods. Results: Statistical analysis showed that krait venom AChE inhibition decreases with the increase of Pd(II) complex (0.025-0.05 µM) and exerted 61% inhibition against the AChE at a fixed concentration (0.5 mM) of ACh. Kinetic analysis using the Lineweaver Burk plot showed that Pd(II) caused a competitive inhibition. The compound Pd(II) complex binds at the active site of the enzyme. It was observed that K m (Michaelis-Menten constant of AChE-ACh into AChE and product) increased from 0.108 to 0.310 mM (45.74 to 318.35%) and V max remained constant with an increase of Pd(II) complex concentrations. In AChE K Iapp was found to increase from 0.0912 to 0.025 µM (29.82-72.58%) and did not affect the V maxapp with an increase of ACh from (0.05-1 mM). K i (inhibitory constant) was estimated to be 0.029µM for snake venom; while the K m was estimated to be 0.4 mM. The calculated IC50 for Pd(II) complex was found to be 0.043 µM at constant ACh concentration (0.5 mM). Conclusions: The results show that the Pd(II) complex can be deliberated as an inhibitor of AChE.(AU)

Microbial green manufacturing of higher alcohols / 生物工程学报

Higher alcohols that contain more than two carbon atoms have better fuel properties than ethanol, making them important supplements and alternatives to fossil fuels. Using microbes to produce higher alcohols from renewable biomass can alleviate the current energy and environmental crises, and has become a major future direction for green biomanufacturing. Since natural microbes can only produce a few higher alcohols in small amounts, it is necessary to reconstruct the synthetic pathways for higher alcohols in model industrial strains through metabolic engineering and synthetic biology to overcome the metabolic bottlenecks. A series of milestones have been accomplished in past decades. The authors of this review have witnessed the entire journey of this field from its first success to the leaping development. On the 30th anniversary of the founding of the discipline of metabolic engineering, this review dates back to the great milestones in achieving heterologous production of higher alcohols in non-native strains. The design and optimization of high alcohol biosynthetic pathways, the expansion of feedstock, the engineering of host strains and the industrialization process are summarized. This review aims to draw further attention to microbial synthesis of higher alcohols, inspire the development of novel techniques and strategies of metabolic engineering, and promote the innovation and upgrade of China's biofuel industry.

Advances and prospects in metabolic engineering for the production of amino acids / 生物工程学报

Fermentative production of amino acids is one of the pillars of the fermentation industry in China. Recently, with the fast development of metabolic engineering and synthetic biology technologies, the metabolic engineering for production of amino acids has been flourishing. Conventional forward metabolic engineering, reversed metabolic engineering based on omics data and in silico simulation, and evolutionary metabolic engineering mimicking the natural evolution, have shown increasingly promising applications. A series of highly efficient and robust amino acids-producing strains have been developed and applied in the industrial production of amino acids. The increasingly fierce market competition has put forward new requirements for strain breeding and selection, such as developing high value-added amino acids, dynamic regulation of cellular metabolism, and adapting to the requirements of new process. This review summarizes the advances and prospects in metabolic engineering for the production of amino acids.