Modular electron transfer circuits for synthetic biology: insulation of an engineered biohydrogen pathway

Electron transfer is central to a wide range of essential metabolic pathways, from photosynthesis to fermentation. The evolutionary diversity and conservation of proteins that transfer electrons makes these pathways a valuable platform for engineered metabolic circuits in synthetic biology. Rational engineering of electron transfer pathways containing hydrogenases has the potential to lead to industrial scale production of hydrogen as an alternative source of clean fuel and experimental assays for understanding the complex interactions of multiple electron transfer proteins in vivo. We designed and implemented a synthetic hydrogen metabolism circuit in Escherichia coli that creates an electron transfer pathway both orthogonal to and integrated within existing metabolism. The design of such modular electron transfer circuits allows for facile characterization of in vivo system parameters with applications toward further engineering for alternative energy production.     

Assessing the impacts of genetically modified microorganisms

The progression towards greater industrial sustainability involves the analysis of biotechnology as a means of achieving clean or cleaner products and processes. Because living systems manage their chemistry more efficiently than man-made factories, and their wastes tend to be recyclable and biodegradable, they can be expected to be more environmentally clean. Industry has begun to use enzymes instead of traditional catalysts in many industrial production processes. The future holds obstacles as well as opportunities for biotechnological applications. A greater ability to manipulate biological materials and processes will have significant impact on manufacturing industries. A growing proportion of biotechnologyderived processes and products is based on the use of genetically modified microorganisms. This extends the analysis from the aspect of cleanliness to the aspect of safety.     

己二酸的生物合成

己二酸是六碳二元羧酸,主要用于生产尼龙、化纤和工程塑料等聚合物,年需求量近300万吨。目前己二酸的工业生产主要是利用硝酸氧化芳烃合成己二酸等化学法获得,不仅污染严重,而且是个不可持续的过程,需要发展可行的替代合成方法。近年来,随着合成生物学和代谢工程的发展,绿色、洁净的己二酸生物合成方法逐渐受到人们的关注和重视。文中就己二酸及其前体物的生物合成研究进展进行了综述,并对可能的合成新途径做了展望。     

Systems biology for industrial strains and fermentation processes--example: amino acids

Systems biology is attracting significant interest finding applications not only in pharmaceutical development but also for basic studies on microbial systems. The latter often concentrate on the quantitative understanding of global regulation phenomena. So far, these activities are dominated by academic groups basically mirroring the necessity to prepare the sound scientific understanding first, before industrial applications can be derived later. However, this short-term view may not be sufficient because systems biology already offers numerous benefits for industrial applications, provided that special constraints are considered. This contribution indicates some of the constraints worth noticing when industrial systems biology projects are carried out. Consequently, differences in project structure and goals between purely academic and industrial systems biology projects are outlined.     

Opportunities for yeast metabolic engineering: Lessons from synthetic biology

Constant progress in genetic engineering has given rise to a number of promising areas of research that facilitated the expansion of industrial biotechnology. The field of metabolic engineering, which utilizes genetic tools to manipulate microbial metabolism to enhance the production of compounds of interest, has had a particularly strong impact by providing new platforms for chemical production. Recent developments in synthetic biology promise to expand the metabolic engineering toolbox further by creating novel biological components for pathway design. The present review addresses some of the recent advances in synthetic biology and how these have the potential to affect metabolic engineering in the yeast Saccharomyces cerevisiae. While S. cerevisiae for years has been a robust industrial organism and the target of multiple metabolic engineering trials, its potential for synthetic biology has remained relatively unexplored and further research in this field could strongly contribute to industrial biotechnology. This review also addresses are general considerations for pathway design, ranging from individual components to regulatory systems, overall pathway considerations and whole-organism engineering, with an emphasis on potential contributions of synthetic biology to these areas. Some examples of applications for yeast synthetic biology and metabolic engineering are also discussed.     

Synthetic biology - the state of play

Just over two years ago there was an article in Nature entitled "Five Hard Truths for Synthetic Biology". Since then, the field has moved on considerably. A number of economic commentators have shown that synthetic biology very significant industrial potential. This paper addresses key issues in relation to the state of play regarding synthetic biology. It first considers the current background to synthetic biology, whether it is a legitimate field and how it relates to foundational biological sciences. The fact that synthetic biology is a translational field is discussed and placed in the context of the industrial translation process. An important aspect of synthetic biology is platform technology, this topic is also discussed in some detail. Finally, examples of application areas are described.     

New challenges and opportunities for industrial biotechnology

ABSTRACT: Industrial biotechnology has not developed as fast as expected due to some challenges including the emergences of alternative energy sources, especially shale gas, natural gas hydrate (or gas hydrate) and sand oil et al. The weaknesses of microbial or enzymatic processes compared with the chemical processing also make industrial biotech products less competitive with the chemical ones. However, many opportunities are still there if industrial biotech processes can be as similar as the chemical ones. Taking advantages of the molecular biology and synthetic biology methods as well as changing process patterns, we can develop bioprocesses as competitive as chemical ones, these including the minimized cells, open and continuous fermentation processes et al.     

Clean technology: industry and environment, a viable partnership?

The industrial sector is becoming increasingly interested in eliminating potential pollution at source and reducing energy use. Biotechnology provides cheaper, cleaner alternatives to a wide range of traditional processes--but its adoption has been slower than expected. If industry is to become truly compatible with the environment, companies and the public will have to be convinced of the ecological and economic value of clean technology.     

2019工业生物学专刊序言

工业生物技术作为可持续发展的重要途径,其创新发展离不开基础学科的支撑。工业生物学研究工业环境下生物体行为的基本规律和作用机制,解决适应工业环境的生物体设计构建及应用的关键科学问题,是工业生物技术学科基础。为了梳理和凝练工业生物学发展状况,本刊特组织出版专刊,从工业蛋白科学、工业细胞科学和工业发酵科学三个方面,分别阐述学科的发展动态,展望未来的发展趋势,为促进工业生物技术发展奠定基础。     

Metabolic Engineering to Modify Flower Color

Thanks to the rapid progress in molecular biology of flavonoidbiosynthesis and plant transformation, it has become feasibleto modify the pathway and flower color through genetic engineering.One of the advantages of molecular breeding is that flower colorcan be specifically modified without changing the other characteristicsof the targeted variety. Novel flower color varieties such asbrick-red petunias and violet carnations have been successfullymade by expression of heterologous flavonoid genes. Flavonoidmetabolic engineering has and will give new perspectives inplant molecular biology besides its industrial application. (Received August 26, 1998; Accepted October 9, 1998)     

Comparison of Microbial Contamination Levels Among Hospital Operating Rooms and Industrial Clean Rooms

Microbial contamination in industrial clean rooms was compared quantitatively and qualitatively with that of hospital operating rooms. The number of aerobic mesophilic microorganisms which accumulated on stainless-steel strips exposed for periods up to 21 weeks to the intramural air of four operating rooms was at least 1 log higher than the accumulation on strips exposed in four clean rooms, and was essentially the same as that found in two factory areas. Volumetric air samplings showed that there were significantly higher numbers of airborne viable particles per cubic foot of air in operating rooms than in industrial clean rooms. In contrast to clean rooms, where most of the airborne contaminants were those associated with human hair, skin, and respiratory tract, the hospital operating rooms showed a very high level of microorganisms associated with dust and soil.     

Techniques for preservation of mammalian germ plasm

Abstract

The preservation of mammalian germ plasm by freezing has become an integral part of animal breeding, medicine, agriculture, reproductive biology and embryology. Considerable understanding of the physical‐chemical and physiological phenomena involved in cryopreservation of sperm, eggs and embryos has been achieved. This understanding has resulted in substantial improvements in the efficiency and efficacy of methods used to cryopreserve germ plasm. In addition, many of these methods have become integrated directly into the practice of animal breeding, and have contributed directly to the international trade in animal genetics. Development of these methods has been derived from close cooperation and interaction between the research and industrial communities. As the powerful techniques of molecular biology are focused on fundamental and applied aspects of embryology and reproductive biology, there are new problems regarding the cryobiology of germ cells to be solved.     

Next‐Generation Industrial Biotechnology‐Transforming the Current Industrial Biotechnology into Competitive Processes

The chemical industry has made a contribution to modern society by providing cost‐competitive products for our daily use. However, it now faces a serious challenge regarding environmental pollutions and greenhouse gas emission. With the rapid development of molecular biology, biochemistry, and synthetic biology, industrial biotechnology has evolved to become more efficient for production of chemicals and materials. However, in contrast to chemical industries, current industrial biotechnology (CIB) is still not competitive for production of chemicals, materials, and biofuels due to their low efficiency and complicated sterilization processes as well as high‐energy consumption. It must be further developed into “next‐generation industrial biotechnology” (NGIB), which is low‐cost mixed substrates based on less freshwater consumption, energy‐saving, and long‐lasting open continuous intelligent processing, overcoming the shortcomings of CIB and transforming the CIB into competitive processes. Contamination‐resistant microorganism as chassis is the key to a successful NGIB, which requires resistance to microbial or phage contaminations, and available tools and methods for metabolic or synthetic biology engineering. This review proposes a list of contamination‐resistant bacteria and takes Halomonas spp. as an example for the production of a variety of products, including polyhydroxyalkanoates under open‐ and continuous‐processing conditions proposed for NGIB.     

Brush-making fibres

Fibres from palm leaf-bases of the tropics clean our streets and fibres from agave plants of Mexico clean our clothes, while fibres from a variety of other plants enter into the manufacture of a variety of brushes for specialized industrial uses.     

工业微生物遗传和环境扰动的调控和适应进化

开发工业微生物,使其利用可再生的原料生产生物燃料、大宗化学品、食品添加剂和营养品、药物以及工业酶等,是发展生物产业的基础。工业微生物高产和胁迫抗性等鲁棒性状受复杂遗传调控网络控制,其改造需要从全基因组尺度进行系统的全局的多位点的扰动,以达到快速积累多样性基因型突变并产生所期望的表型。文中对工业微生物鲁棒性状的遗传调控与胁迫响应机制、基因组全局扰动与多位点快速进化以及细胞水平氧还平衡的全局扰动进行了简要综述,未来需要继续借助系统生物学和合成生物学手段,进一步加强对工业环境下工业微生物鲁棒性状调控机理的解析与建模预测以及系统的工程改造。     

中国科学院工业生物技术发展路径

随着工程生物学、基因编辑等共性技术的快速发展,工业生物技术领域的颠覆式创新在低碳合成、未来食品、药物开发等工业生物技术领域不断取得颠覆式创新,支撑了生物产业高质量创新发展。工业生物技术正在为变革传统工业制造模式,构建碳中性工业制造路线形成重要科技支撑。本文从战略规划、创新机构、人才建设、基础研究、科技创新、产业推进等方面系统介绍了中国科学院在工业生物技术领域的整体安排、建制化研发与科技进展,并提出了加快工业生物技术发展的建议。     

新基因起源：从自然进化到人工设计

生命体系历经40多亿年的自然进化,创造了无数丰富多彩的功能基因,保障了生命体系的传承与繁荣。然而生命体系的自然进化历程极其缓慢,新的功能基因产生需要数百万年时间,无法满足快速发展的工业生产需求。利用合成生物学技术,研究人员可以依据已知的酶催化机理和蛋白质结构进行全新的基因设计与合成,按照工业生产需求快速创造全新的蛋白质催化剂,实现各种自然界生物无法催化的生物化学反应。尽管新基因设计技术展现了激动人心的应用前景,但是目前该技术还存在设计成功率不高、酶催化活性较低、合成成本较高等科技挑战。未来随着合成生物学技术的快速发展,设计、改造、合成和筛选等技术将融合为一体,为新基因设计与创建带来全新的发展机遇。     

合成生物学及其在生物技术中的应用进展

合成生物学是一门21世纪生物学的新兴学科,它着眼生物科学与工程科学的结合,把生物系统当作工程系统"从下往上"进行处理,由"单元"(unit)到"部件"(device)再到"系统"(system)来设计,修改和组装细胞构件及生物系统.合成生物学是分子和细胞生物学、进化系统学、生物化学、信息学、数学、计算机和工程等多学科交叉的产物.目前研究应用包括两个主要方面:一是通过对现有的、天然存在的生物系统进行重新设计和改造,修改已存在的生物系统,使该系统增添新的功能.二是通过设计和构建新的生物零件、组件和系统,创造自然界中尚不存在的人工生命系统.合成生物学作为一门建立在基因组方法之上的学科,主要强调对创造人工生命形态的计算生物学与实验生物学的协同整合.必须强调的是,用来构建生命系统新结构、产生新功能所使用的组件单元既可以是基因、核酸等生物组件,也可以是化学的、机械的和物理的元件.本文跟踪合成生物学研究及应用,对其在DNA水平编程、分子修饰、代谢途径、调控网络和工业生物技术等方面的进展进行综述.     

Industrial biotechnology: Tools and applications

Industrial biotechnology involves the use of enzymes and microorganisms to produce value-added chemicals from renewable sources. Because of its association with reduced energy consumption, greenhouse gas emissions, and waste generation, industrial biotechnology is a rapidly growing field. Here we highlight a variety of important tools for industrial biotechnology, including protein engineering, metabolic engineering, synthetic biology, systems biology, and downstream processing. In addition, we show how these tools have been successfully applied in several case studies, including the production of 1, 3-propanediol, lactic acid, and biofuels. It is expected that industrial biotechnology will be increasingly adopted by chemical, pharmaceutical, food, and agricultural industries.