合成生物学应用产品开发现状与趋势

目的：从产品开发角度分析全球合成生物学发展现状和趋势。方法：在伍德罗·威尔逊国际学者中心的合成生物学产品和应用清单（synthetic biology products and applications inventory）的数据基础上,对全球合成生物学产品的开发状态、市场应用和发展前景等进行补充检索和分析。结果：至2015年,全球至少已有81家企业（或研究机构）的116种合成生物学产品得到了市场应用开发,主要开发者为美国企业（或研究机构）,产品主要集中于化学和医药领域。结论：合成生物学实现了从生物学分析向生物学合成的范式转移,其产品开发将给一系列的行业带来深刻的变革。     

工程大肠杆菌合成游离脂肪酸的研究进展

游离脂肪酸作为一种重要的平台化合物,其衍生产品被广泛应用到能源、化学工业中。作为更加可持续、绿色的生产策略,利用工程微生物合成游离脂肪酸是以石油基和动植物为原料生产脂肪酸类产品的重要补充。大肠杆菌作为经典的模式微生物,通过对其进行代谢工程改造,脂肪酸的积累已经从痕量提高到了约9g/L,展示了其作为脂肪酸合成菌株的巨大应用潜力。随着合成生物学技术的涌现,“感应-调控器”、体外重构、β氧化逆循环、异源合成途径的整合等思路的引入极大地加快了工程大肠杆菌脂肪酸合成的进化速率,并赋予大肠杆菌合成多种脂肪酸产品的能力。对近年来通过代谢工程和合成生物学手段改造大肠杆菌合成游离脂肪酸的研究进展进行综述,对其发展前景进行展望。     

大肠杆菌利用合成生物学策略生产聚羟基脂肪酸酯的研究进展

合成生物学作为近年来发展迅速的一门交叉学科,为微生物的生物合成提供了强有力的平台工具。微生物细胞工厂可以合成一系列不同种类的聚羟基脂肪酸酯(PHA),而大肠杆菌作为最常用的底盘,正不断运用合成生物学的策略发掘PHA的多样性并降低成本、提高产量。本文中,笔者综述了大肠杆菌利用合成生物学策略生产生物基材料PHA的研究进展,并对其开发与应用前景进行了展望。     

合成生物学方法构建电活性大肠杆菌

电活性微生物具有独特的在细胞内外环境之间传递电子的能力。在对天然电活性微生物电子传递机制充分研究的基础上,通过合成生物学方法异源构建天然电活性微生物电子传递结构基础也可以将遗传背景清晰的非电活性大肠杆菌改造为电活性微生物。构建获得的工程化电活性大肠杆菌可以直接应用于微生物燃料电池和生物传感器等领域,同时也可以作为底盘细胞整合相应的目标产物合成通路实现电能驱动的生物合成。本文以合成生物学方法构建电活性大肠杆菌为主题,详细阐述天然电活性微生物电子传递的机理及结构基础,总结了工程化电活性大肠杆菌的构建策略、成功案例以及应用领域,并对合成生物学方法构建电活性大肠杆菌未来的研究方向进行了展望。     

利用重组大肠杆菌进行寡糖合成的研究进展

随着更多寡糖生物学活性的阐明,寡糖合成研究已成为糖生物学研究的热点之一,其中,以重组大肠杆菌作为酶盒或生物反应器,利用Leloir途径合成寡糖的方法,是近年来发展起来的一类重要的寡糖生物合成技术,并取得了较多的进展。将从细菌糖基转移酶的表达和鉴定、糖核苷酸的供给和寡糖的合成途径等几个方面,关注利用细菌功能尤其是利用重组大肠杆菌合成寡糖的研究进展,并分析各技术手段的优缺点及其应用前景。     

从DNA合成技术角度阐述合成生物学

合成生物学是一个拥有巨大潜力的新兴学科,合成生物学技术的发展将会对未来生物、医药、农业、能源、材料和环保等方面产生巨大的推进作用。基因合成是合成生物学中最基本和使用最多的一种技术手段,合成生物学的快速发展对基因合成能力提出了空前需求。综述基因合成技术的发展历史、现状和未来趋势,探讨基因合成技术存合成生物学以及整个生命科学研究中的应用和重要意义。     

合成生物学的科学内涵和社会意义——合成生物学专刊序言

合成生物学（synthetic biology）的产生和快速发展,是人类对生命现象系统认知和深刻探索之后合乎逻辑的必然结果;同时,也是20世纪末和21世纪初,学科交叉迅猛发展的必然结果。顾名思义,     

重组大肠杆菌合成聚（3-巯基丙酸）和聚（3-羟基丁酸-3-巯基丙酸）的研究

利用Clostridium acetobutylicum的丁酸激酶基因 (buk) 和磷酸转丁酰基酶基因(ptb),以及Thiocapsa pfennigii的PHA合成酶基因,设计了一条能够合成多种聚羟基烷酸的代谢途径,用构建的质粒转化大肠杆菌,获得了重组大肠杆菌菌株。前期的研究表明,在合适的前体物条件下,该重组大肠杆菌能够合成包括聚羟基丁酸、聚（羟基丁酸戊酸）等多种生物聚酯［Liu and Steinbüchel, Appl. Environ. Microbiol. 66:739743］。利用该重组大肠杆菌,通过生物催化作用合成了3巯基丙酸的同型共聚酯,同时利用该重组大肠杆菌还获得了含3-巯基丙酸单体的多种异型共聚物。实验首先研究了3巯基丙酸对大肠杆菌生长的影响,在此基础上优化了培养过程中添加3-巯基丙酸的时机和浓度,结果表明,在实验的条件下,细胞合成聚（3-巯基丙酸）可达6.7%(占细胞干重),合成聚（3-羟基丁酸—3-巯基丙酸）（分子中3-巯基丙酸:3-羟基丁酸=3:1）可达24.3%。实验进一步研究了同时或分别表达以上3个基因的重组大肠杆菌合成聚合物的能力,结果表明只有当3个基因同时表达时才能合成聚合物,说明3个基因对合成过程是必须的,从而表明了合成途径是按照设计的路线进行的。还通过GC/MS、GPC、IR等手段对合成的化合物进行了定性的研究。聚（3-巯基丙酸）或聚（3-羟基丁酸-3-巯基丙酸）等聚酯属于一类新型生物聚合物,它在分子骨架中含有硫酯键,不同于聚羟基烷酸酯的氧酯键,从而具有显著不同的物理、化学、光学等性质和具有重要的潜在应用价值。     

Hv古细菌SRP19基因的克隆、表达、重组蛋白的纯化及生物学活性的研究

目的：构建Hv古细菌SRP19蛋白的表达载体pET23d-HvSRP19并在大肠杆菌中表达后进行纯化和研究其生物学活性,为研究SRP循环的分子机制奠定基础。方法：用体外合成的重组DNA技术,先合成具有重叠碱基的10个寡核苷酸短序列,通过拼接,获得Hv SRP19基因全长DNA后,克隆到pET23d载体上。重组质粒在大肠杆菌BL21（DE3）pLysS中的大量表达产物经Q-Sepharose离子交换层析柱纯化后再用蔗糖密度梯度超速离心法分析其生物学活性。结果：正确构建了pET23d-Hv SRP19表达载体,并在大肠杆菌BL21（DE3）pLysS中获得良好的表达;成功地纯化了表达产物,纯度达95%;证明了具有SRP19蛋白的生物学活性,能够与Hv SRP RNA相互作用形成SRP19-SRP RNA的复合物。结论：纯化的Hv SRP19蛋白与Hv SRP RNA相互作用所形成的复合物,被认为是启动SRP颗粒形成和功能发挥的开始。     

合成生物学促进中药活性成分的生物合成

中药是我国的传统药物,现也在不断地谋求发展和创新。合成生物学可以通过“模块化”和“适配性”方法将代谢产物或其前体的生物合成过程从植物转移至微生物中,通过发酵生产中药的活性成分。本文综述了现有中药合成的方法,阐述了合成生物学对中药活性成分合成的促进作用。     

High molecular weight DNA assembly in vivo for synthetic biology applications

DNA assembly is the key technology of the emerging interdisciplinary field of synthetic biology. While the assembly of smaller DNA fragments is usually performed in vitro, high molecular weight DNA molecules are assembled in vivo via homologous recombination in the host cell. Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae are the main hosts used for DNA assembly in vivo. Progress in DNA assembly over the last few years has paved the way for the construction of whole genomes. This review provides an update on recent synthetic biology advances with particular emphasis on high molecular weight DNA assembly in vivo in E. coli, B. subtilis and S. cerevisiae. Special attention is paid to the assembly of whole genomes, such as those of the first synthetic cell, synthetic yeast and minimal genomes.     

Advancing secondary metabolite biosynthesis in yeast with synthetic biology tools

Secondary metabolites are an important source of high-value chemicals, many of which exhibit important pharmacological properties. These valuable natural products are often difficult to synthesize chemically and are commonly isolated through inefficient extractions from natural biological sources. As such, they are increasingly targeted for production by biosynthesis from engineered microorganisms. The budding yeast species Saccharomyces cerevisiae has proven to be a powerful microorganism for heterologous expression of biosynthetic pathways. S. cerevisiae's usefulness as a host organism is owed in large part to the wealth of knowledge accumulated over more than a century of intense scientific study. Yet many challenges are currently faced in engineering yeast strains for the biosynthesis of complex secondary metabolite production. However, synthetic biology is advancing the development of new tools for constructing, controlling, and optimizing complex metabolic pathways in yeast. Here, we review how the coupling between yeast biology and synthetic biology is advancing the use of S. cerevisiae as a microbial host for the construction of secondary metabolic pathways.     

合成生物学中的DNA组装技术

合成生物学旨在应用工程学的研究思路及手段去设计或改造生物系统,是一个综合了科学与工程的拥有发展潜力的新兴学科,在生物医药、农业、能源、环保等方面发挥着巨大作用。DNA组装技术是合成生物学中的关键技术,也是合成生物学快速发展的限制性技术。综述了众多DNA组装技术的发展及其在合成生物学研究中的意义和应用。     

The development of synthetic biology: a patent analysis

In the past decades, synthetic biology has gained interest regarding research and development efforts within the biotechnology domain. However, it is unclear to what extent synthetic biology has matured already into being commercially exploitable. By means of a patent analysis, this study shows that there is an increasing trend regarding synthetic biology related patent applications. The majority of retrieved patents relates to innovations facilitating the realisation of synthetic biology through improved understanding of biological systems. In addition, there is increased activity concerning the development of synthetic biology based applications. When looking at potential application areas, the majority of synthetic biology patents seems most relevant for the medical, energy and industrial sector. Furthermore, the analysis shows that most activity has been carried out by the USA, with Japan and a number of European countries considerably trailing behind. In addition, both universities and companies are major patent applicant actor types. The results presented here form a starting point for follow-up studies concerning the identification of drivers explaining the observed patent application trends in synthetic biology.     

A systematic design method for robust synthetic biology to satisfy design specifications

Background  

Synthetic biology is foreseen to have important applications in biotechnology and medicine, and is expected to contribute significantly to a better understanding of the functioning of complex biological systems. However, the development of synthetic gene networks is still difficult and most newly created gene networks are non-functioning due to intrinsic parameter uncertainties, external disturbances and functional variations of intra- and extra-cellular environments. The design method for a robust synthetic gene network that works properly in a host cell under these intrinsic parameter uncertainties and external disturbances is the most important topic in synthetic biology.     

Authentic teaching and learning through synthetic biology

Synthetic biology is an emerging engineering discipline that, if successful, will allow well-characterized biological components to be predictably and reliably built into robust organisms that achieve specific functions. Fledgling efforts to design and implement a synthetic biology curriculum for undergraduate students have shown that the co-development of this emerging discipline and its future practitioners does not undermine learning. Rather it can serve as the lynchpin of a synthetic biology curriculum. Here I describe educational goals uniquely served by synthetic biology teaching, detail ongoing curricula development efforts at MIT, and specify particular aspects of the emerging field that must develop rapidly in order to best train the next generation of synthetic biologists.     

Construction of synthetic regulatory networks in yeast

Yeast species such as Saccharomyces cerevisiae have been exploited by humans for millennia and so it is therefore unsurprising that they are attractive cells to re-engineer for industrial use. Despite many beneficial traits yeast has for synthetic biology, it currently lags behind Escherichia coli in the number of synthetic networks that have been described. While the eukaryotic nature of yeast means that its regulation is not as simple to predict as it is for E. coli, once initial considerations have been made yeast is pleasingly tractable. In this review we provide a loose guide for constructing and implementing synthetic regulatory networks in S. cerevisiae using examples from previous research to highlight available resources, specific considerations and potential future advances.     

Interactive learning and action: realizing the promise of synthetic biology for global health

The emerging field of synthetic biology has the potential to improve global health. For example, synthetic biology could contribute to efforts at vaccine development in a context in which vaccines and immunization have been identified by the international community as being crucial to international development efforts and, in particular, the millennium development goals. However, past experience with innovations shows that realizing a technology’s potential can be difficult and complex. To achieve better societal embedding of synthetic biology and to make sure it reaches its potential, science and technology development should be made more inclusive and interactive. Responsible research and innovation is based on the premise that a broad range of stakeholders with different views, needs and ideas should have a voice in the technological development and deployment process. The interactive learning and action (ILA) approach has been developed as a methodology to bring societal stakeholders into a science and technology development process. This paper proposes an ILA in five phases for an international effort, with national case studies, to develop socially robust applications of synthetic biology for global health, based on the example of vaccine development. The design is based on results of a recently initiated ILA project on synthetic biology; results from other interactive initiatives described in the literature; and examples of possible applications of synthetic biology for global health that are currently being developed.     

Engineering of a genome-reduced host: practical application of synthetic biology in the overproduction of desired secondary metabolites

Synthetic biology aims to design and build new biological systems with desirable properties, providing the foundation for the biosynthesis of secondary metabolites. The most prominent representation of synthetic biology has been used in microbial engineering by recombinant DNA technology. However, there are advantages of using a deleted host, and therefore an increasing number of biotechnology studies follow similar strategies to dissect cellular networks and construct genome-reduced microbes. This review will give an overview of the strategies used for constructing and engineering reduced-genome factories by synthetic biology to improve production of secondary metabolites.