合成生物学发展现状与前景

合成生物学是综合了科学与工程的一个崭新的生物学研究领域,为生命现象及其运动规律的解析提供了一种采用“白下而上”合成策略的正向工程学的研究思路和方法手段,在经济和社会发展中具有巨大的应用开发潜力。近年来,DNA合成与系统生物学技术的发展使生命系统复杂基因回路的设计、合成与组装逐步成为可能,并应用于生物基化学品、生物燃料、医药中间体、保健产品的生产和环境保护等领域。但是,合成生物学的研究仍然面临科学、技术和伦理的挑战,只有积极地应对这些问题,在加大研究开发支持力度的同时,做好必要的风险监管,才能真正把握合成生物学发展带来的历史机遇。     

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。     

DNA合成技术及应用

DNA从头合成技术是指以寡核苷酸链为起始的合成DNA片段的技术,其不断进步是合成生物学快速发展的基石之一。常规使用的连接介导的DNA合成技术和PCR介导的DNA合成技术日益成熟,精确合成长度已经达到0．5—1kb。微阵列介导的DNA合成技术不断发展,其低成本、高通量的特点吸引了人们的注意;而酵母体内DNA合成技术的成功探索也为体外DNA合成提供了一种补偿方法。DNA合成在优化密码子用于异源表达、构建异源代谢途径、合成人工基因组以及合成减毒病毒用于疫苗研制等方面有广泛应用。综述了DNA从头合成技术的研究进展,并介绍了DNA合成的前沿应用。     

非常规酵母的分子遗传学及合成生物学研究进展

先进的合成生物学技术与传统的分子遗传学技术的结合更有助于实现酵母底盘细胞的快速改造和优化。酵母合成生物学研究最早开始于常规酵母——酿酒酵母(Saccharomyces cerevisiae),近些年来又迅速扩展至一些非常规酵母,包括巴斯德毕赤酵母(Pichiapastoris)、解脂耶氏酵母(Yarrowialipolytica)、乳酸克鲁维酵母(Kluyveromyces lactis)和多形汉逊酵母(Hansenula polymorpha)等。借助合成生物学技术与工具,目前科学家们已经成功开发出了能够高效生产生物材料、生物燃料、生物基化学品、蛋白质制剂、食品添加剂和药物等工业产品的重组非常规酵母工程菌株。本文系统总结了合成生物学工具(主要是基因组编辑工具)、合成生物学组件(主要是启动子和终止子)和相关分子遗传学方法在上述非常规酵母系统(底盘细胞)中的最新研究进展和应用情况,并讨论了其他合成生物学技术在这些非常规酵母表达系统中的潜在适用性和应用前景。这为研究人员利用合成生物学方法在这一新型非模式微生物底盘细胞中设计和构建各种高附加值工业产品的异源合成模块并最终实现目标化合物的高效生物合成提供了科学的理论指导。     

合成生物学技术在环境保护中的应用

合成生物学是一个基于生物学和工程学原理的科学领域，其目的是重新设计和重组微生物，以优化或创建具有增强功能的新生物系统。该领域利用分子工具、系统生物学和遗传框架的重编程，从而构建合成途径以获得具有替代功能的微生物。传统上，合成生物学方法通常旨在开发具有成本效益的微生物细胞工厂进而从可再生资源中生产化学物质。然而，近年来合成生物学技术开始在环境保护中发挥着更直接的作用。本综述介绍了基因工程中的合成生物学工具，讨论了基于基因工程的微生物修复策略，强调了合成生物学技术可以通过响应特定污染物进行生物修复来保护环境。其中，规律间隔成簇短回文重复序列（Clustered Regularly Interspersed Short Palindromic Repeats，CRISPR）技术在基因工程细菌和古细菌的生物修复中得到了广泛应用，生物修复领域也出现了很多新的先进技术，包括生物膜工程、人工微生物群落的构建、基因驱动、酶和蛋白质工程等。有了这些新的技术和工具，生物修复将成为当今最好和最有效的污染物去除方式之一。     

系统生物学和合成生物学研究在生物燃料生产菌株改造中的应用

基于生物质资源生产环境友好的生物燃料,对经济和社会的可持续发展具有重要意义,但其生产成本高的问题十分突出,而高效生产菌株的获得是解决这一问题的根本出路。以下综述了利用系统生物学研究所获得的信息进行菌种改造的过程,重点论述了生产菌株胁迫耐受性方面的研究进展,并讨论了系统生物学、合成生物学和代谢工程技术在改造生物燃料生产菌株中的应用,展望了合成生物学在构建高效生物能源生产菌株方面应用的前景。     

植物合成生物学领域发展态势的文献计量分析

合成生物学作为一种颠覆性技术可应用于农业领域的创新发展,解决当前农业学科中的瓶颈问题。利用文献计量学方法从领域发表论文的时序数量分布、主题分布等探测当前合成生物学的基本态势。基于领域的主题分布可知,其中植物合成生物学这一主题是稳定存在的且主题规模处于稳定增长趋势。聚焦植物合成生物学这一主题方向,在构建引文网络的基础上利用主路径分析方法从知识流动角度探测植物合成生物学领域重要知识节点,内容涵盖介子油苷生物合成途径,重要催化酶功能解析、转录因子的调控作用,组学方法的应用,利用微生物酵母进行生物物质合成,这些内容表征了合成生物的核心理论技术。     

植物合成生物学领域发展态势的文献计量分析

合成生物学作为一种颠覆性技术可应用于农业领域的创新发展,解决当前农业学科中的瓶颈问题。利用文献计量学方法从领域发表论文的时序数量分布、主题分布等探测当前合成生物学的基本态势。基于领域的主题分布可知,其中植物合成生物学这一主题是稳定存在的且主题规模处于稳定增长趋势。聚焦植物合成生物学这一主题方向,在构建引文网络的基础上利用主路径分析方法从知识流动角度探测植物合成生物学领域重要知识节点,内容涵盖介子油苷生物合成途径,重要催化酶功能解析、转录因子的调控作用,组学方法的应用,利用微生物酵母进行生物物质合成,这些内容表征了合成生物的核心理论技术。     

合成生物学在微生物细胞工厂构建中的应用

通过微生物发酵的方法生产大宗化学品和天然产物能够部分替代石油化工炼制和植物提取。合成生物学技术的发展极大地提高了构建微生物细胞工厂生产大宗化学品和天然产物的能力。一方面综述了合成生物学在构建细胞工厂时的关键技术,包括最优合成途径的设计、合成途径的创建与优化、细胞性能的优化;另一方面,介绍了应用这些技术构建细胞工厂生产燃料化学品、大宗化学品和天然产物的典型案例。     

光遗传学技术在调控细菌生命活动中的应用

光遗传学技术利用光作为输入信号,能够精准地调控细胞的生理功能,同时具有高度的时间和空间特异性,使得构建高度动态的调控系统成为可能.近年来,随着新型光敏蛋白的发现和光照系统的创新,基于光遗传学技术的光控系统的效率得到了显著提高.通过合成生物学方法构造各种生物回路,光控系统在细菌中的应用也日益广泛.将光控系统作为输入模块,与其他生物功能模块相结合,能够实现对基因表达、蛋白质活性以及细菌生理功能的调控.本文主要介绍光遗传学技术的基本原理及其在合成生物学和调控细菌生命活动方面的应用.     

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.     

Recent advances in production of 5-aminolevulinic acid using biological strategies

5-Aminolevulinic acid (5-ALA) is the precursor for the biosynthesis of tetrapyrrole compounds and has broad applications in the medical and agricultural fields. Because of the disadvantages of chemical synthesis methods, microbial production of 5-ALA has drawn intensive attention and has been regarded as an alternative in the last years, especially with the rapid development of metabolic engineering and synthetic biology. In this mini-review, recent advances on the application and microbial production of 5-ALA using novel biological approaches (such as whole-cell enzymatic-transformation, metabolic pathway engineering and cell-free process) are described and discussed in detail. In addition, the challenges and prospects of synthetic biology are discussed.     

Metabolic engineering strategies for acetoin and 2,3-butanediol production: advances and prospects

Acetoin and 2,3-butanediol (2,3-BD) have a large number of industrial applications. The production of acetoin and 2,3-BD has traditionally relied on oil supplies. Microbial production of acetoin and 2,3-BD will alleviate the dependence on oil. Acetoin and 2,3-BD are neighboring metabolites in the 2,3-BD metabolic pathway of bacteria. This review summarizes metabolic engineering strategies for improvement of microbial acetoin and 2,3-BD production. We also propose enhancements to current acetoin and 2,3-BD production strategies, by offering a metabolic engineering approach that is guided by systems biology and synthetic biology.     

Engineering of microorganisms for the production of biofuels and perspectives based on systems metabolic engineering approaches

The increasing oil price and environmental concerns caused by the use of fossil fuel have renewed our interest in utilizing biomass as a sustainable resource for the production of biofuel. It is however essential to develop high performance microbes that are capable of producing biofuels with very high efficiency in order to compete with the fossil fuel. Recently, the strategies for developing microbial strains by systems metabolic engineering, which can be considered as metabolic engineering integrated with systems biology and synthetic biology, have been developed. Systems metabolic engineering allows successful development of microbes that are capable of producing several different biofuels including bioethanol, biobutanol, alkane, and biodiesel, and even hydrogen. In this review, the approaches employed to develop efficient biofuel producers by metabolic engineering and systems metabolic engineering approaches are reviewed with relevant example cases. It is expected that systems metabolic engineering will be employed as an essential strategy for the development of microbial strains for industrial applications.     

酿酒酵母代谢工程技术

自20世纪90年代初期诞生以来,代谢工程历经了30年的快速发展。作为代谢工程的首选底盘细胞之一,酿酒酵母细胞工厂已被广泛应用于大量大宗化学品和新型高附加值生物活性物质的生物制造,在能源、医药和环境等领域取得了巨大的突破。近年来,合成生物学、生物信息学以及机器学习等相关技术也极大地促进了代谢工程的技术发展和应用。文中回顾了近30年来酿酒酵母代谢工程重要的技术发展,首先总结了经典代谢工程的常用方法和策略,以及在此基础上发展而来的系统代谢工程和合成生物学驱动的代谢工程技术。最后结合最新技术发展趋势,展望了未来酿酒酵母代谢工程发展的新方向。     

Multi-enzyme systems and recombinant cells for synthesis of valuable saccharides: Advances and perspectives

Saccharides have recently attracted considerable attention because of their biological functions and potential applications in the pharmaceutical, cosmetic and food industries. Over the decades, a large amount of enzymes involved in saccharide synthesis have been discovered and characterised with the aid of available genome sequences. The advancement of metabolic engineering and synthetic biology strategies facilitated the artificial pathway design and construction for production of multiple sugars in vitro and in vivo based on those characterized enzymes. This review presented a panoramic view of enzymes related to saccharide synthesis and gave the detailed information. Furthermore, we provide an extensive overview of the recent advances in the construction of cell-free reaction systems and engineering of microbial cells for the production of natural or unnatural saccharides. In addition, the future trends in the synthesis of sugars with high structural diversity through the combination of multiple pathways are presented and evaluated.     

The path to next generation biofuels: successes and challenges in the era of synthetic biology

Volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. Recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. Metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo pathways for conversion of biomass constituents to short-chain alcohols and advanced biofuels are herewith reviewed. In the foreseeable future, formal integration of functional genomics and systems biology with synthetic biology and metabolic engineering will undoubtedly support the discovery, characterization, and engineering of new metabolic routes and more efficient microbial systems for the production of biofuels.     

人工微生物混菌系统机制解析中的组学应用及进展

人工微生物混菌系统的生物工程应用价值日益受到重视,使得对于混菌系统中成员菌间的相互作用机制研究也成为近年来的一个热点。其研究结果一方面可以为现有人工混菌系统的进一步优化提供理论依据,另一方面也为全新混菌系统的人工构建提供新的思路和策略,进而促进人工微生物混菌系统未来规模化应用。基因组学、转录组学、蛋白质组学和代谢组学等研究方法能够高通量分析各种生物分子、提供大量的数据与信息,多组学分析可以获得混菌系统中细胞的“全景”,在揭示人工微生物混菌系统中各个成员间的相互作用的研究中有着特殊的意义。文中综述了近年来多种组学技术在人工微生物混菌系统机制解析中的应用及研究进展,从代谢网络、能量代谢、信号转导、膜转运、胁迫响应、混菌系统的稳定性以及结构合理性等方面探讨混菌系统机制解析的最新进展,以期为利用合成生物学、基因组编辑等新兴生物技术改造微生物混菌系统实现其工程化应用提供理论依据。     

Synthetic Biology Toolkits for Metabolic Engineering of Cyanobacteria

Cyanobacteria are of great importance to Earth's ecology. Due to their capability in photosynthesis and C1 metabolism, they are ideal microbial chassis that can be engineered for direct conversion of carbon dioxide and solar energy into biofuels and biochemicals. Facilitated by the elucidation of the basic biology of the photoautotrophic microbes and rapid advances in synthetic biology, genetic toolkits have been developed to enable implementation of nonnatural functionalities in engineered cyanobacteria. Hence, cyanobacteria are fast becoming an emerging platform in synthetic biology and metabolic engineering. Herein, the progress made in the synthetic biology toolkits for cyanobacteria and their utilization for transforming cyanobacteria into microbial cell factories for sustainable production of biofuels and biochemicals is outlined. Current techniques in heterologous gene expression, strategies in genome editing, and development of programmable regulatory parts and modules for engineering cyanobacteria towards biochemical production are discussed and prospected. As cyanobacteria synthetic biology is still in its infancy, apart from the achievements made, the difficulties and challenges in applying and developing genetic toolkits in cyanobacteria for biochemical production are also evaluated.