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。     

代谢工程发展20年

代谢工程从上世纪90年代初期发展至今已有20年历史,对微生物发酵工业的发展起到了极大的推动作用。以下回顾了代谢工程发展至今的三个重要阶段,讨论了各阶段中代谢工程在技术方面的进展及其对微生物发酵工业的促进作用。最后还讨论了代谢工程将来发展中的关键问题及解决策略。     

《生物工程学报》2010年“代谢工程”专刊征稿通知

<正>代谢工程自1991年诞生以来,在改造植物、动物、微生物的代谢功能方面得到了广泛的应用。为了展现代谢工程科研工作者取得的最新进展,促进我国代谢工程研究的进步和发展,本刊2009年第9期设立了"代谢工程与细胞工厂"专栏,国内该领域著名学者对代谢工程的技术发展进行了总结,介绍了合成生物学等新理论和新技术,并发表了     

历久弥新：进化中的代谢工程

20世纪90年代,Bailey及Stephanopoulos等提出了经典代谢工程的理念,旨在利用DNA重组技术对代谢网络进行改造,以达到细胞性能改善,目标产物增加的目的。自代谢工程诞生以来的30年,生命科学蓬勃发展,基因组学、系统生物学、合成生物学等新学科不断涌现,为代谢工程的发展注入了新的内涵与活力。经典代谢工程研究已进入到前所未有的系统代谢工程阶段。组学技术、基因组代谢模型、元件组装、回路设计、动态控制、基因组编辑等合成生物学工具与策略的应用,大大提升了复杂代谢的设计与合成能力;机器学习的介入以及进化工程与代谢工程的结合,为系统代谢工程的未来开辟了新的方向。文中对过去30年代谢工程的发展趋势作了梳理,介绍了代谢工程在发展中不断创新的理论与方法及其应用。     

《生物工程学报》2010年“代谢工程”专刊征稿通知

<正>代谢工程自1991年诞生以来,在改造植物、动物、微生物的代谢功能方面得到了广泛的应用。为了展现代谢工程科研工作者取得的最新进展,促进我国代谢工程研究的进步和发展,本刊2009年第9期设立了"代谢工程与细胞工厂"专栏,国内     

氨基酸生产的代谢工程研究进展与发展趋势

氨基酸发酵是我国发酵工业的支柱产业,近年来,随着代谢工程的快速发展,氨基酸的代谢工程育种蓬勃发展。传统的正向代谢工程、基于组学分析与计算机模拟的反向代谢工程以及借鉴自然进化的进化代谢工程,都有越来越多的应用。在氨基酸的工业生产中涌现出了一系列具有高效生产、抗逆性强等优良性状的菌株。日益剧烈的市场竞争对菌株的选育提出了新的要求,如开发高附加值氨基酸品种、菌株代谢的动态调控、适应新工艺的要求等。文中介绍了氨基酸生产相关的代谢工程研究进展以及未来的发展趋势。     

逆代谢工程——基于有用表型的定向遗传工程策略

代谢工程分为推理性代谢工程和逆代谢工程,逆代谢工程是避开对代谢网络充分认识的一种全新的遗传工程。本简要介绍了逆代谢工程的策略,并以实例详细分析了逆代谢工程的具体应用,最后,分析了逆代谢工程的问题和发展前景。     

代谢工程及其在产苯丙氨酸基因工程菌构建中的应用

本文对代谢工程的发展状况从研究方法,在医药、农业及环保中应用等几方面做了概括地介绍;从宿主的选择,加速限速反应,改变代谢流和生产程序的优化几方面较为详细地评述了代谢工程在苯丙氨酸基因工程菌构建方面的应用,并对代谢工程的未来发展进行了展望。     

基因组尺度分析和代谢工程策略

代谢工程是近年来发展起来的新技术,随着各种组学技术的发展,高通量数据整合方法用于分析细胞的代谢网络,改造代谢途径,以提高目标产物的产量。本文就代谢工程的发展状况,基因组尺度的分析技术,以及代谢工程策略进行了综述。分析了生物信息学和系统生物学方法在代谢途径构建和代谢网络分析中的作用,并就存在的问题和可能的解决途径进行了阐述。     

《生物工程学报》2010年“代谢工程”专刊征稿通知

<正>代谢工程自1991年诞生以来,在改造植物、动物、微生物的代谢功能方面得到了广泛的应用。为了展现代谢工程科研工作者取得的最新进展,促进我国代谢工程研究的进步和发展,本刊2009年第9期设立了"代谢工     

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.     

Mapping phenotypic landscapes using DNA micro-arrays

Inverse metabolic engineering is a useful approach for engineering phenotypes in biological systems. The overarching objective of this approach is to combine the power of evolutionary engineering approaches with the precision of constructive metabolic engineering strategies. Often the difficulty in this approach is elucidating the genetic basis of the phenotypes that emerge as a result of evolutionary mechanisms. As a result of advances in genomics technologies, several techniques now exist that substantially improve researchers ability to identify such genes. Metabolic engineers now have the ability to map phenotypic landscapes of considerable genetic diversity, which should improve understanding of the relationships that exist among phenotype, genotype, and environment. In this mini-review, we will discuss several of such genomics tools that may be useful in developing inverse metabolic engineering strategies and, in particular, mapping phenotypic landscapes.     

Towards systems metabolic engineering of microorganisms for amino acid production

Microorganisms capable of efficient production of amino acids have traditionally been developed by random mutation and selection method, which might cause unwanted physiological changes in cellular metabolism. Rational genome-wide metabolic engineering based on systems and synthetic biology tools, which is termed 'systems metabolic engineering', is rising as an alternative to overcome these problems. Recently, several amino acid producers have been successfully developed by systems metabolic engineering, where the metabolic engineering procedures were performed within a systems biology framework, and entire metabolic networks, including complex regulatory circuits, were engineered in an integrated manner. Here we review the current status of systems metabolic engineering successfully applied for developing amino acid producing strains and discuss future prospects.     

Dynamic control in metabolic engineering: Theories,tools, and applications

Metabolic engineering has allowed the production of a diverse number of valuable chemicals using microbial organisms. Many biological challenges for improving bio-production exist which limit performance and slow the commercialization of metabolically engineered systems. Dynamic metabolic engineering is a rapidly developing field that seeks to address these challenges through the design of genetically encoded metabolic control systems which allow cells to autonomously adjust their flux in response to their external and internal metabolic state. This review first discusses theoretical works which provide mechanistic insights and design choices for dynamic control systems including two-stage, continuous, and population behavior control strategies. Next, we summarize molecular mechanisms for various sensors and actuators which enable dynamic metabolic control in microbial systems. Finally, important applications of dynamic control to the production of several metabolite products are highlighted, including fatty acids, aromatics, and terpene compounds. Altogether, this review provides a comprehensive overview of the progress, advances, and prospects in the design of dynamic control systems for improved titer, rate, and yield metrics in metabolic engineering.     

Fermentative production of branched chain amino acids: a focus on metabolic engineering

The branched chain amino acids (BCAAs), l-valine, l-leucine, and l-isoleucine, have recently been attracting much attention as their potential to be applied in various fields, including animal feed additive, cosmetics, and pharmaceuticals, increased. Strategies for developing microbial strains efficiently producing BCAAs are now in transition toward systems metabolic engineering from random mutagenesis. The metabolism and regulatory circuits of BCAA biosynthesis need to be thoroughly understood for designing system-wide metabolic engineering strategies. Here we review the current knowledge on BCAAs including their biosynthetic pathways, regulations, and export and transport systems. Recent advances in the development of BCAA production strains are also reviewed with a particular focus on l-valine production strain. At the end, the general strategies for developing BCAA overproducers by systems metabolic engineering are suggested.     

后基因组时代的工业生物技术

简述了工业生物技术的发展背景和意义,分析了基因组学和功能基因组学发展对工业生物技术的推动作用,重点介绍了本期专刊发表的代谢工程、发酵工程以及工业酶与生物催化领域的17篇论文。     

Metabolic pathways and fermentative production of L-aspartate family amino acids

The L -aspartate family amino acids (AFAAs), L -threonine, L -lysine, L -methionine and L -isoleucine have recently been of much interest due to their wide spectrum of applications including food additives, components of cosmetics and therapeutic agents, and animal feed additives. Among them, L -threonine, L -lysine and L -methionine are three major amino acids produced currently throughout the world. Recent advances in systems metabolic engineering, which combine various high-throughput omics technologies and computational analysis, are now facilitating development of microbial strains efficiently producing AFAAs. Thus, a thorough understanding of the metabolic and regulatory mechanisms of the biosynthesis of these amino acids is urgently needed for designing system-wide metabolic engineering strategies. Here we review the details of AFAA biosynthetic pathways, regulations involved, and export and transport systems, and provide general strategies for successful metabolic engineering along with relevant examples. Finally, perspectives of systems metabolic engineering for developing AFAA overproducers are suggested with selected exemplary studies.     

A systems-level approach for metabolic engineering of yeast cell factories

The generation of novel yeast cell factories for production of high-value industrial biotechnological products relies on three metabolic engineering principles: design, construction, and analysis. In the last two decades, strong efforts have been put on developing faster and more efficient strategies and/or technologies for each one of these principles. For design and construction, three major strategies are described in this review: (1) rational metabolic engineering; (2) inverse metabolic engineering; and (3) evolutionary strategies. Independent of the selected strategy, the process of designing yeast strains involves five decision points: (1) choice of product, (2) choice of chassis, (3) identification of target genes, (4) regulating the expression level of target genes, and (5) network balancing of the target genes. At the construction level, several molecular biology tools have been developed through the concept of synthetic biology and applied for the generation of novel, engineered yeast strains. For comprehensive and quantitative analysis of constructed strains, systems biology tools are commonly used and using a multi-omics approach. Key information about the biological system can be revealed, for example, identification of genetic regulatory mechanisms and competitive pathways, thereby assisting the in silico design of metabolic engineering strategies for improving strain performance. Examples on how systems and synthetic biology brought yeast metabolic engineering closer to industrial biotechnology are described in this review, and these examples should demonstrate the potential of a systems-level approach for fast and efficient generation of yeast cell factories.