基于工业环境扰动的微生物适应性进化

合成生物学技术的快速发展极大提升了微生物细胞工厂的构建能力,为化学品的绿色高效生产提供了重要策略。然而,微生物细胞难以耐受高强度工业环境、抗逆性差,成为了限制其生产性能的关键因素。适应性进化是一种人为施加定向选择压力,使微生物经过长期或短期驯化,获得适应特定环境的表型或生理性能的重要方法。近年来,随着微流控、生物传感器、组学分析等技术的发展,适应性进化为提升微生物细胞在工业环境下的生产性能奠定了基础。本文论述了适应性进化的关键技术及在提高微生物细胞工厂环境耐受性和生产效率方面的重要应用,并展望了适应性进化实现微生物细胞工厂在工业环境下高效运行的重要前景。     

非天然氨基酸细胞工厂的构建与应用

非天然氨基酸在医药、农药、材料等领域得到广泛应用,其绿色、高效合成越来越受到关注.近年来,随着合成生物学的快速发展,微生物细胞工厂为非天然氨基酸的制造提供了重要手段.文中从合成途径的重构、关键酶的设计改造及与前体的协同调控、竞争性旁路途径的敲除、辅因子循环系统的构建等方面介绍了 一系列非天然氨基酸细胞工厂构建与应用的研...     

细胞寿命在大肠杆菌细胞工厂构建中的应用

微生物细胞工厂以可再生资源为原料,为工业化学品的可持续生产提供了一种有前景的替代方案.然而,不适的外界环境显著影响了微生物细胞的存活率,降低了微生物细胞工厂的生产性能.通过延长微生物细胞的时序寿命,可以显著提升微生物细胞工厂的生产性能.首先,基于存活率的变化建立了细胞时序寿命和半时序寿命的评价体系;然后,发现半胱氨酸、...     

Protein structure modeling in the proteomics era

Structural proteomics aims to understand the structural basis of protein interactions and functions. A prerequisite for this is the availability of 3D protein structures that mediate the biochemical interactions. The explosion in the number of available gene sequences set the stage for the next step in genome-scale projects -- to obtain 3D structures for each protein. To achieve this ambitious goal, the slow and costly structure determination experiments are supplemented with theoretical approaches. The current state and recent advances in structure modeling approaches are reviewed here, with special emphasis on comparative protein structure modeling techniques.     

Protein structure modeling in the proteomics era

Structural proteomics aims to understand the structural basis of protein interactions and functions. A prerequisite for this is the availability of 3D protein structures that mediate the biochemical interactions. The explosion in the number of available gene sequences set the stage for the next step in genome-scale projects – to obtain 3D structures for each protein. To achieve this ambitious goal, the slow and costly structure determination experiments are supplemented with theoretical approaches. The current state and recent advances in structure modeling approaches are reviewed here, with special emphasis on comparative protein structure modeling techniques.     

酿酒酵母中胆固醇生物合成与优化的研究进展

胆固醇是动物体内积累的主要甾醇化合物,在维持细胞膜功能、合成甾体激素、生产甾体药物中间体等方面具有重要的生物学意义和医学应用价值。传统动物组织提取胆固醇的方法费时费力并存在严重的环境污染问题,而甾醇分子结构的复杂程度也限制了其化学全合成。近些年,人们利用合成生物学方法构建的微生物细胞工厂已成功用于萜类、甾醇类等天然产物的开发与合成。文中综述了胆固醇微生物细胞工厂的研究进展,包括胆固醇生物合成途径的解析、底盘菌株的选择、异源基因元件的挖掘与优化、相关代谢通路的调控等方面,并讨论了当前研究面临的问题,以期为胆固醇的高效生物合成提供参考。     

MMM: a sequence-to-structure alignment protocol

MOTIVATION: Accurate alignment of a target sequence to a template structure continues to be a bottleneck in producing good quality comparative protein structure models. RESULTS: Multiple Mapping Method (MMM) is a comparative protein structure modeling server with an emphasis on a novel alignment optimization protocol. MMM takes inputs from five profile-to-profile based alignment methods. The alternatively aligned regions from the input alignment set are combined according to their fit in the structural environment of the template structure. The resulting, optimally spliced MMM alignment is used as input to an automated comparative modeling module to produce a full atom model. AVAILABILITY: The MMM server is freely accessible at http://www.fiserlab.org/servers/mmm     

2014工业生物技术专刊序言

工业生物技术是解决人类目前面临的资源、能源及环境危机的有效手段。本期专刊结合第七届中国工业生物技术发展高峰论坛,报道了我国工业生物技术领域专家学者在生物信息学、微生物细胞工厂的模拟设计与构建、工业发酵工程、工业酶的改造与应用、高通量筛选方法等领域取得的最新研究进展。     

化学品生物合成专刊序言

以酶及微生物细胞催化剂结合工程学方法将廉价、废弃原料进行高效生物转化可实现化学品的可持续生产。近年来,合成生物学、系统生物学及酶工程等技术的快速发展大大推动了化学品的可持续生物制造,既实现了多种新型化学品的生物合成,又显著提高化学品的生物合成效率。为展示化学品生物合成的最新进展并促进绿色生物制造的发展,《生物工程学报》特组织出版化学品生物合成专刊,从酶催化与生物合成机制、微生物细胞合成、一碳生物炼制以及关键核心技术等方面,介绍化学品生物合成的最新前沿、挑战以及潜在解决方案。     

合成芳香族化合物的酵母底盘改造策略*

芳香族化合物种类丰富,在多个行业具有广泛的用途,需求量大。通过构建微生物细胞工厂合成芳香族化合物具有独特的优势和工业化应用前景,其中酵母底盘因其清晰的遗传背景、完善的基因操作工具以及成熟的工业发酵体系等优势,常被用于构建细胞工厂。目前改造酵母底盘生产芳香族化合物的研究取得了一系列进展,并针对关键问题提出了一些可行的解决策略。针对酵母合成芳香族化合物的策略与挑战,从芳香族化合物合成路径改造、多样化碳源利用及转运系统改造、基因组多靶点改造、特殊酵母底盘及混菌系统构建、合成生物学高通量技术的应用这五个方面进行系统地梳理和阐述,为生产芳香族化合物的酵母底盘构建与改造提供思路。     

Protein folding and conformational stress in microbial cells producing recombinant proteins: a host comparative overview

Different species of microorganisms including yeasts, filamentous fungi and bacteria have been used in the past 25 years for the controlled production of foreign proteins of scientific, pharmacological or industrial interest. A major obstacle for protein production processes and a limit to overall success has been the abundance of misfolded polypeptides, which fail to reach their native conformation. The presence of misfolded or folding-reluctant protein species causes considerable stress in host cells. The characterization of such adverse conditions and the elicited cell responses have permitted to better understand the physiology and molecular biology of conformational stress. Therefore, microbial cell factories for recombinant protein production are depicted here as a source of knowledge that has considerably helped to picture the extremely rich landscape of in vivo protein folding, and the main cellular players of this complex process are described for the most important cell factories used for biotechnological purposes.     

Recent advances in domesticating non-model microorganisms

Non-model microorganisms have been increasingly explored as microbial cell factories for production of chemicals, fuels, and materials owing to their unique physiology and metabolic capabilities. However, these microorganisms often lack facile genetic tools for strain development, which hinders their adoption as production hosts. In this review, we describe recent advances in domestication of non-model microorganisms, including bacteria, actinobacteria, cyanobacteria, yeast, and fungi, with a focus on the development of genetic tools. In addition, we highlight some successful applications of non-model microorganisms as microbial cell factories.     

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。     

Metabolomics assisted metabolic network modeling and network wide analysis of metabolites in microbiology

Metabolomics is the science of qualitatively and quantitatively analyzing low molecular weight metabolites occur in a given biological system. It provides valuable information to elucidate the functional roles and relations of different metabolites in a metabolic pathway. In recent years, a large amount of research on microbial metabolomics has been conducted. It has become a useful tool for achieving highly efficient synthesis of target metabolites. At the same time, many studies have been conducted over the years in order to integrate metabolomics data into metabolic network modeling, which has yielded many exciting results. Additionally, metabolomics also shows great advantages in analyzing the relationship of metabolites network wide. Integrating metabolomics data into metabolic network construction and applying it in network wide analysis of cell metabolism would further improve our ability to control cellular metabolism and optimize the design of cell factories for the overproduction of valuable biochemicals. This review will examine recent progress in the application of metabolomics approaches in metabolic network modeling and network wide analysis of microbial cell metabolism.     

High efficient production of plant flavonoids by microbial cell factories: Challenges and opportunities

Plant flavonoids are secondary metabolites containing a benzo-γ-pyrone structure, which are widely present in plants and have a variety of physiological and pharmacological activities. However, current flavonoid production from plant extraction or chemical synthesis does not meet the requirements of green and sustainable development. Fortunately, microbial synthesis of flavonoids has shown the potential for large-scale production with the advantages of being controllable and environmentally friendly, and a variety of microorganisms have been developed as microbial cell factories (MCFs) to synthesize plant flavonoids owing to the feasibility of genetic manipulations. However, most of MCFs have not yet been commercialized and industrialized because of the challenges posed by unbalanced metabolic flux among various pathways and conflict between cell growth and production. Here, strategies for coping with the challenges are summarized in terms of enzymes, pathways, metabolic networks, host cells. And combined with protein structure prediction, de novo protein design, artificial intelligence (AI), biocatalytic retrosynthesis, and intelligent stress resistance, it provides new insights for the high efficient production of plant flavonoids and other plant natural products in MCFs.     

MODBASE, a database of annotated comparative protein structure models

MODBASE is a queryable database of annotated comparative protein structure models. The models are derived by MODPIPE, an automated modeling pipeline relying on the programs PSI-BLAST and MODELLER. The database currently contains 3D models for substantial portions of approximately 17 000 proteins from 10 complete genomes, including those of Caenorhabditis elegans, Saccharomyces cerevisiae and Escherichia coli, as well as all the available sequences from Arabidopsis thaliana and Homo sapiens. The database also includes fold assignments and alignments on which the models were based. In addition, special care is taken to assess the quality of the models. ModBase is accessible through a web interface at http://guitar.rockefeller.edu/modbase/     

Nanotechnology,bionanotechnology and microbial cell factories

Nanotechnology is increasingly using both materials and nano-objects synthesized by living beings, most of them produced by microbial cells. Emerging technologies and highly integrative approaches (such as 'omics and systems biology), that have been largely proven successful for the production of proteins and secondary metabolites are now expected to become fully adapted for the improved biological production of nanostructured materials with tailored properties. The so far underestimated potential of microbial cell factories in nanotechnology and nanomedicine is expected to emerge, in the next years, in the context of novel needs envisaged in the nanoscience universe. This should prompt a careful revisiting of the microbial cell factories as the most versatile biological platforms to supply functional materials for nanotechnological applications.     

Developing Bacillus spp. as a cell factory for production of microbial enzymes and industrially important biochemicals in the context of systems and synthetic biology

Increasing concerns over limited petroleum resources and associated environmental problems are motivating the development of efficient cell factories to produce chemicals, fuels, and materials from renewable resources in an environmentally sustainable economical manner. Bacillus spp., the best characterized Gram-positive bacteria, possesses unique advantages as a host for producing microbial enzymes and industrially important biochemicals. With appropriate modifications to heterologous protein expression and metabolic engineering, Bacillus species are favorable industrial candidates for efficiently converting renewable resources to microbial enzymes, fine chemicals, bulk chemicals, and fuels. Here, we summarize the recent advances in developing Bacillus spp. as a cell factory. We review the available genetic tools, engineering strategies, genome sequence, genome-scale structure models, proteome, and secretion pathways, and we list successful examples of enzymes and industrially important biochemicals produced by Bacillus spp. Furthermore, we highlight the limitations and challenges in developing Bacillus spp. as a robust and efficient production host, and we discuss in the context of systems and synthetic biology the emerging opportunities and future research prospects in developing Bacillus spp. as a microbial cell factory.     

Metabolic engineering for the utilization of carbohydrate portions of lignocellulosic biomass

The petrochemical industry has grown to meet the need for massive production of energy and commodities along with an explosive population growth; however, serious side effects such as greenhouse gas emissions and global warming have negatively impacted the environment. Lignocellulosic biomass with myriad quantities on Earth is an attractive resource for the production of carbon-neutral fuels and chemicals through environmentally friendly processes of microbial fermentation. This review discusses metabolic engineering efforts to achieve economically feasible industrial production of fuels and chemicals from microbial cell factories using the carbohydrate portion of lignocellulosic biomass as substrates. The combined knowledge of systems biology and metabolic engineering has been applied to construct robust platform microorganisms with maximum conversion of monomeric sugars, such as glucose and xylose, derived from lignocellulosic biomass. By comprehensively revisiting carbon conversion pathways, we provide a rationale for engineering strategies, as well as their features, feasibility, and recent representative studies. In addition, we briefly discuss how tools in systems biology can be applied in the field of metabolic engineering to accelerate the development of microbial cell factories that convert lignocellulosic biomass into carbon-neutral fuels and chemicals with economic feasibility.     

基于糖原代谢调控的蓝细菌光合细胞工厂优化研究进展

蓝细菌是重要的光合自养微生物,也是最具潜力的光合微生物底盘之一,被广泛应用于光驱固碳细胞工厂的开发.糖原是蓝细菌最重要的天然碳汇物质,糖原代谢对蓝细菌光合碳流的分配和调控具有重要意义.为了优化蓝细菌光合细胞工厂的合成效能,驱动更多的光合碳流重定向至目标代谢产物的合成,已经有多种策略和方法被成功开发用于调控蓝细菌的糖原代...