合成功能菌群的构建及其工程化应用

自然界中存在着大量的天然微生物群落,不同种群的微生物通过通信及分工拓展了单菌的性能边界,降低了整体的代谢负担并增加了对环境的适应性。合成生物学依据工程设计原理构建或改造基本功能元件、基因线路和底盘细胞,从而对生命的运行过程进行具有目的性的重新编程,获得丰富及可控的生物学功能。将这种工程设计的原理引入菌群,获得结构明确及功能可调的合成群落,可以为合成功能菌群的理论研究到应用提供思路及方法。本文回顾了近年来合成功能菌群领域的相关工作,对合成功能菌群的设计原则、构建方法以及应用进行详细介绍,并对未来的发展进行了展望。     

Inhibition of acid production in Streptococcus mutans R9: Inhibition constants and reversibility

Abstract The pac gene encoding the penicillin G acylase (PGA) of Bacillus megaterium ATCC 14945 has been cloned in Escherichia coli HB101 ( proA, leuB ) using a selective minimal medium containing phenylacetyl-L-leucine instead of L-leucine. The nucleotide sequence of this gene has been determined and contains an open reading frame of 2406 nucleotides. The deduced amino acid sequence shows significant similarity with other β-lactam acylases. Although the PGA of B. megaterium is extracellular, the enzyme produced in E. coli appears to have a cytoplasmic localization.     

应用基因组工程构建新型大肠杆菌细胞工厂

基因组工程（genome engineering）是指为了实现某一目标对复制系统进行有意地、广泛地遗传修饰。大肠杆菌作为常用细胞工厂之一,在生物制造领域应用广泛,已成为合成生物学的主要研究对象。应用基因组工程改造大肠杆菌可以进一步拓展其应用范围。介绍了基因组工程最新技术发展,如基因组整合、染色体进化、多元自动化基因组工程、可寻迹多元重组工程等,及其在改造大肠杆菌提高其生产能力、稳定性及环境耐受能力等方面的研究进展。     

石油烃生物降解过程的研究进展

石油烃污染物属于难降解混合物,生物修复已经成为石油烃污染环境的主要修复方法.文中简述了微生物对石油烃的间期适应过程和转运过程,并通过对部分典型石油烃成分的微生物降解机理和代谢路径的梳理和综述,阐释了石油烃生物降解过程中的菌株、基因、代谢路径等研究进展.此外,利用基因工程和代谢工程等手段,可对野生型石油烃降解菌进行改造,...     

合成未来：从大肠杆菌的重构看合成生物学的发展

合成生物学（synthetic biology）是伴随着基因工程、系统生物学以及生物信息学的发展而出现的一个新的交叉学科。大肠杆菌（Escherichia coli）作为一种宿主在合成生物学的发展中功不可没。从某种意义上讲,合成生物学的每一次进展都离不开大肠杆菌。从大肠杆菌的角度出发,对合成生物学的发展进行深入分析,并提出了合成生物学在中圉发展的重点。     

Autonomous bacterial localization and gene expression based on nearby cell receptor density

Escherichia coli were genetically modified to enable programmed motility, sensing, and actuation based on the density of features on nearby surfaces. Then, based on calculated feature density, these cells expressed marker proteins to indicate phenotypic response. Specifically, site‐specific synthesis of bacterial quorum sensing autoinducer‐2 (AI‐2) is used to initiate and recruit motile cells. In our model system, we rewired E. coli's AI‐2 signaling pathway to direct bacteria to a squamous cancer cell line of head and neck (SCCHN), where they initiate synthesis of a reporter (drug surrogate) based on a threshold density of epidermal growth factor receptor (EGFR). This represents a new type of controller for targeted drug delivery as actuation (synthesis and delivery) depends on a receptor density marking the diseased cell. The ability to survey local surfaces and initiate gene expression based on feature density represents a new area‐based switch in synthetic biology that will find use beyond the proposed cancer model here.     

群体感应基因电路的设计与应用进展

群体感应(quorum sensing, QS)是一种细菌协调菌群行为的通信系统。自然界中广泛存在的QS系统通过对外界环境的感知来提升微生物群落生殖繁衍的能力。由于其自主感知和密度依赖的自然特性和模块化、易于工程化改造的特性在合成生物学技术的推动下,取得了快速的发展和应用。QS机制的阐明为基因回路的设计及验证和执行预期的生物功能奠定了基础。然而,如何保证QS基因回路的有效性和功能稳定性是合成生物学应用的重大挑战。因此,本综述中先对自然常见的QS调控机制和基因电路的发展进行整理,然后对其在细胞之间通信中的组装优化进行分析和概括,接着对其在群落中的应用进展进行梳理,最后对QS基因电路如何更好地应用于微生物改造提出了建议和展望。     

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.     

Expression of Escherichia coli Min system in Bacillus subtilis and its effect on cell division

In both rod-shaped Bacillus subtilis and Escherichia coli cells, Min proteins are involved in the regulation of division septa formation. In E. coli , dynamic oscillation of MinCD inhibitory complex and MinE, a topological specificity protein, prevents improper polar septation. However, in B. subtilis no MinE is present and no oscillation of Min proteins can be observed. The function of MinE is substituted by that of an unrelated DivIVA protein, which targets MinCD to division sites and retains them at the cell poles. We inspected cell division when the E. coli Min system was introduced into B. subtilis cells. Expression of these heterologous Min proteins resulted in cell elongation. We demonstrate here that E. coli MinD can partially substitute for the function of its B. subtilis protein counterpart. Moreover, E. coli MinD was observed to have similar helical localization as B. subtilis MinD.