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。     

RDX degrading microbial communities and the prediction of microorganisms responsible for RDX bioremediation

The explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has caused significant soil and groundwater contamination. To remediate these sites, there is a need to determine which microorganisms are responsible for in situ biodegradation of RDX to enable the appropriate planning of bioremediation efforts. Here, studies are examined that have reported on the microbial communities linked with RDX biodegradation. Dominant microorganisms across samples are discussed and summarized. This information is then compared to current knowledge on RDX degrading isolates to predict which organisms may be responsible for RDX degradation in soils and groundwater. From the phyla with known RDX degrading isolates, Firmicutes and Proteobacteria (particularly Gammaproteobacteria) were the most dominant organisms in many contaminated site derived samples. Organisms in the phyla Deltaproteobacteria, Alphaproteobacteria and Actinobacteria were dominant in these studies less frequently. Notably, organisms within the class Betaproteobacteria were dominant in many samples and yet this class does not appear to contain any known RDX degraders. This analysis is valuable for the future development of molecular techniques to track the occurrence and abundance of RDX degraders at contaminated sites.     

How synthetic biology can help bioremediation

The World Health Organization reported that “an estimated 12.6 million people died as a result of living or working in an unhealthy environment in 2012, nearly 1 in 4 of total global deaths”. Air, water and soil pollution were the significant risk factors, and there is an urgent need for effective remediation strategies. But tackling this problem is not easy; there are many different types of pollutants, often widely dispersed, difficult to locate and identify, and in many cases cost-effective clean-up techniques are lacking. Biology offers enormous potential as a tool to develop microbial and plant-based solutions to remediate and restore our environment. Advances in synthetic biology are unlocking this potential enabling the design of tailor-made organisms for bioremediation.In this article, we showcase examples of xenobiotic clean-up to illustrate current achievements and discuss the limitations to advancing this promising technology to make real-world improvements in the remediation of global pollution.     

微生物胞外电子传递效率的合成生物学强化

电活性微生物(产电微生物和亲电微生物)通过与外界环境进行双向电子和能量传递来实现多种微生物电催化过程(包括微生物燃料电池、微生物电解电池、微生物电催化等),从而实现在环境、能源领域的广泛应用,并为开发有效且可持续性生产新能源或大宗精细化学品的工艺提供了新机会。但是,电活性微生物的胞外电子传递效率比较低,这已经成为限制微生物电催化系统在工业应用中的主要瓶颈。以下综述了近年来利用合成生物学改造电活性微生物的相关研究成果,阐明了合成生物学如何用于打破电活性微生物胞外电子传递途径低效率的瓶颈,从而实现电活性微生物与环境的高效电子传递和能量交换,推动电活性微生物电催化系统的实用化进程。     

Effect of petrochemical sludge concentrations on microbial communities during soil bioremediation

Qualitative and quantitative changes of microbial communities in soil microcosms during bioremediation were determined throughout one year. The soil was contaminated with 0%, 2.5%, 5%, 10% (wt/wt) of petrochemical sludge containing polynuclear aromatic hydrocarbons. We analyzed the hydrocarbon concentration in the microcosms, the number of cultivable bacteria using CFU and most probable number assays, the community structure using denaturing gradient gel electrophoresis, and the metabolic activity of soil using dehydrogenase activity and substrate-induced respiration assays. After one year of treatment, the chemical analysis suggested that the hydrocarbon elimination process was over. The biological analysis, however, showed that the contaminated microcosms suffered under long-term disturbance. The number of heterotrophic bacteria that increased after sludge addition (up to 10(8)-10(9) cells ml(-1)) has not returned to the level of the control soil (2-6 x 10(7) cells ml(-1)). The community structure in the contaminated soils differed considerably from that in the control. The substrate-induced respiration of the contaminated soils was significantly lower (approximately 10-fold) and the dehydrogenase activity was significantly higher (20-40-fold) compared to the control. Changes in the community structure of soils depended on the amount of added sludge. The species, which were predominant in the sludge community, could not be detected in the contaminated soils.     

Development of GRAS strains for nutraceutical production using systems and synthetic biology approaches: advances and prospects

Nutraceuticals are food substances with medical and health benefits for humans. Limited by complicated procedures, high cost, low yield, insufficient raw materials, resource waste, and environment pollution, chemical synthesis and extraction are being replaced by microbial synthesis of nutraceuticals. Many microbial strains that are generally regarded as safe (GRAS) have been identified and developed for the synthesis of nutraceuticals, and significant nutraceutical production by these strains has been achieved. In this review, we systematically summarize recent advances in nutraceutical research in terms of physiological effects on health, potential applications, drawbacks of traditional production processes, characteristics of production strains, and progress in microbial fermentation. Recent advances in systems and synthetic biology techniques have enabled comprehensive understanding of GRAS strains and its wider applications. Thus, these microbial strains are promising cell factories for the commercial production of nutraceuticals.     

Combating biotic stresses in plants by synthetic microbial communities: Principles,applications and challenges

Presently, agriculture worldwide is facing the major challenge of feeding the increasing population sustainably. The conventional practices have not only failed to meet the projected needs, but also led to tremendous environmental consequences. Hence, to ensure a food-secure and environmentally sound future, the major thrust is on sustainable alternatives. Due to challenges associated with conventional means of application of biocontrol agents in the management of biotic stresses in agroecosystems, significant transformations in this context are needed. The crucial role played by soil microbiome in efficiently and sustainably managing the agricultural production has unfolded a newer approach of rhizosphere engineering that shows immense promise in mitigating biotic stresses in an eco-friendly manner. The strategy of generating synthetic microbial communities (SynComs), by integrating omics approaches with traditional techniques of enumeration and in-depth analysis of plant–microbe interactions, is encouraging. The review discusses the significance of the rhizospheric microbiome in plant's fitness, and its manipulation for enhancing plant attributes. The focus of the review is to critically analyse the potential tools for the design and utilization of SynComs as a sustainable approach for rhizosphere engineering to ameliorate biotic stresses in plants. Furthermore, based on the synthesis of reports in the area, we have put forth possible solutions to some of the critical issues that impair the large-scale application of SynComs in agriculture.     

代谢工程发展30年

代谢工程学科建立30年以来先后与分子生物学、系统生物学和合成生物学发生深度的交叉融合,并在此基础上获得了飞速发展,极大地促进了生物技术产业的进步和升级.文中首先基于SCI论文发表情况对30年来代谢工程学术研究现状和我国在该领域的地位和影响力进行了分析,随后总结了近10年来系统生物学方法和合成生物学的主要使能技术在代谢工...     

A day of systems and synthetic biology for non‐experts

From understanding ageing to the creation of artificial membrane‐bounded ‘organisms’, systems biology and synthetic biology are seen as the latest revolutions in the life sciences. They certainly represent a major change of gear, but paradigm shifts? This is open to debate, to say the least. For scientists they open up exciting ways of studying living systems, of formulating the ‘laws of life’, and the relationship between the origin of life, evolution and artificial biological systems. However, the ethical and societal considerations are probably indistinguishable from those of human genetics and genetically modified organisms. There are some tangible developments just around the corner for society, and as ever, our ability to understand the consequences of, and manage, our own progress lags far behind our technological abilities. Furthermore our educational systems are doing a bad job of preparing the next generation of scientists and non‐scientists.     

Deciphering microbial interactions in synthetic human gut microbiome communities

The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model‐guided framework to predict higher‐dimensional consortia from time‐resolved measurements of lower‐order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi‐species community dynamics, as opposed to higher‐order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history‐dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human‐associated intestinal species and illuminated design principles of microbial communities.     

A synthetic Escherichia coli predator–prey ecosystem

We have constructed a synthetic ecosystem consisting of two Escherichia coli populations, which communicate bi‐directionally through quorum sensing and regulate each other's gene expression and survival via engineered gene circuits. Our synthetic ecosystem resembles canonical predator–prey systems in terms of logic and dynamics. The predator cells kill the prey by inducing expression of a killer protein in the prey, while the prey rescue the predators by eliciting expression of an antidote protein in the predator. Extinction, coexistence and oscillatory dynamics of the predator and prey populations are possible depending on the operating conditions as experimentally validated by long‐term culturing of the system in microchemostats. A simple mathematical model is developed to capture these system dynamics. Coherent interplay between experiments and mathematical analysis enables exploration of the dynamics of interacting populations in a predictable manner.     

Bioremediation of phenol by a novel partitioning bioreactor using cow dung microbial consortia

A bioreactor has been designed and developed for partitioning of aqueous and organic phases with a provision for aeration and stirring, a cooling system and a sampling port. The potential of a cow dung microbial consortium has been assessed for bioremediation of phenol in a single-phase bioreactor and a two-phase partitioning bioreactor. The advantages of the two-phase partitioning bioreactor are discussed. The Pseudomonas putida IFO 14671 has been isolated, cultured and identified from the cow dung microbial consortium as a high-potential phenol degrader. The methods developed in this study present an advance in bioremediation techniques for the biodegradation of organic compounds such as phenol using a bioreactor. We have also demonstrated the potential of microorganisms from cow dung as a source of biomass.     

微生物药物产量理性化提高的策略及其研究进展

微生物药物(Microbial drug)是一类结构复杂多样,生物活性显著的小分子化合物。微生物药物产量决定了其后续的可开发性与使用成本。传统育种方法提高微生物药物产量效果明显,但随机性强且成本高昂,然而合成生物学的兴起为微生物药物产量理性化提高注入了全新活力。本文从启动子的工程化应用、前体供应、基因组重排等方面,综述了近年来合成生物学策略在放线菌来源的微生物药物产量理性化提高方面所取得的相关研究进展。     

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。     

Integrating computational methods to retrofit enzymes to synthetic pathways

Microbial production of desired compounds provides an efficient framework for the development of renewable energy resources. To be competitive to traditional chemistry, one requirement is to utilize the full capacity of the microorganism to produce target compounds with high yields and turnover rates. We use integrated computational methods to generate and quantify the performance of novel biosynthetic routes that contain highly optimized catalysts. Engineering a novel reaction pathway entails addressing feasibility on multiple levels, which involves handling the complexity of large-scale biochemical networks while respecting the critical chemical phenomena at the atomistic scale. To pursue this multi-layer challenge, our strategy merges knowledge-based metabolic engineering methods with computational chemistry methods. By bridging multiple disciplines, we provide an integral computational framework that could accelerate the discovery and implementation of novel biosynthetic production routes. Using this approach, we have identified and optimized a novel biosynthetic route for the production of 3HP from pyruvate.     

pime: A package for discovery of novel differences among microbial communities

The data used for profiling microbial communities is usually sparse with some microbes having high abundance in a few samples and being nearly absent in others. However, current bioinformatics tools able to deal with this sparsity are lacking. pime (Prevalence Interval for Microbiome Evaluation) was designed to remove those taxa that may be high in relative abundance in just a few samples but have a low prevalence overall. The reliability and robustness of pime were compared against existing methods and tested using 16S rRNA independent data sets. pime filters microbial taxa not shared in a per treatment prevalence interval started at 5% prevalence with increasing increments of 5% at each filtering step. For each prevalence interval, hundreds of decision trees were calculated to predict the likelihood of detecting differences in treatments. The best prevalence‐filtered data set was user‐selected by choosing the prevalence interval that kept a large portion of the 16S rRNA sequences in the data set while also showing the lowest error rate. To obtain the likelihood of introducing type I error while building prevalence‐filtered data sets, an error detection step based was also included. A pime reanalysis of published data sets uncovered other expected microbial associations than previously reported, which may be masked when only relative abundance was considered.     

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...     

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。