Design of a bacterial consortium for consolidated bioprocessing

PI：Schmidt-Dannert，Claudia Proposal Number：1235714机构：明尼苏达大学双子城分校标题：设计用于整合生物处理的细菌联合体生物技术生物过程通常使用代谢工程微生物菌株的纯培养。相比之下，环境过程通常利用本地微生物群体中存在的新陈代谢多样性来完成不是一个单一有机体单独完成的任务。开发用于生物燃料生产的综合生物工艺，其中将顽固的木质纤维生物质的水解和随后的糖转化为生物燃料相结合，这一追求重新推动了对混合培养物使用的研究。目前，人们正在寻求不同的策略来获得既能分解木质纤维又能产生先进生物燃料的菌株，但到目前为止，没有一种工程菌株在这两项任务上都是有效的。在合成生物学领域应用的具有新出现特性的生物网络工程为设计和研究合成微生物联合体提供了工具和策略。通过将代谢功能划分为单独的微生物种群，每个菌株的代谢网络可以针对不同的任务进行优化，这些任务共同导致所需化合物的生产。因此，在生物过程中共培养的不同工程微生物菌株可以被认为是单独的代谢模块，可以与其他模块交换或增强。然而，这种混合微生物群落工程的先决条件是建立种群控制系统。这个项目将设计一个原型合成微生物群落，作为合并生物处理的概念验证。建议的研究结果可以指导使用工程微生物联合体的其他生物过程的开发。具体地说，该项目将设计一种由枯草杆菌、暗色红球菌和大肠杆菌组成的混合培养物用于从头生产生物柴油。工业蛋白表达宿主B.subtilis将被改造成分泌纤维素分解酶以从生物质中释放糖，而含油的不透明红假单胞菌和产乙醇性大肠杆菌菌株一起将糖转化为脂肪酸乙酯(生物柴油)。发展这样一个联合体的关键是设计和配置适当的系统，以根据进程的要求控制每个联合体成员的增长。该项目将使用细菌群体感应系统的组件来设计这样的种群控制系统。将建立一个系统仿真模型来指导我们设计这些控制系统，该项目将为生物处理工程微生物联合体的开发和应用提供一个概念验证。因此，生物技术混合培养的使用可能会重新焕发生机，并从DNA前技术转移到合成生物学领域。这项申请的结果将为人口控制系统的设计提供洞察力和模型，该系统需要根据特定过程的要求调整人口规模。这项拟议的研究将影响生物技术和合成生物学领域。这项研究的结果可能会导致生物燃料生产和其他生物生产过程的新的、更有效的方法。拟议的研究将为一名博士后研究员和四名本科生提供基因和代谢工程方面的培训。

PI: Schmidt-Dannert, ClaudiaProposal Number: 1235714Institution: University of Minnesota-Twin CitiesTitle: Design of a bacterial consortium for consolidated bioprocessingBiotechnological bioprocesses typically use pure cultures of metabolically engineered microbial strains. In contrast, environmental processes generally utilize the metabolic diversity present in native microbial consortia to accomplish tasks that not one single organism can do alone. The quest for the development of consolidated bioprocesses for biofuel production, where hydrolysis of recalcitrant lignocellulosic biomass and subsequent sugar conversion into biofuels are combined, has reinvigorated investigations into the use of mixed cultures. Currently different strategies are being pursued to obtain strains that are both lignocellulolytic and advanced biofuel producers, but so far none of the engineered strains is efficient at both tasks.The engineering of biological networks with new emergent properties employed in the field of synthetic biology has provided tools and strategies with which it becomes possible to design and investigate synthetic microbial consortia. By compartmentalizing metabolic functions into separate microbial populations, the metabolic network of each strain can be optimized for distinct tasks that together result in the production of a desired compound. The different engineered microbial strains co-cultured in a bioprocess can therefore be considered as individual metabolic modules that may be exchanged or augmented with additional modules. Prerequisite for the engineering of such mixed microbial communities, however, is the establishment of population control systems.This project will design a prototype synthetic microbial community as a proof-of-concept for consolidated bioprocessing. Results from the proposed research can guide the development of other bioprocesses using engineered microbial consortia. Specifically, this project will engineer a mixed culture consisting of B. subtilis, Rhodococcus opacus and E. coli for de novo biodiesel production. The industrial protein expression host B. subtilis will be engineered to secrete cellulolytic enzymes for sugar release from biomass, while the oleaginous R. opacus and the ethanologenic E. coli strain together will convert sugars into fatty acid ethyl esters (biodiesel). Key to the development of such a consortium is the engineering and configuration of adequate systems to control growth of each consortium member in accordance to the requirements of the process. The project will design such population control systems using components of bacterial quorum sensing systems. A system simulation model will be built to guide us in the design these control systems.The project will provide a proof-of-concept for the development and application of engineered microbial consortia for bioprocessing. The use of mixed cultures for biotechnology may thus be revitalized and moved from the pre-DNA technology into the synthetic biology area. Results from this application will provide insights and a model for the design of population control systems needed to adjust population sizes to the requirements of a specific process. The proposed research will impact the field of biotechnology and synthetic biology. Findings of this research may lead to new and more efficient approaches for biofuel production and other bioproduction processes. The proposed research will provide training in genetic and metabolic engineering for one postdoctoral researcher and four undergraduate students.