ERASynBio: Intensification of the Synthetic Biology Design Cycle

该ERASynBio欧盟-美国合作项目由美国国家科学基金会生物/MCB系统和合成生物学项目以及ENG/CBET生物技术、生化和生物质工程项目共同资助。该项目解决了合成生物学的一个基本需求，即如何优化和减少合成生物学的设计/构建/测试周期。目标是开发并提供一种快速、全面的系统部件设计及其功能分析方法。提出的强化过程源于信息聚合物、DNA或XNA（合成DNA变体）的紧密整合和测定，以及它们在时间和空间上的功能表征。为了实现这一目标，该团队将开发和实施IODA技术平台（dna序列和功能测定的集成），将罗氏现有的下一代测序硬件基础设施与用于表征编码功能的原位和体外平台相结合。该项目的第4个工作包由哈佛大学的Church教授牵头。他的实验室的作用是开发一个合适的平台，用于体外蛋白质合成和酶分析能力，使用基于链霉亲和素的蛋白质支架来进化新的自然酶催化特性。这个概念的一部分是，该平台有能力招募新的辅助因子，如附着在生物素基团上的有机金属催化剂到蛋白质支架中。在体外建立聚焦链霉亲和素文库将通过产生固定化荧光反应产物来筛选合成能力强的催化剂。将这一过程整合到IODA平台中，将成为一个自动化的、高通量的合成和分析平台，用于在各种反应条件下筛选进化的蛋白质功能。该技术的原理证明将产生一种能够在生理条件下高效进行合环复分解的人工酶。这个项目如果成功，将为合成生物学领域提供极为有用的工具。此外，该项目还为与项目相关的学生和博士后研究人员提供了特殊的培训机会。该技术本身将通过新型仪器产生直接的经济影响，并通过开发新型工业上有用的催化剂产生间接影响。

This ERASynBio EU-US collaborative project is funded jointly by the NSF Systems and Synthetic Biology Program in BIO/MCB and the Biotechnology, Biochemical and Biomass Engineering Program in ENG/CBET. The project addresses a fundamental need in synthetic biology, namely, how to optimize and reduce the Synthetic Biology design/build/test cycle. The goal is to develop and provide a method for the rapid and comprehensive design of system parts and their functional analysis. The proposed intensification process is derived from the close integration and determination of an informational polymer, DNA or XNA (synthetic DNA variants), and their functional characterization in time and space. To achieve this, the team will develop and implement the IODA technology platform (Integration Of the Determination of DNA-sequence And function) by coupling the available Roche hardware infrastructure of next generation sequencing with in situ and in vitro platforms for characterization of the encoded functions. Work package 4 of the project is spearheaded by Prof. Church from Harvard University. His laboratory's role is to develop a suitable platform for in vitro protein synthesis and enzyme assaying capabilities using a Streptavidin-based protein scaffold for the evolution of new-to-nature enzyme catalytic properties. Part of this concept is that the platform has the capacity to recruit novel co-factors such as organometallic catalysts attached to a biotin group into the protein scaffold. The in vitro creation of focused streptavidin libraries will be screened for metathesis-competent catalysts by generating immobilized fluorescent reaction products. Integration of this process into the IODA platform will enable an automated, high-throughput, synthesis and analytical platform for the screening of evolved protein functions under various reaction conditions. The proposed proof of principle of this technology will generate an artificial enzyme that can carry out the ring-closing metathesis at high efficiency under physiological conditions. The project, if successful, will provide enormously useful tools for the field of synthetic biology. In addition this project offers exceptional training opportunities to students and postdoctoral researchers associated with the project. The technology itself will have direct economic impact with novel instrumentation, and indirect impact derived from the development of novel industrially useful catalysts.