ERASynBio: Induced Evolution of Synthetic Yeast Genomes

该项目由MCB的系统和合成生物学计划以及CBET的生物技术，生物化学和生物质工程计划资助，是ERASynBio资助的更大合作的一部分。 研究人员先前已经开发出设计和合成整个酵母染色体的能力，并将其插入染色体位点，使其易于修改或重组染色体片段。 在这项工作中，他们利用这种能力来进化酵母菌株，这些酵母菌株特别适合于生产化学品或燃料或其他生物制造任务。 此外，他们还将收集数据，帮助他们解决有关染色体在实验室或制造环境中如何进化的问题，以及哪些特征会产生更稳定的染色体和更好的酵母菌株。 与此同时，研究人员将开发在线课程，教授与合成生物学领域相关的伦理学，并扩大他们的实验室课程，使本科生能够合成酵母染色体的一部分，并学习进入这一研究领域所需的工具。技术说明：合成酵母基因组的诱导进化（IESY）将使用第一个合成真核生物酿酒酵母2.0（Sc2.0）作为代谢工程和基因组最小化的平台，更重要的是用于产生和理解工业上高价值的表型。Sc2.0中的合成染色体允许通过合成染色体重排和loxP介导的进化修饰（SCRaMbLE）进行快速和全面的基因组进化。SCRaMbLE将在美国和欧洲使用恒化器和批量转移方法，在这里开发用于生物燃料和生物技术的高价值表型的菌株。将开发新染色体和基因类正交SCRaMbLE技术。进化轨迹将被分析以将基因组结构与基因组功能联系起来：DNA测序将揭示进化菌株中的基因组序列、重排和拷贝数变化;染色体构象捕获将显示大规模重排如何影响3D结构;深度测序技术将序列和结构与基因表达和亚型丰度联系起来。计算分析将确定高适应性的进化驱动因素，并有可能进一步优化。IESY建立在国际Sc2.0联盟独特的资源基础上，将成为高效进化高价值表型的国际资源。该项目代表了合成生物学的一种新范式，其中基因组被预先编程以探索组合多样性空间，从而进化出新的有用功能。

This project, funded by the Systems and Synthetic Biology Program in MCB and the Biotechnology, Biochemical and Biomass Engineering Program in CBET, is part of a larger ERASynBio funded collaborative. The researchers have previously developed the capability to design and synthesize entire yeast chromosomes, and have inserted into the chromosomes sites that make it easy to modify or recombine pieces of the chromosome. In this work, they leverage this capability to evolve yeast strains that will be particularly well suited for production of chemicals or fuels or other biomanufacturing tasks. In addition, they will collect data that will help them address questions about how chromosomes evolve in laboratory or manufacturing settings, and what characteristics give rise to more stable chromosomes and better growing yeast strains. At the same time, the researchers will develop on line courses to teach ethics related to the field of synthetic biology, and expand their laboratory classes that enable undergraduates to synthesize parts of the yeast chromosome and learn the tools needed to enter into this research field. Technical Description: Induced Evolution of Synthetic Yeast genomes (IESY) will use the first synthetic eukaryote, Saccharomyces cerevisiae 2.0 (Sc2.0), as a platform for metabolic engineering and genome minimization, and more importantly for generating and understanding industrially high-value phenotypes. Synthetic chromosomes in Sc2.0 permit rapid and comprehensive genome evolution through synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE). SCRaMbLE will be exploited here to evolve strains selected for high-value phenotypes for biofuels and biotechnology, using both chemostats and batch transfer methods in the USA and Europe. Technologies for neochromosomes and orthogonal SCRaMbLE of gene classes will be developed. Evolutionary trajectories will be analyzed to relate genome structure with genome function: DNA sequencing will reveal the genome sequence, rearrangements, and copy number changes in the evolved strains; chromosome conformation capture will show how massive rearrangements affect 3D structure; and deep sequencing technologies will relate sequence and structure to gene expression and isoform abundance. Computational analysis will identify the evolutionary drivers for high fitness, with the potential for further optimization. IESY builds on resources uniquely available from the international Sc2.0 consortium and will be an international resource for efficient evolution of high-value phenotypes. This project represents a new paradigm in synthetic biology in which a genome is pre-programmed to explore combinatorial diversity space to evolve new and useful function.