ERASynBio: Induced Evolution of Synthetic Yeast Genomes

ERASynBio：合成酵母基因组的诱导进化

• 批准号: 1445537
• 负责人: Jef Boeke
• 金额: $ 42.74万
• 依托单位: New York University Medical Center
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-07-15 至 2017-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1445537&HistoricalAwards=false
• 关键词: ERASynBio; Induced; Evolution; Synthetic; Yeast

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.

该项目由MCB的系统和合成生物学计划以及CBET的生物技术，生化和生物量工程计划的资助，是较大的Erasynbio资助协作的一部分。 研究人员以前已经开发了设计和合成整个酵母染色体的能力，并插入染色体位点，使其易于修饰或重组染色体的碎片。 在这项工作中，他们利用这种能力来发展酵母菌菌株，这些菌株将特别适合生产化学药品或燃料或其他生物制造任务。 此外，他们将收集数据，以帮助他们解决有关实验室或制造环境中染色体如何发展的问题，以及哪些特征会导致更稳定的染色体和更好地生长的酵母菌菌株。 同时，研究人员将在线课程发展，以教授与合成生物学领域相关的道德，并扩大实验室课程，使本科生能够合成酵母染色体的一部分，并学习进入该研究领域所需的工具。技术描述：诱导的合成酵母基因组（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，并且更重要的是生成和理解工业高价值现象。 SC2.0中的合成染色体可以通过LOXP介导的进化（Scramble）进行合成染色体重排和修饰，可以快速而全面的基因组进化。在这里，将使用Chemofule和生物技术的高价值表型，使用Chemodotats和Chemotatats和批处理转移方法在这里开发争夺，以进化为生物燃料和生物技术的高价值表型的发展。将开发针对基因类别的新染色体和正交拼凑的技术。将分析进化轨迹，以将基因组结构与基因组功能相关联：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；深层测序技术将序列和结构与基因表达和同工型丰度相关联。计算分析将确定高健身的进化驱动因素，并具有进一步优化的潜力。 Iesy建立在国际SC2.0联盟中独特获得的资源基础上，将成为有效发展高价值表型的国际资源。该项目代表了合成生物学的一个新范式，其中预先编程了基因组来探索组合多样性空间以发展新的和有用的功能。