14-ERASynBio - IESY - Inducible Evolution of Synthetic Yeast genomes

合成酵母基因组诱导进化（IESY）将使用第一个合成真核生物Saccharomyces cerevisiae 2.0 （Sc2.0）作为代谢工程和基因组最小化的平台，更重要的是产生和理解工业上高价值的表型。Sc2.0中的合成染色体通过loxp介导的进化（SCRaMbLE）实现了合成染色体的重排和修饰，从而实现了快速而全面的基因组进化。在美国和欧洲，SCRaMbLE将被用于进化为生物燃料和生物技术的高价值表型选择的菌株，同时使用趋化剂和批量转移方法。开发新染色体技术和基因类正交SCRaMbLE技术。将分析进化轨迹，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三维结构；深度测序技术将序列和结构与基因表达和异构体丰度联系起来。计算分析将确定高适应度的进化驱动因素，并具有进一步优化的潜力。IESY以国际Sc2.0联盟提供的资源为基础，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新范式，其中基因组被预编程以探索组合多样性空间以进化新的有用功能。

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 analysed 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.