Complete synthesis of designer eukaryotic genome, Sc2.0

设计师真核基因组的完全合成，Sc2.0

• 批准号: 1616111
• 负责人: Jef Boeke
• 金额: $ 273.92万
• 依托单位: New York University Medical Center
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-08-01 至 2024-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1616111&HistoricalAwards=false
• 关键词: Complete; synthesis; designer; eukaryotic; genome

This project aims to complete the synthesis of the world's first synthetic eukaryotic genome project, Sc2.0, a human-designed genome powering growth of the model organism Saccharomyces cerevisiae. Rather than simply re-writing a known genome sequence, the extensive set of design features written into the Sc2.0 genome is intended to confer increased genomic stability and genetic flexibility while maintaining normal growth. The Sc2.0 genome is designed to enable unique experiments that will "teach us biology". The project involves teams of scientists from around the world working together towards a common goal. The Build A Genome course, initiated by this project, is a distinctive educational vehicle for teaching synthetic biology and genomics to undergraduate students. The Sc2.0 genome is also a platform for bio-manufacturing by increasing the production of biofuels, vaccines, specialty chemicals, pharmaceuticals, and biologics. The Sc2.0 project has also taken a lead role in generating a "statement of principles" for the project addressing bioethics, safety and related concerns of the public. The synthetic Saccharomyces genome is well on its way to being completed. A global group of scientists is building strains encoding individual synthetic chromosomes, with the ultimate goal of combining them into a single cell to construct the world's first designer, entirely synthetic eukaryotic genome. Five additional chromosomes have been completely designed, synthesized and assembled, sequenced, and evaluated for fitness under diverse conditions. This project will be critical to its completion. Teams in the Boeke lab are working to complete chromosomes 1, 4 and 8. Also, while there are essentially 16 teams around the world each producing one chromosome, an important series of final steps relates to combining the synthetic chromosomes into a single strain. An extensive set of design features written into the Sc2.0 genome is intended to confer increased genomic stability and genetic flexibility while maintaining the ability to grow at a normal rate. For instance, destabilizing elements such as repetitive sequences are deleted from Sc2.0 chromosomes while tRNA genes are re-located to a separate "neochromosome". Additionally, an inducible evolution or genome scrambling system (Dymond and Boeke, 2012), plus a watermarking system to distinguish synthetic and wild type DNA, provide unprecedented capacity to generate derivative genomes with novel structures and track synthetic DNA. All 16 synthetic chromosomes have been designed. The completion of the synthesis and assembly of one and a half synthetic chromosomes has been reported (Annaluru et al., 2014; Dymond et al., 2011). Debugging of various types was required in some of the synthetic chromosomes to produce a high fitness isolate, by restoring to the native sequence certain designer changes found to be deleterious to expression, etc. In the coming years work will focus on building a synthetic yeast mitochondrial DNA, and deletion of all introns and splicing machinery from the genome, and the power of genome scrambling will be evaluated in new ways.The Sc2.0 project, looking ahead, will answer many evolutionary questions never before approachable, such as how introns and transposons evolve and spread throughout host genomes. Additional questions include: How extensive is the universe of minimal eukaryotic gene sets? Do introns/splicing machinery play essential roles? Can one build transposon-free and/or intron-free genomes? Can one add a 21st amino acid to the genetic code? What happens when transposons are introduced into such genomes? How do engineered genomes perform in meiosis? Will synthetic and native yeast genomes make fertile hybrids? Can one build a new type of genetics based entirely on changing gene sets and gene dosage rather than base changes?

该项目旨在完成世界上第一个合成真核生物基因组项目SC2.0的综合，这是一种人为设计的基因组，为酿酒酵母的模型有生物体的增长提供了动力。与SC2.0基因组写入的广泛的设计特征不简单地重写已知的基因组序列，旨在赋予增强的基因组稳定性和遗传柔韧性，同时保持正常生长。 SC2.0基因组旨在实现“教给我们生物学”的独特实验。 该项目涉及来自世界各地的科学家团队，以实现共同的目标。该项目发起的建立基因组课程是为本科生教授合成生物学和基因组学的独特教育工具。 SC2.0基因组也是通过增加生物燃料，疫苗，特种化学品，药物和生物制剂的生产来进行生物制造的平台。 SC2.0项目还为解决公众的生物伦理学，安全性和相关问题的项目生成“原则声明”也发挥了主导作用。合成的糖疗基因组正在完成。一群全球科学家正在建立编码单个合成染色体的菌株，其最终目标是将它们组合到单个细胞中，以构建世界上第一个完全合成的真核基因组。在各种条件下，已经完全设计，合成和组装，测序并评估了五个其他染色体。 该项目对于完成至关重要。 Boeke Lab中的团队正在努力完成1、4和8染色体。而且，尽管世界各地基本上有16个团队每个人都会产生一个染色体，但重要的最终步骤与将合成染色体结合到单个菌株中有关。 一组写入SC2.0基因组中的广泛设计特征旨在赋予提高基因组稳定性和遗传柔韧性，同时保持正常速率增长的能力。例如，不稳定的元素（例如重复序列）被从SC2.0染色体中删除，而TRNA基因被重新定位为单独的“新染色体”。此外，诱导性进化或基因组拼凑系统（Dymond and Boeke，2012年），以及区分合成和野生型DNA的水印系统，提供了前所未有的能力，可以用新的结构和跟踪合成DNA产生衍生基因组。所有16种合成染色体均已设计。已经报道了一半合成染色体的合成和组装的完成（Annaluru等，2014； Dymond等，2011）。在某些合成染色体中需要进行各种类型的调试，以产生高健身分离株，通过恢复本机序列，某些设计师的变化被发现对表达有害的某些变更。展望未来，将回答许多前所未有的进化问题，例如内含子和转座如何在整个宿主基因组中演变和传播。其他问题包括：最小真核基因集的宇宙有多广泛？内含子/剪接机械是否扮演着重要角色？ 一个人可以构建不含转座和/或无内含子基因组吗？ 一个人可以在遗传密码中添加第21个氨基酸吗？将转座引入此类基因组时会发生什么？ 工程基因组在减数分裂中的表现如何？ 合成和天然酵母基因组会成为肥沃的杂种吗？一个人能否完全基于变化的基因组和基因剂量而不是基础变化来建立一种新的遗传学？