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基因组项目 Sc2.0 的合成，这是一个人类设计的基因组，为模式生物酿酒酵母的生长提供动力。写入 Sc2.0 基因组的大量设计特征并非简单地重写已知的基因组序列，而是旨在提高基因组稳定性和遗传灵活性，同时保持正常生长。 Sc2.0 基因组旨在实现“教会我们生物学”的独特实验。 该项目涉及来自世界各地的科学家团队，为实现共同目标而共同努力。该项目发起的“构建基因组”课程是向本科生教授合成生物学和基因组学的独特教育工具。 Sc2.0 基因组也是一个生物制造平台，可增加生物燃料、疫苗、特种化学品、药品和生物制剂的产量。 Sc2.0 项目还在为该项目制定“原则声明”方面发挥了主导作用，解决了公众的生物伦理、安全和相关问题。合成的酵母基因组即将完成。一个全球科学家小组正在构建编码单个合成染色体的菌株，最终目标是将它们组合成单个细胞，以构建世界上第一个设计的、完全合成的真核基因组。另外五条染色体已经完全设计、合成、组装、测序，并评估了在不同条件下的适应性。 该项目对其完成至关重要。 Boeke 实验室的团队正在努力完成 1、4 和 8 号染色体。此外，虽然全世界基本上有 16 个团队，每个团队都生产一条染色体，但一系列重要的最终步骤涉及将合成染色体组合成单个菌株。 Sc2.0 基因组中写入了一组广泛的设计功能，旨在提高基因组稳定性和遗传灵活性，同时保持正常速率的生长能力。例如，重复序列等不稳定元素从 Sc2.0 染色体中删除，而 tRNA 基因则重新定位到单独的“新染色体”。此外，诱导进化或基因组置乱系统（Dymond 和 Boeke，2012），加上区分合成和野生型 DNA 的水印系统，提供了前所未有的能力来生成具有新颖结构的衍生基因组并跟踪合成 DNA。所有 16 条合成染色体均已设计完成。据报道，完成了一条半合成染色体的合成和组装（Annaluru et al., 2014; Dymond et al., 2011）。一些合成染色体需要进行各种类型的调试，通过恢复天然序列、某些被发现对表达有害的设计者改变等来产生高适应性分离株。未来几年的工作将集中于构建合成酵母线粒体DNA、从基因组中删除所有内含子和剪接机制，以及基因组扰乱的力量将以新的方式进行评估。展望未来，Sc2.0 项目将回答许多以前无法解决的进化问题，例如内含子和剪接机制如何转座子在宿主基因组中进化和传播。其他问题包括：最小真核基因组的范围有多大？内含子/剪接机制发挥重要作用吗？ 能否构建无转座子和/或无内含子的基因组？ 可以在遗传密码中添加第 21 个氨基酸吗？当转座子被引入这样的基因组时会发生什么？ 工程基因组在减数分裂中如何表现？ 合成和天然酵母基因组会产生可育的杂交种吗？人们能否完全基于改变基因组和基因剂量而不是基础变化来建立一种新型遗传学？