Expanding the functions of a 57 codon recoded E.coli genome

扩展 57 个密码子重新编码的大肠杆菌基因组的功能

• 批准号: 2123243
• 负责人: George Church
• 金额: $ 199.67万
• 依托单位: Harvard University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-01 至 2024-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2123243&HistoricalAwards=false
• 关键词: Expanding; functions; 57; codon; recoded

A fundamental and highly conserved code is embedded in all genomes and underlies biological life. This code is known as the ‘standard genetic code’, which defines how genetic information translates amino acid building blocks into proteins during their biological manufacturing process. Harnessing the universality of the standard genetic code has revolutionized the material, food, chemical, and energy industry. Although minor deviations from the standard code exist in a few organisms, the standard genetic code has withstood nearly 3.5 billion years of genetic drift by being highly conserved across all domains of life. The genetic codon is a triplet unit of a genetic material (DNA or RNA) that can define a protein building block. The mapping of 64 triplet codons to the 20 canonical amino acids, the building blocks of proteins, results in the same amino acid being encoded by multiple synonymous codons. By rationally building synthetic genomes in living cells, with a reduced set of synonymous codons, the liberated codons can be reassigned to incorporate non-natural amino acids into proteins. By systematic codon replacement, researchers are progressing towards the final assembly of a computationally designed bacterial genome that relies on 57 codons instead of the universal 64 codons. In this project, the fully assembled 57-codon synthetic bacteria cell will be explored and further modified for safe bio-containment and genetic isolation to prevent exchange of genetic information with the environment. The researchers will also build an open-access database to enable streamlined computational approaches for non-canonical amino acid incorporation. As a form of outreach, the researchers will organize a two-day open webinar series annually with philosophers, early-career researchers, STEM graduate students, and scientific experts engaged in synthetic cell engineering projects globally to discuss future perspectives and ethical issues associated with synthetic cells.The standard genetic code maps the 64 triplet codons in the genome with the 20 canonical amino acids. Translating the information encoded in the standard genetic code to proteins further involves adaptor tRNA molecules, ribosomes, and amino-acyl tRNA synthetases. Researchers are progressing towards assembling a 57-codon Escherichia coli genome by replacing seven codons that encode the canonical amino acids serine, leucine, alanine and the amber stop codon with their synonymous alternatives. The liberated codons will incorporate multiple non-canonical amino acids and establish biocontainment for engineered genetic information. The researchers will gain fundamental insights on cellular plasticity by studying the adaptations of the proteome towards long-term non-canonical amino acid dependence. The study will also provide biological insights into genetic code evolution by tracking for processes such as codon-capture and ambiguous decoding during the long-term adaptation and dependence of the recoded genome to non-canonical amino acids. The project will also build an open-access database for genetic code expansion and make available computational tools to facilitate the research with non-canonical amino acids. In sum, it is expected that this project will provide new tools and knowledge for academic and industrial efforts related to genetic code and synthetic cell engineering while simultaneously facilitating the safe use of synthetic biological systems and communicating these aspects to a wide range of researchers and STEM students.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

所有基因组中都嵌入了基本且配置高度的代码，并构成了生物学生命的基础。该代码被称为“标准遗传密码”，该代码定义了遗传信息如何在其生物制造过程中将氨基酸构建块转化为蛋白质。利用标准遗传法规的宇宙彻底改变了材料，食品，化学和能源行业。尽管在几种生物体中存在一些较小的标准代码，但标准遗传代码在所有生命的所有领域中都高度保守，使遗传漂移近35亿年。遗传密码子是可以定义蛋白质构建块的遗传材料（DNA或RNA）的三联单元。将64个三重三倍密码子映射到20个规范氨基酸（蛋白质的基础）中，导致相同的氨基酸由多个合成密码子编码。通过在活细胞中合理构建合成基因组（合成密码子），可以重新分配解放的密码子，以将非天然氨基酸掺入蛋白质中。通过系统的密码子置换，研究人员正在朝着最终组装计算设计的细菌基因组的最终组装，该细菌基因组依赖于57个密码子，而不是通用64个密码子。在该项目中，将探索完全组装的57-codon合成细菌细胞，并进一步修改以进行安全的生物含量和遗传分离，以防止遗传信息与环境交换。研究人员还将构建一个开放式数据库，以实现非经典氨基酸掺入的简化计算方法。作为一种外展的形式，研究人员将每年与哲学家，早期研究人员，STEM研究生和科学专家组织为期两天的开放式网络研讨会系列，从事合成细胞工程项目的研究，在全球范围内从事合成细胞工程项目，以讨论与合成细胞相关的未来观点和道德问题。将标准遗传密码中编码的信息转换为蛋白质，进一步涉及衔接子tRNA分子，核糖体和氨基 - 酰基-Asyl tRNA合成酶。研究人员正在通过替换七个编码规范氨基酸丝氨酸，亮氨酸，丙氨酸和琥珀色终止密码子的七个密码子，并用其合成的替代方法来组装57多子大肠杆菌基因组。解放的密码子将结合多种非典型氨基酸，并建立用于工程遗传信息的生物植物。研究人员将通过研究蛋白质组对长期非经典氨基酸依赖性的适应性来获得对细胞可塑性的基本见解。这项研究还将通过跟踪在长期适应和依赖于非典型氨基酸的过程中的密码子捕获和模棱两可的解码等过程来提供对遗传代码演化的生物学见解。该项目还将建立一个开放式数据库，以扩展遗传代码，并提供计算工具，以促进使用非经典氨基酸的研究。 In sum, it is expected that this project will provide new tools and knowledge for academic and industrial effort related to genetic code and synthetic cell engineering while simultaneously supporting the safe use of synthetic biologic systems and communicating these aspects to a wide range of researchers and STEM students.This award reflects NSF's statutory mission and has been deemed precious of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

项目成果

Towards next-generation cell factories by rational genome-scale engineering

• DOI: 10.1038/s41929-022-00836-w
• 发表时间: 2022-09
• 期刊: Nature Catalysis
• 影响因子: 37.8
• 作者: S. Yilmaz;Á. Nyerges;J. van der Oost;G. Church;Nico J. Claassens