Towards Life with a Reduced Protein Alphabet

以减少的蛋白质字母走向生活

• 批准号: 2032259
• 负责人: Harris Wang
• 金额: $ 300万
• 依托单位: Columbia University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2032259&HistoricalAwards=false
• 关键词: Towards; Life; Reduced; Protein; Alphabet

All living organisms on earth use at least 20 amino acids as basic building blocks to make proteins. It is not known, however, whether these building blocks are all essential or whether they can be further reduced. Answering this question will help shed fundamental insights regarding the origin of all organic life on the planet and help us to further understand the organizing rules of life. The goal of this research project is to apply cutting-edge methods in gene and genome synthesis to assess whether life can exist with a reduced number of amino acids. Ultimately, success in this research endeavor will lead to new capabilities in protein design and testing, and provide information regarding the fundamental rules of life. The educational outreach aspect of this work will focus on synthetic microbiology and microbiome topics to provide an important and concrete venue to further increase science literacy, interest, and dialog in synthetic biology, genomics, and biotechnology in the general public. Recent advances in synthetic biology have enabled the total chemical synthesis of viral, bacterial, and eukaryotic genomes. New design principles have been applied to these synthetic genomes to test with great success our understanding of the fundamental rules governing life including the genetic code, genomic architecture, and genome minimization. A universal property of all known life is the use of the canonical 20 amino acids throughout the cell life cycle from growth to replication and cell division. No free-living organism has been found to date that uses an amino acid alphabet composed of fewer than 20 amino acids. The overall aim of this project is to explore whether every one of the 20 canonical amino acids are essential for life or whether some are dispensable and can be removed at a genome-scale. We will computationally model protein sequence-function and perform proteome-wide residue reassignments to build recoded proteins that utilizes only 19 or fewer amino acids in its alphabet. Through development of new computational protein models and algorithms, including semi-supervised and deep-learning approaches, we will generate new protein variants and experimentally test them in high-throughput using next-generation gene synthesis and multiplex evaluation strategies in living bacteria. Finally, we will attempt to build a partial bacterial genome with these residue recoding principles genome-wide in a piecewise fashion and assess feasibility of amino acid minimization to advance retro-synthetic biology. This effort seeks to make large-scale coding changes to proteins to a degree that has never been attempted in the past and will lead to the development of new foundational computational, experimental, and synthetic biology and genomics tools relevant for the field for the next decade.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.

地球上所有的生物体都使用至少20种氨基酸作为制造蛋白质的基本组成部分。 然而，目前还不知道这些基本要素是否都是必不可少的，或者是否可以进一步减少。 探讨这个问题将有助于我们对地球上所有有机生命的起源有基本的了解，并有助于我们进一步了解生命的组织规则。 该研究项目的目标是应用基因和基因组合成的尖端方法来评估生命是否可以在氨基酸数量减少的情况下存在。 最终，这项奋进的成功将导致蛋白质设计和测试的新能力，并提供有关生命基本规则的信息。 这项工作的教育推广方面将侧重于合成微生物学和微生物组主题，以提供一个重要而具体的场所，进一步提高公众对合成生物学，基因组学和生物技术的科学素养，兴趣和对话。 合成生物学的最新进展使病毒、细菌和真核生物基因组的全化学合成成为可能。 新的设计原则已应用于这些合成基因组，以极大成功地测试我们对生命基本规则的理解，包括遗传密码、基因组架构和基因组最小化。 所有已知生命的一个普遍性质是在从生长到复制和细胞分裂的整个细胞生命周期中使用典型的20种氨基酸。迄今为止，还没有发现自由生活的有机体使用少于20种氨基酸组成的氨基酸字母表。 该项目的总体目标是探索20种典型氨基酸中的每一种是否都是生命所必需的，或者是否有些是必需的，可以在基因组规模上去除。 我们将计算蛋白质序列功能模型，并进行蛋白质组范围内的残基重排，以建立只利用其字母表中19个或更少氨基酸的重编码蛋白质。 通过开发新的计算蛋白质模型和算法，包括半监督和深度学习方法，我们将生成新的蛋白质变体，并在活细菌中使用下一代基因合成和多重评估策略进行高通量实验测试。 最后，我们将尝试建立一个部分细菌基因组与这些残基编码原则全基因组在一个分段的方式，并评估氨基酸最小化的可行性，以推进逆合成生物学。 这项努力旨在对蛋白质进行大规模的编码改变，达到过去从未尝试过的程度，并将导致新的基础计算，实验，该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查进行评估，被认为值得支持的搜索.

项目成果

Extensive regulation of enzyme activity by phosphorylation in Escherichia coli.

• DOI: 10.1038/s41467-021-25988-4
• 发表时间: 2021-09-24
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Schastnaya E;Raguz Nakic Z;Gruber CH;Doubleday PF;Krishnan A;Johns NI;Park J;Wang HH;Sauer U
• 通讯作者: Sauer U

Fast and efficient template-mediated synthesis of genetic variants

快速高效的模板介导的遗传变异合成

• DOI: 10.1038/s41592-023-01868-1
• 发表时间: 2023
• 期刊: Nature Methods
• 影响因子: 48
• 作者: Liu, Liyuan;Huang, Yiming;Wang, Harris H.
• 通讯作者: Wang, Harris H.

State-of-the-Art Estimation of Protein Model Accuracy Using AlphaFold

• DOI: 10.1103/physrevlett.129.238101
• 发表时间: 2022-12-02
• 期刊: PHYSICAL REVIEW LETTERS
• 影响因子: 8.6
• 作者: Roney, James P.;Ovchinnikov, Sergey
• 通讯作者: Ovchinnikov, Sergey

Scaffolding protein functional sites using deep learning.

• DOI: 10.1126/science.abn2100
• 发表时间: 2022-07-22
• 期刊: Science (New York, N.Y.)