Towards Life with a Reduced Protein Alphabet

地球上所有的生物都使用至少20种氨基酸作为制造蛋白质的基本构件。然而，目前尚不清楚这些基石是否都是必不可少的，或者是否可以进一步减少。回答这个问题将有助于我们对地球上所有有机生命的起源提供基本的见解，并帮助我们进一步了解生命的组织规则。这项研究项目的目标是应用基因和基因组合成中的尖端方法来评估生命是否可以在减少氨基酸数量的情况下存在。最终，这项研究的成功将带来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。这项工作的教育宣传方面将侧重于合成微生物学和微生物组主题，以提供一个重要和具体的场所，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。新的设计原则已经被应用到这些合成基因组中，以检验我们对支配生命的基本规则的理解，包括遗传密码、基因组结构和基因组最小化。所有已知生命的普遍特性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标准的20种氨基酸。到目前为止，还没有发现自由生活的生物体使用由不到20个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，或者是否有些是可有可无的，可以在基因组规模上移除。我们将对蛋白质序列功能进行计算建模，并执行蛋白质组范围的残基重新分配，以构建仅利用其字母表中19个或更少氨基酸的重组蛋白质。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，我们将产生新的蛋白质变体，并使用下一代基因合成和活细菌中的多重评估策略对它们进行高通量实验测试。最后，我们将尝试用这些残基重新编码原则以分段的方式在全基因组范围内构建部分细菌基因组，并评估氨基酸最小化的可行性，以推进逆向合成生物学。这一努力寻求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，并将导致在未来十年开发与该领域相关的新的基础计算、实验和合成生物学和基因组学工具。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.