Evolution Reloaded: From Artificial Genes To Novel Biological Functions

进化重装上阵：从人工基因到新的生物功能

• 批准号: 1050510
• 负责人: Michael Hecht
• 金额: $ 70.39万
• 依托单位: Princeton University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-04-01 至 2015-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1050510&HistoricalAwards=false
• 关键词: Evolution; Reloaded; Artificial; Genes; Novel

EVOLUTION RELOADED: FROM ARTIFICIAL GENES TO NOVEL BIOLOGICAL FUNCTIONSIntellectual Merit of the Research Project: Nothing in biology makes sense except in the light of evolution, wrote Theodore Dobzhansky. Accordingly, scientists "make sense" of life by understanding biological traits from metabolism at the molecular level to behavior at the societal level in response to eons of selective pressure for enhanced survival. The diversity of life on earth was enabled by a myriad evolutionary trajectories emanating from starting points defined by ancestral sequences that existed billions of years ago. Might different trajectories have evolved if different ancestral sequences had been available? Until now this question could not be answered; collections of primordial sequences were not available for laboratory experimentation. Now however, novel genes and proteins are available. Sequences unbiased by billions of years of evolutionary history can be designed and constructed de novo. Such sequences provide a novel feedstock to restart evolution in the laboratory. Genes that never existed in nature, but which nonetheless encode biological functions that sustain life will enable experiments to assess whether (i) alternative progenitor sequences might lead to different evolutionary trajectories, and (ii) different molecular ancestors might produce fundamentally different progeny. The current project addresses these issues at the level of genes, proteins, genomes, and proteomes. The aims of this work include the following:(1) Discovery of novel sequences that do not resemble natural genes, but nonetheless enable cell growth. Life-sustaining functions will be passaged in both prokaryotic and eukaryotic cells.(2) Probing the functional promiscuity of novel proteins and delineate the extent to which unevolved sequences are multifunctional "generalists."(3) Determination of the biochemical and biophysical properties of novel proteins; and correlation of structural order with catalytic proficiency in sequences that have not benefited from selection.(4) Restart evolution by selecting novel sequences to further enhance microbial growth. Broader Impacts Resulting from the Research Activity: EDUCATION: Surveys indicate that nearly 50% of Americans do not accept evolution as the overarching theory that "makes sense" of life on earth. Evolution's detractors argue that because it is not possible to go back in time and actually observe evolutionary trajectories from ancestral progenitors to modern organisms, evolution must remain "only" a theory. Although evolution in vitro is now a standard technique for protein engineering in academic labs and biotechnology companies, skeptics argue that such studies rely on feedstocks of sequences provided by nature, and therefore provide only limited support for Darwinian theories about the origin and diversification of life on earth. The current project will provide the first example of laboratory studies demonstrating explicitly that (i) novel genes bearing no sequences resemblance to those from natural organisms can evolve to produce progeny that enhance the fitness of a host organism, and (ii) de novo rather than derived macromolecules can provide essential biological functions. Dissemination of these results will have a broad impact on science education and literacy. This study will provide also multiple research training opportunities for students at all levels and postdoctoral researchers. IMPACTS ON DIVERSITY AND OUTREACH: Woman and minorities play significant roles in this research, and numerous outreach activities are planned.BIOTECHNOLOGY: Current biotechnology relies on genes and proteins isolated (or modified) from natural sequences. Yet the number of sequences in natural genomes and proteomes is dwarfed by the possibilities in all of sequence space. This research project explores the functional potential of novel sequences, thereby laying foundations for new technologies in which novel proteins will be developed for specific applications.

进化论重装：从人造基因到新颖的生物功能该研究项目的智力价值：除了进化论之外，生物学中的任何事物都没有意义，西奥多·多布赞斯基（Theodore Dobzhansky）写道。因此，科学家通过了解生物特征来“理解”生命，从分子水平的新陈代谢到社会水平的行为，以应对亿万年的选择压力，以提高生存率。地球上生命的多样性是由无数的进化轨迹促成的，这些进化轨迹源自数十亿年前存在的祖先序列所定义的起点。如果有不同的祖先序列，可能会进化出不同的轨迹吗？到目前为止，这个问题还无法得到解答；原始序列的集合无法用于实验室实验。然而现在，新的基因和蛋白质已经可用。不受数十亿年进化历史影响的序列可以从头设计和构建。这些序列提供了一种新的原料，可以在实验室中重新启动进化。自然界中从未存在过但编码维持生命的生物功能的基因将使实验能够评估（i）替代祖序列是否可能导致不同的进化轨迹，以及（ii）不同的分子祖先可能产生根本不同的后代。当前的项目在基因、蛋白质、基因组和蛋白质组水平上解决这些问题。这项工作的目标包括以下内容：（1）发现与天然基因不同但仍能促进细胞生长的新序列。维持生命的功能将在原核和真核细胞中传代。(2) 探索新型蛋白质的功能混杂性，并描绘未进化的序列在多大程度上是多功能的“通才”。(3) 新型蛋白质的生化和生物物理特性的测定蛋白质；以及结构顺序与未从选择中受益的序列中的催化能力的相关性。(4)通过选择新序列来重新启动进化，以进一步促进微生物生长。 研究活动产生的更广泛影响： 教育：调查表明，近 50% 的美国人不接受进化论作为“解释”地球生命的总体理论。进化论的批评者认为，由于不可能回到过去并实际观察从祖先到现代生物的进化轨迹，因此进化论必须“仅”是一种理论。尽管体外进化现在是学术实验室和生物技术公司蛋白质工程的标准技术，但怀疑论者认为此类研究依赖于大自然提供的序列原料，因此只能为达尔文关于生命起源和多样化的理论提供有限的支持。地球。 当前的项目将提供实验室研究的第一个例子，明确证明（i）与自然生物体没有序列相似性的新基因可以进化产生增强宿主生物体适应性的后代，以及（ii）从头开始而不是从头开始衍生的大分子可以提供必要的生物学功能。这些成果的传播将对科学教育和扫盲产生广泛​​的影响。本研究还将为各级学生和博士后研究人员提供多种研究培训机会。对多样性和推广的影响：女性和少数族裔在这项研究中发挥着重要作用，并且计划开展许多推广活动。生物技术：当前的生物技术依赖于从自然序​​列中分离（或修改）的基因和蛋白质。 然而，自然基因组和蛋白质组中的序列数量与所有序列空间中的可能性相比相形见绌。该研究项目探索新序列的功能潜力，从而为开发新蛋白质用于特定应用的新技术奠定基础。