Evolution Reloaded: From Artificial Genes To Novel Biological Functions

进化重新加载：从人工基因到新的生物功能研究项目的智力价值：除非从进化的角度来看，生物学中没有任何东西是有意义的，西奥多·多布赞斯基写道。因此，科学家通过了解生物特征，从分子水平的新陈代谢到社会水平的行为，来回应亿万年来增强生存的选择压力，从而对生命“有意义”。地球上生命的多样性是由数十亿年前存在的祖先序列定义的起点发出的无数进化轨迹所促成的。如果有不同的祖先序列，会不会进化出不同的轨迹？到目前为止，这个问题还无法回答；原始序列的收集还不能用于实验室实验。然而，现在有了新的基因和蛋白质。不受数十亿年进化历史影响的序列可以从头开始设计和构建。这样的序列提供了一种新的原料，可以在实验室重新开始进化。那些在自然界中从未存在过，但仍编码维持生命的生物功能的基因，将使实验能够评估(I)不同的祖先序列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。目前的项目在基因、蛋白质、基因组和蛋白质组的水平上解决这些问题。这项工作的目标包括：(1)发现与自然基因不相似但仍能使细胞生长的新序列。维持生命的功能将在原核和真核细胞中传递。(2)探索新蛋白质的功能混杂，并描绘出未进化的序列在多大程度上是多功能的“通才”。(3)新蛋白质的生化和生物物理性质的确定；以及结构顺序与未从选择中受益的序列中催化熟练程度的相关性。(4)通过选择新序列来重新开始进化，以进一步促进微生物的生长。研究活动产生的更广泛的影响：教育：调查表明，近50%的美国人不接受进化论作为地球上生命“有意义”的首要理论。进化论的批评者辩称，由于不可能回到过去并实际观察从祖先到现代生物体的进化轨迹，进化论必须仍然只是一种理论。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，但怀疑者认为，这些研究依赖于自然提供的序列的原料，因此对达尔文关于地球上生命的起源和多样化的理论提供的支持有限。目前的项目将提供第一个实验室研究的例子，明确表明：(I)与自然生物体的序列没有相似之处的新基因可以进化成后代，从而增强宿主生物体的适合性，(Ii)从头开始而不是衍生的大分子可以提供基本的生物功能。这些成果的传播将对科学教育和扫盲产生广泛影响。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。对多样性和外延的影响：妇女和少数群体在这项研究中发挥了重要作用，并计划了许多外展活动。生物技术：目前的生物技术依赖于从自然序列中分离(或修饰)的基因和蛋白质。然而，与所有序列空间中的可能性相比，自然基因组和蛋白质组中的序列数量相形见绌。这项研究项目探索了新序列的功能潜力，从而为新技术奠定了基础，在新技术中，将为特定应用开发新的蛋白质。

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.