Evolution Reloaded: From Artificial Genes To Novel Biological Functions

重新加载的进化：从人工基因到新的生物功能研究项目的智力价值：西奥多·多布赞斯基写道，除非从进化的角度出发，否则生物学中的任何东西都没有意义。因此，科学家们通过理解从分子水平上的新陈代谢到社会水平上的行为等生物特征来“理解”生命，以应对千百年来增强生存的选择压力。地球上生命的多样性得益于无数的进化轨迹，它们的起点由数十亿年前存在的祖先序列确定。如果有不同的祖先序列，可能会有不同的轨迹进化吗？直到现在，这个问题还不能得到回答；原始序列的收集无法用于实验室实验。然而，现在有了新的基因和蛋白质。经过数十亿年的进化史，无偏倚的序列可以被重新设计和构建。这样的序列为在实验室中重新开始进化提供了一种新的原料。在自然界中从未存在过，但却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。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以下内容：(1)发现与自然基因不相似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)探索新蛋白质的功能混杂性，并描绘未进化序列在多大程度上是多功能的“通才”。“(3)测定新型蛋白质的生化和生物物理特性；结构顺序与催化能力的相关性没有受益于选择的序列。(4)通过选择新的序列重新启动进化，进一步促进微生物的生长。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地球上生命“有意义”的总体理论。进化论的批评者认为，因为不可能回到过去，实际上不可能观察到从祖先祖先到现代生物的进化轨迹，所以进化论必须“仅仅”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，这种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地球生命起源和多样化的理论提供有限的支持。目前的项目将提供实验室研究的第一个例子，明确证明(i)与自然生物体的序列不相似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。对多样性和推广的影响：妇女和少数民族在这项研究中发挥了重要作用，并计划了许多推广活动。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，与整个序列空间的可能性相比，自然基因组和蛋白质组的序列数量显得微不足道。这个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，新的蛋白质将被开发用于特定的应用。

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.