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Deep characterization of the sequence space and evolutionary trajectories of reconstructed ancestral proteins - Resubmission 01

重建祖先蛋白质的序列空间和进化轨迹的深度表征 - 重新提交 01

基本信息

批准号：
9901582
负责人：
Joseph W Thornton
金额：
$ 31.92万
依托单位：
UNIVERSITY OF CHICAGO
依托单位国家：
美国
项目类别：
财政年份：
2017
资助国家：
美国
起止时间：
2017-04-04 至 2021-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9901582
关键词：
Affect Amino Acid Sequence Amino Acids Bacteriophages Biochemical Biochemistry Biological Models Biology Biophysical Process Biophysics Cardiovascular Diseases Cellular biology Core Protein DNA DNA Binding Domain DNA Sequence DNA-Binding Proteins Development Disease Event Evolution Family Foundations Gene Expression Gene Expression Regulation Genetic Genetic Determinism Genetic Epistasis Genotype Goals Hand Homeostasis Hormone Receptor DNA-Binding Domain Immune System Diseases Immunity Inflammation Knowledge Laboratories Length Libraries Malignant Neoplasms Maps Mediating Metabolic Metabolism Methodology Methods Molecular Molecular Biology Molecular Evolution Mutation Nature Neighborhoods Outcome Pathway interactions Phylogenetic Analysis Play Probability Process Protein Biochemistry Protein Family Proteins Recording of previous events Reproduction Response Elements Role Site Specificity Structure Techniques Testing Time Variant Work exhaustion genetic predictors insight mutation screening novel physical property prevent receptor receptor binding reconstruction reproductive steroid hormone receptor tool transcription factor

项目摘要

We propose the first comprehensive characterization of sequence space around an ancestral protein. This work will 1) characterize the effects on function of all possible mutations and pairs of mutations across the protein's entire length and of all possible combinations of mutations at a key subset of sites, 2) illuminate how the distribution of function through this multidimensional sequence space would have affected the processes of protein evolution (a key goal in molecular evolution), and 3) quantify the complete set of main-effect and epistatic genetic determinants of DNA specificity in a transcription factor and elucidate their biochemical causes – an important goal for protein biochemistry and molecular gene regulation. We use the steroid hormone receptor DNA-binding domain as an ideal model system, because it is of great biomedical importance; it is experimentally and phylogenetically tractable; and its specificity for DNA targets diversified through a well-understood evolutionary process, with a known set of historical mutations and biophysical mechanisms. The proposed work will reveal why this history occurred relative to the many other mutational trajectories the protein could have taken as it evolved its new specificity. With the map of sequence space in hand, we will then apply locus-specific, replicated experimental evolution to the ancestral protein, placing it under strong selection to explore sequence space and evolve the same novel specificity that it acquired during historical evolution. By identifying commonalities and differences among the historical trajectory, experimental evolution trajectories, and the many other possible pathways through sequence space, we will gain fundamental insight into the roles of contingency and determinism in evolution and illuminate underlying mechanistic factors that caused those phenomena. Specific questions include: how many ways were there to evolve the derived DNA specificity, and how many were accessible under selection and drift? Did the historical outcome evolve because it was the optimal genotype, because it was the best or only accessible genotype, or simply due to chance? If more optimal genotypes exist, what prevented the evolving protein from reaching them? To what extent must new specificities evolve through promiscuous intermediates, and how many mutations does it take to evolve a new specificity? We will also characterize sequence space and experimental evolutionary trajectories around ancient receptors that existed at different times during history; this will reveal how the protein's evolvability and robustness fluctuated over evolutionary time due to epistatically acting mutations. Finally, by fully characterizing the main and epistatic genetic determinants of the protein's DNA specificity, we will identify common biophysical mechanisms that underlie DNA recognition, contributing to an important goal in molecular biology, biochemistry, cell biology, and development. The methods and conceptual tools we develop will be applicable to studying other transcription factors and the evolution of many other protein families.

我们提出了第一个综合表征序列空间周围的祖先蛋白。这