Pleiotropy, Epistasis, and the Biophysical Adaptation of ssDNA Bacteriophages

ssDNA 噬菌体的多效性、上位性和生物物理适应

• 批准号: 8370018
• 负责人: Darin R Rokyta
• 金额: $ 22.94万
• 依托单位: FLORIDA STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-01 至 2017-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8370018
• 关键词: Affect; Affinity; Bacteriophages; Binding; Biochemistry; Biological Models; Biophysics; Buffers; Capsid; Conflict (Psychology); Data; Death Rate; Development; Elements; Engineering; Enzymes; Evolution; Genetic; Genetic Epistasis; Genetic Variation; Genotype; Goals; Growth; Heating; Individual; Infection; Measures; Modeling; Molecular; Movement; Mutation; Phenotype; Population; Population Dynamics; Process; Property; Proteins; Protocols documentation; Research; Role; Staging; Study models; System; Testing; Vaccine Design; Viral; Virulence; Walking; base; design; experience; fitness; improved; infectious disease evolution; insight; molecular dynamics; novel; pathogen; pleiotropism; pressure; protein folding; protein structure; reaction rate; research study; theories; trait

DESCRIPTION (provided by applicant): The proposed project will explore the roles of pleiotropy and epistasis in adaptive evolution and integrate ideas and questions from biophysics and biochemistry into an evolutionary framework in a bacteriophage system. The experiments, inspired by the population dynamics experienced by many pathogens, will use a unique experimental-evolution protocol involving rapidly fluctuating selective pressures to induce a two-component fitness based on growth rate and one of three biophysical parameters: capsid stability, low-pH tolerance, and novel host binding. The selection protocol consists of periods of growth within hosts punctuated by strong selection for one of three biophysical properties in the absence phage replication. For Aim 1, this protocol will be used to study the pleiotropic effects of individual beneficial mutations in five microvirid bacteriophage genotypes on growth rate and the three biophysical properties and to determine how this conflict, and pleiotropy in general, affects the genetic variation available for adaptatio. For Aim 2, beneficial mutations identified for Aim 1 will be engineered into new genetic contexts to reveal the extent to which biophysical properties of mutations are additive across backgrounds. The results from Aim 3 will be used to determine whether long-term adaptation can allow deleterious pleiotropic effects to be overcome through compensatory evolution to allow the two traits to be simultaneously maximized. The results from the proposed project will serve as a bridge between biophysics and evolution by subsuming biophysical parameters within fitness, and the relationship between growth rate and stability will provide insight into basic aspects of protein folding, function, and evolution. Theoreticians have long sought generalities that characterize the evolutionary process, and if such generalities exist, they should arise naturally from lower-level phenomena. The proposed experiments are designed to reveal such phenomena if they exist. Generalities about the evolution of protein thermal stability have not been forthcoming despite their relevance to a variety of fields, ranging from the evolution of extremophiles to basic questions about evolvability and the rational design of enzymes for industrial uses. Thermal stability is thought actually to promote evolvability by buffering against deleterious pleiotropic effects of mutations. The results will also aid in adjusting current models of adaptation to improve their realism and increase the accuracy of their predictions. Pleiotropy is a defining feature of Fisher's geometric model, and the proposed experiments will quantify the pleiotropic effects of mutations contributing to adaptation, providin information about the types of movements possible in multidimensional phenotypic space. They will also provide estimates of the main parameters in the mutational landscape model. Although epistasis has been widely documented, its molecular basis remains elusive. The results will provide a wealth of information about epistasis and its causes for beneficial mutations, about which few data exist. Many pathogens must survive under harsh conditions between infections and can potentially evolve greater virulence as a result. The proposed experimental system will serve as a model for studying the implications of this type of selection and provide insights into the evolution of infectious diseases. PUBLIC HEALTH RELEVANCE: The proposed project will investigate viral adaptation from a biophysical perspective and characterize the underlying bases of pleiotropy and epistasis for mutations increasing the thermal stability of viral capsids. Understanding the evolution of protein stability is of paramoun importance because thermally stable proteins are generally more useful in industrial applications and more tolerant of mutations with more dramatic effects, which can increase their evolvability. The proposed research will also develop a model system for studying the evolutionary implications of the population dynamics experienced by many pathogens, in which periods of growth within hosts are punctuated by periods outside the host, during which growth ceases and pathogens must concentrate on surviving the elements.

描述（由申请人提供）： 拟议的项目将探索多效性和上位性在适应性进化中的作用，并将生物物理学和生物化学的想法和问题整合到噬菌体系统的进化框架中。这些实验受到许多病原体经历的种群动态的启发，将使用一种独特的实验进化方案，涉及快速波动的选择压力，以诱导基于生长速率和三个生物物理参数之一的二元适应性：衣壳稳定性、低pH耐受性和新型宿主结合。选择方案包括宿主内的生长时期，在没有噬菌体复制的情况下，通过对三种生物物理特性之一的强烈选择来打断。对于目标 1，该协议将 可用于研究五种微病毒噬菌体基因型中个体有益突变对生长速率和三种生物物理特性的多效性影响，并确定这种冲突以及一般的多效性如何影响可用于适应的遗传变异。对于目标 2，为目标 1 确定的有益突变将被工程化到新的遗传背景中，以揭示突变的生物物理特性在不同背景下相加的程度。目标 3 的结果将用于确定长期适应是否可以通过补偿进化来克服有害的多效性效应，从而使这两个性状同时最大化。 该项目的结果将通过将生物物理参数纳入适应性范围内，成为生物物理学和进化之间的桥梁，而生长速率和稳定性之间的关系将提供对蛋白质折叠、功能和进化的基本方面的深入了解。理论家长期以来一直在寻找表征进化过程的普遍性，如果这种普遍性存在，它们应该自然地从较低层次的现象中产生。所提出的实验旨在揭示此类现象（如果存在）。尽管蛋白质热稳定性的进化与许多领域相关，从极端微生物的进化到关于进化性的基本问题和工业用途酶的合理设计，但关于蛋白质热稳定性进化的一般性尚未出现。人们认为热稳定性实际上可以通过缓冲突变的有害多效性效应来促进进化性。研究结果还将有助于调整当前的适应模型，以提高其现实性并提高预测的准确性。多效性是费舍尔几何模型的一个定义特征，拟议的实验将量化有助于适应的突变的多效性效应，提供有关多维表型空间中可能的运动类型的信息。他们还将提供突变景观模型中主要参数的估计。尽管上位性已被广泛记录，但其分子基础仍然难以捉摸。结果将提供有关上位性及其有益突变原因的大量信息，而有关这些信息的数据很少。许多病原体必须在两次感染之间的恶劣条件下生存，并可能因此进化出更大的毒力。所提出的实验系统将作为研究此类选择的影响的模型，并为传染病的演变提供见解。 公共卫生相关性： 拟议的项目将从生物物理学的角度研究病毒的适应性，并表征增加病毒衣壳热稳定性的突变的多效性和上位性的基本基础。了解蛋白质稳定性的进化至关重要，因为热稳定蛋白质通常在工业应用中更有用，并且更能耐受具有更显着效果的突变，这可以提高其进化能力。拟议的研究还将开发一个模型系统，用于研究许多病原体所经历的种群动态的进化影响，其中宿主内的生长时期被宿主外的时期所打断，在此期间生长停止，病原体必须集中精力在环境中生存。