Collaborative Research: The Causes of Natural Variation in Protein Expression

该项目的目标是了解细胞的遗传物质，即DNA，如何控制每个细胞产生的蛋白质数量，细胞的环境如何刺激它增加或减少蛋白质产量，以及这种反应在个体之间有何不同。为了发挥作用，生物体将DNA中的特定遗传信息复制到称为RNA的分子中，然后使用RNA作为模板来制造蛋白质。蛋白质是执行细胞工作并赋予细胞身份的分子机器。目前还不清楚是什么原因导致细胞产生的蛋白质数量在个体之间存在差异。众所周知，这可能是由RNA合成量的差异引起的。然而，个体从相同数量的RNA中生成蛋白质的速度可能不同，当蛋白质老化时，它们回收蛋白质的速度也可能不同。这项研究将测量两种不同的芽殖酵母菌对交配信息素的反应时的RNA和蛋白质水平。它将包括对许多蛋白质的广泛调查和对目标组的详细测量。在从事这项研究的同时，主要是本科院校的学生和博士后将在进化系统生物学的新兴领域获得跨学科的培训。初中学生也将从事科学发现；他们将从空气和树皮中收集野生酵母，并确定它们在真菌生命树中的相互关系，以满足加利福尼亚州和华盛顿州最近通过的“下一代科学标准”的要求。具体而言，该项目旨在系统地描述蛋白质表达时间动态差异的原因，使用高通量表型，建模，细胞分辨率定量性状定位和靶向功能分析的独特组合。本文将出芽酵母（Saccharomyces cerevisiae）交配信息素反应网络作为模型系统。该研究将确定mRNA水平、蛋白质产生率和蛋白质降解率的变化对蛋白质水平的贡献。将这种方法应用于基因网络将阐明蛋白质表达变异如何产生的一般趋势。识别蛋白质表达变异的因果多态性将指向这种变异的分子机制。这些项目成果将在进化遗传学和系统生物学领域产生深远的影响。

The goal of this project is to understand how the genetic material of a cell, its DNA, controls the amount of protein each cell produces, how a cell's environment stimulates it to ramp protein production up or down, and how this response differs between individuals. To function, an organism copies specific genetic information from genes in its DNA to molecules called RNA and then uses that RNA as templates to make proteins. Proteins are the molecular machines that carry out the work of cells and give cells their identities. It is not clear what causes the amount of protein that cells make to differ between individuals. It is known that this can be caused by differences in how much RNA is made. However, individuals may differ in how fast they make protein from the same amount of RNA and also how quickly they recycle protein when it gets old. The research will measure RNA and protein levels in two different strains of budding yeast as they respond to mating pheromone. It will involve both broad surveys of many proteins and detailed measurements of a targeted set. While engaging in this research, students at a primarily undergraduate institution and a postdoctoral fellow will gain interdisciplinary training in the emerging field of evolutionary systems biology. Students from a junior high school will also be engaged in scientific discovery; they will collect wild yeasts from the air and from tree bark and identify their relationships to each other in the fungal tree of life, fulfilling the requirements of the Next Generation Science Standards recently adopted by California and Washington.Specifically, the project seeks to systematically characterize the causes of divergence in protein expression temporal dynamics using a unique combination of high-throughput phenotyping, modeling, cellular resolution quantitative trait mapping, and targeted functional analysis. The mating pheromone response network of the budding yeast Saccharomyces cerevisiae will be used as a model system. The research will identify the contribution of variation in mRNA levels, protein production rates, and protein degradation rates to protein levels. Applying this approach to a network of genes will elucidate the general trends in how protein expression variation arises. Identifying the causal polymorphisms underlying protein expression variation will point to the molecular mechanisms for such variation. These project outcomes will have far reaching effects in the fields of evolutionary genetics and systems biology.