CAREER: Experimentally integrated modeling of quality control during eukaryotic mRNA protein synthesis

为了生长和分裂，活细胞需要快速产生蛋白质。然而，在化学物质受损或营养缺乏的情况下，细胞使用一种安全阀来减缓蛋白质生产的速度。这种所谓的质量控制机制起到了故障保险的作用，以确保蛋白质的准确生产和正确的数量。然后，随着细胞环境变得更有利，蛋白质合成的障碍需要消除。了解细胞如何恢复正常功能是这个项目的目标。这项研究的成功完成将使科学家能够准确预测细胞在不同条件下产生的蛋白质数量。这项研究将同时使用计算和实验方法，这将为参与研究的研究生提供宝贵的跨学科培训机会。相关培训将通过研究生课程“计算生物学的工具”提供，该课程面向弗雷德·哈钦森癌症研究中心和华盛顿大学开办的分子和细胞生物学博士项目的一年级学生。参与暑期研究项目将吸引本科生实习生和高中生参与与该项目目标相关的研究。在通过翻译产生蛋白质的过程中，核糖体通常沿着mRNAs快速移动，同时催化氨基酸添加到生长的肽链中。有时，核糖体会遇到路障，并在很长一段时间内停止运动。为了挽救这些停滞不前的核糖体，细胞依赖于几种酶，这些酶统称为质量控制因素。翻译研究领域的一个重大悬而未决的问题是，质量控制因素如何识别和挽救停滞的核糖体，而不会对正常翻译的核糖体产生任何不利影响。最近的结果提供了一条重要的线索：有效的质量控制只发生在翻译起始率高的mRNAs上。利用对发芽酵母中蛋白质和mRNA水平的高分辨率测量数据，建立了计算模型来检验多个核糖体之间的碰撞是质量控制的触发因素的假设。计算模型将提供预测性信息来指导旨在探索这一想法的实验。遗传和生化实验将用于剖析介导核糖体碰撞对质量控制影响的酶，并识别细胞中其翻译受核糖体碰撞影响的mRNAs。这一结果将为这一重要质量控制过程的机制和动态提供前所未有的见解。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

To grow and divide, living cells need to produce proteins rapidly. However, in cases of chemical damage or nutrient scarcity, cells use a kind of safety valve to slow the speed of protein production. This so-called quality control mechanism serves as a fail-safe to make sure that proteins are produced accurately and in the right quantities. Then, as the cellular environment becomes more favorable, the block on protein synthesis needs to be removed. Understanding how cells resume normal function is the goal of this project. Successful completion of this research will enable scientists to accurately predict the quantity of proteins that cells produce under different conditions. The research will use both computational and experimental approaches, which will provide valuable interdisciplinary training opportunities for graduate students taking part in the research. Related training will be offered through a graduate course, "Tools for Computational Biology," for first year students in the Molecular and Cellular Biology Ph.D. program run by the Fred Hutchinson Cancer Research Center and University of Washington. Participation in summer research programs will engage undergraduate interns and high school students in research related to the project goals.During the process of protein production by translation, ribosomes typically move rapidly along mRNAs while catalyzing addition of amino acids to growing peptide chains. At times, ribosomes can encounter roadblocks and stall their motion for long periods. To rescue these stalled ribosomes, cells rely on several enzymes that are collectively referred to as quality control factors. A major unresolved question in the field of translation research is how quality control factors recognize and rescue stalled ribosomes, without any adverse effect on normally translating ribosomes. Recent results have provided an important clue: efficient quality control occurs only on mRNAs with high rates of translation initiation. Using data from high resolution measurements of protein and mRNA levels in the budding yeast Saccharomyces cerevisiae, computational models have been formulated to test the hypothesis that collisions between multiple ribosomes serve as the trigger for quality control. Computational models will provide predictive information to guide experiments aimed at exploring this idea. Genetic and biochemical experiments will be used to dissect the enzymes that mediate the effect of ribosome collisions on quality control and to identify mRNAs in the cell whose translation is affected by ribosome collisions. The results will provide unprecedented insights into the mechanisms and dynamics of this important quality control process.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.