Regulation of Protein Synthesis by Synonymous Codon Usage

项目摘要 （* 来自父母补助金 *） 核糖体翻译mRNA是所有活细胞中的一个重要过程，并且经常失调 在许多癌症和神经退行性疾病中。翻译的起始阶段通常被认为是 调节蛋白质表达和mRNA稳定性的主要点。然而，我们和其他人最近在查- 在基因表达的调节中，翻译的延伸阶段具有关键的和多方面的作用。 在我们的上一个资助期间，我们确定了同义密码子使用在调节延伸率中的新作用 和哺乳动物mRNA在氨基酸限制期间的蛋白质表达。同义密码子的研究 效应导致了一个重大发现，即多个核糖体之间的碰撞是细胞识别的信号， 启动和拯救停滞的核糖体。此外，我们观察到，高起始速率会反直觉地降低 蛋白质表达和经历核糖体碰撞的mRNA的稳定性。从这些进步中出现的是一个 mRNA作为大分子复合物之间多因子相互作用的动态平台的作用 在翻译过程中。在下一个项目期间，我们将剖析这种相互作用之间发生的伸长ri- 核糖体、起始核糖体和mRNA衰变因子。这些研究的目标将是全面 定义一组核糖体介导的相互作用，这对准确预测基因表达很重要， mRNA周转、短上游开放阅读框和核糖体病的特定背景。为实现这一 目标，我们将利用我们独特的跨学科方法，结合定量高通量实验 计算动力学模型。成功完成我们的研究将提供一个机械框架 预测核糖体和mRNA衰变因子中疾病相关突变的细胞后果， 以及特定mRNA的非编码和同义位点。

Project Summary (*from parent grant*) Translation of mRNAs by ribosomes is an essential process in all living cells, and it is frequently dysregulated in many cancers and neurodegenerative diseases. The initiation stage of translation is usually thought of as the major point for regulation of protein expression and mRNA stability. However, we and others have recently char- acterized a critical and multi-faceted role for the elongation stage of translation in regulation of gene expression. During our last funding period, we identified a novel role for synonymous codon usage in regulating elongation rate and protein expression from mammalian mRNAs during amino acid limitation. Our studies of synonymous codon effects led to the major discovery that collisions between multiple ribosomes serve as a signal for cells to recog- nize and rescue stalled ribosomes. Furthermore, we observed that high initiation rates counter-intuitively decrease protein expression and stability of mRNAs undergoing ribosome collisions. Emerging from these advances is a role for the mRNA as a dynamic platform for multi-factorial interactions between large macromolecular complexes during translation. In the next project period, we will dissect such interactions that occur between elongating ri- bosomes, initiating ribosomes, and mRNA decay factors. The goal of these studies will be to comprehensively define the set of ribosome-mediated interactions that are important for accurate prediction of gene expression in the specific contexts of mRNA turnover, short upstream open reading frames, and ribosomopathies. Towards this goal, we will leverage our unique interdisciplinary approach combining quantitative high throughput experiments with computational kinetic models. Successful completion of our research will provide a mechanistic framework to predict the cellular consequences of disease-associated mutations in ribosomes and mRNA decay factors, as well as in noncoding and synonymous sites of specific mRNAs.