Decoding the regulation of protein folding by synonymous codon usage

项目总结-破译同义密码子使用对蛋白质折叠的调节 同义突变在复杂的多基因疾病中广泛存在，但通常被认为是 表型沉默，因为它们保留了编码蛋白质的氨基酸序列。然而，同义词 突变可以通过各种机制显著扰乱蛋白质的动态平衡，包括扰乱 编码蛋白质的折叠机制。最近，我的实验室发现同义密码子诱导的 蛋白质折叠的变化可以大到足以(A)超过由提供的蛋白质动态平衡缓冲 分子伴侣和(B)导致细胞生长速度急剧下降两倍。对于这些蛋白质来说， 改变密码子使用模式会产生结构改变的折叠蛋白质，这会导致变化 在活性和/或对细胞蛋白酶降解的敏感性方面。这些结果的深刻含义是 这种密码子的使用代表了基因组中编码的另一种水平的信息，将它们连接在一起“沉默” 具有适当蛋白质功能的遗传差异和对潜在广泛细胞范围的调控 机械装置。然而，从历史上看，研究体内蛋白质折叠机制的扰动 巨大的技术挑战。由于这个原因，到目前为止，只确定了几个连接的例子 密码子使用和蛋白质折叠之间的关系。因此，我们缺乏对以下情况的全面了解 同义密码子的使用有助于功能蛋白质组的产生以及同义程度 突变会扰乱蛋白质的动态平衡。这个先锋奖项目旨在突破现有的 技术挑战，开发一种新的方法来(I)第一次广泛地衡量数量和类型 在整个蛋白质组中，具有对同义密码子使用敏感的折叠机制的蛋白质以及(Ii) 深入询问哪种密码子的使用模式和特征最能支持体内正确的蛋白质折叠。这个 该项目雄心勃勃的总体目标是通过开发一种 对最能支持功能性基因生产的同义密码子使用模式的预测性理解 蛋白质组和导致人类遗传病的失调。

PROJECT SUMMARY - Decoding the regulation of protein folding by synonymous codon usage Synonymous mutations are widespread in complex, polygenic diseases but are typically regarded as phenotypically silent, as they preserve the amino acid sequence of the encoded protein. Yet, synonymous mutations can significantly perturb protein homeostasis through a variety of mechanisms, including perturbing the folding mechanism of the encoded protein. Recently, my lab discovered that synonymous codon-induced changes to protein folding can be large enough to (a) exceed the protein homeostatic buffering provided by molecular chaperones and (b) lead to a dramatic two-fold decrease in cell growth rate. For these proteins, changing the codon usage pattern produces a folded protein with an altered structure, which leads to changes in activity and/or susceptibility to degradation by cellular proteases. The profound implication of these results is that codon usage represents another level of information encoded within genomes, linking together “silent” genetic differences with proper protein function and regulation of a potentially broad range of cellular mechanisms. Historically, however, studying perturbations to protein folding mechanisms in vivo has presented immense technical challenges. For this reason, to date only a few examples have been identified of connections between codon usage and protein folding. As a result, we lack a comprehensive picture of the extent to which synonymous codon usage contributes to the production of a functional proteome and how synonymous mutations perturb protein homeostasis. This Pioneer Award project is designed to break through existing technical challenges, developing a novel approach to (i) broadly measure for the first time the number and types of proteins with folding mechanisms sensitive to synonymous codon usage, across an entire proteome and (ii) deeply interrogate which codon usage patterns and features best support proper protein folding in vivo. The ambitious, overarching goal of this project is to enable a next generation of genomic inference by developing a predictive understanding of the synonymous codon usage patterns that best support production of a functional proteome and the dysregulation that leads to human genetic disease.