Investigating the properties of the ribosomes and their impact on translation dynamics across scales and systems

研究核糖体的特性及其对跨尺度和系统翻译动力学的影响

• 批准号: RGPIN-2020-05348
• 负责人: DaoDuc, Khanh
• 金额: $ 2.7万
• 依托单位: University of British Columbia
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2021
• 资助国家: 加拿大
• 起止时间: 2021-01-01 至 2022-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=740525
• 关键词: Investigating; properties; ribosomes; their; impact

The translation of mRNA into protein is a fundamental, yet complex biological process, mediated by ribosomes. To explain what can affect its efficiency, it is crucial to unravel the interactions between the ribosomes and other molecular complexes, but also to take into account other factors at a larger scale. The main goal of this proposal is to draw a global picture of the role played by ribosomes in translational systems across different scales, encompassing molecular, cellular and evolutionary aspects. More specifically, I will investigate 1) the biophysical properties and evolution of the ribosome exit tunnel, 2) different modes of translation, transport and remodeling of the ribosome in response to specific spatial cellular organizations and 3) the limiting factors that drive protein translation at the system level. These complementary approaches will both elucidate the functional impact of the ribosome structure, and conversely, determine how spatial or resources management impose evolutionary and design constraints at the molecular level. I will analyze the biophysical properties of the exit tunnel from cryo EM data, and elucidate the interplay between the tunnel electrostatics and geometry. These biophysical properties will also be studied in the context of evolution, with cryo EM structures of the ribosomes available for many species. Studying the evolution of the ribosome and its tunnel will require inferring ancestral shapes that can potentially explain different modes of translation. At the mesoscopic scale, we will focus on two important modes of translation: First, the translation of membrane protein genes, which involves transport to the endoplasmic reticulum (ER). Interestingly, this gives rise to geometric patterns of polyribosomes on the ER membrane. To explain these patterns, we will study a new biophysical model of translation, and compare the patterns with imaging data. The second local mode of translation to investigate occurs in dendritic regions, located far from the cell nucleus. By combining theoretical analysis of modes of transport, with differential expression data, we will build statistical tools to distinguish, for different genes, their mode of transport, and infer the associated local translation dynamics. At the system scale, we are interested in the metabolic cost of translation. In vitro time-series measurements of protein levels plateau, with multiple potential limiting factors. Upon fitting a mathematical model to various experimental conditions, I will disentangle the contribution of these factors. This modeling approach will serve as a first step for high-throughput measurement of translation rates. In vivo, living systems also need to manage the ribosomal population. In particular, "ribophagy" pathway can not only decrease the ribosomal pool, but also allows the recycling of ribosomal components. To assess the robustness and optimality of this pathway, I will use optimal control.

mRNA转化为蛋白质是一个基本而复杂的生物过程，由核糖体介导。为了解释影响其效率的因素，关键是要解开核糖体和其他分子复合物之间的相互作用，但也要考虑到更大范围内的其他因素。本提案的主要目标是绘制核糖体在不同尺度的翻译系统中所起作用的全局图像，包括分子，细胞和进化方面。更具体地说，我将研究1)核糖体出口通道的生物物理特性和进化，2)响应特定空间细胞组织的核糖体的不同翻译，运输和重塑模式，以及3)在系统水平上驱动蛋白质翻译的限制因素。这些互补的方法将阐明核糖体结构的功能影响，反过来，确定空间或资源管理如何在分子水平上施加进化和设计约束。我将从低温电镜数据分析出口隧道的生物物理特性，并阐明隧道静电和几何之间的相互作用。这些生物物理性质也将在进化的背景下进行研究，核糖体的低温电镜结构可用于许多物种。研究核糖体及其隧道的进化将需要推断出可能解释不同翻译模式的祖先形状。在介观尺度上，我们将重点关注两种重要的翻译模式：第一，膜蛋白基因的翻译，涉及到内质网（ER）的转运。有趣的是，这会在内质网膜上产生多核糖体的几何图案。为了解释这些模式，我们将研究一种新的翻译生物物理模型，并将其与成像数据进行比较。要研究的第二种局部翻译模式发生在远离细胞核的树突区域。通过将理论分析与差异表达数据相结合，我们将建立统计工具来区分不同基因的运输模式，并推断相关的局部翻译动态。在系统尺度上，我们感兴趣的是翻译的代谢成本。体外时间序列测量蛋白水平平稳，有多种潜在的限制因素。在将数学模型拟合到各种实验条件后，我将解开这些因素的贡献。这种建模方法将作为高通量翻译率测量的第一步。在体内，生命系统也需要管理核糖体种群。特别是“核糖体自噬”途径不仅可以减少核糖体池，还可以使核糖体成分循环利用。为了评估这条路径的鲁棒性和最优性，我将使用最优控制。