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

mRNA到蛋白质的翻译是一个基本的，但复杂的生物过程，由核糖体介导。为了解释什么会影响其效率，关键是要解开核糖体和其他分子复合物之间的相互作用，但也要考虑更大规模的其他因素。该提案的主要目标是绘制一幅关于核糖体在不同尺度的翻译系统中所起作用的全局图，包括分子、细胞和进化方面。更具体地说，我将研究1）核糖体出口隧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，并反过来，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。我将从低温电磁数据中分析出口隧道的生物物理特性，并阐明隧道静电和几何形状之间的相互作用。这些生物物理特性也将在进化的背景下进行研究，许多物种的核糖体的冷冻电镜结构。研究核糖体及其通道的进化需要推断祖先的形状，这可能解释不同的翻译模式。 在介观尺度上，我们将集中在两个重要的翻译模式：第一，膜蛋白基因的翻译，其中涉及运输到内质网（ER）。有趣的是，这引起了ER膜上的多聚核糖体的几何图案。为了解释这些模式，我们将研究一个新的生物物理模型的翻译，并比较模式与成像数据。要研究的第二种局部翻译模式发生在远离细胞核的树突状区域。通过结合运输模式的理论分析，与差异表达数据，我们将建立统计工具来区分，为不同的基因，他们的运输模式，并推断相关的本地翻译动力学。在系统尺度上，我们对翻译的代谢成本感兴趣。蛋白质水平的体外时间序列测量平台，具有多个潜在的限制因素。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翻译速率高通量测量的第一步。在体内，生命系统也需要管理核糖体群体。特别是，“核糖体吞噬”途径不仅可以减少核糖体库，而且还允许核糖体组分的再循环。为了评估这种途径的鲁棒性和最优性，我将使用最优控制。

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.