Learning principles from the pyrenoid, a phase-separated organelle

学习类核蛋白（一种相分离细胞器）的原理

• 批准号: 10544349
• 负责人: Martin Casimir Jonikas
• 金额: $ 50.44万
• 依托单位: PRINCETON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-01-01 至 2024-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10544349
• 关键词: Activase; Algae; Amyotrophic Lateral Sclerosis; Architecture; Back; Binding; Binding Sites; Biochemical Process; Biological; Biological Models; Biology; Biophysical Process; Carbon Dioxide; Cell physiology; Cells; Cellular Structures; Chlamydomonas; Chlamydomonas reinhardtii; Chloroplasts; Collaborations; Coupling; Cryo-electron tomography; Cues; Data; Disease; Energy-Generating Resources; Engineering; Ensure; Enzymes; Equilibrium; Exclusion; Experimental Models; Fluorescence Recovery After Photobleaching; Free Energy; Functional disorder; Gene Expression; Genetic Materials; Health; Holoenzymes; Image; In Vitro; Individual; Learning; Liquid substance; Location; Magic; Malignant Neoplasms; Measurement; Mediating; Membrane; Metabolism; Microscopic; Modeling; Molecular; Multienzyme Complexes; Mutation; Nature; Organelles; Phase; Physical condensation; Physiological Processes; Positioning Attribute; Process; Property; Proteins; RNA; Regulation; Ribosomes; Ribulose-Bisphosphate Carboxylase; Role; Signal Transduction; Source; Specificity; Starch; Structure; System; Thylakoids; Variant; Visualization; biological adaptation to stress; biophysical model; carbon fixation; experimental study; flexibility; human disease; in vivo; interdisciplinary approach; liquid dynamics; model organism; molecular dynamics; physical property; recruit; repaired; response; sample fixation; self assembly; stoichiometry; theories

PROJECT ABSTRACT Phase separation is an emerging organizing principle for intracellular biology. Processes that are now understood to exploit phase separation include storage of genetic material, gene expression, ribosome synthesis, signaling, stress response, and metabolism. While each phase-separating system has unique features, there are universal themes relevant to all such systems, including regulation of the phase boundary, the dynamics of mixing within and between condensates, and the interactions of condensates with their surroundings. To uncover general principles regarding these common themes, we focus on a well-suited model organism and system: the genetically tractable alga Chlamydomonas reinhardtii and its pyrenoid, a non-membrane bound, phase-separated organelle responsible for efficient carbon fixation. The pyrenoid offers many practical advantages: 1. its phase separation is driven by two well- characterized components, the rigid enzyme complex Rubisco and the flexible linker protein EPYC1, via a known specific binding interface; 2. the pyrenoid’s in vivo liquidity is reproduced in vitro with no energy source; 3. in vivo assembly/disassembly is controllable by external cues; and 4. the pyrenoid is singular, large, and stable enough to systematically investigate its functional interactions with other cellular components. Based on these advantages, the pyrenoid has already proven to be a source of many discoveries including the ability of a flexible multivalent linker to condense a rigid component, inheritance of non-membrane bound organelles by fission, specific recruitment via a conserved binding motif, and a magic-number effect. The key universal questions we will address with this system are: What is the role of the valence, strength, and spacing of the interacting motifs in determining condensate properties? How does the stability of small oligomers control phase boundaries? What keeps condensates in a liquid state? How do cells control the number, size, and location of condensates, including their relation to other cellular structures? Our approach will closely integrate theory and experiment, as providing fundamental answers to these questions requires a multidisciplinary approach that places specific data within a broad theoretical framework. We anticipate that our focus on underlying biophysical mechanisms will facilitate generalizability of our results to a wide range of phase-separated intracellular systems.

项目摘要 相分离是目前细胞内生物学过程的一种新兴组织原理。 据了解，利用相分离包括遗传物质的储存、基因表达、核糖体 每个相分离系统都有独特的合成、信号传导、应激反应和代谢。 特征，有与所有此类系统相关的普遍主题，包括相位调节 边界、冷凝物内部和之间的混合动力学以及冷凝物的相互作用 为了揭示这些共同主题的一般原则，我们关注一个问题。 非常适合的模型生物体和系统：遗传易驯化的藻类莱茵衣藻和 它的蛋白核是一种非膜结合的相分离细胞器，负责有效的碳固定。 核糖体具有许多实际优点：1.它的相分离是由两个良好的驱动器驱动的。 特征成分，刚性酶复合物 Rubisco 和柔性连接蛋白 EPYC1，通过 2. 体内的核糖体的流动性在体外无需能量即可复制； 来源；3. 体内组装/分解可通过外部信号控制；4. 蛋白核是单一的， 大且稳定，足以系统地研究其与其他细胞的功能相互作用 基于这些优点，核糖体已被证明是许多成分的来源。 发现包括灵活的多价连接体压缩刚性成分的能力、继承 通过裂变、通过保守的结合基序进行特异性募集和 我们将用这个系统解决的关键普遍问题是：作用是什么。 相互作用基序的化合价、强度和间距如何确定凝聚态性质？ 小低聚物的稳定性控制相界吗？是什么使冷凝物保持液态？ 细胞如何控制凝结物的数量、大小和位置，包括它们与其他物质的关系？ 细胞结构？我们的方法将紧密结合理论和实验，作为提供基础 这些问题的答案需要采用多学科方法，将特定数据置于广泛的范围内 我们预计，我们对潜在生物物理机制的关注将有助于促进这一理论框架。 我们的结果可推广到各种相分离的细胞内系统。