Physicochemical properties driving membraneless organelle assembly in bacteria

驱动细菌无膜细胞器组装的物理化学特性

基本信息

批准号：
10727036
负责人：
Julie Biteen
金额：
$ 11.84万
依托单位：
UNIVERSITY OF MICHIGAN AT ANN ARBOR
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-09-15 至 2025-08-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10727036
关键词：
Affect Ally Automobile Driving Bacteria Bacterial Chromosomes Bacterial DNA Bacterial Physiology Behavior Biochemical Biochemistry Biogenesis Cell Separation Cell Survival Cell physiology Cells Chromosome Condensation Chromosome Structures Chromosomes Complement Complex Cytoplasm DNA DNA Binding DNA-Binding Proteins DNA-Directed RNA Polymerase Diffuse Diffusion Engineering Environment Eukaryotic Cell Feedback Genetic Goals Growth Higher Order Chromatin Structure Image In Vitro Kinetics Life Liquid substance Maps Measures Mediating Membrane Microscopy Modeling Molecular Motion Nucleic Acids Organelles Organism Phase Phase Transition Physical condensation Physiological Process Property Proteins Proteomics Research Rheology Ribosomes Role Spatial Distribution Spectrum Analysis Starvation Stress Structure System Testing Time Trees Work antibiotic design cell injury chemical property chromatin immunoprecipitation chromosome conformation capture defined contribution environmental change experimental study genome-wide genomic locus in silico in vivo innovation liquid crystal macromolecule mechanical behavior mechanical properties multidisciplinary novel physical property rational design response single molecule small molecule superresolution imaging superresolution microscopy theories tool viscoelasticity

项目摘要

Project Summary Recently, breakthrough work has led to a wave of discoveries of biomolecular condensates. Such membraneless organelles that cluster specific biomolecules away from the surrounding cellular milieu have long been theorized and are now experimentally tractable. These dynamic structures contain a wide range of proteins and nucleic acids and assemble through the process of phase separation. While many proteins are prone to phase separation (either by themselves or via complexation with other proteins, nucleic acids, or small molecules), these condensates have primarily been found in eukaryotic cells. Since bacteria do not typically contain membrane-enclosed organelles, we hypothesize that bacteria instead use phase-separated membraneless organelles as novel organizers of their cytoplasm to regulate biochemical activity while they respond to changing environmental conditions. In this proposal, our multidisciplinary team combines state-of-the-art in vitro approaches, in vivo experiments, and in silico modeling and theory to explore the structural organization of the bacterial cytoplasm and characterize phase-separated membraneless organelles in bacteria. We will focus on a candidate protein system, the DNA-binding protein from starved cells (Dps), that drives the organization of the bacterial chromosome and leads DNA to form a separate subcellular compartment within bacterial cells upon stress. We will first study this system’s chemical and mechanical properties, map the phase space for condensate formation, ascertain whether it occurs through spinodal decomposition or nucleation and condensate droplet growth, and determine its kinetics in vitro. Next, we will elucidate how phase separation controls the access of cytoplasmic and nucleoid-associated biomolecules to the bacterial chromosome and image the structure of membraneless DNA-organizing organelles in living bacteria to measure the effect of condensation on chromosome structure and dynamics in vivo. Finally, we will characterize the impact of chromosome phase separation on the mobility of cytoplasmic and DNA-binding proteins in vivo and determine the role of chromosomal condensation in bacterial physiology and survival. Together, our results will define the contributions of the unique physicochemical properties of the bacterial cytoplasm to compartmentalization within these cells. Phase separation provides an alternate mechanism for spatial and functional organization in the bacterial domain of life. Indeed, phase separation is emerging as a universal organizing principle across the tree of life, and our work will ultimately shed light on the origin of life and provide new targets for rationally designed antibiotics.

项目概要最近，突破性的工作引发了一波生物分子凝聚体的发现热潮。将特定生物分子聚集成远离周围细胞环境的无膜细胞器这些动态结构早已被理论化，现在可以通过实验进行处理。蛋白质和核酸通过相分离过程组装。易于发生相分离（通过其本身或通过与其他蛋白质、核酸或小分子络合）分子），这些缩合物主要存在于真核细胞中，因为细菌通常不存在。含有膜封闭的细胞器，我们勇敢地认为细菌使用相分离无膜细胞器作为其细胞质的新型组织者，在它们调节生化活性的同时应对不断变化的环境条件。在这项提案中，我们的多学科团队结合了最先进的体外方法、体内实验、并通过计算机建模和理论探索细菌细胞质的结构组织和表征细菌中相分离的无膜细胞器我们将重点关注候选蛋白质。系统，来自饥饿细胞 (Dps) 的 DNA 结合蛋白，驱动细菌的组织染色体并导致DNA在压力下在细菌细胞内形成独立的亚细胞区室。将首先研究该系统的化学和机械特性，绘制凝结水的相空间形成，确定它是否通过旋节线分解或成核和冷凝液滴发生接下来，我们将阐明相分离如何控制其进入。将细胞质和类核相关生物分子附着到细菌染色体上，并对细菌染色体的结构进行成像活细菌中的无膜 DNA 组织细胞器，用于测量冷凝对最后，我们将描述染色体相位的影响。分离对体内细胞质和 DNA 结合蛋白的迁移率并确定其作用我们的结果将共同定义细菌生理学和存活中的染色体凝聚。细菌细胞质独特的理化性质对区室化的贡献在这些细胞内，相分离为空间和功能组织提供了另一种机制。事实上，在生命的细菌领域，相分离正在成为一种普遍的组织原则。生命之树，我们的工作最终将揭示生命的起源，并为理性研究提供新的目标设计的抗生素。

项目成果

期刊论文数量（4）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Achieving Single-Molecule Tracking of Subcellular Regulation in Bacteria during Real-Time Environmental Perturbations.

在实时环境扰动期间实现细菌亚细胞调节的单分子追踪。

DOI：
发表时间：
2023-01-17
期刊：
影响因子：
7.4
作者：
Calkins, Anna L;Demey, Lucas M;Rosenthal, Brooke M;DiRita, Victor J;Biteen, Julie S
通讯作者：
Biteen, Julie S

Live to fight another day: The bacterial nucleoid under stress.

活着再战：压力下的细菌核。

DOI：
发表时间：
2024-05-01
期刊：
影响因子：
3.6
作者：
Walker, Azra M;Abbondanzieri, Elio A;Meyer, Anne S
通讯作者：
Meyer, Anne S

Bridging DNA contacts allow Dps from E. coli to condense DNA.

桥接 DNA 接触使大肠杆菌的 Dps 能够浓缩 DNA。

DOI：
发表时间：
2024-01-25
期刊：
影响因子：
0
作者：
Shahu, Sneha;Vtyurina, Natalia;Das, Moumita;Meyer, Anne S;Ganji, Mahipal;Abbondanzieri, Elio A
通讯作者：
Abbondanzieri, Elio A

Bridging DNA contacts allow Dps from E. coli to condense DNA.

桥接 DNA 接触使大肠杆菌的 Dps 能够浓缩 DNA。

DOI：
发表时间：
2024-04-04
期刊：
影响因子：
14.9
作者：
Shahu, Sneha;Vtyurina, Natalia;Das, Moumita;Meyer, Anne S;Ganji, Mahipal;Abbondanzieri, Elio A
通讯作者：
Abbondanzieri, Elio A