The function and regulation of translationally active RNA granules

翻译活性RNA颗粒的功能和调控

• 批准号: BB/P018270/1
• 负责人: Mark Peter Ashe
• 金额: $ 63万
• 依托单位: University of Manchester
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2017
• 资助国家: 英国
• 起止时间: 2017 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FP018270%2F1
• 关键词: function; regulation; translationally; active; RNA

Almost all life forms require the capacity to produce energy and a mechanism to convert the information in genes into chains of different amino acids called proteins. Proteins are the principal effectors of biological function, responsible for catalysing most biochemical reactions including those that produce energy and those required for protein production itself. Genes are translated into protein from an intermediate molecule, messenger RNA (mRNA), in a process that is highly similar across all eukaryotic cells (animals, plants and fungi). Both proteins and mRNAs can be localised in cells to allow the generation of local concentrations of specific proteins, and this plays critical roles in the spatial development of cellular zones such as long projections on nerve cells or membrane protrusions on gut cells. mRNA localisation to such sites involves granules which contain the mRNAs in an inert, repressed state. Inert mRNAs can also become localised during cellular adversity, where two different classes of granule have been identified, 'stress granules' and 'P-bodies'. These granules are thought to play roles in both the storage of useful and destruction of surplus mRNAs. Additionally, their deployment has also been linked to human disease, especially in diseases of the brain and muscles, as well as fundamental roles in the development of multicellular animals, especially development of the embryo. We use the simple single-celled organism, brewer's yeast, as a model to study these fundamental processes. mRNA localisation both to defined polarised regions and to P-bodies or stress granules has been widely studied in yeast to uncover key principles that control protein synthesis. Yeast has served as a paradigm in such studies owing to its relatively simple genome, its level of similarity to human cells and the ease with which genes can be mutated, deleted or tagged in some way. In fact whole yeast strains collections have been constructed where all of the yeast genes have been systematically deleted or tagged, and these have facilitated a range of unbiased screens, where individual strains are tested for activity changes.Our recent studies have uncovered a particularly novel finding in yeast- mRNAs encoding non-localised proteins involved in energy generation and protein synthesis are present in mRNA granules even in actively growing cells. Counter to most mRNA localisation events, these mRNAs are not inert, instead they are translated into protein in these granules. We have extended this work in a number of directions. Remarkably, we have found that almost every mRNA across the two pathways is co-localised to and translated in granules. We have taken advantage of yeast as a system to perform unbiased screens and identify genes that are important for these granules. These genes encode proteins with functions such as RNA binding and protein folding. We have also taken hypothesis driven approaches to identify key determinants involved in the localisation of mRNA to granules. As such, we show that DNA sequences dictating mRNA production called promoters, as well as the chemical modification of mRNA are important in determining the fate of specific mRNAs to granules. In this project, we will decipher the precise determinants of mRNA selection to granules and how this impacts on the physiology of cells. We will examine how the mRNAs are marked for a granular fate and investigate the proteins that decipher these marks. We will also investigate the functional rationale for the localisation focussing on energy and protein production, especially during cell division. These fundamental studies will guide and inform studies in other systems including human, as well as provide alternative mechanisms to tweak industrial biotechnology systems where yeast is commonly used. The studies in this proposal may well allow optimisation at this level, especially for multi-protein biochemical pathways.

几乎所有的生命形式都需要产生能量的能力和将基因中的信息转化为称为蛋白质的不同氨基酸链的机制。蛋白质是生物功能的主要效应物，负责催化大多数生化反应，包括产生能量的反应和蛋白质生产本身所需的反应。基因从中间分子信使RNA（mRNA）翻译成蛋白质，其过程在所有真核细胞（动物，植物和真菌）中高度相似。蛋白质和mRNA都可以定位在细胞中，以允许产生特定蛋白质的局部浓度，这在细胞区域的空间发育中起着关键作用，例如神经细胞上的长突起或肠细胞上的膜突起。mRNA定位到这些位点涉及含有处于惰性、受抑制状态的mRNA的颗粒。惰性mRNA也可以在细胞逆境中定位，其中已经鉴定出两种不同类型的颗粒，“应激颗粒”和“P体”。这些颗粒被认为在有用mRNA的储存和剩余mRNA的破坏中发挥作用。此外，它们的部署也与人类疾病有关，特别是在大脑和肌肉疾病中，以及在多细胞动物发育中的基本作用，特别是胚胎发育。我们使用简单的单细胞生物，啤酒酵母，作为研究这些基本过程的模型。mRNA定位于确定的极化区域和P体或应激颗粒已经在酵母中被广泛研究，以揭示控制蛋白质合成的关键原则。由于其相对简单的基因组，其与人类细胞的相似性水平以及基因可以以某种方式突变，删除或标记的容易性，酵母已成为此类研究的范例。事实上，已经构建了完整的酵母菌株收集，其中所有的酵母基因都被系统地删除或标记，这些有助于进行一系列无偏筛选，我们最近的研究在酵母中发现了一个特别新颖的发现--编码非-参与能量产生和蛋白质合成的局部蛋白质存在于mRNA颗粒中，甚至存在于活跃生长的细胞中。与大多数mRNA定位事件相反，这些mRNA不是惰性的，而是在这些颗粒中被翻译成蛋白质。我们已将这项工作扩展到若干方面。值得注意的是，我们已经发现，几乎每一个跨两个途径的mRNA是共定位和翻译的颗粒。我们利用酵母作为一个系统来进行无偏筛选，并确定对这些颗粒重要的基因。这些基因编码具有RNA结合和蛋白质折叠等功能的蛋白质。我们还采取了假设驱动的方法，以确定关键的决定因素参与mRNA的本地化颗粒。因此，我们表明，DNA序列决定mRNA的生产称为启动子，以及mRNA的化学修饰是重要的，在确定特定的mRNA的命运颗粒。在这个项目中，我们将破译mRNA选择颗粒的精确决定因素，以及这对细胞生理学的影响。我们将研究mRNA是如何标记为颗粒状的命运，并研究破译这些标记的蛋白质。我们还将研究定位的功能原理，重点是能量和蛋白质的产生，特别是在细胞分裂期间。这些基础研究将指导和指导包括人类在内的其他系统的研究，并提供替代机制来调整常用酵母的工业生物技术系统。本提案中的研究可能会在这一水平上进行优化，特别是对于多蛋白生化途径。

项目成果

Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses.

• DOI: 10.1186/s13059-017-1338-4
• 发表时间: 2017-10-27
• 期刊: Genome biology
• 影响因子: 12.3
• 作者: Costello JL;Kershaw CJ;Castelli LM;Talavera D;Rowe W;Sims PFG;Ashe MP;Grant CM;Hubbard SJ;Pavitt GD
• 通讯作者: Pavitt GD

Integrated multi-omics reveals common properties underlying stress granule and P-body formation.

综合的多词揭示了应力颗粒和p体形成的共同特性。

• DOI: 10.1080/15476286.2021.1976986
• 发表时间: 2021-11-12
• 期刊: RNA biology
• 影响因子: 4.1
• 作者: Kershaw CJ;Nelson MG;Lui J;Bates CP;Jennings MD;Hubbard SJ;Ashe MP;Grant CM
• 通讯作者: Grant CM

The mTOR-S6 kinase pathway promotes stress granule assembly.

• DOI: 10.1038/s41418-018-0076-9
• 发表时间: 2018-11
• 期刊: Cell death and differentiation
• 影响因子: 12.4
• 作者: Sfakianos AP;Mellor LE;Pang YF;Kritsiligkou P;Needs H;Abou-Hamdan H;Désaubry L;Poulin GB;Ashe MP;Whitmarsh AJ
• 通讯作者: Whitmarsh AJ

Core Fermentation (CoFe) granules focus coordinated glycolytic mRNA localization and translation to fuel glucose fermentation.

核心发酵（COFE）颗粒聚焦的糖酵解mRNA定位和转化为燃料葡萄糖发酵。

• DOI: 10.1016/j.isci.2021.102069
• 发表时间: 2021-02-19
• 期刊: iScience
• 影响因子: 5.8
• 作者: Morales-Polanco F;Bates C;Lui J;Casson J;Solari CA;Pizzinga M;Forte G;Griffin C;Garner KEL;Burt HE;Dixon HL;Hubbard S;Portela P;Ashe MP
• 通讯作者: Ashe MP

Translation factor and RNA binding protein mRNA interactomes support broader RNA regulons for posttranscriptional control.

翻译因子和RNA结合蛋白mRNA相互作用组支持更广泛的RNA调节，用于转录后控制。

• DOI: 10.1016/j.jbc.2023.105195
• 发表时间: 2023-10
• 期刊: JOURNAL OF BIOLOGICAL CHEMISTRY
• 影响因子: 4.8
• 作者: Kershaw, Christopher J.;Nelson, Michael G.;Castelli, Lydia M.;Jennings, Martin D.;Lui, Jennifer;Talavera, David;Grant, Chris M.;Pavitt, Graham D.;Hubbard, Simon J.;Ashe, Mark P.
• 通讯作者: Ashe, Mark P.