Mapping global mRNA fate: integrating translational and spatial dynamics

绘制全球 mRNA 命运：整合翻译和空间动态

• 批准号: BB/N000757/1
• 负责人: Mark Peter Ashe
• 金额: $ 54.9万
• 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: 2016
• 资助国家: 英国
• 起止时间: 2016 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FN000757%2F1
• 关键词: Mapping; global; mRNA; fate; integrating

The information content of genes in living cells is decoded to produce chains of different amino acids called proteins that dictate the identity and function of a cell. Proteins are the principal effectors of biological function, responsible for catalysing most biochemical reactions, as well as serving numerous structural and regulatory roles. They are translated into protein from an intermediate molecule, messenger RNA (mRNA), by a process that is highly similar across all eukaryotic cells (animals, plants and fungi). It is becoming increasingly clear that this translation process is a key regulatory step in the control of protein level (and hence biological function and cellular state), both by changing the level of translation of specific mRNAs and also by targeting the location. Both proteins and mRNAs can be localised within cells to facilitate the generation of local concentrations of particular proteins, and this plays critical roles in the spatial development of specific cellular zones such as axons on neurons or microvilli on intestinal cells. mRNA localisation to specific sites in cells usually involves granules which contain the mRNAs in an inert, translationally repressed state. mRNAs can also become localised during times of 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. Since mRNA localisation to defined cellular regions has been widely studied in yeast, linking cellular stress to mRNA localisation in both P-bodies and stress granules, we aim to use this simple model organism to uncover the fundamental molecular biology of this process for the control of protein synthesis. Our recent studies have uncovered two novel findings. Surprisingly, mRNAs encoding unlocalised proteins involved in routine pathways such as sugar metabolism and translation itself are present in mRNA granules, even in actively growing cells. Our experiments suggest that mRNA translation into protein occurs in these granules. In a second study, we have found that most of these localised mRNAs do not interact in a classical "closed loop" model of selection for protein synthesis, making it unclear how these mRNAs are translated. In this project we will use cutting-edge molecular technologies to decipher which mRNAs and proteins are present in the granules, find out how they are translated, and explore the biological reasons for their localisation. We will examine how mRNAs become localised and also assess how they are passed on to their daughter cells. Specifically, we will determine whether proteins from the same pathway or complex are co-ordinately produced and regulated at these sites. We will also test the hypothesis that key transcripts are passed on to daughter cells via these granules, as a means to provide a "start-up pack" of key mRNAs for developing progeny.Although yeast is a simple eukaryote, all known mechanisms of translational control utilised in yeast are present in mammalian cells. Hence, our fundamental studies in yeast will guide and inform studies in other systems including human, as well as provide alternative mechanisms to tweak industrial biotechnology expression systems where yeast is commonly used. The studies in this proposal may well allow optimisation at this level, especially for multi-protein complexes.

活细胞中基因的信息内容被解码，产生不同的氨基酸链，称为蛋白质，决定细胞的身份和功能。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，以及担任许多结构和调节角色。它们从中间分子信使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。越来越清楚的是，这种翻译过程是控制蛋白质水平（以及生物学功能和细胞状态）的关键调节步骤，既可以通过改变特定mRNA的翻译水平，也可以通过靶向定位。蛋白质和mRNA都可以定位在细胞内，以促进特定蛋白质的局部浓度的产生，这在特定细胞区域的空间发育中起着关键作用，例如神经元上的轴突或肠细胞上的微绒毛。mRNA定位于细胞中的特定位点通常涉及含有处于惰性、抑制状态的mRNA的颗粒。mRNA也可以在细胞逆境期间变得局部化，其中已经鉴定了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。由于mRNA定位到确定的细胞区域已被广泛研究，在酵母中，连接细胞应力mRNA定位在P-体和应力颗粒，我们的目标是使用这个简单的模式生物体来揭示这一过程的基本分子生物学控制蛋白质合成。我们最近的研究发现了两个新的发现。令人惊讶的是，编码参与常规途径（如糖代谢和翻译本身）的非定位蛋白质的mRNA存在于mRNA颗粒中，即使在活跃生长的细胞中也是如此。我们的实验表明，mRNA翻译成蛋白质发生在这些颗粒。在第二项研究中，我们发现大多数这些局部mRNA在蛋白质合成的经典“闭环”选择模型中不相互作用，因此不清楚这些mRNA是如何翻译的。在这个项目中，我们将使用尖端分子技术来破译颗粒中存在哪些mRNA和蛋白质，找出它们是如何翻译的，并探索它们定位的生物学原因。我们将研究mRNA是如何定位的，并评估它们是如何传递到子细胞的。具体来说，我们将确定来自相同途径或复合物的蛋白质是否在这些位点协同产生和调节。我们还将测试的假设，关键转录传递到子细胞通过这些颗粒，作为一种手段，以提供一个“启动包”的关键mRNA的发展profion.Although酵母是一个简单的真核生物，所有已知的机制，利用酵母翻译控制存在于哺乳动物细胞。因此，我们对酵母的基础研究将指导和告知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表达系统。本提案中的研究可能很好地允许在这一水平上进行优化，特别是对于多蛋白复合物。

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

Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions.

• DOI: 10.1038/s41598-018-26170-5
• 发表时间: 2018-05-21
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: Talavera D;Kershaw CJ;Costello JL;Castelli LM;Rowe W;Sims PFG;Ashe MP;Grant CM;Pavitt GD;Hubbard SJ
• 通讯作者: Hubbard SJ

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

The role of PKA in the translational response to heat stress in Saccharomyces cerevisiae.

• DOI: 10.1371/journal.pone.0185416
• 发表时间: 2017
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Barraza CE;Solari CA;Marcovich I;Kershaw C;Galello F;Rossi S;Ashe MP;Portela P
• 通讯作者: Portela P