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含量被解码以产生不同氨基酸的链，称为蛋白质，这些蛋白质决定了细胞的身份和功能。蛋白质是生物学功能的主要效应因素，负责催化大多数生化反应，并发挥许多结构和调节作用。它们通过在所有真核细胞（动物，植物和真菌）中高度相似的过程将它们转化为中间分子Messenger RNA（mRNA）的蛋白质。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，无论是通过改变特定mRNA的翻译水平，也通过针对位置而改变。蛋白质和mRNA都可以定位于细胞中，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。在细胞中特定部位的mRNA定位通常涉及颗粒，这些颗粒包含惰性，翻译状态的mRNA。在细胞逆境时期，mRNA也可以局部化，其中已经确定了两个不同类别的颗粒，即“压力颗粒”和“ P-Bodies”。这些颗粒被认为在剩余mRNA的有用和破坏的存储中起着作用。此外，它们的部署也与人类疾病有关，尤其是在大脑和肌肉疾病中，以及在多细胞动物的发展中，尤其是胚胎发展中的基本作用。由于在酵母中已广泛研究了在定义的细胞区域中的mRNA定位，将细胞应激与p-体和胁迫颗粒中的mRNA定位联系起来，因此我们旨在使用这种简单的模型生物体来揭示该过程的基本分子生物学，以控制蛋白质合成。我们最近的研究发现了两个新发现。令人惊讶的是，即使在积极生长的细胞中，也存在编码参与常规途径（例如糖代谢和翻译本身）的常规途径（例如糖代谢和翻译本身）的mRNA。我们的实验表明，在这些颗粒中，mRNA转化为蛋白质。在第二项研究中，我们发现这些局部mRNA中的大多数不会在蛋白质合成的经典“闭环”模型中相互作用，因此尚不清楚如何翻译这些mRNA。在这个项目中，我们将使用尖端的分子技术来解密mRNA和蛋白质存在于颗粒中，找出它们的翻译方式，并探索其定位的生物学原因。我们将研究mRNA如何局部化，并评估它们如何传递给其子细胞。具体而言，我们将确定来自同一途径或复合物的蛋白质是否在这些位点共同生产和调节。我们还将检验以下假设：关键转录本通过这些颗粒传递给子细胞，作为提供用于发展后代的关键mRNA的“启动式”包装。尽管酵母是一种简单的真核生物，所有已知的翻译控制机制在哺乳动物细胞中都存在于酵母中。因此，我们在酵母上的基本研究将指导和告知其他系统中的研究，并为通常使用酵母菌的工业生物技术表达系统提供替代机制。该提案中的研究很可能允许在此级别进行优化，尤其是对于多蛋白质复合物。

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

Ribosomal flavours: an acquired taste for specific mRNAs?

• DOI: 10.1042/bst20180160
• 发表时间: 2018-12-17
• 期刊: BIOCHEMICAL SOCIETY TRANSACTIONS
• 影响因子: 3.9
• 作者: Bates, Christian;Hubbard, Simon J.;Ashe, Mark P.
• 通讯作者: Ashe, Mark P.

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

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

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

• 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