A systems analysis of the translational release factor as a coordinator of termination mRNA stability and ribosome recycling

近年来，许多基因组测序已经完成，当然也包括人类基因组。基因组中的每一个基因都被用来指导特定蛋白质的合成。蛋白质是细胞中的功能因子，例如作为催化剂加速细胞内的单个化学反应。基因中的信息，编码为碱基A，T，C和G的不同序列，用于在两个阶段的过程中制造蛋白质。首先，基因信息以信使RNA（mRNA）的形式复制到类似的碱基链中。mRNA是一种长链样分子，然后被用作信息存储器来指导蛋白质的组装，该蛋白质由一条氨基酸链组成，在一个称为翻译的过程中。氨基酸的精确序列（由mRNA碱基序列指导）决定了蛋白质的最终功能。氨基酸序列由mRNA序列定义，mRNA序列又由基因序列定义，从而将基因与蛋白质连接起来。翻译过程是本研究的重点。在翻译过程中，被称为核糖体的小颗粒（它们本身由RNA和蛋白质组成）沿着mRNA移动，依次添加氨基酸以形成最终的蛋白质。这条生产线的过程被停止（终止），以响应mRNA中特定的碱基序列，导致完整蛋白质的释放。终止对于确保蛋白质具有正确的长度至关重要。现在已知，终止后，核糖体被引导回到mRNA的起始处，有效地将它们在mRNA链上循环。这使得翻译过程更有效，但在mRNA生产线上产生非常复杂的核糖体交通流。出于这个原因，核糖体流动的数学模型将与生化实验一起用于这项研究，以帮助解开控制翻译的机制。这项建议旨在研究翻译终止有两个重要原因。首先，在许多人类遗传疾病中，受影响的基因（例如囊性纤维化，杜氏肌营养不良症）发生突变，因为它在基因序列的早期含有额外的终止密码子。这具有过早终止翻译的效果，导致缩短的无功能蛋白质。人们对开发使翻译终止不那么准确的药物越来越感兴趣。这将允许核糖体绕过早期终止密码子并到达天然终止密码子以产生正确长度的蛋白质。研究终止的分子机制，正如这个建议所描述的，可以提供直接用于药物开发的关键见解，以治疗某些形式的人类遗传疾病。终止也很重要，因为与此过程相关的是mRNA上核糖体的再循环。在信息结束时终止后，核糖体主动返回到mRNA的起始处，以从相同的模板制造新的蛋白质，形成一种环形核糖体赛道;赛道的每一个回路都导致一种新的蛋白质被制造。人们对回收过程知之甚少，但它是蛋白质合成效率的关键。通过了解循环是如何工作的，有可能提高细胞中蛋白质合成的效率，这对制造B型肝炎疫苗和胰岛素等药物至关重要。总之，翻译终止过程在每个细胞中的基因表达中至关重要，因此具有基本的“纯”研究兴趣。然而，它也是理解蛋白质如何在药物制造中重要的生物技术过程中有效制造的关键，也是治疗一系列极度衰弱的人类遗传疾病的药物的有吸引力的目标。

Recent years have seen a host of genome sequences being completed, including of course the human genome. Each gene in a genome is used to direct the synthesis of a specific protein. It is the proteins that are the functional agents in a cell, for example acting as catalysts to speed individual chemical reactions within the cell. Information in the gene, coded as different sequences of the bases A, T, C and G, is used to make a protein in a two-stage process. First, the gene information is copied into a similar chain of bases in the form of a messenger RNA (mRNA). The mRNA, a long chain-like molecule, is then used as an information store to direct the assembly of a protein, consisting of a chain of amino acids, in a process called translation. The precise sequence of amino acids (directed by the mRNA base sequence) determines the eventual function of the protein. The amino acid sequence is defined by the mRNA sequence, which in turn is defined by the gene sequence, thus linking gene to protein. The process of translation forms the focus of this research proposal. During translation, small particles called ribosomes (themselves made of RNA and protein) travel along the mRNA, sequentially adding amino acids to make the final protein. This production line process is stopped (terminated) in response to a specific sequence of bases in the mRNA, causing the release of the completed protein. Termination is crucial for ensuring the protein made is of the correct length. It is now known that following termination, ribosomes are directed back to the beginning of the mRNA, effectively recycling them on the mRNA chain. This makes the translation process more efficient, but generates very complex ribosome traffic flow on the mRNA production line. For this reason, mathematical modelling of ribosome flow will be used in this research alongside the biochemical experimentation to help unravel the mechanisms by which translation is controlled. This proposal seeks to study translation termination for two important reasons. First, in many human genetic diseases, the affected gene (e.g cystic fibrosis, Duchenne muscular dystrophy) is mutated because it contains an additional stop codon early in the gene sequence. This has the effect of prematurely terminating translation, resulting in a shortened, non-functional protein. There is increasing interest in developing drugs that would make translation termination less accurate. This would allow the ribosome to bypass the early stop codon and reach the natural stop codon to make correct length protein. Research into the molecular mechanisms of termination, as this proposal describes, can provide crucial insight used directly in the development of drugs to treat some forms of human genetic disease. Termination is also important because associated with this process is the recycling of the ribosomes on the mRNA. After termination at the end of the message, ribosomes are actively returned to the beginning of the mRNA to make a new protein from the same template, forming a type of circular ribosomal race track; each circuit of the track results in a new protein being made. The recycling process is very poorly understood, and yet it is key to protein synthetic efficiency. By understanding how recycling works, it may be possible to boost the efficiency of protein synthesis in cells, which is crucial for the manufacture of drugs like hepatitis B vaccine and insulin, to name but two. In summary then, the process of translation termination is crucially important in the expression of genes in every cell, and thus has fundamental 'pure' research interest. It is however also a key to understand how proteins can be made efficiently in biotechnological processes important in drug manufacture, and is also an attractive target for drugs that can treat a range of extremely debilitating human genetic diseases.