Ribosome traffic flow on the mRNA as a regulator of cellular protein production: an integrated modelling and experimental analysis

在这项提案中，一个由生物学家和物理学家组成的跨学科团队将建立预测细胞蛋白质组成的新技术。蛋白质被所有有机体内的细胞用来执行构成生命的基本生化过程。知道一个细胞正在制造哪些蛋白质和多少数量，就定义了那个特定细胞的特性。因此，能够预测细胞的蛋白质组成是理解细胞生物学的一个非常强大的工具。蛋白质本身是由一串名为氨基酸的化学成分组成的，其中有20种不同的类型。正是蛋白质链中氨基酸的独特序列赋予了蛋白质的生化和催化特性。即使是像面包师酵母这样相对简单的有机体，也可以有大约6000种不同的蛋白质，每种蛋白质都有自己特定的氨基酸序列。细胞使用其基因中编码的信息来制造正确的氨基酸序列的蛋白质。每个基因编码一种蛋白质类型，因此面包师酵母有6000个基因编码相同数量的不同蛋白质。为了制造蛋白质，基因中的编码信息首先被复制到一个被称为信使RNA或mRNA的短的线性分子中。然后，一组称为核糖体的生物分子读取信使核糖核酸中的信息，这一过程称为翻译。核糖体沿着信使核糖核酸从一端移动到另一端，读取信使核糖核酸中编码的信息，并通过顺序添加氨基酸来翻译信使核糖核酸形成蛋白链。氨基酸通过转移RNA分子(TRNAs)进入核糖体。然后，这种蛋白质被释放出来，在细胞中发挥其功能。事实上，这种信使核糖核酸可以被多个核糖体同时翻译，核糖体就像汽车在路上一样紧随其后。这种交通类比相当贴切；有时，就像汽车被困在交通堵塞中一样，核糖体在翻译信使核糖核酸时会放慢速度，甚至完全停顿，通常是对难以翻译的信使核糖核酸片段做出反应。当这种情况发生时，核糖体的队列可能会堆积起来，从而降低蛋白质的生产速度。所有的mRNA都由许多不同的慢速和快速翻译区域组成，例如，由不同tRNA物种的不同丰度引起的。然后，核糖体队列可以开始合并，有时会延伸到信使核糖核酸的开头，阻止核糖体加入信使核糖核酸。这将减少由该信使核糖核酸指导的蛋白质合成量。因此，核糖体在mRNAs上的流量是不同蛋白质合成数量的关键调节因素。因此，为了了解细胞将表达哪些蛋白质群体，以及以什么数量表达，需要能够预测核糖体在mRNA上的流量，以及整个核糖体群体如何与酵母中的6000个mRNA中的每一个相互作用。准确预测核糖体在翻译时如何相互作用和排队是一项具有挑战性的任务，需要联合应用数学和生物学技术。在这项提议之前的工作中，我们开发了一个数学模型来模拟核糖体在mRNAs上的流量。这个模型对核糖体流量如何影响mRNAs的翻译做出了一些重要的预测，这些预测将在这项提议中得到检验。拟议的研究还将进一步发展该模型，纳入对翻译过程的详细数学描述。该模型将通过实验分析酵母中的翻译反应来进行测试和验证。总体而言，这种跨学科的方法不仅将提供对细胞用来表达其基因的基本机制的真正洞察，而且将对生物学和物理学中的许多其他交通流量系统的研究产生影响。

In this proposal, an interdisciplinary team of biologists and physicists will establish novel technologies to predict the protein composition of a cell. Proteins are used by the cells within all organisms to carry out the essential biochemical processes that constitute life. Knowing which proteins and in what quantities are being made by a cell, defines the properties of that particular cell. Being able to predict the protein composition of a cell therefore represents a very powerful tool to understand cell biology. Proteins themselves are made of a string of chemical building blocks called amino acids, of which there are twenty different types. It is the distinct sequence of the amino acids in the protein chain that gives the protein its biochemical and catalytic properties. Even a relatively simple organism such as baker's yeast, the subject of this proposal, can have about 6,000 different varieties of protein, each with its own specific amino acid sequence. The cell makes proteins of the correct amino acid sequence using information encoded in its genes. Each gene codes for a single protein type, so baker's yeast has 6,000 genes encoding the same number of distinct proteins. To make a protein, the coding information in a gene is first copied into a short linear molecule termed a messenger RNA, or mRNA. Then an assembly of bio-molecules called ribosome reads the information within the mRNA, a process called translation. The ribosome moves along the mRNA from one end to the other, reading the information coded in the mRNA, and translating it by sequentially adding the amino acids to make a protein chain. The amino acids are brought to the ribosomes by transfer RNA molecules (tRNAs). The protein is then released to carry out its function in the cell. In fact, the mRNA can by translated by multiple ribosomes at the same time, with ribosomes following each other like cars down a road. This traffic analogy is rather apt; sometimes, just as cars get stuck in a traffic jam, so ribosomes can slow down or even pause completely as they translate the mRNA, usually in response to a section of the mRNA that is difficult to translate. When this happens, queues of ribosomes can build up, reducing the rate at which that protein is produced. All mRNAs are comprised of many different slowly and rapidly translated regions, for instance, caused by different abundances of distinct tRNA species. Ribosome queues can then begin to merge, sometimes extending back to the beginning of the mRNA and preventing ribosomes from joining the mRNA. This will reduce the amount of protein synthesis directed by that mRNA. Ribosomal traffic flow on mRNAs is therefore a key regulator of the quantities of the different proteins being made. To understand which population of proteins a cell will express, and in which quantities, therefore requires an ability to predict ribosomal traffic flow on the mRNA, and how whole populations of ribosomes interact with each of the 6,000 mRNAs in yeast. Predicting exactly how ribosomes interact and queue as they translate is a challenging task that requires joint application of both mathematical and biological techniques. In work leading up to this proposal, we have developed a mathematical model to simulate ribosome traffic on mRNAs. This model makes a number of important predictions about how ribosome traffic flow affects the translation of mRNAs, predictions that will be tested in this proposal. The proposed research will also develop the model much further, incorporating detailed mathematical descriptions of the translation process. The model will be tested and validated by experimentally analysing translation reactions in yeast. Overall, the interdisciplinary approach will not only provide genuine insight into the fundamental mechanisms a cell uses to express its genes, but will have implications for the study of many other traffic flow systems in Biology and Physics.