In-Sequence Coding of Stochastic Gene Expression Via Synonymous Mutations

通过同义突变进行随机基因表达的顺序编码

• 批准号: 1409321
• 负责人: Philippe Cluzel
• 金额: $ 70.34万
• 依托单位: Harvard University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-07-15 至 2018-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1409321&HistoricalAwards=false
• 关键词: Sequence; Coding; Stochastic; Gene; Expression

Because 18 of the 20 amino acids are encoded at the DNA level with multiple synonymous codons, the genetic code used during protein synthesis is highly redundant -- a codon is the sequence of three DNA base pairs coding an amino acid. While it is well known that proteins can be encoded by different synonymous codons, the role of this redundant code on the efficiency of protein synthesis has remained unclear. Remarkably, the investigator found that under nutrient starvation, synonymous codons played very distinct roles on both synthesis levels and the variations from one cell to another of the quantity of synthetized proteins. Some codons were found to be robust to the limitation of certain amino acids, allowing for stronger protein expression, while others were sensitive to this limitation yielding low levels of protein expression. Importantly, cells are believed to starve during the formation of bacterial biofilms or during cancerous proliferation for which synonymous codons should play an important role in regulating protein synthesis. Therefore, the goal of this project is to quantify and establish the role of synonymous codons in protein synthesis during starvation of nutrients. The training of students with scientific backgrounds in mathematics or biology is an important component of this effort. Students will have the opportunity for hands-on participation in dynamics simulation of gene expression extracted from data made possible by this project. Over the last decade, there has been considerable interest from physicists and biologists to develop a quantitative framework to predict the stochastic behavior of gene expression at the single cell level. In bacteria, a clear picture has emerged: noise in gene expression is mainly caused by transcriptional bursts that are Poisson distributed and translation solely amplifies these fluctuations. While this canonical model holds when bacteria grow in rich media, it fails to explain the observed noise when bacteria are exposed to environmental perturbations such as nutrient limitation. The outcome of this project will be to create a novel physical framework to predict the noise in gene expression governed by the in-sequence distribution of sensitive synonymous codons under environmental perturbations. Here the investigator proposes to characterize the noise associated with robust and sensitive codons when used to encode the expression of the yellow fluorescent protein. Firstly, the investigator will focus on quantifying the stochastic cell-to-cell behavior in gene expression arising from synonymous codon choice. Secondly, work will be done to identify how the dynamics associated with the translation of synonymous sensitive codons exhibits near-critical behavior. Finally, the third aim examines the contribution of the variations of key intracellular parameters as control parameters of noise driven by synonymous codons under well-characterized environmental perturbations.This award is supported jointly by the Physics of Living Systems Program in the Physics Division and the Cellular Dynamics and Function Program in the Division of Molecular and Cellular Biosciences.

由于 20 个氨基酸中的 18 个是在 DNA 水平上用多个同义密码子编码的，因此蛋白质合成过程中使用的遗传密码是高度冗余的——密码子是编码氨基酸的三个 DNA 碱基对的序列。虽然众所周知蛋白质可以由不同的同义密码子编码，但这种冗余密码对蛋白质合成效率的作用仍不清楚。值得注意的是，研究人员发现，在营养匮乏的情况下，同义密码子在合成水平以及从一个细胞到另一个细胞的合成蛋白质数量的变化方面发挥着非常独特的作用。一些密码子被发现对某些氨基酸的限制具有鲁棒性，从而允许更强的蛋白质表达，而另一些密码子对此限制敏感，产生低水平的蛋白质表达。重要的是，细胞被认为在细菌生物膜形成或癌性增殖过程中会挨饿，而同义密码子在调节蛋白质合成中应发挥重要作用。因此，该项目的目标是量化和确定营养饥饿期间同义密码子在蛋白质合成中的作用。对具有数学或生物学科学背景的学生的培训是这项努力的重要组成部分。学生将有机会亲自参与从该项目提供的数据中提取的基因表达的动态模拟。 在过去的十年中，物理学家和生物学家对开发一个定量框架来预测单细胞水平上基因表达的随机行为表现出极大的兴趣。在细菌中，一幅清晰的图景已经出现：基因表达中的噪音主要是由泊松分布的转录爆发引起的，而翻译只会放大这些波动。虽然当细菌在丰富的培养基中生长时，这种规范模型成立，但它无法解释当细菌暴露于营养限制等环境扰动时观察到的噪音。该项目的成果将是创建一个新颖的物理框架来预测环境扰动下敏感同义密码子的顺序分布所控制的基因表达噪音。在这里，研究人员建议表征当用于编码黄色荧光蛋白的表达时与稳健和敏感密码子相关的噪声。首先，研究人员将重点量化同义密码子选择引起的基因表达中的随机细胞间行为。其次，将开展工作以确定与同义敏感密码子翻译相关的动态如何表现出近临界行为。最后，第三个目标研究了关键细胞内参数的变化作为在明确的环境扰动下由同义密码子驱动的噪声控制参数的贡献。该奖项由物理部门的生命系统物理学项目和细胞研究中心共同支持分子和细胞生物科学部的动力学和功能项目。