Mechanisms of circadian clock and codon usage biases

摘要 这项建议将侧重于对两种基本生物学机制的理解 真核生物中的现象：生物钟和密码子使用偏向。生物钟控制不同的细胞， 真核生物的生理和行为过程。我们的长期目标是了解 允许测量时间和昼夜节律输出的分子和生化机制 真核生物生物钟的节律。我们以前的研究对 了解真核生物的生物钟机制。同义密码子不能与EQUAL一起使用 研究了所有基因组中的频率，这种现象被称为密码子使用偏向。即使这一现象 密码子使用偏倚的研究已经有几十年的历史了，密码子使用偏爱的功能和机制 都不清楚。我们之前的工作表明，密码子的使用是遗传密码层的一个新层，它可以 确定基因表达水平和蛋白质结构。我们实验室使用的是脉孢子虫、果蝇和 哺乳动物系统来研究这两种现象。 对于昼夜节律时钟项目，我们建议关注昼夜节律振荡器的几个关键方面 脉孢子虫和哺乳动物时钟系统中的机制。我们将确定其作用和机制。 FRQ-CK1a相互作用在决定脉孢子虫昼夜节律中的作用此外，我们将扩大我们的研究范围 通过确定周期-CK1相互作用在哺乳动物昼夜节律中的作用进入哺乳动物系统 钟。这些研究将建立一种在真菌和动物中确定周期的保守机制。 尽管脉孢子虫中的FRQ和动物中的PER蛋白被认为不是同源的，但大多数 这两种蛋白质中的结构域都被预测为本质上无序的，并且都是逐渐地 磷酸化。我们将使用生物化学和生物化学来确定FRQ和PER如何在生物钟中发挥作用 分子方法。对于密码子使用项目，我们将建立在我们在角色上的开创性发现之上 以及密码子使用偏向决定基因表达和蛋白质结构的机制。我们会 确定密码子使用对脉孢子菌基因转录影响的机制 此前进行了大规模的基因筛查。这项研究将揭示 密码子使用对基因转录的保守影响。我们将评估密码子的使用如何影响基因 通过创建体内密码子使用报告在小鼠中表达。这项研究将建立起 密码子的使用对哺乳动物组织和细胞类型特异性基因表达的影响。在……里面 此外，我们将开发一种基于密码子使用的作用来调节翻译延伸速度的方法 在调节蛋白质折叠方面，这将有可能用于治疗许多疾病。加在一起，这些 研究将解决对我们理解这两个生物学至关重要的基本问题 真核生物中的现象。

ABSTRACT This proposal will be focused on the understanding of mechanisms of two fundamental biological phenomena in eukaryotes: the circadian clock and codon usage bias. Circadian clocks control diverse cellular, physiological, and behavioral processes in eukaryotic organisms. Our long-term goal is to understand the molecular and biochemical mechanisms that permit the measurement of time and the output of circadian rhythms in eukaryotic circadian clocks. Our previous studies made fundamental contributions to the understanding of the eukaryotic circadian clock mechanisms. Synonymous codons are not used with equal frequencies in all genomes examined, a phenomenon called codon usage bias. Even though the phenomenon of codon usage bias has been known for several decades, the functions and mechanisms of codon usage bias are unclear. Our previous work demonstrate that codon usage is a novel layer of the genetic code that can determine both gene expression levels and protein structures. Our lab uses Neurospora, Drosophila and mammalian systems to study these two phenomena. For the circadian clock project, we propose to focus on several key aspects of the circadian oscillator mechanism in both Neurospora and mammalian clock systems. We will determine the role and mechanism of FRQ-CK1a interaction in circadian period determination in Neurospora. In addition, we will expand our study into a mammalian system by determining the role of the PERIOD-CK1 interaction in the mammalian circadian clock. These studies will establish a conserved mechanism for period determination in fungi and animals. Although FRQ in Neurospora and PER proteins in animals are not considered homologous, most of the domains in both proteins are predicted to be intrinsically disordered and both are progressively phosphorylated. We will determine how FRQ and PER function in the circadian clock using biochemical and molecular methods. For the codon usage project, we will build on our ground-breaking discoveries on the roles and mechanisms of codon usage biases in determining gene expression and protein structures. We will determine the mechanism of the codon usage effect on gene transcription in Neurospora based on a previously performed large-scale genetic screen. This study will reveal the mechanisms that underlie the conserved effect of codon usage on gene transcription. We will evaluate how codon usage influences gene expression in mice by creating an in vivo codon usage reporter. This study will establish the mechanism that contributes to effects of codon usage on tissue- and cell type-specific gene expression in mammals. In addition, we will develop a method to modulate translation elongation speed based on the role of codon usage in regulating protein folding that will have potential for use in treatment of many diseases. Together, these studies will address fundamental questions that are critical for our understanding of these two biological phenomena in eukaryotes.