Mechanisms of circadian clock and codon usage biases

生物钟和密码子使用偏差的机制

• 批准号: 10166524
• 负责人: YI LIU
• 金额: $ 65.72万
• 依托单位: UT SOUTHWESTERN MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-04-04 至 2026-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10166524
• 关键词: Address; Animals; Behavioral; Biochemical; Biological Phenomena; Biological Process; CSNK1A1 gene; Cell physiology; Circadian Rhythms; Codon Nucleotides; Disease; Drosophila genus; Eukaryota; Frequencies; Gene Expression; Gene Proteins; Genetic Code; Genetic Screening; Genetic Transcription; Genome; Goals; Human; Lead; Mammals; Mental Health; Mental disorders; Methods; Molecular; Mus; Neurospora; Organism; Output; Physiological; Physiological Processes; Physiology; Play; Process; Proteins; Reporter; Role; Sleep Disorders; Speed; System; Therapeutic; Tissues; Translations; Work; base; cell type; circadian; circadian pacemaker; fungus; human disease; in vivo; novel; protein folding; protein structure; temporal measurement

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.

抽象的 该提案将重点关注两种基本生物机制的理解 真核生物现象：生物钟和密码子使用偏差。生物钟控制着不同的细胞， 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 真核生物钟的节律。我们之前的研究为 了解真核生物钟机制。同义密码子不与同等密码子一起使用 所有检查的基因组中的频率，这种现象称为密码子使用偏差。尽管现象 密码子使用偏倚的作用已为人所知数十年，密码子使用偏倚的功能和机制 不清楚。我们之前的工作表明，密码子的使用是遗传密码的一个新层，可以 确定基因表达水平和蛋白质结构。我们的实验室使用脉孢菌、果蝇和 哺乳动物系统来研究这两种现象。 对于生物钟项目，我们建议重点关注生物钟振荡器的几个关键方面 脉孢菌和哺乳动物时钟系统中的机制。我们将确定角色和机制 FRQ-CK1a 在脉孢菌昼夜节律测定中的相互作用。此外，我们还将扩大我们的研究范围 通过确定 PERIOD-CK1 相互作用在哺乳动物昼夜节律中的作用，将其引入哺乳动物系统 钟。这些研究将建立一种用于真菌和动物周期测定的保守机制。 尽管脉孢菌中的 FRQ 和动物中的 PER 蛋白不被认为是同源的，但大多数 预计这两种蛋白质中的结构域本质上是无序的，并且都逐渐变得无序。 磷酸化。我们将使用生物化学和生物钟来确定 FRQ 和 PER 在生物钟中的功能。 分子方法。对于密码子使用项目，我们将基于我们对角色的突破性发现 以及确定基因表达和蛋白质结构中密码子使用偏差的机制。我们将 确定密码子使用对脉孢菌基因转录影响的机制 之前进行过大规模的基因筛查。这项研究将揭示其背后的机制 密码子使用对基因转录的保守效应。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基因在小鼠中表达。本研究将建立机制 有助于密码子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 此外，我们将开发一种根据密码子使用的作用来调节翻译延伸速度的方法 调节蛋白质折叠，有望用于治疗许多疾病。在一起，这些 研究将解决对于我们理解这两种生物学至关重要的基本问题 真核生物中的现象。