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: 10395606
• 负责人: YI LIU
• 金额: $ 65.81万
• 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/10395606
• 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 该建议将重点介绍对两个基本生物学机制的理解 真核生物中的现象：昼夜节律和密码子使用偏见。昼夜节律控制多种细胞， 真核生物的生理和行为过程。我们的长期目标是了解 允许时间和昼夜节律输出的分子和生化机制 真核生物昼夜节律的节奏。我们以前的研究为 理解真核昼夜节律的时钟机制。同义密码子不相等地使用 所有检查的基因组中的频率，一种称为密码子使用偏置的现象。即使现象 密码子的使用偏差已知数十年，这是密码子使用偏见的功能和机制 不清楚。我们以前的工作表明，密码子的使用是遗传密码的新层，可以 确定基因表达水平和蛋白质结构。我们的实验室使用Neurospora，果蝇和 哺乳动物系统研究这两种现象。 对于昼夜节目项目，我们建议专注于昼夜节律振荡器的几个关键方面 Neurospora和哺乳动物时钟系统的机制。我们将确定 神经孢子中的昼夜节律测定中的FRQ-CK1A相互作用。此外，我们将扩大研究 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保守的机制，用于真菌和动物的周期测定。 尽管神经孢子中的FRQ和动物中的每蛋白不被认为是同源的，但大多数 两种蛋白质中的结构域被预测是本质上无序的，并且均逐渐 磷酸化。我们将使用生化和 分子方法。对于密码子使用项目，我们将建立关于角色的开创性发现 密码子使用的机制在确定基因表达和蛋白质结构中存在偏见。我们将 确定基于A的神经孢子中基因转录的密码子使用效应的机制 先前进行的大规模遗传筛选。这项研究将揭示其基础的机制 密码子使用对基因转录的保守作用。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用法记者在小鼠中的表达。这项研究将确定一种机制 有助于密码子使用对哺乳动物中组织和细胞类型特异性基因表达的影响。在 此外，我们还将根据密码子的作用来开发一种调节翻译伸长速度的方法 在调节蛋白质折叠时，该蛋白质有可能用于治疗许多疾病。在一起，这些 研究将解决对我们对这两个生物学的理解至关重要的基本问题 真核生物的现象。