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: 10597614
• 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/10597614
• 关键词: 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; Mammals; Mental Health; Mental disorders; Methods; Molecular; Mus; Neurospora; Organism; Output; Phosphorylation; Physiological; Physiological Processes; Physiology; Play; Process; Proteins; Reporter; Role; Sleep Disorders; Speed; System; Therapeutic; Tissues; Translations; Work; 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.

摘要 该提案将侧重于理解两种基本生物学机制， 真核生物现象：生物钟和密码子使用偏好。生物钟控制着不同的细胞， 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物化学机制 真核生物的生物钟。我们以前的研究为 了解真核生物的生物钟机制。同义密码子不与equal 频率在所有基因组检查，一种现象称为密码子使用偏好。尽管这种现象 密码子使用偏性的研究已有几十年的历史， 不清楚。我们以前的工作表明，密码子使用是遗传密码的一个新的层次，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 链孢菌和哺乳动物生物钟系统的机制。我们将确定的作用和机制， FRQ-CK 1a在脉孢菌昼夜节律周期测定中的相互作用此外，我们将扩大我们的研究， 通过确定PERIOD-CK 1相互作用在哺乳动物昼夜节律中的作用， 时钟这些研究将为真菌和动物的周期确定建立一个保守的机制。 尽管认为链孢菌中的FRQ和动物中的PER蛋白不同源，但大多数链孢菌中的FRQ和PER蛋白都是同源的。 这两种蛋白质中的结构域被预测为本质上是无序的， 磷酸化我们将使用生物化学和生物信息学方法来确定FRQ和PER在生物钟中的作用， 分子方法对于密码子使用项目，我们将建立在我们的突破性发现的作用， 以及决定基因表达和蛋白质结构的密码子使用偏好的机制。我们将 基于一个密码子选择对链孢霉基因转录的影响机制， 之前进行过大规模的基因筛查这项研究将揭示的机制，背后的 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使用报告基因在小鼠中表达。本研究将建立一种机制， 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具有潜在的用途，可用于治疗许多疾病。所有这些 研究将解决对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。