The functional and adaptive roles of RNA recoding

RNA重编码的功能和适应性作用

基本信息

批准号：
10723394
负责人：
Kavita Rangan
金额：
$ 12.44万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN DIEGO
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-08-01 至 2025-07-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10723394
关键词：
Acclimatization Affect Amino Acid Substitution Aspergillus Aspergillus nidulans Bioinformatics Biological Assay Biology Carrier Proteins Cell physiology Cephalopoda Code Codon Nucleotides Complex Cues DNA DNA Polymerase II DNA Repair DNA Repair Gene DNA biosynthesis DNA-Directed DNA Polymerase Data Development Development Plans Dynein ATPase Early Endosome Environment Epigenetic Process Exposure to Fungal RNA Genetic Genomics Homologous Gene Human In Vitro Intracellular Transport Kinesin Label Maps Mentors Messenger RNA Microscope Microtubules Mining Molds Molecular Motor Mutagenesis Mutation Neurospora Neurospora crassa Oceans Organism Phase Phenotype Physiological Polymerase Primer Extension Property Proteins Publishing RNA RNA Editing Recombinants Regulation Reporter Research Role Seawater Secretory Vesicles Site Squid Temperature Testing Tissues Training Variant Work Yeasts career career development cell motility cell type epigenetic regulation experimental study fungus genetic information in vivo interest mutant mutation assay novel programs protein aminoacid sequence protein complex protein function response screening single molecule success symposium trafficking transcriptome sequencing

项目摘要

PROJECT SUMMARY Organisms use a variety of molecular mechanisms to adapt to their environments. RNA editing occurs widely across organisms and generates non-synonymous codon changes in mRNAs, thereby altering the amino acid sequence of proteins. In cephalopods and fungi, this ‘recoding’ generates incredible diversity in proteins across most cellular processes. However, the functions of RNA recoding in these organisms are largely unknown. How is RNA recoding used to support physiological needs and facilitate adaptation? The research proposed here investigates how cephalopod and fungal RNA recoding regulates the function of proteins involved in two core cellular processes: microtubule-based transport and DNA replication and repair. This work will illuminate how RNA recoding modulates protein function to support phenotypic plasticity and adaptation and will advance our understanding of the regulation and functions of highly conserved cellular machineries. In Aim 1, Dr. Rangan will investigate how RNA recoding diversifies the function of microtubule motor protein complexes. In the K99 phase, she will evaluate the effects of RNA recoding on dynein and kinesin motor complexes using in vivo cargo transport assays and single-molecule motility assays. She will also investigate how RNA recoding of motor proteins is coordinated at different temperatures in squid to facilitate transport. In Aim 2, Dr. Rangan will investigate how RNA recoding alters the function of DNA replication and repair proteins. In the K99 phase, she will characterize the effects of RNA recoding on DNA polymerases epsilon and zeta using assays for mutation rate, fidelity, and processivity. In the R00 phase, she will evaluate how temperature-dependent recoding of DNA polymerases alters function and extend this characterization to other proteins involved in DNA replication and repair. In Aim 3, Dr. Rangan will explore how RNA recoding of DNA replication machinery influences genomic mutation rate and bias in the filamentous fungus Neurospora crassa. In the K99 phase, she will use RNA-seq to evaluate temperature-dependent changes in RNA editing in Neurospora ascospores. During the R00 phase, she will perform mutation accumulation experiments with recoding site mutants and wild type fungi to elucidate the role of RNA recoding in mutagenesis. Dr. Rangan is committed to developing an independent research program centered around investigating how RNA editing in diverse organisms supports phenotypic plasticity and adaptation. To facilitate her transition to independence, she will attend diverse scientific conferences and participate in UCSD classes on topics of career development and lab management. She will receive guidance and support from her mentoring committee and her primary mentor, Sam Reck-Peterson. This development plan, combined with training in bioinformatics and computational genomics (with Ludmil Alexandrov, UC San Diego) as well as Neurospora biology and genetics (with Katherine Borkovich, UC Riverside) will prepare her for success in an independent career.

项目概要生物体利用多种分子机制来适应发生的 RNA 编辑。广泛跨生物体并在 mRNA 中产生非同义密码子变化，从而改变氨基酸在头足类动物和真菌中，这种“记录”产生了令人难以置信的蛋白质多样性。然而，这些生物体中 RNA 记录的功能很大程度上是。未知。RNA 记录如何用于支持生理需求并促进适应？这里提出的研究研究头足类动物和真菌 RNA 记录如何调节相关蛋白质的功能这项工作将涉及两个核心细胞过程：基于微管的运输以及 DNA 复制和修复。阐明 RNA 记录如何调节蛋白质功能以支持表型可塑性和适应，并将我们对高度保守的细胞机器的调节和高级功能的理解。在目标 1 中，Rangan 博士将研究 RNA 记录如何使微管运动功能多样化在 K99 阶段，她将评估 RNA 记录对动力蛋白和驱动蛋白运动的影响。她还将研究使用体内货物运输测定和单分子运动的复合物。鱿鱼中运动蛋白的 RNA 记录如何在不同温度下协调以促进运输。在目标 2 中，Rangan 博士将研究 RNA 记录如何改变 DNA 复制和修复的功能在 K99 阶段，她将描述 RNA 记录对 DNA 聚合酶 epsilon 和 epsilon 的影响。 zeta 使用突变率、保真度和持续性分析在 R00 阶段，她将评估如何进行。 DNA聚合酶的温度依赖性记录改变了功能并将这种特征扩展到其他参与 DNA 复制和修复的蛋白质。在目标 3 中，Rangan 博士将探索 DNA 复制机制的 RNA 记录如何影响基因组在K99阶段，她将使用RNA-seq来研究丝状真菌粗糙脉孢菌的突变率和偏差。她评估了脉孢子囊孢子 R00 阶段 RNA 编辑的温度依赖性变化。将用记录位点突变体和野生型真菌进行突变积累实验，以阐明 RNA记录在诱变中的作用。 Rangan 博士致力于开发一个以调查为中心的独立研究项目不同生物体中的 RNA 编辑如何支持表型可塑性和适应以促进她的转变。为了独立，她将参加各种科学会议并参加加州大学圣地亚哥分校的课程，主题包括她将得到指导委员会的指导和支持。和她的主要导师 Sam Reck-Peterson 这个发展计划与生物信息学培训相结合。和计算基因组学（与加州大学圣地亚哥分校的 Ludmil Alexandrov 合作）以及脉孢菌生物学和遗传学（与加州大学河滨分校的凯瑟琳·博科维奇一起）将为她在独立职业生涯中取得成功做好准备。