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.

项目摘要生物体使用各种分子机制来适应其环境。 RNA编辑发生跨生物体广泛，并在mRNA中产生非同义密码子变化，从而改变氨基蛋白质的酸序列。在头足类和真菌中，这种“重新编码”产生了令人难以置信的蛋白质多样性在大多数细胞过程中。但是，在这些生物中重新编码RNA的功能在很大程度上是未知。 RNA如何用于支持身体需求并促进适应？研究此处提出的调查了头足类和真菌RNA如何调节涉及的蛋白质的功能在两个核心细胞过程中：基于微管的运输以及DNA复制和修复。这项工作将阐明RNA重新编码如何调节蛋白质功能以支持表型可塑性和适应性，并将促进我们对高度保守的细胞机械的调节和功能的理解。在AIM 1中，Rangan博士将研究RNA重新编码如何使微管电机的功能多样化蛋白质复合物。在K99阶段，她将评估RNA重新编码对Dynein和动力蛋白电动机的影响使用体内货物传输测定法和单分子运动测定法。她还将调查运动蛋白的RNA如何在不同温度下在鱿鱼中协调以促进运输。在AIM 2中，Rangan博士将研究RNA重新编码如何改变DNA复制和修复的功能蛋白质。在K99阶段，她将表征RNA重新编码对DNA聚合酶Epsilon和使用分析的突变率，保真度和加工性的Zeta。在R00阶段，她将评估 DNA聚合酶的温度依赖性重现改变了功能，并将此表征扩展到其他参与DNA复制和修复的蛋白质。在AIM 3中，Rangan博士将探索RNA重新复制机制如何影响基因组丝状真菌神经孢子骨的突变率和偏差。在K99阶段，她将使用RNA-Seq到评估神经孢子孢子中RNA编辑的温度依赖性变化。在R00阶段，她将使用重新编码位点突变体和野生型真菌进行突变积累实验，以阐明 RNA在诱变中的作用。 Rangan博士致力于制定以调查为中心的独立研究计划 RNA在潜水生物体中的编辑如何支持表型可塑性和适应性。促进她的过渡为了独立，她将参加多元化的科学会议，并参加UCSD课程职业发展和实验室管理。她将获得心理委员会的指导和支持和她的主要导师萨姆·莱克·佩特森（Sam Reck-Peterson）。该开发计划与生物信息学培训相结合和计算基因组学（与Ludmil Alexandrov，UC圣地亚哥）以及Neurospora生物学和遗传学（与凯瑟琳·博科维奇（Katherine Borkovich），加州大学里弗赛德（UC Riverside）一起）将为她在独立职业中的成功做好准备。