The functional and adaptive roles of RNA recoding

项目总结 生物体使用各种分子机制来适应他们的环境。发生RNA编辑 在生物体中广泛存在，并在mRNAs中产生非同义密码子变化，从而改变氨基酸 蛋白质的酸性序列。在头足类动物和真菌中，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。然而，在这些生物中，RNA重新编码的功能很大程度上是 未知。RNA重新编码是如何用于支持生理需求和促进适应的？这项研究 研究了头足类和真菌类的rna重新编码如何调节相关蛋白质的功能。 在两个核心的细胞过程中：基于微管的运输和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的调节和功能的理解。 在目标1中，兰根博士将研究RNA重新编码如何使微管马达的功能多样化 蛋白质复合体。在K99阶段，她将评估RNA重新编码对动力蛋白和运动蛋白运动的影响 使用体内货物转运分析和单分子运动性分析的复合体。她还将调查 如何在不同的温度下协调马达蛋白的RNA重新编码以促进运输。 在目标2中，兰根博士将研究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，她将描述RNA重新编码对DNA聚合酶epsilon和 齐塔人使用变异率、保真度和处理能力的测试。在R00阶段，她将评估如何 依赖于温度的DNA聚合酶的重新编码改变了功能，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，兰根博士将探索DNA复制机制的RNA重新编码如何影响基因组 丝状真菌粗枝脉孢菌的突变率和偏倚。在K99阶段，她将使用RNA-seq来 评估脉孢菌子囊孢子中RNA编辑的温度依赖性变化。在R00阶段，她 将对重组位点突变体和野生型真菌进行突变积累实验，以阐明 RNA重新编码在突变中的作用。 兰根博士致力于开发一个以研究为中心的独立研究计划 不同生物体中的RNA编辑如何支持表型可塑性和适应性。为她的过渡提供便利 为了独立，她将参加各种科学会议，并参加加州大学圣迭戈分校的课程，主题是 职业发展和实验室管理。她将得到指导委员会的指导和支持。 以及她的主要导师萨姆·雷克·彼得森。这一发展计划与生物信息学培训相结合 和计算基因组学(与Ludmil Alexandrov，加州大学圣地亚哥分校)以及脉孢子虫生物学和 遗传学(与加州大学河滨分校的凯瑟琳·博尔科维奇)将为她在独立职业生涯中的成功做好准备。

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.