CAREER: Learning from NMD evasion by endogenous and viral transcripts

职业：从内源性和病毒转录本的 NMD 逃避中学习

• 批准号: 2338218
• 负责人: Sujatha Jagannathan
• 金额: $ 130万
• 依托单位: University of Colorado at Denver
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2024
• 资助国家: 美国
• 起止时间: 2024-03-01 至 2029-02-28
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2338218&HistoricalAwards=false
• 关键词: CAREER; Learning; NMD; evasion; endogenous

Robustness in biological systems relies on quality control. An important quality control step in the flow of genetic information is to eliminate faulty and/or foreign messenger RNA (mRNA) molecules so that proteins that may be harmful to the cell are not produced. One of the ways that cells can identify faulty RNAs is by sensing the length of the sequence within an RNA that encodes for a protein versus not. While this mechanism works well in simple organisms such as yeast, the human genome has evolved to have naturally long regions of mRNAs that do not encode for a protein but serve regulatory purposes. How then does the cell know to not degrade such normal transcripts and yet identify potentially toxic RNAs that arise from mutated genes or viral genomes? This project will leverage evolutionary analysis, molecular biology, and genomics tools to identify and understand signals that could allow physiological RNAs that resemble aberrant RNAs to escape quality control. The project will also promote broader societal impacts by engaging 8th- and 9th-grade students in Aurora Science and Tech, a local school that primarily serves underprivileged and low-income populations in Aurora, CO, in hands-on research to facilitate their training and exposure to scientific research. Nonsense-mediated RNA decay (NMD) is a quality control process that degrades transcripts containing premature termination codons (PTC) to prevent the production of toxic truncated proteins. NMD senses aberrant transcripts either via the presence of exon junction complexes (EJCs) downstream of the terminating ribosome or via the long 3’ untranslated region (UTR) generated by premature termination. Many non-aberrant endogenous transcripts and certain viral transcripts also mimic PTC-containing transcripts by virtue of possessing long 3’ UTRs and are also targeted by NMD. However, through the course of evolution, several transcripts with long UTRs, both viral and endogenous, have evolved mechanisms to bypass NMD by antagonizing the central NMD factor, UPF1. In this project, natural NMD evasion mechanisms will be investigated for novel insights into this fundamental quality control mechanism. The goals are to identify mechanisms of endogenous and viral bypass of long UTR NMD (Aim 1), determine the role of a mammal-specific UPF1 isoform in the arms race between NMD and its targets through experimental evolution in human and drosophila cells (Aim 2), and engage 8th-9th grade students from a local high-needs school in investigating the cross-regulation of different UPF1 paralogs and viral antagonists in yeast (Aim 3).This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

生物系统的稳健性依赖于质量控制。遗传信息流中一个重要的质量控制步骤是消除有缺陷的和/或外来的信使 RNA (mRNA) 分子，从而不会产生可能对细胞有害的蛋白质。细胞识别有缺陷的 RNA 的方法之一是通过检测编码蛋白质的 RNA 与不编码蛋白质的 RNA 中的序列长度。虽然这种机制在酵母等简单生物体中运作良好，但人类基因组已经进化到具有自然长的 mRNA 区域，这些区域不编码蛋白质，而是用于调节目的。那么细胞如何知道不降解这些正常转录本，同时识别由突变基因或病毒基因组产​​生的潜在有毒RNA呢？该项目将利用进化分析、分子生物学和基因组学工具来识别和理解可能使类似于异常 RNA 的生理 RNA 逃避质量控制的信号。该项目还将通过让奥罗拉科学与技术学校（一家主要为科罗拉多州奥罗拉市的贫困和低收入人群服务的当地学校）的八年级和九年级学生参与实践研究，以促进他们的培训和接触科学研究，从而促进更广泛的社会影响。无义介导的 RNA 衰减 (NMD) 是一种质量控制过程，可降解包含过早终止密码子 (PTC) 的转录本，以防止产生有毒的截短蛋白质。 NMD 通过终止核糖体下游的外显子连接复合物 (EJC) 或通过过早终止产生的长 3' 非翻译区 (UTR) 来感知异常转录本。许多非异常内源转录本和某些病毒转录本也通过拥有长 3’UTR 来模仿包含 PTC 的转录本，并且也是 NMD 的目标。然而，在进化过程中，一些具有长 UTR 的转录物（病毒的和内源的）已经进化出通过拮抗中央 NMD 因子 UPF1 来绕过 NMD 的机制。在该项目中，将研究自然 NMD 规避机制，以获得对这一基本质量控制机制的新见解。目标是确定长 UTR NMD 的内源性和病毒旁路机制（目标 1），通过人类和果蝇细胞中的实验进化确定哺乳动物特异性 UPF1 亚型在 NMD 与其靶标之间的军备竞赛中的作用（目标 2），并让当地高需求学校的 8-9 年级学生参与研究不同 UPF1 旁系同源物和病毒拮抗剂的交叉调节 酵母（目标 3）。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。