Translational regulation in exposure biology - Xenobiotic-induced reprograming of tRNA modifications and selective translation of codon-biased response genes in rat and human models

暴露生物学中的翻译调控——在大鼠和人类模型中异种物质诱导的 tRNA 修饰重编程和密码子偏向反应基因的选择性翻译

• 批准号: 10693254
• 负责人: Thomas J Begley
• 金额: $ 44.96万
• 依托单位: STATE UNIVERSITY OF NEW YORK AT ALBANY
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-01 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10693254
• 关键词: Acids; Amino Acids; Arsenates; Arsenic; Arsenic Trioxide; Arsenites; Behavior; Biological Markers; Biology; Blood; Cacodylic Acid; Cell Line; Cell Survival; Cell model; Cells; Codon Nucleotides; Data; Databases; Defect; Detection; Diethylnitrosamine; Dose; Drug Metabolic Detoxication; Environmental Exposure; Exposure to; Foundations; Gene Expression; Genes; Heart; HepG2; Hepatocyte; Human; In Vitro; Kidney; Leukocytes; Lipopolysaccharides; Liver; Lymphocyte; Mitochondria; Modeling; Modification; Mus; Nucleoside Q; Organ; Pharmaceutical Preparations; Population; Proteins; Proteome; Proteomics; RNA; Rattus; Reactive Oxygen Species; Research; Role; Sampling; Selenocysteine; Sodium; Technology; Testing; Therapeutic; Time; Tissues; Toxicant exposure; Transcript; Transfer RNA; Translating; Translational Regulation; Translations; Whole Blood; Xenobiotics; Yeasts; base; biological adaptation to stress; biomarker signature; epitranscriptome; epitranscriptomics; glutathione peroxidase; human model; in vivo; knock-down; programs; response; sodium arsenite; toxicant; translational model; usability

ABSTRACT Human cells respond to xenobiotic exposures by altering gene expression, with the ~50 RNA modifications comprising the epitranscriptome emerging as key regulators of the stress response. We have developed unique RNA modification detection (LC-MS/MS, AQRNA-seq), tRNA gene expression (AQRNA-seq), and computational (Codon Analytics) technologies to show that yeast, rat livers, mice and cultured human cells respond to xenobiotic exposures with coordinated changes in the levels of tRNA modifications and tRNAs, to regulate codon-biased translation of important stress response proteins. Using liver from rats exposed to six drugs and toxicants in the NTP DrugMatrix program, we observed that 23 different tRNA modifications were uniquely altered in toxicant-, dose- and time-dependent manner after exposure. Among the changes, arsenite increased the level of queuosine (Q), a key tRNA wobble modification that decodes codons for four amino acids (His, Tyr, Asn, Asp). This behavior was recapitulated in human liver cells (HEPG2), with Q incorporation into tRNA in response to sodium arsenite required for cell viability, reactive oxygen species (ROS) detoxification, and mitochondrial function, and decreased Q levels promoting changes in translation. Similarly, the wobble U tRNA wobble base 5-methoxycarbonyl-methyluridine (mcm5U) was also increased in response to sodium arsenite in rat liver and HepG2 cells, with knockdown of the corresponding wobble U writer – ALKBH8 – promoting decreased cell viability, increased ROS, and changes in mitochondrial function. We have further shown that ALKBH8 defects disrupt the translation of selenocysteine (Sec)-containing glutathione peroxidases (GPXs) that detoxify ROS and promote mitochondrial function. In this renewal application, we will test the hypothesis of organ-specific tRNA reprogramming and codon-biased translation in rats and human cells exposed to arsenite and other toxicants, and then test the idea that whole blood and white blood cells (WBCs) serve as an accessible sampling compartment for human epitranscriptome biomarker studies.

抽象的 人类细胞通过改变基因表达来响应异生素暴露，其中约 50 个 RNA 修饰 我们开发了独特的表观转录组作为应激反应的关键调节因子。 RNA 修饰检测（LC-MS/MS、AQRNA-seq）、tRNA 基因表达（AQRNA-seq）和计算 （Codon Analytics）技术表明酵母、大鼠肝脏、小鼠和培养的人类细胞对 异生素暴露与 tRNA 修饰和 tRNA 水平的协调变化， 使用暴露于应激反应的大鼠的肝脏来调节重要应激反应蛋白的密码子偏倚翻译。 在 NTP DrugMatrix 程序中，我们观察到 6 种不同的 tRNA 修饰 暴露后，亚砷酸盐会以毒物、剂量和时间依赖性方式发生独特的变化。 增加了 queuosine (Q) 的水平，这是一种关键的 tRNA 摆动修饰，可解码四个氨基酸的密码子 人肝细胞 (HEPG2) 中通过 Q 掺入重现了这种行为。 转化为 tRNA，以响应细胞活力、活性氧 (ROS) 解毒所需的亚砷酸钠， 和线粒体功能，以及 Q 水平降低促进翻译的变化。 tRNA 摆动碱基 5-甲氧基羰基-甲基尿苷 (mcm5U) 也因​​钠的反应而增加 大鼠肝脏和 HepG2 细胞中的亚砷酸盐，并敲低相应的摆动 U 写入器 – ALKBH8 – 促进细胞活力下降、ROS 增加以及线粒体功能的变化。 研究表明 ALKBH8 缺陷会破坏含硒代半胱氨酸 (Sec) 的谷胱甘肽过氧化物酶的翻译 （GPX）可以解毒 ROS 并促进线粒体功能。在此更新应用中，我们将测试 大鼠和人类细胞中器官特异性 tRNA 重编程和密码子偏倚翻译的假说 暴露于亚砷酸盐和其他有毒物质，然后测试全血和白细胞的想法 （白细胞）作为人类表观转录组生物标志物研究的可访问采样室。

项目成果

Reciprocal regulation of TORC signaling and tRNA modifications by Elongator enforces nutrient-dependent cell fate.

Elongator 对 TORC 信号传导和 tRNA 修饰的相互调节增强了营养依赖性细胞命运。

• 发表时间: 2019
• 影响因子: 13.6
• 作者: Candiracci, Julie;Migeot, Valerie;Chionh, Yok;Bauer, Fanelie;Brochier, Thomas;Russell, Brandon;Shiozaki, Kazuhiro;Dedon, Peter;Hermand, Damien
• 通讯作者: Hermand, Damien

Three distinct 3-methylcytidine (m3C) methyltransferases modify tRNA and mRNA in mice and humans.

三种不同的 3-甲基胞苷 (m3C) 甲基转移酶可修饰小鼠和人类的 tRNA 和 mRNA。

• 发表时间: 2017
• 作者: Xu, Luang;Liu, Xinyu;Sheng, Na;Oo, Kyaw Soe;Liang, Junxin;Chionh, Yok Hian;Xu, Juan;Ye, Fuzhou;Gao, Yong;Dedon, Peter C;Fu, Xin
• 通讯作者: Fu, Xin

Nanopore-based direct sequencing of RNA transcripts with 10 different modified nucleotides reveals gaps in existing technology.

基于纳米孔的 10 种不同修饰核苷酸的 RNA 转录本直接测序揭示了现有技术的差距。

• 发表时间: 2023-11-01
• 作者: Burdick, Joshua T;Comai, Annelise;Bruzel, Alan;Sun, Guangxin;Dedon, Peter C;Cheung, Vivian G
• 通讯作者: Cheung, Vivian G