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反应异种生物的暴露，并进行约50个RNA的修饰 符合性的表演组作为应力反应的关键调节剂。我们已经发展了独特 RNA修饰检测（LC-MS/MS，AQRNA-SEQ），TRNA基因表达（AQRNA-SEQ）和计算 （密码子分析）技术表明酵母，老鼠生命，小鼠和培养的人类细胞对 tRNA修饰水平和tRNA的水平有协调的变化的异生物暴露， 调节重要应力反应蛋白的密码子偏置翻译。使用暴露于大鼠的肝脏 NTP Drugmatrix计划中的六种药物和有毒物质，我们观察到23种不同的tRNA修饰是 暴露后的毒物，剂量和时间依赖性方式的独特改变。在变化中，阿森特 提高了Queuosine（Q）的水平，这是一种钥匙tRNA摇摆的修饰，可解码四个氨基的密码子 酸（他的Tyr，ASN，ASP）。在人肝细胞（HEPG2）中概括了这种行为，并结合了Q 响应细胞活力，活性氧（ROS）解毒所需的砷酸钠响应tRNA， 和线粒体功能，并提高了Q水平，促进了翻译的变化。同样，摇摆 tRNA摇摆基碱5-甲氧基核酸 - 甲基尿苷（MCM5U）也因钠的响应而增加 大鼠肝脏和HEPG2细胞中的砷岩，与相应的Wobble U作者敲低 - AlkbH8 - 促进细胞活力降低，ROS增加以及线粒体功能的变化。我们还有更多 表明ALKBH8缺陷破坏了硒代半胱氨酸（SEC）的翻译 - 含有谷胱甘肽的过氧化物酶 （GPX）将ROS排毒并促进线粒体功能。在此续订应用程序中，我们将测试 在大鼠和人类细胞中的器官特异性tRNA重编程和密码子偏置翻译的假设 暴露于砷和其他有毒物质，然后测试全血和白细胞的想法 （WBC）作为人类表演组生物标志物研究的无障碍抽样室。

项目成果

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

• DOI: 10.1093/g3journal/jkad200
• 发表时间: 2023-11-01
• 期刊: G3-GENES GENOMES GENETICS
• 影响因子: 2.6
• 作者: Burdick, Joshua T.;Comai, Annelise;Bruzel, Alan;Sun, Guangxin;Dedon, Peter C.;Cheung, Vivian G.
• 通讯作者: Cheung, Vivian G.

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

• DOI: 10.1126/sciadv.aav0184
• 发表时间: 2019-06-01
• 期刊: SCIENCE ADVANCES
• 影响因子: 13.6
• 作者: Candiracci, Julie;Migeot, Valerie;Hermand, Damien
• 通讯作者: Hermand, Damien