A tRNA modification with aminovaleramide facilitates AUA decoding in protein synthesis

IF 12.9 1区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Nature chemical biology Pub Date : 2024-09-19 DOI:10.1038/s41589-024-01726-x

Kenjyo Miyauchi, Satoshi Kimura, Naho Akiyama, Kazuki Inoue, Kensuke Ishiguro, Thien-Son Vu, Veerasak Srisuknimit, Kenta Koyama, Gosuke Hayashi, Akiko Soma, Asuteka Nagao, Mikako Shirouzu, Akimitsu Okamoto, Matthew K. Waldor, Tsutomu Suzuki

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Abstract

Modified tRNA anticodons are critical for proper mRNA translation during protein synthesis. It is generally thought that almost all bacterial tRNAs^Ile use a modified cytidine—lysidine (L)—at the first position (34) of the anticodon to decipher the AUA codon as isoleucine (Ile). Here we report that tRNAs^Ile from plant organelles and a subset of bacteria contain a new cytidine derivative, designated 2-aminovaleramididine (ava²C). Like L34, ava²C34 governs both Ile-charging ability and AUA decoding. Cryo-electron microscopy structural analyses revealed molecular details of codon recognition by ava²C34 with a specific interaction between its terminal amide group and an mRNA residue 3′-adjacent to the AUA codon. These findings reveal the evolutionary variation of an essential tRNA modification and demonstrate the molecular basis of AUA decoding mediated by a unique tRNA modification.

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修饰的 tRNA 反密码子对于蛋白质合成过程中 mRNA 的正常翻译至关重要。一般认为，几乎所有细菌的 tRNAsIle 都在反密码子的第一个位置（34）使用修饰胞苷苷（L）来将 AUA 密码子破译为异亮氨酸（Ile）。在这里，我们报告了来自植物细胞器和一部分细菌的 tRNAsIle 含有一种新的胞苷衍生物，被命名为 2-氨基戊酰胺苷（ava2C）。与 L34 一样，ava2C34 也控制着 Ile 的充电能力和 AUA 解码。冷冻电镜结构分析揭示了ava2C34识别密码子的分子细节，其末端酰胺基团与AUA密码子相邻3′的mRNA残基之间存在特异性相互作用。这些发现揭示了一种重要的 tRNA 修饰的进化变异，并证明了由一种独特的 tRNA 修饰介导的 AUA 解码的分子基础。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nature chemical biology 生物-生化与分子生物学

CiteScore

23.90

自引率

1.40%

发文量

238

审稿时长

12 months

期刊介绍： Nature Chemical Biology stands as an esteemed international monthly journal, offering a prominent platform for the chemical biology community to showcase top-tier original research and commentary. Operating at the crossroads of chemistry, biology, and related disciplines, chemical biology utilizes scientific ideas and approaches to comprehend and manipulate biological systems with molecular precision. The journal embraces contributions from the growing community of chemical biologists, encompassing insights from chemists applying principles and tools to biological inquiries and biologists striving to comprehend and control molecular-level biological processes. We prioritize studies unveiling significant conceptual or practical advancements in areas where chemistry and biology intersect, emphasizing basic research, especially those reporting novel chemical or biological tools and offering profound molecular-level insights into underlying biological mechanisms. Nature Chemical Biology also welcomes manuscripts describing applied molecular studies at the chemistry-biology interface due to the broad utility of chemical biology approaches in manipulating or engineering biological systems. Irrespective of scientific focus, we actively seek submissions that creatively blend chemistry and biology, particularly those providing substantial conceptual or methodological breakthroughs with the potential to open innovative research avenues. The journal maintains a robust and impartial review process, emphasizing thorough chemical and biological characterization.

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