A Preliminary Survey of Transfer RNA Modifications and Modifying Enzymes of the Tropical Plant Cocos nucifera L.
文献类型： 外文期刊
作者： Chu, Meng 1 ; Qin, Yichao 1 ; Lin, Xiuying 1 ; Ma, Li 1 ; Deng, Dehai 1 ; Lv, Daizhu 4 ; Fu, Pengcheng 1 ; Lin, Huan 1 ;
作者机构： 1.Hainan Univ, State Key Lab Marine Resource Utilizat South China, Haikou 570228, Peoples R China
2.Hainan Univ, Sch Life Sci, Haikou 570228, Peoples R China
3.Hainan Univ, Coll Ecol & Environm, Haikou 570228, Peoples R China
4.Chinese Acad Trop Agr Sci, Anal & Testing Ctr, Haikou 571101, Peoples R China
关键词： Cocos nucifera; epitranscriptomics; LC-MS; MS; nucleoside misidentification; RNA modification
期刊名称：GENES （ 影响因子：3.5； 五年影响因子：3.9 ）
ISSN：
年卷期： 2023 年 14 卷 6 期
页码：
收录情况： SCI
摘要： The coconut (Cocos nucifera L.) is a commercial crop widely distributed among coastal tropical regions. It provides millions of farmers with food, fuel, cosmetics, folk medicine, and building materials. Among these, oil and palm sugar are representative extracts. However, this unique living species of Cocos has only been preliminarily studied at molecular levels. Benefiting from the genomic sequence data published in 2017 and 2021, we investigated the transfer RNA (tRNA) modifications and modifying enzymes of the coconut in this survey. An extraction method for the tRNA pool from coconut flesh was built. In total, 33 species of modified nucleosides and 66 homologous genes of modifying enzymes were confirmed using a nucleoside analysis using high-performance liquid chromatography combined with high-resolution mass spectrometry (HPLC-HRMS) and homologous protein sequence alignment. The positions of tRNA modifications, including pseudouridines, were preliminarily mapped using a oligonucleotide analysis, and the features of their modifying enzymes were summarized. Interestingly, we found that the gene encoding the modifying enzyme of 2 & PRIME;-O-ribosyladenosine at the 64th position of tRNA (Ar(p)64) was uniquely overexpressed under high-salinity stress. In contrast, most other tRNA-modifying enzymes were downregulated with mining transcriptomic sequencing data. According to previous physiological studies of Ar(p)64, the coconut appears to enhance the quality control of the translation process when subjected to high-salinity stress. We hope this survey can help advance research on tRNA modification and scientific studies of the coconut, as well as thinking of the safety and nutritional value of naturally modified nucleosides.
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