Ma Lili, Zuo Jinhua, Bai Chunmei, Fu Anzhen, Wang Qing, Zhou Zhongjing, Deng Zhiping, Tan Jinjuan, Bouzayen Mondher, Zheng Yanyan
Institute of Agri-food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, China.
College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China.
Plant J. 2024 Dec;120(5):2014-2030. doi: 10.1111/tpj.17095. Epub 2024 Nov 4.
N-methyladenosine (mA) methylation is an essential mechanism of gene regulation known to impact several biological processes in living organisms. However, little is known about the abundance, distribution, and functional significance of mRNA mA modification during fruit ripening of tomato the main model species for fleshy fruits. Our study shows that mA modifications are prevalent in tomato mRNA and are detected in lncRNA and circRNA. The distribution of mA peaks in mRNA segments indicates that mA is mainly enriched at the start codon and CDS regions. Assessing changes in global RNA methylation during fruit ripening in wild-type tomatoes and in the ripening-impaired Nr mutant affected in the ethylene receptor gene (SlETR3) revealed a decrease in the overall methylation levels from mature green (MG) stage to 6 days postbreaker (Br + 6). Nr mutant fruits show significantly lower methylation levels than Ailsa Craig (AC) fruits. Notably, differences in mA methylation are well correlated to the expression levels of a number of key ripening-related genes. The integration of RNA-seq and MeRIP-seq data suggests a potential positive impact of mA modifications on gene expression. In comparison to the AC fruits, the hypomethylation and reduced expression of ethylene-related genes, ACO3, EBF1, and ERF.D6, in the Nr mutants likely underpin the distinct phenotypic traits observed between the two fruit genotypes at the Br6 stage. Overall, our study brings further arguments supporting the potential significance of mA methylation modifications in fruit ripening, a developmental process that is instrumental to plant reproduction and to fruit sensory and nutritional qualities.
N-甲基腺苷（mA）甲基化是一种重要的基因调控机制，已知其会影响生物体中的多种生物学过程。然而，对于番茄（肉质果实的主要模式物种）果实成熟过程中mRNA mA修饰的丰度、分布和功能意义却知之甚少。我们的研究表明，mA修饰在番茄mRNA中普遍存在，并且在lncRNA和circRNA中也能检测到。mRNA片段中mA峰的分布表明，mA主要富集在起始密码子和编码区。对野生型番茄果实成熟过程以及乙烯受体基因（SlETR3）功能受损的成熟缺陷型Nr突变体果实成熟过程中整体RNA甲基化变化的评估显示，从绿熟（MG）阶段到破色后6天（Br + 6），整体甲基化水平下降。Nr突变体果实的甲基化水平明显低于艾尔莎·克雷格（AC）果实。值得注意的是，mA甲基化的差异与许多关键成熟相关基因的表达水平密切相关。RNA-seq和MeRIP-seq数据的整合表明，mA修饰对基因表达可能具有积极影响。与AC果实相比，Nr突变体中乙烯相关基因ACO3、EBF1和ERF.D6的低甲基化和表达降低，可能是导致在Br6阶段两种果实基因型之间观察到明显表型差异的原因。总体而言，我们的研究进一步支持了mA甲基化修饰在果实成熟中的潜在重要性，果实成熟是一个对植物繁殖以及果实感官和营养品质至关重要的发育过程。
