MdMTA‐mediated m⁶A modification enhances drought tolerance by promoting mRNA stability and translation efficiency of genes involved in lignin deposition and oxidative stress

Abstract

Summary Although the N6‐methyladenosine (m6A) modification is the most prevalent RNA modification in eukaryotes, the global m6A modification landscape and its molecular regulatory mechanism in response to drought stress remain unclear. Transcriptome‐wide m6A methylome profiling revealed that m6A is mainly enriched in the coding sequence and 3′ untranslated region in response to drought stress in apple, by recognizing the plant‐specific sequence motif UGUAH (H=A, U or C). We identified a catalytically active component of the m6A methyltransferase complex, MdMTA. An in vitro methyl transfer assay, dot blot, LC‐MS/MS and m6A‐sequencing (m6A‐seq) suggested that MdMTA is an m6A writer and essential for m6A mRNA modification. Further studies revealed that MdMTA is required for apple drought tolerance. m6A‐seq and RNA‐seq analyses under drought conditions showed that MdMTA mediates m6A modification and transcripts of mRNAs involved in oxidative stress and lignin deposition. Moreover, m6A modification promotes mRNA stability and the translation efficiency of these genes in response to drought stress. Consistently, MdMTA enhances lignin deposition and scavenging of reactive oxygen species under drought conditions. Our results reveal the global involvement of m6A modification in the drought response of perennial apple trees and illustrate its molecular mechanisms, thereby providing candidate genes for the breeding of stress‐tolerant apple cultivars.

Epitranscriptomic mRNA modifications governing plant stress responses: underlying mechanism and potential application

“…Similar to the observations under normal growth and development in plants (Luo et al ., 2014 ; Wan et al ., 2015 ; Shen et al ., 2016 ; Duan et al ., 2017 ; Wang et al ., 2017c ; Miao et al ., 2019 ; Parker et al ., 2020 ; Hu et al ., 2022 ) and other eukaryotes (Dominissini et al ., 2012 ; Ke et al ., 2015 ; Lence et al ., 2016 ; Li et al ., 2019 ; Linder et al ., 2015 ; Meyer et al ., 2012 ; Schwartz et al ., 2013 ; Zhao et al ., 2017 ), m 6 A is predominantly enriched at the 3′‐UTR and the near‐stop codon under stress (Anderson et al ., 2018 ; Cheng et al ., 2021 ; He et al ., 2021 ; Hou et al ., 2022 ; Hu et al ., 2021 ; Liu et al ., 2020 ; Mao et al ., 2021 ; Wang et al ., 2022a ; Yang et al ., 2021 ; Zhang et al ., 2021a , 2021b , 2021c ; Zheng et al ., 2021 ). These findings indicate that m 6 A distribution on mRNAs is conserved across organisms under both normal and stress conditions.…”

“…In fact, the global m 6 A levels increased under salt stress in Arabidopsis (Hu et al ., 2021 ) and upon viral infection in rice (Zhang et al ., 2021a ) but decreased under drought stress in sea buckthorn (Zhang et al ., 2021b ), under moderate low‐temperature stress in tomato (Yang et al ., 2021 ) and upon cucumber green mottle mosaic virus (CGMMV) infection in watermelon (He et al ., 2021 ). In contrast, global m 6 A levels remain unchanged in apples exposed to drought stress (Hou et al ., 2022 ; Mao et al ., 2021 ), Pak‐choi exposed to heat stress (Liu et al ., 2020 ), rice exposed to heavy metal (cadmium) stress (Cheng et al ., 2021 ), and wheat infected by yellow mosaic virus (Zhang et al ., 2021c ). These findings indicate dynamic m 6 A modifications in a stress‐ or species‐specific manner.…”

“…For instance, m 6 A located in the 3′‐UTR and near the stop codon is primarily involved in modulating transcript stability (Hou et al ., 2021 ; Luo et al ., 2020 ; Zhou et al ., 2019 , 2021 ) and transcriptome integrity (Pontier et al ., 2019 ). m 6 A present in the 5′‐UTR is involved in the regulation of translation (Hou et al ., 2022 ), and m 6 A in the coding region affects the stability and splicing of mRNA (Ma et al ., 2021 ; Zhou et al ., 2021 ).…”

“…Analogous to epigenetic regulation, which involves DNA methylation and histone modifications, a series of covalent RNA modifications has recently been elucidated as epitranscriptomic regulation; such regulation plays pivotal roles in shaping gene expression through the modulation of RNA metabolism at the post‐transcriptional level (Davalos et al ., 2018 ). Recent bioinformatic and molecular evidence has illustrated the link between specific mRNA modifications and transcript abundances in plants under stress (Anderson et al ., 2018 ; Cheng et al ., 2021 ; He et al ., 2021 ; Hou et al ., 2022 ; Hu et al ., 2021 ; Liu et al ., 2020 ; Mao et al ., 2021 ; Wang et al ., 2022a ; Yang et al ., 2021 ; Zhang et al ., 2021a , 2021b , 2021c ). However, the precise mechanism underlying post‐transcriptional gene regulation via mRNA modification under stress awaits further investigation.…”

N6-methyladenosine RNA modification promotes viral genomic RNA stability and infection

“…It has recently been shown that strawberry MTA interacts with MTB and RNA interference of these down-regulates the m 6 A level of series transcripts 26 . Apple MTA also interacts with MTB but methyltransferase activity depends on the presence of both MTA and MTB 27 . Although MTA has been studied in detail, its protein partner, MTB has been characterized less intensively and its function in plants remains largely unknown 13,28 .…”