ECT12, an YTH-domain protein, is a potential mRNA m6A reader that affects abiotic stress responses by modulating mRNA stability in Arabidopsis

RNA modification: A contemporary review of pseudouridine (Ψ) and its role in functional plant biology

Pseudouridine (Ψ) is a modified nucleoside present in diverse RNA species, including mRNA (messenger RNA), snRNA (small nuclear RNA), rRNA (ribosomal RNA) and tRNA (transfer RNA). In plants, Ψ serves a critical function in RNA modification, supporting the stability, structural integrity, and functionality of RNA molecules. This review provides the various roles that Ψ fulfils in the modification of plant RNA biology, encompassing effects on biosynthesis pathways, regulatory mechanisms, stability, and translation efficiency. Additionally, we discuss recent advancements in the dynamic regulation of Ψ deposition in response to environmental stimuli and stressors. Elucidating Ψ's roles contributes to the comprehension of plant biology and may facilitate developments in biotechnology and crop improvement.

N6-Methyladenosine Modification Regulates Prunus Necrotic Ringspot Virus Infection in Cucumis sativus

N6-methyladenosine (m6A) is a common epigenetic modification found in eukaryotic RNA. Recent studies have increasingly highlighted the importance of m6A modification in plant defense against viruses. In this investigation, we found that prunus necrotic ringspot virus (PNRSV) infection affected the m6A modification process. Plant transcriptomes and epitranscriptomes were sequenced to coanalyze the dynamic changes of m6A modifications after PNRSV infection. Further studies revealed that the silencing of evolutionarily conserved C-terminal region (ECTs), encoding m6A readers, led to increased PNRSV accumulation, indicating that ECTs confer resistance to PNRSV. Additionally, we demonstrated that UPF3 and SMG7, which are involved in non-sense-mediated mRNA decay pathways, as well as phenylalanine ammonia-lyase (PAL), a well-known key enzyme in plant defense and an identified m6A-modified gene following PNRSV infection, play crucial roles in regulating PNRSV infection. These findings provide new insights into understanding PNRSV infection and further elucidate the role of m6A in modulating viral infection in plants.

Genome-Wide Identification and Expression Analysis of the YTH Domain-Containing Protein Gene Family in Salvia miltiorrhiza

YTH domain-containing proteins act as the primary readers of N6-methyladenosine (m6A), playing an important role in plant development and stress responses. However, little is known about the YTH proteins in medicinal plants. Genome-wide identification of the YTH gene family in the medicinal model plant, Salvia miltiorrhiza Bunge, identified a total of nineteen SmYTH genes from five chromosomes, with SmYTH8-SmYTH19 clustered on chromosome 8. Phylogenetic analysis showed that SmYTH proteins belong to the YTHDF category. No YTHDC members were identified. Conserved domain identification, amino acid sequence alignment, and phase separation prediction revealed that SmYTH1-SmYTH4 exhibited the characteristic m6A reader protein feature, containing conserved aromatic cages (WWW) capable of binding m6A residues. SmYTH5-SmYTH19 proteins contain a unique conserved F-box protein interaction domain that has not been reported previously. qRT-PCR analysis revealed tissue-specific patterns, with SmYTH1-SmYTH4 genes highly expressed in roots and leaves, whereas SmYTH8-SmYTH19 were mainly expressed in leaves. The results were consistent with RNA-seq data. The expression of various SmYTHs and the content of phenolic acid active ingredients were significantly altered under MeJA and SA treatments. The results provide useful information for further studies on the biological functions of m6A and YTH proteins in S. miltiorrhiza.

A review of m6A modification in plant development and potential quality improvement

N6-methyladenosine (m6A) represents the most prevalent internal modification observed in eukaryotic mRNAs. As a pivotal regulator of gene expression, m6A exerts influence over a number of processes, including splicing, transport, translation, degradation, and the stability of mRNAs. It thus plays a crucial role in plant development and resistance to biotic and abiotic stressors. The writers, erasers, and readers of m6A, which deposit, eliminate and decode this modification, are also of critical importance and have been identified and characterized in multiple plant species. The advent of next-generation sequencing (NGS) and m6A detection technologies has precipitated a surge in research on m6A in recent years. Extensive research has elucidated the specific roles of m6A in plants and its underlying molecular mechanisms, indicating significant potential for crop improvement. This review presents a comprehensive overview of recent studies on m6A and its regulatory proteins in plant development and stress tolerance. It highlights the potential applications of this modification and its writers, erasers, and readers for plant improvement, with a particular focus on leaf development, floral transition, trichome morphogenesis, fruit ripening, and resilience to pests, diseases and abiotic stresses.

The N6-methyladenosine reader ECT1 regulates seed germination via gibberellic acid- and phytochrome B-mediated signaling

Seed germination, a pivotal stage in plant growth, is governed by phytohormones such as gibberellic acid (GA) and influenced by phytochromes, which are key photoreceptors in plants. The N6-methyladenosine (m6A) RNA modification is fundamental to plant growth and development. However, the molecular mechanisms underlying the regulation of PHYTOCHROME B (phyB) and the function of m6A signaling in GA-mediated seed germination remain elusive. Here, we discovered EVOLUTIONARILY CONSERVED C-TERMINAL REGION 1 (ECT1) as an m6A reader protein that directly binds to m6A and forms homodimers to enhance its stability in Arabidopsis (Arabidopsis thaliana). We observed that the ect1-1 mutant exhibits attenuated GA3 responsiveness in seed germination. Restoration of ECT1 function in ect1-1 confirmed the role of ECT1 in promoting seed germination. Our findings indicate that ECT1 promotes seed germination by destabilizing m6A-modified REPRESSOR OF GA1-3 1 (RGA1), a key inhibitor of GA-mediated seed germination. Moreover, ECT1 establishes a regulatory circuit with DOF AFFECTING GERMINATION 2 (DAG2), another regulator of GA-mediated seed germination. DAG2 directly binds to the ECT1 promoter and controls its transcription, and ECT1 modulates DAG2 mRNA stability through m6A binding. Furthermore, we identified PHYB as a common downstream target of DAG2 and ECT1. ECT1 binds directly to m6A-modified PHYB and influences its stability, and DAG2 binds to the PHYB promoter to regulate its transcription. Our findings demonstrate that ECT1 fine-tunes m6A-regulated seed germination via complex and multifaceted molecular mechanisms, particularly through interactions with GA and phyB, broadening our understanding of m6A-regulated processes in Arabidopsis.

RNA modifications in plant biotic interactions

The chemical modifications of DNA and proteins are powerful mechanisms for regulating molecular and biological functions, influencing a wide array of signaling pathways in eukaryotes. Recent advancements in epitranscriptomics have shown that RNA modifications play crucial roles in diverse biological processes. Since their discovery in the 1970s, scientists have sought to decipher, identify, and elucidate the functions of these modifications across biological systems. Over the past decade, mounting evidence has demonstrated the importance of RNA modification pathways in plants, prompting significant efforts to decipher their physiological relevance. With the advent of high-resolution mapping techniques for RNA modifications and the gradual uncovering of their biological roles, our understanding of this additional layer of regulation is beginning to take shape. In this review, we summarize recent findings on the major RNA modifications identified in plants, with an emphasis on N6-methyladenosine (m6A), the most extensively studied modification. We discuss the functional significance of the effector components involved in m6A modification and its diverse roles in plant biotic interactions, including plant-virus, plant-bacterium, plant-fungus, and plant-insect relationships. Furthermore, we highlight new technological developments driving research progress in this field and outline key challenges that remain to be addressed.

RNA modifications in plant adaptation to abiotic stresses

Epitranscriptomic chemical modifications of RNAs have emerged as potent regulatory mechanisms in the process of plant stress adaptation. Currently, over 170 distinct chemical modifications have been identified in mRNAs, tRNAs, rRNAs, microRNAs (miRNAs), and long noncoding RNAs (lncRNAs). Genetic and molecular studies have identified the genes responsible for addition and removal of chemical modifications from RNA molecules, which are known as "writers" and "erasers," respectively. N6-methyladenosine (m6A) is the most prevalent chemical modification identified in eukaryotic mRNAs. Recent studies have identified m6A writers and erasers across different plant species, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), cotton (Gossypium hirsutum), and tomato (Solanum lycopersicum). Accumulating discoveries have improved our understanding of the functions of RNA modifications in plant stress responses. This review highlights the latest research on RNA modification, emphasizing the biological and cellular roles of diverse chemical modifications of mRNAs, tRNAs, rRNAs, miRNAs, and lncRNAs in plant responses to environmental and hormonal signals. We also propose and discuss critical questions and future challenges for enhancing our understanding of the cellular and mechanistic roles of RNA modifications in plant stress responses. Integrating molecular insights into the regulatory roles of RNA modifications in stress responses with novel genome- and RNA-editing technologies will facilitate the breeding of stress-tolerant crops through precise engineering of RNA modifications.

Epigenetic control of plant abiotic stress responses

On top of genetic information, organisms have evolved complex and sophisticated epigenetic regulation to adjust gene expression in response to developmental and environmental signals. Key epigenetic mechanisms include DNA methylation, histone modifications and variants, chromatin remodeling, and chemical modifications of RNAs. Epigenetic control of environmental responses is particularly important for plants, which are sessile and unable to move away from adverse environments. Besides enabling plants to rapidly respond to environmental stresses, some stress-induced epigenetic changes can be maintained, providing plants with a pre-adapted state to recurring stresses. Understanding these epigenetic mechanisms offers valuable insights for developing crop varieties with enhanced stress tolerance. Here, we focus on abiotic stresses and summarize recent progress in characterizing stress-induced epigenetic changes and their regulatory mechanisms and roles in plant abiotic stress resistance.

ECT8, an mRNA m6A reader, enhances salt stress tolerance by modulating mRNA stability in Arabidopsis

N6-methyladenosine (m6A), the most prevalent modification found in eukaryotic mRNAs, is recognized and interpreted by m6A-binding proteins called m6A readers. The EVOLUTIONARILY CONSERVED C-TERMINAL REGION (ECT) proteins have increasingly been identified as m6A readers in plants. A recent study has demonstrated that the loss-of-function ect8 mutant is sensitive to salt stress by enhancing the stability of negative salt stress regulators in Arabidopsis (Arabidopsis thaliana). In this study, we generated and analyzed the ECT8-overexpressing transgenic Arabidopsis plants to further explore the function of ECT8 in salt stress response. The electrophoretic mobility shift assay in vitro showed that ECT8 binds to the m6A-modified synthetic RNAs, preferring UGUm6AA and UACm6AGA motifs over the GGm6ACU motif. Contrary to the ect8 mutant exhibiting salt hypersensitivity by enhancing the stability of salt stress negative regulators, the ECT8-overexpressing transgenic Arabidopsis plants displayed salt tolerance by increasing the stability and expression levels of salt stress positive regulators. Moreover, RNA-immunoprecipitation assay demonstrated that ECT8 binds to the m6A-modified salt stress-responsive mRNAs in planta. Collectively, our current and previous findings highlight that ECT8-mediated stabilization and destabilization of the genes encoding salt stress positive or negative regulators, respectively, contribute to the salt stress tolerance of Arabidopsis.

An mRNA methylase and demethylase regulate sorghum salt tolerance by mediating N6-methyladenosine modification

N 6-methyladenosine (m6A) modification is a crucial and widespread molecular mechanism governing plant development and stress tolerance. The specific impact of m6A regulation on plants with inherently high salt tolerance remains unclear. Existing research primarily focuses on the overexpression or knockout of individual writer or eraser components to alter m6A levels. However, a comprehensive study simultaneously altering overall m6A modification levels within the same experiment is lacking. Such an investigation is essential to determine whether opposing changes in m6A modification levels exert entirely different effects on plant salt tolerance. In this study, we identified the major writer member mRNA adenosine methylase A (SbMTA) in sorghum (Sorghum bicolor) as critical for sorghum survival. The sbmta mutant exhibits a phenotype characterized by reduced overall m6A, developmental arrest, and, ultimately, lethality. Overexpression of SbMTA increased m6A levels and salt tolerance, while overexpression of the m6A eraser alkylated DNA repair protein AlkB homolog 10B (SbALKBH10B) in sorghum showed the opposite phenotype. Comparative analyses between sorghum with different m6A levels reveal that SbMTA- and SbALKBH10B-mediated m6A alterations significantly impact the stability and expression levels of genes related to the abscisic acid signaling pathway and growth under salt stress. In summary, this study unveils the intricate relationship between m6A modifications and salt tolerance in sorghum, providing valuable insights into how m6A modification levels on specific transcripts influence responses to salt stress.

Reading m6A marks in mRNA: A potent mechanism of gene regulation in plants

Modifications to RNA have recently been recognized as a pivotal regulator of gene expression in living organisms. More than 170 chemical modifications have been identified in RNAs, with N6-methyladenosine (m6A) being the most abundant modification in eukaryotic mRNAs. The addition and removal of m6A marks are catalyzed by methyltransferases (referred to as "writers") and demethylases (referred to as "erasers"), respectively. In addition, the m6A marks in mRNAs are recognized and interpreted by m6A-binding proteins (referred to as "readers"), which regulate the fate of mRNAs, including stability, splicing, transport, and translation. Therefore, exploring the mechanism underlying the m6A reader-mediated modulation of RNA metabolism is essential for a much deeper understanding of the epigenetic role of RNA modification in plants. Recent discoveries have improved our understanding of the functions of m6A readers in plant growth and development, stress response, and disease resistance. This review highlights the latest developments in m6A reader research, emphasizing the diverse RNA-binding domains crucial for m6A reader function and the biological and cellular roles of m6A readers in the plant response to developmental and environmental signals. Moreover, we propose and discuss the potential future research directions and challenges in identifying novel m6A readers and elucidating the cellular and mechanistic role of m6A readers in plants.

The m6A-YTH regulatory system in plants: A status

Plants use mRNA methylation to regulate gene expression. As in other eukaryotes, the only abundant methylated nucleotide in plant mRNA bodies is N6-methyladenosine (m6A). The conserved core components of m6A-based genetic control are a multi-subunit nuclear methyltransferase, and a set of nuclear and cytoplasmic RNA-binding proteins consisting of an m6A recognition module, the YT521-B homology (YTH) domain, and long intrinsically disordered regions (IDRs). In plants, this system is essential for growth during embryonic and post-embryonic development, but emerging evidence also points to key functions in plant-virus interactions and stimulus-dependent gene regulation. Cytoplasmic YTH-domain proteins are particularly important for these functions, and recent progress has identified two elements of the underlying molecular mechanisms: IDR-mediated phase separation and conserved short linear motifs mediating interactions with other key mRNA-binding proteins.

Crosstalk between RNA m6A modification and epigenetic factors in plant gene regulation

N6-methyladenosine (m6A) is the most abundant modification observed in eukaryotic mRNAs. Advances in transcriptome-wide m6A mapping and sequencing technologies have enabled the identification of several conserved motifs in plants, including the RRACH (R = A/G and H = A/C/U) and UGUAW (W = U or A) motifs. However, the mechanisms underlying deposition of m6A marks at specific positions in the conserved motifs of individual transcripts remain to be clarified. Evidence from plant and animal studies suggests that m6A writer or eraser components are recruited to specific genomic loci through interactions with particular transcription factors, 5-methylcytosine DNA methylation marks, and histone marks. In addition, recent studies in animal cells have shown that microRNAs play a role in depositing m6A marks at specific sites in transcripts through a base-pairing mechanism. m6A also affects the biogenesis and function of chromatin-associated regulatory RNAs and long noncoding RNAs. Although we have less of an understanding of the link between m6A modification and epigenetic factors in plants than in animals, recent progress in identifying the proteins that interact with m6A writer or eraser components has provided insights into the crosstalk between m6A modification and epigenetic factors, which plays a crucial role in transcript-specific methylation and regulation of m6A in plants.

N6-Methyladenosine RNA Modification Regulates Maize Resistance to Maize Chlorotic Mottle Virus Infection

Maize chlorotic mottle virus (MCMV) is one of the main viruses causing significant losses in maize. N6-methyladenosine (m6A) RNA modification has been proven to play important regulatory roles in plant development and stress response. In this study, we found that MCMV infection significantly up-regulated the m6A level in maize, and methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were performed to investigate the distribution of m6A modified peaks and gene expression patterns in MCMV-infected maize plants. The results showed that 1325 differentially methylated genes (DMGs) and 47 differentially methylated and expressed genes (DMEGs) were identified and analyzed. Moreover, the results of virus-induced gene silencing (VIGS) assays showed that ZmECT18 and ZmGST31 were required for MCMV infection, while silencing of ZmMTC, ZmSCI1 or ZmTIP1 significantly promoted MCMV infection in maize. Our findings provided novel insights into the regulatory roles of m6A modification in maize response to MCMV infection.

Detection, distribution, and functions of RNA N 6-methyladenosine (m6A) in plant development and environmental signal responses

The epitranscriptomic mark N 6-methyladenosine (m6A) is the most common type of messenger RNA (mRNA) post-transcriptional modification in eukaryotes. With the discovery of the demethylase FTO (FAT MASS AND OBESITY-ASSOCIATED PROTEIN) in Homo Sapiens, this modification has been proven to be dynamically reversible. With technological advances, research on m6A modification in plants also rapidly developed. m6A modification is widely distributed in plants, which is usually enriched near the stop codons and 3'-UTRs, and has conserved modification sequences. The related proteins of m6A modification mainly consist of three components: methyltransferases (writers), demethylases (erasers), and reading proteins (readers). m6A modification mainly regulates the growth and development of plants by modulating the RNA metabolic processes and playing an important role in their responses to environmental signals. In this review, we briefly outline the development of m6A modification detection techniques; comparatively analyze the distribution characteristics of m6A in plants; summarize the methyltransferases, demethylases, and binding proteins related to m6A; elaborate on how m6A modification functions in plant growth, development, and response to environmental signals; and provide a summary and outlook on the research of m6A in plants.