The immunophilin-interacting protein AtFIP37 from Arabidopsis is essential for plant development and is involved in trichome endoreduplication

Identification of m6A RNA methylation genes in Oryza sativa and expression profiling in response to different developmental and environmental stimuli

Eukaryotic messenger RNAs (mRNAs) transcend their predominant function of protein encoding by incorporating auxiliary components that ultimately contribute to their processing, transportation, translation, and decay. In doing so, additional layers of modifications are incorporated in mRNAs at post-transcriptional stage. Among them, N6-methyladenosine (m6A) is the most frequently found mRNA modification that plays crucial roles in plant development and stress response. In the overall mechanism of m6A methylation, key proteins classified based on their functions such as writers, readers, and erasers dynamically add, read, and subtract methyl groups respectively to deliver relevant functions in response to external stimuli. In this study, we identified 30 m6A regulatory genes (9 writers, 5 erasers, and 16 readers) in rice that encode 53 proteins (13 writers, 7 erasers, and 33 readers) where segmental duplication was found in one writer and four reader gene pairs. Reproductive cells such as sperm, anther and panicle showed high levels of expression for most of the m6A regulatory genes. Notably, writers like OsMTA, OsMTD, and OsMTC showed varied responses in different stress and infection contexts, with initial upregulation in response to early exposure followed by downregulation later. OsALKBH9A, a noteworthy eraser, displayed varied expression in response to different stresses at different time intervals, but upregulation in certain infections. Reader genes like OsECT5, OsCPSF30-L3, and OsECT8 showed continuous upregulation in exertion of all kinds of stress relevant here. Conversely, other reader genes along with OsECT11 and OsCPSF30-L2 were observed to be consistently downregulated. The apparent correlation between the expression patterns of m6A regulatory genes and stress modulation pathways in this study underscores the need for additional research to unravel their intricate regulatory mechanisms that could ultimately contribute to the substantial development of enhanced stress tolerance in rice through mRNA modification.

N6-methyladenosine mRNA methylation positively regulated the response of poplar to salt stress

As the most abundant form of methylation modification in messenger RNA (mRNA), the distribution of N6-methyladenosine (m6A) has been preliminarily revealed in herbaceous plants under salt stress, but its function and mechanism in woody plants were still unknown. Here, we showed that global m6A levels increased during poplar response to salt stress. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) revealed that m6A significantly enriched in the coding sequence region and 3'-untranslated regions in poplar, by recognising the conserved motifs, AGACU, GGACA and UGUAG. A large number of differential m6A transcripts have been identified, and some have been proved involving in salt response and plant growth and development. Further combined analysis of MeRIP-seq and RNA-seq revealed that the m6A hypermethylated and enrich in the CDS region preferred to positively regulate expression abundance. Writer inhibitor, 3-deazaneplanocin A treatment increased the sensitivity of poplar to salt stress by reducing mRNA stability to regulate the expression of salt-responsive transcripts PagMYB48, PagGT2, PagNAC2, PagGPX8 and PagARF2. Furthermore, we verified that the methyltransferase PagFIP37 plays a positively role in the response of poplar to salt stress, overexpressed lines have stronger salt tolerance, while RNAi lines were more sensitive to salt, which relied on regulating mRNA stability in an m6A manner of salt-responsive transcripts PagMYB48, PagGT2, PagNAC2, PagGPX8 and PagARF2. Collectively, these results revealed the regulatory role of m6A methylation in poplar response to salt stress, and revealed the importance and mechanism of m6A methylation in the response of woody plants to salt stress for the first time.

Genome-wide identification of the N6-methyladenosine regulatory genes reveals NtFIP37B increases drought resistance of tobacco (Nicotiana tabacum L.)

BACKGROUND

N6-methyladenosine (m6A) is one of the common internal RNA modifications found in eukaryotes. The m6A modification can regulate various biological processes in organisms through the modulation of alternative splicing, alternative polyadenylation, folding, translation, localization, transport, and decay of multiple types of RNA, without altering the nucleotide sequence. The three components involved in m6A modification, namely writer, eraser, and reader, mediate the abundance of RNA m6A modification through complex collaborative actions. Currently, research on m6A regulatory genes in plants is still in its infancy.

RESULTS

In this study, we identified 52 candidate m6A regulatory genes in common tobacco (Nicotiana tabacum L.). Gene structure, conserved domains, and motif analysis showed structural and functional diversity among different subgroups of tobacco m6A regulatory genes. The amplification of m6A regulatory genes were mainly driven by polyploidization and dispersed duplication, and duplicated genes evolved through purified selection. Based on the potential regulatory network and expression pattern analysis of m6A regulatory genes, a significant number of m6A regulatory genes might play important roles in growth, development, and stress response processes. Furthermore, we have confirmed the critical role of NtFIP37B, an m6A writer gene in tobacco, in enhancing drought resistance.

CONCLUSIONS

This study provides useful information for better understanding the evolution of m6A regulatory genes and the role of m6A modification in tobacco stress response, and lays the foundation for further elucidating the function of m6A regulatory genes in tobacco.

TurboID-mediated proximity labeling for screening interacting proteins of FIP37 in Arabidopsis

Proximity labeling was recently developed to detect protein-protein interactions and members of subcellular multiprotein structures in living cells. Proximity labeling is conducted by fusing an engineered enzyme with catalytic activity, such as biotin ligase, to a protein of interest (bait protein) to biotinylate adjacent proteins. The biotinylated protein can be purified by streptavidin beads, and identified by mass spectrometry (MS). TurboID is an engineered biotin ligase with high catalytic efficiency, which is used for proximity labeling. Although TurboID-based proximity labeling technology has been successfully established in mammals, its application in plant systems is limited. Here, we report the usage of TurboID for proximity labeling of FIP37, a core member of m6A methyltransferase complex, to identify FIP37 interacting proteins in Arabidopsis thaliana. By analyzing the MS data, we found 214 proteins biotinylated by GFP-TurboID-FIP37 fusion, including five components of m6A methyltransferase complex that have been previously confirmed. Therefore, the identified proteins may include potential proteins directly involved in the m6A pathway or functionally related to m6A-coupled mRNA processing due to spatial proximity. Moreover, we demonstrated the feasibility of proximity labeling technology in plant epitranscriptomics study, thereby expanding the application of this technology to more subjects of plant research.

The Roles of N6-Methyladenosine Modification in Plant-RNA Virus Interactions

N6-methyladenosine (m6A) is a dynamic post-transcriptional RNA modification. Recently, its role in viruses has led to the study of viral epitranscriptomics. m6A has been observed in viral genomes and alters the transcriptomes of both the host cell and virus during infection. The effects of m6A modifications on host plant mRNA can either increase the likelihood of viral infection or enhance the resistance of the host to the virus. However, to date, the regulatory mechanisms of m6A in viral infection and host immune responses have not been fully elucidated. With the development of sequencing-based biotechnologies, the study of m6A in plant viruses has received increasing attention. In this mini review, we summarize the positive and negative consequences of m6A modification in different RNA viral infections. Given its increasingly important roles in multiple viruses, m6A represents a new potential target for antiviral defense.

Advances in understanding epigenetic regulation of plant trichome development: a comprehensive review

Plant growth and development are controlled by a complex gene regulatory network, which is currently a focal point of research. It has been established that epigenetic factors play a crucial role in plant growth. Trichomes, specialized appendages that arise from epidermal cells, are of great significance in plant growth and development. As a model system for studying plant development, trichomes possess both commercial and research value. Epigenetic regulation has only recently been implicated in the development of trichomes in a limited number of studies, and microRNA-mediated post-transcriptional regulation appears to dominate in this context. In light of this, we have conducted a review that explores the interplay between epigenetic regulations and the formation of plant trichomes, building upon existing knowledge of hormones and transcription factors in trichome development. Through this review, we aim to deepen our understanding of the regulatory mechanisms underlying trichome formation and shed light on future avenues of research in the field of epigenetics as it pertains to epidermal hair growth.

Characteristics of N6-methyladenosine Modification During Sexual Reproduction of Chlamydomonas reinhardtii

The unicellular green alga Chlamydomonas reinhardtii (hereafter Chlamydomonas) possesses both plant and animal attributes, and it is an ideal model organism for studying fundamental processes such as photosynthesis, sexual reproduction, and life cycle. N6-methyladenosine (m6A) is the most prevalent mRNA modification, and it plays important roles during sexual reproduction in animals and plants. However, the pattern and function of m6A modification during the sexual reproduction of Chlamydomonas remain unknown. Here, we performed transcriptome and methylated RNA immunoprecipitation sequencing (MeRIP-seq) analyses on six samples from different stages during sexual reproduction of the Chlamydomonas life cycle. The results show that m6A modification frequently occurs at the main motif of DRAC (D = G/A/U, R = A/G) in Chlamydomonas mRNAs. Moreover, m6A peaks in Chlamydomonas mRNAs are mainly enriched in the 3' untranslated regions (3'UTRs) and negatively correlated with the abundance of transcripts at each stage. In particular, there is a significant negative correlation between the expression levels and the m6A levels of genes involved in the microtubule-associated pathway, indicating that m6A modification influences the sexual reproduction and the life cycle of Chlamydomonas by regulating microtubule-based movement. In summary, our findings are the first to demonstrate the distribution and the functions of m6A modification in Chlamydomonas mRNAs and provide new evolutionary insights into m6A modification in the process of sexual reproduction in other plant organisms.

m6A mRNA modification promotes chilling tolerance and modulates gene translation efficiency in Arabidopsis

N 6-methyladenosine (m6A), the most prevalent mRNA modification in eukaryotes, is an emerging player of gene regulation at transcriptional and translational levels. Here, we explored the role of m6A modification in response to low temperature in Arabidopsis (Arabidopsis thaliana). Knocking down mRNA adenosine methylase A (MTA), a key component of the modification complex, by RNA interference (RNAi) led to drastically reduced growth at low temperature, indicating a critical role of m6A modification in the chilling response. Cold treatment reduced the overall m6A modification level of mRNAs especially at the 3' untranslated region. Joint analysis of the m6A methylome, transcriptome and translatome of the wild type (WT) and the MTA RNAi line revealed that m6A-containing mRNAs generally had higher abundance and translation efficiency than non-m6A-containing mRNAs under normal and low temperatures. In addition, reduction of m6A modification by MTA RNAi only moderately altered the gene expression response to low temperature but led to dysregulation of translation efficiencies of one third of the genes of the genome in response to cold. We tested the function of the m6A-modified cold-responsive gene ACYL-COA:DIACYLGLYCEROL ACYLTRANSFERASE 1 (DGAT1) whose translation efficiency but not transcript level was reduced in the chilling-susceptible MTA RNAi plant. The dgat1 loss-of-function mutant exhibited reduced growth under cold stress. These results reveal a critical role of m6A modification in regulating growth under low temperature and suggest an involvement of translational control in chilling responses in Arabidopsis.

Functional interdependence of N6-methyladenosine methyltransferase complex subunits in Arabidopsis

Addition of N6-methyladenosine (m6A), the most prevalent internal mRNA modification in eukaryotes, is catalyzed by an evolutionarily conserved m6A methyltransferase complex. In the model plant Arabidopsis thaliana, the m6A methyltransferase complex is composed of 2 core methyltransferases, mRNA adenosine methylase (MTA) and MTB, and several accessory subunits such as FK506-BINDING PROTEIN 12 KD INTERACTING PROTEIN 37KD (FIP37), VIRILIZER (VIR), and HAKAI. It is yet largely unknown whether these accessory subunits influence the functions of MTA and MTB. Herein, I reveal that FIP37 and VIR are indispensable for stabilizing the methyltransferases MTA and MTB, thus functioning as key subunits to maintain the functionality of the m6A methyltransferase complex. Furthermore, VIR affects FIP37 and HAKAI protein accumulation, while MTA and MTB mutually influence each other. In contrast, HAKAI has little effect on protein abundance or localization of MTA, MTB, and FIP37. These findings uncover unique functional interdependence at the post-translational level among individual components in the Arabidopsis m6A methyltransferase complex, suggesting that maintenance of protein homeostasis among various subunits of the m6A methyltransferase complex is essential for maintaining the protein stoichiometry required for the proper function of the m6A methyltransferase complex in m6A deposition in plants.

Shaping the landscape of N6-methyladenosine RNA methylation in Arabidopsis

N 6-methyladenosine (m6A) modification on messenger RNAs (mRNAs) is deposited by evolutionarily conserved methyltransferases (writers). How individual m6A writers sculpt the overall landscape of the m6A methylome and the resulting biological impact in multicellular organisms remains unknown. Here, we systematically surveyed the quantitative m6A methylomes at single-nucleotide resolution and their corresponding transcriptomes in Arabidopsis (Arabidopsis thaliana) bearing respective impaired m6A writers. The m6A sites associated with the five Arabidopsis writers were located mostly within 3' untranslated regions with peaks at around 100 bp downstream of stop codons. m6A predominantly promoted the usage of distal poly(A) sites but had little effect on RNA splicing. Notably, impaired m6A writers resulted in hypomethylation and downregulation of transcripts encoding ribosomal proteins, indicating a possible correlation between m6A and protein translation. Besides the common effects on mRNA metabolism and biological functions uniquely exerted by different Arabidopsis m6A writers compared with their counterparts in human cell lines, our analyses also revealed the functional specificity of individual Arabidopsis m6A writers in plant development and response to stresses. Our findings thus reveal insights into the biological roles of various Arabidopsis m6A writers and their cognate counterparts in other multicellular m6A methyltransferase complexes.

The blue light receptor CRY1 interacts with FIP37 to promote N6 -methyladenosine RNA modification and photomorphogenesis in Arabidopsis

Light is a particularly important environmental cue that regulates a variety of diverse plant developmental processes, such as photomorphogenesis. Blue light promotes photomorphogenesis mainly through the activation of the photoreceptor cryptochrome 1 (CRY1). However, the mechanism underlying the CRY1-mediated regulation of growth is not fully understood. Here, we found that blue light induced N⁶ -methyladenosine (m⁶ A) RNA modification during photomorphogenesis partially via CRY1. Cryptochrome 1 mediates blue light-induced expression of FKBP12-interacting protein 37 (FIP37), which is a component of m⁶ A writer. Moreover, we showed that CRY1 physically interacted with FIP37 in vitro and in vivo, and mediated blue light activation of FIP37 binding to RNA. Furthermore, CRY1 and FIP37 modulated m⁶ A on photomorphogenesis-related genes PIF3, PIF4, and PIF5, thereby accelerating the decay of their transcripts. Genetically, FIP37 repressed hypocotyl elongation under blue light, and fip37 mutation could partially rescue the short-hypocotyl phenotype of CRY1-overexpressing plants. Together, our results provide a new insight into CRY1 signal in modulating m⁶ A methylation and stability of PIFs, and establish an essential molecular link between m⁶ A modification and determination of photomorphogenesis in plants.

RNA methyltransferases in plants: Breakthroughs in function and evolution

Each day it is becoming increasingly difficult not to notice the completely new, fast growing, extremely intricate and challenging world of epitranscriptomics as the understanding of RNA methylation is expanding at a hasty rate. Writers (methyltransferases), erasers (demethylases) and readers (RNA-binding proteins) are responsible for adding, removing and recognising methyl groups on RNA, respectively. Several methyltransferases identified in plants are now being investigated and recent studies have shown a connection between RNA-methyltransferases (RNA-MTases) and stress and development processes. However, compared to their animal and bacteria counterparts, the understanding of RNA methyltransferases is still incipient, particularly those located in organelles. Comparative and systematic analyses allowed the tracing of the evolution of these enzymes suggesting the existence of several methyltransferases yet to be characterised. This review outlines the functions of plant nuclear and organellar RNA-MTases in plant development and stress responses and the comparative and evolutionary discoveries made on RNA-MTases across kingdoms.

Genome-wide identification of the AlkB homologs gene family, PagALKBH9B and PagALKBH10B regulated salt stress response in Populus

The AlkB homologs (ALKBH) gene family regulates N⁶-methyladenosine (m⁶A) RNA methylation and is involved in plant growth and the abiotic stress response. Poplar is an important model plant for studying perennial woody plants. Poplars typically have a long juvenile period of 7-10 years, requiring long periods of time for studies of flowering or mature wood properties. Consequently, functional studies of the ALKBH genes in Populus species have been limited. Based on AtALKBHs sequence similarity with Arabidopsis thaliana, 23 PagALKBHs were identified in the genome of the poplar 84K hybrid genotype (P. alba  ×  P. tremula var. glandulosa), and gene structures and conserved domains were confirmed between homologs. The PagALKBH proteins were classified into six groups based on conserved sequence compared with human, Arabidopsis, maize, rice, wheat, tomato, barley, and grape. All homologs of PagALKBHs were tissue-specific; most were highly expressed in leaves. ALKBH9B and ALKBH10B are m⁶A demethylases and overexpression of their homologs PagALKBH9B and PagALKBH10B reduced m⁶A RNA methylation in transgenic lines. The number of adventitious roots and the biomass accumulation of transgenic lines decreased compared with WT. Therefore, PagALKBH9B and PagALKBH10B mediate m⁶A RNA demethylation and play a regulatory role in poplar growth and development. Overexpression of PagALKBH9B and PagALKBH10B can reduce the accumulation of H₂O₂ and oxidative damage by increasing the activities of SOD, POD, and CAT, and enhancing protection for Chl a/b, thereby increasing the salt tolerance of transgenic lines. However, overexpression lines were more sensitive to drought stress due to reduced proline content. This research revealed comprehensive information about the PagALKBH gene family and their roles in growth and development and responsing to salt stress of poplar.

Transcriptome-Wide m6A Methylome Profiling in Sorghum following GA3 Treatment under Salt Stress

Sorghum (“Jitian 3”) is a salt-tolerant seed cultivar used regularly in marginal lands, such as those with saline soils. Herein, we examined the potential of employing gibberellic acid (GA₃) as an inducer of sorghum development during salt stress. Thus far, there have been no reports on the signaling network involved in the GA₃-mediated regulation of sorghum development. In this study, we demonstrated that the stimulating properties of 50 mg/L GA₃ on sorghum development was far superior to other GA₃ concentrations under a 150 mM NaCl salinity condition. Furthermore, using methylated RNA immunoprecipitation sequencing (MeRIP-seq), we established an m⁶A methylation (m⁶A-M) profile in sorghum following exposure to 50 mg/L GA₃. Overall, 23,363 m⁶A peaks and 16,200 m⁶A genes were screened among the GA₃-treated and control leaves. These identified peaks were shown to be primarily enriched in the coding, as were the 3′- and 5′-untranslated regions. In addition, we employed m⁶A and transcript expression cross-analysis to identify 70 genes with differential transcript expression and simultaneous m⁶A-M. Intriguingly, the principal gene, LOC8066282, which is associated with LOC8084853, was shown to be intricately linked to the phosphatidylinositol signaling, which in turn regulates sorghum development and response to salt stress. This investigation presents a novel RNA m⁶A-M profile in sorghum, which may facilitate new insights into the underlying signaling behind salt stress resistance. This work will also benefit future investigations on foreign GA₃ administration of sorghum.

Transcriptome-wide N6-methyladenosine (m6A) methylation in soybean under Meloidogyne incognita infection

N6-methyladenosine (m6A) is a reversible epigenetic modification of mRNA and other RNAs that plays a significant role in regulating gene expression and biological processes. However, m6A abundance, dynamics, and transcriptional regulatory mechanisms remain unexplored in the context of soybean resistance to Meloidogyne incognita. In this study, we performed a comparative analysis of transcriptome-wide m6A and metabolome profiles of soybean root tissues with and without M. incognita infection. Global m6A hypermethylation was widely induced in response to M. incognita infection and was enriched around the 3' end of coding sequences and in 3' UTR regions. There were 2069 significantly modified m6A sites, 594 differentially expressed genes, and 103 differentially accumulated metabolites between infected and uninfected roots, including coumestrol, psoralidin, and 2-hydroxyethylphosphonate. Among 101 m6A-modified DEGs, 34 genes were hypomethylated and upregulated, and 39 genes were hypermethylated and downregulated, indicating a highly negative correlation between m6A methylation and gene transcript abundance. A number of these m6A-modified DEGs, including WRKY70, ERF60, POD47 and LRR receptor-like serine/threonine-protein kinases, were involved in plant defense responses. Our study provides new insights into the critical role of m6A modification in early soybean responses to M. incognita.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-022-00077-2.

Exploring epitranscriptomics for crop improvement and environmental stress tolerance

Climate change and stressful environmental conditions severely hamper crop growth, development and yield. Plants respond to environmental perturbations, through their plasticity provided by key-genes, governed at post-/transcriptional levels. Gene-regulation in plants is a multilevel process controlled by diverse cellular entities that includes transcription factors (TF), epigenetic regulators and non-coding RNAs beside others. There are successful studies confirming the role of epigenetic modifications (DNA-methylation/histone-modifications) in gene expression. Recent years have witnessed emergence of a highly specialized field the "Epitranscriptomics". Epitranscriptomics deals with investigating post-transcriptional RNA chemical-modifications present across the life forms that change structural, functional and biological characters of RNA. However, deeper insights on of epitranscriptomic modifications, with >140 types known so far, are to be understood fully. Researchers have identified epitranscriptome marks (writers, erasers and readers) and mapped the site-specific RNA modifications (m6A, m⁵C, 3' uridylation, etc.) responsible for fine-tuning gene expression in plants. Simultaneous advancement in sequencing platforms, upgraded bioinformatic tools and pipelines along with conventional labelled techniques have further given a statistical picture of these epitranscriptomic modifications leading to their potential applicability in crop improvement and developing climate-smart crops. We present herein the insights on epitranscriptomic machinery in plants and how epitranscriptome and epitranscriptomic modifications underlying plant growth, development and environmental stress responses/adaptations. Third-generation sequencing technology, advanced bioinformatics tools and databases being used in plant epitranscriptomics are also discussed. Emphasis is given on potential exploration of epitranscriptome engineering for crop-improvement and developing environmental stress tolerant plants covering current status, challenges and future directions.

Epitranscriptomics: An Additional Regulatory Layer in Plants' Development and Stress Response

Epitranscriptomics has added a new layer of regulatory machinery to eukaryotes, and the advancement of sequencing technology has revealed more than 170 post-transcriptional modifications in various types of RNAs, including messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and long non-coding RNA (lncRNA). Among these, N6-methyladenosine (m⁶A) and N5-methylcytidine (m⁵C) are the most prevalent internal mRNA modifications. These regulate various aspects of RNA metabolism, mainly mRNA degradation and translation. Recent advances have shown that regulation of RNA fate mediated by these epitranscriptomic marks has pervasive effects on a plant's development and responses to various biotic and abiotic stresses. Recently, it was demonstrated that the removal of human-FTO-mediated m⁶A from transcripts in transgenic rice and potatoes caused a dramatic increase in their yield, and that the m⁶A reader protein mediates stress responses in wheat and apple, indicating that regulation of m⁶A levels could be an efficient strategy for crop improvement. However, changing the overall m⁶A levels might have unpredictable effects; therefore, the identification of precise m⁶A levels at a single-base resolution is essential. In this review, we emphasize the roles of epitranscriptomic modifications in modulating molecular, physiological, and stress responses in plants, and provide an outlook on epitranscriptome engineering as a promising tool to ensure food security by editing specific m⁶A and m⁵C sites through robust genome-editing technology.

The m6 A reader MhYTP2 regulates MdMLO19 mRNA stability and antioxidant genes translation efficiency conferring powdery mildew resistance in apple

N⁶ -methyladenosine (m⁶ A) reader protein plays an important role in trichome morphology, developmental timing and morphogenesis in Arabidopsis. However, the function of m⁶ A readers in plant-microbe interaction remains unclear. Here, a Malus YTH-domain family protein MhYTP2 was initially characterized as an m⁶ A reader. MhYTP2 overexpression increased mRNA m⁶ A modification level and translation efficiency. The m⁶ A in the exon regions appeared to destabilize the mRNAs, whereas m⁶ A in the untranslated regions positively correlated with the associated mRNA abundance. MhYTP2 overexpression enhanced apple powdery mildew resistance, possibly by rapidly degrading the bound mRNAs of MdMLO19 and MdMLO19-X1 and improving the translation efficiency of the antioxidant genes. To conclude, the results shed light on the apple m⁶ A profile, the effect of MhYTP2 on m⁶ A profile, and the m⁶ A roles in MdMLO19 and MdMLO19-X1 mRNAs stability and glutamate dehydrogenase 1-like MdGDH1L mRNA translation efficiency.

Multi-Omics Analysis Reveals the Dynamic Changes of RNA N 6 -Methyladenosine in Pear (Pyrus bretschneideri) Defense Responses to Erwinia amylovora Pathogen Infection

N6-methylated adenine (m⁶A) is the most prevalent modification of mRNA methylation and can regulate many biological processes in plants, such as mRNA processing, development, and stress response. Some studies have increased our understanding of its various roles in model plants in recent years. Nevertheless, the distribution of m⁶A and the impact of m⁶A on the regulation of plant defense responses against pathogen inoculation are virtually unknown in pear. In this study, MeRIP-seq and RNA-seq data from healthy and inoculated plants were analyzed to assess the changes in the transcript levels and posttranscriptional modification of pear in response to the fire blight pathogen Erwinia amylovora. Following the analysis of 97,261 m⁶A peaks, we found that m⁶A preferred to modify duplicate genes rather than singleton genes and that m⁶A-methylated genes underwent stronger purifying selection. A total of 2,935 specific m⁶A sites were detected at the transcriptome level after inoculation, which may increase defense-related transcript abundance to enhance pear resistance. In addition, 1,850 transcripts were detected only in the mock-inoculated groups. The hypomethylated transcripts were mainly related to transcriptional regulation and various biological processes, such as chloroplast organization and sucrose biosynthetic processes. In addition, we found that the extent of m⁶A methylation was significantly positively correlated with the transcript level, suggesting a regulatory role for m⁶A in the plant response.

Discovery of potential protein biomarkers associated with sugarcane white leaf disease susceptibility using a comparative proteomic approach

Sugarcane white leaf disease (SCWLD) is caused by phytoplasma, a serious sugarcane phytoplasma pathogen, which causes significant decreases in crop yield and sugar quality. The identification of proteins involved in the defense mechanism against SCWLD phytoplasma may help towards the development of varieties resistant to SCWLD. We investigated the proteomes of four sugarcane varieties with different levels of susceptibility to SCWLD phytoplasma infection, namely K88-92 and K95-84 (high), KK3 (moderate), and UT1 (low) by quantitative label-free nano-liquid chromatography-tandem mass spectrometry (nano LC-MS/MS). A total of 248 proteins were identified and compared among the four sugarcane varieties. Two potential candidate protein biomarkers for reduced susceptibility to SCWLD phytoplasma were identified as proteins detected only in UT1. The functions of these proteins are associated with protein folding, metal ion binding, and oxidoreductase. The candidate biomarkers could be useful for further study of the sugarcane defense mechanism against SCWLD phytoplasma, and in molecular and conventional breeding strategies for variety improvement.

Epigenome and Epitranscriptome: Potential Resources for Crop Improvement

Crop breeding faces the challenge of increasing food demand, especially under climatic changes. Conventional breeding has relied on genetic diversity by combining alleles to obtain desired traits. In recent years, research on epigenetics and epitranscriptomics has shown that epigenetic and epitranscriptomic diversity provides additional sources for crop breeding and harnessing epigenetic and epitranscriptomic regulation through biotechnologies has great potential for crop improvement. Here, we review epigenome and epitranscriptome variations during plant development and in response to environmental stress as well as the available sources for epiallele formation. We also discuss the possible strategies for applying epialleles and epitranscriptome engineering in crop breeding.

Arabidopsis thaliana subclass I ACTIN DEPOLYMERIZING FACTORs and vegetative ACTIN2/8 are novel regulators of endoreplication

Endoreplication is a type of cell cycle where genome replication occurs without mitosis. An increase of ploidy level by endoreplication is often associated with cell enlargement and an enhanced plant growth. Here we report Arabidopsis thaliana subclass I ACTIN DEPOLYMERIZING FACTORs (ADFs) and vegetative ACTIN2/8 as novel regulators of endoreplication. A. thaliana has 11 ADF members that are divided into 4 subclasses. Subclass I consists of four members, ADF1, -2, -3, and -4, all of which constitutively express in various tissues. We found that both adf4 knockout mutant and transgenic plants in which expressions of all of four subclass I ADFs are suppressed (ADF1-4Ri) showed an increased leaf area of mature first leaves, which was associated with a significant increase of epidermal pavement cell area. Ploidy analysis revealed that the ploidy level was significantly increased in mature leaves of ADF1-4Ri. The increased ploidy was also observed in roots of adf4 and ADF1-4Ri, as well as in dark-grown hypocotyls of adf4. Furthermore, double mutants of vegetative ACT2 and ACT8 (act2/8) exhibited an increase of leaf area and ploidy level in mature leaves. Therefore, actin-relating pathway could regulate endoreplication. The possible mechanisms that actin and ADFs regulate endoreplication are discussed.

N6-methyladenosine modification underlies messenger RNA metabolism and plant development

RNA modifications constitute an essential layer of gene regulation in living organisms. As the most prevalent internal modification on eukaryotic mRNAs, N⁶-methyladenosine (m⁶A) exists in many plant species and requires the evolutionarily conserved methyltransferases, demethylases, and m⁶A binding proteins for writing, erasing, and reading m⁶A, respectively. In plants, m⁶A affects many aspects of mRNA metabolism, including alternative polyadenylation, secondary structure, translation, and decay, which underlies various plant developmental processes and stress responses. Here, we discuss the recent progress in understanding the roles of m⁶A modification in mRNA metabolism and their mechanistic link with plant development and stress responses. We also highlight some outstanding questions and provide an outlook on future prospects of m⁶A research in plants.

RNA N6-Methyladenosine Responds to Low-Temperature Stress in Tomato Anthers

Cold stress is a serious threat to subtropical crop pollen development and induces yield decline. N6-methyladenosine (m⁶A) is the most frequent mRNA modification and plays multiple physiological functions in plant development. However, whether m⁶A regulates pollen development is unclear, and its putative role in cold stress response remains unknown. Here, we observed that moderate low-temperature (MLT) stress induced pollen abortion in tomato. This phenotype was caused by disruption of tapetum development and pollen exine formation, accompanied by reduced m⁶A levels in tomato anther. Analysis of m⁶A-seq data revealed 1,805 transcripts displayed reduced m⁶A levels and 978 transcripts showed elevated m⁶A levels in MLT-stressed anthers compared with those in anthers under normal temperature. These differentially m⁶A enriched transcripts under MLT stress were mainly related to lipid metabolism, adenosine triphosphatase (ATPase) activity, and ATP-binding pathways. An ATP-binding transcript, SlABCG31, had significantly upregulated m⁶A modification levels, which was inversely correlated to the dramatically downregulated expression level. These changes correlated with higher abscisic acid (ABA) levels in anthers and disrupted pollen wall formation under low-temperature stress. Our findings characterized m⁶A as a novel layer of complexity in gene expression regulation and established a molecular link between m⁶A methylation and tomato anther development under low-temperature conditions.

N6 -Methyladenosine mRNA methylation is important for salt stress tolerance in Arabidopsis

As the most abundant internal modification of mRNA, N⁶ -methyladenosine (m⁶ A) methylation of RNA is emerging as a new layer of epitranscriptomic gene regulation in cellular processes, including embryo development, flowering-time control, microspore generation and fruit ripening, in plants. However, the cellular role of m⁶ A in plant responses to environmental stimuli remains largely unexplored. In this study, we show that m⁶ A methylation plays an important role in salt stress tolerance in Arabidopsis. All mutants of m⁶ A writer components, including MTA, MTB, VIRILIZER (VIR) and HAKAI, displayed salt-sensitive phenotypes in an m⁶ A-dependent manner. The vir mutant, in which the level of m⁶ A was most highly reduced, exhibited salt-hypersensitive phenotypes. Analysis of the m⁶ A methylome in the vir mutant revealed a transcriptome-wide loss of m⁶ A modification in the 3' untranslated region (3'-UTR). We demonstrated further that VIR-mediated m⁶ A methylation modulates reactive oxygen species homeostasis by negatively regulating the mRNA stability of several salt stress negative regulators, including ATAF1, GI and GSTU17, through affecting 3'-UTR lengthening linked to alternative polyadenylation. Our results highlight the important role played by epitranscriptomic mRNA methylation in the salt stress response of Arabidopsis and indicate a strong link between m⁶ A methylation and 3'-UTR length and mRNA stability during stress adaptation.

OseIF3h Regulates Plant Growth and Pollen Development at Translational Level Presumably through Interaction with OsMTA2

The initiation stage of protein biosynthesis is a sophisticated process tightly regulated by numerous initiation factors and their associated components. However, the mechanism underlying translation initiation has not been completely understood in rice. Here, we showed knock-out mutation of the rice eukaryotic translation initiation factor 3 subunit h (OseIF3h) resulted in plant growth retardation and seed-setting rate reduction as compared to the wild type. Further investigation demonstrated an interaction between OseIF3h and OsMTA2 (mRNA adenosine methylase 2), a rice homolog of METTL3 (methyltransferase-like 3) in mammals, which provided new insight into how N6-methyladenosine (m6A) modification of messenger RNA (mRNA) is engaged in the translation initiation process in monocot species. Moreover, the RIP-seq (RNA immunoprecipitation sequencing) data suggested that OseIF3h was involved in multiple biological processes, including photosynthesis, cellular metabolic process, precursor metabolites, and energy generation. Therefore, we infer that OseIF3h interacts with OsMTA2 to target a particular subset of genes at translational level, regulating plant growth and pollen development.

Deciphering Epitranscriptome: Modification of mRNA Bases Provides a New Perspective for Post-transcriptional Regulation of Gene Expression

Gene regulation depends on dynamic and reversibly modifiable biological and chemical information in the epigenome/epitranscriptome. Accumulating evidence suggests that messenger RNAs (mRNAs) are generated in flashing bursts in the cells in a precisely regulated manner. However, the different aspects of the underlying mechanisms are not fully understood. Cellular RNAs are post-transcriptionally modified at the base level, which alters the metabolism of mRNA. The current understanding of epitranscriptome in the animal system is far ahead of that in plants. The accumulating evidence indicates that the epitranscriptomic changes play vital roles in developmental processes and stress responses. Besides being non-genetically encoded, they can be of reversible nature and involved in fine-tuning the expression of gene. However, different aspects of base modifications in mRNAs are far from adequate to assign the molecular basis/functions to the epitranscriptomic changes. Advances in the chemogenetic RNA-labeling and high-throughput next-generation sequencing techniques are enabling functional analysis of the epitranscriptomic modifications to reveal their roles in mRNA biology. Mapping of the common mRNA modifications, including N 6-methyladenosine (m6A), and 5-methylcytidine (m5C), have enabled the identification of other types of modifications, such as N 1-methyladenosine. Methylation of bases in a transcript dynamically regulates the processing, cellular export, translation, and stability of the mRNA; thereby influence the important biological and physiological processes. Here, we summarize the findings in the field of mRNA base modifications with special emphasis on m6A, m5C, and their roles in growth, development, and stress tolerance, which provide a new perspective for the regulation of gene expression through post-transcriptional modification. This review also addresses some of the scientific and technical issues in epitranscriptomic study, put forward the viewpoints to resolve the issues, and discusses the future perspectives of the research in this area.

Analysis and review of trichomes in plants

BACKGROUND

Trichomes play a key role in the development of plants and exist in a wide variety of species.

RESULTS

In this paper, it was reviewed that the structure and morphology characteristics of trichomes, alongside the biological functions and classical regulatory mechanisms of trichome development in plants. The environment factors, hormones, transcription factor, non-coding RNA, etc., play important roles in regulating the initialization, branching, growth, and development of trichomes. In addition, it was further investigated the atypical regulation mechanism in a non-model plant, found that regulating the growth and development of tea (Camellia sinensis) trichome is mainly affected by hormones and the novel regulation factors.

CONCLUSIONS

This review further displayed the complex and differential regulatory networks in trichome initiation and development, provided a reference for basic and applied research on trichomes in plants.

Processing of coding and non-coding RNAs in plant development and environmental responses

Precursor RNAs undergo extensive processing to become mature RNAs. RNA transcripts are subjected to 5′ capping, 3′-end processing, splicing, and modification; they also form dynamic secondary structures during co-transcriptional and post-transcriptional processing. Like coding RNAs, non-coding RNAs (ncRNAs) undergo extensive processing. For example, secondary small interfering RNA (siRNA) transcripts undergo RNA processing, followed by further cleavage to become mature siRNAs. Transcriptome studies have revealed roles for co-transcriptional and post-transcriptional RNA processing in the regulation of gene expression and the coordination of plant development and plant–environment interactions. In this review, we present the latest progress on RNA processing in gene expression and discuss phased siRNAs (phasiRNAs), a kind of germ cell-specific secondary small RNA (sRNA), focusing on their functions in plant development and environmental responses.

The impact of epitranscriptomic marks on post-transcriptional regulation in plants

Ribonucleotides within the various RNA molecules in eukaryotes are marked with more than 160 distinct covalent chemical modifications. These modifications include those that occur internally in messenger RNA (mRNA) molecules such as N6-methyladenosine (m6A) and 5-methylcytosine (m5C), as well as those that occur at the ends of the modified RNAs like the non-canonical 5' end nicotinamide adenine dinucleotide (NAD+) cap modification of specific mRNAs. Recent findings have revealed that covalent RNA modifications can impact the secondary structure, translatability, functionality, stability and degradation of the RNA molecules in which they are included. Many of these covalent RNA additions have also been found to be dynamically added and removed through writer and eraser complexes, respectively, providing a new layer of epitranscriptome-mediated post-transcriptional regulation that regulates RNA quality and quantity in eukaryotic transcriptomes. Thus, it is not surprising that the regulation of RNA fate mediated by these epitranscriptomic marks has been demonstrated to have widespread effects on plant development and the responses of these organisms to abiotic and biotic stresses. In this review, we highlight recent progress focused on the study of the dynamic nature of these epitranscriptome marks and their roles in post-transcriptional regulation during plant development and response to environmental cues, with an emphasis on the mRNA modifications of non-canonical 5' end NAD+ capping, m6A and several other internal RNA modifications.

A Rice Immunophilin Homolog, OsFKBP12, Is a Negative Regulator of Both Biotic and Abiotic Stress Responses

A class of proteins that were discovered to bind the immunosuppressant drug FK506, called FK506-binding proteins (FKBPs), are members of a sub-family of immunophilins. Although they were first identified in human, FKBPs exist in all three domains of life. In this report, a rice FKBP12 homolog was first identified as a biotic stress-related gene through suppression subtractive hybridization screening. By ectopically expressing OsFKBP12 in the heterologous model plant system, Arabidopsis thaliana, for functional characterization, OsFKBP12 was found to increase susceptibility of the plant to the pathogen, Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). This negative regulatory role of FKBP12 in biotic stress responses was also demonstrated in the AtFKBP12-knockout mutant, which exhibited higher resistance towards Pst DC3000. Furthermore, this higher-plant FKBP12 homolog was also shown to be a negative regulator of salt tolerance. Using yeast two-hybrid tests, an ancient unconventional G-protein, OsYchF1, was identified as an interacting partner of OsFKBP12. OsYchF1 was previously reported as a negative regulator of both biotic and abiotic stresses. Therefore, OsFKBP12 probably also plays negative regulatory roles at the convergence of biotic and abiotic stress response pathways in higher plants.

The m6 A reader ECT2 post-transcriptionally regulates proteasome activity in Arabidopsis

Methylation of internal adenosine at nitrogen-6 position (m⁶ A) is the most abundant post-transcriptional modification in eukaryotic RNAs. These modifications are recognized by m⁶ A-binding proteins ('readers') that affect downstream functions. In plants, the scope of gene expression regulation by reader proteins is not clear. Here, overexpression and loss-of-function mutants were used to characterize the role of the Arabidopsis m⁶ A reader ECT2 in proteasome regulation. ECT2 regulates the mRNA levels of the proteasome regulator PTRE1 and of several 20S proteasome subunits, resulting in enhanced 26S proteasome activity. This regulation is dependent on ECT2 m⁶ A binding function. Interestingly, though ECT2 positively regulates proteasome activity in both young and mature plants, PTRE1 has different regulatory effects in different developmental stages. In mature plants, PTRE1 inhibits 26S proteasome activity, while in seedlings PTRE1 knockout mutants have reduced 26S proteasome activity. Taken together, our results suggest a novel epitranscriptomic mechanism of proteasome regulation by ECT2 that is used to fine tune proteasome activity by affecting the expression of PTRE1 and 20S proteasome subunits.

Recurrent requirement for the m6A-ECT2/ECT3/ECT4 axis in the control of cell proliferation during plant organogenesis

mRNA methylation at the N6-position of adenosine (m⁶A) enables multiple layers of post-transcriptional gene control, often via RNA-binding proteins that use a YT521-B homology (YTH) domain for specific m⁶A recognition. In Arabidopsis, normal leaf morphogenesis and rate of leaf formation require m⁶A and the YTH-domain proteins ECT2, ECT3 and ECT4. In this study, we show that ect2/ect3 and ect2/ect3/ect4 mutants also exhibit slow root and stem growth, slow flower formation, defective directionality of root growth, and aberrant flower and fruit morphology. In all cases, the m⁶A-binding site of ECT proteins is required for in vivo function. We also demonstrate that both m⁶A methyltransferase mutants and ect2/ect3/ect4 exhibit aberrant floral phyllotaxis. Consistent with the delayed organogenesis phenotypes, we observe particularly high expression of ECT2, ECT3 and ECT4 in rapidly dividing cells of organ primordia. Accordingly, ect2/ect3/ect4 mutants exhibit decreased rates of cell division in leaf and vascular primordia. Thus, the m⁶A-ECT2/ECT3/ECT4 axis is employed as a recurrent module to stimulate plant organogenesis, at least in part by enabling rapid cellular proliferation.

Marking RNA: m6A writers, readers, and functions in Arabidopsis

N6-methyladenosine (m6A) emerges as an important modification in eukaryotic mRNAs. m6A has first been reported in 1974, and its functional significance in mammalian gene regulation and importance for proper development have been well established. An arsenal of writer, eraser, and reader proteins accomplish deposition, removal, and interpretation of the m6A mark, resulting in dynamic function. This led to the concept of an epitranscriptome, the compendium of RNA species with chemical modification of the nucleobases in the cell, in analogy to the epigenome. While m6A has long been known to also exist in plant mRNAs, proteins involved in m6A metabolism have only recently been detected by mutant analysis, homology search, and mRNA interactome capture in the reference plant Arabidopsis thaliana. Dysregulation of the m6A modification causes severe developmental abnormalities of leaves and roots and altered timing of reproductive development. Furthermore, m6A modification affects viral infection. Here, we discuss recent progress in identifying m6A sites transcriptome-wide, in identifying the molecular players involved in writing, removing, and reading the mark, and in assigning functions to this RNA modification in A. thaliana. We highlight similarities and differences to m6A modification in mammals and provide an outlook on important questions that remain to be addressed.

Functional Implications of Active N6-Methyladenosine in Plants

N6-methyladenosine (m6A) is the most common type of eukaryotic mRNA modification and has been found in many organisms, including mammals, and plants. It has important regulatory effects on RNA splicing, export, stability, and translation. The abundance of m6A on RNA depends on the dynamic regulation between methyltransferase ("writer") and demethylase ("eraser"), and m6A binding protein ("reader") exerts more specific regulatory function by binding m6A modification sites on RNA. Progress in research has revealed important functions of m6A modification in plants. In this review, we systematically summarize the latest advances in research on the composition and mechanism of action of the m6A system in plants. We emphasize the function of m6A modification on RNA fate, plant development, and stress resistance. Finally, we discuss the outstanding questions and opportunities exist for future research on m6A modification in plant.

MTA, an RNA m6A Methyltransferase, Enhances Drought Tolerance by Regulating the Development of Trichomes and Roots in Poplar

N6-methyladenosine (m⁶A) is the most prevalent internal modification present in the mRNAs of all higher eukaryotes, where it is present within both coding and noncoding regions. In mammals, methylation requires the catalysis of a multicomponent m⁶A methyltransferase complex. Proposed biological functions for m⁶A modification include pre-mRNA splicing, RNA stability, cell fate regulation, and embryonic development. However, few studies have been conducted on m⁶A modification in trees. In particular, the regulation mechanism of RNA m⁶A in Populus development remains to be further elucidated. Here, we show that PtrMTA (Populus trichocarpa methyltransferase) was colocalized with PtrFIP37 in the nucleus. Importantly, the PtrMTA-overexpressing plants significantly increased the density of trichomes and exhibited a more developed root system than that of wild-type controls. Moreover, we found that PtrMTA-overexpressing plants had better tolerance to drought stress. We also found PtrMTA was a component of the m⁶A methyltransferase complex, which participated in the formation of m⁶A methylation in poplar. Taken together, these results demonstrate that PtrMTA is involved in drought resistance by affecting the development of trichomes and roots, which will provide new clues for the study of RNA m⁶A modification and expand our understanding of the epigenetic molecular mechanism in woody plants.

CONSTANS-FKBP12 interaction contributes to modulation of photoperiodic flowering in Arabidopsis

Flowering time is a key process in plant development. Photoperiodic signals play a crucial role in the floral transition in Arabidopsis thaliana, and the protein CONSTANS (CO) has a central regulatory function that is tightly regulated at the transcriptional and post-translational levels. The stability of CO protein depends on a light-driven proteasome process that optimizes its accumulation in the evening to promote the production of the florigen FLOWERING LOCUS T (FT) and induce seasonal flowering. To further investigate the post-translational regulation of CO protein we have dissected its interactome network employing in vivo and in vitro assays and molecular genetics approaches. The immunophilin FKBP12 has been identified in Arabidopsis as a CO interactor that regulates its accumulation and activity. FKBP12 and CO interact through the CCT domain, affecting the stability and function of CO. fkbp12 insertion mutants show a delay in flowering time, while FKBP12 overexpression accelerates flowering, and these phenotypes can be directly related to a change in accumulation of FT protein. The interaction is conserved between the Chlamydomonas algal orthologs CrCO-CrFKBP12, revealing an ancient regulatory step in photoperiod regulation of plant development.

Epigenetic Modifications of mRNA and DNA in Plants

Advances in the detection and mapping of messenger RNA (mRNA) N⁶-methyladenosine (m⁶A) and 5-methylcytosine (m⁵C), and DNA N⁶-methyldeoxyadenosine (6mA) redefined our understanding of these modifications as additional tiers of epigenetic regulation. In plants, the most prevalent internal mRNA modifications, m⁶A and m⁵C, play crucial and dynamic roles in many processes, including embryo development, stem cell fate determination, trichome branching, leaf morphogenesis, floral transition, stress responses, fruit ripening, and root development. The newly identified and widespread epigenetic marker 6mA DNA methylation is associated with gene expression, plant development, and stress responses. Here, we review the latest research progress on mRNA and DNA epigenetic modifications, including the detection, dynamics, distribution, functions, regulatory proteins, and evolution, with a focus on m⁶A, m⁵C, and 6mA. We also provide some perspectives on future research of the newly identified and unknown epigenetic modifications of mRNA and DNA in plants.

Evolution of the RNA N 6-Methyladenosine Methylome Mediated by Genomic Duplication

RNA N ⁶-methyladenosine (m⁶A) modification is the most abundant form of RNA epigenetic modification in eukaryotes. Given that m⁶A evolution is associated with the selective constraints of nucleotide sequences in mammalian genomes, we hypothesize that m⁶A evolution can be linked, at least in part, to genomic duplication events in complex polyploid plant genomes. To test this hypothesis, we presented the maize (Zea mays) m⁶A modification landscape in a transcriptome-wide manner and identified 11,968 m⁶A peaks carried by 5,893 and 3,811 genes from two subgenomes (maize1 and maize2, respectively). Each of these subgenomes covered over 2,200 duplicate genes. Within these duplicate genes, those carrying m⁶A peaks exhibited significant differences in retention rate. This biased subgenome fractionation of m⁶A-methylated genes is associated with multiple sequence features and is influenced by asymmetric evolutionary rates. We also characterized the coevolutionary patterns of m⁶A-methylated genes and transposable elements, which can be mediated by whole genome duplication and tandem duplication. We revealed the evolutionary conservation and divergence of duplicated m⁶A functional factors and the potential role of m⁶A modification in maize responses to drought stress. This study highlights complex interplays between m⁶A modification and gene duplication, providing a reference for understanding the mechanisms underlying m⁶A evolution mediated by genome duplication events.

Occurrence and Functions of m6A and Other Covalent Modifications in Plant mRNA

Posttranscriptional control of gene expression is indispensable for the execution of developmental programs and environmental adaptation. Among the many cellular mechanisms that regulate mRNA fate, covalent nucleotide modification has emerged as a major way of controlling the processing, localization, stability, and translatability of mRNAs. This powerful mechanism is conserved across eukaryotes and controls the cellular events that lead to development and growth. As in other eukaryotes, N 6-methylation of adenosine is the most abundant and best studied mRNA modification in flowering plants. It is essential for embryonic and postembryonic plant development and it affects growth rate and stress responses, including susceptibility to plant RNA viruses. Although the mRNA modification field is young, the intense interest triggered by its involvement in stem cell differentiation and cancer has led to rapid advances in understanding how mRNA modifications control gene expression in mammalian systems. An equivalent effort from plant molecular biologists has been lagging behind, but recent work in Arabidopsis (Arabidopsis thaliana) and other plant species is starting to give insights into how this essential layer of posttranscriptional regulation works in plants, and both similarities and differences with other eukaryotes are emerging. In this Update, we summarize, connect, and evaluate the experimental work that supports our current knowledge of the biochemistry, molecular mechanisms, and biological functions of mRNA modifications in plants. We devote particular attention to N 6-methylation of adenosine and attempt to place the knowledge gained from plant studies within the context of a more general framework derived from studies in other eukaryotes.

In search of the mRNA modification landscape in plants

BACKGROUND

Precise regulation of gene expression is indispensable for the proper functioning of organisms in both optimal and challenging conditions. The most commonly known regulative mechanisms include the modulation of transcription, translation and adjustment of the transcript, and protein half-life. New players have recently emerged in the arena of gene expression regulators - chemical modifications of mRNAs.

MAIN TEXT

The latest studies show that modified ribonucleotides affect transcript splicing, localization, secondary structures, interaction with other molecules and translation efficiency. Thus far, attention has been focused mostly on the most widespread mRNA modification - adenosine methylation at the N⁶ position (m⁶A). However, initial reports on the formation and possible functions of other modified ribonucleotides, such as cytosine methylated at the 5' position (m⁵C), 8-hydroxyguanosine (8-OHG) and 8-nitroguanosine (8-NO₂G), have started to appear in the literature. Additionally, some reports indicate that pseudouridine (Ψ) is present in mRNAs and might perform important regulatory functions in eukaryotic cells. The present review summarizes current knowledge regarding the above-mentioned modified ribonucleotides (m⁶A, m⁵C, 8-OHG, 8-NO₂G) in transcripts across various plant species, including Arabidopsis, rice, sunflower, wheat, soybean and potato.

CONCLUSIONS

Chemical modifications of ribonucleotides affect mRNA stability and translation efficiency. They thus constitute a newly discovered layer of gene expression regulation and have a profound effect on the development and functioning of various organisms, including plants.

N6-methyladenosine regulatory machinery in plants: composition, function and evolution

N6-methyladenosine (m6A) RNA methylation, one of the most pivotal internal modifications of RNA, is a conserved post-transcriptional mechanism to enrich and regulate genetic information in eukaryotes. The scope and function of this modification in plants has been an intense focus of study, especially in model plant systems. The characterization of plant m6A writers, erasers and readers, as well as the elucidation of their functions, is currently one of the most fascinating hotspots in plant biology research. The functional analysis of m6A in plants will be booming in the foreseeable future, which could contribute to crop genetic improvement through epitranscriptome manipulation. In this review, we systematically analysed and summarized recent advances in the understanding of the structure and composition of plant m6A regulatory machinery, and the biological functions of m6A in plant growth, development and stress response. Finally, our analysis showed that the evolutionary relationships between m6A modification components were highly conserved across the plant kingdom.

The subunit of RNA N6-methyladenosine methyltransferase OsFIP regulates early degeneration of microspores in rice

N⁶-Methyladenosine (m⁶A) RNA methylation plays important roles during development in different species. However, knowledge of m⁶A RNA methylation in monocots remains limited. In this study, we reported that OsFIP and OsMTA2 are the components of m⁶A RNA methyltransferase complex in rice and uncovered a previously unknown function of m⁶A RNA methylation in regulation of plant sporogenesis. Importantly, OsFIP is essential for rice male gametogenesis. Knocking out of OsFIP results in early degeneration of microspores at the vacuolated pollen stage and simultaneously causes abnormal meiosis in prophase I. We further analyzed the profile of rice m⁶A modification during sporogenesis in both WT and OsFIP loss-of-function plants, and identified a rice panicle specific m⁶A modification motif “UGWAMH”. Interestingly, we found that OsFIP directly mediates the m⁶A methylation of a set of threonine protease and NTPase mRNAs and is essential for their expression and/or splicing, which in turn regulates the progress of sporogenesis. Our findings revealed for the first time that OsFIP plays an indispensable role in plant early sporogenesis. This study also provides evidence for the different functions of the m⁶A RNA methyltransferase complex between rice and Arabidopsis.

N⁶-Methyladenosine (m⁶A) is the most abundant internal modification of eukaryotic mRNA, and m⁶A mRNA methylation affects almost every stage of mRNA metabolism. However, the components of the m⁶A methyltransferase complex and their functions in monocots are completely unknown. In this study, we identified the components of the m⁶A RNA methyltransferase complex in rice, and uncovered a hitherto unknown function of m⁶A RNA methylation in regulating early microspore apoptosis. We also systematically analyzed the characteristics of m⁶A modification during sporogenesis for the first time, and revealed the sporogenesis stage-specific distribution of m⁶A peaks along genes and the specific modification motif in rice, which are different from that of other species and other developmental stages. The target genes of m⁶A methyltransferase complex member OsFIP were also identified in this study. Given the important roles of posttranscriptional mRNA regulation in gene expression and sporogenesis in plants, the findings of this study should stimulate more studies exploring the role of plant m⁶A methyltransferase and other components.

TOR inhibitors: from mammalian outcomes to pharmacogenetics in plants and algae

Target of rapamycin (TOR) is a conserved eukaryotic phosphatidylinositol 3-kinase-related kinase that regulates growth and metabolism in response to environment in plants and algae. The study of the plant and algal TOR pathway has largely depended on TOR inhibitors first developed for non-photosynthetic eukaryotes. In animals and yeast, fundamental work on the TOR pathway has benefited from the allosteric TOR inhibitor rapamycin and more recently from ATP-competitive TOR inhibitors (asTORis) that circumvent the limitations of rapamycin. The asTORis, developed for medical application, inhibit TOR complex 1 (TORC1) more efficiently than rapamycin and also inhibit rapamycin-resistant TORCs. This review presents knowledge on TOR inhibitors from the mammalian field and underlines important considerations for plant and algal biologists. It discusses the use of rapamycin and asTORis in plants and algae and concludes with guidelines for physiological studies and genetic screens with TOR inhibitors.

Messenger RNA Modifications in Plants

Over 160 distinct RNA modifications are known and collectively termed the epitranscriptome. Some of these modifications have been discovered in mRNA, uncovering a new layer of gene regulation. Transcriptome-wide mapping of epitranscriptomic codes and the discovery of their writers, erasers, and readers that dynamically install, remove, and interpret RNA modifications, respectively, are fundamental to understanding the epitranscriptome. Recent technologies have enabled the transcriptome-wide profiling of several mRNA modifications in Arabidopsis thaliana, providing key insights into regulating these modifications and their effects on plant development. Here we review technological innovations and recent progress in epitranscriptomics, with specific focus on N⁶-methyladenosine (m⁶A), 5-methylcytosine (m⁵C), uridylation, and their roles in multiple aspects of plant development.

A dynamic reversible RNA N6 -methyladenosine modification: current status and perspectives

N⁶ -methyladenosine (m⁶ A), as the most abundant RNA epigenetic modifications, has been shown to play critical roles in various biological functions. Research about enzymes that can catalyze and remove m⁶ A have revealed its comprehensive roles in messenger RNA (mRNA) metabolism and other physiological processes. The "readers" including YTH domain-containing proteins, hnRNPC, hnRNPG, hnRNPA2B1, IGF2BP1, IGF2BP2, and IGF2BP3, which can affect the fates of mRNA in an m⁶ A-dependent manner. In this review, we focus on recent advances in the research of the m⁶ A modifications, especially about the latest functions of its writers, erasers, readers in RNA metabolism, cancer, and lipid metabolism. In the end, we provide insights into the underlying molecular mechanisms of m⁶ A modifications.

N⁶-methyladenosine (m⁶A): Revisiting the Old with Focus on New, an Arabidopsis thaliana Centered Review

N⁶-methyladenosine (m⁶A) is known to occur in plant and animal messenger RNAs (mRNAs) since the 1970s. However, the scope and function of this modification remained un-explored till very recently. Since the beginning of this decade, owing to major technological breakthroughs, the interest in m⁶A has peaked again. Similar to animal mRNAs, plant mRNAs are also m⁶A methylated, within a specific sequence motif which is conserved across these kingdoms. m⁶A has been found to be pivotal for plant development and necessary for processes ranging from seed germination to floral development. A wide range of proteins involved in methylation of adenosine have been identified alongside proteins that remove or identify m⁶A. This review aims to put together the current knowledge regarding m⁶A in Arabidopsis thaliana.

Genome-wide analyses of genes encoding FK506-binding proteins reveal their involvement in abiotic stress responses in apple

Background

The FK506-binding proteins (FKBPs) play diverse roles in numerous critical processes for plant growth, development, and abiotic stress responses. However, the FKBP gene family in the important fruit crop apple (Malus × domestica Borkh.) has not been studied as thoroughly as in other species. Our research objective was to investigate the mechanisms by which apple FKBPs enable apple plants to tolerate the effects of abiotic stresses.

Results

Using bioinformatics-based methods, RT-PCR, and qRT-PCR technologies, we identified 38 FKBP genes and cloned 16 of them in the apple genome. The phylogenetic analysis revealed three major groups within that family. The results from sequence alignments, 3-D structures, phylogenetics, and analyses of conserved domains indicated that apple FKBPs are highly and structurally conserved. Furthermore, genomics structure analysis showed that those genes are also highly and structurally conserved in several other species. Comprehensive qRT-PCR analysis found various expression patterns for MdFKBPs in different tissues and in plant responses to water-deficit and salt stresses. Based on the results from interaction network and co-expression analyses, we determined that the pairing in the MdFKBP62a/MdFKBP65a/b-mediated network is involved in water-deficit and salt-stress signaling, both of which are uniformly up-regulated through interactions with heat shock proteins in apple.

Conclusions

These results provide new insight for further study of FKBP genes and their functions in abiotic stress response and multiple metabolic and physiological processes in apple.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5097-8) contains supplementary material, which is available to authorized users.

The YTH Domain Protein ECT2 Is an m6A Reader Required for Normal Trichome Branching in Arabidopsis

Methylations at position N⁶ of internal adenosines (m⁶As) are the most abundant and widespread mRNA modifications. These modifications play crucial roles in reproduction, growth, and development by controlling gene expression patterns at the posttranscriptional level. Their function is decoded by readers that share the YTH domain, which forms a hydrophobic pocket that directly accommodates the m⁶A residues. While the physiological and molecular functions of YTH readers have been extensively studied in animals, little is known about plant readers, even though m⁶As are crucial for plant survival and development. Viridiplantae contains high numbers of YTH domain proteins. Here, we performed comprehensive evolutionary analysis of YTH domain proteins and demonstrated that they are highly likely to be actual readers with redundant as well as specific functions. We also show that the ECT2 protein from Arabidopsis thaliana binds to m⁶A-containing RNAs in vivo and that this property relies on the m⁶A binding pocket carried by its YTH domain. ECT2 is cytoplasmic and relocates to stress granules upon heat exposure, suggesting that it controls mRNA fate in the cytosol. Finally, we demonstrate that ECT2 acts to decode the m⁶A signal in the trichome and is required for their normal branching through controlling their ploidy levels.