RNA N6 -methyladenosine modification suppresses replication of rice black streaked dwarf virus and is associated with virus persistence in its insect vector

Transcriptome-wide N6-methyladenosine profiling reveals growth-defense trade-offs in the response of rice to brown planthopper (Nilaparvata lugens) infestation

BACKGROUND

N6-Methyladenosine (m6A) is a common messenger RNA (mRNA) modification that affects various physiological processes in stress responses. However, the role of m6A modifications in plants responses to herbivore stress remains unclear.

RESULTS

Here, we found that an infestation of brown planthopper (Nilaparvata lugens) female adults enhanced the resistance of rice to N. lugens. The m6A methylome analysis of N. lugens-infested and uninfested rice samples was performed to explore the interaction between rice and N. lugens. The m6A methylation mainly occurred in genes that were actively expressed in rice following N. lugens infestation, while an analysis of the whole-genomic mRNA distribution of m6A showed that N. lugens infestation caused an overall decrease in the number of m6A methylation sites across the chromosomes. The m6A methylation of genes involved in the m6A modification machinery and several defense-related phytohormones (jasmonic acid and salicylic acid) pathways was increased in N. lugens-infested rice compared to that in uninfested rice. In contrast, m6A modification levels of growth-related phytohormone (auxin and gibberellin) biosynthesis-related genes were significantly attenuated during N. lugens infestation, accompanied by the down-regulated expression of these transcripts, indicating that rice growth was restricted during N. lugens attack to rapidly optimize resource allocation for plant defense. Integrative analysis of the differential patterns of m6A methylation and the corresponding transcripts showed a positive correlation between m6A methylation and transcriptional regulation.

CONCLUSION

The m6A modification is an important strategy for regulating the expression of genes involved in rice defense and growth during rice-N. lugens interactions. These findings provide new ideas for formulating strategies to control herbivorous pests. © 2024 Society of Chemical Industry.

Wing expansion functional analysis of ion transport peptide gene in Sogatella furcifera (Horváth) (Hemiptera: Delphacidae)

Ion transport peptide (ITP), a superfamily of arthropod neuropeptides, serves a crucial role in regulating various physiological processes such as diuresis, ecdysis behavior, and wing expansion. However, the molecular characteristics, expression profile, and role of ITP in Sogatella furcifera are poorly understood. To elucidate the characteristics and biological function of ITP in S. furcifera, we employed reverse transcription-polymerase chain reaction (RT-PCR) and RNA interference (RNAi) methods. The identified SfITP gene encodes 117 amino acids. The expression of SfITP gradually increased followed the formation of 3-day-old of 5th instar nymph, peaking initially at 40 min after eclosion, and reaching another peak 24 h after eclosion, with particularly high expression levels in thorax and wing tissues. Notably, SfITP RNAi in 3rd instar nymphs of S. furcifera significantly inhibited the transcript levels of SfITP, resulting in 55% mortality and 78% wing deformity. These findings suggests that SfITP is involved in the regulation of wing expansion in S. furcifera, providing insights into the regulation of insect wing expansion and contributing to the molecular understanding of this process.

N6-methyladenosine modification of RNA controls dopamine synthesis to influence labour division in ants

The N6-methyladenosine (m6A) modification of RNA has been reported to remodel gene expression in response to environmental conditions; however, the biological role of m6A in social insects remains largely unknown. In this study, we explored the role of m6A in the division of labour by worker ants (Solenopsis invicta). We first determined the presence of m6A in RNAs from the brains of worker ants and found that m6A methylation dynamics differed between foragers and nurses. Depletion of m6A methyltransferase or chemical suppression of m6A methylation in foragers resulted in a shift to 'nurse-like' behaviours. Specifically, mRNAs of dopamine receptor 1 (Dop1) and dopamine transporter (DAT) were modified by m6A, and their expression increased dopamine levels to promote the behavioural transition from foragers to nurses. The abundance of Dop1 and DAT mRNAs and their stability were reduced by the inhibition of m6A modification caused by the silencing of Mettl3, suggesting that m6A modification in worker ants modulates dopamine synthesis, which regulates labour division. Collectively, our results provide the first example of the epitranscriptomic regulation of labour division in social insects and implicate m6A regulatory mechanism as a potential novel target for controlling red imported fire ants.

N6-methyladenosine modification of the mRNA for a key gene in purine nucleotide metabolism regulates virus proliferation in an insect vector

The titer of viruses that persist and propagate in their insect vector must be high enough for transmission yet not harm the insect, but the mechanism of this dynamic balance is unclear. Here, expression of inosine monophosphate dehydrogenase (LsIMPDH), a rate-limiting enzyme for guanosine triphosphate (GTP) synthesis, is shown to be downregulated by increased levels of N6-methyladenosine (m6A) on LsIMPDH mRNA in rice stripe virus (RSV)-infected small brown planthoppers (SBPHs; Laodelphax striatellus), the RSV vector, which decreases GTP content, thus limiting viral proliferation. Moreover, planthopper methyltransferase-like protein 3 (LsMETTL3) and m6A reader protein LsYTHDF3 are found to catalyze and recognize the m6A on LsIMPDH mRNA, respectively, and cooperate in destabilizing LsIMPDH transcripts. Co-silencing assays show that negative regulation of viral proliferation by both LsMETTL3 and LsYTHDF3 is partially dependent on LsIMPDH. This distinct mechanism limits virus replication in an insect vector, providing a potential gene target to block viral transmission.

Methyltransferase-like (METTL) homologues participate in Nicotiana benthamiana antiviral responses

Methyltransferase (MTase) enzymes catalyze the addition of a methyl group to a variety of biological substrates. MTase-like (METTL) proteins are Class I MTases whose enzymatic activities contribute to the epigenetic and epitranscriptomic regulation of multiple cellular processes. N⁶-adenosine methylation (m⁶A) is a common chemical modification of eukaryotic and viral RNA whose abundance is jointly regulated by MTases and METTLs, demethylases, and m⁶A binding proteins. m⁶A affects various cellular processes including RNA degradation, post-transcriptional processing, and antiviral immunity. Here, we used Nicotiana benthamiana and plum pox virus (PPV), an RNA virus of the Potyviridae family, to investigated the roles of MTases in plant-virus interaction. RNA sequencing analysis identified MTase transcripts that are differentially expressed during PPV infection; among these, accumulation of a METTL gene was significantly downregulated. Two N. benthamiana METTL transcripts (NbMETTL1 and NbMETTL2) were cloned and further characterized. Sequence and structural analyses of the two encoded proteins identified a conserved S-adenosyl methionine (SAM) binding domain, showing they are SAM-dependent MTases phylogenetically related to human METTL16 and Arabidopsis thaliana FIONA1. Overexpression of NbMETTL1 and NbMETTL2 caused a decrease of PPV accumulation. In sum, our results indicate that METTL homologues participate in plant antiviral responses.

Roles of RNA m6A modifications in plant-virus interactions

Viral RNAs have been known to contain N6-methyladenosine (m6A) modifications since the 1970s. The function of these modifications remained unknown until the development of genome-wide methods to map m6A residues. Increasing evidence has recently revealed a strong association between m6A modifications and plant viral infection. This highlight introduces advances in the roles of RNA m6A modifications in plant-virus interactions.

Plant reoviruses hijack autophagy in insect vectors

Plant reoviruses, transmitted only by insect vectors, seriously threaten global cereal production. Understanding how insect vectors efficiently transmit the viruses is key to controlling the viral diseases. Autophagy commonly plays important roles in plant host defense against virus infection, but recent studies have shown that plant reoviruses can hijack the autophagy pathway in insect cells to enable their persistence in the insect and continued transmission to plants. Here, we summarize and discuss new insights on viral activation, evasion, regulation, and manipulation of autophagy within the insect vectors and the role of autophagy in virus survival in insect vectors. Deeper knowledge of the functions of autophagy in vectors may lead to novel strategies for blocking transmission of insect-borne plant viruses.

Pathogen-induced m6A dynamics affect plant immunity

Posttranscriptional regulation of mRNA mediated by methylation at the N6 position of adenine (N6-methyladenosine [m6A]) has profound effects on transcriptome regulation in plants. Focused studies across eukaryotes offer glimpses into the processes governed by m6A throughout developmental and disease states. However, we lack an understanding of the dynamics and the regulatory potential of m6A during biotic stress in plants. Here, we provide a comprehensive look into the effects of m6A on both the short-term and long-term responses to pathogen signaling in Arabidopsis (Arabidopsis thaliana). We demonstrate that m6A-deficient plants are more resistant to bacterial and fungal pathogen infections and have altered immune responses. Furthermore, m6A deposition is specifically coordinated on transcripts involved in defense and immunity prior to and proceeding the pathogen signal flagellin. Consequently, the dynamic modulation of m6A on specific stress-responsive transcripts is correlated with changes in abundance and cleavage of these transcripts. Overall, we show that the m6A methylome is regulated prior to and during simulated and active pathogen stress and functions in the coordination and balancing of normal growth and pathogen responses.

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.

Plant YTHDF proteins are direct effectors of antiviral immunity against an N6-methyladenosine-containing RNA virus

In virus-host interactions, nucleic acid-directed first lines of defense that allow viral clearance without compromising growth are of paramount importance. Plants use the RNA interference pathway as a basal antiviral immune system, but additional RNA-based mechanisms of defense also exist. The infectivity of a plant positive-strand RNA virus, alfalfa mosaic virus (AMV), relies on the demethylation of viral RNA by the recruitment of the cellular N6-methyladenosine (m6 A) demethylase ALKBH9B, but how demethylation of viral RNA promotes AMV infection remains unknown. Here, we show that inactivation of the Arabidopsis cytoplasmic YT521-B homology domain (YTH)-containing m6 A-binding proteins ECT2, ECT3, and ECT5 is sufficient to restore AMV infectivity in partially resistant alkbh9b mutants. We further show that the antiviral function of ECT2 is distinct from its previously demonstrated function in the promotion of primordial cell proliferation: an ect2 mutant carrying a small deletion in its intrinsically disordered region is partially compromised for antiviral defense but not for developmental functions. These results indicate that the m6 A-YTHDF axis constitutes a novel branch of basal antiviral immunity in plants.

The covalent nucleotide modifications within plant mRNAs: What we know, how we find them, and what should be done in the future

Although covalent nucleotide modifications were first identified on the bases of transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), a number of these epitranscriptome marks have also been found to occur on the bases of messenger RNAs (mRNAs). These covalent mRNA features have been demonstrated to have various and significant effects on the processing (e.g. splicing, polyadenylation, etc.) and functionality (e.g. translation, transport, etc.) of these protein-encoding molecules. Here, we focus our attention on the current understanding of the collection of covalent nucleotide modifications known to occur on mRNAs in plants, how they are detected and studied, and the most outstanding future questions of each of these important epitranscriptomic regulatory signals.

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

Plants inevitably encounter environmental adversities, including abiotic and biotic stresses, which significantly impede plant growth and reduce crop yield. Thus, fine-tuning the fate and function of stress-responsive RNAs is indispensable for plant survival under such adverse conditions. Recently, post-transcriptional RNA modifications have been studied as a potent route to regulate plant gene expression under stress. Among over 160 mRNA modifications identified to date, N⁶ -methyladenosine (m⁶ A) in mRNAs is notable because of its multifaceted roles in plant development and stress response. Recent transcriptome-wide mapping has revealed the distribution and patterns of m⁶ A in diverse stress-responsive mRNAs in plants, building a foundation for elucidating the molecular link between m⁶ A and stress response. Moreover, the identification and characterization of m⁶ A writers, readers and erasers in Arabidopsis and other model crops have offered insights into the biological roles of m⁶ A in plant abiotic stress responses. Here, we review the recent progress of research on mRNA modifications, particularly m⁶ A, and their dynamics, distribution, regulation and biological functions in plant stress responses. Further, we posit potential strategies for breeding stress-tolerant crops by engineering mRNA modifications and propose the future direction of research on RNA modifications to gain a much deeper understanding of plant stress biology.

A Review of Vector-Borne Rice Viruses

Rice (Oryza sativa L.) is one of the major staple foods for global consumption. A major roadblock to global rice production is persistent loss of crops caused by plant diseases, including rice blast, sheath blight, bacterial blight, and particularly various vector-borne rice viral diseases. Since the late 19th century, 19 species of rice viruses have been recorded in rice-producing areas worldwide and cause varying degrees of damage on the rice production. Among them, southern rice black-streaked dwarf virus (SRBSDV) and rice black-streaked dwarf virus (RBSDV) in Asia, rice yellow mottle virus (RYMV) in Africa, and rice stripe necrosis virus (RSNV) in America currently pose serious threats to rice yields. This review systematizes the emergence and damage of rice viral diseases, the symptomatology and transmission biology of rice viruses, the arm races between viruses and rice plants as well as their insect vectors, and the strategies for the prevention and control of rice viral diseases.

Functional Characterization of Two RNA Methyltransferase Genes METTL3 and METTL14 Uncovers the Roles of m6A in Mediating Adaptation of Plutella xylostella to Host Plants

N⁶-methyladenosine (m⁶A) is one of the major epigenetic modifications in eukaryotes. Although increasing functions of m⁶A have been identified in insects, its role in Plutella xylostella L. for host plant adaptation remains unclear. In the current study, we show that the m⁶A content of P. xylostella was relatively low in different developmental stages and tissues, with no significant differences. Two RNA methyltransferase genes, PxMETTL3 (methyltransferase-like 3) and PxMETTL14 (methyltransferase-like 14), were identified and characterized. PxMETTL3 could be transcribed into two transcripts, and PxMETTL14 had only one transcript; both of these genes were highly expressed in egg and adult stages and reproductive tissues. The CRISPR/Cas9-mediated knockout of PxMETTL3 (ΔPxMETTL3-2) or PxMETTL14 (ΔPxMETTL14-14) confirmed their function in m⁶A installation into RNA. Furthermore, upon transfer from an artificial diet to the host plant, the mutant strains were affected in terms of larval and pupal weight or adult emergence rate, while the wildtype (WT) strain did not exhibit any difference. In addition, the fecundity and egg hatching rate of the WT strain decreased significantly, whereas only the ΔPxMETTL14-14 mutant strain displayed significantly decreased fecundity. There seemed to be a tradeoff between the stress adaptation and reproduction in P. xylostella mediated by m⁶A modification. During host transfer, the expression of PxMETTL14 was consistent with the change in m⁶A content, which implied that PxMETTL14 could respond to host plant defense effectively, and may regulate m⁶A content. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the differentially expressed transcripts with changes in m⁶A levels revealed that the potential functions of m⁶A-related genes may be involved in steroid biosynthesis for larval performance and metabolic pathways for adult reproduction. Overall, our work reveals an epigenetic regulation mechanism for the rapid adaptation of P. xylostella to variations in the host environment.

m6 A-mediated regulation of crop development and stress responses

Dynamic chemical modifications in eukaryotic messenger RNAs (mRNAs) constitute an essential layer of gene regulation, among which N⁶ -methyladenosine (m⁶ A) was unveiled to be the most abundant. m⁶ A functionally modulates important biological processes in various mammals and plants through the regulation of mRNA metabolism, mainly mRNA degradation and translation efficiency. Physiological functions of m⁶ A methylation are diversified and affected by intricate sequence contexts and m⁶ A machineries. A number of studies have dissected the functional roles and the underlying mechanisms of m⁶ A modifications in regulating plant development and stress responses. Recently, it was demonstrated that the human FTO-mediated plant m⁶ A removal caused dramatic yield increases in rice and potato, indicating that modulation of m⁶ A methylation could be an efficient strategy for crop improvement. In this review, we summarize the current progress concerning the m⁶ A-mediated regulation of crop development and stress responses, and provide an outlook on the potential application of m⁶ A epitranscriptome in the future improvement of crops.

Differential Microbial Communities in Paddy Soils Between Guiyang Plateaus and Chengdu Basins Drive the Incidence of Rice Bacterial Diseases

Southwest China has the most complex rice-growing regions in China. With great differences in topography, consisting mainly of basins and plateaus, ecological factors differ greatly between regions. In this study, bulk paddy soils collected from long-term rice fields in Chengdu (basins) and Guiyang (plateaus) were used to study the correlation between microbial diversity and the incidence of rice bacterial diseases. Results showed that the microbial community composition in paddy soils and the microbial functional categories differed significantly between basins and plateaus. They shared >70% of the dominant genera (abundance >1%), but the abundance of the dominant genera differed significantly. Functional analysis found that bulk paddy soils from Chengdu were significantly enriched in virulence factor-related genes; soils from Guiyang were enriched in biosynthesis of secondary metabolites, especially antibiotics. Correspondingly, Chengdu was significantly enriched in leaf bacterial pathogens Acidovorax, Xanthomonas, and Pseudomonas. Greenhouse experiments and correlation analysis showed that soil chemical properties had a greater effect on microbial community composition and positively correlated with the higher incidence of rice bacterial foot rot in Guiyang, whereas temperature had a greater effect on soil microbial functions and positively correlated with the higher severity index of leaf bacterial diseases in Chengdu. Our results provide a new perspective on how differences in microbial communities in paddy soils can influence the incidence of rice bacterial diseases in areas with different topographies.

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.