Skip to main content
Log in

m6A modification of plant virus enables host recognition by NMD factors in plants

  • Research Paper
  • Published:
Science China Life Sciences Aims and scope Submit manuscript

Abstract

N6-methyladenosine (m6A) is the most abundant eukaryotic mRNA modification and is involved in various biological processes. Increasing evidence has implicated that m6A modification is an important anti-viral defense mechanism in mammals and plants, but it is largely unknown how m6A regulates viral infection in plants. Here we report the dynamic changes and functional anatomy of m6A in Nicotiana benthamiana and Solanum lycopersicum during Pepino mosaic virus (PepMV) infection. m6A modification in the PepMV RNA genome is conserved in these two species. Overexpression of the m6A writers, mRNA adenosine methylase A (MTA), and HAKAI inhibit the PepMV RNA accumulation accompanied by increased viral m6A modifications, whereas deficiency of these writers decreases the viral RNA m6A levels but enhances virus infection. Further study reveals that the cytoplasmic YTH-domain family protein NbECT2A/2B/2C as m6A readers are involved in anti-viral immunity. Protein-protein interactions indicate that NbECT2A/2B/2C interact with nonsense-mediated mRNA decay (NMD)-related proteins, including NbUPF3 and NbSMG7, but not with NbUPF1. m6A modification-mediated restriction to PepMV infection is dependent on NMD-related factors. These findings provide new insights into the functionality of m6A anti-viral activity and reveal a distinct immune response that NMD factors recognize the m6A readers-viral m6A RNA complex for viral RNA degradation to limit virus infection in plants.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

Data availability

The authors declare that all data supporting the findings of this study are available in the manuscript, and its Supplementary Information files are available from the corresponding author upon request.

References

  • Aguilar, J.M., Hernández-Gallardo, M.D., Cenis, J.L., Lacasa, A., and Aranda, M.A. (2002). Complete sequence of the Pepino mosaic virus RNA genome. Arch Virol 147, 2009–2015.

    Article  CAS  PubMed  Google Scholar 

  • Alarcón, C.R., Goodarzi, H., Lee, H., Liu, X., Tavazoie, S., and Tavazoie, S.F. (2015). HNRNPA2B1 is a mediator of m6A-dependent nuclear RNA processing events. Cell 162, 1299–1308.

    Article  PubMed  PubMed Central  Google Scholar 

  • Arribas-Hernández, L., Bressendorff, S., Hansen, M.H., Poulsen, C., Erdmann, S., and Brodersen, P. (2018). An m6A-YTH module controls developmental timing and morphogenesis in Arabidopsis. Plant Cell 30, 952–967.

    Article  PubMed  PubMed Central  Google Scholar 

  • Balistreri, G., Horvath, P., Schweingruber, C., Zünd, D., McInerney, G., Merits, A., Mühlemann, O., Azzalin, C., and Helenius, A. (2014). The host nonsense-mediated mRNA decay pathway restricts mammalian RNA virus replication. Cell Host Microbe 16, 403–411.

    Article  CAS  PubMed  Google Scholar 

  • Batista, P.J., Molinie, B., Wang, J., Qu, K., Zhang, J., Li, L., Bouley, D.M., Lujan, E., Haddad, B., Daneshvar, K., et al. (2014). m6A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell 15, 707–719.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bawankar, P., Lence, T., Paolantoni, C., Haussmann, I.U., Kazlauskiene, M., Jacob, D., Heidelberger, J.B., Richter, F.M., Nallasivan, M.P., Morin, V., et al. (2021). Hakai is required for stabilization of core components of the m6A mRNA methylation machinery. Nat Commun 12, 3778.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bodi, Z., Zhong, S., Mehra, S., Song, J., Graham, N., Li, H., May, S., and Fray, R.G. (2012). Adenosine methylation in Arabidopsis mRNA is associated with the 3′ end and reduced levels cause developmental defects. Front Plant Sci 3, 48.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brocard, M., Ruggieri, A., and Locker, N. (2017). m6A RNA methylation, a new hallmark in virus-host interactions. J Gen Virol 98, 2207–2214.

    Article  CAS  PubMed  Google Scholar 

  • Choe, J., Lin, S., Zhang, W., Liu, Q., Wang, L., Ramirez-Moya, J., Du, P., Kim, W., Tang, S., Sliz, P., et al. (2018). mRNA circularization by METTL3-eIF3h enhances translation and promotes oncogenesis. Nature 561, 556–560.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Courtney, D.G., Kennedy, E.M., Dumm, R.E., Bogerd, H.P., Tsai, K., Heaton, N.S., and Cullen, B.R. (2017). Epitranscriptomic enhancement of influenza A virus gene expression and replication. Cell Host Microbe 22, 377–386.e5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dominissini, D., Moshitch-Moshkovitz, S., Schwartz, S., Salmon-Divon, M., Ungar, L., Osenberg, S., Cesarkas, K., Jacob-Hirsch, J., Amariglio, N., Kupiec, M., et al. (2012). Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201–206.

    Article  CAS  PubMed  Google Scholar 

  • Du, H., Zhao, Y., He, J., Zhang, Y., Xi, H., Liu, M., Ma, J., and Wu, L. (2016). YTHDF2 destabilizes m6A-containing RNA through direct recruitment of the CCR4-NOT deadenylase complex. Nat Commun 7, 12626.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dutch, R.E., and Whitfield, A.E. (2021). In memoriam: Michael M. Goodin (1967–2020). Annu Rev Virol 8, viii–ix.

    Article  CAS  Google Scholar 

  • Garcia, D., Garcia, S., and Voinnet, O. (2014). Nonsense-mediated decay serves as a general viral restriction mechanism in plants. Cell Host Microbe 16, 391–402.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ge, L., Cao, B., Qiao, R., Cui, H., Li, S., Shan, H., Gong, P., Zhang, M., Li, H., Wang, A., et al. (2023). SUMOylation-modified Pelota-Hbs1 RNA surveillance complex restricts the infection of potyvirids in plants. Mol Plant 16, 632–642.

    Article  CAS  PubMed  Google Scholar 

  • Geula, S., Moshitch-Moshkovitz, S., Dominissini, D., Mansour, A.A.F., Kol, N., Salmon-Divon, M., Hershkovitz, V., Peer, E., Mor, N., Manor, Y.S., et al. (2015). m6 A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation. Science 347, 1002–1006.

    Article  CAS  PubMed  Google Scholar 

  • Hanssen, I.M., and Thomma, B.P.H.J. (2010). Pepino mosaic virus: a successful pathogen that rapidly evolved from emerging to endemic in tomato crops. Mol Plant Pathol 11, 179–189.

    Article  CAS  PubMed  Google Scholar 

  • Hao, H., Hao, S., Chen, H., Chen, Z., Zhang, Y., Wang, J., Wang, H., Zhang, B., Qiu, J., Deng, F., et al. (2019). N6-methyladenosine modification and METTL3 modulate enterovirus 71 replication. Nucleic Acids Res 47, 362–374.

    Article  CAS  PubMed  Google Scholar 

  • He, H., Ge, L., Li, Z., Zhou, X., and Li, F. (2023). Pepino mosaic virus antagonizes plant m6A modification by promoting the autophagic degradation of the m6A writer HAKAI. Abiotech 4, 83–96.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • He, W., Wu, J., Ren, Y., Zhou, X., Zhang, S., Qian, Y., Li, F., and Wu, J. (2020). Highly sensitive serological approaches for Pepino mosaic virus detection. J Zhejiang Univ Sci B 21, 811–822.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Horiuchi, K., Kawamura, T., Iwanari, H., Ohashi, R., Naito, M., Kodama, T., and Hamakubo, T. (2013). Identification of Wilms’ tumor 1-associating protein complex and its role in alternative splicing and the cell cycle. J Biol Chem 288, 33292–33302.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hou, Y., Sun, J., Wu, B., Gao, Y., Nie, H., Nie, Z., Quan, S., Wang, Y., Cao, X., and Li, S. (2021). CPSF30-L-mediated recognition of mRNA m6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis. Mol Plant 14, 688–699.

    Article  CAS  PubMed  Google Scholar 

  • Hu, J., Cai, J., Park, S.J., Lee, K., Li, Y., Chen, Y., Yun, J., Xu, T., and Kang, H. (2021). N6-methyladenosine mRNA methylation is important for salt stress tolerance in Arabidopsis. Plant J 106, 1759–1775.

    Article  CAS  PubMed  Google Scholar 

  • Huang, H., Weng, H., Sun, W., Qin, X., Shi, H., Wu, H., Zhao, B.S., Mesquita, A., Liu, C., Yuan, C.L., et al. (2018). Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation. Nat Cell Biol 20, 285–295.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Imam, H., Khan, M., Gokhale, N.S., McIntyre, A.B.R., Kim, G.W., Jang, J.Y., Kim, S.J., Mason, C.E., Horner, S.M., and Siddiqui, A. (2018). N6-methyladenosine modification of hepatitis B virus RNA differentially regulates the viral life cycle. Proc Natl Acad Sci USA 115, 8829–8834.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jia, G., Fu, Y., Zhao, X., Dai, Q., Zheng, G., Yang, Y., Yi, C., Lindahl, T., Pan, T., Yang, Y.G., et al. (2011). N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol 7, 885–887.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jones, R.A.C., Koenig, R., and Lesemann, D.E. (1980). Pepino mosaic virus, a new potexvirus from pepino (Solanum muricatum). Ann Appl Biol 94, 61–68.

    Article  CAS  Google Scholar 

  • Lence, T., Akhtar, J., Bayer, M., Schmid, K., Spindler, L., Ho, C.H., Kreim, N., Andrade-Navarro, M.A., Poeck, B., Helm, M., et al. (2016). m6A modulates neuronal functions and sex determination in Drosophila. Nature 540, 242–247.

    Article  CAS  PubMed  Google Scholar 

  • Leon, K., and Ott, M. (2021). An ‘Arms Race’ between the nonsense-mediated mRNA decay pathway and viral infections. Semin Cell Dev Biol 111, 101–107.

    Article  CAS  PubMed  Google Scholar 

  • Li, D., Zhang, H., Hong, Y., Huang, L., Li, X., Zhang, Y., Ouyang, Z., and Song, F. (2014). Genome-wide identification, biochemical characterization, and expression analyses of the yTH domain-containing RNA-binding protein family in Arabidopsis and rice. Plant Mol Biol Rep 32, 1169–1186.

    Article  CAS  Google Scholar 

  • Li, F., Qiao, R., Wang, Z., Yang, X., and Zhou, X. (2022). Occurrence and distribution of geminiviruses in China. Sci China Life Sci 65, 1498–1503.

    Article  PubMed  Google Scholar 

  • Li, F., Zhang, C., Li, Y., Wu, G., Hou, X., Zhou, X., and Wang, A. (2018). Beclin1 restricts RNA virus infection in plants through suppression and degradation of the viral polymerase. Nat Commun 9, 1268.

    Article  PubMed  PubMed Central  Google Scholar 

  • Li, F., Zhang, C., Tang, Z., Zhang, L., Dai, Z., Lyu, S., Li, Y., Hou, X., Bernards, M., and Wang, A. (2020). A plant RNA virus activates selective autophagy in a UPR-dependent manner to promote virus infection. New Phytol 228, 622–639.

    Article  CAS  PubMed  Google Scholar 

  • Liu, J., Yue, Y., Han, D., Wang, X., Fu, Y., Zhang, L., Jia, G., Yu, M., Lu, Z., Deng, X., et al. (2013). A METTL3-METTL14 complex mediates mammalian nuclear RNA N6 -adenosine methylation. Nat Chem Biol 10, 93–95.

    Article  PubMed  PubMed Central  Google Scholar 

  • Martinez-Perez, M., Aparicio, F., Lopez-Gresa, M.P., Bellés, J.M., Sánchez-Navarro, J. A., and Pallás, V. (2017). Arabidopsis m6A demethylase activity modulates viral infection of a plant virus and the m6A abundance in its genomic RNAs. Proc Natl Acad Sci USA 114, 10755–10760.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ok, S.H., Jeong, H.J., Bae, J.M., Shin, J.S., Luan, S., and Kim, K.N. (2005). Novel CIPK1-associated proteins in Arabidopsis contain an evolutionary conserved C-terminal region that mediates nuclear localization. Plant Physiol 139, 138–150.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rüzicka, K., Zhang, M., Campilho, A., Bodi, Z., Kashif, M., Saleh, M., Eeckhout, D., El-Showk, S., Li, H., Zhong, S., et al. (2017). Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. New Phytol 215, 157–172.

    Article  PubMed  PubMed Central  Google Scholar 

  • Scutenaire, J., Deragon, J.M., Jean, V., Benhamed, M., Raynaud, C., Favory, J.J., Merret, R., and Bousquet-Antonelli, C. (2018). The YTH domain protein ECT2 is an m6A reader required for normal trichome branching in Arabidopsis. Plant Cell 30, 986–1005.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shen, L., Liang, Z., Gu, X., Chen, Y., Teo, Z.W.N., Hou, X., Cai, W.M., Dedon, P.C., Liu, L., and Yu, H. (2016). N6-methyladenosine RNA modification regulates shoot stem cell fate in Arabidopsis. Dev Cell 38, 186–200.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shi, H., Wang, X., Lu, Z., Zhao, B.S., Ma, H., Hsu, P.J., Liu, C., and He, C. (2017). YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA. Cell Res 27, 315–328.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Song, P., Yang, J., Wang, C., Lu, Q., Shi, L., Tayier, S., and Jia, G. (2021). Arabidopsis N6-methyladenosine reader CPSF30-L recognizes FUE signals to control poly-adenylation site choice in liquid-like nuclear bodies. Mol Plant 14, 571–587.

    Article  CAS  PubMed  Google Scholar 

  • Spence, N.J., Basham, J., Mumford, R.A., Hayman, G., Edmondson, R., and Jones, D.R. (2006). Effect of Pepino mosaic virus on the yield and quality ofglasshouse-grown tomatoes in the UK. Plant Pathol 55, 595–606.

    Article  Google Scholar 

  • Sun, T., Wu, R., and Ming, L. (2019). The role of m6A RNA methylation in cancer. Biomed Pharmacother 112, 108613.

    Article  CAS  PubMed  Google Scholar 

  • van der Vlugt, R.A.A., Stijger, C.C.M.M., Verhoeven, J.T.J., and Lesemann, D.E. (2000). First report of Pepino mosaic virus on tomato. Plant Dis 84, 103.

    Article  CAS  PubMed  Google Scholar 

  • Wang, X., Lu, Z., Gomez, A., Hon, G.C., Yue, Y., Han, D., Fu, Y., Parisien, M., Dai, Q., Jia, G., et al. (2014). N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 505, 117–120.

    Article  PubMed  Google Scholar 

  • Wang, X., Zhao, B.S., Roundtree, I.A., Lu, Z., Han, D., Ma, H., Weng, X., Chen, K., Shi, H., and He, C. (2015). N6-methyladenosine modulates messenger RNA translation efficiency. Cell 161, 1388–1399.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang, Y., Zhang, L., Ren, H., Ma, L., Guo, J., Mao, D., Lu, Z., Lu, L., and Yan, D. (2021). Role of Hakai in m6A modification pathway in Drosophila. Nat Commun 12, 2159.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wei, L.H., Song, P., Wang, Y., Lu, Z., Tang, Q., Yu, Q., Xiao, Y., Zhang, X., Duan, H.C., and Jia, G. (2018). The m6A reader ECT2 controls trichome morphology by affecting mRNA stability in Arabidopsis. Plant Cell 30, 968–985.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu, R., Li, A., Sun, B., Sun, J.G., Zhang, J., Zhang, T., Chen, Y., Xiao, Y., Gao, Y., Zhang, Q., et al. (2019). A novel m6A reader Prrc2a controls oligodendroglial specification and myelination. Cell Res 29, 23–41.

    Article  PubMed  Google Scholar 

  • Xia, T., Li, X., Wang, X., Zhu, Y., Zhang, H., Cheng, W., Chen, M., Ye, Y., Li, Y., Zhang, A., et al. (2021). N6-methyladenosine-binding protein YTHDF1 suppresses EBV replication and promotes EBV RNA decay. EMBO Rep 22, e50128.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xiong, R., Wu, J., Zhou, Y., and Zhou, X. (2009). Characterization and subcellular localization of an RNA silencing suppressor encoded by Rice stripe tenuivirus. Virology 387, 29–40.

    Article  CAS  PubMed  Google Scholar 

  • Xu, K., Yang, Y., Feng, G.H., Sun, B.F., Chen, J.Q., Li, Y.F., Chen, Y.S., Zhang, X.X., Wang, C.X., Jiang, L.Y., et al. (2017). Mettl3-mediated m6A regulates spermato-gonial differentiation and meiosis initiation. Cell Res 27, 1100–1114.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ye, F., Chen, E.R., and Nilsen, T.W. (2017). Kaposi’s Sarcoma-associated herpesvirus utilizes and manipulates RNA N6-adenosine methylation to promote lytic replication. J Virol 91, e00466–17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yue, H., Nie, X., Yan, Z., and Weining, S. (2019). N6-methyladenosine regulatory machinery in plants: composition, function and evolution. Plant Biotechnol J 17, 1194–1208.

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang, K., Zhuang, X., Dong, Z., Xu, K., Chen, X., Liu, F., and He, Z. (2021). The dynamics of N6-methyladenine RNA modification in interactions between rice and plant viruses. Genome Biol 22, 189.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang, M., Cao, B., Zhang, H., Fan, Z., Zhou, X., and Li, F. (2023). Geminivirus satellite-encoded αC1 activates UPR, induces bZIP60 nuclear export, and manipulates the expression of bZIP60 downstream genes to benefit virus infection. Sci China Life Sci 66, 1408–1425.

    Article  CAS  PubMed  Google Scholar 

  • Zhang, T., Shi, C., Hu, H., Zhang, Z., Wang, Z., Chen, Z., Feng, H., Liu, P., Guo, J., Lu, Q., et al. (2022). N6-methyladenosine RNA modification promotes viral genomic RNA stability and infection. Nat Commun 13, 6576.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zheng, G., Dahl, J.A., Niu, Y., Fedorcsak, P., Huang, C.M., Li, C.J., Vågbø, C.B., Shi, Y., Wang, W.L., Song, S.H., et al. (2013). ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell 49, 18–29.

    Article  CAS  PubMed  Google Scholar 

  • Zheng, H., Li, S., Zhang, X., and Sui, N. (2020). Functional implications of active N6 -methyladenosine in plants. Front Cell Dev Biol 8, 291.

    Article  PubMed  PubMed Central  Google Scholar 

  • Zheng, Q., Hou, J., Zhou, Y., Li, Z., and Cao, X. (2017). The RNA helicase DDX46 inhibits innate immunity by entrapping m6A-demethylated antiviral transcripts in the nucleus. Nat Immunol 18, 1094–1103.

    Article  CAS  PubMed  Google Scholar 

  • Zhong, X., Yu, J., Frazier, K., Weng, X., Li, Y., Cham, C.M., Dolan, K., Zhu, X., Hubert, N., Tao, Y., et al. (2018). Orcadian clock regulation of hepatic lipid metabolism by modulation of m6A mRNA methylation. Cell Rep 25, 1816–1828.e4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhong, S., Li, H., Bodi, Z., Button, J., Vespa, L., Herzog, M., and Fray, R.G. (2008). MTA is an Arabidopsis messenger RNA adenosine methylase and interacts with a homolog of a sex-specific splicing factor. Plant Cell 20, 1278–1288.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgement

This work was supported by the National Key Research and Development Program of China (2021YFD1400400) to Fangfang Li and the National Natural Science Foundation of China (32172385 and 31930089) to Fangfang Li and Xueping Zhou, respectively. We thank Dr. Andrew O. Jackson (University of California, Berkeley, USA) for valuable suggestions and English editing of the manuscript, and we thank Dr. Shaofang Li (Institute of Plant Protection, Chinese Academy of Agricultural Sciences, China) for helpful discussion and suggestions. We thank Dr. Michael M. Goodin (University of Kentucky, USA) for the seeds of the RFP-H2B transgenic line (Dutch and Whitfield, 2021). We also thank Dr. Yule Liu (Tsinghua University, China) for providing the TRV VIGS vector and Dr. Jianxiang Wu (Zhejiang University, China) for providing anti-PepMV CP antibodies (He et al., 2020).

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Xueping Zhou or Fangfang Li.

Ethics declarations

The author(s) declare that they have no conflict of interest.

Supplementary Information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

He, H., Ge, L., Chen, Y. et al. m6A modification of plant virus enables host recognition by NMD factors in plants. Sci. China Life Sci. 67, 161–174 (2024). https://doi.org/10.1007/s11427-022-2377-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11427-022-2377-1

Navigation