Turnip mosaic virus manipulates DRM2 expression to regulate host CHH and CHG methylation for robust infection

Abstract

DNA methylation is an important epigenetic marker for the suppression of transposable elements (TEs) and the regulation of plant immunity. However, little is known how RNA viruses counter defense such antiviral machinery. In this study, the change of DNA methylation in turnip mosaic virus (TuMV)-infected cells was analyzed by whole genome bisulfite sequencing. Results showed that the total number of methylated sites of CHH and CHG increased in TuMV-infected cells, the majority of differentially methylated regions (DMRs) in the CHH and CHG contexts were associated with hypermethylation. Gene expression analysis showed that the expression of two methylases (DRM2 and CMT3) and three demethylases (ROS3, DML2, DML3) was significantly increased and decreased in TuMV-infected cells, respectively. Pathogenicity tests showed that the enhanced resistance to TuMV of the loss-of-function mutant of DRM2 is associated with unregulated expression of several defense-related genes. Finally, we found TuMV-encoded NIb, the viral RNA-dependent RNA polymerase, was able to induce the expression of DRM2. In conclusion, this study discovered that TuMV can modulate host DNA methylation by regulating the expression of DRM2 to promote virus infection.

Keywords

Counter defense / DRM2 / Hypermethylation / RNA-directed DNA methylation / Turnip mosaic virus

References

[1] Annacondia ML, Martinez G (2021) Reprogramming of RNA silencing triggered by cucumber mosaic virus infection in Arabidopsis. Genome Biol 22:340. https://doi.org/10.1186/s13059-021-02564-z

[2] CaoX, AufsatzW, ZilbermanD, MetteMF, HuangMS, MatzkeM, JacobsenSE. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol, 2003, 13: 2212-2217

[3] Chan SWL, Henderson IR, Zhang X, Shah G, Chien JSC, Jacobsen SE (2006) RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in Arabidopsis. PLoS Genet 2:e83–e83. https://doi.org/10.1371/journal.pgen.0020083

[4] ChenZQ, ZhaoJ-H, ChenQ, ZhangZH, LiJ, GuoZX, XieQ, DingSW, GuoHS. DNA geminivirus infection induces an imprinted E3 ligase gene to epigenetically activate viral gene transcription. Plant Cell, 2020, 32: 3256-3272

[5] ChenJ, ZhangJ, KongM, FreemanA, ChenH, LiuF. More stories to tell: NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1, a salicylic acid receptor. Plant Cell Environ, 2021, 44: 1716-1727

[6] ChengX, XiongR, LiY, LiF, ZhouX, WangA. Sumoylation of turnip mosaic virus RNA polymerase promotes viral infection by counteracting the host NPR1-mediated immune response. Plant Cell, 2017, 29: 508-525

[7] CorrêaRL, Sanz-CarbonellA, KogejZ, MüllerSY, AmbrósS, López-GomollónS, GómezG, BaulcombeDC, ElenaSF. Viral fitness determines the magnitude of transcriptomic and epigenomic reprograming of defense responses in plants. Mol Biol Evolution, 2020, 37: 1866-1881

[8] da Silva MF, Goncalves MC, Brito MDS, Medeiros CN, Harakava R, Landell MGA, Pinto LR (2020) Sugarcane mosaic virus mediated changes in cytosine methylation pattern and differentially transcribed fragments in resistance-contrasting sugarcane genotypes. PLoS ONE 15:e0241493. https://doi.org/10.1371/journal.pone.0241493

[9] DelerisA, HalterT, NavarroL. DNA methylation and demethylation in plant immunity. Annu Rev Phytopathol, 2016, 54: 579-603

[10] Diezma-NavasL, Perez-GonzalezA, ArtazaH, AlonsoL, CaroE, LlaveC, Ruiz-FerrerV. Crosstalk between epigenetic silencing and infection by tobacco rattle virus in Arabidopsis. Mol Plant Pathol, 2019, 20: 1439-1452

[11] DingP, DingY. Stories of salicylic acid: a plant defense hormone. Trends Plant Sci, 2020, 25: 549-565

[12] Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR (2012) Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci U S A 109:e2183–e2191. https://doi.org/10.1073/pnas.1209329109

[13] Gui X, Liu C, Qi Y, Zhou X (2022) Geminiviruses employ host DNA glycosylases to subvert DNA methylation-mediated defense. Nature Commun 13:575. https://doi.org/10.1038/s41467-022-28262-3

[14] HeweziT, LaneT, PiyaS, RambaniA, RiceJH, StatonM. Cyst nematode parasitism induces dynamic changes in the root epigenome. Plant Physiol, 2017, 174: 405-420

[15] Huang M, Zhang Y, Wang Y, Xie J, Cheng J, Fu Y, Jiang D, Yu X, Li B (2022a) Active DNA demethylation regulates MAMP-triggered immune priming in Arabidopsis. J Genet Genomics. https://doi.org/10.1016/j.jgg.2022.02.021

[16] Huang X, Li F, Zhang X, Chen J, Wang J, Wei J, Yang X, Zhou G, Zhang T (2022b) A virus-derived small RNA targets the rice transcription factor ROC1 to induce disease-like symptom. Phytopathol Res 4:7. https://doi.org/10.1186/s42483-022-00112-6

[17] Le TN, Schumann U, Smith NA, Tiwari S, Au PCK, Zhu QH, Taylor JM, Kazan K, Llewellyn DJ, Zhang R, Dennis ES, Wang M-B (2014) DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis. Genome Biol 15:458. https://doi.org/10.1186/s13059-014-0458-3

[18] LellisAD, KasschauKD, WhithamSA, CarringtonJC. Loss-of-susceptibility mutants of Arabidopsis thaliana reveal an essential role for eIF(iso)4E during potyvirus infection. Current Biol, 2002, 12: 1046-1051

[19] LeoneM, ZavalloD, VenturuzziA, AsurmendiS. RdDM pathway components differentially modulate tobamovirus symptom development. Plant Mol Biol, 2020, 104: 467-481

[20] Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. https://doi.org/10.1186/s13059-014-0550-8

[21] Mei Y, Wang Y, Li F, Zhou X (2020) The C4 protein encoded by tomato leaf curl Yunnan virus reverses transcriptional gene silencing by interacting with NbDRM2 and impairing its DNA-binding ability. PLoS Pathog 16:e1008829. https://doi.org/10.1371/journal.ppat.1008829

[22] MhamdiA. NPR1 has everything under control. Plant Physiol, 2019, 181: 6-7

[23] PerteaM, PerteaGM, AntonescuCM, ChangTC, MendellJT, SalzbergSL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol, 2015, 33(3):290-295

[24] RajaP, SanvilleBC, BuchmannRC, BisaroDM. Viral genome methylation as an epigenetic defense against geminiviruses. J Virol, 2008, 82: 8997-9007

[25] Revers F, García JA (2015) Molecular biology of potyviruses. In: Karl M, Thomas CM (eds) Adv Virus Res, vol 92. Academic Press, Waltham, MA, USA, pp 101–199. https://doi.org/10.1016/bs.aivir.2014.11.006

[26] SánchezAL, StassenJHM, FurciL, SmithLM, TonJ. The role of DNA (de)methylation in immune responsiveness of Arabidopsis. Plant J, 2016, 88(3):361-374

[27] Shen W, Shi Y, Dai Z, Wang A (2020) The RNA-dependent RNA polymerase NIb of potyviruses plays multifunctional, contrasting roles during viral infection. Viruses 12(1):77. https://doi.org/10.3390/v12010077

[28] StroudH, DoT, DuJ, ZhongX, FengS, JohnsonL, PatelDJ, JacobsenSE. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol, 2014, 21(1):64-72 http://www.nature.com/nsmb/journal/v21/n1/abs/nsmb.2735.html#supplementary-information

[29] Sun Y, Fan M, He Y (2019) DNA methylation analysis of the Citrullus lanatus response to cucumber green mottle mosaic virus infection by whole-genome bisulfite sequencing. Genes (basel) 10:344. https://doi.org/10.3390/genes10050344

[30] TirnazS, BatleyJ. DNA methylation: toward crop disease resistance improvement. Trends Plant Sci, 2019, 24(12):1137-1150

[31] Viggiano L, de Pinto MC (2017) Dynamic DNA methylation patterns in stress response. In: Rajewsky N, Jurga S, Barciszewski J (eds) Plant Epigenetics. Springer International Publishing, pp 281–302. https://doi.org/10.1007/978-3-319-55520-1_15

[32] WangT, ZhangX. Genome-wide dynamic network analysis reveals the potential genes for MeJA-induced growth-to-defense transition. BMC Plant Biol, 2021, 21: 450-450

[33] WangB, LiF, HuangC, YangX, QianY, XieY, ZhouX. V2 of tomato yellow leaf curl virus can suppress methylation-mediated transcriptional gene silencing in plants. J Gen Virol, 2014, 95(Pt 1):225-230

[34] Wang C, Wang C, Xu W, Zou J, Qiu Y, Kong J, Yang Y, Zhang B, Zhu S (2018) Epigenetic changes in the regulation of Nicotiana tabacum response to cucumber mosaic virus infection and symptom recovery through single-base resolution methylomes. Viruses 10(8):402. https://doi.org/10.3390/v10080402

[35] YangL, XuY, LiuY, MengD, JinT, ZhouX. Hc-Pro viral suppressor from tobacco vein banding mosaic virus interferes with DNA methylation and activates the salicylic acid pathway. Virology, 2016, 497: 244-250

[36] YangL, MengD, WangY, WuY, LangC, JinT, ZhouX. The viral suppressor HcPro decreases DNA methylation and activates auxin biosynthesis genes. Virology, 2020, 546: 133-140

[37] YangX, LiY, WangA. Research advances in potyviruses: from the laboratory bench to the field. Annu Rev Phytopathol, 2021, 59: 1-29

[38] YuA, LepèreG, JayF, WangJ, BapaumeL, WangY, AbrahamA-L, PentermanJ, FischerRL, VoinnetO, NavarroL. Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense. Proc Natl Acad Sci USA, 2013, 110: 2389-2394

[39] ZhangH, LangZ, ZhuJK. Dynamics and function of DNA methylation in plants. Nat Rev Mol Cell Biol, 2018, 19: 489-506

[40] ZhouX. Hijack to escape: a geminivirus seizes a host imprinted E3 ligase to escape epigenetic repression. Sci China Life Sci, 2021, 64(2):323-325

Funding

National Natural Science Foundation of China(31860491); Natural Science Foundation of Heilongjiang Municipal Science and Technology Commission(LH2019C027); China National Tobacco Corporation(110202002010-JY-13); Academic Backbone Projects of Northeast Agricultural University(18XG04)