Abstract
Main conclusion
Vascular development-related TRN1 transcription is suppressed by cytosine methylation in fully developed leaves of tomato. ToLCNDV infection disrupts methylation machinery and reactivates TRN1 expression - likely causing abnormal leaf growth pattern.
Abstract
Leaf curl disease of tomato caused by tomato leaf curl New Delhi virus (ToLCNDV) inflicts huge economical loss. Disease symptoms resemble leaf developmental defects including abnormal vein architecture. Leaf vein patterning-related TORNADO1 gene’s (SlTRN1) transcript level is augmented in virus-infected leaves. To elucidate the molecular mechanism of the upregulation of SlTRN1 in vivo, we have deployed SlTRN1 promoter-reporter transgenic tomato plants and investigated the gene’s dynamic expression pattern in leaf growth stages and infection. Expression of the gene was delimited in the vascular tissues and suppressed in fully developed leaves. WRKY16 transcription factor readily activated SlTRN1 promoter in varied sized leaves and upon virus infection, while silencing of WRKY16 gene resulted in dampened promoter activity. Methylation-sensitive PCR analyses confirmed the accumulation of CHH methylation at multiple locations in the SlTRN1 promoter in older leaves. However, ToLCNDV infection reverses the methylation status and restores expression level in the leaf vascular bundle. The virus dampens the level of key maintenance and de novo DNA methyltransferases SlDRM5, SlMET1, SlCMT2 with concomitant augmentation of two DNA demethylases, SlDML1 and SlDML2 levels in SlTRN1 promoter-reporter transgenics. Transient overexpression of SlDML2 mimics the virus-induced hypomethylation state of the SlTRN1 promoter in mature leaves, while silencing of SlDML2 lessens promoter activity. Furthermore, in line with the previous studies, we confirm the crucial role of viral suppressors of RNA silencing AC2 and AC4 proteins in promoting DNA demethylation and directing it to restore activated transcription of SlTRN1. Unusually elevated expression of SlTRN1 may negatively impact normal growth of leaves.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
Additional data supporting the findings in this study are available in the Supplementary Information of this article. The raw datasets are available from the first author or corresponding author on reasonable request.
Abbreviations
- CMT:
-
CHROMOMETHYLASE
- DML:
-
DEMETER-LIKE PROTEINS
- DRM:
-
DOMAINS REARRANGED METHYLTRANSFERASE
- GUS:
-
β-Glucuronidase
- MET1:
-
DNA METHYLTRANSFERASE1
- TGS:
-
Transcriptional gene silencing
- ToLCNDV:
-
Tomato leaf curl New Delhi virus
- TRN1:
-
TORNADO1
- VSR:
-
Viral suppressors of RNA silencing
References
Bartels A, Han Q, Nair P, Stacey L, Gaynier H, Mosley M, Huang QQ, Pearson JK, Hsieh T-F, An Y-QC, Xiao W (2018) Dynamic DNA methylation in plant growth and development. Int J Mol Sci 19(7):2144. https://doi.org/10.3390/ijms19072144
Buchmann RC, Asad S, Wolf JN, Mohannath G, Bisaro DM (2009) Geminivirus AL2 and L2 proteins suppress transcriptional gene silencing and cause genome-wide reductions in cytosine methylation. J Virology 83(10):5005–5013. https://doi.org/10.1128/JVI.01771-08
Candaele J, Demuynck K, Mosoti D, Beemster GTS, Inzé D, Nelissen H (2014) Differential methylation during maize leaf growth targets developmentally regulated genes. Plant Physiol 164(3):1350–1364. https://doi.org/10.1104/pp.113.233312
Cnops G, Neyt P, Raes J, Petrarulo M, Nelissen H, Malenica N, Luschnig C, Tietz O, Ditengou F, Palme K, Azmi A, Prinsen E, Van Lijsebettens M (2006) The TORNADO1 and TORNADO2 genes function in several patterning processes during early leaf development in Arabidopsis thaliana. Plant Cell 18(4):852–866. https://doi.org/10.1105/tpc.105.040568
Dasgupta P, Chaudhuri S (2019) Analysis of DNA methylation profile in plants by Chop-PCR. In: Gassmann W (ed) Plant innate immunity: Methods and protocols. Springer, New York, pp 79–90. https://doi.org/10.1007/978-1-4939-9458-8_9
Díaz-Pendón JA, Ding SW (2008) Direct and indirect roles of viral suppressors of RNA silencing in pathogenesis. Annu Rev Phytopathol 46:303–326. https://doi.org/10.1146/annurev.phyto.46.081407.104746
Ding S-W (2010) RNA-based antiviral immunity. Nat Rev Immunol 10(9):632–644. https://doi.org/10.1038/nri2824
Elbashir SM, Martinez J, Patkaniowska A, Lendeckel W, Tuschl T (2001) Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J 20(23):6877–6888. https://doi.org/10.1093/emboj/20.23.6877
Gorovits R, Moshe A, Amrani L, Kleinberger R, Anfoka G, Czosnek H (2017) The six Tomato yellow leaf curl virus genes expressed individually in tomato induce different levels of plant stress response attenuation. Cell Stress Chaperones 22(3):345–355. https://doi.org/10.1007/s12192-017-0766-0
Guzmán-Benito I, Donaire L, Amorim-Silva V, Vallarino JG, Esteban A, Wierzbicki AT, Ruiz-Ferrer V, Llave C (2019) The immune repressor BIR1 contributes to antiviral defense and undergoes transcriptional and post-transcriptional regulation during viral infections. New Phytol 224(1):421–438. https://doi.org/10.1111/nph.15931
Huang H, Liu R, Niu Q, Tang K, Zhang B, Zhang H, Chen K, Zhu J-K, Lang Z (2019) Global increase in DNA methylation during orange fruit development and ripening. Proc Natl Acad Sci USA 116(4):1430–1436. https://doi.org/10.1073/pnas.1815441116
Ismayil A, Haxim Y, Wang Y, Li H, Qian L, Han T, Chen T, Jia Q, Yihao Liu A, Zhu S, Deng H, Gorovits R, Hong Y, Hanley-Bowdoin L, Liu Y (2018) Cotton Leaf Curl Multan virus C4 protein suppresses both transcriptional and post-transcriptional gene silencing by interacting with SAM synthetase. PLoS Pathog 14(8):e1007282. https://doi.org/10.1371/journal.ppat.1007282
Lang Z, Wang Y, Tang K, Tang D, Datsenka T, Cheng J, Zhang Y, Handa AK, Zhu J-K (2017) Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit. Proc Natl Acad Sci USA 114(22):E4511–E4519. https://doi.org/10.1073/pnas.1705233114
Li W, Liu H, Cheng ZJ, Su YH, Han HN, Zhang Y, Zhang XS (2011) DNA methylation and histone modifications regulate de novo shoot regeneration in Arabidopsis by modulating WUSCHEL expression and auxin signaling. PLoS Genet 7(8):e1002243–e1002243. https://doi.org/10.1371/journal.pgen.1002243
Li Z, Du Z, Tang Y, She X, Wang X, Zhu Y, Yu L, Lan G, He Z (2020) C4, the pathogenic determinant of Tomato Leaf Curl Guangdong Virus, may suppress post-transcriptional gene silencing by interacting with BAM1 protein. Front Microbiol 11:851. https://doi.org/10.3389/fmicb.2020.00851
Liu H, Zhang H, Dong YX, Hao YJ, Zhang XS (2018) DNA METHYLTRANSFERASE1-mediated shoot regeneration is regulated by cytokinin-induced cell cycle in Arabidopsis. New Phytol 217(1):219–232. https://doi.org/10.1111/nph.14814
Llave C (2010) Virus-derived small interfering RNAs at the core of plant-virus interactions. Trends Plant Sci 15(12):701–707. https://doi.org/10.1016/j.tplants.2010.09.001
Luna AP, Rodríguez-Negrete EA, Morilla G, Wang L, Lozano-Durán R, Castillo AG, Bejarano ER (2017) V2 from a curtovirus is a suppressor of post-transcriptional gene silencing. J General Virol 98(10):2607–2614. https://doi.org/10.1099/jgv.0.000933
Mandal A, Sarkar D, Kundu S, Kundu P (2015) Mechanism of regulation of tomato TRN1 gene expression in late infection with tomato leaf curl New Delhi virus (ToLCNDV). Plant Sci 241:221–237. https://doi.org/10.1016/j.plantsci.2015.10.008
Martinez G, Castellano M, Tortosa M, Pallas V, Gomez G (2014) A pathogenic non-coding RNA induces changes in dynamic DNA methylation of ribosomal RNA genes in host plants. Nucleic Acids Res 42(3):1553–1562. https://doi.org/10.1093/nar/gkt968
Mei Y, Yang X, Huang C, Zhang X, Zhou X (2018) Tomato leaf curl Yunnan virus-encoded C4 induces cell division through enhancing stability of Cyclin D 1.1 via impairing NbSKη -mediated phosphorylation in Nicotiana benthamiana. PLoS Pathog 14(1):e1006789. https://doi.org/10.1371/journal.ppat.1006789
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(10):e1008829. https://doi.org/10.1371/journal.ppat.1008829
Moglia A, Gianoglio S, Acquadro A, Valentino D, Milani AM, Lanteri S, Comino C (2019) Identification of DNA methyltransferases and demethylases in Solanum melongena L., and their transcription dynamics during fruit development and after salt and drought stresses. PLoS ONE 14(10):e0223581. https://doi.org/10.1371/journal.pone.0223581
Prakash V, Singh A, Singh AK, Dalmay T, Chakraborty S (2020) Tobacco RNA-dependent RNA polymerase 1 affects the expression of defence-related genes in Nicotiana benthamiana upon Tomato leaf curl Gujarat virus infection. Planta 252(1):11. https://doi.org/10.1007/s00425-020-03417-y
Raja P, Sanville BC, Buchmann RC, Bisaro DM (2008) Viral genome methylation as an epigenetic defense against geminiviruses. J Virol 82(18):8997–9007. https://doi.org/10.1128/JVI.00719-08
Ren Z, Li Z, Miao Q, Yang Y, Deng W, Hao Y (2011) The auxin receptor homologue in Solanum lycopersicum stimulates tomato fruit set and leaf morphogenesis. J Exp Bot 62(8):2815–2826. https://doi.org/10.1093/jxb/erq455
Rodríguez-Negrete E, Lozano-Durán R, Piedra-Aguilera A, Cruzado L, Bejarano ER, Castillo AG (2013) Geminivirus Rep protein interferes with the plant DNA methylation machinery and suppresses transcriptional gene silencing. New Phytol 199(2):464–475. https://doi.org/10.1111/nph.12286
Ruiz-Ferrer V, Voinnet O (2009) Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol 60:485–510. https://doi.org/10.1146/annurev.arplant.043008.092111
Saini K, Markakis MN, Zdanio M, Balcerowicz DM, Beeckman T, De Veylder L, Prinsen E, Beemster GTS, Vissenberg K (2017) Alteration in auxin homeostasis and signaling by overexpression of PINOID Kinase causes leaf growth defects in Arabidopsis thaliana. Front Plant Sci 8:1009. https://doi.org/10.3389/fpls.2017.01009
Tu YC, Tsai WS, Wei JY, Chang KY, Tien CC, Hsiao HY, Fu SF (2017) The C2 protein of tomato leaf curl Taiwan virus is a pathogenicity determinant that interferes with expression of host genes encoding chromomethylases. Physiol Plant 161(4):515–531. https://doi.org/10.1111/ppl.12615
Vanitharani R, Chellappan P, Pita JS, Fauquet CM (2004) Differential roles of AC2 and AC4 of cassava geminiviruses in mediating synergism and suppression of posttranscriptional gene silencing. J Virol 78(17):9487–9498. https://doi.org/10.1128/jvi.78.17.9487-9498.2004
Vanyushin BF (2006) DNA methylation in plants. Curr Topics Microbiol Immunol 301:67–122. https://doi.org/10.1007/3-540-31390-7_4
Vinutha T, Kumar G, Garg V, Canto T, Palukaitis P, Ramesh SV, Praveen S (2018) Tomato geminivirus encoded RNAi suppressor protein, AC4 interacts with host AGO4 and precludes viral DNA methylation. Gene 678:184–195. https://doi.org/10.1016/j.gene.2018.08.009
Vinutha T, Vanchinathan S, Bansal N, Kumar G, Permar V, Watts A, Ramesh SV, Praveen S (2020) Tomato auxin biosynthesis/signaling is reprogrammed by the geminivirus to enhance its pathogenicity. Planta 252(4):51. https://doi.org/10.1007/s00425-020-03452-9
Wang H, Hao L, Shung C-Y, Sunter G, Bisaro DM (2003) Adenosine kinase is inactivated by geminivirus AL2 and L2 proteins. Plant Cell 15(12):3020–3032. https://doi.org/10.1105/tpc.015180
Wang Y, Xue X, Zhu JK, Dong J (2016) Demethylation of ERECTA receptor genes by IBM1 histone demethylase affects stomatal development. Development (cambridge, England) 143(23):4452–4461. https://doi.org/10.1242/dev.129932
Wang B, Yang X, Wang Y, Xie Y, Zhou X (2018) Tomato Yellow Leaf Curl Virus V2 interacts with host histone deacetylase 6 to suppress methylation-mediated transcriptional gene silencing in plants. J Virol. https://doi.org/10.1128/jvi.00036-18
Wang L, Ding Y, He L, Zhang G, Zhu JK, Lozano-Duran R (2020) A virus-encoded protein suppresses methylation of the viral genome through its interaction with AGO4 in the Cajal body. Elife. https://doi.org/10.7554/eLife.55542
Yang J-Y, Iwasaki M, Machida C, Machida Y, Zhou X, Chua N-H (2008) βC1, the pathogenicity factor of TYLCCNV, interacts with AS1 to alter leaf development and suppress selective jasmonic acid responses. Genes Dev 22(18):2564–2577. https://doi.org/10.1101/gad.1682208
Yang Y, Tang K, Datsenka TU, Liu W, Lv S, Lang Z, Wang X, Gao J, Wang W, Nie W, Chu Z, Zhang H, Handa AK, Zhu J-K, Zhang H (2019) Critical function of DNA methyltransferase 1 in tomato development and regulation of the DNA methylome and transcriptome. J Integr Plant Biol 61(12):1224–1242. https://doi.org/10.1111/jipb.12778
Zhang Z, Chen H, Huang X, Xia R, Zhao Q, Lai J, Teng K, Li Y, Liang L, Du Q, Zhou X, Guo H, Xie Q (2011) BSCTV C2 attenuates the degradation of SAMDC1 to suppress DNA methylation-mediated gene silencing in Arabidopsis. Plant Cell 23(1):273–288. https://doi.org/10.1105/tpc.110.081695
Zhong X, Wang ZQ, Xiao R, Wang Y, Xie Y, Zhou X (2017) iTRAQ analysis of the tobacco leaf proteome reveals that RNA-directed DNA methylation (RdDM) has important roles in defense against geminivirus-betasatellite infection. J Proteomics 152:88–101. https://doi.org/10.1016/j.jprot.2016.10.015
Acknowledgements
This work is supported by DST, GoI, INSPIRE fellowship to SC and intramural funding of Bose Institute to PK. Authors are thankful to Professor Shubho Chaudhuri, Pratiti Dasgupta, members of Chaudhuri lab and the Central Instrument Facility of Bose Institute. Statistical analysis support from Dr. Sanat K. Das of Bose Institute is highly acknowledged. We thank Prof. Somnath Bhattacharyya, Bidhan Chandra Krishi Viswavidyalaya for assistance with plant physiological parameter analysis.
Funding
Department of Science and Technology, Government of India.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors have no financial or non-financial interests to declare that are relevant to the content of this article.
Additional information
Communicated by Dorothea Bartels.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Chowdhury, S., Mukherjee, A., Basak, S. et al. Disruption of tomato TGS machinery by ToLCNDV causes reprogramming of vascular tissue-specific TORNADO1 gene expression. Planta 256, 78 (2022). https://doi.org/10.1007/s00425-022-03985-1
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00425-022-03985-1