Abstract
The co-evolution of plant pathosystems has generated a plethora of molecular mechanisms by which plants defend themselves from the attack of invading pathogens. One of the players involved in plant response to pathogen attack includes the double-stranded RNA Binding (DRB) proteins. The model plant Arabidopsis thaliana encodes DRB proteins by five genes (DRB1 to DRB5). Their participation in plant responses has been demonstrated for viruses and bacteria but not yet for fungi and stramenopiles. Thus, this study investigated the expression profile of A. thaliana DRB genes throughout a time course experiment after inoculation with eukaryotic pathogens of different lifestyles. Employing RT-qPCR and electronic Northern analysis, we observed that DRB genes were differentially expressed between infected and control plants during Alternaria brassicicola, Colletotrichum higginsianum, Phytophtora infestans, Botrytis cinerea, and Golovinomyces orontii infection. DRB3, DRB4, and DRB5 were the genes with higher variation across infected and control plants. Gene expression analysis showed that there is no differentiated pattern between the modulations of DRB genes comparing pathogens with different lifestyles. The results presented in this study are the first approach relating the DRB genes to the response of plants to fungi and oomycetes.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Alvarez-Diaz, J. C., Richard, M. M. S., Thareau, V., Teano, G., Paysant-Le-Roux, C., Rigaill, G., et al. (2021). Genome-wide identification of key components of RNA silencing in two Phaseolus vulgaris genotypes of contrasting origin and their expression analyses in response to fungal infection. Genes, 13(1), 64. https://doi.org/10.3390/genes13010064
Aveling, T. A. S., Snyman, H. G., & Rijkenberg, F. H. J. (1994). Morphology of infection of onion leaves by Alternaria porri. Canadian Journal of Botany, 72(8), 1164–1170. https://doi.org/10.1139/b94-142
Barton, D. A., Roovers, E. F., Gouil, Q., da Fonseca, G. C., Reis, R. S., Jackson, C., Overall, R. L., Fusaro, A. F., & Waterhouse, P. M. (2017). Live cell imaging reveals the relocation of dsRNA binding proteins upon viral infection. Molecular Plant-Microbe Interactions, 30(6), 435–443. https://doi.org/10.1094/mpmi-02-17-0035-r
Belmas, E., Briand, M., Kwasiborski, A., Colou, J., N’Guyen, G., Iacomi, B., et al. (2018). Genome sequence of the necrotrophic plant pathogen Alternaria brassicicola Abra43. Genome Announcements, 6(6), e01559–e01517. https://doi.org/10.1128/genomea.01559-17
Bustin, S. A., Benes, V., Garson, J. A., Hellemans, J., Huggett, J., Kubista, M., Mueller, R., Nolan, T., Pfaffl, M. W., Shipley, G. L., Vandesompele, J., & Wittwer, C. T. (2009). The MIQE guidelines: Minimum information for publication of quantitative real-time PCR experiments. Clinical Chemistry, 55(4), 611–622. https://doi.org/10.1373/clinchem.2008.112797
Dehpour, A. A., Alavi, S. V., & Majd, A. (2007). Light and scanning Electron microscopy studies on the penetration and infection processes of Alternaria Alternata, causing Brown spot on Minneola tangelo in the West Mazandaran - Iran. World Applied Sciences Journal, 2(1), 68–72 https://www.researchgate.net/publication/237596289
Derveaux, S., Vandesompele, J., & Hellemans, J. (2010). How to do successful gene expression analysis using real-time PCR. Methods, 50(4), 227–230. https://doi.org/10.1016/j.ymeth.2009.11.001
Eamens, A. L., Kim, K. W., Curtin, S. J., & Waterhouse, P. M. (2012a). DRB2 is required for MicroRNA biogenesis in Arabidopsis thaliana. PLoS One, 7(4), e35933. https://doi.org/10.1371/journal.pone.0035933
Eamens, A. L., Kim, K. W., & Waterhouse, P. M. (2012b). DRB2, DRB3 and DRB5 function in a non-canonical microRNA pathway in Arabidopsis thaliana. Plant Signaling and Behavior, 7(10), 1224–1229. https://doi.org/10.4161/psb.21518
Fátyol, K., Fekete, K. A., & Ludman, M. (2020). Double-stranded-RNA-binding protein 2 participates in antiviral defense. Journal of Virology, 94(11), 1–20. https://doi.org/10.1128/jvi.00017-20
Ferrari, S., Galletti, R., Denoux, C., De Lorenzo, G., Ausubel, F. M., & Dewdney, J. (2007). Resistance to Botrytis cinerea induced in Arabidopsis by elicitors is independent of salicylic acid, ethylene, or jasmonate signaling but requires PHYTOALEXIN DEFICIENT3. Plant Physiology, 144(1), 367–379. https://doi.org/10.1104/pp.107.095596
Han, M.-H., Goud, S., Song, L., & Fedoroff, N. (2004). The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proceedings of the National Academy of Sciences, 101(4), 1093–1098. https://doi.org/10.1073/pnas.0307969100
Incarbone, M., Clavel, M., Monsion, B., Kuhn, L., Scheer, H., Vantard, É., Poignavent, V., Dunoyer, P., Genschik, P., & Ritzenthaler, C. (2021). Immunocapture of dsRNA-bound proteins provides insight into tobacco rattle virus replication complexes and reveals Arabidopsis DRB2 to be a wide-spectrum antiviral effector. Plant Cell, 33(11), 3402–3420. https://doi.org/10.1093/plcell/koab214
Koh, S., André, A., Edwards, H., Ehrhardt, D., & Somerville, S. (2005). Arabidopsis thaliana subcellular responses to compatible Erysiphe cichoracearum infections. The Plant Journal, 44(3), 516–529. https://doi.org/10.1111/J.1365-313X.2005.02545.X
Kwon, T. (2016). A double-stranded RNA binding protein, HYL1, regulates plant immunity via the jasmonic acid pathway. Journal of Plant Biology 2016, 59(5), 506–514. https://doi.org/10.1007/S12374-016-0303-1
Lim, G.-H., Hoey, T., Zhu, S., Clavel, M., Yu, K., Navarre, D., Kachroo, A., Deragon, J. M., & Kachroo, P. (2018). COP1, a negative regulator of photomorphogenesis, positively regulates plant disease resistance via double-stranded RNA binding proteins. PLoS Pathogens, 14(3), e1006894. https://doi.org/10.1371/journal.ppat.1006894
Lim, G.-H., Zhu, S., Zhang, K., Hoey, T., Deragon, J.-M., Kachroo, A., & Kachroo, P. (2019). The analogous and opposing roles of double-stranded RNA-binding proteins in bacterial resistance. Journal of Experimental Botany, 70(5), 1627–1638. https://doi.org/10.1093/jxb/erz019
Livak, K. J., & Schmittgen, T. D. (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods, 25(4), 402–408. https://doi.org/10.1006/meth.2001.1262
Ma, S., & Bohnert, H. J. (2007). Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression. Genome Biology, 8(4), R49. https://doi.org/10.1186/gb-2007-8-4-r49
Macioszek, V. K., Gapińska, M., Zmienko, A., Sobczak, M., Skoczowski, A., Oliwa, J., & Kononowicz, A. K. (2020). Complexity of Brassica oleracea–Alternaria brassicicola susceptible interaction reveals downregulation of photosynthesis at ultrastructural, transcriptional, and physiological levels. Cells., 9(10), 2329. https://doi.org/10.3390/cells9102329
Macioszek, V. K., Lawrence, C. B., & Kononowicz, A. K. (2018). Infection cycle of Alternaria brassicicola on Brassica oleracea leaves under growth room conditions. Plant Pathology, 67(5), 1088–1096. https://doi.org/10.1111/ppa.12828
Nakazawa, Y., Hiraguri, A., Moriyama, H., & Fukuhara, T. (2007). The dsRNA-binding protein DRB4 interacts with the dicer-like protein DCL4 in vivo and functions in the trans-acting siRNA pathway. Plant Molecular Biology, 63(6), 777–785. https://doi.org/10.1007/s11103-006-9125-8
Nowakowska, M., Wrzesińska, M., Kamiński, P., Szczechura, W., Lichocka, M., Tartanus, M., Kozik, E. U., & Nowicki, M. (2019). Alternaria brassicicola – Brassicaceae pathosystem: Insights into the infection process and resistance mechanisms under optimized artificial bio-assay. European Journal of Plant Pathology, 153, 131–151. https://doi.org/10.1007/s10658-018-1548-y
Nowicki, M., Nowakowska, M., Niezgoda, A., & Kozik, E. (2012). Alternaria black spot of crucifers: Symptoms, importance of disease, and perspectives of resistance breeding. Vegetable Crops Research Bulletin, 76(1), 5–19. https://doi.org/10.2478/v10032-012-0001-6
O’Connell, R., Herbert, C., Sreenivasaprasad, S., Khatib, M., Esquerré-Tugayé, M.-T., & Dumas, B. (2004). A novel Arabidopsis-Colletotrichum Pathosystem for the molecular dissection of plant-fungal interactions. Molecular Plant-Microbe Interactions, 17(3), 272–282. https://doi.org/10.1094/mpmi.2004.17.3.272
O’Connell, R. J., Thon, M. R., Hacquard, S., Amyotte, S. G., Kleemann, J., Torres, M. F., Damm, U., Buiate, E. A., Epstein, L., Alkan, N., Altmüller, J., Alvarado-Balderrama, L., Bauser, A. C., Becker, C., Birren, B. W., Chen, Z., Choi, J., Crouch, J. A., Ducick, J., et al. (2012). Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nature Genetics, 44(9), 1060–1065. https://doi.org/10.1038/ng.2372
Pélissier, T., Clavel, M., Chaparro, C., Pouch-PéLissier, M. N., Vaucheret, H., & Deragon, J. M. (2011). Double-stranded RNA binding proteins DRB2 and DRB4 have an antagonistic impact on polymerase IV-dependent siRNA levels in Arabidopsis. RNA, 17(8), 1502–1510. https://doi.org/10.1261/RNA.2680711
Perfect, S. E., Hughes, H. B., O’Connell, R. J., & Green, J. R. (1999). Colletotrichum: A model genus for studies on pathology and fungal–plant interactions. Fungal Genetics and Biology, 27(2–3), 186–198. https://doi.org/10.1006/fgbi.1999.1143
Pochon, S., Terrasson, E., Guillemette, T., Iacomi-Vasilescu, B., Georgeault, S., Juchaux, M., Berruyer, R., Debeaujon, I., Simoneau, P., & Campion, C. (2012). The Arabidopsis thaliana-Alternaria brassicicola pathosystem: A model interaction for investigating seed transmission of necrotrophic fungi. Plant Methods, 8(1), 1–13. https://doi.org/10.1186/1746-4811-8-16/FIGURES/8
Raja, P., Jackel, J. N., Li, S., Heard, I. M., & Bisaro, D. M. (2014). Arabidopsis double-stranded RNA binding protein DRB3 participates in methylation-mediated defense against Geminiviruses. Journal of Virology, 88(5), 2611–2622. https://doi.org/10.1128/JVI.02305-13
Sharma, P., Deep, S., Bhati, D. S., Sharma, M., & Chowdappa, P. (2014). Penetration and infection processes of Alternaria brassicicola on cauliflower leaf and Alternaria brassicae on mustard leaf: A histopathological study. Plant Pathology Journal, 13(2), 100–111. https://doi.org/10.3923/PPJ.2014.100.111
Shimada, C., Lipka, V., O’Connell, R., Okuno, T., Schulze-Lefert, P., & Takano, Y. (2007). Nonhost resistance in Arabidopsis-Colletotrichum interactions acts at the cell periphery and requires actin filament function. Molecular Plant-Microbe Interactions, 19(3), 270–279. https://doi.org/10.1094/MPMI-19-0270
Shlezinger, N., Minz, A., Gur, Y., Hatam, I., Dagdas, Y. F., Talbot, N. J., & Sharon, A. (2011). Anti-apoptotic machinery protects the necrotrophic fungus Botrytis cinerea from host-induced apoptotic-like cell death during plant infection. PLoS Pathogens, 7(8), e1002185. https://doi.org/10.1371/JOURNAL.PPAT.1002185
Toufighi, K., Brady, S. M., Austin, R., Ly, E., & Provart, N. J. (2005). The botany Array resource: E-Northerns, expression angling, and promoter analyses. The Plant Journal, 43(1), 153–163. https://doi.org/10.1111/J.1365-313X.2005.02437.X
Vale, F. X. R., Fernandes Filho, E. I., & Liberato, J. R. (2003). QUANT - a software for plant disease severity assessment. In 8th international congress of plant pathology (p. 105). New Zealand: Christchurch.
Vandesompele, J., De Preter, K., Pattyn, F., Poppe, B., Van Roy, N., De Paepe, A., & Speleman, F. (2002). Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biology, 3, research0034.1. https://doi.org/10.1186/gb-2002-3-7-research0034
Velho, A. C., & Stadnik, M. J. (2020). Non-host resistance of arabidopsis and apple is associated with callose accumulation and changes in preinfective structures of Colletotrichum species. Physiological and Molecular Plant Pathology, 110, 101463. https://doi.org/10.1016/J.PMPP.2020.101463
Vetukuri, R. R., Åsman, A. K. M., Tellgren-Roth, C., Jahan, S. N., Reimegård, J., Fogelqvist, J., Savenkov, E., Söderbom, F., Avrova, A. O., Whisson, S. C., & Dixelius, C. (2012). Evidence for small RNAs homologous to effector-encoding genes and transposable elements in the oomycete Phytophthora infestans. PLoS One, 7(12), e51399. https://doi.org/10.1371/JOURNAL.PONE.0051399
Waese, J., Fan, J., Pasha, A., Yu, H., Fucile, G., Shi, R., Cumming, M., Kelley, L. A., Sternberg, M. J., Krishnakumar, V., Ferlanti, E., Miller, J., Town, C., Stuerzlinger, W., & Provart, N. J. (2017). ePlant: Visualizing and exploring multiple levels of data for hypothesis generation in plant biology. The Plant Cell, 29(8), 1806–1821. https://doi.org/10.1105/tpc.17.00073
Winter, D., Vinegar, B., Nahal, H., Ammar, R., Wilson, G. V., & Provart, N. J. (2007). An “electronic fluorescent pictograph” browser for exploring and analyzing large-scale biological data sets. PLoS One, 2(8), e718. https://doi.org/10.1371/JOURNAL.PONE.0000718
Yan, Y., Yuan, Q., Tang, J., Huang, J., Hsiang, T., Wei, Y., & Zheng, L. (2018). Colletotrichum higginsianum as a model for understanding host–pathogen interactions: A review. International Journal of Molecular Sciences. 19(7), 2142. https://doi.org/10.3390/ijms19072142
Zhu, S., Jeong, R. D., Lim, G. H., Yu, K., Wang, C., Chandra-Shekara, A. C., Navarre, D., Klessig, D. F., Kachroo, A., & Kachroo, P. (2013). Double-stranded RNA-binding protein 4 is required for resistance signaling against viral and bacterial pathogens. Cell Reports, 4(6), 1168–1184. https://doi.org/10.1016/j.celrep.2013.08.018
Acknowledgments
This work was supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq; project N° 477933/2013-0) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES). We thank Dra Juliana Dal-Ri Lindenau for her help in the statistical analysis. We also thank to Programa de Pós-Graduação em Biologia Celular e do Desenvolvimento (PPGBCD) for supporting us.
Author information
Authors and Affiliations
Contributions
KRS: Investigation, methodology, data analysis, writing - original draft; SKOC, MBF, and ACV: Investigation, methodology and data analysis; FRK, MJS, and RM: Funding acquisition and conceptualization; FRK: Methodology, data analysis, writing and supervision. All authors read, provided critical feedback, and approved the final version of the manuscript.
Corresponding author
Ethics declarations
Competing interests
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) 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
Silva, K.R., Cabral, S.K.O., de Freitas, M.B. et al. Fungal infection modulates the gene expression of the double-stranded RNA binding proteins (DRB) in Arabidopsis thaliana. Eur J Plant Pathol 165, 475–488 (2023). https://doi.org/10.1007/s10658-022-02620-9
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10658-022-02620-9