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Elucidating potential effectors, pathogenicity and virulence factors expressed by the phytopathogenic fungus Thecaphora frezii through analysis of its transcriptome

Abstract

Thecaphora frezii is a phytopathogenic fungus belonging to the Ustilaginomycetes class, which causes peanut smut disease. In its biological cycle it has three structures, teliospores (is the resistance structure), basidiospores and hyphae. The mycelium is the structure that penetrates the plant’s gynophore and initiates the infection. For this action, the expression of effectors, pathogenicity and virulence factor proteins is necessary. The aim of this study was to identify potential Thecaphora frezii’s proteins that could exert pathogenicity, virulence and/or effector functions. Based on the transcriptome of two ontogenetic stages (teliospore and hyphae) of Thecaphora frezii, and a series of bioinformatic analyses, 18 potential effectors and 91 factors possibly involved in the level of pathogenicity and virulence were identified. Higher expression levels of candidate effectors were found in the infective stage of the fungus. In the other hand, the major variability observed in pathogenicity and virulence factors expressed between Ustilago maydis and Thecaphora frezii were the number of virulence factors secreted (higher in U. maydis). In the future, when the genome of the fungus will be known, functional studies of these proteins could be carried out to validate their function.

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Data is available either in supplementary material or at GenBank.

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References

  • Agrios, G. (2005). Plant pathology (5th ed.). Elsevier. https://doi.org/10.1016/C2009-0-02037-6.

  • Almagro Armenteros, J. J., Tsirigos, K. D., Sønderby, C. K., Petersen, T. N., Winther, O., Brunak, S., von Heijne G., Nielsen H. (2019). SignalP 5.0 improves signal peptide predictions using deep neural networks. Nature Biotechnology, 37(4), 420–423. https://doi.org/10.1038/s41587-019-0036-z.

  • Arias, S. L., Mary, V. S., Velez, P. A., Rodriguez, M. G., Otaiza-González, S. N., & Theumer, M. G. (2021). Where does the peanut smut pathogen, Thecaphora frezii , fit in the spectrum of smut diseases? Plant Disease, 105(9), 2268–2280. https://doi.org/10.1094/PDIS-11-20-2438-FE.

  • Backman, P. A., Bell, D. K., Ben-Yephet, Y., Beute, M. K., Black, M. C., Boswell, T. E., et al. (1997). Compendium of peanut diseases (2nd Edition). APS Press.

  • Bauters, L., Kyndt, T., De Meyer, T., Morreel, K., Boerjan, W., Lefevere, H., & Gheysen, G. (2020). Chorismate mutase and isochorismatase, two potential effectors of the migratory nematode Hirschmanniella oryzae , increase host susceptibility by manipulating secondary metabolite content of rice. Molecular Plant Pathology, 21(12), 1634–1646. https://doi.org/10.1111/mpp.13003.

  • Bölker, M. (2001). Ustilago maydis – a valuable model system for the study of fungal dimorphism and virulence. Microbiology, 147(6), 1395–1401. https://doi.org/10.1099/00221287-147-6-1395.

  • Borah, N., Albarouki, E., & Schirawski, J. (2018). Comparative methods for molecular determination of host-specificity factors in plant-pathogenic fungi. International Journal of Molecular Sciences, 19(3), 863. https://doi.org/10.3390/ijms19030863.

  • Carranza, J. M., & Lindquist, J. C. (1962). Thecaphora frezii n. sp., parásita de Arachis sp. Boletin de la Sociedad Argentina de Botanica, 10, 11–18.

    Google Scholar 

  • Cavallo, A., Novo, R., & Pérez, M. (2005). Eficiencia de fungicidas en el control de la flora fúngica transportada por semillas de maní (Arachis hypogaea L.) en la Argentina. Agriscientia, XXII(1), 9–16. https://doi.org/10.31047/1668.298x.v22.n1.2674.

  • Cazzola, N., Gateau, M., March, G., Marinelli, A., García, J., Rago, A., & Oddino, C. (2012). Intensidad y pérdidas ocasionadas por carbón del maní según regiones de producción. In XXVII Jornada Nacional de Maní (pp. 34–35).

  • Córdoba Bolsa de Cereales. (2015). Campaña 2014/2015. Producción Final de Maní, Córdoba, Argentina. Informe especial, 69.

  • Courville, K. J., Frantzeskakis, L., Gul, S., Haeger, N., Kellner, R., Heßler, N., Day B., Usadel B., Gupta Y. K., Esse H. P., Brachmann A., Kemen E., Feldbrügge M., Göhre V. (2019). Smut infection of perennial hosts: The genome and the transcriptome of the Brassicaceae smut fungus Thecaphora thlaspeos reveal functionally conserved and novel effectors. New Phytologist, 222(3), 1474–1492. https://doi.org/10.1111/nph.15692.

  • Dalio, R. J. D., Herlihy, J., Oliveira, T. S., McDowell, J. M., & Machado, M. (2018). Effector biology in focus: A primer for computational prediction and functional characterization. Molecular Plant-Microbe Interactions®, 31(1), 22–33. https://doi.org/10.1094/MPMI-07-17-0174-FI.

  • de Castro, E., Sigrist, C. J. A., Gattiker, A., Bulliard, V., Langendijk-Genevaux, P. S., Gasteiger, E., et al. (2006). ScanProsite: Detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Research, 34(Web Server), W362–W365. https://doi.org/10.1093/nar/gkl124.

  • De Wit, P. J. G. M., Meharabi, R., Van Den Burg, H. A., & Stergiopoulos, I. (2009). Fungal effector proteins: Past, present and future. Molecular Plant Pathology, 10(6), 735–747. https://doi.org/10.1111/j.1364-3703.2009.00591.x.

  • Di Rienzo, J. A., Casanoves, F., Balzarini, M. G., Gonzalez, L., Tablada, M., & Robledo, C. W. (2016). InfoStat versión 2016. Grupo Infostat, FCA, Universidad Nacional de Córdoba, Argentina. URL http://www.infostat.com.ar. Accessed 15 March 2021. Córdoba, Argentina: Universidad Nacional de Córdoba.

  • Dodds, P. N., & Rathjen, J. P. (2010). Plant immunity: Towards an integrated view of plant–pathogen interactions. Nature Reviews Genetics, 11(8), 539–548. https://doi.org/10.1038/nrg2812.

  • Doehlemann, G., Ökmen, B., Zhu, W., & Sharon, A. (2017). Plant pathogenic Fungi. Microbiology Spectrum, 5(1), 573–644. https://doi.org/10.1128/microbiolspec.FUNK-0023-2016.

  • Franceschetti, M., Maqbool, A., Jiménez-Dalmaroni, M. J., Pennington, H. G., Kamoun, S., & Banfield, M. J. (2017). Effectors of filamentous plant pathogens: Commonalities amid diversity. Microbiology and Molecular Biology Reviews, 81(2), 1–17. https://doi.org/10.1128/MMBR.00066-16.

  • Frantzeskakis, L., Courville, K. J., Plücker, L., Kellner, R., Kruse, J., Brachmann, A., Feldbrügge M., Göhre V. (2017). The plant-dependent life cycle of Thecaphora thlaspeos : A smut fungus adapted to Brassicaceae. Molecular Plant-Microbe Interactions, 30(4), 271–282. https://doi.org/10.1086/648488.

  • Godfrey, D., Böhlenius, H., Pedersen, C., Zhang, Z., Emmersen, J., & Thordal-Christensen, H. (2010). Powdery mildew fungal effector candidates share N-terminal Y/F/WxC-motif. BMC Genomics, 11(1), 317. https://doi.org/10.1186/1471-2164-11-317.

  • Ismail, I. A., & Able, A. J. (2016). Secretome analysis of virulent Pyrenophora teres f . teres isolates. Proteomics, 16(20), 2625–2636. https://doi.org/10.1002/pmic.201500498.

  • Jaswal, R., Kiran, K., Rajarammohan, S., Dubey, H., Singh, P. K., Sharma, Y., Deshmukh R., Sonah H., Gupta N., Sharma T.R. (2020). Effector biology of biotrophic plant fungal pathogens: Current advances and future prospects. Microbiological Research, 241(December 2019), 126567. https://doi.org/10.1016/j.micres.2020.126567.

  • Jiang, R. H. Y., Tripathy, S., Govers, F., & Tyler, B. M. (2008). RXLR effector reservoir in two Phytophthora species is dominated by a single rapidly evolving superfamily with more than 700 members. Proceedings of the National Academy of Sciences, 105(12), 4874–4879. https://doi.org/10.1073/pnas.0709303105.

  • Jones, D. A., Bertazzoni, S., Turo, C. J., Syme, R. A., & Hane, J. K. (2018). Bioinformatic prediction of plant–pathogenicity effector proteins of fungi. Current Opinion in Microbiology, 46, 43–49. https://doi.org/10.1016/j.mib.2018.01.017.

  • Kall, L., Krogh, A., & Sonnhammer, E. L. L. (2007). Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Research, 35(Web Server), W429–W432. https://doi.org/10.1093/nar/gkm256.

  • Kanja, C., & Hammond-Kosack, K. E. (2020). Proteinaceous effector discovery and characterization in filamentous plant pathogens. Molecular Plant Pathology, 21(10), 1353–1376. https://doi.org/10.1111/mpp.12980.

  • Krogh, A., Larsson, B., von Heijne, G., & Sonnhammer, E. L. L. (2001). Predicting transmembrane protein topology with a hidden markov model: Application to complete genomes. Journal of Molecular Biology, 305(3), 567–580. https://doi.org/10.1006/jmbi.2000.4315.

  • Lanver, D., Tollot, M., Schweizer, G., Lo Presti, L., Reissmann, S., Ma, L.-S., Schuster M., Tanaka S., Liang L., Ludwig N., Kahmann R. (2017). Ustilago maydis effectors and their impact on virulence. Nature Reviews Microbiology, 15(7), 409–421. https://doi.org/10.1038/nrmicro.2017.33.

  • Laurie, J. D., Ali, S., Linning, R., Mannhaupt, G., Wong, P., Güldener, U., Münsterkötter M., Moore R., Kahmann R., Bakkeren G., Schirawski J. (2012). Genome comparison of barley and maize smut fungi reveals targeted loss of RNA silencing components and species-specific presence of transposable elements. The Plant Cell, 24(5), 1733–1745. https://doi.org/10.1105/tpc.112.097261.

  • Lefebvre, F., Joly, D. L., Labbé, C., Teichmann, B., Linning, R., Belzile, F., et al. (2013). The transition from a phytopathogenic smut ancestor to an anamorphic biocontrol agent deciphered by comparative whole-genome analysis. Plant Cell, 25(6), 1946–1959. https://doi.org/10.1105/tpc.113.113969.

  • Li, J., & Zhang, K.-Q. (2014). Independent expansion of Zincin metalloproteinases in Onygenales Fungi may be associated with their pathogenicity. PLoS One, 9(2), e90225. https://doi.org/10.1371/journal.pone.0090225.

  • Liu, L., Xu, L., Jia, Q., Pan, R., Oelmüller, R., Zhang, W., & Wu, C. (2019). Arms race: Diverse effector proteins with conserved motifs. Plant Signaling & Behavior, 14(2), 1557008. https://doi.org/10.1080/15592324.2018.1557008.

  • 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.

  • Marinelli, A., March, G. J., & Oddino, C. (2008). Aspectos biológicos y epidemiológicos del carbón del maní (Arachis hypogaea L.) causado por Thecaphora frezii Carranza & Lindquist. AgriScientia, 25(1), 1–5. https://doi.org/10.31047/1668.298x.v25.n1.2735.

  • Mosquera, G., Giraldo, M. C., Khang, C. H., Coughlan, S., & Valent, B. (2009). Interaction transcriptome analysis identifies Magnaporthe oryzae BAS1-4 as biotrophy-associated secreted proteins in rice blast disease. The Plant Cell, 21(4), 1273–1290. https://doi.org/10.1105/tpc.107.055228.

  • Neu, E., & Debener, T. (2019). Prediction of the Diplocarpon rosae secretome reveals candidate genes for effectors and virulence factors. Fungal Biology, 123(3), 231–239. https://doi.org/10.1016/j.funbio.2018.12.003.

  • Pierleoni, A., Martelli, P. L., & Casadio, R. (2008). PredGPI: A GPI-anchor predictor. BMC Bioinformatics, 9(1), 392. https://doi.org/10.1186/1471-2105-9-392.

  • Rago, A. M., Cazón, L. I., Paredes, J. A., Molina, J. P. E., Conforto, E. C., Bisonard, E. M., & Oddino, C. (2017). Peanut smut: From an emerging disease to an actual threat to Argentine Peanut production. Plant Disease, 101(3), 400–408. https://doi.org/10.1094/PDIS-09-16-1248-FE.

  • Sander, C., & Schneider, R. (1991). Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins: Structure, Function, and Genetics, 9(1), 56–68. https://doi.org/10.1002/prot.340090107.

  • Simbaqueba, J., Rodríguez, E. A., Burbano-David, D., González, C., & Caro-Quintero, A. (2021). Putative novel effector genes revealed by he genomic analysis of the phytopathogenic fungus Fusarium oxysporum f. sp. physali (Foph) that infects Cape Gooseberry plants. Frontiers in Microbiology, 11(January). https://doi.org/10.3389/fmicb.2020.593915.

  • Sonah, H., Deshmukh, R. K., & Bélanger, R. R. (2016). Computational prediction of effector proteins in fungi: Opportunities and challenges. Frontiers in Plant Science, 7(FEB2016), 1–14. https://doi.org/10.3389/fpls.2016.00126.

  • Song, Y.-D., Hsu, C.-C., Lew, S. Q., & Lin, C.-H. (2021). Candida tropicalis RON1 is required for hyphal formation, biofilm development, and virulence but is dispensable for N-acetylglucosamine catabolism. Medical Mycology, 59(4), 379–391. https://doi.org/10.1093/mmy/myaa063.

  • Soria, N. W., Díaz, M. S., Figueroa, A. C., Alasino, V. R., Yang, P., & Beltramo, D. M. (2021a). Identificación y expresión del efector central fúngico Pep1 en Thecaphora frezii. Methodo Investigación Aplicada a las Ciencias Biológicas, 6(4), 155–161. https://doi.org/10.22529/me.2021.6(4)02.

  • Soria, N. W., Díaz, M. S., Figueroa, A. C., Alasino, V. R., Yang, P., & Beltramo, D. M. (2021b). Identification of Chitin synthase and Chitinase genes in three ontogenetic stages from Thecaphora frezii, the causal agent of peanut smut disease. Physiological and Molecular Plant Pathology, 116(July), 101727. https://doi.org/10.1016/j.pmpp.2021.101727.

  • Soria, N. W., Figueroa, A. C., Díaz, M. S., Alasino, V. R., Yang, P., & Beltramo, D. M. (2022). Identification and expression of some plant cell wall-degrading enzymes present in three ontogenetics stages of Thecaphora frezii, a Peanut pathogenic fungus. American Journal of Plant Sciences, 13(01), 1–22. https://doi.org/10.4236/ajps.2022.131001.

  • Sperschneider, J., & Dodds, P. N. (2022). EffectorP 3.0: Prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes. Molecular Plant-Microbe Interactions®, 35(2), 146–156. https://doi.org/10.1094/MPMI-08-21-0201-R.

  • Sperschneider, J., Dodds, P. N., Gardiner, D. M., Manners, J. M., Singh, K. B., & Taylor, J. M. (2015). Advances and challenges in computational prediction of effectors from plant pathogenic fungi. PLoS Pathogens, 11(5), e1004806. https://doi.org/10.1371/journal.ppat.1004806.

  • von Heijne, G. (1990). The signal peptide. The Journal of Membrane Biology, 115(3), 195–201. https://doi.org/10.1007/BF01868635.

  • Wei, L., Liu, Y., Dubchak, I., Shon, J., & Park, J. (2002). Comparative genomics approaches to study organism similarities and differences. Journal of Biomedical Informatics, 35(2), 142–150. https://doi.org/10.1016/S1532-0464(02)00506-3.

  • Winnenburg, R. (2006). PHI-base: A new database for pathogen host interactions. Nucleic Acids Research, 34(90001), D459–D464. https://doi.org/10.1093/nar/gkj047.

  • Xia, W., Yu, X., & Ye, Z. (2020). Smut fungal strategies for the successful infection. Microbial Pathogenesis, 142(February), 104039. https://doi.org/10.1016/j.micpath.2020.104039.

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Acknowledgments

The present work was supported by grants from Universidad Católica de Córdoba, Fundación Maní Argentino and Centro de Excelencia de Productos y Procesos de Córdoba (CEPROCOR).

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NWS and DMB conceived the project. ACF, MSD, VRA, PY and EHB did experiments. NWS and DMB analyzed data and wrote the manuscript. ACF, MSD, VRA, PY and EHB provided the biological material. All authors read and approved the final manuscript.

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Correspondence to Néstor W. Soria or Dante M. Beltramo.

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Soria, N.W., Badariotti, E.H., Alasino, V.R. et al. Elucidating potential effectors, pathogenicity and virulence factors expressed by the phytopathogenic fungus Thecaphora frezii through analysis of its transcriptome. Eur J Plant Pathol (2022). https://doi.org/10.1007/s10658-022-02562-2

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Keywords

  • Effectors
  • Pathogenicity
  • Virulence
  • Thecaphora frezii
  • Peanut