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Nuclear proteome analysis of apple cultivar ‘Antonovka’ accessions in response to apple scab (Venturia inaequalis)

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Abstract

This study presents the first comprehensive description of the differential nuclear proteome of apple leaves during the interaction with the fungal pathogen Venturia inaequalis. Nuclear proteins isolated from V. inaequalis infected leaves of three different apple genotypes, two ‘Antonovka’ accessions of varying resistance and cultivar ‘Puikis’ used as a control, were subjected to 2DE-DIGE. The analysis of proteins revealed 186 protein spots with significant differences in protein abundance (P ≤ 0.01), of which 67 proteins were identified through LC-MS/MS analysis. The proteins were classified into 9 functional categories that included redox regulation, cell signalling, cell homeostasis, protein degradation, epigenetic control, energy metabolism, photosynthesis, other stress-related proteins and proteins with unknown biological function. Comparison of the ‘Antonovka’ accessions revealed 13 proteins with different expression patterns. Among these were proteins mainly involved in ROS scavenging mechanisms, ubiquitin/26S proteasome-mediated protein degradation, protein folding and carbohydrate metabolism that may contribute to a varying resistance of ‘Antonovka’ accessions to apple scab. These results provide novel insights into the response of apple leaves to fungal pathogen infection and promote further investigation of the molecular mechanisms of apple resistance to V. inaequalis.

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References

  • Allen, E. M., & Mieyal, J. J. (2012). Protein-thiol oxidation and cell death: regulatory role of glutaredoxins. Antioxidants & Redox Signaling, 17(12), 1748–1763.

    Article  CAS  Google Scholar 

  • Bae, M. S., Cho, E. J., Choi, E. Y., & Park, O. K. (2003). Analysis of the Arabidopsis nuclear proteome and its response to cold stress. The Plant Journal, 36(5), 652–663.

    Article  CAS  PubMed  Google Scholar 

  • Barajas-López Jde, D., Blanco, N. E., & Strand, Å. (2013). Plastid-to-nucleus communication, signals controlling the running of the plant cell. Biochimica et Biophysica Acta, 1833(2), 425–437.

    Article  PubMed  Google Scholar 

  • Bhattacharjee, S., Garner, C. M., & Gassmann, W. (2013). New clues in the nucleus: transcriptional reprogramming in effector-triggered immunity. Frontiers in Plant Science. doi:10.3389/fpls.2013.00364.

    PubMed  PubMed Central  Google Scholar 

  • Bhuiyan, N. H., Hamada, A., Yamada, N., Rai, V., Hibino, T., & Takabe, T. (2007). Regulation of betaine synthesis by precursor supply and choline monooxygenase expression in Amaranthus Tricolor. Journal of Experimental Botany, 58(15–16), 4203–4212.

    Article  CAS  PubMed  Google Scholar 

  • Bilgin, D. D., Zavala, J. A., Zhu, J., Clough, S. J., Ort, D. R., & DeLucia, E. H. (2010). Biotic stress globally downregulates photosynthesis genes. Plant, Cell & Environment, 33(10), 1597–1613.

    Article  CAS  Google Scholar 

  • Bowen, J. K., Mesarich, C. H., Bus, V. G. M., Beresford, R. M., Plummer, K. M., & Templeton, M. D. (2011). Venturia inaequalis: the causal agent of apple scab. Molecular Plant Pathology, 12(2), 105–122.

    Article  PubMed  Google Scholar 

  • Buron-Moles, G., Wisniewski, M., Viñas, I., Teixidó, N., Usall, J., Droby, S., et al. (2015). Characterizing the proteome and oxi-proteome of apple in response to a host (Penicillium expansum) and a non-host (Penicillium digitatum) pathogen. Journal of Proteomics, 114, 136–151.

    Article  CAS  PubMed  Google Scholar 

  • Bus, V. G. M., van de Weg, W. E., Peil, A., Dunemann, F., Zini, E., Laurens, F. N. D., et al. (2012). The role of Schmidt ‘Antonovkaʼ in apple scab resistance breeding. Tree Genetics & Genomes, 8(4), 627–642.

    Article  Google Scholar 

  • Cao, S., Zhang, Q., Zhu, Z., Guo, J., Chen, Y., & Xue, H. (2008). Preliminary proteomics analysis of the total proteins of flower bud induction of apple trees. Frontiers of Agriculture in China, 2(4), 467–473.

    Article  Google Scholar 

  • Castillejo, M. A., Amiour, N., Dumas-Gaudot, E., Rubiales, D., & Jorrin, J. V. (2004). A proteomic approach to studying plant response to crenate broomrape (Orobanche crenata) in pea (Pisum sativum). Phytochemistry, 65(12), 1817–1828.

    Article  Google Scholar 

  • Caverzan, A., Passaia, G., Rosa, S. B., Ribeiro, C. W., Lazzarotto, F., & Margis-Pinheiro, M. (2012). Plant responses to stresses: role of ascorbate peroxidase in the antioxidant protection. Genetics and Molecular Biology, 35(4), 1011–1019.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cho, E. J., Yuen, C. Y. L., Kang, B. H., Ondzighi, C. A., Staehelin, L. A., & Christopher, D. A. (2011). Protein disulfide isomerase-2 of Arabidopsis mediates protein folding and localizes to both the secretory pathway and nucleus, where it interacts with maternal effect embryo arrest factor. Molecules and Cells, 32(5), 459–475.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Choudhary, M. K., Basu, D., Datta, A., Chakraborty, N., & Chakraborty, S. (2009). Dehydration-responsive nuclear proteome of rice (Oryza sativa L.) illustrates protein network, novel regulators of cellular adaptation, and evolutionary perspective. Molecular and Cellular Proteomics, 8(7), 1579–1598.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Conesa, A., Götz, S., García-Gómez, J. M., Terol, J., Talón, M., & Robles, M. (2005). Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18), 3674–3676.

    Article  CAS  PubMed  Google Scholar 

  • Constabel, C. P., & Barbehenn, R. (2008). Defensive roles of polyphenol oxidase in plants. In A. Schaller (Ed.), Induced plant resistance to herbivory (pp. 253–270). Dordrecht: Springer Netherlands.

    Chapter  Google Scholar 

  • Crosby, J. A., Janick, J., Pecknold, P. C., Korban, S. S., O’Connon, P. A., Ries, S. M., et al. (1992). Breeding apples for scab resistance: 1945–1990. Fruit Varieties Journal, 46(3), 145–166.

    Google Scholar 

  • Cross, J. V., & Templeton, D. J. (2004). Oxidative stress inhibits MEKK1 by site-specific glutathionylation in the ATP-binding domain. Biochemical Journal, 381(Pt 3), 675–683.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Deslandes, L., & Rivas, S. (2011). The plant cell nucleus: a true arena for the fight between plants and pathogens. Plant Signaling & Behavior, 6(1), 42–48.

    Article  CAS  Google Scholar 

  • Dodds, P. N., & Rathjen, J. P. (2010). Plant immunity: towards an integrated view of plant-pathogen interactions. Nature Reviews Genetics, 11(8), 539–548.

    Article  CAS  PubMed  Google Scholar 

  • Flor, H. H. (1971). Current status of the gene-for-gene concept. Annual Review of Phytopathology, 9, 275–296.

    Article  Google Scholar 

  • Gessler, C., & Pertot, I. (2012). Vf scab resistance of malus. Trees, 26(1), 95–108.

    Article  Google Scholar 

  • Gessler, C., Patocchi, A., Sansavini, S., Tartarini, S., & Gianfranceschi, L. (2006). Venturia inaequalis resistance in apple. Critical Reviews in Plant Sciences, 25(6), 473–503.

    Article  CAS  Google Scholar 

  • Gizak, A., & Dzugaj, A. (2003). FBPase is in the nuclei of cardiomyocytes. FEBS Letters, 539(1–3), 51–55.

    Article  CAS  PubMed  Google Scholar 

  • Guarino, C., Arena, S., De Simone, L., D’Ambrosio, C., Santoro, S., Rocco, M., et al. (2007). Proteomic analysis of the major soluble components in Annurca apple flesh. Molecular Nutrition & Food Research, 51(2), 255–262.

    Article  CAS  Google Scholar 

  • Haake, V., Zrenner, R., Sonnewald, U., & Stitt, M. (1998). A moderate decrease of plastid aldolase activity inhibits photosynthesis, alters the levels of sugars and starch, and inhibits growth of potato plants. Plant Journal, 14(2), 147–157.

    Article  CAS  PubMed  Google Scholar 

  • Hammond-Kosack, K. E., & Jones, J. D. G. (1997). Plant disease resistance genes. Annual Review of Plant Physiology and Plant Molecular Biology, 48, 575–607.

    Article  CAS  PubMed  Google Scholar 

  • Heath, M. C. (2003). Nonhost resistance in plants to microbial pathogens. In R. A. B. Ezekowitz & J. A. Hoffmann (Eds.), Innate immunity (pp. 47–57). New York: Humana Press.

    Google Scholar 

  • Hemmat, M., Brown, S. K., Aldwinckle, H. S., Mehlenbacher, S. A., & Weeden, N. F. (2003). Identification and mapping of markers for resistance to apple scab from ‘Antonovka’ and ‘Hansen’s baccata #2. Acta Horticulturae, 622, 153–161.

    Article  CAS  Google Scholar 

  • Hough, L. F., & Shay, J. R. (1949). Breeding for scab resistant apples. Phytopathology, 39, 10.

    Google Scholar 

  • Huber, L. A., Pfaller, K., & Vietor, I. (2003). Organelle proteomics: implications for subcellular fractionation in proteomics. Circulation Research, 92(9), 962–968.

    Article  CAS  PubMed  Google Scholar 

  • Isaacson, T., Damasceno, C. M., Saravanan, R. S., He, Y., Catalá, C., Saladié, M., et al. (2006). Sample extraction techniques for enhanced proteomic analysis of plant tissues. Nature Protocols, 1(2), 769–774.

    Article  CAS  PubMed  Google Scholar 

  • Janick, J., Cummins, J. N., Brown, S. K., & Hemmat, M. (1996). Apples. In J. Janick & J. Moore (Eds.), Fruit breeding, tree and tropical fruits (pp. 1–77). New York: Wiley.

    Google Scholar 

  • Jones, J., & Dangl, J. (2006). The plant immune system. Nature, 444(7117), 323–329.

    Article  CAS  PubMed  Google Scholar 

  • Juniper, B. E., & Mabberley, D. J. (2006). The story of the apple. Portland: Timber Press.

    Google Scholar 

  • Kim, M., Ahn, J. W., Jin, U. H., Choi, D., Paek, K. H., & Pai, H. S. (2003). Activation of the programmed cell death pathway by inhibition of proteasome function in plants. Journal of Biological Chemistry, 278(21), 19406–19415.

    Article  CAS  PubMed  Google Scholar 

  • Lateur, M., & Populer, C. (1994). Screening fruit tree genetic resources in Belgium for disease resistance and other desirable characters. Euphytica, 77(1), 147–153.

    Article  Google Scholar 

  • Libik-Konieczny, M., Surowka, E., Nosek, M., Goraj, S., & Miszalski, Z. (2012). Pathogen-induced changes in malate content and NADP-dependent malic enzyme activity in C3 or CAM performing Mesembryanthemum crystallinum L. plants. Acta Physiologiae Plantarum, 34(4), 1471–1477.

    Article  CAS  Google Scholar 

  • López, A., Ramírez, V., García-Andrade, J., Flors, V., & Vera, P. (2011). The RNA silencing enzyme RNA polymerase V is required for plant immunity. PLoS Genetics. doi:10.1371/journal.pgen.1002434.

    Google Scholar 

  • MacHardy, W. E. (1996). Apple scab: biology, epidemiology, and management. St.Paul: APS Press.

    Google Scholar 

  • Maurino, V. G., Saigo, M., Andreo, C. S., & Drincovich, M. F. (2001). Non-photosynthetic ‘malic enzyme’ from maize: a constituvely expressed enzyme that responds to plant defence inducers. Plant Molecular Biology, 45(4), 409–420.

    Article  CAS  PubMed  Google Scholar 

  • Milli, A., Cecconi, D., Bortesi, L., Persi, A., Rinalducci, S., Zamboni, A., et al. (2012). Proteomic analysis of the compatible interaction between Vitis vinifera and Plasmopara viticola. Journal of Proteomics, 75(4), 1284–1302.

    Article  CAS  PubMed  Google Scholar 

  • Morgan, J., & Richards, A. (1993). The book of apples. London: Ebury Press.

    Google Scholar 

  • Morris, A. C., & Djordjevic, M. A. (2001). Proteome analysis of cultivar-specific interactions between Rhizobium leguminosarum biovar trifolii and subterranean clover cultivar Woogenellup. Electrophoresis, 22(3), 586–598.

    Article  CAS  PubMed  Google Scholar 

  • Mysore, K. S., & Ryu, C. M. (2004). Nonhost resistance: how much do we know? Trends in Plant Science, 9(2), 97–104.

    Article  CAS  PubMed  Google Scholar 

  • Napier, R. M., Trueman, S., Henderson, J., Boyce, J. M., Hawes, C., Fricker, M. D., et al. (1995). Purification, sequencing and functions of calreticulin from maize. Journal of Experimental Botany, 46(10), 1603–1613.

    Article  CAS  Google Scholar 

  • Nice, E., & Catimel, B. (2004). Affinity-based biosensors, microarrays and proteomics. In D. Speicher (Ed.), Proteome analysis (pp. 243–275). Amsterdam: Elsevier.

    Chapter  Google Scholar 

  • Nishizawa, A., Yabuta, Y., & Shigeoka, S. (2008). Galactinol and raffinose constitute a novel function to protect plants from oxidative damage. Plant Physiology, 147(3), 1251–1263.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pikunova, A., Madduri, M., Sedov, E., Noordijk, Y., Peil, A., Troggio, M., et al. (2014). ‘Schmidt’s Antonovka’ is identical to ‘common Antonovka’, an apple cultivar widely used in Russia in breeding for biotic and abiotic stresses. Tree Genetics & Genomes, 10(2), 261–271.

    Article  Google Scholar 

  • Qiu, Y., Xi, J., Du, L., & Poovaiah, B. W. (2012). The function of calreticulin in plant immunity. Plant Signaling & Behavior, 7(8), 907–910.

    Article  CAS  Google Scholar 

  • Rivas, S. (2012). Nuclear dynamics during plant innate immunity. Plant Physiology, 158(1), 87–94.

    Article  CAS  PubMed  Google Scholar 

  • Roth, C., & Wiermer, M. (2012). Nucleoporins Nup160 and Seh1 are required for disease resistance in Arabidopsis. Plant Signaling & Behavior, 7(10), 1212–1214.

    Article  CAS  Google Scholar 

  • Sansavini, S., Donati, F., Costa, F., & Tartarini, S. (2004). Advances in apple breeding for enhanced fruit qualityand resistance to biotic stresses: new varieties for the european market. Journal of Fruit and Ornamental Plant Research, 12, 13–52.

    Google Scholar 

  • Shevchenko, A., Tomas, H., Havlis, J., Olsen, J. V., & Mann, M. (2006). In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nature Protocols, 1(6), 2856–2860.

    Article  CAS  PubMed  Google Scholar 

  • Shulaev, V., Korban, S. S., Sosinski, B., Abbott, A. G., Aldwinckle, H. S., Folta, K. M., et al. (2008). Multiple models for Rosaceae genomics. Plant Physiology, 147(3), 985–1003.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sikorskaite, S., Gelvonauskiene, D., Stanys, V., & Baniulis, D. (2012). Characterization of microsatellite loci in apple (Malus × domestica Borkh.) cultivars. Žemdirbystė = Agriculture, 99(2), 131–138.

    Google Scholar 

  • Sikorskaite, S., Rajamäki, M. L., Baniulis, D., Stanys, V., & Valkonen, J. P. T. (2013a). Protocol: optimised methodology for isolation of nuclei from leaves of species in the Solanaceae and Rosaceae families. Plant Methods. doi:10.1186/1746-4811-9-31.

    PubMed  PubMed Central  Google Scholar 

  • Sikorskaite, S., Gelvonauskienė, D., Bendokas, V., Stanys, V., & Baniulis, D. (2013b). Malus sp. - V.inaequalis interaction characteristics among local apple cultivars in Lithuania. Acta Horticulturae, 976, 567–572.

    Article  Google Scholar 

  • Smedegaard-Petersen, V., & Tolstrup, K. (1985). The limiting effect of disease resistance on yield. Annual Review of Phytopathology, 23, 475–490.

    Article  Google Scholar 

  • Sobhanian, H., Aghaei, K., & Komatsu, S. (2011). Changes in the plant proteome resulting from salt stress: toward the creation of salt-tolerant crops? Journal of Proteomics, 74(8), 1323–1337.

    Article  CAS  PubMed  Google Scholar 

  • Supek, F., Bošnjak, M., Škunca, N., & Šmuc, T. (2011). REVIGO summarizes and visualizes long lists of gene ontology terms. PloS One. doi:10.1371/journal.pone.0021800.

    PubMed  PubMed Central  Google Scholar 

  • Suty, L., Lequeu, J., Lançon, A., Etienne, P., Petitot, A. S., & Blein, J. P. (2003). Preferential induction of 20S proteasome subunits during elicitation of plant defense reactions: towards the characterization of “plant defense proteasomes”. The International Journal of Biochemistry & Cell Biology, 35(5), 637–650.

    Article  CAS  Google Scholar 

  • Thordal-Christensen, H. (2003). Fresh insights into processes of nonhost resistance. Current Opinion in Plant Biology, 6(4), 351–357.

    Article  CAS  PubMed  Google Scholar 

  • Tuinyla, V., Lukoševičius, A., & Bandaravičius, A. (1990). Lietuvos pomologija. obelys ir kriaušės. Vilnius: Mokslas.

    Google Scholar 

  • Velasco, R., Zharkikh, A., Affourtit, J., Dhingra, A., Cestaro, A., Kalyanaraman, A., et al. (2010). The genome of the domesticated apple (Malus × domestica Borkh.). Nature Genetics, 42(10), 833–839.

    Article  CAS  PubMed  Google Scholar 

  • Vickers, C. E., Possell, M., Cojocariu, C. I., Velikova, V. B., Laothawornkitkul, J., Ryan, A., et al. (2009). Isoprene synthesis protects transgenic tobacco plants from oxidative stress. Plant, Cell & Environment, 32(5), 520–531.

    Article  CAS  Google Scholar 

  • Voulgaris, I., O’Donnell, A., Harvey, L. M., & McNeil, B. (2012). Inactivating alternative NADH dehydrogenases: enhancing fungal bioprocesses by improving growth and biomass yield? Scientific Reports. doi:10.1038/srep00322.

    PubMed  PubMed Central  Google Scholar 

  • Wang, W., Vinocur, B., Shoseyov, O., & Altman, A. (2004). Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. Trends in Plant Science, 9(5), 244–252.

    Article  CAS  PubMed  Google Scholar 

  • Winterberg, B., Du Fall, L. A., Song, X., Pascovici, D., Care, N., Molloy, M., et al. (2014). The necrotrophic effector protein SnTox3 re-programs metabolism and elicits a strong defence response in susceptible wheat leaves. BMC Plant Biology. doi:10.1186/s12870-014-0215-5.

    PubMed  PubMed Central  Google Scholar 

  • Wojtaszek, P. (1997). Oxidative burst: an early plant response to pathogen infection. Biochemical Journal, 322(Pt 3), 681–692.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu, J., Audenaert, K., Hofte, M., & De Vleesschauwer, D. (2013). Abscisic acid promotes susceptibility to the rice leaf blight pathogen Xanthomonas oryzae pv oryzae by suppressing salicylic acid-mediated defenses. PloS One. doi:10.1371/annotation/659105c2-8364-4cc7-94e7-66620370637a.

    Google Scholar 

  • Yazaki, K. (2006). ABC transporters involved in the transport of plant secondary metabolites. FEBS Letters, 580(4), 1183–1191.

    Article  CAS  PubMed  Google Scholar 

  • Zemach, A., & Grafi, G. (2007). Methyl-CpG-binding domain proteins in plants: interpreters of DNA methylation. Trends in Plant Science, 12(2), 80–85.

    Article  CAS  PubMed  Google Scholar 

  • Zhang, C. X., Tian, Y., & Cong, P. H. (2015). Proteome analysis of pathogen-responsive proteins from apple leaves induced by the Alternaria blotch Alternaria alternata. PloS One. doi:10.1371/journal.pone.0122233.

    Google Scholar 

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Acknowledgments

The research was part of the Lithuanian Research Centre for Agriculture and Forestry (LAMMC) long-term program „Genetics and purposeful change of genotypes of agricultural and forest plants“. The authors thank Dr. Danas Baniulis for help in analysing mass spectrometry data and his kind support.

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  1. Insitute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas st. 30, Babtai, Kaunas distr, Lithuania

    Sidona Sikorskaite-Gudziuniene, Perttu Haimi, Dalia Gelvonauskiene & Vidmantas Stanys

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  1. Sidona Sikorskaite-Gudziuniene
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Electronic supplementary material

Supplementary Fig. 1

Four biological replicate gels of nuclear proteins labeled with Cy3 or Cy5 of each apple genotype. (PDF 301 kb)

Supplementary Table

List of apple scab responsive apple nuclear proteins identified by MS/MS analysis. (PDF 363 kb)

Supplementary Fig. 3

The scatterplot view of GO terms in the biological process ontology drawn by REVIGO. The scatterplot indicates the cluster representatives in a two-dimensional space derived by applying multidimensional scaling to a matrix of the GO terms’ semantic similarities. The cluster representatives are shown in distinct colour and other cluster members in dimmed colour. Bubble colour indicates provided p-value. Bubble radius indicates the generality of GO terms, where bigger bubbles imply more general terms. Scale on the right – the mean of log10 p value. (GIF 58 kb)

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Sikorskaite-Gudziuniene, S., Haimi, P., Gelvonauskiene, D. et al. Nuclear proteome analysis of apple cultivar ‘Antonovka’ accessions in response to apple scab (Venturia inaequalis). Eur J Plant Pathol 148, 771–784 (2017). https://doi.org/10.1007/s10658-016-1131-3

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