Abstract
Recent work has clearly shown the capacity of proteomics-based methodologies to establish the roles played by specific proteins in different biological processes. Beyond the study of genes, it has been established that proteins are the relevant set to be analyzed in research aiming to solve specific biological questions. Proteomics approaches can be categorized according to three different methodologies; gel-based, mainly two-dimension gel electrophoresis (2-DE); gel free, based on liquid chromatography-mass spectrometry (LC-MS); and quantitative proteomics, by isobaric markers. Most of these methodologies have been applied to studies of the proteome of Botrytis cinerea. Since the publication of the first proteomics report on Botrytis, technological advances have accelerated the identification of global protein content. Clearly, the publication of the B. cinerea genome has been of tremendous value to the proteomics research community; this has supported the accurate identification, through MS, of this fungus’ peptides. This landmark event has greatly facilitated the development of proteomics studies exploring the biology of the fungus; to date, mainly mycelium samples have been used. Only a few reports have aimed at the study of fractions of the total proteome, and all of these are focused on the secretome. The role of several particular proteins related to fungal pathogenicity, metabolism, biology, etc. has been elucidated, but the number of Botrytis proteins found, as a proportion of the total proteins predicted from the genome, remains below 10 %. There is much work to be done.
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References
Alderete JF, Millsap KW, Lehker MW et al (2001) Enzymes on microbial pathogens and Trichomonas vaginalis: molecular mimicry and functional diversity. Cell Microbiol 3(6):359–370
Amselem J, Cuomo CA, Van Kan JA, et al (2011) Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet 7:e1002230
Beroza P, Villar HO, Wick MM et al (2002) Chemoproteomics as a basis for post-genomic drug discovery. Drug Discov Today 7(15):807–814
Brower V (2001) Proteomics: biology in the post-genomic era. EMBO Rep 2(7):558–560
Chen X, Fang Y, Yao L et al (2007) Does drug-target have a likeness? Methods Inf Med 46(3):360–363
Cherrad S, Girard V, Dieryckx C et al (2012) Proteomic analysis of proteins secreted by Botrytis cinerea in response to heavy metal toxicity. Metallomics 4(8):835–846
Cilindre C, Jegou S, Hovasse A et al (2008) Proteomics approach to identify champagne wine proteins as modified by Botrytis cinerea infection. J Proteome Res 7(3):1199–1208
Dass C (2000) Principles and practice of biological mass spectrometry, Wiley-Interscience series on mass spectrometry. Wiley, New York, 448 p
Davanture M, Dumur J, Bataillé-Simoneau N et al (2014) Phosphoproteome profiles of the phytopathogenic fungi Alternaria brassicicola and Botrytis cinerea during exponential growth in axenic cultures. Proteomics 14(13–14):1639–1645
Dujon B (1996) The yeast genome project: what did we learn? Trends Genet 12:263–270
Durán-Patrón R, Cantoral JM, Hernández-Galán R et al (2004) The biodegradation of the phytotoxic metabolite botrydial by its parent organism, Botrytis cinerea. J Chem Res 2004(6):441–443
Espino JJ, Gutiérrez-Sánchez G, Brito N et al (2010) The Botrytis cinerea early secretome. Proteomics 10(16):3020–3034
Fenn JB, Mann M, Meng CK et al (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246:64–71
Fernandez-Acero FJ, Jorge I, Calvo E et al (2006) Two-dimensional electrophoresis protein profile of the phytopathogenic fungus Botrytis cinerea. Proteomics 6:S88–S96
Fernandez-Acero FJ, Carbu M, Garrido C et al (2007a) Proteomic advances in phytopathogenic fungi. Curr Proteome 4:79–88
Fernandez-Acero FJ, Jorge I, Calvo E et al (2007b) Proteomic analysis of phytopathogenic fungus Botrytis cinerea as a potentia tool for identifying pathogenicity factors, therapeutic targets and for basic research. Arch Microbiol 187:207–215
Fernandez-Acero FJ, Colby T, Harzen A et al (2009) Proteomic analysis of the phytopathogenic fungus Botrytis cinerea during cellulose degradation. Proteomics 9:2892–2902
Fernández-Acero FJ, Colby T, Harzen A et al (2010) 2-DE proteomic approach to the Botrytis cinerea secretome induced with different carbon sources and plant-based elicitors. Proteomics 10(12):2270–2280
Fernández-Acero FJ, Carbú M, El-Akhal MR et al (2011) Development of proteomics-based fungicides: new strategies for environmentally friendly control of fungal plant diseases. Int J Mol Sci 12(1):795–816. doi:10.3390/ijms12010795
Frías M, González C, Brito N (2011) BcSpl1, a cerato-platanin family protein, contributes to Botrytis cinerea virulence and elicits the hypersensitive response in the host. New Phytol 192(2):483–495
Garrido C, Cantoral JM, Carbú M et al (2011) New proteomic approaches to plant pathogenic fungi. Curr Proteomics 2011(4):306–315
González Fernández R, Prats E, Jorrin J (2010) Proteomics of plant pathogenic fungi. J Biomed Biotechnol 2010:1–36. doi:10.1155/2010/932527
Gonzalez-Fernandez R, Aloria K, Arizmendi JM et al (2013) Application of label-free shotgun nUPLC-MSE and 2-DE approaches in the study of Botrytis cinerea mycelium. J Proteome Res 12(6):3042–3056
Gonzalez-Fernandez R, Aloria K, Valero-Galvan J et al (2014) Proteomic analysis of mycelium and secretome of different Botrytis cinerea wild-type strains. J Proteome 97:195–221
Hack CJ (2004) Integrated transcriptome and proteome data: the challenges ahead. Brief Funct Genomic Proteomic 3(3):212–219. doi:10.1093/bfgp/3.3.212
Haider S, Pal R (2013) Integrated analysis of transcriptomic and proteomic data. Curr Genomics 14(2):91–110. doi:10.2174/1389202911314020003
Hernández R, Nombela C, Diez-Orejas R et al (2004) Two-dimensional reference map of Candida albicans hyphal forms. Proteomics 4:374–382
Hillenkamp F, Karas M, Beavis RC et al (1991) Matrix-associated laser desorption/ionization mass spectrometry of biopolymers. Anal Chem 63:A1193–A1202
Huan X, HangYang X, MingZhi L et al (2007) Learning the drug target-likeness of a protein. Proteomics 7(23):4255–4263
James P (1997) Protein identification in the post-genome era: the rapid rise of proteomics. Q Rev Biophys 30(4):279–331
Kim Y, Nandakumar MP, Marten MR (2007) Proteomics of filamentous fungi. Tren Biotechnol 25(9):395–400
Li B, Wang W, Zong Y et al (2012) Exploring pathogenic mechanisms of Botrytis cinerea secretome under different ambient pH based on comparative proteomic analysis. J Proteome Res 11(8):4249–4260
Lyon GD, Goodman BA, Williamson B (2004) Botrytis cinerea perturbs redox processes as an attack strategy in plants. In: Elad Y, Williamson B, Tudzynski P, Delen N (eds) Botrytis: biology, pathology and control. Kluwer Academic Publishers: Dordrecht, The Netherlands
Manteau S, Abouna S, Lambert B et al (2003) Differential regulation by ambient pH of putative virulence factor secretion by the phytopathogenic fungus Botrytis cinerea. FEMS Microbiol Ecol 43(3):359–366
Marx V (2013) Targeted proteomics. Nat Methods 10:19–22
Minguez P, Parca L, Diella F et al (2012) Deciphering a global network of functionally associated post-translational modifications. Mol Syst Biol 8:1–14
Mulema JMK, Okori P, Denby KJ (2011) Proteomic analysis of the Arabidopsis thaliana-Botrytis cinerea interaction using two-dimensional liquid chromatography. Afr J Biotechnol 10(76):17551–17563
Rossignol T, Kobi D, Jacquet-Gutfreund L et al (2009) The proteome of a wine yeast strain during fermentation, correlation with the transcriptome. J Appl Microbiol 107(1):47–55
Shah P, Atwood JA III, Orlando R et al (2009a) Comparative proteomic analysis of Botrytis cinerea secretome. J Proteome Res 8(3):1123–1130
Shah P, Gutierrez-Sanchez G, Orlando R, Bergmann C (2009b) A proteomic study of pectin-degrading enzymes secreted by Botrytis cinerea grown in liquid culture. Proteomics 9(11):3126–3135
Shah P, Powell ALT, Orlando R et al (2012) Proteomic analysis of ripening tomato fruit infected by Botrytis cinerea. J Proteome Res 11(4):2178–2192
Staats M, van Kan JA (2013) Genome update of Botrytis cinerea strains B05.10 and T4. Eukaryot Cell 11(11):1413–1414. doi:10.1128/EC.00164-12
Staats M, van Kan JA (2013) Genome update of Botrytis cinerea strains B05.10 and T4. Eukaryot Cell. 2012 Nov;11(11):1413–4. doi: 10.1128/EC.00164-12.
ten Have A, Espino JJ, Dekkers E et al (2010) The Botrytis cinerea aspartic proteinase family. Fungal Genet Biol 47(1):53–65
Tietjen K, Schreier PH (2013) New targets for fungicides. In: Modern methods in crop protection research. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, pp 197–216
Tudzynski P, Kokkelink L (2009) Botrytis cinerea: molecular aspects of a necrotrophic life style. In: Deising HB (ed) The mycota. Springer, Berlin, pp 29–50
Van Sluyter SC, Warnock NI, Schmidt S et al (2013) Aspartic acid protease from Botrytis cinerea removes haze-forming proteins during white winemaking. J Agric Food Chem 61(40):9705–9711
Wilkins MR, Sanchez JC, Gooley AA et al (1995) Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev 13:19–50
Acknowledgements
The authors gratefully acknowledge funding from the Spanish Government DGICYT – AGL2012-39798-C02-02 (www.micinn.es/portal/site/MICINN/). Eva Liñeiro was supported by a FPI grant from the University of Cadiz (2010-152). Special thanks are given to Celedonio Gonzalez (University of La Laguna) and Fiona McCarthy (PI of Agbase) for their guidance, support and patience in unravelling bioinformatics data.
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Liñeiro, E., Cantoral, J.M., Fernández-Acero, F.J. (2016). Contribution of Proteomics Research to Understanding Botrytis Biology and Pathogenicity. In: Fillinger, S., Elad, Y. (eds) Botrytis – the Fungus, the Pathogen and its Management in Agricultural Systems. Springer, Cham. https://doi.org/10.1007/978-3-319-23371-0_16
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