Proteogenomics and in silico structural and functional annotation of the barley powdery mildew Blumeria graminis f. sp. hordei |
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Authors: | Bindschedler Laurence V McGuffin Liam J Burgis Timothy A Spanu Pietro D Cramer Rainer |
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Affiliation: | aDepartment of Chemistry, University of Reading, P.O. Box 221, Reading RG6 6AS, United Kingdom;bSchool of Biological Sciences, University of Reading, P.O. Box 221, Reading RG6 6AS, United Kingdom;cCentre for Bioinformatics, Imperial College, Woltson Building, South Kensington Campus, London SW7 2AZ, United Kingdom;dDepartment of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom;eThe BioCentre, University of Reading, P.O. Box 221, Reading RG6 6AS, United Kingdom |
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Abstract: | Blumeria graminis is an economically important obligate plant-pathogenic fungus, whose entire genome was recently sequenced and manually annotated using ab initio in silico predictions (Spanu et al. 2010, Science 330, 1543-1546). Employing large scale proteogenomic analysis we are now able to verify independently the existence of proteins predicted by ∼24% of open reading frame models. We compared the haustoria and sporulating hyphae proteomes and identified 71 proteins exclusively in haustoria, the feeding and effector-delivery organs of the pathogen. These proteins are significantly smaller than the rest of the protein pool and predicted to be secreted. Most do not share any similarities with Swiss–Prot or Trembl entries nor possess any identifiable Pfam domains. We used a novel automated prediction pipeline to model the 3D structures of the proteins, identify putative ligand binding sites and predict regions of intrinsic disorder. This revealed that the protein set found exclusively in haustoria is significantly less disordered than the rest of the identified Blumeria proteins or random (and representative) protein sets generated from the yeast proteome. For most of the haustorial proteins with unknown functions no good templates could be found, from which to generate high quality models. Thus, these unknown proteins present potentially new protein folds that can be specific to the interaction of the pathogen with its host. |
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Keywords: | Abbreviations: A:B, acrylamide:bis-acrylamide ratio CASP, Critical Assessment of Techniques for Protein Structure EH, Epidermis containing haustoria FDR, False discovery rate HY, sporulating hyphae MS, mass spectrometry nESI, nanoelectrospray ionisation nLC, nanoliquid chromatography ORF, open reading frame RP, reverse phase |
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