Proteogenomic analysis of the Venturia pirina (pear scab fungus) secretome reveals potential effectors

Cooke, Ira R, Jones, Dan, Bowen, Joanna K, Deng, Cecilia, Faou, Pierre, Hall, Nathan E, Jayachandran, Vignesh, Liem, Michael, Taranto, Adam P, Plummer, Kim M, and Mathivanan, Suresh (2014) Proteogenomic analysis of the Venturia pirina (pear scab fungus) secretome reveals potential effectors. Journal of Proteome Research, 13 (8). pp. 3635-3644.

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Abstract

A proteogenomic analysis is presented for Venturia pirina, a fungus that causes scab disease on European pear (Pyrus communis). V. pirina is host-specific, and the infection is thought to be mediated by secreted effector proteins. Currently, only 36 V. pirina proteins are catalogued in GenBank, and the genome sequence is not publicly available. To identify putative effectors, V. pirina was grown in vitro on and in cellophane sheets mimicking its growth in infected leaves. Secreted extracts were analyzed by tandem mass spectrometry, and the data (ProteomeXchange identifier PXD000710) was queried against a protein database generated by combining in silico predicted transcripts with six frame translations of a whole genome sequence of V. pirina (GenBank Accession JEMP00000000). We identified 1088 distinct V. pirina protein groups (FDR 1%) including 1085 detected for the first time. Thirty novel (not in silico predicted) proteins were found, of which 14 were identified as potential effectors based on characteristic features of fungal effector protein sequences. We also used evidence from semitryptic peptides at the protein N-terminus to corroborate in silico signal peptide predictions for 22 proteins, including several potential effectors. The analysis highlights the utility of proteogenomics in the study of secreted effectors.

Item ID: 43954
Item Type: Article (Research - C1)
ISSN: 1535-3907
Keywords: ave1; proteogenomics; secreted effectors; Venturia pirina
Funders: Australian Research Council (ARC), La Trobe, VLSCI’s Life Sciences Computation Centre, Plant Biosecurity Cooperative Research Centre
Projects and Grants: Australian NH&MRC fellowship (1016599), ARC DP130100535
Date Deposited: 23 Jun 2016 05:05
FoR Codes: 06 BIOLOGICAL SCIENCES > 0607 Plant Biology > 060704 Plant Pathology @ 50%
06 BIOLOGICAL SCIENCES > 0601 Biochemistry and Cell Biology > 060102 Bioinformatics @ 50%
SEO Codes: 82 PLANT PRODUCTION AND PLANT PRIMARY PRODUCTS > 8202 Horticultural Crops > 820210 Pome Fruit, Pip Fruit @ 100%
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