Proteogenomic Analysis of the Venturia pirina (Pear Scab Fungus) Secretome Reveals Potential Effectors

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.