ApoplastP: Prediction of effectors and plant proteins in the apoplast using machine learning
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© 2017 New Phytologist Trust. The plant apoplast is integral to intercellular signalling, transport and plant-pathogen interactions. Plant pathogens deliver effectors both into the apoplast and inside host cells, but no computational method currently exists to discriminate between these localizations. We present ApoplastP, the first method for predicting whether an effector or plant protein localizes to the apoplast. ApoplastP uncovers features of apoplastic localization common to both effectors and plant proteins, namely depletion in glutamic acid, acidic amino acids and charged amino acids and enrichment in small amino acids. ApoplastP predicts apoplastic localization in effectors with a sensitivity of 75% and a false positive rate of 5%, improving the accuracy of cysteine-rich classifiers by > 13%. ApoplastP does not depend on the presence of a signal peptide and correctly predicts the localization of unconventionally secreted proteins. The secretomes of fungal saprophytes as well as necrotrophic, hemibiotrophic and extracellular fungal pathogens are enriched for predicted apoplastic proteins. Rust pathogens have low proportions of predicted apoplastic proteins, but these are highly enriched for predicted effectors. ApoplastP pioneers apoplastic localization prediction using machine learning. It will facilitate functional studies and will be valuable for predicting if an effector localizes to the apoplast or if it enters plant cells.
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Sperschneider, J.; Dodds, P.; Singh, Karam; Taylor, J. (2017)© 2017 New Phytologist Trust. The plant apoplast is integral to intercellular signalling, transport and plant-pathogen interactions. Plant pathogens deliver effectors both into the apoplast and inside host cells, but no ...
LOCALIZER: Subcellular localization prediction of both plant and effector proteins in the plant cellSperschneider, J.; Catanzariti, A.; Deboer, K.; Petre, B.; Gardiner, D.; Singh, Karam; Dodds, P.; Taylor, J. (2017)Pathogens secrete effector proteins and many operate inside plant cells to enable infection. Some effectors have been found to enter subcellular compartments by mimicking host targeting sequences. Although many computational ...
Evaluation of secretion prediction highlights differing approaches needed for oomycete and fungal effectorsSperschneider, J.; Williams, A.; Hane, James; Singh, K.; Taylor, J. (2015)© 2015 Sperschneider, Williams, Hane, Singh and Taylor. The steadily increasing number of sequenced fungal and oomycete genomes has enabled detailed studies of how these eukaryotic microbes infect plants and cause devastating ...