However, signal peptides, pro-domains and the rapid evolution of effectors pose challenges ( Fig. In principle, a plant-trained classifier should work on both host and pathogen, as effectors might exploit the plant machinery to enter organelles. However, experimental methods are labour-intensive, prone to artefacts, and not appropriate for high-throughput screening of the large effector repertoires predicted in fungi and oomycetes. Determining effector subcellular localization in plant cells can provide important clues about their virulence function. Recently, several rust effector candidates were shown to mimic transit peptides to translocate into chloroplasts 12. Whilst there are many bacterial effectors targeting specific compartments, the extent to which eukaryotic effectors enter plant organelles is less understood 5, 6, 7, 8, 9, 10, 11. Transit peptides rarely share sequence conservation and vary in length 1, 3.Įukaryotic filamentous plant pathogens deliver cytoplasmic effectors into host tissues to subvert plant functions to their advantage 4. Plant proteins are translocated from the cytosol into specific organelles by means of N-terminal transit peptides in the case of chloroplasts and mitochondria 1, 2, or nuclear localization signals (NLSs) in the case of nuclei. Plant cells feature subcellular compartments such as mitochondria or chloroplasts which contain distinct suites of proteins related to their specialised biological functions. LOCALIZER is the first method for predicting effector localisation in plants and is a valuable tool for prioritizing effector candidates for functional investigations. Secretome-wide predictions and confocal microscopy reveal that rust fungi might have evolved multiple effectors that target chloroplasts or nuclei. For 107 eukaryotic effectors, LOCALIZER outperforms other methods and predicts a previously unrecognized chloroplast transit peptide for the ToxA effector, which we show translocates into tobacco chloroplasts. LOCALIZER shows greater prediction accuracy for chloroplast and mitochondrial targeting compared to other methods for 652 plant proteins. ![]() We introduce LOCALIZER for predicting plant and effector protein localization to chloroplasts, mitochondria, and nuclei. Although many computational methods exist to predict plant protein subcellular localization, they perform poorly for effectors. Some effectors have been found to enter subcellular compartments by mimicking host targeting sequences. Pathogens secrete effector proteins and many operate inside plant cells to enable infection.
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