PT - JOURNAL ARTICLE AU - Jana Sperschneider AU - Ann-Maree Catanzariti AU - Kathleen DeBoer AU - Benjamin Petre AU - Donald M. Gardiner AU - Karam B Singh AU - Peter N. Dodds AU - Jennifer M. Taylor TI - LOCALIZER: subcellular localization prediction of both plant and effector proteins in the plant cell AID - 10.1101/092726 DP - 2016 Jan 01 TA - bioRxiv PG - 092726 4099 - http://biorxiv.org/content/early/2016/12/09/092726.short 4100 - http://biorxiv.org/content/early/2016/12/09/092726.full AB - Pathogens are able to deliver effector proteins into plant cells to enable infection. Some effectors have been found to enter subcellular compartments by mimicking host targeting sequences. Although many computational methods exist to predict plant protein subcellular localization, they perform poorly for effectors. We introduce LOCALIZER for predicting plant and effector protein localization to chloroplasts, mitochondria, and nuclei. LOCALIZER shows greater prediction accuracy for chloroplast and mitochondrial targeting compared to other methods for 652 plant proteins. For 108 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. Secretome-wide predictions and confocal microscopy reveal that rust fungi might have evolved multiple effectors that target chloroplasts or nuclei. LOCALIZER is the first method for predicting effector localisation in plants and is a valuable tool for prioritizing effector candidates for functional investigations. LOCALIZER is available at http://localizer.csiro.au/.