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LOCALIZER: subcellular localization prediction of both plant and effector proteins in the plant cell

Sperschneider, Jana; Catanzariti, Ann-Maree; DeBoer, D.; DeBoer, Kathleen; Petre, Benjamin; Gardiner, Donald M; Singh, Karam B; Dodds, Peter N; Taylor, Jennifer

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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 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...[Show more]

dc.contributor.authorSperschneider, Jana
dc.contributor.authorCatanzariti, Ann-Maree
dc.contributor.authorDeBoer, D.
dc.contributor.authorDeBoer, Kathleen
dc.contributor.authorPetre, Benjamin
dc.contributor.authorGardiner, Donald M
dc.contributor.authorSingh, Karam B
dc.contributor.authorDodds, Peter N
dc.contributor.authorTaylor, Jennifer
dc.date.accessioned2021-08-02T04:12:22Z
dc.date.available2021-08-02T04:12:22Z
dc.identifier.issn2045-2322
dc.identifier.urihttp://hdl.handle.net/1885/242586
dc.description.abstractPathogens 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 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 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. 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/.
dc.description.sponsorshipJS is supported by an OCE Postdoctoral Fellowship.
dc.format.mimetypeapplication/pdf
dc.language.isoen_AU
dc.publisherNature Publishing Group
dc.rights© The Author(s) 2017
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.sourceScientific Reports
dc.titleLOCALIZER: subcellular localization prediction of both plant and effector proteins in the plant cell
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume7
dc.date.issued2017
local.identifier.absfor060704 - Plant Pathology
local.identifier.absfor060108 - Protein Trafficking
local.identifier.absfor060102 - Bioinformatics
local.identifier.ariespublicationa383154xPUB5570
local.publisher.urlhttp://www.nature.com/srep/index.html
local.type.statusPublished Version
local.contributor.affiliationSperschneider, Jana , Commonwealth Scientific and Industrial Research Organization
local.contributor.affiliationCatanzariti, Ann-Maree, College of Science, ANU
local.contributor.affiliationDeBoer, D., University of California (Berkeley)
local.contributor.affiliationDeBoer, Kathleen, Monash University
local.contributor.affiliationPetre, Benjamin, The Sainsbury Laboratory
local.contributor.affiliationGardiner, Donald M , Commonwealth Scientific and Industrial Research Organization
local.contributor.affiliationSingh, Karam B , CSIRO
local.contributor.affiliationDodds, Peter N, CSIRO
local.contributor.affiliationTaylor, Jennifer, CSIRO
local.bibliographicCitation.issue44598
local.bibliographicCitation.startpage1
local.bibliographicCitation.lastpage14
local.identifier.doi10.1038/srep44598
local.identifier.absseo970106 - Expanding Knowledge in the Biological Sciences
dc.date.updated2020-11-23T10:46:01Z
local.identifier.scopusID2-s2.0-85015371305
local.identifier.thomsonID000396543100002
dcterms.accessRightsOpen Access
dc.provenanceThis work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
dc.rights.licenseCreative Commons Attribution 4.0 International License
CollectionsANU Research Publications

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