Dataset Information

New insights into the subcellular localization of Tubby-like proteins and their participation in the Arabidopsis-Piriformospora indica interaction.

ABSTRACT: Tubby-like proteins (TLPs) have been associated with hormone signaling and responses to abiotic and biotic stress in plants. Recently, Arabidopsis thaliana TLP3 was found to translocate from the plasma membrane of cells in response to distinct abiotic stresses, thereby activating cellular signaling. In addition, several AtTLPs were demonstrated to be necessary for normal colonization of roots by the mutualistic fungus Piriformospora indica. Here, we present evidence for the involvement of another two AtTLPs in this interaction. Furthermore, we show that plasma membrane targeting of TLPs might be conserved in other plant species, although we did not find it for all members of the protein family. Finally, the position of a GFP-tag influences the localization of AtTLP3, which needs to be considered when working with TLPs.

SUBMITTER: Reitz MU

PROVIDER: S-EPMC3999060 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature

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New insights into the subcellular localization of Tubby-like proteins and their participation in the Arabidopsis-Piriformospora indica interaction.

Reitz Marco U MU Pai Subhash S Imani Jafargholi J Schäfer Patrick P

Plant signaling & behavior 20130626 8

Tubby-like proteins (TLPs) have been associated with hormone signaling and responses to abiotic and biotic stress in plants. Recently, Arabidopsis thaliana TLP3 was found to translocate from the plasma membrane of cells in response to distinct abiotic stresses, thereby activating cellular signaling. In addition, several AtTLPs were demonstrated to be necessary for normal colonization of roots by the mutualistic fungus Piriformospora indica. Here, we present evidence for the involvement of anothe ...[more]

PMID: 23733076

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Project description:Despite the growing volume of experimentally validated knowledge about the subcellular localization of plant proteins, a well performing in silico prediction tool is still a necessity. Existing tools, which employ information derived from protein sequence alone, offer limited accuracy and/or rely on full sequence availability. We explored whether gene expression profiling data can be harnessed to enhance prediction performance. To achieve this, we trained several support vector machines to predict the subcellular localization of Arabidopsis thaliana proteins using sequence derived information, expression behavior, or a combination of these data and compared their predictive performance through a cross-validation test. We show that gene expression carries information about the subcellular localization not available in sequence information, yielding dramatic benefits for plastid localization prediction, and some notable improvements for other compartments such as the mitochondrion, the Golgi, and the plasma membrane. Based on these results, we constructed a novel subcellular localization prediction engine, SLocX, combining gene expression profiling data with protein sequence-based information. We then validated the results of this engine using an independent test set of annotated proteins and a transient expression of GFP fusion proteins. Here, we present the prediction framework and a website of predicted localizations for Arabidopsis. The relatively good accuracy of our prediction engine, even in cases where only partial protein sequence is available (e.g., in sequences lacking the N-terminal region), offers a promising opportunity for similar application to non-sequenced or poorly annotated plant species. Although the prediction scope of our method is currently limited by the availability of expression information on the ATH1 array, we believe that the advances in measuring gene expression technology will make our method applicable for all Arabidopsis proteins.

Dataset Information

New insights into the subcellular localization of Tubby-like proteins and their participation in the Arabidopsis-Piriformospora indica interaction.

Publications

New insights into the subcellular localization of Tubby-like proteins and their participation in the Arabidopsis-Piriformospora indica interaction.

Similar Datasets

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