Abstract
BackgroundHeat shock proteins (Hsps) perform a fundamental role in protecting plants against abiotic stresses. Although researchers have made great efforts on the functional analysis of individual family members, Hsps have not been fully characterized in rice (Oryza sativa L.) and little is known about their interactors.ResultsIn this study, we combined orthology-based approach with expression association data to screen rice Hsps for the expression patterns of which strongly correlated with that of heat responsive probe-sets. Twenty-seven Hsp candidates were identified, including 12 small Hsps, six Hsp70s, three Hsp60s, three Hsp90s, and three clpB/Hsp100s. Then, using a combination of interolog and expression profile-based methods, we inferred 430 interactors of Hsp70s in rice, and validated the interactions by co-localization and function-based methods. Subsequent analysis showed 13 interacting domains and 28 target motifs were over-represented in Hsp70s interactors. Twenty-four GO terms of biological processes and five GO terms of molecular functions were enriched in the positive interactors, whose expression levels were positively associated with Hsp70s. Hsp70s interaction network implied that Hsp70s were involved in macromolecular translocation, carbohydrate metabolism, innate immunity, photosystem II repair and regulation of kinase activities.ConclusionsTwenty-seven Hsps in rice were identified and 430 interactors of Hsp70s were inferred and validated, then the interacting network of Hsp70s was induced and the function of Hsp70s was analyzed. Furthermore, two databases named Rice Heat Shock Proteins (RiceHsps) and Rice Gene Expression Profile (RGEP), and one online tool named Protein-Protein Interaction Predictor (PPIP), were constructed and could be accessed at http://bioinformatics.fafu.edu.cn/.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-344) contains supplementary material, which is available to authorized users.
Highlights
Heat shock proteins (Hsps) perform a fundamental role in protecting plants against abiotic stresses
Gene expression in rice subjected to abiotic stresses Four sets of gene expression data from rice seedlings exposed to drought, salt, cold and heat treatment were collected (Table 1) from the Gene Expression Omnibus (GEO) [30]
We found that the absolute Pearson Correlation Coefficients (PCC) of 1,072 protein-protein interactions (PPIs) related to Hsp70s, including 430 interactors, were greater than 0.90
Summary
Heat shock proteins (Hsps) perform a fundamental role in protecting plants against abiotic stresses. Researchers have made great efforts on the functional analysis of individual family members, Hsps have not been fully characterized in rice (Oryza sativa L.) and little is known about their interactors. Heat shock proteins (Hsps) are stimulated in response to a wide array of stress conditions and perform a fundamental role in protecting plants against abiotic stresses [1,2]. Researchers have made great efforts on the functional analysis of individual Hsp family members in rice [11,12,13,14], Hsps still have not been fully characterized and little is known about their interactors [14]
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