1. Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case study
- Author
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Huan Tao, Xinhai Chen, Shoukai Lin, Shufu Que, Qi Song, Huaqin He, Kuan Li, Yong-Fei Wang, and Jian Huang
- Subjects
endocrine system ,Identification ,Gene regulatory network ,Biology ,Proteomics ,Genome ,Genome wide ,User-Computer Interface ,Stress, Physiological ,Heat shock protein ,Databases, Genetic ,Genetics ,Gene Regulatory Networks ,HSP70 Heat-Shock Proteins ,Protein Interaction Maps ,Oligonucleotide Array Sequence Analysis ,Plant Proteins ,Internet ,Oryza sativa ,Binding Sites ,Heat shock proteins ,Rice (Oryza sativa L.) ,food and beverages ,Oryza ,Seedlings ,DNA microarray ,CLPB ,Transcriptome ,Function (biology) ,Genome, Plant ,Biotechnology ,Research Article ,Signal Transduction - Abstract
Background Heat 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. Results In 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. Conclusions Twenty-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/.
- Published
- 2014