Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case study

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.

Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica

“…Correspondingly, several genes encoding HSPs, such as OsHSP80.2 and OsHSP40 , had indica ‐specific PACs and were highly expressed in indica (Table S3). Heat shock proteins act as molecular chaperones in protein folding and perform a fundamental role in protecting plants against heat or drought stresses (Von Koskulldoring et al ., ; Wang et al ., ). Thus, the enhancement of HSPs may contribute to the relatively high level of heat tolerance in indica (Wang and Li, ).…”

OsASR5 enhances drought tolerance through a stomatal closure pathway associated with ABA and H2O2 signalling in rice

“…HSPs are stimulated in response to abiotic stress and play an important role in protecting plants against many stresses (Alvim et al, 2001;Cho and Hong, 2006;Sato and Yokoya, 2008;Timperio et al, 2008;Wang et al, 2014). A 2OG-Fe (II) oxygenase family protein in rice affects water transport in leaves by affecting the composition and structure of leaf secondary cell walls (Fang et al, 2012).…”

The Genome of Dendrobium officinale Illuminates the Biology of the Important Traditional Chinese Orchid Herb

“…tomato (Simon et al, 2014). Besides, several unique gene families in D. officinale were also identified relating to defense responses to pathogen infections: the mannose-specific lectin gene family, which belongs to a single superfamily of evolutionarily related proteins (Barre et al, 1996) and has several functions, including protection from fungi and symbiosis with fungi and bacteria (Rudiger and Gabius, 2001); the heat shock 70 kDa protein, involved in macromolecular translocation, carbohydrate metabolism, innate immunity, photosystem II repair, and regulation of kinase activities (Wang et al, 2014b); CCR4-associated factor 1, involved in regulating mRNA deadenylation in vivo and playing a role in plant defense (Liang et al, 2009). The expansions of these gene families ( Figure 3A) and evolution of those unique families in D. officinale may be attributed to the symbiotic feature that plants share with the fungi.…”