Functional subnetworks involving sHSPs during tomato fruit ripening.

ARCE, DÉBORA P; PONCE, SERGIO D; TAPIA, ELIZABETH; PRATTA, GUILLERMO R

Viña del Mar

Conferencia; ISCB-LA SOIBIO EMBnet 2018; 2018

ISCB and Soibio

Background Small heat shock proteins (sHSPs) prevent irreversible protein aggregation induced by stress and development in different organisms. Functional annotation sHSPs in plants remains scarce. Protein interactions with sHSPs in tomato are poorly understood. In this work, we aim to shed light on putative tomato sHSP functionalities from the study of protein interactions during fruit ripening. Method Ripening cluster of co-expression data (Fragkostefanakis et al 2015) was used to build networks of sHSP proteins using interactomic data (TomatoNet, Kim et al. 2016). The networks were built using Cytoscape. MCODE algorithm was applied to identify clusters inside the ripening network. Subnetworks containing sHSPs were considered for further analysis concerning the identification transcriptional regulation modules based on HSE matrix scanning (Arce et al, 2018) and associated protein expression values (Szymanski et al, 2017). DAVID tool was used for functional enrichment analysis. Results We used a curated tomato interactome network including 22,549 proteins and 721,626 interactions. Specific interactions between co-regulated proteins and their first neighbors resulted in a ripening related subnetwork (cluster #2). MCODE analysis resulted in a subnetwork containing sHSPs (3 cytosolic, 1 chloroplastic and 1 mitochondrial), HSC80, HSP70s, and dnaJs. A clear up-regulation was observed for sHSP-Solyc06g076570 during ripening. Functional enrichment analysis showed that the subnetwork is related to protein folding and its transcriptional regulation is related to the HSE presence. Conclusion Our study presents a network-based view of the tomato sHSP protein family allowing the assignment of putative functionalities to uncharacterized members of this chaperone family.