Independent transcriptomic and proteomic networks reveal common differentially expressed chaperone and interactor genes during tomato cv. Micro-Tom fruit ripening

Abstract

Heat Shock Proteins (HSPs) are a superfamily of chaperones that have been characterized in different organisms. In plants, HSPs contribute to abiotic stress responses and development. The aim of this work was to perform an integrative analysis using bioinformatic and inferential approaches based on protein-protein interactions (PPI) network building, using transcriptomic and proteomic public data from Solanum lycopersicum cultivar (cv.) Micro-Tom during fruit ripening. We were able to identify specific chaperone networks for each maturing stage at both transcriptional and proteomic levels. Also, we noted that the number of induced chaperones was higher at the transcriptomic level than the proteomic one and increased as the fruit matured. Additionally, we identified clusters at both levels during advanced stages of ripening that were over-represented by HSP families (HSP70 and HSP20), chaperones (Proteasome assembly chaperone) and common protein interactors associated with protein folding, protein synthesis and degradation, and response to stress (Glutathione-S-transferase or GST; Endoplasmic reticulum auxin binding protein ER-ABP; tetratricopeptide repeat protein-ripening regulated protein or TRP-RRP). Finally, we found that some of these up-regulated chaperones show the presence of heat shock element (HSE) motifs in their 5′-untranslated regions (5´UTRs). Our combined inferential bioinformatics approach allowed us to integrate RNA, protein expression and co-expression levels of chaperones involved in cv. Micro-Tom fruit ripening. Statement of significance of the study: The Chaperone network is largely characterized by diverse families including Heat Shock Proteins (HSPs), which participate in the refolding of denatured proteins in physiological processes such as developmental changes and abiotic stress response. In the present work, we performed the integrative analysis of transcriptomic and proteomic publicly available data from Solanum lycopersicum cv. Micro-Tom to describe interactome networks at both primary stages (transcription and translation) of gene expression in tomato fruits. Our strategy based on interactomics allowed us to identify specific networks at both levels for each maturing stage at fruit ripening, discovering new interactions and characterizing chaperones and co-chaperons forming these complex biological protein networks during tomato fruit ripening.