SWATH-based quantitative proteomics gives insight into a significant proteome shift in UCB-1 pistachio rootstock under salt stress
Journal article, 2023
The hybrid pistachio rootstock UCB-1 is especially tolerant to abiotic stresses including salinity. However, the effect of salinity on its whole proteome is obscure, which limits our ability to develop high-confident protein biomarkers to facilitate the genetic improvement of pistachio cultivars with enhanced salt-tolerance. In the present study, using sequential window acquisition of all theoretical mass spectra (SWATH-MS) technology, the expression of 1150 proteins was quantified, with the expression of 459 proteins significantly impacted by salt exposure. Functional enrichment determined that salinity stress increases the level of proteins associated with response to salt stress and reduces the level of ribosomal subunits. We used KEGG pathway enrichment analysis to link salt exposure with a set of alterations in several pathways including ribosome components, biosynthesis of phenylpropanoids, and carbon fixation in photosynthetic organisms. To track the potential consequences of protein alteration with more crucial biological functions in the enriched pathways, the incorporation of SWATH-MS data and protein-protein interactions (PPIs) analysis were then conducted. Centrality analysis of the three top-ranked enriched pathways highlighted that any alterations in the abundance of EMB3010, PA2, NAD-ME1, and PGAM proteins may result in desirable consequences on salt tolerance in UCB-1. Therefore, centrality analysis of whole proteome survey-derived responsive PPIs was useful in the identification, prioritization, and selection of potential biomarker candidates by which the need for expensive and time-consuming experimental validation will be minimized. At the early selection stages in tree breeding programs, integration of proteomics-generated resources with conventional programs can assist in developing fast selection assays.