Seasonal and water restriction-related changes in Eucalyptus grandis leaf proteins: Shedding light on the dark proteome

Abstract

Climate change is escalating the frequency and intensity of warming and drought periods around the globe, currently representing a threat to many plant species. Understanding how plants cope with such abiotic stresses is crucial.We investigate how Eucalyptus grandis, a plant species with several industry applications, copes with seasonal variation and water restriction imposition at the proteomic level under field conditions. Therefore, we attempted to identify known proteins and novel peptides associated with the effect of seasonality and water restriction impositions, as well as to provide insights into how novel peptides behave under such conditions. The leaf proteome of E. grandis plants was studied under both a conventional proteomic workflow and a dedicated proteogenomics approach. The highest proteomic variability was identified in the summer season and the most abundant known proteins associated with seasonal variation were related to photosynthesis. Post-translational modifications, protein turnover, and chaperones were the main functional classifications identified among biological treatments. Furthermore, 144 novel peptides not predicted by current proteomics pipelines, were identified by both spectral correlations against modified databases (43) and a de novo peptide sequencing approach (101). It is predicted that most single amino acid substituted (SAS) peptides, mainly associated with the photosynthesis process, decrease protein stability by altering the quantitative change upon ΔΔG values and non-covalent interactions. Multiple reaction monitoring validation assays were performed for selected novel peptide identifications demonstrating that it is a very robust mass spectrometry-based method of validation. Data are available via ProteomeXchange with identifier PXD031100.