Changes in the Phosphoproteome and Metabolome Link Early Signaling Events to Rearrangement of Photosynthesis and Central Metabolism in Salinity and Oxidative Stress Response in Arabidopsis

Abstract

Salinity and oxidative stress are major factors affecting and limiting the productivity of agricultural crops. The molecular and biochemical processes governing the plant response to abiotic stress have often been researched in a reductionist manner. Here, we report a systemic approach combining metabolic labeling and phosphoproteomics to capture early signaling events with quantitative metabolome analysis and enzyme activity assays to determine the effects of salt and oxidative stress on plant physiology. K + and Na + transporters showed coordinated changes in their phosphorylation pattern, indicating the importance of dynamic ion homeostasis for adaptation to salt stress. Unique phosphorylation sites were found for Arabidopsis (Arabidopsis thaliana) SNF1 kinase homolog10 and 11, indicating their central roles in the stress-regulated responses. Seven Sucrose Nonfermenting1-Related Protein Kinase2 kinases showed varying levels of phosphorylation at multiple serine/threonine residues in their kinase domain upon stress, showing temporally distinct modulation of the various isoforms. Salinity and oxidative stress also lead to changes in protein phosphorylation of proteins central to photosynthesis, in particular the kinase State Transition Protein7 required for state transition and light-harvesting II complex proteins. Furthermore, stress-induced changes of the phosphorylation of enzymes of central metabolism were observed. The phosphorylation patterns of these proteins were concurrent with changes in enzyme activity. This was reflected by altered levels of metabolites, such as the sugars sucrose and fructose, glycolysis intermediates, and amino acids. Together, our study provides evidence for a link between early signaling in the salt and oxidative stress response that regulates the state transition of photosynthesis and the rearrangement of primary metabolism.

Na2CO3-Responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics

“…However, only about 53 salinity-responsive genes encoding chloroplast proteins have been characterized [5], which are insufficient to address the sophisticated salinity-responsive networks in chloroplasts. Additionally, NaCl stress altered phosphorylation levels of several chloroplast proteins in Arabidopsis [19,20], Brachypodium distachyon [21] and sugar beet ( Beta vulgaris ) [22], implying that state transition, PSII damage repair, thermal dissipation, and thylakoid membrane organization were crucial for plant acclimation to salt stress [23]. However, the critical roles of reversible protein phosphorylation in salinity-/alkali-responsive metabolic networks are virtually unknown.…”

A Tale of Two Sugars: Trehalose 6-Phosphate and Sucrose

“…Trehalose also confers desiccation tolerance on yeast cells (Tapia et al, 2015), in part by protecting them from oxidative damage by reactive oxygen species (Benaroudj et al, 2001). Many of the abiotic (and biotic) stresses faced by plants lead to reactive oxygen species production, and the accumulation of sugars such as trehalose and Suc is one of the mechanisms providing protection from oxidative stress (Romero et al, 2002;Cortina and Culianez-Macia, 2005;Couée et al, 2006;Luo et al, 2008;Chen and Hoehenwarter, 2015).…”

Rapid and reproducible phosphopeptide enrichment by tandem metal oxide affinity chromatography: application to boron deficiency induced phosphoproteomics

“…Furthermore our data show that the broad and deep phosphoproteome coverage was facilitated by high enrichment selectivity of our improved tandem MOAC protocol with more than 75% of peptides identified in each sample being phosphopeptides. By contrast, other previous studies in Arabidopsis required three times more measurement time while identifying only one‐third of the quantified sites (Chen and Hoehenwarter, ; Nukarinen et al ., ). By optimizing the enrichment procedure, we achieved similar coverage to published large‐scale phosphoproteomics studies in tissue, despite using less starting material and analysis time (Lan et al ., ).…”

“…Owing to the importance of protein phosphorylation in cellular signaling, we considered a global analysis of protein phosphorylation useful to provide insight into mechanisms by which this dynamic post‐translational modification modulates boron homeostasis. Major advances in mass spectrometric techniques, instrumentation and data analysis applications in the last years have revolutionized the study of the cellular proteome including global analysis of protein phosphorylation events (Olsen et al ., ; Chen et al ., ; Engelsberger and Schulze, ; Wu et al ., ; Chen and Hoehenwarter, ). Phosphoproteomics allows unbiased localization and site‐specific quantification of in vivo phosphorylation of thousands of proteins (Sharma et al ., ).…”