Recent advances and challenges in plant phosphoproteomics

Abstract

Plants are sessile organisms that need to respond to environmental changes quickly and efficiently. They can accomplish this by triggering specialized signaling pathways often mediated by protein phosphorylation and dephosphorylation. Phosphorylation is a fast response that can switch on or off a myriad of biological pathways and processes. Proteomics and MS are the main tools employed in the study of protein phosphorylation. Advances in the technologies allow simultaneous identification and quantification of thousands of phosphopeptides and proteins that are essential to understanding the sophisticated biological systems and regulations. In this review, we summarize the advances in phosphopeptide enrichment and quantitation, MS for phosphorylation site mapping and new data acquisition methods, databases and informatics, interpretation of biological insights and crosstalk with other PTMs, as well as future directions and challenges in the field of phosphoproteomics.

Identification and Mapping of Phosphorylated Isoforms of the Major Storage Protein of Potato Based on Two- Dimensional Electrophoresis

“…Thus, no phosphorylated ortholog sites were identified in other plant phosphoproteomics data for Arabidopsis thaliana, Brassica napus, Glycine max, Medicago truncatula, Oryza sativa and Zea mays. It is noteworthy that enrichment methods of underrepresented phosphorylated proteins or peptides can be conducted prior to highresolution MS analysis to precisely identify and map phosphorylation sites, but the amount of protein collected in a spot is often insufficient for downstream enrichment methods [37]. Consequently, it would be difficult to assign phosphorylation sites to the specific isoforms found along 2-DE patatin patterns.…”

Update: Post-translational protein modifications in plant metabolism

“…Phosphorylation is one of the most widespread reversible PTMs and plays a major role in plant signal transduction and metabolism by altering protein activities, protein interactions, or subcellular location (Mithoe and Menke, 2011;Schönberg and Baginsky, 2012;van Wijk et al, 2014;Silva-Sanchez et al, 2015). Phosphorylation is catalyzed by kinases, which transfer a phosphoryl group typically from ATP, but also from ADP (e.g.…”

“…Several dozen large-scale phosphorylation studies have been published for Arabidopsis, Medicago spp., maize (Zea mays), rice (Oryza sativa), and other plant species; most of these data can be mined using various plant phosphorylation databases (Silva-Sanchez et al, 2015). A recent review summarized the phosphorylation of enzymes in the photorespiratory pathway located in chloroplasts, peroxisomes, and mitochondria and discussed each of these enzymes in fair detail (Hodges et al, 2013; Table III).…”

Phosphoproteomics technologies and applications in plant biology research

“…A successful phosphoproteomics study depends not only on the selective enrichment of phosphopeptides, but also on accurate detection and quantitation of the peptides, as well as precise mapping of the phosphorylation sites. Advances in these areas have been extensively reviewed (Batalha et al, 2012; Fíla and Honys, 2012; Kline and De Luca, 2014; Silva-Sanchez et al, 2015). Most of the technologies were developed in animal and yeast systems, and subsequently applied in plants.…”