Mapping the plant proteome: tools for surveying coordinating pathways

Abstract

Plants rapidly respond to environmental fluctuations through coordinated, multi-scalar regulation, enabling complex reactions despite their inherently sessile nature. In particular, protein post-translational signaling and protein-protein interactions combine to manipulate cellular responses and regulate plant homeostasis with precise temporal and spatial control. Understanding these proteomic networks are essential to addressing ongoing global crises, including those of food security, rising global temperatures, and the need for renewable materials and fuels. Technological advances in mass spectrometry-based proteomics are enabling investigations of unprecedented depth, and are increasingly being optimized for and applied to plant systems. This review highlights recent advances in plant proteomics, with an emphasis on spatially and temporally resolved analysis of post-translational modifications and protein interactions. It also details the necessity for generation of a comprehensive plant cell atlas while highlighting recent accomplishments within the field.

Keywords: plant proteins; post translational modification; protein–protein interactions; proteomics.

Figure 1.. Overview of common mass spectrometry-based strategies for the analysis of canonical and non-canonical phosphorylation.

Figure 2.. Representative mass spectrometry-based strategies for the direct and indirect analysis of reversible cysteine oxidation.

Both approaches can be facilitated using peptide-level enrichment as well; however, recent work has favored protein-level enrichment due to the decrease in artifactual oxidation.

Figure 3.. Common strategies for mass spectrometry-based interactomics that have been employed in plant systems.

Many of the approaches can be applied together for complementary analysis of protein networks.