Recent Trends in Plant Protein Complex Analysis in a Developmental Context

Abstract

Because virtually all proteins interact with other proteins, studying protein-protein interactions (PPIs) is fundamental in understanding protein function. This is especially true when studying specific developmental processes, in which proteins often make developmental stage- or tissue specific interactions. However, studying these specific PPIs in planta can be challenging. One of the most widely adopted methods to study PPIs in planta is affinity purification coupled to mass spectrometry (AP/MS). Recent developments in the field of mass spectrometry have boosted applications of AP/MS in a developmental context. This review covers two main advancements in the field of affinity purification to study plant developmental processes: increasing the developmental resolution of the harvested tissues and moving from affinity purification to affinity enrichment. Furthermore, we discuss some new affinity purification approaches that have recently emerged and could have a profound impact on the future of protein interactome analysis in plants.

Keywords: Arabidopsis thaliana; affinity enrichment; interactomics; plant development; proximity-dependent labeling; tandem affinity purification.

FIGURE 1

Comparison of available biomass sources for AP/MS experiments. The advantages and disadvantages of different biomass sources are scaled on five parameters. Cell cultures are the most cost- and time-efficient means of generating biomass for AP/MS experiments. They also allow the highest experimental flexibility because of the ease with which they are manipulated by chemical compounds. Arabidopsis seedlings are the best all-round biomass source, offering the best performance for standard AP/MS experiments. When studying more specific developmental processes, crop seedlings can be better suited. However, these are more time consuming and often allow less experimental flexibility because of their size. Although isolated organs and tissues offer the highest degree of developmental context, determining the optimal tissue and developmental stage to harvest biomass increases the complexity of the experimental setup and the time needed.

FIGURE 2

Overview of the different AP/MS approaches (A) and available TAP tags (B). TAP tags: (1) TAPi tag; (2) GSrhino tag; (3) GS^yellow tag. CBP, calmodulin binding protein; FP, false positive; FN, false negative; ProtA, protein A domain; ProtG, protein G domain; 2x Rhino, double recognition site for the Rhinovirus 3C protease; TEV, recognition site for the tobacco etch virus protease; SBP, streptavidin-binding peptide; YFP, yellow fluorescent protein.

FIGURE 3

Overview of the advantages and disadvantages of various AP/MS approaches.