Exploring the protein–protein interaction landscape in plants

Abstract

Protein-protein interactions (PPIs) represent an essential aspect of plant systems biology. Identification of key protein players and their interaction networks provide crucial insights into the regulation of plant developmental processes and into interactions of plants with their environment. Despite the great advance in the methods for the discovery and validation of PPIs, still several challenges remain. First, the PPI networks are usually highly dynamic, and the in vivo interactions are often transient and difficult to detect. Therefore, the properties of the PPIs under study need to be considered to select the most suitable technique, because each has its own advantages and limitations. Second, besides knowledge on the interacting partners of a protein of interest, characteristics of the interaction, such as the spatial or temporal dynamics, are highly important. Hence, multiple approaches have to be combined to obtain a comprehensive view on the PPI network present in a cell. Here, we present the progress in commonly used methods to detect and validate PPIs in plants with a special emphasis on the PPI features assessed in each approach and how they were or can be used for the study of plant interactions with their environment.

Proximity labeling of protein complexes and cell type-specific organellar proteomes in Arabidopsis enabled by TurboID

“…Today's state-of-the-art for identification of in-planta protein interactors and complexes is affinity purification with proteinspecific antibodies or single-and tandem affinity purification tags and subsequent mass spectrometry (MS) analysis (Struk et al 2019;Xu et al 2010). However, while affinity purification-mass spectrometry (AP-MS) strategies are undoubtedly useful in many instances, AP-MS is challenging for very low abundant proteins, those expressed only in rare cell types or developmental stages, and those with poor solubility like integral membrane proteins.…”

Visualizing protein-protein interactions in plants by rapamycin-dependent delocalization

“…In the past 20 years, the number of articles which feature protein-protein interactions (PPIs) as a topic or focusing on PPI technology development has been steadily increasing (Xing et al, 2016). Although a plethora of tools to investigate PPIs is available (Miura, 2018;Titeca et al, 2019;Wiens and Campbell, 2018), those which can be used in planta are relatively limited (Fukao, 2012;Lampugnani et al, 2018;Struk et al, 2019;Xing et al, 2016). In plant systems, including Arabidopsis thaliana, multiple interactomes have been described based on large-scale screenings (Arabidopsis Interactome Mapping Consortium, 2011;Boruc et al, 2010a;Jones et al, 2014;Piya et al, 2014).…”

“…Interactomes plot the landscape surrounding a certain bait protein, yet seldom provide information on specific or direct interaction partners. The evaluation of specific biological functions and the mode of action of a protein of interest usually requires multi-technical approaches (Struk et al, 2019). Thus, a proper selection of the optimal PPI tools to use represents a foremost important task.…”

The Arabidopsis Proteins AtNHR2A and AtNHR2B Are Multi-Functional Proteins Integrating Plant Immunity With Other Biological Processes

“…Because the detailed functions of AtNHR2A and AtNHR2B are still unknown, the main objective of this work is to gain insight into their function by investigating their respective protein-protein interaction network (interactome). Investigating protein-protein interactions are powerful tools to gain insight into the function of proteins of interest given that most biological processes occur by the formation of protein complexes (Struk et al, 2018).…”