Interactome of Arabidopsis Thaliana

Abstract

More than 95,000 protein-protein interactions of Arabidopsis thaliana have been published and deposited in databases. This dataset was supplemented by approximately 900 additional interactions, which were identified in the literature from the years 2002-2021. These protein-protein interactions were used as the basis for a Cytoscape network and were supplemented with data on subcellular localization, gene ontologies, biochemical properties and co-expression. The resulting network has been exemplarily applied in unraveling the PPI-network of the plant vacuolar proton-translocating ATPase (V-ATPase), which was selected due to its central importance for the plant cell. In particular, it is involved in cellular pH homeostasis, providing proton motive force necessary for transport processes, trafficking of proteins and, thereby, cell wall synthesis. The data points to regulation taking place on multiple levels: (a) a phosphorylation-dependent regulation by 14-3-3 proteins and by kinases such as WNK8 and NDPK1a, (b) an energy-dependent regulation via HXK1 and the glucose receptor RGS1 and (c) a Ca²⁺-dependent regulation by SOS2 and IDQ6. The known importance of V-ATPase for cell wall synthesis is supported by its interactions with several proteins involved in cell wall synthesis. The resulting network was further analyzed for (experimental) biases and was found to be enriched in nuclear, cytosolic and plasma membrane proteins but depleted in extracellular and mitochondrial proteins, in comparison to the entity of protein-coding genes. Among the processes and functions, proteins involved in transcription were highly abundant in the network. Subnetworks were extracted for organelles, processes and protein families. The degree of representation of organelles and processes reveals limitations and advantages in the current knowledge of protein-protein interactions, which have been mainly caused by a high number of database entries being contributed by only a few publications with highly specific motivations and methodologies that favor, for instance, interactions in the cytosol and the nucleus.

Keywords: Arabidopsis thaliana; Cytoscape; interactome; protein–protein interaction.

Figure 1

Subcellular distribution of proteins in the network and according to protein-coding AGI listed in the genome. The diagram is based on the consensus prediction provided by SUBA4. Nuclear proteins (green) were enriched in the network, and a depletion was visible for extracellular (grey) and mitochondrial proteins (blue).

Figure 2

Enrichment of GO category process (A) and GO category function (B). The ratio has been calculated as the number of GOs in the network/the number of GOs of protein-coding genes in A. thaliana. GOs with a ratio >1 were considered as enriched in the network and labeled in red. Yellow columns correspond to ratios <1.

Figure 3

Subnetworks of Thioredoxins (A) and 14-3-3 proteins (B). Node color corresponds to subcellular localization (Cytosol—grey, nucleus—cyan, plastid—green, mitochondrion—red, peroxisomes—orange, ER—light blue, Golgi—light purple, vacuole—dark purple, plasma membrane—purple, extracellular—white), node size indicates the molecular weight. Edge size displays co-expression strength.

Figure 4

Protein–protein interactions of V-ATPase subunits. The catalytic head comprises VHA-A (red) and VHA-B (green). Subunits of the peripheral stalk (VHA-C, VHA-E, VHA-G, VHA-H) are given in orange-yellow, and the central stalk (VHA-D, VHA-F) is shown in blue. The membrane integral sector V₀ consists of VHA-a, the proteolipids VHA-c and VHA-c”, the bearing VHA-d and the subunit VHA-e. A selection of interacting proteins is given per subunits, regardless of the isoform.

Figure 5

Contribution of individual methods (A) and publications (B) to the databases. (A) “Biochemical” denominates data from co-fractionation/mass spectroscopy (CF/MS) [167]. Enzymatic studies (green), Förster resonance energy transfer (dark blue), genetic interference (brown), X-ray experiments, imaging techniques and FarWestern contribute a comparatively low amount of data. (B) Publications are given by the name of the first author; Smakowska corresponds to Smakowska-Luzan [165,166,168,169,170,171,172,173,174].