Interactome of Arabidopsis Thaliana

Yilmaz M, Paulic M, Seidel T (2022)
Plants 11(3): 350.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
OA 2.44 MB
Autor*in
Yilmaz, Merve; Paulic, Merle; Seidel, ThorstenUniBi
Abstract / Bemerkung
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.
Stichworte
protein–protein interaction; Arabidopsis thaliana; interactome; Cytoscape
Erscheinungsjahr
2022
Zeitschriftentitel
Plants
Band
11
Ausgabe
3
Art.-Nr.
350
eISSN
2223-7747
Finanzierungs-Informationen
Open-Access-Publikationskosten wurden durch die Universität Bielefeld gefördert.
Page URI
https://pub.uni-bielefeld.de/record/2960841

Zitieren

Yilmaz M, Paulic M, Seidel T. Interactome of Arabidopsis Thaliana. Plants. 2022;11(3): 350.
Yilmaz, M., Paulic, M., & Seidel, T. (2022). Interactome of Arabidopsis Thaliana. Plants, 11(3), 350. https://doi.org/10.3390/plants11030350
Yilmaz, M., Paulic, M., and Seidel, T. (2022). Interactome of Arabidopsis Thaliana. Plants 11:350.
Yilmaz, M., Paulic, M., & Seidel, T., 2022. Interactome of Arabidopsis Thaliana. Plants, 11(3): 350.
M. Yilmaz, M. Paulic, and T. Seidel, “Interactome of Arabidopsis Thaliana”, Plants, vol. 11, 2022, : 350.
Yilmaz, M., Paulic, M., Seidel, T.: Interactome of Arabidopsis Thaliana. Plants. 11, : 350 (2022).
Yilmaz, Merve, Paulic, Merle, and Seidel, Thorsten. “Interactome of Arabidopsis Thaliana”. Plants 11.3 (2022): 350.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Creative Commons Namensnennung 4.0 International Public License (CC-BY 4.0):
Volltext(e)
Access Level
OA Open Access
Zuletzt Hochgeladen
2022-01-31T07:08:44Z
MD5 Prüfsumme
567439ba3f2fc108a71e25ac0134ca89

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 35161331
PubMed | Europe PMC

Suchen in

Google Scholar