Proteomic and phosphoproteomic analyses of chromatin-associated proteins from Arabidopsis thaliana

Jean Bigeard (1) , Naganand Rayapuram (2) , Ludovic Bonhomme (2) , Heribert Hirt (1, 3) , Delphine Pflieger (2)

1 URGV - Unité de recherche en génomique végétale
2 LAMBE - Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement
3 KAUST - King Abdullah University of Science and Technology [Saudi Arabia]

The nucleus is the organelle where basically all DNA-related processes take place in eukaryotes, such as replication, transcription, and splicing as well as epigenetic regulation. The identification and description of the nuclear proteins is one of the requisites toward a comprehensive understanding of the biological functions accomplished in the nucleus. Many of the regulatory mechanisms of protein functions rely on their PTMs among which phosphorylation is probably one of the most important properties affecting enzymatic activity, interaction with other molecules, localization, or stability. So far, the nuclear and subnuclear proteome and phosphoproteome of the model plant Arabidopsis thaliana have been the subject of very few studies. In this work, we developed a purification protocol of Arabidopsis chromatin-associated proteins and performed proteomic and phosphoproteomic analyses identifying a total of 879 proteins of which 198 were phosphoproteins that were mainly involved in chromatin remodeling, transcriptional regulation, and RNA processing. From 230 precisely localized phosphorylation sites (phosphosites), 52 correspond to hitherto unidentified sites. This protocol and data thereby obtained should be a valuable resource for many domains of plant research.

Mots clés: Phosphoproteins; Proteome; proteomics; protein stability; protein phosphorylation; protein motif; protein localization; protein function; protein domain; protein analysis; plant; chemistry; classification; Arabidopsis; nuclear protein; Arabidopsis thaliana; Article; cellular distribution; chromatin assembly and disassembly; controlled study; enzyme activity; molecular biology; nonhuman; RNA processing; transcription regulation; Arabidopsis protein; unclassified drug; RNA; phosphoprotein; chromatin associated protein; cell protein; metabolism; molecular genetics; protein database; Amino Acid Sequence; Arabidopsis Proteins; Chromatin; Databases; Protein; Molecular Sequence Data; Nuclear Proteins

Domaines: Chimie-Physique [physics.chem-ph]

Jean Bigeard, Naganand Rayapuram, Ludovic Bonhomme, Heribert Hirt, Delphine Pflieger. Proteomic and phosphoproteomic analyses of chromatin-associated proteins from Arabidopsis thaliana. Proteomics, 2014, 14 (19), pp.2141-2155. ⟨10.1002/pmic.201400072⟩. ⟨hal-02112304⟩