Genome-Wide Identification, In Silico Characterization of AtCOP1-Targeting Regulatory Proteins Network and their Expression Profiling in The COP1 Downregulated Arabidopsis thaliana

The functional diversification of the RING-finger constitutive photomorphogenesis 1 (COP1) enzyme highly depends on its (in)direct interaction with regulatory proteins involved in the Arabidopsis photomorphogenesis signaling pathways. In last decade, only a few AtCOP1-ligand complexes have been investigated using functional analysis and proved by biochemical interaction analysis, despite much more have been remaining unclear. Identifying the functions of COP1 will undoubtedly provide an opportunity for the discovery of novel COP1 targets either triggered on COP1 or targeted by COP1, which their characteristics have not been reported so far. Here, we have focused on the tertiary structure analysis of COP1 protein and characterization of its potent ligands based on the protein–protein interaction characteristics of the known AtCOP1-based protein complexes, which their interaction with COP1 were biochemically approved. Based on motif analysis and molecular docking results, a total of 88 regulatory proteins with different confidence were identified to be interactive and co-regulated with AtCOP1 E3 ligase. The correlation regulatory network analysis reveals that COP1 functions as a master switch in controlling the Arabidopsis growth and development. The up/down regulations of the potent COP1-ligands gene expression levels in cop1 knockdown T0 plants indicate the COP1 expanded roles in a wide diversity of biological processes. These characteristics consist of the photomorphogenesis signaling pathway, cell cycle regulation, cell division, histone H3-K27 methylation, stomata formation, and iron starvation. Meanwhile, the VPS11 transporter probably transports the COP1 into the endosome, lysosome, and vacuole between the nucleus and cytoplasm during the photomorphogenesis signaling pathway in darkness condition.