Hua, Z.*

Abstract

Protein ubiquitylation is a post-translational modification (PTM) process that covalently modifies a protein substrate with either mono-ubiquitin moieties or poly-ubiquitin chains often at the lysine residues. In Arabidopsis, bioinformatic predictions have suggested that over 5% of its proteome constitutes the protein ubiquitylation system. Despite advancements in functional genomic studies in plants, only a small fraction of this bioinformatically predicted system has been functionally characterized. To expand our understanding about the regulatory function of protein ubiquitylation to that rivaling several other major systems, such as transcription regulation and epigenetics, I described the status, issues, and new approaches of protein ubiquitylation studies in plant biology. I summarized the methods utilized in defining the ubiquitylation machinery by bioinformatics, identifying ubiquitylation substrates by proteomics, and characterizing the ubiquitin E3 ligase-substrate pathways by functional genomics. Based on the functional and evolutionary analyses of the F-box gene superfamily, I proposed a deleterious duplication model for the large expansion of this family in plant genomes. Given this model, I presented new perspectives of future functional genomic studies on the plant ubiquitylation system to focus on core and active groups of Ub E3 ligase genes.