Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA.
Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA.
J Exp Bot. 2023 Nov 21;74(21):6487-6504. doi: 10.1093/jxb/erad354.
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 rivalling several other major systems, such as transcription regulation and epigenetics, I describe the status, issues, and new approaches of protein ubiquitylation studies in plant biology. I summarize 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 propose a deleterious duplication model for the large expansion of this family in plant genomes. Given this model, I present new perspectives of future functional genomic studies on the plant ubiquitylation system to focus on core and active groups of ubiquitin E3 ligase genes.
蛋白质泛素化是一种翻译后修饰（PTM）过程，通过赖氨酸残基将单泛素或多泛素链共价修饰到蛋白质底物上。在拟南芥中，生物信息学预测表明，其蛋白质组的 5%以上构成了蛋白质泛素化系统。尽管植物功能基因组学研究取得了进展，但该生物信息学预测系统的一小部分已得到功能表征。为了将蛋白质泛素化的调控功能扩展到与转录调控和表观遗传学等其他几个主要系统相媲美，我描述了植物生物学中蛋白质泛素化研究的现状、问题和新方法。我总结了通过生物信息学定义泛素化机制、通过蛋白质组学鉴定泛素化底物以及通过功能基因组学表征泛素 E3 连接酶-底物途径所采用的方法。基于 F-box 基因超家族的功能和进化分析，我提出了一个有害复制模型，用于解释该家族在植物基因组中的大量扩张。基于该模型，我提出了未来植物泛素化系统功能基因组学研究的新视角，重点关注泛素 E3 连接酶基因的核心和活跃群体。
