Journal Article

An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome

Zhang, Chongyang, Wang, Guo-Liang, Fang, Hong, He, Feng, Qin, Mengchao, Zhang, Pingping, Wang, Ruyi, Xiao, Yunping, Xie, Qi, Wang, Jisong, Wang, Jiyang, Zhao, Qingzhen, Xing, Hefei, Tao, Hui, Zhao, Tianxiao, You, Xiaoman, Ning, Yuese, Zhang, Fan, Wang, Debao, Xu, Xiao, Hao, Zeyun, Wang, Xuli, Liu, Wende, Wang, Min, Liu, Zheng, Kang, Houxiang, Fang, Liang

2022

Overview

Background Ubiquitination is essential for many cellular processes in eukaryotes, including 26S proteasome-dependent protein degradation, cell cycle progression, transcriptional regulation, and signal transduction. Although numerous ubiquitinated proteins have been empirically identified, their cognate ubiquitin E3 ligases remain largely unknown. Results Here, we generate a complete ubiquitin E3 ligase-encoding open reading frames (UbE3-ORFeome) library containing 98.94% of the 1515 E3 ligase genes in the rice ( Oryza sativa L . ) genome. In the test screens with four known ubiquitinated proteins, we identify both known and new E3s. The interaction and degradation between several E3s and their substrates are confirmed in vitro and in vivo. In addition, we identify the F-box E3 ligase OsFBK16 as a hub-interacting protein of the phenylalanine ammonia lyase family OsPAL1–OsPAL7. We demonstrate that OsFBK16 promotes the degradation of OsPAL1, OsPAL5, and OsPAL6. Remarkably, we find that overexpression of OsPAL1 or OsPAL6 as well as loss-of-function of OsFBK16 in rice displayed enhanced blast resistance, indicating that OsFBK16 degrades OsPALs to negatively regulate rice immunity. Conclusions The rice UbE3-ORFeome is the first complete E3 ligase library in plants and represents a powerful proteomic resource for rapid identification of the cognate E3 ligases of ubiquitinated proteins and establishment of functional E3–substrate interactome in plants.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Ammonia / Animal Genetics and Genomics / Antibodies / Bioinformatics / Biomedical and Life Sciences / Cell cycle / Cloning / Degradation / Disease resistance / E3 ligase / Enzymes / eukaryotic cells / Evolutionary Biology / family / Gene amplification / Gene regulation / genome / Genomes / Human Genetics / immunity / Interactome / Life Sciences / loss-of-function mutation / Metabolism / Microbial Genetics and Genomics / Open reading frames / ORFeome / Oryza - genetics / Oryza - metabolism / Oryza sativa / Phenylalanine / phenylalanine ammonia-lyase / Plant Genetics and Genomics / Proteasome 26S / protein degradation / Proteins / Proteomic / Proteomics / Rice / Rice blast / Signal transduction / Systems development / transcription (genetics) / Ubiquitin / Ubiquitin-protein ligase / Ubiquitin-Protein Ligases - genetics / Ubiquitin-Protein Ligases - metabolism / Ubiquitinated Proteins - genetics / Ubiquitinated Proteins - metabolism / Ubiquitination / Ubiquitins - genetics / Ubiquitins - metabolism