An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome
Abstract 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, t...
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| Format: | Article |
| Language: | English |
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BMC
2022-07-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-022-02717-8 |
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| author | Ruyi Wang Xiaoman You Chongyang Zhang Hong Fang Min Wang Fan Zhang Houxiang Kang Xiao Xu Zheng Liu Jiyang Wang Qingzhen Zhao Xuli Wang Zeyun Hao Feng He Hui Tao Debao Wang Jisong Wang Liang Fang Mengchao Qin Tianxiao Zhao Pingping Zhang Hefei Xing Yunping Xiao Wende Liu Qi Xie Guo-Liang Wang Yuese Ning |
| author_facet | Ruyi Wang Xiaoman You Chongyang Zhang Hong Fang Min Wang Fan Zhang Houxiang Kang Xiao Xu Zheng Liu Jiyang Wang Qingzhen Zhao Xuli Wang Zeyun Hao Feng He Hui Tao Debao Wang Jisong Wang Liang Fang Mengchao Qin Tianxiao Zhao Pingping Zhang Hefei Xing Yunping Xiao Wende Liu Qi Xie Guo-Liang Wang Yuese Ning |
| author_sort | Ruyi Wang |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-11T00:59:22Z |
| format | Article |
| id | doaj.art-d5f48ed1187c46cfacf415ee1080824a |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-11T00:59:22Z |
| publishDate | 2022-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-d5f48ed1187c46cfacf415ee1080824a2022-12-22T01:26:22ZengBMCGenome Biology1474-760X2022-07-0123112110.1186/s13059-022-02717-8An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactomeRuyi Wang0Xiaoman You1Chongyang Zhang2Hong Fang3Min Wang4Fan Zhang5Houxiang Kang6Xiao Xu7Zheng Liu8Jiyang Wang9Qingzhen Zhao10Xuli Wang11Zeyun Hao12Feng He13Hui Tao14Debao Wang15Jisong Wang16Liang Fang17Mengchao Qin18Tianxiao Zhao19Pingping Zhang20Hefei Xing21Yunping Xiao22Wende Liu23Qi Xie24Guo-Liang Wang25Yuese Ning26State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesOE Biotech Co., LtdOE Biotech Co., LtdOE Biotech Co., LtdState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesState Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesDepartment of Plant Pathology, The Ohio State UniversityState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesAbstract 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.https://doi.org/10.1186/s13059-022-02717-8E3 ligaseUbiquitinationORFeomeInteractomeProteomicRice |
| spellingShingle | Ruyi Wang Xiaoman You Chongyang Zhang Hong Fang Min Wang Fan Zhang Houxiang Kang Xiao Xu Zheng Liu Jiyang Wang Qingzhen Zhao Xuli Wang Zeyun Hao Feng He Hui Tao Debao Wang Jisong Wang Liang Fang Mengchao Qin Tianxiao Zhao Pingping Zhang Hefei Xing Yunping Xiao Wende Liu Qi Xie Guo-Liang Wang Yuese Ning An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome Genome Biology E3 ligase Ubiquitination ORFeome Interactome Proteomic Rice |
| title | An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome |
| title_full | An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome |
| title_fullStr | An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome |
| title_full_unstemmed | An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome |
| title_short | An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome |
| title_sort | orfeome of rice e3 ubiquitin ligases for global analysis of the ubiquitination interactome |
| topic | E3 ligase Ubiquitination ORFeome Interactome Proteomic Rice |
| url | https://doi.org/10.1186/s13059-022-02717-8 |
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