Ubiquitinome Profiling Reveals the Landscape of Ubiquitination Regulation in Rice Young Panicles

• Published in: Genomics, proteomics & bioinformatics Vol. 18; no. 3; pp. 305 - 320
• Main Authors: Zhu, Liya, Cheng, Han, Peng, Guoqing, Wang, Shuansuo, Zhang, Zhiguo, Ni, Erdong, Fu, Xiangdong, Zhuang, Chuxiong, Liu, Zexian, Zhou, Hai
• Format: Journal Article
• Language: English
• Published: China Elsevier B.V 01.06.2020; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources,Instrumental Analysis and Research Center,Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences,South China Agricultural University,Guangzhou 510642,China%Sun Yat-sen University Cancer Center,State Key Laboratory of Oncology in South China,Collaborative Innovation Center for Cancer Medicine,Guangzhou 510060,China; College of Life Science and Technology,Huazhong University of Science and Technology,Wuhan 430074,China; School of Life Sciences,Zhengzhou University,Zhengzhou 450001,China; College of Life Science and Technology,Huazhong University of Science and Technology,Wuhan 430074,China%The State Key Laboratory of Plant Cell and Chromosome Engineering,Institute of Genetics and Developmental Biology,Chinese Academy of Sciences,National Centre for Plant Gene Research,Beijing 100101,China%Sun Yat-sen University Cancer Center,State Key Laboratory of Oncology in South China,Collaborative Innovation Center for Cancer Medicine,Guangzhou 510060,China; Elsevier; Oxford University Press
• Subjects: Acetylation; Grain development; Lysine - chemistry; Lysine - metabolism; Lysine ubiquitination; Male sterility; Original Research; Oryza - growth & development; Oryza - metabolism; Plant Proteins - chemistry; Plant Proteins - metabolism; Protein Interaction Maps; Protein Processing, Post-Translational; Proteome - analysis; Proteome - metabolism; Rice; Ubiquitin - metabolism; Ubiquitination; Ubiquitinome; Grain development; Male sterility; Lysine ubiquitination; Ubiquitinome; Rice
• ISSN: 1672-0229; 2210-3244
• DOI: 10.1016/j.gpb.2019.01.005

Ubiquitination, an essential post-transcriptional modification (PTM), plays a vital role in nearly every biological process, including development and growth. Despite its functions in plant reproductive development, its targets in rice panicles remain unclear. In this study, we used proteome-wide profiling of lysine ubiquitination in rice (O. sativa ssp. indica) young panicles. We created the largest ubiquitinome dataset in rice to date, identifying 1638 lysine ubiquitination sites on 916 unique proteins. We detected three conserved ubiquitination motifs, noting that acidic glutamic acid (E) and aspartic acid (D) were most frequently present around ubiquitinated lysine. Enrichment analysis of Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of these ubiquitinated proteins revealed that ubiquitination plays an important role in fundamental cellular processes in rice young panicles. Interestingly, enrichment analysis of protein domains indicated that ubiquitination was enriched on a variety of receptor-like kinases and cytoplasmic tyrosine and serine-threonine kinases. Furthermore, we analyzed the crosstalk between ubiquitination, acetylation, and succinylation, and constructed a potential protein interaction network within our rice ubiquitinome. Moreover, we identified ubiquitinated proteins related to pollen and grain development, indicating that ubiquitination may play a critical role in the physiological functions in young panicles. Taken together, we reported the most comprehensive lysine ubiquitinome in rice so far, and used it to reveal the functional role of lysine ubiquitination in rice young panicles.