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; School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
Genomics Proteomics Bioinformatics. 2020 Jun;18(3):305-320. doi: 10.1016/j.gpb.2019.01.005. Epub 2020 Nov 2.
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.
泛素化是一种重要的转录后修饰（PTM），几乎参与了所有的生物过程，包括发育和生长。尽管它在植物生殖发育中具有功能，但在水稻颖花中其靶标仍不清楚。在这项研究中，我们使用了水稻（O. sativa ssp. indica）幼穗泛素化的蛋白质组范围分析。我们创建了迄今为止在水稻中最大的泛素组数据集，鉴定了 916 个独特蛋白上的 1638 个赖氨酸泛素化位点。我们检测到三个保守的泛素化基序，注意到围绕泛素化赖氨酸最常出现酸性谷氨酸（E）和天冬氨酸（D）。对这些泛素化蛋白的基因本体论（GO）注释和京都基因与基因组百科全书（KEGG）途径的富集分析表明，泛素化在水稻幼穗的基本细胞过程中发挥着重要作用。有趣的是，蛋白质结构域的富集分析表明，泛素化在各种受体样激酶和细胞质酪氨酸和丝氨酸-苏氨酸激酶上富集。此外，我们分析了泛素化、乙酰化和琥珀酰化之间的串扰，并在我们的水稻泛素组内构建了一个潜在的蛋白质相互作用网络。此外，我们鉴定了与花粉和籽粒发育相关的泛素化蛋白，表明泛素化可能在幼穗的生理功能中发挥关键作用。总之，我们报道了迄今为止在水稻中最全面的赖氨酸泛素组，并利用它揭示了赖氨酸泛素化在水稻幼穗中的功能作用。
