生物
核蛋白
计算生物学
核仁
核糖核蛋白
核运输
核孔
基因组
细胞核
遗传学
细胞生物学
核心
基因
核糖核酸
转录因子
作者
Shuaijian Dai,Shichang Liu,Chen Zhou,Fengchao Yu,Guang Zhu,Wenhao Zhang,Haiteng Deng,Alma L. Burlingame,Weichuan Yu,Tingliang Wang,Ning Li
标识
DOI:10.1016/j.molp.2023.03.013
摘要
Nuclear proteins are major constituents and key regulators of nucleome topological organization and manipulators of nuclear events. To decipher the global connectivity of nuclear proteins and the hierarchically organized modules of their interactions, we conducted two rounds of cross-linking mass spectrometry (XL-MS) analysis, one of which followed a quantitative double chemical cross-linking mass spectrometry (in vivo qXL-MS) workflow, and identified 24,140 unique crosslinks in total from the nuclei of soybean seedlings. This in vivo quantitative interactomics enabled the identification of 5340 crosslinks that can be converted into 1297 nuclear protein–protein interactions (PPIs), 1220 (94%) of which were non-confirmative (or novel) nuclear PPIs compared with those in repositories. There were 250 and 26 novel interactors of histones and the nucleolar box C/D small nucleolar ribonucleoprotein complex, respectively. Modulomic analysis of orthologous Arabidopsis PPIs produced 27 and 24 master nuclear PPI modules (NPIMs) that contain the condensate-forming protein(s) and the intrinsically disordered region–containing proteins, respectively. These NPIMs successfully captured previously reported nuclear protein complexes and nuclear bodies in the nucleus. Surprisingly, these NPIMs were hierarchically assorted into four higher-order communities in a nucleomic graph, including genome and nucleolus communities. This combinatorial pipeline of 4C quantitative interactomics and PPI network modularization revealed 17 ethylene-specific module variants that participate in a broad range of nuclear events. The pipeline was able to capture both nuclear protein complexes and nuclear bodies, construct the topological architectures of PPI modules and module variants in the nucleome, and probably map the protein compositions of biomolecular condensates.
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