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capturing the hierarchically assorted modules of protein–protein interactions in the organized nucleome

Molecular Plant 2023年第5期16卷 930-961页

作者： Shuaijian Dai Shichang Liu chen Zhou Fengchao Yu Guang Zhu Wenhao Zhang Haiteng Deng Al Burlingame Weichuan Yu Tingliang Wang Ning Li Division of Life Science The Hong Kong University of Science and TechnologyHong Kong SARChina Department of chemical and Biological Engineering The Hong Kong University of Science and TechnologyHong KongChina Tsinghua-Peking Joint centre for Life Sciences Centre for Structural BiologySchoolof Life Sciences and Schoolof MedicineTsinghua UniversityBejing 100084China The Hk.UST Shenzhen-Hong Kong collaborative Innovation Research Institute FutianShenzhenGuangdong 518057China Department of Electronic and computer Engineering The Hong Kong University of Science and TechnologyHong Kong SARChina Department of Pharmaceutical chemistry University of CaliforniaSan FranciscoSan FranciscoCAUSA

Nuclear proteins are major constituents and key regulators of nucleome topological organization and manipulators of nuclear *** 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 *** 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 *** were 250 and 26 novel interactors of histones and the nucleolar box c/D small nucleolar ribonucleoprotein complex,*** 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,*** NPIMs successfully captured previously reported nuclear protein complexes and nuclear bodies in the ***,these NPIMs were hierarchically assorted into four higher-order communities in a nucleomic graph,including genome and nucleolus *** combinatorial pipeline of 4c quantitative interactomics and PPI network modularization revealed 17 ethylene-specific module variants that participate in a broad range of nuclear *** 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.

关键词： nucleome 4c interactomics in vivo qXL-MS biomolecular modulomics cHAMPION 4D biomolecular modulomes

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