Specific pupylation as IDEntity reporter (SPIDER) for the identification of protein-biomolecule interactions

作者全名："Jiang, He-Wei; Chen, Hong; Zheng, Yun-Xiao; Wang, Xue-Ning; Meng, Qingfeng; Xie, Jin; Zhang, Jiong; Zhang, ChangSheng; Xu, Zhao-Wei; Chen, Zi-Qing; Wang, Lei; Kong, Wei-Sha; Zhou, Kuan; Ma, Ming-Liang; Zhang, Hai-Nan; Guo, Shu-Juan; Xue, Jun-Biao; Hou, Jing-Li; Liu, Zhe-Yi; Niu, Wen-Xue; Wang, Fang-Jun; Wang, Tao; Li, Wei; Wang, Rui-Na; Dang, Yong-Jun; Czajkowsky, Daniel M.; Pei, JianFeng; Dong, Jia-Jia; Tao, Sheng-Ce"

作者地址："[Jiang, He-Wei; Chen, Hong; Zheng, Yun-Xiao; Wang, Xue-Ning; Meng, Qingfeng; Wang, Lei; Kong, Wei-Sha; Zhou, Kuan; Ma, Ming-Liang; Zhang, Hai-Nan; Guo, Shu-Juan; Xue, Jun-Biao; Tao, Sheng-Ce] Shanghai Jiao Tong Univ, Shanghai Ctr Syst Biomed, Key Lab Syst Biomed, Minist Educ, Shanghai 200240, Peoples R China; [Xie, Jin; Pei, JianFeng] Peking Univ, Acad Adv Interdisciplinary Studies, Ctr Quantitat Biol, Beijing 100871, Peoples R China; [Zhang, Jiong] Anhui Med Univ, Sch Pharm, Inflammat & Immune Mediated Dis Lab Anhui Prov, Hefei 230032, Peoples R China; [Zhang, Jiong; Dong, Jia-Jia] Chinese Acad Sci, Univ Chinese Acad Sci, Shanghai Inst Organ Chem, Ctr Excellence Mol Synth,Key Lab Organofluorine Ch, Shanghai 200240, Peoples R China; [Zhang, ChangSheng] Peking Univ, Coll Chem & Mol Engn, Beijing 100871, Peoples R China; [Xu, Zhao-Wei] Fujian Med Univ, Key Lab Gastrointestinal Canc, Minist Educ, Fuzhou 350122, Peoples R China; [Chen, Zi-Qing] Princeton Univ, Dept Mol Biol, Princeton, NJ 08540 USA; [Hou, Jing-Li] Shanghai Jiao Tong Univ, Instrumental Anal Ctr, Shanghai 200240, Peoples R China; [Liu, Zhe-Yi; Niu, Wen-Xue; Wang, Fang-Jun] Chinese Acad Sci, Dalian Inst Chem Phys, CAS Key Lab Separat Sci Analyt Chem, Dalian 116023, Peoples R China; [Wang, Tao] Peking Univ, Inst Syst Biol, Shenzhen Bay Lab, Shenzhen Grad Sch, Shenzhen 518055, Peoples R China; [Li, Wei] Pharmaceut Univ, Sch Pharm, Dept Med Chem, Nanjing 211198, Peoples R China; [Wang, Rui-Na] Fudan Univ, Sch Basic Med Sci, Dept Biochem & Mol Biol, Key Lab Metab & Mol Med,Minist Educ, Shanghai 200240, Peoples R China; [Dang, Yong-Jun] Chongqing Med Univ, Ctr Novel Target & Therapeut Intervent, Chongqing 400016, Peoples R China; [Czajkowsky, Daniel M.] Shanghai Jiao Tong Univ, Sch Biomed Engn, Shanghai 200240, Peoples R China"

通信作者："Tao, SC (通讯作者)，Shanghai Jiao Tong Univ, Shanghai Ctr Syst Biomed, Key Lab Syst Biomed, Minist Educ, Shanghai 200240, Peoples R China.; Pei, JF (通讯作者)，Peking Univ, Acad Adv Interdisciplinary Studies, Ctr Quantitat Biol, Beijing 100871, Peoples R China.; Dong, JJ (通讯作者)，Chinese Acad Sci, Univ Chinese Acad Sci, Shanghai Inst Organ Chem, Ctr Excellence Mol Synth,Key Lab Organofluorine Ch, Shanghai 200240, Peoples R China."

来源：SCIENCE CHINA-LIFE SCIENCES

ESI学科分类：BIOLOGY & BIOCHEMISTRY

WOS号：WOS:000968027500001

JCR分区：Q1

影响因子：9.1

年份：2023

卷号：　

期号：　

开始页：　

结束页：　

文献类型：Article; Early Access

关键词：proximity labeling; protein-biomolecule interaction; proteomics; pupylation

摘要："Protein-biomolecule interactions play pivotal roles in almost all biological processes. For a biomolecule of interest, the identification of the interacting protein(s) is essential. For this need, although many assays are available, highly robust and reliable methods are always desired. By combining a substrate-based proximity labeling activity from the pupylation pathway of Mycobacterium tuberculosis and the streptavidin (SA)-biotin system, we developed the Specific Pupylation as IDEntity Reporter (SPIDER) method for identifying protein-biomolecule interactions. Using SPIDER, we validated the interactions between the known binding proteins of protein, DNA, RNA, and small molecule. We successfully applied SPIDER to construct the global protein interactome for m(6)A and mRNA, identified a variety of uncharacterized m(6)A binding proteins, and validated SRSF7 as a potential m(6)A reader. We globally identified the binding proteins for lenalidomide and CobB. Moreover, we identified SARS-CoV-2-specific receptors on the cell membrane. Overall, SPIDER is powerful and highly accessible for the study of protein-biomolecule interactions."

基金机构："National Key Research and Development Program of China [2020YFE0202200]; National Natural Science Foundation of China [31900112, 21907065, 31970130, 31670831]; Guangzhou Institutes of Biomedicine and Health of Chinese Academy of Sciences"

基金资助正文："AcknowledgementsThis work was supported by the National Key Research and Development Program of China (2020YFE0202200), the National Natural Science Foundation of China (31900112, 21907065, 31970130 and 31670831). We thank Dr. Heng Zhu for his long-term guidance. We thank Prof. Pilong Li of School of Life Sciences of Tsinghua University for kindly providing the YTHDF family plasmids. We thank Prof. Xichen Bao of Guangzhou Institutes of Biomedicine and Health of Chinese Academy of Sciences for kindly providing the Sox2 plasmid. We thank Prof. Xiaodong Zhao of Shanghai Jiao Tong University and Prof. Jian Yang of Tongji University for critical comments."