Identification of Protein Direct Interactome with Genetic Code Expansion and Search Engine OpenUaa

文献类型： 外文期刊

第一作者： Liu, Chao

作者： Liu, Chao;Yang, Hao;Gong, Pengyun;Liu, Chao;Yang, Hao;Gong, Pengyun;Wu, Ting;Shu, Xin;Zhang, Long;Yang, Bing;Wu, Ting;Shu, Xin;Zhang, Long;Yang, Bing;Li, Shang-Tong;Li, Shang-Tong;Wang, Daniel R.;Wang, Nanxi;Wang, Lei;Wang, Daniel R.;Wang, Nanxi;Wang, Lei;Zhou, Rong;Li, Kui;Jiang, Hong;Hendriks, Ivo A.;Nielsen, Michael L.

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关键词： database search engine; genetic code expansion; mass spectrometry; protein direct interactome

期刊名称：ADVANCED BIOLOGY

ISSN： 2701-0198

年卷期： 2021 年 5 卷 3 期

页码：

收录情况： SCI

摘要： Protein crosslinks occur endogenously such as modifications by ubiquitin-like proteins for signaling, or exogenously through genetically encoded chemical crosslinkers (GECX) for studying elusive protein-protein interactions. However, it remains challenging to identify these protein crosslinks efficiently at the proteomic scale. Herein, software OpenUaa is developed for identifying protein crosslinks generated by genetically encoded unnatural amino acids and endogenous protein conjugation. OpenUaa features inclusive and open search capability, dramatically improving identification sensitivity and coverage. Integrating GECX with OpenUaa, the direct interactome of thioredoxin is identified in Escherichia coli cells, yielding 289 crosslinked peptides and corresponding to 205 direct binding protein of thioredoxin. These identified direct binders provide evidence for thioredoxin's regulation of redox state and mitochondria energy metabolism. When identifying endogenous conjugation of small ubiquitin-like modifier (SUMO), OpenUaa also markedly improves coverage of SUMOylated peptides by approximate to 92%, revealing new SUMO targets. GECX-OpenUaa will enable efficient identification of direct interactomes of various proteins in live cells.

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