ETD-Based Proteomic Profiling Improves Arginine Methylation Identification and Reveals Novel PRMT5 Substrates

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Protein arginine methylations are important post-translational modifications (PTMs) in eukaryotes, regulating many biological processes. However, traditional collision-based mass spectrometry methods inevitably cause neutral losses of methylarginines, preventing the deep mining of biologically important sites. Herein we developed an optimized mass spectrometry workflow based on electron-transfer dissociation (ETD) with supplemental activation for proteomic profiling of arginine methylation in human cells. Using symmetric dimethylarginine (sDMA) as an example, we show that the ETD-based optimized workflow significantly improved the identification and site localization of sDMA. Quantitative proteomics identified 138 novel sDMA sites as potential PRMT5 substrates in HeLa cells. Further biochemical studies on SERBP1, a newly identified PRMT5 substrate, confirmed the coexistence of sDMA and asymmetric dimethylarginine in the central RGG/RG motif, and loss of either methylation caused increased the recruitment of SERBP1 to stress granules under oxidative stress. Overall, our optimized workflow not only enabled the identification and localization of extensive, nonoverlapping sDMA sites in human cells but also revealed novel PRMT5 substrates whose sDMA may play potentially important biological functions.
OriginalsprogEngelsk
TidsskriftJournal of Proteome Research
Vol/bind23
Udgave nummer3
Sider (fra-til)1014-1027
ISSN1535-3893
DOI
StatusUdgivet - 2024

Bibliografisk note

Funding Information:
This work was supported by grants from the National Natural Science Foundation of China (32001044 and 32271497); the National Key Research and Development Program, Ministry of Science and Technology of China (2021YFA1200903); Science and Technology Projects in Guangzhou (202103000029); Novo Nordisk Foundation (NNF14CC0001 and NNF17SA0027704) and the program of excellence from the University of Copenhagen (CDO2016); and EPIC-XS project number 823839.

Publisher Copyright:
© 2024 American Chemical Society.

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