ETD-Based Proteomic Profiling Improves Arginine Methylation Identification and Reveals Novel PRMT5 Substrates
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ETD-Based Proteomic Profiling Improves Arginine Methylation Identification and Reveals Novel PRMT5 Substrates. / Lu, Lingzi; Ye, Zilu; Zhang, Rou; Olsen, Jesper V.; Yuan, Yanqiu; Mao, Yang.
In: Journal of Proteome Research, Vol. 23, No. 3, 2024, p. 1014-1027.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - ETD-Based Proteomic Profiling Improves Arginine Methylation Identification and Reveals Novel PRMT5 Substrates
AU - Lu, Lingzi
AU - Ye, Zilu
AU - Zhang, Rou
AU - Olsen, Jesper V.
AU - Yuan, Yanqiu
AU - Mao, Yang
N1 - Publisher Copyright: © 2024 American Chemical Society.
PY - 2024
Y1 - 2024
N2 - 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.
AB - 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.
KW - arginine methylation
KW - electron transfer dissociation
KW - PRMT5
KW - proteomics
U2 - 10.1021/acs.jproteome.3c00724
DO - 10.1021/acs.jproteome.3c00724
M3 - Journal article
C2 - 38272855
AN - SCOPUS:85184917800
VL - 23
SP - 1014
EP - 1027
JO - Journal of Proteome Research
JF - Journal of Proteome Research
SN - 1535-3893
IS - 3
ER -
ID: 383430131