Dataset Information

Tudor-based Proteomic Strategy Pan-specifically Enriches and Identifies Protein Arginine Methylation

ABSTRACT: In current study, we developed a molecular affinity strategy based on the Tudor domain of SMN, a naturally occurring methylarginine reader protein, for comprehensive proteomic profiling of cellular arginine methylation. We demonstrated that the Tudor domain-based approach exhibits broad specificity for proteins harboring mono- or di-methylated arginines, encompassing both RGG/RG-rich and non-RG motifs, facilitating the discovery of novel methylation sites. Using this strategy, we identified asymmetric dimethylarginine (aDMA) at the N-terminal of eIF3D, an essential component of the eukaryotic translation initiation complex. Biochemical analysis revealed that aDMA modification at R99 of eIF3D plays a regulatory role in protein translation initiation. Our findings establish a generally applicable approach for proteomic profiling of arginine methylation and unveil its novel regulatory role for this modification in eukaryotic protein translation.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: 凌子卢

LAB HEAD: Yanqiu Yuan

PROVIDER: PXD053390 | Pride | 2025-12-15

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20220419_EIF3D_2h_10HCD_20ng-2_220420183952.raw	Raw
	20230331_LUMOS1_nLC3_ZY_LLZ_2_hmSILAC_Trypsin_ETD_2ul_01.pdResult	Other
	20230331_LUMOS1_nLC3_ZY_LLZ_2_hmSILAC_Trypsin_ETD_2ul_01.raw	Raw
	20230331_LUMOS1_nLC3_ZY_LLZ_2_hmSILAC_Trypsin_ETD_heavy_2ul_01.pdResult	Other
	20230331_LUMOS1_nLC3_ZY_LLZ_Hela_WT_trypsin_SMN_enrich_10ul_replicate1.pdResult	Other

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Publications

Tudor-based proteomic strategy pan-specifically enriches and identifies protein arginine methylation.

Lu Lingzi L Li Ting T Zhang Rou R Wang Yutong Y Ye Xiaoping X Luo Yixin Y Sun Lingyu L Qi Liang L Ye Zilu Z Mao Yang Y Yuan Yanqiu Y

EMBO reports 20251020 23

Protein arginine methylation is an important post-translational modification (PTM) in eukaryotes, regulating a variety of biological processes. Proteomic profiling of arginine methylation has advanced our understanding of its roles in biology and disease. However, pan-specific enrichment of methylarginine-containing peptides remains challenging. Herein we report a molecular affinity strategy based on the Tudor domain of SMN, a naturally occurring methylarginine reader protein, for comprehensive ...[more]

PMID: 41116072

Similar Datasets

Project description:PRMT5 is the major enzyme that catalyzes the symmetric dimethylation of arginine (sDMA) in mammalian cells. Its activity is crucial for many biological processes including transcriptional regulation, mRNA processing, as well as DNA damage and repair. However, the protein substrates identified for PRMT5 have yet been limited in numbers, hindering the understanding of PRMT5 functions in normal as well as diseased cells. Herein we developed an optimized strategy for proteomic profiling of cellular sDMA and apply it to the discovery of novel PRMT5 substrates. Our results show that a combination of proteolytic digestion by the metalloprotease ulilysin and using electron-transfer dissociation with supplemental activation as the mass spectrometry method significantly increased sDMA site identification and localization after immuno-affinity enrichment. By employing SILAC-based differential quantitative proteomic approach and a PRMT5 specific inhibitor, we identified 325 sDMA sites being regulated by PRMT5, 220 being novel sites, which greatly expanded the number of PRMT5 substrates. Biochemical studies confirmed the newly discovered PRMT5 substrate, Plasminogen activator inhibitor 1 RNA-binding protein (SERBP1) and revealed that the RGG/RG motif in the central region of SERBP1 contains both PRMT5-catalyzed sDMA and Type I PRMT-catalyzed asymmetric dimethylation of arginine (aDMA). Unexpectedly, using the optimized methylarginine profiling strategy, we also discovered arginine trimethylation, a previously unknown type of modification, on the central RGG/RG region of SERBP1. By mutational studies we demonstrated that the trimethyl modification on R172 of SERBP1 regulates its recruitment to stress granule (SG) under oxidative stress, indicating a functional role of arginine trimethylation in the cell. Overall, the optimized profiling strategy not only enabled the identification of extensive, non-overlapping sDMA sites and novel PRMT5 substrates, but also revealed a potentially important new PTM, arginine trimethylation. The work lays the foundation for further investigations on the functional interplay of different methylation modifications on arginines, especially in the heavily methylated RGG/RG motif of many RNA-binding proteins.