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

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 proteomic profiling of cellular arginine methylation. We demonstrate 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 identify asymmetric dimethylarginine (aDMA) in protein eIF3D, an essential component of the eukaryotic translation initiation complex. Biochemical analyses reveal 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.