An Unbiased Proteomic Platform for Activity-based Arginylation Profiling

Lin, Z.; Xie, Y.; Gongora, J.; Liu, X.; Zahn, E.; Palai, B. B.; Ramirez, D.; Searfoss, R.; Vitorino, F. N.; Dann, G. P.; Zhao, C.; Han, X.; Mactaggart, B.; Lan, X.; Fu, D.; Greenberg, L.; Zhang, Y.; Lavine, K. J.; Greenberg, M. J.; Lyu, D.; Kashina, A. S.; Garcia, B. A.

doi:10.1101/2024.06.01.596974

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bioRxiv · 10.1101/2024.06.01.596974

An Unbiased Proteomic Platform for Activity-based Arginylation Profiling

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Abstract

Protein arginylation is an essential posttranslational modification (PTM) catalyzed by arginyl-tRNA-protein transferase 1 (ATE1) in mammalian systems. Arginylation features a post-translational conjugation of an arginyl to a protein, making it extremely challenging to differentiate from translational arginine residues with the same mass in a protein sequence. Here we present a general ATE1-based arginylation profiling platform for the unbiased discovery of arginylation substrates and their precise modification sites. This method integrates isotopic arginine labeling into an ATE1 assay utilizing biological lysates (ex vivo) rather than live cells, thus eliminating translational bias derived from the ribosomal activity and enabling bona fide arginylation identification using isotopic features. The method has been successfully applied to an array of peptide, protein, cell, patient, and animal tissue samples using 20 {micro}g sample input, with 235 unique arginylation sites revealed from human proteomes. Representative sites were validated and followed up for their biological functions. The developed platform is globally applicable to the aforementioned sample types and therefore paves the way for functional studies of this difficult-to-characterize protein modification.

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Lin, Z., Xie, Y., Gongora, J., Liu, X., Zahn, E., Palai, B. B., Ramirez, D., Searfoss, R., Vitorino, F. N., Dann, G. P., Zhao, C., Han, X., Mactaggart, B., Lan, X., Fu, D., Greenberg, L., Zhang, Y., Lavine, K. J., Greenberg, M. J., Lyu, D., Kashina, A. S., Garcia, B. A.. 2024-06-02. An Unbiased Proteomic Platform for Activity-based Arginylation Profiling. https://doi.org/10.1101/2024.06.01.596974

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