An unbiased proteomic platform for ATE1-based arginylation profiling

Zongtao Lin¹, Yixuan Xie², Joanna Gongora², Xingyu Liu², Emily Zahn², Bibhuti Bhusana Palai², Daniel H Ramirez², Richard M Searfoss², Francisca N Vitorino², Rashmi Karki², Geoffrey P Dann³, Chenfeng Zhao⁴, Xian Han², Brittany MacTaggart⁵, Xin Lan⁶, Dechen Fu⁶, Lina Greenberg², Yi Zhang⁶, Kory J Lavine⁷, Michael J Greenberg², Dongwen Lv^{8

9}, Anna Kashina⁵, Benjamin A Garcia¹⁰

Affiliations

¹ Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA. zongtao@wustl.edu.
² Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA.
³ Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
⁴ McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA.
⁵ School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
⁶ Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA.
⁷ Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
⁸ Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
⁹ Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA.
¹⁰ Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA. bagarcia@wustl.edu.

PMID: 40855110
DOI: 10.1038/s41589-025-01996-z

An unbiased proteomic platform for ATE1-based arginylation profiling

Zongtao Lin et al. Nat Chem Biol. 2025.

. 2025 Aug 25.

doi: 10.1038/s41589-025-01996-z. Online ahead of print.

Authors

Affiliations

¹ Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA. zongtao@wustl.edu.
² Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA.
³ Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
⁴ McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA.
⁵ School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
⁶ Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA.
⁷ Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
⁸ Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
⁹ Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA.
¹⁰ Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA. bagarcia@wustl.edu.

PMID: 40855110
DOI: 10.1038/s41589-025-01996-z

Abstract

Protein arginylation is an essential post-translational modification 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. 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 ribosomal bias and enabling bona fide arginylation identification. The method has been successfully applied to peptide, protein, cell, patient and mouse samples, with 235 unique arginylation sites revealed from human proteomes using 20 µg of input. Representative sites were validated and followed up for their biological functions. This global platform, applicable to various sample types, paves the way for functional studies of this difficult-to-characterize protein modification.

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Conflict of interest statement

Competing interests: Z.L., D.L. and B.A.G. are cofounders of LasNova Therapeutics, LLC. B.A.G. is paid to be on the advisory board for Quantum Si. The remaining authors declare no competing interests.

Update of

An Unbiased Proteomic Platform for ATE1-based Arginylation Profiling.
Lin Z, Xie Y, Gongora J, Liu X, Zahn E, Palai BB, Ramirez DH, Searfoss RM, Vitorino FN, Karki R, Dann GP, Zhao C, Han X, MacTaggart B, Lan X, Fu D, Greenberg L, Zhang Y, Lavine KJ, Greenberg MJ, Lv D, Kashina A, Garcia BA. Lin Z, et al. bioRxiv [Preprint]. 2025 May 15:2024.06.01.596974. doi: 10.1101/2024.06.01.596974. bioRxiv. 2025. Update in: Nat Chem Biol. 2025 Aug 25. doi: 10.1038/s41589-025-01996-z. PMID: 38854050 Free PMC article. Updated. Preprint.

References

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An unbiased proteomic platform for ATE1-based arginylation profiling

Affiliations

An unbiased proteomic platform for ATE1-based arginylation profiling

Authors

Affiliations

Abstract

Conflict of interest statement

Update of

References

Grants and funding

LinkOut - more resources

Full Text Sources