Comprehensive ADP-ribosylome analysis identifies tyrosine as an ADP-ribose acceptor site

  • EMBO Rep. 2018 Aug;19(8):e45310. doi: 10.15252/embr.201745310.
Deena M Leslie Pedrioli  1 ,  Mario Leutert  1  2 ,  Vera Bilan  1 ,  Kathrin Nowak  1  2 ,  Kapila Gunasekera  1 ,  Elena Ferrari  1 ,  Ralph Imhof  1 ,  Lars Malmström  3 ,  Michael O Hottiger  4
Affiliations
  • 1. Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
  • 2. Molecular Life Science PhD Program of the Life Science Zurich Graduate School, Zurich, Switzerland.
  • 3. S3IT and Institute for Computational Science, University of Zurich, Zurich, Switzerland.
  • 4. Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland [email protected].
PMID: 29954836 DOI: 10.15252/embr.201745310
Abstract

Despite recent mass spectrometry (MS)-based breakthroughs, comprehensive ADP-ribose (ADPr)-acceptor amino acid identification and ADPr-site localization remain challenging. Here, we report the establishment of an unbiased, multistep ADP-ribosylome data analysis workflow that led to the identification of tyrosine as a novel ARTD1/PARP1-dependent in vivo ADPr-acceptor amino acid. MS analyses of in vitro ADP-ribosylated proteins confirmed tyrosine as an ADPr-acceptor amino acid in RPS3A (Y155) and HPF1 (Y238) and demonstrated that trans-modification of RPS3A is dependent on HPF1. We provide an ADPr-site Localization Spectra Database (ADPr-LSD), which contains 288 high-quality ADPr-modified peptide spectra, to serve as ADPr spectral references for correct ADPr-site localizations.

Keywords
ADP‐ribosylation; ARTD1/PARP1; HPF1; genotoxic stress; tyrosine ADP‐ribosylation.