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

EMBO Rep. 2018 Aug;19(8):e45310. doi: 10.15252/embr.201745310. Epub 2018 Jun 28.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • ADP-Ribosylation*
  • Adenosine Diphosphate Ribose / metabolism*
  • Amino Acid Sequence
  • Carrier Proteins / metabolism
  • DNA Damage
  • HeLa Cells
  • Humans
  • Mass Spectrometry
  • Nuclear Proteins / metabolism
  • Peptides / chemistry
  • Peptides / metabolism
  • Phosphoproteins / metabolism
  • Poly (ADP-Ribose) Polymerase-1 / metabolism
  • Proteome / metabolism
  • RNA, Small Interfering / metabolism
  • Reproducibility of Results
  • Tyrosine / metabolism*

Substances

  • Carrier Proteins
  • HPF1 protein, human
  • Nuclear Proteins
  • Peptides
  • Phosphoproteins
  • Proteome
  • RNA, Small Interfering
  • Adenosine Diphosphate Ribose
  • Tyrosine
  • PARP1 protein, human
  • Poly (ADP-Ribose) Polymerase-1