Literature DB >> 29954836

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

Deena M Leslie Pedrioli1, Mario Leutert1,2, Vera Bilan1, Kathrin Nowak1,2, Kapila Gunasekera1, Elena Ferrari1, Ralph Imhof1, Lars Malmström3, Michael O Hottiger4.   

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.
© 2018 The Authors.

Entities:  

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

Mesh：

Substances：

Year:  2018        PMID： 29954836      PMCID： PMC6073207          DOI： 10.15252/embr.201745310

Source DB:  PubMed          Journal:  EMBO Rep        ISSN： 1469-221X            Impact factor:   8.807


  39 in total

1.  Optimization of LTQ-Orbitrap Mass Spectrometer Parameters for the Identification of ADP-Ribosylation Sites.

Authors:  Florian Rosenthal; Paolo Nanni; Simon Barkow-Oesterreicher; Michael O Hottiger
Journal:  J Proteome Res       Date:  2015-08-10       Impact factor: 4.466

2.  Mapping PARP-1 auto-ADP-ribosylation sites by liquid chromatography-tandem mass spectrometry.

Authors:  John D Chapman; Jean-Philippe Gagné; Guy G Poirier; David R Goodlett
Journal:  J Proteome Res       Date:  2013-03-18       Impact factor: 4.466

3.  Proteome-Wide Identification of In Vivo ADP-Ribose Acceptor Sites by Liquid Chromatography-Tandem Mass Spectrometry.

Authors:  Sara C Larsen; Mario Leutert; Vera Bilan; Rita Martello; Stephanie Jungmichel; Clifford Young; Michael O Hottiger; Michael L Nielsen
Journal:  Methods Mol Biol       Date:  2017

Review 4.  On PAR with PARP: cellular stress signaling through poly(ADP-ribose) and PARP-1.

Authors:  Xin Luo; W Lee Kraus
Journal:  Genes Dev       Date:  2012-03-01       Impact factor: 11.361

5.  Identification of ADP-Ribose Acceptor Sites on In Vitro Modified Proteins by Liquid Chromatography-Tandem Mass Spectrometry.

Authors:  Mario Leutert; Vera Bilan; Peter Gehrig; Michael O Hottiger
Journal:  Methods Mol Biol       Date:  2017

6.  Combining Higher-Energy Collision Dissociation and Electron-Transfer/Higher-Energy Collision Dissociation Fragmentation in a Product-Dependent Manner Confidently Assigns Proteomewide ADP-Ribose Acceptor Sites.

Authors:  Vera Bilan; Mario Leutert; Paolo Nanni; Christian Panse; Michael O Hottiger
Journal:  Anal Chem       Date:  2017-01-13       Impact factor: 6.986

7.  Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation.

Authors:  Bryan A Gibson; Yajie Zhang; Hong Jiang; Kristine M Hussey; Jonathan H Shrimp; Hening Lin; Frank Schwede; Yonghao Yu; W Lee Kraus
Journal:  Science       Date:  2016-06-02       Impact factor: 47.728

8.  PARP1 and PARP2 stabilise replication forks at base excision repair intermediates through Fbh1-dependent Rad51 regulation.

Authors:  George E Ronson; Ann Liza Piberger; Martin R Higgs; Anna L Olsen; Grant S Stewart; Peter J McHugh; Eva Petermann; Nicholas D Lakin
Journal:  Nat Commun       Date:  2018-02-21       Impact factor: 14.919

9.  Proteome-wide identification of the endogenous ADP-ribosylome of mammalian cells and tissue.

Authors:  Rita Martello; Mario Leutert; Stephanie Jungmichel; Vera Bilan; Sara C Larsen; Clifford Young; Michael O Hottiger; Michael L Nielsen
Journal:  Nat Commun       Date:  2016-09-30       Impact factor: 14.919

10.  Deficiency of terminal ADP-ribose protein glycohydrolase TARG1/C6orf130 in neurodegenerative disease.

Authors:  Reza Sharifi; Rosa Morra; C Denise Appel; Michael Tallis; Barry Chioza; Gytis Jankevicius; Michael A Simpson; Ivan Matic; Ege Ozkan; Barbara Golia; Matthew J Schellenberg; Ria Weston; Jason G Williams; Marianna N Rossi; Hamid Galehdari; Juno Krahn; Alexander Wan; Richard C Trembath; Andrew H Crosby; Dragana Ahel; Ron Hay; Andreas G Ladurner; Gyula Timinszky; R Scott Williams; Ivan Ahel
Journal:  EMBO J       Date:  2013-03-12       Impact factor: 11.598
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  29 in total

1.  ELTA: Enzymatic Labeling of Terminal ADP-Ribose.

Authors:  Yoshinari Ando; Elad Elkayam; Robert Lyle McPherson; Morgan Dasovich; Shang-Jung Cheng; Jim Voorneveld; Dmitri V Filippov; Shao-En Ong; Leemor Joshua-Tor; Anthony K L Leung
Journal:  Mol Cell       Date:  2019-01-31       Impact factor: 17.970

Review 2.  Poly(ADP-Ribosylation) in Age-Related Neurological Disease.

Authors:  Leeanne McGurk; Olivia M Rifai; Nancy M Bonini
Journal:  Trends Genet       Date:  2019-06-07       Impact factor: 11.639

Review 3.  The chemistry of the vitamin B3 metabolome.

Authors:  Mikhail V Makarov; Samuel A J Trammell; Marie E Migaud
Journal:  Biochem Soc Trans       Date:  2018-12-17       Impact factor: 5.407

4.  An Advanced Strategy for Comprehensive Profiling of ADP-ribosylation Sites Using Mass Spectrometry-based Proteomics.

Authors:  Ivo A Hendriks; Sara C Larsen; Michael L Nielsen
Journal:  Mol Cell Proteomics       Date:  2019-02-23       Impact factor: 5.911

5.  Ion-Pairing with Triethylammonium Acetate Improves Solid-Phase Extraction of ADP-Ribosylated Peptides.

Authors:  Robert Lyle McPherson; Shao-En Ong; Anthony K L Leung
Journal:  J Proteome Res       Date:  2020-01-07       Impact factor: 4.466

6.  ADP-ribosylation of histone variant H2AX promotes base excision repair.

Authors:  Qian Chen; Chunjing Bian; Xin Wang; Xiuhua Liu; Muzaffer Ahmad Kassab; Yonghao Yu; Xiaochun Yu
Journal:  EMBO J       Date:  2020-12-02       Impact factor: 11.598

7.  Molecular Tools for the Study of ADP-Ribosylation: A Unified and Versatile Method to Synthesise Native Mono-ADP-Ribosylated Peptides.

Authors:  Jim Voorneveld; Johannes Gregor Matthias Rack; Luke van Gijlswijk; Nico J Meeuwenoord; Qiang Liu; Herman S Overkleeft; Gijsbert A van der Marel; Ivan Ahel; Dmitri V Filippov
Journal:  Chemistry       Date:  2021-05-06       Impact factor: 5.020

8.  A Study into the ADP-Ribosylome of IFN-γ-Stimulated THP-1 Human Macrophage-like Cells Identifies ARTD8/PARP14 and ARTD9/PARP9 ADP-Ribosylation.

Authors:  Hideyuki Higashi; Takashi Maejima; Lang Ho Lee; Yukiyoshi Yamazaki; Michael O Hottiger; Sasha A Singh; Masanori Aikawa
Journal:  J Proteome Res       Date:  2019-03-21       Impact factor: 4.466

9.  Serine-linked PARP1 auto-modification controls PARP inhibitor response.

Authors:  Evgeniia Prokhorova; Florian Zobel; Rebecca Smith; Siham Zentout; Ian Gibbs-Seymour; Kira Schützenhofer; Alessandra Peters; Joséphine Groslambert; Valentina Zorzini; Thomas Agnew; John Brognard; Michael L Nielsen; Dragana Ahel; Sébastien Huet; Marcin J Suskiewicz; Ivan Ahel
Journal:  Nat Commun       Date:  2021-07-01       Impact factor: 14.919

10.  Interplay of Histone Marks with Serine ADP-Ribosylation.

Authors:  Edward Bartlett; Juan José Bonfiglio; Evgeniia Prokhorova; Thomas Colby; Florian Zobel; Ivan Ahel; Ivan Matic
Journal:  Cell Rep       Date:  2018-09-25       Impact factor: 9.423
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