The regulatory landscape of the human HPF1-and ARH3-dependent ADP-ribosylome

Ivo A. Hendriks, Sara C. Buch-Larsen, Evgeniia Prokhorova, Jonas D. Elsborg, Alexandra K. L. F. S. Rebak, Kang Zhu, Dragana Ahel, Claudia Lukas, Ivan Ahel, Michael L. Nielsen*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

ADP-ribosylation is regulated by HPF1 and ARH3, but the cellular target spectrum of these enzymes is not fully understood. Here, the authors use quantitative proteomics to define the HPF1- and ARH3-dependent ADP-ribosylome, providing evidence that mono-ADP-ribosylation of serine predominates in cells.

Despite the involvement of Poly(ADP-ribose) polymerase-1 (PARP1) in many important biological pathways, the target residues of PARP1-mediated ADP-ribosylation remain ambiguous. To explicate the ADP-ribosylation regulome, we analyze human cells depleted for key regulators of PARP1 activity, histone PARylation factor 1 (HPF1) and ADP-ribosylhydrolase 3 (ARH3). Using quantitative proteomics, we characterize 1,596 ADP-ribosylation sites, displaying up to 1000-fold regulation across the investigated knockout cells. We find that HPF1 and ARH3 inversely and homogenously regulate the serine ADP-ribosylome on a proteome-wide scale with consistent adherence to lysine-serine-motifs, suggesting that targeting is independent of HPF1 and ARH3. Notably, we do not detect an HPF1-dependent target residue switch from serine to glutamate/aspartate under the investigated conditions. Our data support the notion that serine ADP-ribosylation mainly exists as mono-ADP-ribosylation in cells, and reveal a remarkable degree of histone co-modification with serine ADP-ribosylation and other post-translational modifications.

Original languageEnglish
Article number5893
JournalNature Communications
Volume12
Issue number1
Number of pages16
ISSN2041-1723
DOIs
Publication statusPublished - 2021

Keywords

  • ACETYLATION POSTTRANSLATIONAL MODIFICATIONS
  • POLY(ADENOSINE DIPHOSPHATE RIBOSYLATION)
  • DNA-DAMAGE RESPONSE
  • POLY(ADP-RIBOSE) POLYMERASE
  • IDENTIFICATION
  • SERINE
  • CHROMATIN
  • PROTEOME
  • STRATEGY
  • HISTONES

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