Combining Chemical Genetics with Proximity-Dependent Labeling Reveals Cellular Targets of Poly(ADP-ribose) Polymerase 14 (PARP14)

ACS Chem Biol. 2018 Oct 19;13(10):2841-2848. doi: 10.1021/acschembio.8b00567. Epub 2018 Sep 28.

Abstract

Poly(ADP-ribose) polymerase 14 (PARP14) is a member of the PARP family of enzymes that transfer ADP-ribose from NAD+ to nucleophilic amino acids on target proteins, a process known as mono-ADP-ribosylation (MARylation). PARP14 is involved in normal immune function through the IL-4 signaling pathway and is a prosurvival factor in multiple myeloma and hepatocellular carcinoma. A mechanistic understanding of the physiological and pathophysiological roles of PARP14 has been limited by the dearth of PARP14-specific MARylation targets. Herein we engineered a PARP14 variant that uses an NAD+ analog that is orthogonal to wild-type PARPs for identifying PARP14-specific MARylation targets. Combining this chemical genetics approach with a BioID approach for proximity-dependent labeling of PARP14 interactors, we identified 114 PARP14-specific protein substrates, several of which are RNA regulatory proteins. One of these targets is PARP13, a protein known to play a role in regulating RNA stability. PARP14 MARylates PARP13 on several acidic amino acids. This study not only reveals crosstalk among PARP family members but also highlights the advantage of using disparate approaches for identifying the direct targets of individual PARP family members.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • ADP-Ribosylation
  • Carbon-Nitrogen Ligases / genetics
  • Chromatography, Liquid
  • Click Chemistry
  • DEAD-box RNA Helicases / chemistry
  • DEAD-box RNA Helicases / metabolism
  • Escherichia coli Proteins / genetics
  • HEK293 Cells
  • Humans
  • Molecular Biology / methods
  • NAD / analogs & derivatives
  • NAD / metabolism
  • Point Mutation
  • Poly(ADP-ribose) Polymerases / genetics
  • Poly(ADP-ribose) Polymerases / metabolism*
  • Protein Binding
  • Protein Engineering / methods
  • Proto-Oncogene Proteins / chemistry
  • Proto-Oncogene Proteins / metabolism
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism*
  • Recombinant Fusion Proteins / genetics
  • Repressor Proteins / genetics
  • Tandem Mass Spectrometry

Substances

  • Escherichia coli Proteins
  • Proto-Oncogene Proteins
  • RNA-Binding Proteins
  • Recombinant Fusion Proteins
  • Repressor Proteins
  • ZC3HAV1 protein, human
  • NAD
  • PARP14 protein, human
  • Poly(ADP-ribose) Polymerases
  • DDX6 protein, human
  • DEAD-box RNA Helicases
  • Carbon-Nitrogen Ligases
  • birA protein, E coli