Robust high-throughput assays to assess discrete steps in ubiquitination and related cascades

BMC Mol Cell Biol. 2020 Mar 30;21(1):21. doi: 10.1186/s12860-020-00262-5.

Abstract

Background: Ubiquitination and ubiquitin-like protein post-translational modifications play an enormous number of roles in cellular processes. These modifications are constituted of multistep reaction cascades. Readily implementable and robust methods to evaluate each step of the overall process, while presently limited, are critical to the understanding and modulation of the reaction sequence at any desired level, both in terms of basic research and potential therapeutic drug discovery and development.

Results: We developed multiple robust and reliable high-throughput assays to interrogate each of the sequential discrete steps in the reaction cascade leading to protein ubiquitination. As models for the E1 ubiquitin-activating enzyme, the E2 ubiquitin-conjugating enzyme, the E3 ubiquitin ligase, and their ultimate substrate of ubiquitination in a cascade, we examined Uba1, Rad6, Rad18, and proliferating cell nuclear antigen (PCNA), respectively, in reconstituted systems. Identification of inhibitors of this pathway holds promise in cancer therapy since PCNA ubiquitination plays a central role in DNA damage tolerance and resulting mutagenesis. The luminescence-based assays we developed allow for the quantitative determination of the degree of formation of ubiquitin thioester conjugate intermediates with both E1 and E2 proteins, autoubiquitination of the E3 protein involved, and ubiquitination of the final substrate. Thus, all covalent adducts along the cascade can be individually probed. We tested previously identified inhibitors of this ubiquitination cascade, finding generally good correspondence between compound potency trends determined by more traditional low-throughput methods and the present high-throughput ones.

Conclusions: These approaches are readily adaptable to other E1, E2, and E3 systems, and their substrates in both ubiquitination and ubiquitin-like post-translational modification cascades.

Keywords: E1 ubiquitin-conjugating enzymes; E2 ubiquitin-conjugating enzymes; E3 ubiquitin ligases; High-throughput screening; Post-translational modifications; Step-specific assays and evaluation; Ubiquitin-like proteins; Ubiquitination.

MeSH terms

  • DNA Damage
  • Proliferating Cell Nuclear Antigen* / analysis
  • Proliferating Cell Nuclear Antigen* / metabolism
  • Protein Processing, Post-Translational*
  • Ubiquitin / chemistry
  • Ubiquitin / metabolism
  • Ubiquitin-Conjugating Enzymes / chemistry
  • Ubiquitin-Protein Ligases / chemistry
  • Ubiquitination*
  • Ubiquitins / chemistry
  • Ubiquitins / metabolism

Substances

  • Proliferating Cell Nuclear Antigen
  • Ubiquitin
  • Ubiquitins
  • Ubiquitin-Conjugating Enzymes
  • Ubiquitin-Protein Ligases