Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay

Joanna Koszela, Nhan T Pham, David Evans, Stefan Mann, Irene Perez-Pi, Steven Shave, Derek F J Ceccarelli, Frank Sicheri, Mike Tyers, Manfred Auer

Research output: Contribution to journalArticlepeer-review

Abstract

BACKGROUND: The ubiquitin-proteasome system (UPS) controls the stability, localization and/or activity of the proteome. However, the identification and characterization of complex individual ubiquitination cascades and their modulators remains a challenge. Here, we report a broadly applicable, multiplexed, miniaturized on-bead technique for real-time monitoring of various ubiquitination-related enzymatic activities. The assay, termed UPS-confocal fluorescence nanoscanning (UPS-CONA), employs a substrate of interest immobilized on a micro-bead and a fluorescently labeled ubiquitin which, upon enzymatic conjugation to the substrate, is quantitatively detected on the bead periphery by confocal imaging.

RESULTS: UPS-CONA is suitable for studying individual enzymatic activities, including various E1, E2, and HECT-type E3 enzymes, and for monitoring multi-step reactions within ubiquitination cascades in a single experimental compartment. We demonstrate the power of the UPS-CONA technique by simultaneously following ubiquitin transfer from Ube1 through Ube2L3 to E6AP. We applied this multi-step setup to investigate the selectivity of five ubiquitination inhibitors reportedly targeting different classes of ubiquitination enzymes. Using UPS-CONA, we have identified a new activity of a small molecule E2 inhibitor, BAY 11-7082, and of a HECT E3 inhibitor, heclin, towards the Ube1 enzyme.

CONCLUSIONS: As a sensitive, quantitative, flexible, and reagent-efficient method with a straightforward protocol, UPS-CONA constitutes a powerful tool for interrogation of ubiquitination-related enzymatic pathways and their chemical modulators, and is readily scalable for large experiments.

Original languageEnglish
Article number88
Number of pages13
JournalBMC Biology
Volume16
Issue number1
DOIs
Publication statusPublished - 10 Aug 2018

Keywords

  • Bead-based assay
  • Confocal fluorescence
  • Inhibitors
  • Ubiquitin
  • Ubiquitination assay

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