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

Overview of attention for article published in BMC Biology, August 2018
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Title
Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay
Published in
BMC Biology, August 2018
DOI 10.1186/s12915-018-0554-z
Pubmed ID
Authors

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

Abstract

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. 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. 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.

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Geographical breakdown

Country Count As %
Unknown 36 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 13 36%
Researcher 6 17%
Student > Bachelor 5 14%
Student > Master 5 14%
Professor 1 3%
Other 2 6%
Unknown 4 11%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 15 42%
Agricultural and Biological Sciences 7 19%
Chemistry 4 11%
Business, Management and Accounting 2 6%
Neuroscience 2 6%
Other 2 6%
Unknown 4 11%