K48- and K63-linked ubiquitin chain interactome reveals branch- and length-specific interactors.

Waltho, A.; Popp, O.; Lenz, C.; Pluska, L.; Dötsch, V.; Mertins, P.; Sommer, T.

doi:10.1101/2024.01.08.574586

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bioRxiv · 10.1101/2024.01.08.574586

K48- and K63-linked ubiquitin chain interactome reveals branch- and length-specific interactors.

Waltho, A.·Popp, O.·Lenz, C.·Pluska, L.·Dötsch, V.·Mertins, P.·Sommer, T.

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Abstract

The ubiquitin (Ub) code denotes the complex Ub architectures, including Ub chains of different length, linkage-type and linkage combinations, which enable ubiquitination to control a wide range of protein fates. Although many linkage-specific interactors have been described, how interactors are able to decode more complex architectures is not fully understood. We conducted a Ub interactor screen, in humans and yeast, using Ub chains of varying length, as well as, homotypic and heterotypic branched chains of the two most abundant linkage types - K48- and K63-linked Ub. We identified some of the first K48/K63 branch-specific Ub interactors, including histone ADP-ribosyltransferase PARP10/ARTD10, E3 ligase UBR4 and huntingtin-interacting protein HIP1. Furthermore, we revealed the importance of chain length by identifying interactors with a preference for Ub3 over Ub2 chains, including Ub-directed endoprotease DDI2, autophagy receptor CCDC50 and p97-adaptor FAF1. Crucially, we compared datasets collected using two common DUB inhibitors - Chloroacetamide and N-ethylmaleimide. This revealed inhibitor-dependent interactors, highlighting the importance of inhibitor consideration during pulldown studies. This dataset is a key resource for understanding how the Ub code is read.

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Waltho, A., Popp, O., Lenz, C., Pluska, L., Dötsch, V., Mertins, P., Sommer, T.. 2024-01-08. K48- and K63-linked ubiquitin chain interactome reveals branch- and length-specific interactors.. https://doi.org/10.1101/2024.01.08.574586

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