The UBA domain of conjugating enzyme Ubc1/Ube2K facilitates assembly of K48/K63‐branched ubiquitin chains

The assembly of a specific polymeric ubiquitin chain on a target protein is a key event in the regulation of numerous cellular processes. Yet, the mechanisms that govern the selective synthesis of particular polyubiquitin signals remain enigmatic. The homologous ubiquitin-conjugating (E2) enzymes Ubc1 (budding yeast) and Ube2K (mammals) exclusively generate polyubiquitin linked through lysine 48 (K48). Uniquely among E2 enzymes, Ubc1 and Ube2K harbor a ubiquitin-binding UBA domain with unknown function. We found that this UBA domain preferentially interacts with ubiquitin chains linked through lysine 63 (K63). Based on structural modeling, in vitro ubiquitination experiments, and NMR studies, we propose that the UBA domain aligns Ubc1 with K63-linked polyubiquitin and facilitates the selective assembly of K48/K63-branched ubiquitin conjugates. Genetic and proteomics experiments link the activity of the UBA domain, and hence the formation of this unusual ubiquitin chain topology, to the maintenance of cellular proteostasis.Deutsche Forschungsgemeinschaft (DFG) http://dx.doi.org/10.13039/501100001659Max‐Planck‐Gesellschaft (MPG) http://dx.doi.org/10.13039/501100004189Peer Reviewe

Ubiquitin-binding domains in polyubiquitin chain synthesis

Ubiquitinierung ist eine essentielle posttranslationale Proteinmodifikation (PTM), die vielfältige Prozesse in eukaryotischen Zellen steuert. Ubiquitin wird zu unterschiedlichen polymeren Ketten zusammengesetzt, wobei E2-Ubiquitin-konjugierende Enzyme häufig eine entscheidende Rolle spielen. Im Rahmen meiner Promotion habe ich die molekularen Grundlagen der Ub Kettensynthese durch die E2-Enzyme Ubc1 und Ubc7 untersucht. Dies geschah mithilfe von in vitro Ubiquitinierungs-Reaktionen, biochemischen und strukturellen Untersuchungen sowie zellbiologischen Experimenten. Ich konnte zeigen, dass zugehörige Ubiquitin-Binde-Domänen (UBDs) die Funktion der E2-Enzyme maßgeblich regulieren. Als einziges unter elf E2-Enzymen in S. cerevisiae enthält Ubc1 eine Ub-bindende UBA Domäne, deren Funktion bisher unklar blieb. Ubc1 modifiziert ausschließlich Lysin 48 (K48) in Ub und wurde mit Proteinqualitätskontrolle sowie der Regulation des Zellzyklus in Verbindung gebracht. Meine Ergebnisse zeigen, dass Ubc1 mithilfe seiner UBA-Domäne vorzugsweise mit K63-verknüpftem Polyubiquitin interagiert, wodurch K48/K63 verzweigte Ub-Ketten entstehen. Basierend auf vorhandenen Strukturinformationen und meinen eigenen röntgenkristallographischen Untersuchungen zeige ich eine Modellstruktur für die Reaktion auf. Meine Ergebnisse stellen eine wesentliche Untersuchungsgrundlage für verzweigten Ub-Ketten dar, über deren Vorkommen und Funktion bisher wenig bekannt ist. Ubc7 assembliert mithilfe seines Kofaktors Cue1 K48-verknüpfte Ub-Ketten im Rahmen des Endoplasmatisches-Retikulum-assoziierten Proteinabbaus (ERAD). In einem kollaborativen Projekt haben wir die Ub-bindende CUE-Domäne in Cue1, die hierfür eine Schlüsselrolle spielt, untersucht. Sie ermöglicht die Ausrichtung des E2-Enzyms an der distalen Spitze der Ub-Kette für eine schnelle Kettenverlängerung, besitzt einzigartige auf den Prozess angepasste Bindungseigenschaften und ihre Beeinträchtigung stört den Abbau des ERAD-Substrates Ubc6.Ubiquitination is an essential posttranslational protein modification (PTM) that regulates widespread intracellular processes in eukaryotic cells. Ubiquitin (Ub) can be assembled into polymeric chains through its seven internal lysine residues and the N-terminus enabling the formation of a complex "Ubiquitin Code". Factors that guide the molecular machinery which produces this code remain poorly understood. In this study, I demonstrate that ubiquitin binding domains (UBDs) associated with the E2 enzymes Ubc1 and Ubc7 substantially contribute to the assembly of particular Ub chains. Uniquely among the eleven E2 enzymes of S. cerevisiae Ubc1 contains a ubiquitin binding UBA domain. Ubc1 exclusively modifies lysine 48 (K48) in Ub and has been implicated in protein quality control and cell cycle progression. However, the function of its UBA domain remained elusive. I identified Ubc1 to preferentially target specific Ub molecules in K63-linked polyubiquitin via its UBA domain. This activity results in the assembly of K48/K63 branched Ub chains. Based on existing structural information and my own X-ray crystallographic experiments, I propose a structure for the transition state of branched chain assembly by Ubc1. My findings provide a basis for the study of this unusual Ub chain type. Ubc7 has previously been shown to be activated by its co-factor Cue1 to assemble Ub chains linked through lysine 48 (K48) in the context of endoplasmic reticulum associated protein degradation (ERAD). In collaboration with Dr. Maximilian von Delbrück and Dr. Andreas Kniss, we identified the ubiquitin binding CUE domain in Cue1 to play a key role in aligning Ubc7 with the distal tip of a K48-linked Ub chain for rapid chain elongation. Furthermore, we showed how binding of Ub by the CUE domain is well adapted towards the chain elongation process and how its disruption impairs degradation of the ERAD substrate Ubc6

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

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