HECT ubiquitin ligases as accessory proteins of the plant proteasome

Abstract

The proteasome plays vital roles in eukaryotic cells by orchestrating the regulated degradation of large repertoires of substrates involved in numerous biological processes. Proteasome dysfunction is associated with a wide variety of human pathologies and in plants severely affects growth, development and responses to stress. The activity of E3 ubiquitin ligases marks proteins fated for degradation with chains of the post-translational modifier, ubiquitin. Proteasomal processing of ubiquitinated substrates involves ubiquitin chain recognition, deubiquitination, ATP-mediated unfolding and translocation, and proteolytic digestion. This complex series of steps is made possible not only by the many specialised subunits of the 1.5 MDa proteasome complex but also by a range of accessory proteins that are recruited to the proteasome. A surprising class of accessory proteins are members of the HECT-type family of ubiquitin ligases that utilise a unique mechanism for post-translational attachment of ubiquitin to their substrates. So why do proteasomes that already contain all the necessary machinery to recognise ubiquitinated substrates, harbour HECT ligase activity? It is now clear that some ubiquitin ligases physically relay their substrates to proteasome-associated HECT ligases, which prevent substrate stalling at the proteasome. Moreover, HECT ligases ubiquitinate proteasome subunits, thereby modifying the proteasome’s ability to recognise substrates. They may therefore enable proteasomes to be both non-specific and extraordinarily selective in a complex substrate environment. Understanding the relationship between the proteasome and accessory HECT ligases will reveal how the proteasome controls so many diverse plant developmental and stress responses.

BIG participates in the Arg/N-degron pathways and the hypoxia response inArabidopsis thaliana

“…These observations are also consistent with previous reports of E3 ligases associated with the proteasome, including HECT E3 ligases [72] and yeast UBR1 [87]. In yeast, the HECT E3 ligase UFD4 binds UBR1 and increases processivity of polyubiquitination [88]; similarly in plants, substrates from diverse E3 ligases are relayed to UPLs which prevent substrate stalling at the proteasome [72]. Given that UBR4 interacts with a diverse array of protein partners including E2 ubiquitin conjugating enzymes and E3 ligases to degrade both Ndegron pathway substrates and other protein targets [43,45,89], it is plausible that BIG serves as a versatile recognition component of the Arg/N-degron pathways and possibly other proteostatic mechanisms, interacting with one or more E3 ligases to mediate proteasomal degradation of a broad range of substrates (Fig.…”

“…In agreement with this, BIG copurified with proteasome subunits and UPL1/3 in transiently transfected Nicotiana benthamiana [60] and UBR4 is present at the proteasome at significant, but sub-stoichiometric amounts in mammals [85,86]. These observations are also consistent with previous reports of E3 ligases associated with the proteasome, including HECT E3 ligases [72] and yeast UBR1 [87]. In yeast, the HECT E3 ligase UFD4 binds UBR1 and increases processivity of polyubiquitination [88]; similarly in plants, substrates from diverse E3 ligases are relayed to UPLs which prevent substrate stalling at the proteasome [72].…”

“…1F). Interestingly, regulatory proteasomal subunits and Homologous to E6AP C-terminus (HECT) ubiquitin E3 ligases known to be associated with the proteasome [72] were also highly enriched in the R-TurboID sample (Fig. 1F; Dataset S1).…”

Ubiquitome profiling reveals a regulatory pattern of UPL3 with UBP12 on metabolic-leaf senescence

“…As described in previous review, the HECT E3 N-terminus not only simply serves as an adapter for direct binding but it also provides various ways to regulate HECT E3s’ substrate recruitment and catalytic activity ( Lan & Miao, 2019 ; Wang & Spoel, 2022 ). In this study, we showed that UPL3 seemed to interact with histone variants, histone modifiers (BRM), PPC2, HXK1, several U-box proteins (UBC35), and DUBs (UBP12) in the nucleus ( Figs 6 and S8 ).…”

HECT‐type ubiquitin ligase KAKTUS mediates the proteasome‐dependent degradation of cyclin‐dependent kinase inhibitor KRP2 during trichome morphogenesis in Arabidopsis

“…Degradation of UPS substrates requires the concerted action of E1, E2, and E3 enzymes, which execute the functions of ubiquitin (Ub) activation, Ub‐conjugation, and Ub‐ligation, respectively (Vierstra, 2009). One important class of Ub‐ligating enzymes is the HECT E3s, which all contain a conserved domain with homology to the C‐terminus of human E6‐Associated Protein (E6‐AP) that functions in the degradation of p53 protein (Marín, 2013; Wang & Spoel, 2022). The Arabidopsis genome contains seven HECT‐containing proteins termed ubiquitin‐protein ligase 1(UPL1)‐UPL7, and UPL3 has a specific role in trichome development (Downes et al., 2003).…”