Ubiquitin E3 ligases control every aspect of eukaryotic biology by promoting protein ubiquitination and degradation. At the end of a three-enzyme cascade, ubiquitin ligases mediate the transfer of ubiquitin from an E2 ubiquitin-conjugating enzyme to specific substrate proteins. Early investigations of E3s of the RING (really interesting new gene) and HECT (homologous to the E6AP carboxyl terminus) types shed light on their enzymatic activities, general architectures, and substrate degron-binding modes. Recent studies have provided deeper mechanistic insights into their catalysis, activation, and regulation. In this review, we summarize the current progress in structure–function studies of ubiquitin ligases as well as exciting new discoveries of novel classes of E3s and diverse substrate recognition mechanisms. Our increased understanding of ubiquitin ligase function and regulation has provided the rationale for developing E3-targeting therapeutics for the treatment of human diseases.

Strigolactones (SLs), a newly discovered class of carotenoid-derived phytohormones, are essential for developmental processes that shape plant architecture and interactions with parasitic weeds and symbiotic arbuscular mycorrhizal fungi. Despite the rapid progress in elucidating the SL biosynthetic pathway, the perception and signalling mechanisms of SL remain poorly understood. Here we show that DWARF 53 (D53) acts as a repressor of SL signalling and that SLs induce its degradation. We find that the rice (Oryza sativa) d53 mutant, which produces an exaggerated number of tillers compared to wild-type plants, is caused by a gain-of-function mutation and is insensitive to exogenous SL treatment. The D53 gene product shares predicted features with the class I Clp ATPase proteins and can form a complex with the α/β hydrolase protein DWARF 14 (D14) and the F-box protein DWARF 3 (D3), two previously identified signalling components potentially responsible for SL perception. We demonstrate that, in a D14- and D3-dependent manner, SLs induce D53 degradation by the proteasome and abrogate its activity in promoting axillary bud outgrowth. Our combined genetic and biochemical data reveal that D53 acts as a repressor of the SL signalling pathway, whose hormone-induced degradation represents a key molecular link between SL perception and responses.

Ubiquitin (Ub), a centrally important component of the ubiquitin-proteasome system (UPS), is covalently attached to numerous cellular proteins through a highly regulated process. The attached Ub serves as a recognition element in trans, to which a variety of downstream effectors bind. These complexes play roles in a broad array of cellular functions, the best studied is targeting of the conjugated proteins to degradation by the 26S proteasome. Regulated degradation plays key roles in basic processes such as cell cycle, differentiation, transcription, and maintenance of the cellular quality control. In addition to its conjugated form, there is also a free pool of Ub that is essential to ascertain its immediate availability for the many tasks it serves. Ub is considered as a stable protein, particularly due to its unique globular structure and ability to be recycled by deubiquitinating enzymes (DUBs). However, alterations in its steady state which occur under different pathophysiological conditions have suggested more complex - yet elusive - regulatory mechanisms that govern Ub stability. Recent findings have demonstrated that Ub can be degraded by the proteasome via three routes - along with its conjugated substrate, when extended with a C-terminal tail, and as a monomer.