Origin and evolution of fungal HECT ubiquitin ligases

Abstract

Ubiquitin ligases (E3s) are basic components of the eukaryotic ubiquitination system. In this work, the emergence and diversification of fungal HECT ubiquitin ligases is described. Phylogenetic and structural data indicate that six HECT subfamilies (RSP5, TOM1, UFD4, HUL4, HUL4A and HUL5) existed in the common ancestor of all fungi. These six subfamilies have evolved very conservatively, with only occasional losses and duplications in particular fungal lineages. However, an early, drastic reduction in the number of HECT genes occurred in microsporidians, in parallel to the reduction of their genomes. A significant correlation between the total number of genes and the number of HECT-encoding genes present in fungi has been observed. However, transitions from unicellularity to multicellularity or vice versa apparently had no effect on the evolution of this family. Likely orthologs or co-orthologs of all fungal HECT genes have been detected in animals. Four genes are deduced to be present in the common ancestor of fungi, animals and plants. Protein-protein interactions detected in both the yeast Saccharomyces cerevisiae and humans suggest that some ancient functions of HECT proteins have been conserved since the animals/fungi split.

Solenoid architecture of HUWE1 contributes to ligase activity and substrate recognition

“…In addition to the helical repeats, the large disordered region (aa 2259–3179), which is mostly absent in the closest HUWE1 homolog in S. cerevisiae ( Marín, 2018 ) (TOM1), may also contribute to binding a specific subset of substrates. The modularity observed in the structural data and evolution of HUWE1 ( Giles and Grill, 2020 ; Grau-Bové et al, 2013 ; Marín, 2010 , 2018 ) adapts well to its function as a major cellular rheostat that plays an important role in protein quality control and the destabilization of key regulators of cell growth and death. On the basis of our structure, it will now be possible to interrogate the binding modes of a diverse set of substrates in future studies.…”

Regulation of the endocytosis and prion-chaperoning machineries by yeast E3 ubiquitin ligase Rsp5 as revealed by orthogonal ubiquitin transfer

“…Thus, we envision that the yeast selection platform would be useful for the engineering of other types of HECT E3s that play important roles in cell regulation and disease development (Rotin and Kumar, 2009). The E2-binding loop identified for the Rsp5 HECT domain is a common structural motif in various HECT E3s of mammalian origin, such as E6AP, Smurf1/2, and Nedd1/2, and of yeast origin, such as Tom1 and Ufd4 (Marin, 2018). By randomizing the E2-binding loop on other HECT E3s and using highthroughput yeast sorting for catalysis-based selection, we can expand the reach of the OUT cascades to other HECT E3s to probe their biological functions.…”

Modular HUWE1 architecture serves as hub for degradation of cell-fate decision factors

“…This stretch is dispensable for DDIT4 activity 26 , but its phosphorylation state has been linked to protein stability 27 . In addition to the helical repeats, the large disordered region (aa 2259-3179), which is mostly absent in the closest HUWE1 homolog in yeast 28 (TOM1), may also contribute to binding towards a specific subset of substrates. The modularity observed in the structural data and evolution of HUWE1 22,[28][29][30] adapts well to its function as a major cellular rheostat that controls stability of many key regulators of cell growth and death.…”

“…In addition to the helical repeats, the large disordered region (aa 2259-3179), which is mostly absent in the closest HUWE1 homolog in yeast 28 (TOM1), may also contribute to binding towards a specific subset of substrates. The modularity observed in the structural data and evolution of HUWE1 22,[28][29][30] adapts well to its function as a major cellular rheostat that controls stability of many key regulators of cell growth and death. On the basis of our structure it will now be possible to interrogate the binding modes of a diverse set of substrates in future studies.…”