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.

Figure 1

ML phylogenetic analysis of a dataset of 2899 HECT domain sequences. The best tree, shown here, was obtained with the LG + R10 model of sequence evolution and perturbation strength = 0.5 (see Methods). In brackets, the number of sequences included in each of the five highly-supported groups, named according to the Saccharomyces cerevisiae genes included in each of them.

Figure 2

ML tree based on the analysis of 203 sequences from fungi and Fonticula alba. The LG + R9 model with perturbation strength = 0.8 provided the top ML value. NJ and MP results were so similar that they are also shown here. Numbers above the branches refer to ML/NJ/MP bootstrap support. Groups that include Fonticula alba sequences are indicated in blue and those that only include fungal sequences, in red. The branch that comprises all the HUL4-related sequences was supported by ML analysis but not by NJ or MP analyses (indicated as 99/−/−).

Figure 3

ML tree of fungi sensu stricto and Fonticula sequences. In this case, the LG + R8 model with perturbation strength = 0.5 provided the best ML value. Numbers refer to bootstrap support (as in Fig. 2: ML/NJ/MP). At the right, eight examples of the most typical structures found in fungal HECT proteins. Domains are indicated as colored boxes. From top to bottom: Saccharomyces cerevisiae RSP5, S. cerevisiae TOM1, Laccaria bicolor TOM1 (Accession number XM_001877693.1), S. cerevisiae HUL4, Coccidioides immitis HUL4A (XM_001247392.2), S. cerevisiae HUL5, Fusarium verticilloides HUL5 (XM_018889203.1) and S. cerevisiae UFD4. Figures are drawn to scale; the HECT domains shown correspond to 300–310 amino acids.

Figure 4

The most parsimonious hypothesis that explains the distribution of genes into classes summarized in Table 1. Whole genome duplications^, are indicated as blue ellipses, black rectangles indicate gene losses and red arrows are gene emergences or duplications. The emergences of the HUL4A and HUL5 genes, after the Fonticula/fungi split, are indicated in brackets because animal data indicate an earlier origin for these genes that it is shown here (see main text). The topology of the tree was obtained from refs^,,–.

Figure 5

Maximum Likelihood phylogenetic tree of fungal and animal HECT sequences. The best ML value was obtained with the LG + R10 model of sequence evolution and perturbation strength = 0.5. Numbers indicate ultrafast bootstrap support. Blue: fungal groups. In all cases but HUL4A, they correspond to the fungal HECT subfamilies shown in Fig. 2. HUL4A subfamily sequences are here divided into two groups. Red: animal subfamilies; these groups include a sequence of the choanoflagellate Monosiga brevicollis. Black: animal subfamilies for which no orthologous choanoflagellate sequences were found.

Figure 6

Neighbor-Joining tree of fungal and animal HECTs. Numbers refer to bootstrap support. Color conventions as in Fig. 5. There are six differences with that Figure, which are indicated with asterisks. For example, HACE1 [*] indicates that at least one sequence included in the HACE1 subfamily in Fig. 5 is missing in the corresponding group in Fig. 6. In this case, the difference consists in just one sequence, Monosiga brevicollis XM_001745698.1, which can be found below in the tree. Four sequences that in this tree appear isolated but were included in one of the subfamilies in Fig. 5 have the name of the corresponding subfamily indicated within brackets. Notice that HUL4A sequences are divided here into three groups instead of two, as in the previous figure.