Animal HECT ubiquitin ligases: evolution and functional implications

Abstract

Background: HECT ubiquitin ligases (HECT E3s) are key components of the eukaryotic ubiquitin-proteasome system and are involved in the genesis of several human diseases. In this study, I analyze the patterns of diversification of HECT E3s since animals emerged in order to provide the right framework to understand the functional data available for proteins of this family.

Results: I show that the current classification of HECT E3s into three groups (NEDD4-like E3s, HERCs and single-HECT E3s) is fundamentally incorrect. First, the existence of a "Single-HECT E3s" group is not supported by phylogenetic analyses. Second, the HERC proteins must be divided into two subfamilies (Large HERCs, Small HERCs) that are evolutionarily very distant, their structural similarity being due to convergence and not to a common origin. Sequence and structural analyses show that animal HECT E3s can be naturally classified into 16 subfamilies. Almost all of them appeared either before animals originated or in early animal evolution. More recently, multiple gene losses have occurred independently in some lineages (nematodes, insects, urochordates), the same groups that have also lost genes of another type of E3s (RBR family). Interestingly, the emergence of some animal HECT E3s precedes the origin of key cellular systems that they regulate (TGF-beta and EGF signal transduction pathways; p53 family of transcription factors) and it can be deduced that distantly related HECT proteins have been independently co-opted to perform similar roles. This may contribute to explain why distantly related HECT E3s are involved in the genesis of multiple types of cancer.

Conclusions: The complex evolutionary history of HECT ubiquitin ligases in animals has been deciphered. The most appropriate model animals to study them and new theoretical and experimental lines of research are suggested by these results.

Figure 1

HECT E3 subfamilies. The results of all the phylogenetic analyses were highly congruent, so they are depicted in a single tree. Number above branches refer to bootstrap support (NJ/MP/ML; in percentages; only consistently high bootstrap values are indicated). The number of sequences included in each subfamily is also indicated (in brackets). All the families except the one that I have named HECTX contain at least one human protein. Thus, I used the names of the human proteins to call the corresponding subfamilies.

Figure 2

Structures of typical members of the subfamilies. To obtain this figure, all the HECT proteins present in humans, the placozoan Trichoplax adhaerens, the cnidarian Nematostella vectensis and the choanoflagellate Monosiga brevicollis were structurally analyzed using InterProScan [18]. The structures from orthologous proteins in the three animals were generally identical, and therefore all but four of the proteins shown here are from humans. The four exceptions derive from Monosiga brevicollis. Three of them are detailed in the figure. The fourth belongs to the HECTX subfamily, which is not present in vertebrates. Minimal variations were detected in some NEDD4 subfamily proteins (e. g. lack of the C2 domain; lack of one of the WW domains). Also, this figure shows the structure of just one of the Large HERC proteins, HERC1, but does not depict the structure of HERC2 (described before by e. g. [31]).

Figure 3

Most parsimonious reconstruction of the patterns of emergence and loss of HECT E3s in animals. Arrows indicate the emergence of new genes (indicated in the boxes) and rectangles, a gene loss. Question marks indicate cases in which it is unclear that a gene is present or not, due to partial data. The names NEDD4a-d refer to the four ancestral genes of the NEDD4 subfamily that still exist in many animals (Table 1) and that emerged before the metazoa/choanoflagellata split. In humans, the genes NEDD4 and NEDD4L derive from a duplication of NEDD4a, WWP1, WWP2 and ITCH derive from NEDD4b, Smurf1 and Smurf2 from NEDD4c and NEDL1 and NEDL2 from NEDD4d. The partial data available for lophotrochozoans (in brackets) allows concluding that all genes are present in at least one species of this group of organisms, and therefore they were all present in their common ancestor. However, losses in particular lineages may have occurred.

Figure 4

Known substrates of HECT E3s that are related to the TGF-β signaling pathway. Lines connect the enzymes and their corresponding substrates. The presence (+) or absence (-) of genes encoding those substrates in the choanoflagellate Monosiga brevicollis (M. b.) and the placozoan Trichoplax adhaerens (T. a.) is also indicated. NEDD4a - NEDD4d refer to the four genes already present in early animals. A question mark indicates that one or more related genes are detected, but it is unclear whether they are true orthologs of the corresponding human genes. It is clear from this data that NEDD4 genes of different origin ubiquitinate now the same substrates.

Figure 5

Substrates of HECT E3s that are related to EGFR metabolism. Conventions as in Figure 4.

Figure 6

Details of the HECT ubiquitin ligases that are known to ubiquitinate p53 family proteins. See Figure 4 and main text for the details.