Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties

Abstract

Background: The TRIM family is composed of multi-domain proteins that display the Tripartite Motif (RING, B-box and Coiled-coil) that can be associated with a C-terminal domain. TRIM genes are involved in ubiquitylation and are implicated in a variety of human pathologies, from Mendelian inherited disorders to cancer, and are also involved in cellular response to viral infection.

Results: Here we defined the entire human TRIM family and also identified the TRIM sets of other vertebrate (mouse, rat, dog, cow, chicken, tetraodon, and zebrafish) and invertebrate species (fruitfly, worm, and ciona). By means of comparative analyses we found that, after assembly of the tripartite motif in an early metazoan ancestor, few types of C-terminal domains have been associated with this module during evolution and that an important increase in TRIM number occurred in vertebrate species concomitantly with the addition of the SPRY domain. We showed that the human TRIM family is split into two groups that differ in domain structure, genomic organization and evolutionary properties. Group 1 members present a variety of C-terminal domains, are highly conserved among vertebrate species, and are represented in invertebrates. Conversely, group 2 is absent in invertebrates, is characterized by the presence of a C-terminal SPRY domain and presents unique sets of genes in each mammal examined. The generation of independent sets of group 2 genes is also evident in the other vertebrate species. Comparing the murine and human TRIM sets, we found that group 1 and 2 genes evolve at different speeds and are subject to different selective pressures.

Conclusion: We found that the TRIM family is composed of two groups of genes with distinct evolutionary properties. Group 2 is younger, highly dynamic, and might act as a reservoir to develop novel TRIM functions. Since some group 2 genes are implicated in innate immune response, their evolutionary features may account for species-specific battles against viral infection.

Figure 1

TRIM domains in evolution. A) Logo representation of the sequences of Plant B-box (60 B-box sequences; representative species: A. thaliana, O. sativa, P. sativum, B. nigra); Metazoan B-box1 (all the B-box1 sequences in representative species: H. sapiens, D. melanogaster, and C. elegans); Mammalian B-box2 (all B-box2 sequences in representative species: H. sapiens) and Invertebrate B-box2 (all B-box2 sequences in representative species: D. melanogaster, and C. elegans). The overall height of each position is proportional to its information content and, within a given position, the conservation of each residue is represented as the relative height of amino acid symbols. Shaded columns indicate the residues involved in the coordination of zinc atoms. Blue bars represent amino acid segments of variable length; the mean value for each segment is reported. Red bars represent segments of fixed amino acid length that are present only in a proportion (indicated in red above the bar) of proteins. B) TRIM complements of humans, fruitfly (D. melanogaster) and worm (C. elegans). The total number of TRIM and TRIM-like genes in each species is indicated (top). The presence of the TRIM associated C-terminal domains is indicated with the same color code (bottom). The length of each bar in the bottom part is proportional to the number (also indicated) of the relative TRIM C-terminal domains found in each species.

Figure 2

Relatedness of the human TRIM and TRIM-like proteins. A) Unrooted phylogenetic tree generated upon alignment of the B-box2 and Coiled-coil region of human TRIM and TRIM-like proteins. The numbers indicate the TRIM family members; numbers with an asterisk indicate the 'incomplete' TRIM proteins named with their alternative TRIM name (see Table 1); light blue circles indicate the presence of the B-box1 domain; the colored open circles represent the different C-terminal domains as indicated in the figure. Partition in groups 1 and group 2 is indicated. B) Representative protein structures of the two groups obtained in A); dashed parentheses indicate that B-box 1 may not be present.

Figure 3

Group 1 and group 2 TRIM gene conservation in human and mouse. A) Distribution of the percentage of amino acid identity between human TRIM and TRIM-like proteins and their murine counterparts. Group 2 (yellow) and group 1 (grey). The bars represent the number of human TRIM genes (Y axis) for each percentage of identity interval (X axis); NO indicates absence of a murine counterpart. B) Distribution of the Ka/Ks ratios observed in human-mouse orthologous TRIM pairs considering the two groups separately. The bars represent the number of TRIM pairs (Y axis) for each Ka/Ks value interval (X axis).

Figure 4

Phylogenetic analysis of human (h, blue), mouse (m, blue), fruitfly (CGs, red), and worm (green) group 1 TRIM and TRIM-like proteins. Human and mouse TRIM proteins are indicated with their TRIM numbers; 'incomplete' TRIM proteins are indicated with their alternative TRIM number with an asterisk (see Table 1); fruitfly and worm sequences are indicated with GenBank accession numbers. Bootstrap support values above 50% based on 1000 replicates are shown. The main domain distal to the tripartite motif is indicated on the right; ND indicates no known domain detected. Panels A-E show the evolutionary relationships among the members of TRIM subgroups that belong to group 1; the worm TRIM genes composed of the R-B2-CC motif only (Figure 2B) represent a separate group related to group 1 and are not shown in the figure. TRIM37 (C-terminal domain: MATH) did not segregated within any subgroups in preliminary analyses and was therefore used as an outgroup in all phylogenetic analyses. The trees were drawn to the scale of amino acid sequence divergence indicated at the bottom right corner. A) Subgroup A includes FN3 and FN3-related TRIM sequences. Fruitfly CG31721 and its worm ortholog C39F7 are the only invertebrate proteins present in the FN3 subgroup and segregate with mammalian TRIM9 and 67. B) Subgroup B includes ARF-related TRIM sequences. Genes encoding a protein homologous to TRIM23 are found in worm and in the honeybee Apis mellifera (ENS10667 = ENSAPMT00000010667) but not in D. melanogaster, suggesting that the ARF domain has been acquired by a tripartite-gene precursor before vertebrate-invertebrate lineage separation, and has occasionally been lost in some species. C) Subgroup C includes PHD-BROMO and PHD-BROMO-related TRIM sequences. Fruitfly CG5206 behaves as an outgroup for all human and mouse PHD-BROMO proteins, suggesting that it may be regarded as an ortholog of their protein ancestor. D) Subgroup D includes IGFLMN-related TRIM sequences. This subgroup is the only example of TRIM expansion in invertebrates, because it includes worm and fly genes that do not have any direct correspondent in mammals. E) Subgroup E includes TRIM proteins with B1, B2, and SPRY in various combinations (see Table 1). No invertebrate sequences are found within this subgroup.

Figure 5

Phylogenetic analysis of human (h) and mouse (m) TRIM and TRIM-like proteins from Group 2. TRIM proteins are indicated with their TRIM number ('incomplete' TRIM proteins are indicated with their alternative TRIM number with an asterisk, see Table 1). No invertebrate TRIM proteins are represented in this group. Bootstrap support values above 50% based on 1000 replicates are shown. Group 1 TRIM37 sequences are used as outgroup. The scale of amino acid sequence divergence is indicated at the bottom right corner. Twenty-four pairs of orthologs can be identified (gray-shadowed branches). The remaining proteins can be subdivided in three different types, based on the phylogenetic relationship with their neighbors: (i) Proteins that are present only in one species and apparently started to diverge from their paralogs before human-mouse split (green clades); (ii) Clades of paralogous proteins that are present only in human and share a single homologous counterpart in mouse (red-shadowed branches); (iii) Clades of paralogous proteins that are present only in mouse and do not have any obvious homologous counterpart in humans (blue-shadowed branches).

Figure 6

Phylogenetic analysis of TRIM and TRIM-like proteins of representative species of mammals, aves, and fish. Human (Hs, dark blue), chicken (Gg, dark green), tetraodon (Tn, light blue); ciona (Ci, orange), fruitfly (red) and worm (light green) are included. Bootstrap support values based on 1000 replicates are shown. Group 1 TRIM37 sequences are used as outgroups. The scale of amino acid sequence divergence is indicated at the bottom right corner.

Figure 7

Proposed model for TRIM structure evolution (see text). The C-terminal domains probably derived from a single ancestor domain are indicated with the same color.