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

Sardiello M, Cairo S, Fontanella B, Ballabio A, Meroni G - BMC Evol. Biol. (2008)

Bottom Line: 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.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.We found that the TRIM family is composed of two groups of genes with distinct evolutionary properties.

View Article: PubMed Central - HTML - PubMed

Affiliation: Telethon Institute of Genetics and Medicine, Via P, Castellino 111, 80131 Naples, Italy. sardiello@tigem.it

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.

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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.
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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.

Mentions: To trace back in evolution the origin of the TRIM family, we used human B-box1 and B-box2 sequences as queries to investigate the occurrence of these domains in the genomes of prokaryotic and eukaryotic representative species. We did not find any sequences similar to the B-box domains in prokaryotes. B-box sequences are present in plants with a consensus that is more similar to B-box1 than B-box2 (Fig. 1A). We examined 50 B-box containing proteins from 4 plant species (A. thaliana, O. sativa, P. sativum, B. nigra): the B-box is found alone or associated with a second B-box, with the CCT (CONSTANS, CO-like, and TOC1) domain [36], or with both. Differently from mammals, proximal and distal plant B-boxes (we analyzed a total of 60 B-box sequences) are very similar to each other and, consistently, do not separate in distinct branches in phylogenetic analysis (data not shown). No association with RING or Coiled-coil domains was detected in all the plant proteins analyzed.


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

Sardiello M, Cairo S, Fontanella B, Ballabio A, Meroni G - BMC Evol. Biol. (2008)

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.
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Related In: Results  -  Collection

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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.
Mentions: To trace back in evolution the origin of the TRIM family, we used human B-box1 and B-box2 sequences as queries to investigate the occurrence of these domains in the genomes of prokaryotic and eukaryotic representative species. We did not find any sequences similar to the B-box domains in prokaryotes. B-box sequences are present in plants with a consensus that is more similar to B-box1 than B-box2 (Fig. 1A). We examined 50 B-box containing proteins from 4 plant species (A. thaliana, O. sativa, P. sativum, B. nigra): the B-box is found alone or associated with a second B-box, with the CCT (CONSTANS, CO-like, and TOC1) domain [36], or with both. Differently from mammals, proximal and distal plant B-boxes (we analyzed a total of 60 B-box sequences) are very similar to each other and, consistently, do not separate in distinct branches in phylogenetic analysis (data not shown). No association with RING or Coiled-coil domains was detected in all the plant proteins analyzed.

Bottom Line: 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.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.We found that the TRIM family is composed of two groups of genes with distinct evolutionary properties.

View Article: PubMed Central - HTML - PubMed

Affiliation: Telethon Institute of Genetics and Medicine, Via P, Castellino 111, 80131 Naples, Italy. sardiello@tigem.it

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.

Show MeSH
Related in: MedlinePlus