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Fish 'n' TRIMs.

Du Pasquier L - J. Biol. (2009)

Bottom Line: A novel diversified multigene family of tripartite-motif (TRIM) intracellular receptors with putative antiviral activity has been identified in teleost fish and published in BMC Biology.The history of these receptors involves ancient linkage to paralogs of the major histocompatibility complex, and the family has invertebrate precursors.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of Basel, Institute of Zoology and Evolutionary Biology, Vesalgasse 1, Basel CH-4051, Switzerland. dupasquier@dial.eunet.ch

ABSTRACT
A novel diversified multigene family of tripartite-motif (TRIM) intracellular receptors with putative antiviral activity has been identified in teleost fish and published in BMC Biology. The history of these receptors involves ancient linkage to paralogs of the major histocompatibility complex, and the family has invertebrate precursors.

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Comparison of sequences and chromosomal positions of TRIM and MHC genes between species. (a) Human MHC-paralogous regions. The 1pq, 6p21 and 9q segments are the classical MHC-paralogous regions [8]. For simplicity only selected markers are shown, particularly MHC markers shared with the fish markers shown in Figure 1. For the purposes of this article I identified a set of genes on human chromosome 11p so far not considered as a MHC-paralogous region but that indeed seem to correspond to a group of MHC-paralogous genes that are missing from the group present on chromosome 19p13. Asterisks indicate genes for which paralogs have also been identified on chromosome 12p13, which is also known to contain some MHC-paralogous genes. Two chromosomes also have ATP5L homologs (green) linked to TRIM genes, as also found for three fish species in [6]. TRIMs in blue are those with antiviral activity. Lines indicate paralogous loci. (b) Alignment of B30.2 (Pry-Spry) domains across metazoa. Invertebrates are represented by the following sequences: a diploblastic cnidarian (sea anemone, Nematostella, XM_001632290), a protostome insect (Drosophila, NP_723600.2), a chelicerate (tick, Ixodes, EEC02812), a deuterostome echinoderm (sea urchin, Strongylocentrotus, XR_026371), a tunicate (sea squirt, Ciona, XM_002126032) and a cephalochordate (amphioxus, Branchiostoma, XM_002222150). Vertebrates are represented by: a teleost fish TRIM-B30.2 (zebrafish, Danio, XM_001332270), human CD277 (Homo, NP_001138480, given as an example of B30.2 associated with a molecule other than TRIMs), and rat Trim9 (Rattus, NP_569104, of which several invertebrate TRIMs are close homologs). Red, residues conserved in more than 50% of the sequences; blue, regions considered as signatures of the B30.2 domain [2]. Strand prediction (shown above the sequences) is taken from the Phyre server [17]. (c) Schematic representations using SMART [18] of TRIM-related proteins from Nematostella (close to class I of [5]) and Branchiostoma (close to class IV of [6]). The Pry domain is not always suggested by the graphic SMART program, as for Nematostella here, but it is visible in the alignment. Data obtained from the ENSEMBL [19], UCSC [20] and Vectorbase [21] servers.
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Figure 2: Comparison of sequences and chromosomal positions of TRIM and MHC genes between species. (a) Human MHC-paralogous regions. The 1pq, 6p21 and 9q segments are the classical MHC-paralogous regions [8]. For simplicity only selected markers are shown, particularly MHC markers shared with the fish markers shown in Figure 1. For the purposes of this article I identified a set of genes on human chromosome 11p so far not considered as a MHC-paralogous region but that indeed seem to correspond to a group of MHC-paralogous genes that are missing from the group present on chromosome 19p13. Asterisks indicate genes for which paralogs have also been identified on chromosome 12p13, which is also known to contain some MHC-paralogous genes. Two chromosomes also have ATP5L homologs (green) linked to TRIM genes, as also found for three fish species in [6]. TRIMs in blue are those with antiviral activity. Lines indicate paralogous loci. (b) Alignment of B30.2 (Pry-Spry) domains across metazoa. Invertebrates are represented by the following sequences: a diploblastic cnidarian (sea anemone, Nematostella, XM_001632290), a protostome insect (Drosophila, NP_723600.2), a chelicerate (tick, Ixodes, EEC02812), a deuterostome echinoderm (sea urchin, Strongylocentrotus, XR_026371), a tunicate (sea squirt, Ciona, XM_002126032) and a cephalochordate (amphioxus, Branchiostoma, XM_002222150). Vertebrates are represented by: a teleost fish TRIM-B30.2 (zebrafish, Danio, XM_001332270), human CD277 (Homo, NP_001138480, given as an example of B30.2 associated with a molecule other than TRIMs), and rat Trim9 (Rattus, NP_569104, of which several invertebrate TRIMs are close homologs). Red, residues conserved in more than 50% of the sequences; blue, regions considered as signatures of the B30.2 domain [2]. Strand prediction (shown above the sequences) is taken from the Phyre server [17]. (c) Schematic representations using SMART [18] of TRIM-related proteins from Nematostella (close to class I of [5]) and Branchiostoma (close to class IV of [6]). The Pry domain is not always suggested by the graphic SMART program, as for Nematostella here, but it is visible in the alignment. Data obtained from the ENSEMBL [19], UCSC [20] and Vectorbase [21] servers.

Mentions: The linkage to MHC and its three paralogous regions [9] is not only ancient, it is also conserved, as several genes encoding proteins with TRIM and B30.2 domains and with antiviral activity are also MHC-linked in various vertebrate lineages, such as birds and mammals [10-12] (Figure 2a), and some are also moderately amplified (such as TRIM5 genes, with five contiguous members) in a way that is reminiscent of the ftr amplification [13]. Was the immunological antiviral function of such receptors a reason to be selected for co-segregation with the region of the MHC containing genes encoding proteins that are associated with inflammatory responses, such as tumor necrosis factor and components of the antigen-presentation machinery? It may have contributed to the creation of a massive assembly of immunity-related genes, which would have had the advantage of being inheritable as a single unit. This linkage may no longer have any selective value in some species, given that it is not apparent in the stickleback, a species of teleosts that has diverged more recently than the zebrafish. In zebrafish, it may simply be a 'fossil' of an ancient, once useful architecture.


Fish 'n' TRIMs.

Du Pasquier L - J. Biol. (2009)

Comparison of sequences and chromosomal positions of TRIM and MHC genes between species. (a) Human MHC-paralogous regions. The 1pq, 6p21 and 9q segments are the classical MHC-paralogous regions [8]. For simplicity only selected markers are shown, particularly MHC markers shared with the fish markers shown in Figure 1. For the purposes of this article I identified a set of genes on human chromosome 11p so far not considered as a MHC-paralogous region but that indeed seem to correspond to a group of MHC-paralogous genes that are missing from the group present on chromosome 19p13. Asterisks indicate genes for which paralogs have also been identified on chromosome 12p13, which is also known to contain some MHC-paralogous genes. Two chromosomes also have ATP5L homologs (green) linked to TRIM genes, as also found for three fish species in [6]. TRIMs in blue are those with antiviral activity. Lines indicate paralogous loci. (b) Alignment of B30.2 (Pry-Spry) domains across metazoa. Invertebrates are represented by the following sequences: a diploblastic cnidarian (sea anemone, Nematostella, XM_001632290), a protostome insect (Drosophila, NP_723600.2), a chelicerate (tick, Ixodes, EEC02812), a deuterostome echinoderm (sea urchin, Strongylocentrotus, XR_026371), a tunicate (sea squirt, Ciona, XM_002126032) and a cephalochordate (amphioxus, Branchiostoma, XM_002222150). Vertebrates are represented by: a teleost fish TRIM-B30.2 (zebrafish, Danio, XM_001332270), human CD277 (Homo, NP_001138480, given as an example of B30.2 associated with a molecule other than TRIMs), and rat Trim9 (Rattus, NP_569104, of which several invertebrate TRIMs are close homologs). Red, residues conserved in more than 50% of the sequences; blue, regions considered as signatures of the B30.2 domain [2]. Strand prediction (shown above the sequences) is taken from the Phyre server [17]. (c) Schematic representations using SMART [18] of TRIM-related proteins from Nematostella (close to class I of [5]) and Branchiostoma (close to class IV of [6]). The Pry domain is not always suggested by the graphic SMART program, as for Nematostella here, but it is visible in the alignment. Data obtained from the ENSEMBL [19], UCSC [20] and Vectorbase [21] servers.
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Related In: Results  -  Collection

Show All Figures
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Figure 2: Comparison of sequences and chromosomal positions of TRIM and MHC genes between species. (a) Human MHC-paralogous regions. The 1pq, 6p21 and 9q segments are the classical MHC-paralogous regions [8]. For simplicity only selected markers are shown, particularly MHC markers shared with the fish markers shown in Figure 1. For the purposes of this article I identified a set of genes on human chromosome 11p so far not considered as a MHC-paralogous region but that indeed seem to correspond to a group of MHC-paralogous genes that are missing from the group present on chromosome 19p13. Asterisks indicate genes for which paralogs have also been identified on chromosome 12p13, which is also known to contain some MHC-paralogous genes. Two chromosomes also have ATP5L homologs (green) linked to TRIM genes, as also found for three fish species in [6]. TRIMs in blue are those with antiviral activity. Lines indicate paralogous loci. (b) Alignment of B30.2 (Pry-Spry) domains across metazoa. Invertebrates are represented by the following sequences: a diploblastic cnidarian (sea anemone, Nematostella, XM_001632290), a protostome insect (Drosophila, NP_723600.2), a chelicerate (tick, Ixodes, EEC02812), a deuterostome echinoderm (sea urchin, Strongylocentrotus, XR_026371), a tunicate (sea squirt, Ciona, XM_002126032) and a cephalochordate (amphioxus, Branchiostoma, XM_002222150). Vertebrates are represented by: a teleost fish TRIM-B30.2 (zebrafish, Danio, XM_001332270), human CD277 (Homo, NP_001138480, given as an example of B30.2 associated with a molecule other than TRIMs), and rat Trim9 (Rattus, NP_569104, of which several invertebrate TRIMs are close homologs). Red, residues conserved in more than 50% of the sequences; blue, regions considered as signatures of the B30.2 domain [2]. Strand prediction (shown above the sequences) is taken from the Phyre server [17]. (c) Schematic representations using SMART [18] of TRIM-related proteins from Nematostella (close to class I of [5]) and Branchiostoma (close to class IV of [6]). The Pry domain is not always suggested by the graphic SMART program, as for Nematostella here, but it is visible in the alignment. Data obtained from the ENSEMBL [19], UCSC [20] and Vectorbase [21] servers.
Mentions: The linkage to MHC and its three paralogous regions [9] is not only ancient, it is also conserved, as several genes encoding proteins with TRIM and B30.2 domains and with antiviral activity are also MHC-linked in various vertebrate lineages, such as birds and mammals [10-12] (Figure 2a), and some are also moderately amplified (such as TRIM5 genes, with five contiguous members) in a way that is reminiscent of the ftr amplification [13]. Was the immunological antiviral function of such receptors a reason to be selected for co-segregation with the region of the MHC containing genes encoding proteins that are associated with inflammatory responses, such as tumor necrosis factor and components of the antigen-presentation machinery? It may have contributed to the creation of a massive assembly of immunity-related genes, which would have had the advantage of being inheritable as a single unit. This linkage may no longer have any selective value in some species, given that it is not apparent in the stickleback, a species of teleosts that has diverged more recently than the zebrafish. In zebrafish, it may simply be a 'fossil' of an ancient, once useful architecture.

Bottom Line: A novel diversified multigene family of tripartite-motif (TRIM) intracellular receptors with putative antiviral activity has been identified in teleost fish and published in BMC Biology.The history of these receptors involves ancient linkage to paralogs of the major histocompatibility complex, and the family has invertebrate precursors.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of Basel, Institute of Zoology and Evolutionary Biology, Vesalgasse 1, Basel CH-4051, Switzerland. dupasquier@dial.eunet.ch

ABSTRACT
A novel diversified multigene family of tripartite-motif (TRIM) intracellular receptors with putative antiviral activity has been identified in teleost fish and published in BMC Biology. The history of these receptors involves ancient linkage to paralogs of the major histocompatibility complex, and the family has invertebrate precursors.

Show MeSH