Fish 'n' TRIMs
© BioMed Central Ltd 2009
Published: 29 May 2009
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.
Multigene families are common in metazoa. They result from genomic duplications and contain a variety of genes, such as those encoding the immunoglobulin superfamily, cadherins, leucine-rich repeats, scavenger receptors, actins, tubulins, keratins, collagens, heat shock proteins and rhodopsins. The largest receptor families, which can contain tens to hundreds of members, comprise mostly either olfactory receptors of the rhodopsin family or immunoreceptors, such as cysteine-rich scavenger receptors (SRCRs) and Toll-like receptors (TLRs) in echinoderms and the nucleotide-binding and oligomerization domain leucine-rich repeat receptors (also known as NOD-like receptors or NLRs) in teleosts, as well as other immunoglobulin superfamily members in teleosts, amphibians, birds and mammals .
In such families the immunologist sees a potential source of useful diversity for innate immune recognition and immediately thinks in terms of its adaptive value. The evolutionary biologist reminds us that not all diversity is adaptive and asks for direct evidence of involvement in immunity. At this point the cell biologist confronts the difficult issue of how the expression of large sets of genes is controlled.
Tripartite-motif (TRIM) intracellular receptors have been implicated in control of proliferation, differentiation, development, oncogenesis, apoptosis and antiviral activity in various mammalian species. They comprise a RING finger with E3 ubiquitin ligase activity, a B-box (a type of zinc-finger domain) and a coiled-coil domain mediating oligomerization. Some TRIMs are coupled to the B30.2 module – a fusion of the Pry and Spry domains  – which mediates diverse functions in at least six families of human receptor by binding to targets through an interface resembling that of an antibody . The mode of action of the B30.2 domain is mostly unknown, but it may confer antiviral activity on TRIM , which is why these molecules are of particular interest. In humans there are 75 TRIMs . All metazoan TRIMs fall into 11 classes , all of which contain the above mentioned ring box, one or two B boxes, and a coiled-coil region. The classes are defined according to the absence (class V) or the presence of one to three extra domains.
For the TRIMs discussed in this minireview – that is, those that have been duplicated – these extra domains are: C-terminal subgroup one signature (classes I, II and III), fibronectin type III (classes I and III), B30.2 (classes I and IV), plant homeo- and bromodomains (class VI), and filamin and NHL (NCL1, HT2A, LIN41 repeat) (class VII).
A recent paper by van der Aa et al.  in BMC Biology has now identified a novel large multigene family of TRIM proteins in teleosts, the most abundant infraclass of bony fish, with over 25,000 species. The TRIM proteins are encoded by the fintrim (ftr) and the bloodthirsty-related (btr) genes and include a TRIM domain coupled to a B30.2 module. Expression of the genes can be induced by experimental viral infection (by intravenous injection of the viral suspension) in teleost cells and may thus contribute to antiviral defense in these fish. The fish TRIM family is an interesting model because, first, it is amplified uniquely in fish (see  for a recent discussion of duplications in the teleost genome) and thus provides a new model for studying the origin, raison d'être and evolution of large multigene families putatively involved in vertebrate immunity; and second, because comparative data may help to determine which segments of the receptors are essential (rather than accessory) to antiviral activity, in particular with respect to the B30.2 domain.
Fish ftr diversity and chromosome location
The report by van der Aa et al.  describes two subsets of the 240 zebrafish TRIMs, which the authors named the fintrim (ftr) and the bloodthirsty-related (btr) genes. The 84 ftr genes and 33 btr genes encode class IV TRIMs (RING finger-B-box-coiled-coil-B30.2 proteins) . The ftr genes stem from an unknown ancestor and make up a teleost-specific family encoding proteins induced by viral infection. Ftrs evolved through positive selection of residues in the B30.2 domain homologous to those involved in viral recognition of the mammalian anti-retroviral protein TRIM5α; they are therefore likely to form a family of immune receptors since, in a changing viral environment, diversity of recognition of determinants is a selective advantage for an immune system . The family illustrates a recurrent observation: during evolution, families of genes with non-immune functions in other organisms may become diversified in some species to fulfill functions in immune recognition and defense. Another example of such evolution is shown by members of the immunoglobulin superfamily in invertebrates and vertebrates . In the case of Ftr proteins, the pressure to diversify must have been intense because different species of phylogenetically distant teleosts have generated ftr families through different mechanisms: tandem duplications in zebrafish and retrotranspositions in medaka. This convergence suggests again that Ftr diversity has adaptive value. One possibility is that this great diversity compensates for deficiencies in adaptive immunity to viruses.
The other subset of zebrafish TRIMs, the Btrs, stems from an ortholog of mammalian Trim-39. Members of this subset are not documented to have any involvement in immunity, but the fact that the genes are highly amplified whereas trim-39 is not raises some interesting questions, and studying the origin and diversification of both subsets may prove useful.
The B30.2 domain: origin and mobility
The antiviral properties of TRIM proteins seem to be due mainly to the RING finger-B-box region (in TRIM25) and the B30.2 module (in TRIM5). These two regions work in different ways: through the ubiquitination pathway for the RING finger-B-box region, and by interference with virus decapsidation and replication for the B30.2 module .
Very little is known about B30.2 evolution beyond vertebrates. Briefly, the hypothetical evolutionary history of B30.2 is often presented in phases [3–5]: an ancient Spry domain inherited from an ancestral form later became associated with a Pry domain to give the final B30.2 configuration seen only in vertebrates. My analysis of sequences from various invertebrates (Figure 2) shows clearly the presence of a B30.2 domain associated with TRIM-like molecules. In cnidarians, there seems to be two classes of TRIM: class I, with fibronectin type III and B30.2 domains; and class V, without a B30.2 domain. However, in echinoderms, such as the sea urchin, the B30.2 domain is rare. Among the chordates, many classes and many members exist in amphioxus (Cephalochordata), whereas the sea squirt Ciona (Urochordata) has only ten TRIMs  and only one has so far been found to contain a B30.2 domain. As yet, no association of a B30.2 domain with an extracellular immunoglobulin superfamily domain has been found in invertebrates. The shuffling of the B30.2 exon seems specific to vertebrate butyrophilins (a family of receptors named from a milk protein but that contains several immunologically relevant molecules). This association of a B30.2 domain with a MHC-linked immunoglobulin superfamily member must be old since it is shared between mammals [10, 11] and the zebrafish. Indeed, chromosome 3 of Danio (zebrafish) contains two butyrophilin homologs – btn1, which encodes a protein containing the B30.2 domain, and btn2, which does not – and several MHC markers (Figure 1). The existence of TRIM-B30.2 but the absence of butyrophilin in invertebrates suggests that the B30.2 domain was shuffled from a TRIM into one of the nearby MHC-linked immunoglobulin superfamily members (resembling, for instance, zebrafish btn2).
In mammals, the B30.2 domain can be associated with surface, cytoplasmic and nuclear receptors and even with some soluble proteins, such as toxins [2, 3]. It remains a mystery why the B30.2 domain is associated with or has colonized so many different genes in some organisms but remains rare among others. However, 'rare' is not the term one would use for the B30.2 domain in teleosts. Following exon shuffling, B30.2 domains similar to those of Ftr proteins expanded tremendously into another large family of zebrafish intracellular receptors, the NOD-like receptors (NLRs) [14, 15], which can function as immunoreceptors . These receptors resemble plant disease resistance proteins and are involved in responses to pathogens. Together, the findings that TRIM-B30.2 is present in invertebrates but that B30.2 domains are absent from the NLRs of vertebrates except teleosts suggests that TRIM-B30.2 is older than NLR and that the exon shuffling caused a B30.2 domain to move from a TRIM-B30.2 gene to an NLR gene rather than in the opposite direction.
The existence of hundreds of similar B30.2 domains associated with different intracellular immunoreceptors complicates the analysis of their expression, especially when these receptors are likely to be expressed in the same tissue and sometimes even in the same cells. How are the different receptors compartmentalized and how do they avoid competition? What is the specific role of the B30.2 domains in the various receptors? Fish that diversified massively the B30.2 domains into two categories of receptors, the TRIMs and NLRs, probably under different selection pressures, offer a good model for experiments addressing these questions.
Van der Aa et al.  have opened Pandora's box, and their work suggests future directions for studies of the phylogenies, linkage and functions of TRIM proteins and their relationships with other immune-system components. Their work calls for more experiments with the teleost model: a more thorough analysis of all TRIM sequences in fish might reveal new trends in the evolution of the family and could enable investigation of the relationships with the related TRIMs without B30.2 or RING-finger-B-box moieties. Tissue localization, regulation of expression and binding specificity must also be determined. This will be difficult, but what is revealed is likely to be fascinating for any biologist. Finally, many unanswered questions about antiviral activity could profit from B30.2 comparative models, among which invertebrates may offer natural variations on the theme of TRIM-B30.2 receptors. Comparative TRIMinologists have many happy days ahead.
- Flajnik MF, Du Pasquier L: Evolution of the immune system. Fundamental Immunology. Edited by: Paul WE. 2008, Philadelphia: Wolters Kluwer, Lippincott Williams &Wilkins, 56-124. 6
- Henry J, Ribouchon MT, Offer C, Pontarotti P: B30.2-like domain proteins: a growing family. Biochem Biophys Res Commun. 1997, 235: 162-165. 10.1006/bbrc.1997.6751.View ArticlePubMed
- Rhodes DA, de Bono B, Trowsdale J: Relationship between SPRY and B30.2 protein domains. Evolution of a component of immune defence?. Immunology. 2005, 116: 411-417.PubMed CentralPubMed
- Ozato K, Shin DM, Chang TH, Morse HC: TRIM family proteins and their emerging roles in innate immunity. Nat Rev Immunol. 2008, 8: 849-860. 10.1038/nri2413.PubMed CentralView ArticlePubMed
- Sardiello M, Cairo S, Fontanella B, Ballabio A, Meroni G: Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties. BMC Evol Biol. 2008, 8: 225-10.1186/1471-2148-8-225.PubMed CentralView ArticlePubMed
- Aa van der LM, Levraud JP, Yahmi M, Lauret E, Briolat V, Herbomel P, Benmansour A, Poudinot P: A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish. BMC Biol. 2009, 7: 7-10.1186/1741-7007-7-7.PubMed CentralView ArticlePubMed
- Braasch I, Salzburger W: In ovo omnia: diversification by duplication in fish and other vertebrates. J Biol. 2009, 8: 25-10.1186/jbiol121.PubMed CentralView ArticlePubMed
- Zucchetti I, De Santis R, Grusea S, Pontarotti P, Du Pasquier L: Origin and evolution of the vertebrate leukocyte receptors: the lesson from tunicates. Immunogenetics. 2009, doi:10.1007/s00251-009-0373-z
- Flajnik MF, Kasahara M: Comparative genomics of the MHC: glimpses into the evolution of the adaptive immune system. Immunity. 2001, 15: 351-362. 10.1016/S1074-7613(01)00198-4.View ArticlePubMed
- Abi Rached L, McDermott MF, Pontarotti P: The MHC big bang. Immunol Rev. 1999, 167: 33-44. 10.1111/j.1600-065X.1999.tb01380.x.View ArticlePubMed
- Meyer M, Gaudieri S, Rhodes DA, Trowsdale J: Cluster of TRIM genes in the human MHC class I region sharing the B30.2 domain. Tissue Antigens. 2003, 61: 63-71. 10.1034/j.1399-0039.2003.610105.x.View ArticlePubMed
- Ruby T, Bed'Hom B, Wittzell H, Morin V, Oudin A, Zoorob R: Characterisation of a cluster of TRIM-B30.2 genes in the chicken MHC B locus. Immunogenetics. 2005, 57: 116-128. 10.1007/s00251-005-0770-x.View ArticlePubMed
- Sawyer SL, Emerman M, Malik HS: Discordant evolution of the adjacent antiretroviral genes TRIM22 and TRIM5 in mammals. PLoS Pathog. 2007, 3: e197-10.1371/journal.ppat.0030197.PubMed CentralView ArticlePubMed
- Stein C, Caccamo M, Laird G, Leptin M: Conservation and divergence of gene families encoding components of innate immune response systems in zebrafish. Genome Biol. 2007, 13: R251-10.1186/gb-2007-8-11-r251.View Article
- Laing KJ, Purcell MK, Winton JR, Hansen JD: A genomic view of the NOD-like receptor family in teleost fish: identification of a novel NLR subfamily in zebrafish. BMC Evol Biol. 2008, 8: 42-10.1186/1471-2148-8-42.PubMed CentralView ArticlePubMed
- Sirard JC, Vignal C, Dessein R, Chamaillard M: Nod-like receptors: cytosolic watchdogs for immunity against pathogens. PLoS Pathog. 2007, 3: e152-10.1371/journal.ppat.0030152.PubMed CentralView ArticlePubMed
- Phyre. [http://www.sbg.bio.ic.ac.uk/phyre/]
- SMART. [http://smart.embl-heidelberg.de/]
- ENSEMBL. [http://www.ensembl.org/index.html]
- UCSC. [http://genome.ucsc.edu/]
- Vectorbase. [http://ixscapularis.vectorbase.org/index.php]