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Open Access Research article

A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish

Lieke M van der Aa12, Jean-Pierre Levraud3, Malika Yahmi1, Emilie Lauret1, Valérie Briolat3, Philippe Herbomel3, Abdenour Benmansour1 and Pierre Boudinot1*

Author Affiliations

1 Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, Jouy-en-Josas, France

2 Cell Biology and Immunology Group, Wageningen University, Marijkeweg 40, 6709 PG, Wageningen, The Netherlands

3 Unité Macrophages et Développement de l'Immunité, URA 2578 du Centre National de la Recherche Scientifique, Institut Pasteur, 25, rue du Docteur Roux, 75015 Paris, France

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BMC Biology 2009, 7:7  doi:10.1186/1741-7007-7-7

Published: 5 February 2009

Abstract

Background

In mammals, the members of the tripartite motif (TRIM) protein family are involved in various cellular processes including innate immunity against viral infection. Viruses exert strong selective pressures on the defense system. Accordingly, antiviral TRIMs have diversified highly through gene expansion, positive selection and alternative splicing. Characterizing immune TRIMs in other vertebrates may enlighten their complex evolution.

Results

We describe here a large new subfamily of TRIMs in teleosts, called finTRIMs, identified in rainbow trout as virus-induced transcripts. FinTRIMs are formed of nearly identical RING/B-box regions and C-termini of variable length; the long variants include a B30.2 domain. The zebrafish genome harbors a striking diversity of finTRIMs, with 84 genes distributed in clusters on different chromosomes. A phylogenetic analysis revealed different subsets suggesting lineage-specific diversification events. Accordingly, the number of fintrim genes varies greatly among fish species. Conserved syntenies were observed only for the oldest fintrims. The closest mammalian relatives are trim16 and trim25, but they are not true orthologs. The B30.2 domain of zebrafish finTRIMs evolved under strong positive selection. The positions under positive selection are remarkably congruent in finTRIMs and in mammalian antiviral TRIM5α, concentrated within a viral recognition motif in mammals. The B30.2 domains most closely related to finTRIM are found among NOD-like receptors (NLR), indicating that the evolution of TRIMs and NLRs was intertwined by exon shuffling.

Conclusion

The diversity, evolution, and features of finTRIMs suggest an important role in fish innate immunity; this would make them the first TRIMs involved in immunity identified outside mammals.