Abstract
BackgroundIn 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.ResultsWe 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.ConclusionThe 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.
Highlights
In mammals, the members of the tripartite motif (TRIM) protein family are involved in various cellular processes including innate immunity against viral infection
The TRIM proteins are characterized by a tripartite motif that comprises from the N- to C-terminus, a RING zinc finger domain, one or two B-boxes and a coiled-coil domain
Results finTRIM, a new group of TRIM proteins induced by viruses in rainbow trout In order to identify virus-induced transcripts in fish leukocytes, we previously used the method of subtractive suppressive hybridization on rainbow trout leukocytes that were either incubated with viral hemorrhagic septicemia virus (VHSV) or mock-infected
Summary
The members of the tripartite motif (TRIM) protein family are involved in various cellular processes including innate immunity against viral infection. The TRIM proteins are characterized by a tripartite motif that comprises from the N- to C-terminus, a RING zinc finger domain, one or two B-boxes and a coiled-coil domain. They are known as RBCC proteins [1]. The RING finger and B-box are cysteine-rich domains and both domains bind zinc atoms, suggesting interaction with other proteins, RNA and DNA [2,3,4,5] They are usually encoded as a single exon, and together form the 'RBB' region. Most TRIM genes code for at least two isoforms that are generated by alternative splicing, resulting in full-length and partial transcripts that lack the C-terminal encoding sequence
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