A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish.
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 TRIM5alpha, 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.


CONCLUSIONS
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.
van der Aa
Lieke M
LM
Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, Jouy-en-Josas, France. lvanderaa@jouy.inra.fr
Levraud
Jean-Pierre
JP
Yahmi
Malika
M
Lauret
Emilie
E
Briolat
Valérie
V
Herbomel
Philippe
P
Benmansour
Abdenour
A
Boudinot
Pierre
P
D020816:Amino Acid Motifs / Q000235:genetics*; D000595:Amino Acid Sequence; D000818:Animals; D019556:COS Cells; D002522:Chlorocebus aethiops; D019143:Evolution, Molecular; D020440:Gene Duplication; D014644:Genetic Variation / Q000235:genetics*; D008969:Molecular Sequence Data; D005810:Multigene Family; D017686:Oncorhynchus mykiss; D010802:Phylogeny; D054829:RING Finger Domains / Q000235:genetics; D012641:Selection, Genetic; D015027:Zebrafish