title: A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish.
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 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.
authors.affiliation: Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique, Jouy-en-Josas, France. lvanderaa@jouy.inra.fr
authors.forename: Lieke M
authors.initials: LM
authors.lastname: van der Aa
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Levraud
authors.forename: Malika
authors.initials: M
authors.lastname: Yahmi
authors.forename: Emilie
authors.initials: E
authors.lastname: Lauret
authors.forename: Valérie
authors.initials: V
authors.lastname: Briolat
authors.forename: Philippe
authors.initials: P
authors.lastname: Herbomel
authors.forename: Abdenour
authors.initials: A
authors.lastname: Benmansour
authors.forename: Pierre
authors.initials: P
authors.lastname: Boudinot
mesh_terms: 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