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Bioinformatics and expression analysis of finTRIM genes in grass carp, Ctenopharyngodon idella.

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      Abstract

      The tripartite motifs (TRIMs) constitute a large family of proteins containing a Really Interesting New Gene (RING) domain, a B-box domain and coiled-coil region followed by different C-terminal domains. TRIM proteins play multiple roles in various cellular processes, including cell growth, differentiation, apoptosis and antiviral immunity. Fish novel large multigene TRIM genes (finTRIM/ftr) appear only in teleosts and play a vital role in antiviral responses. Phylogenetic analysis revealed the existence of different subsets of novel fish TRIM 14 genes (finTRIM14/ftr14), ftr51, ftr67, ftr72, ftr82, ftr83, and ftr99 in grass carp (Ctenopharyngodon idella), suggesting lineage-specific diversification events. Therefore, the number of finTRIM genes varies greatly among species. The ftr genes in grass carp, which are closely related to zebrafish and possess various evolutionary branches, have evolved faster than human TRIMs. The predicted protein domains were almost identical RING zinc finger domains, with the exception of ftr72, the B-box domain (excluding ftr67, ftr82, ftr83), and the B30.2 domain, which evolved under positive selection (with the exception of ftr67, and ftr72). The genes were predominantly expressed in the spleen, gill and head kidney. These findings indicate that the ftr genes in grass carp are involved diverse cellular processes, including innate immune responses.

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      Affiliations
      [1 ] Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434020, China.
      [2 ] Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434020, China; School of Animal Science, Yangtze University, Jingzhou 434020, China.
      [3 ] College of Marine and Biotechnology, Guangxi University for Nationalities, Nanning, Guangxi 530006, China; Guangxi Colleges and Universities Key Laboratory of Utilization of Microbial and Botanical Resources, Guangxi University for Nationalities, Nanning, Guangxi 530006, China. Electronic address: hanwen_yuan@126.com.
      [4 ] Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou 434020, China; School of Animal Science, Yangtze University, Jingzhou 434020, China. Electronic address: xuqiaoqing@yangtzeu.edu.cn.
      Journal
      Fish Shellfish Immunol.
      Fish & shellfish immunology
      Elsevier BV
      1095-9947
      1050-4648
      May 02 2017
      : 66
      28476675
      S1050-4648(17)30238-3
      10.1016/j.fsi.2017.05.004

      finTRIM, RING domain, Expression, B-box domain

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