Genomic Analysis, Evolution and Characterization of E3 Ubiquitin Protein Ligase (TRIM) Gene Family in Common Carp (Cyprinus carpio)

SIMPLE SUMMARY: TRIM family proteins form a large family of proteins that play a central role in antiviral host defense. These proteins are characterized and identified in tetrapods but the knowledge related to this family among teleost species is very limited. In this study, we analyze the evolutionary relationships, characterization, and functional annotation of common carp TRIM family. The evolutionary analysis revealed that the TRIM family among tetrapods and teleost species is conserved in sequence similarity and domain architectures. The occurrence of certain motifs across the TRIMs members implies a conserved nature and indicate a group specific function. However, the exon-intron organization is more diverse suggesting the complex alternative splicing and duplication. The functional annotation shows that most TRIM proteins are associated with ubiquitination, which can potentially mediate multicellular processes including immune response, cell cycle regulation, modulation of different substrates of important signaling pathways and post translational modifications. The study results will open up new avenues for future research and can be used to elucidate several mechanisms related to common carp development and immune response. ABSTRACT: Tripartite motifs (TRIM) is a large family of E3 ubiquitin ligases that play an important role in ubiquitylation. TRIM proteins regulate a wide range of biological processes from cellular response to viral infection and are implicated in various pathologies, from Mendelian disease to cancer. Although the TRIM family has been identified and characterized in tetrapods, but the knowledge about common carp and other teleost species is limited. The genes and proteins in the TRIM family of common carp were analyzed for evolutionary relationships, characterization, and functional annotation. Phylogenetic analysis was used to elucidate the evolutionary relationship of TRIM protein among teleost and higher vertebrate species. The results show that the TRIM orthologs of highly distant vertebrates have conserved sequences and domain architectures. The pairwise distance was calculated among teleost species of TRIMs, and the result exhibits very few mismatches at aligned position thus, indicating that the members are not distant from each other. Furthermore, TRIM family of common carp clustered into six groups on the basis of phylogenetic analysis. Additionally, the analysis revealed conserved motifs and functional domains in the subfamily members. The difference in functional domains and motifs is attributed to the evolution of these groups from different ancestors, thus validating the accuracy of clusters in the phylogenetic tree. However, the intron-exon organization is not precisely similar, which suggests duplication of genes and complex alternative splicing. The percentage of secondary structural elements is comparable for members of the same group, but the tertiary conformation is varied and dominated by coiled-coil segments required for catalytic activity. Gene ontology analysis revealed that these proteins are mainly associated with the catalytic activity of ubiquitination, immune system, zinc ion binding, positive regulation of transcription, ligase activity, and cell cycle regulation. Moreover, the biological pathway analyses identified four KEGG and 22 Reactome pathways. The predicted pathways correspond to functional domains, and gene ontology which proposes that proteins with similar structures might perform the same functions.