Interaction analysis of TRIM proteins and innate immunity mediators of common carp (Cyprinus carpio L.) to evaluate its affinity for ubiquitination and innate immune response

Common carp (Cyprinus carpio L.) is considered the most important aquaculture piscine specie. The continuous exposure of this specie to pathogens, including viruses and bacteria, impact its growth and production. The role of tripartite motifs (TRIM) protein in higher mammals has been investigated and a lot of information is available that demonstrates the function of these proteins in diverse cellular mechanisms including antiviral responses. Fish species do not possess a specialized adaptive immune response as seen in mammals and information related to TRIM proteins is very limited. Therefore, understanding the function of TRIMs is a very important area of research. PPIs play a key role in determining the functions of target proteins. In this study, the outcome of interactions among TRIM proteins of Common carp with important innate immunity mediators is investigated. The TRIM proteins are activated as a response to viral infection and are classified on C-terminal domains. TRIMs including, TRIM3, 9, 21, 23, 25, 33, 37, and 82 contain discrete C-terminal domains that are included in this study. Some important mediators including RIG-I, MDA5, cGAS, STING, and TBK1 are selected in this study for their interactions with TRIMs by using computational approaches. These innate immunity mediators are very important in sensing viral infections. They also induce different signaling pathways that trigger cytokine production and activate downstream signaling pathways. A total of forty interactions are performed and the results suggest that TRIM proteins interact selectively with the mediators. The results further hypothesized the binding affinity, important residues, and regions of these proteins involved in interactions that can modulate different cellular activities. In most of the interactions, the residues present in the BBC and coiled-coil domains are predominantly involved in making contact with their interacting partners. The binding affinity and interacting profile proposed that the coil-coil region is very important for attachment to perform the catalytic activity of the TRIM proteins. The findings of this study will open new avenues in better understanding the molecular mechanisms associated with innate immunity and antiviral responses in Common carp against viral infections.