Aedes aegypti microRNA, miR-2944b-5p interacts with 3'UTR of chikungunya virus and cellular target vps-13 to regulate viral replication

Background RNA interference is among the most important mechanisms that serve to restrict virus replication within mosquitoes, where microRNAs (miRNAs) are important in regulating viral replication and cellular functions. These miRNAs function by binding to complementary sequences mostly in the untranslated regions of the target. Chikungunya virus (CHIKV) genome consists of two open reading frames flanked by 5 and 3 untranslated regions on the two sides. A recent study from our laboratory has shown that Aedes miRNAs are regulated during CHIKV infection. The present study was undertaken to further understand the role of these miRNAs in CHIKV replication. Methods/Findings We observe that miR-2944b-5p binds to the 3 ' untranslated region of CHIKV and the binding is abated when the binding sites are abolished. Loss-of-function studies of miR-2944b-5p using antagomirs, both in vitro and in vivo, reveal an increase in CHIKV viral replication, thereby directly implying a role of miR-2944b-5p in CHIKV replication. We further showed that the mitochondrial membrane potential of the mosquito cells is maintained by this miRNA during CHIKV replication, and cellular factor vps-13 plays a contributing role. Conclusions Our study has opened new avenues to understand vector-virus interactions and provides novel insights into CHIKV replication in Aedes aegypti. Furthermore, our study has shown miR-2944b-5p to be playing role, where one of its target vps-13 also contributes, in maintaining mitochondrial membrane potential in Aedes aegypti. Author summary Aedes aegypti mosquito transmits pathogenic viruses like chikungunya virus (CHIKV). Inside the vector, the virus replicates in a way so that it is able to survive within the mosquito without causing damage to it. However, once in the mammalian host, it becomes pathogenic and induces death to the infected cells. Amongst several mosquito specific factors that allows or rejects the virus survival, microRNAs play a decisive role. In several studies, miRNAs have shown to be playing role in controlling virus replication either by binding to viral genome or to suppress the expression of any host factor. In the present study, we identified an Aedes miRNA, miR-2944b-5p, which binds to 3'UTR of CHIKV and regulates the replication of the virus in the mosquito. Analysis of the mode of action of this regulation revealed that miR-2944b-5p played a role in maintaining mitochondrial membrane potential during CHIKV replication by targeting cellular factor vps-13.