In-silico identification, characterization, and expression analysis of RNA recognition motif (RRM) containing RNA binding proteins in Aedes aegypti

Abstract

BackgroundRNA binding proteins (RBPs) are the proteins that bind RNAs and regulate their functioning. RBPs in mosquitoes are gaining attention due to their ability to bind flaviviruses and regulate their replication and transmission. Despite their relevance, RBPs in mosquitoes have not been explored much. In this study, we screened the whole genome of Aedes aegypti, the primary vector of several pathogenic viruses, and identified the proteins containing RNA recognition motif (RRM), the most abundant protein domain in eukaryotes. ResultsUsing several in-silico strategies, a total of 135 RRM containing RBPs were identified in Ae. aegypti. The proteins were characterized based on their available annotations and the sequence similarity with the Drosophila melanogaster. Ae. aegypti RRM containing RBPs included serine/arginine-rich (SR) proteins, polyadenylate binding proteins (PABP), heteronuclear ribonucleoproteins (hnRNP), small nuclear ribonucleoproteins (snRNP), splicing factors, eukaryotic initiation factors, transformers, nucleolysins, etc. Phylogenetic analysis revealed that the proteins and the domain organisation is conserved among Ae. aegypti, Bombyx mori and Drosophila melanogaster. However, the gene length and the intron-exon organisation varied across the insect species. Expression analysis of the genes encoding RBPs using publicly available RNA sequencing data for different developmental time points of the mosquito life cycle starting from the ovary and eggs up to the adults revealed stage-specific expression with several genes preferentially expressed in early embryonic stages and blood-fed female ovary. ConclusionsThis is the first database for the Ae. aegypti RBPs that can serve as the reference base for future investigations. The stage-specific genes can be further explored to determine their role in mosquito growth and development with a focus to develop novel mosquito control strategies.