Abstract
RNA-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 are not 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. Using 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 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, and nucleolysins. Phylogenetic analysis revealed that the proteins and the domain organization are conserved among Ae. aegypti, Bombyx mori, and Drosophila melanogaster. However, the gene length and the intron-exon organization 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 ovaries. This is the first database for the Ae. aegypti RBPs that can serve as the reference base for future investigations. Stage-specific genes can be further explored to determine their role in mosquito growth and development with a focus on developing novel mosquito control strategies.
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Acknowledgements
The authors would like to thank the Indian Council of Medical Research (ICMR), New Delhi for intramural support. Melveettil Kishor Sumitha would like to thank ICMR for the Senior Research Fellowship and Madurai Kamaraj University (MKU) for supporting the research.
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Conceptualization, methodology, formal analysis and investigation, visualization, and writing the manuscript: Bhavna Gupta. Data retrieval and analysis, visualization, and writing the manuscript: Melveettil Kishor Sumitha. Data retrieval and visualization: Mariapillai Kalimuthu and Murali Aarthy. Manuscript review: Ashwani Kumar and Rajaiah Paramasivan.
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Figure S1. Amino acid sequence alignment of squid protein and its orthologs in Aedes aegypti. Jalview has been used for alignment. Identical residues are marked with dots whereas high conservation in the amino acid sequences of both proteins is shown in bright yellow color and higher numerical value. (TIF 162 kb)
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Sumitha, M.K., Kalimuthu, M., Aarthy, M. et al. In silico identification, characterization, and expression analysis of RNA recognition motif (RRM) containing RNA-binding proteins in Aedes aegypti. Parasitol Res 122, 2847–2857 (2023). https://doi.org/10.1007/s00436-023-07969-2
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DOI: https://doi.org/10.1007/s00436-023-07969-2