A curated tissue-specific proteome, phosphoproteome, and kinome map of Drosophila melanogaster with an integrated outlook in circadian physiology

Abstract

The fruit fly Drosophila melanogaster is a simple multicellular model system widely used in biomedical research. Here, we aimed to curate a comprehensive tissue and organ-specific proteome, phosphoproteome, and kinome atlas of D. melanogaster. Using information from published literature and databases, we have systematically curated the protein expression profiles, phosphorylation patterns, and the associated kinases and phosphatases in 11 tissue types across the different developmental stages and mature D. melanogaster and its derived cell lines. Gene annotation and pathway enrichment analysis were performed using the DAVID. Protein-protein interaction analysis was carried out using STRING, BioGrid, OmniPath, and InWeb-IM. Drosophila kinase and phosphatase gene orthologs in humans and mice were identified through the FlyBase database, utilizing the DRSC integrative ortholog prediction tool. We mapped a total of 18,377 proteins, 9021 phosphoproteins, 433 kinases, and 141 phosphatases in D. melanogaster. Subsequent categorization of the proteins into different tissue types indicated the enrichment of some tissue-specific pathways and expression clusters. We identified 295 and 289 Drosophila kinase orthologs in humans and mice through an ortholog screening. In the rhythmicity analysis, we observed 24-hour periodicity in 5289 transcripts, 678 proteins, 437 phosphoproteins, 166 kinases, and 89 phosphatases. The findings of our study are integrated as a convenient resource for understanding the proteome-level organizations in Drosophila, their oscillating expression, and their tissue-specific roles in maintaining cellular and physiological functions. We anticipate that this study will help to enhance the systems-level analysis of D. melanogaster as a model organism.