Das Sandip, Kannihalli Arpita, Banerjee Srishti, Chakraborty Nikita, Ray Sandipan
Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, 502284, India.
Funct Integr Genomics. 2025 Feb 19;25(1):41. doi: 10.1007/s10142-025-01554-9.
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.
果蝇黑腹果蝇是一种简单的多细胞模型系统，广泛应用于生物医学研究。在此，我们旨在精心构建一份全面的黑腹果蝇组织和器官特异性蛋白质组、磷酸化蛋白质组和激酶组图谱。利用已发表文献和数据库中的信息，我们系统地整理了不同发育阶段、成熟黑腹果蝇及其衍生细胞系中11种组织类型的蛋白质表达谱、磷酸化模式以及相关的激酶和磷酸酶。使用DAVID进行基因注释和通路富集分析。使用STRING、BioGrid、OmniPath和InWeb-IM进行蛋白质-蛋白质相互作用分析。通过FlyBase数据库，利用DRSC综合直系同源预测工具，鉴定了人类和小鼠中果蝇激酶和磷酸酶基因的直系同源物。我们在黑腹果蝇中总共绘制了18377种蛋白质、9021种磷酸化蛋白质、433种激酶和141种磷酸酶。随后将蛋白质分类到不同组织类型中，表明某些组织特异性通路和表达簇的富集。通过直系同源筛选，我们在人类和小鼠中分别鉴定出295个和289个果蝇激酶直系同源物。在节律性分析中，我们在5289个转录本、678种蛋白质、437种磷酸化蛋白质、166种激酶和89种磷酸酶中观察到24小时周期性。我们的研究结果整合为一个便捷的资源，用于理解果蝇中的蛋白质组水平组织、其振荡表达以及它们在维持细胞和生理功能中的组织特异性作用。我们预计这项研究将有助于加强对作为模式生物的黑腹果蝇的系统水平分析。
