Comparison of Drosophila melanogaster Embryo and Adult Proteome by SWATH-MS Reveals Differential Regulation of Protein Synthesis, Degradation Machinery, and Metabolism Modules

• Published in: Journal of proteome research Vol. 18; no. 6; pp. 2525 - 2534
• Main Authors: Fabre, Bertrand, Korona, Dagmara, Lees, Jonathan G, Lazar, Ikrame, Livneh, Ido, Brunet, Manon, Orengo, Christine A, Russell, Steven, Lilley, Kathryn S
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 07.06.2019
• Subjects: Animals; Drosophila melanogaster - genetics; Drosophila melanogaster - growth & development; Drosophila melanogaster - metabolism; Drosophila melanogaster - microbiology; Embryo, Nonmammalian - metabolism; Embryo, Nonmammalian - microbiology; Gene Expression Regulation, Developmental - genetics; Protein Biosynthesis - genetics; Proteolysis; Proteome - genetics; Proteome - metabolism; Proteomics - methods; Transcriptome - genetics; Wolbachia - pathogenicity; SWATH-MS; embryo; proteomics; Drosophila melanogaster; post-transcriptional regulation; adult fly
• ISSN: 1535-3893; 1535-3907
• DOI: 10.1021/acs.jproteome.9b00076

An important area of modern biology consists of understanding the relationship between genotype and phenotype. However, to understand this relationship it is essential to investigate one of the principal links between them: the proteome. With the development of recent mass-spectrometry approaches, it is now possible to quantify entire proteomes and thus relate them to different phenotypes. Here, we present a comparison of the proteome of two extreme developmental states in the well-established model organism Drosophila melanogaster: adult and embryo. Protein modules such as ribosome, proteasome, tricarboxylic acid cycle, glycolysis, or oxidative phosphorylation were found differentially expressed between the two developmental stages. Analysis of post-translation modifications of the proteins identified in this study indicates that they generally follow the same trend as their corresponding protein. Comparison between changes in the proteome and the transcriptome highlighted patterns of post-transcriptional regulation for the subunits of protein complexes such as the ribosome and the proteasome, whereas protein from modules such as TCA cycle, glycolysis, and oxidative phosphorylation seem to be coregulated at the transcriptional level. Finally, the impact of the endosymbiont Wolbachia pipientis on the proteome of both developmental states was also investigated.