title: Global Proteomic Profiling of Drosophila Ovary: A High-resolution, Unbiased, Accurate and Multifaceted Analysis.
abstract: BACKGROUND
  Drosophila melanogaster ovary serves as an attractive model system for the investigation of the cell cycle, death, signaling, migration, differentiation, development and stemness. By employing the 3750/+ heterozygote fly strain that carries specific functions in the follicle cell compartment, and a reliable control in GAL4/UAS-based transgenic technology, we herein characterized the protein-expression profiling of D. melanogaster ovary by applying high-resolution proteomic tools and bioinformatics programs.
  
  
  METHODS
  Whole-cell total protein extracts derived from 3750/+ fly ovaries were prepared under highly denaturing conditions and after tryptic digestion, their cognate peptides were processed to liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) analysis in a high-resolution LTQ Orbitrap Elite instrument. Obtained protein data were analyzed through use of UniProt, DAVID, KEGG and PANTHER bioinformatics platforms.
  
  
  RESULTS
  The 7,583 unique peptides identified show that fly ovary contains at least 2,103 single proteins, which are distributed to all egg chamber compartments, in cytoplasm, membrane and nucleus, compartmentalized into major cellular organelles, and categorized into critical macromolecular assemblies. Among the recognized specific functions, nucleic acid binding, hydrolase, oxidoreductase, transporter and vesicle-mediated trafficking activities were the most prevalent. Determinants implicated in cellular metabolism and gene expression are represented by ~41% and ~17% of the ovarian proteome, respectively. Surprisingly, several proteins were found engaged in aging, immune response and neurogenesis. All major signaling pathways were detected, while apoptotic and non-apoptotic cell death programs were also identified. Remarkably, proteins involved in tumor formation, neurodegenerative and inflammatory diseases were also recognized. The successful remodeling of the proteasome and nearly complete molecular reconstruction of the citrate cycle and fatty acid degradation pathways demonstrate the efficacy, accuracy and fidelity of our combined proteomics/bioinformatics approach.
  
  
  CONCLUSIONS
  Global proteomic characterization of D. melanogaster ovary allows the discovery of novel regulators and pathways, and provides a systemic view of networks that govern ovarian pathophysiology and embryonic development in fly species as well in humans.
authors.affiliation: Department of Cell Biology and Biophysics, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece.
authors.forename: Athanassios D
authors.initials: AD
authors.lastname: Velentzas
authors.affiliation: Proteomics Research Unit, Center of Basic Research II, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
authors.forename: Athanasios K
authors.initials: AK
authors.lastname: Anagnostopoulos
authors.affiliation: Department of Cell Biology and Biophysics, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece.
authors.forename: Panagiotis D
authors.initials: PD
authors.lastname: Velentzas
authors.affiliation: Department of Cell Biology and Biophysics, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece.
authors.forename: Vassiliki E
authors.initials: VE
authors.lastname: Mpakou
authors.affiliation: Department of Cell Biology and Biophysics, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece.
authors.forename: Niki E
authors.initials: NE
authors.lastname: Sagioglou
authors.affiliation: Department of Cell Biology and Biophysics, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece.
authors.forename: Maria M
authors.initials: MM
authors.lastname: Tsioka
authors.affiliation: Department of Cell Biology and Biophysics, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece.
authors.forename: Stamatia
authors.initials: S
authors.lastname: Katarachia
authors.affiliation: Department of Cell Biology and Biophysics, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece.
authors.forename: Areti K
authors.initials: AK
authors.lastname: Manta
authors.affiliation: Department of Cell Biology and Biophysics, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece.
authors.forename: Eumorphia G
authors.initials: EG
authors.lastname: Konstantakou
authors.affiliation: Department of Cell Biology and Biophysics, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece.
authors.forename: Issidora S
authors.initials: IS
authors.lastname: Papassideri
authors.affiliation: Proteomics Research Unit, Center of Basic Research II, Biomedical Research Foundation of the Academy of Athens, Athens, Greece gthtsangaris@bioacademy.gr dstravop@biol.uoa.gr.
authors.forename: George T H
authors.initials: GT
authors.lastname: Tsangaris
authors.affiliation: Department of Cell Biology and Biophysics, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece gthtsangaris@bioacademy.gr dstravop@biol.uoa.gr.
authors.forename: Dimitrios J
authors.initials: DJ
authors.lastname: Stravopodis
mesh_terms: D000818:Animals; D017209:Apoptosis; D002453:Cell Cycle; D002454:Cell Differentiation; D002465:Cell Movement; D002853:Chromatography, Liquid; D019295:Computational Biology; D004331:Drosophila melanogaster; D005260:Female; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006579:Heterozygote; D007249:Inflammation; D010053:Ovary / Q000378:metabolism*; D020543:Proteome; D040901:Proteomics; D015398:Signal Transduction; D053719:Tandem Mass Spectrometry
chemical_list: D020543:Proteome
keywords: Bioinformatics; Drosophila; liquid chromatography; mass spectrometry; ovary; proteome; proteomics