The developmental proteome of Drosophila melanogaster
- Nuria Casas-Vila1,8,
- Alina Bluhm1,8,
- Sergi Sayols2,8,
- Nadja Dinges3,
- Mario Dejung4,
- Tina Altenhein5,
- Dennis Kappei6,
- Benjamin Altenhein5,7,
- Jean-Yves Roignant3 and
- Falk Butter1
- 1Quantitative Proteomics, Institute of Molecular Biology, 55128 Mainz, Germany;
- 2Bioinformatics Core Facility, Institute of Molecular Biology, 55128 Mainz, Germany;
- 3RNA Epigenetics, Institute of Molecular Biology, 55128 Mainz, Germany;
- 4Proteomics Core Facility, Institute of Molecular Biology, 55128 Mainz, Germany;
- 5Institute of Genetics, Johannes Gutenberg University, 55128 Mainz, Germany;
- 6Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599;
- 7Institute of Zoology, University of Cologne, 50674 Cologne, Germany
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↵8 These authors contributed equally to this work.
Abstract
Drosophila melanogaster is a widely used genetic model organism in developmental biology. While this model organism has been intensively studied at the RNA level, a comprehensive proteomic study covering the complete life cycle is still missing. Here, we apply label-free quantitative proteomics to explore proteome remodeling across Drosophila’s life cycle, resulting in 7952 proteins, and provide a high temporal-resolved embryogenesis proteome of 5458 proteins. Our proteome data enabled us to monitor isoform-specific expression of 34 genes during development, to identify the pseudogene Cyp9f3Ψ as a protein-coding gene, and to obtain evidence of 268 small proteins. Moreover, the comparison with available transcriptomic data uncovered examples of poor correlation between mRNA and protein, underscoring the importance of proteomics to study developmental progression. Data integration of our embryogenesis proteome with tissue-specific data revealed spatial and temporal information for further functional studies of yet uncharacterized proteins. Overall, our high resolution proteomes provide a powerful resource and can be explored in detail in our interactive web interface.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.213694.116.
- Received July 29, 2016.
- Accepted March 30, 2017.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
