In Depth Exploration of the Alternative Proteome of Drosophila melanogaster


  • Fabre Bertrand
  • Choteau Sebastien
  • Duboé Carine
  • Pichereaux Carole
  • Montigny Audrey
  • Korona Dagmara
  • Deery Michael
  • Camus Mylène
  • Brun Christine
  • Burlet-Schiltz Odile
  • Russell Steven
  • Combier Jean-Philippe
  • Lilley Kathryn
  • Plaza Serge


  • Alternative proteins
  • Short open reading frame–encoded polypeptide
  • Microprotein
  • Peptidomics
  • Mass spectrometry

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Recent studies have shown that hundreds of small proteins were occulted when protein-coding genes were annotated. These proteins, called alternative proteins, have failed to be annotated notably due to the short length of their open reading frame (less than 100 codons) or the enforced rule establishing that messenger RNAs (mRNAs) are monocistronic. Several alternative proteins were shown to be biologically active molecules and seem to be involved in a wide range of biological functions. However, genome-wide exploration of the alternative proteome is still limited to a few species. In the present article, we describe a deep peptidomics workflow which enabled the identification of 401 alternative proteins in Drosophila melanogaster . Subcellular localization, protein domains, and short linear motifs were predicted for 235 of the alternative proteins identified and point toward specific functions of these small proteins. Several alternative proteins had approximated abundances higher than their canonical counterparts, suggesting that these alternative proteins are actually the main products of their corresponding genes. Finally, we observed 14 alternative proteins with developmentally regulated expression patterns and 10 induced upon the heat-shock treatment of embryos, demonstrating stage or stress-specific production of alternative proteins.

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