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Deep transcriptome annotation suggests that small and large proteins encoded in the same genes often cooperate

Sondos Samandi, Annie V. Roy, Vivian Delcourt, Jean-François Lucier, Jules Gagnon, Maxime C. Beaudoin, Benoît Vanderperre, Marc-André Breton, Julie Motard, View ORCID ProfileJean-François Jacques, Mylène Brunelle, Isabelle Gagnon-Arsenault, Isabelle Fournier, Aida Ouangraoua, Darel J. Hunting, Alan A. Cohen, Christian R. Landry, Michelle S. Scott, View ORCID ProfileXavier Roucou
doi: https://doi.org/10.1101/142992
Sondos Samandi
1Department of Biochemistry, Université de Sherbrooke, Québec, Canada
7PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
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Annie V. Roy
1Department of Biochemistry, Université de Sherbrooke, Québec, Canada
7PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
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Vivian Delcourt
1Department of Biochemistry, Université de Sherbrooke, Québec, Canada
7PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
8Université Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM) F-59000 Lille, France
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Jean-François Lucier
2Department of Biology and Center for Computational Science, Université de Sherbrooke, Québec, Canada
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Jules Gagnon
2Department of Biology and Center for Computational Science, Université de Sherbrooke, Québec, Canada
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Maxime C. Beaudoin
1Department of Biochemistry, Université de Sherbrooke, Québec, Canada
7PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
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Benoît Vanderperre
1Department of Biochemistry, Université de Sherbrooke, Québec, Canada
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Marc-André Breton
1Department of Biochemistry, Université de Sherbrooke, Québec, Canada
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Julie Motard
1Department of Biochemistry, Université de Sherbrooke, Québec, Canada
7PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
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Jean-François Jacques
1Department of Biochemistry, Université de Sherbrooke, Québec, Canada
7PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
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  • ORCID record for Jean-François Jacques
Mylène Brunelle
1Department of Biochemistry, Université de Sherbrooke, Québec, Canada
7PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
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Isabelle Gagnon-Arsenault
6Département de biologie and IBIS, Université Laval, Québec, Canada
7PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
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Isabelle Fournier
8Université Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM) F-59000 Lille, France
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Aida Ouangraoua
3Department of Computer Science, Université de Sherbrooke, Québec, Canada
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Darel J. Hunting
4Department of Nuclear Medicine & Radiobiology, Université de Sherbrooke, Québec, Canada
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Alan A. Cohen
5Department of Family Medicine, Université de Sherbrooke, Québec, Canada
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Christian R. Landry
6Département de biologie and IBIS, Université Laval, Québec, Canada
7PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
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Michelle S. Scott
1Department of Biochemistry, Université de Sherbrooke, Québec, Canada
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Xavier Roucou
1Department of Biochemistry, Université de Sherbrooke, Québec, Canada
7PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec, Canada
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  • ORCID record for Xavier Roucou
  • For correspondence: xavier.roucou@usherbrooke.ca
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Abstract

Recent studies in eukaryotes have demonstrated the translation of alternative open reading frames (altORFs) in addition to annotated protein coding sequences (CDSs). We show that a large number of small proteins could in fact be coded by altORFs. The putative alternative proteins translated from altORFs have orthologs in many species and evolutionary patterns indicate that altORFs are particularly constrained in CDSs that evolve slowly. Thousands of predicted alternative proteins are detected in proteomic datasets by reanalysis using a database containing predicted alternative proteins. Protein domains and co-conservation analyses suggest a potential functional relationship between small and large proteins encoded in the same genes. This is illustrated with specific examples, including altMiD51, a 70 amino acid mitochondrial fission-promoting protein encoded in MiD51/Mief1/SMCR7L, a gene encoding an annotated protein promoting mitochondrial fission. Our results suggest that many coding genes code for more than one protein that are often functionally related.

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Posted September 22, 2017.
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Deep transcriptome annotation suggests that small and large proteins encoded in the same genes often cooperate
Sondos Samandi, Annie V. Roy, Vivian Delcourt, Jean-François Lucier, Jules Gagnon, Maxime C. Beaudoin, Benoît Vanderperre, Marc-André Breton, Julie Motard, Jean-François Jacques, Mylène Brunelle, Isabelle Gagnon-Arsenault, Isabelle Fournier, Aida Ouangraoua, Darel J. Hunting, Alan A. Cohen, Christian R. Landry, Michelle S. Scott, Xavier Roucou
bioRxiv 142992; doi: https://doi.org/10.1101/142992
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Deep transcriptome annotation suggests that small and large proteins encoded in the same genes often cooperate
Sondos Samandi, Annie V. Roy, Vivian Delcourt, Jean-François Lucier, Jules Gagnon, Maxime C. Beaudoin, Benoît Vanderperre, Marc-André Breton, Julie Motard, Jean-François Jacques, Mylène Brunelle, Isabelle Gagnon-Arsenault, Isabelle Fournier, Aida Ouangraoua, Darel J. Hunting, Alan A. Cohen, Christian R. Landry, Michelle S. Scott, Xavier Roucou
bioRxiv 142992; doi: https://doi.org/10.1101/142992

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