In Depth Exploration of the Alternative Proteome of Drosophila melanogaster
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 establish...
| Main Authors: | , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-05-01
|
| Series: | Frontiers in Cell and Developmental Biology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fcell.2022.901351/full |
| _version_ | 1818253929200222208 |
|---|---|
| author | Bertrand Fabre Bertrand Fabre Sebastien A. Choteau Carine Duboé Carole Pichereaux Carole Pichereaux Carole Pichereaux Audrey Montigny Dagmara Korona Michael J. Deery Mylène Camus Mylène Camus Christine Brun Christine Brun Odile Burlet-Schiltz Odile Burlet-Schiltz Steven Russell Jean-Philippe Combier Kathryn S. Lilley Serge Plaza |
| author_facet | Bertrand Fabre Bertrand Fabre Sebastien A. Choteau Carine Duboé Carole Pichereaux Carole Pichereaux Carole Pichereaux Audrey Montigny Dagmara Korona Michael J. Deery Mylène Camus Mylène Camus Christine Brun Christine Brun Odile Burlet-Schiltz Odile Burlet-Schiltz Steven Russell Jean-Philippe Combier Kathryn S. Lilley Serge Plaza |
| author_sort | Bertrand Fabre |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-12T16:47:52Z |
| format | Article |
| id | doaj.art-c3280b188e334a1b912ba22d6e1bf509 |
| institution | Directory Open Access Journal |
| issn | 2296-634X |
| language | English |
| last_indexed | 2024-12-12T16:47:52Z |
| publishDate | 2022-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cell and Developmental Biology |
| spelling | doaj.art-c3280b188e334a1b912ba22d6e1bf5092022-12-22T00:18:26ZengFrontiers Media S.A.Frontiers in Cell and Developmental Biology2296-634X2022-05-011010.3389/fcell.2022.901351901351In Depth Exploration of the Alternative Proteome of Drosophila melanogasterBertrand Fabre0Bertrand Fabre1Sebastien A. Choteau2Carine Duboé3Carole Pichereaux4Carole Pichereaux5Carole Pichereaux6Audrey Montigny7Dagmara Korona8Michael J. Deery9Mylène Camus10Mylène Camus11Christine Brun12Christine Brun13Odile Burlet-Schiltz14Odile Burlet-Schiltz15Steven Russell16Jean-Philippe Combier17Kathryn S. Lilley18Serge Plaza19Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, FranceCambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, United KingdomAix-Marseille Université, INSERM, TAGC, Turing Centre for Living Systems, Marseille, FranceLaboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, FranceFédération de Recherche (FR3450), Agrobiosciences, Interactions et Biodiversité (AIB), CNRS, Toulouse, FranceInstitut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, FranceInfrastructure Nationale de Protéomique, ProFI, FR 2048, Toulouse, FranceLaboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, FranceCambridge Systems Biology Centre and Department of Genetics, University of Cambridge, Cambridge, United KingdomCambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, United KingdomInstitut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, FranceInfrastructure Nationale de Protéomique, ProFI, FR 2048, Toulouse, FranceAix-Marseille Université, INSERM, TAGC, Turing Centre for Living Systems, Marseille, FranceCNRS, Marseille, FranceInstitut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, FranceInfrastructure Nationale de Protéomique, ProFI, FR 2048, Toulouse, FranceCambridge Systems Biology Centre and Department of Genetics, University of Cambridge, Cambridge, United KingdomLaboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, FranceCambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, United KingdomLaboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, FranceRecent 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.https://www.frontiersin.org/articles/10.3389/fcell.2022.901351/fullalternative proteinsshort open reading frame–encoded polypeptidemicroproteinpeptidomicsmass spectrometry |
| spellingShingle | Bertrand Fabre Bertrand Fabre Sebastien A. Choteau Carine Duboé Carole Pichereaux Carole Pichereaux Carole Pichereaux Audrey Montigny Dagmara Korona Michael J. Deery Mylène Camus Mylène Camus Christine Brun Christine Brun Odile Burlet-Schiltz Odile Burlet-Schiltz Steven Russell Jean-Philippe Combier Kathryn S. Lilley Serge Plaza In Depth Exploration of the Alternative Proteome of Drosophila melanogaster Frontiers in Cell and Developmental Biology alternative proteins short open reading frame–encoded polypeptide microprotein peptidomics mass spectrometry |
| title | In Depth Exploration of the Alternative Proteome of Drosophila melanogaster |
| title_full | In Depth Exploration of the Alternative Proteome of Drosophila melanogaster |
| title_fullStr | In Depth Exploration of the Alternative Proteome of Drosophila melanogaster |
| title_full_unstemmed | In Depth Exploration of the Alternative Proteome of Drosophila melanogaster |
| title_short | In Depth Exploration of the Alternative Proteome of Drosophila melanogaster |
| title_sort | in depth exploration of the alternative proteome of drosophila melanogaster |
| topic | alternative proteins short open reading frame–encoded polypeptide microprotein peptidomics mass spectrometry |
| url | https://www.frontiersin.org/articles/10.3389/fcell.2022.901351/full |
| work_keys_str_mv | AT bertrandfabre indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT bertrandfabre indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT sebastienachoteau indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT carineduboe indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT carolepichereaux indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT carolepichereaux indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT carolepichereaux indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT audreymontigny indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT dagmarakorona indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT michaeljdeery indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT mylenecamus indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT mylenecamus indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT christinebrun indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT christinebrun indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT odileburletschiltz indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT odileburletschiltz indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT stevenrussell indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT jeanphilippecombier indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT kathrynslilley indepthexplorationofthealternativeproteomeofdrosophilamelanogaster AT sergeplaza indepthexplorationofthealternativeproteomeofdrosophilamelanogaster |