Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins
Recent functional, proteomic and ribosome profiling studies in eukaryotes have concurrently 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 thes...
| Main Authors: | , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2017-10-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/27860 |
| _version_ | 1811181090466955264 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Sondos Samandi |
| collection | DOAJ |
| description | Recent functional, proteomic and ribosome profiling studies in eukaryotes have concurrently 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 these altORFs. The putative alternative proteins translated from altORFs have orthologs in many species and contain functional domains. Evolutionary analyses indicate that altORFs often show more extreme conservation patterns than their CDSs. Thousands of alternative proteins are detected in proteomic datasets by reanalysis using a database containing predicted alternative proteins. 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 genes are multicoding genes and code for a large protein and one or several small proteins. |
| first_indexed | 2024-04-11T09:12:36Z |
| format | Article |
| id | doaj.art-6aa1a82d2e824bd38587ba83dbdc8a9e |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-11T09:12:36Z |
| publishDate | 2017-10-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-6aa1a82d2e824bd38587ba83dbdc8a9e2022-12-22T04:32:26ZengeLife Sciences Publications LtdeLife2050-084X2017-10-01610.7554/eLife.27860Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteinsSondos Samandi0Annie V Roy1Vivian Delcourt2Jean-François Lucier3Jules Gagnon4Maxime C Beaudoin5Benoît Vanderperre6Marc-André Breton7Julie Motard8Jean-François Jacques9https://orcid.org/0000-0002-0465-0313Mylène Brunelle10Isabelle Gagnon-Arsenault11Isabelle Fournier12https://orcid.org/0000-0003-1096-5044Aida Ouangraoua13Darel J Hunting14Alan A Cohen15Christian R Landry16Michelle S Scott17Xavier Roucou18https://orcid.org/0000-0001-9370-5584Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada; PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, CanadaDepartment of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada; PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, CanadaDepartment of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada; PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, Canada; INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM) F-59000 Lille, Université de Lille, Lille, FranceDepartment of Biology, Université de Sherbrooke, Québec, Canada; Center for Scientific computing, Information Technologies Services,, Université de Sherbrooke, Québec, CanadaDepartment of Biology, Université de Sherbrooke, Québec, Canada; Center for Scientific computing, Information Technologies Services,, Université de Sherbrooke, Québec, CanadaDepartment of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada; PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, CanadaDepartment of Biochemistry, Université de Sherbrooke, Sherbrooke, CanadaDepartment of Biochemistry, Université de Sherbrooke, Sherbrooke, CanadaDepartment of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada; PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, CanadaDepartment of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada; PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, CanadaDepartment of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada; PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, CanadaPROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, Canada; Département de biochimie, microbiologie et bioinformatique, Université Laval, Québec, Canada; IBIS, Université Laval, Québec, CanadaINSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM) F-59000 Lille, Université de Lille, Lille, FranceDepartment of Computer Science, Université de Sherbrooke, Québec, CanadaDepartment of Nuclear Medicine and Radiobiology, Université de Sherbrooke, Québec, CanadaDepartment of Family Medicine, Université de Sherbrooke, Québec, CanadaPROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, Canada; Département de biochimie, microbiologie et bioinformatique, Université Laval, Québec, Canada; IBIS, Université Laval, Québec, CanadaDepartment of Biochemistry, Université de Sherbrooke, Sherbrooke, CanadaDepartment of Biochemistry, Université de Sherbrooke, Sherbrooke, Canada; PROTEO, Québec Network for Research on Protein Function, Structure and Engineering, Québec, CanadaRecent functional, proteomic and ribosome profiling studies in eukaryotes have concurrently 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 these altORFs. The putative alternative proteins translated from altORFs have orthologs in many species and contain functional domains. Evolutionary analyses indicate that altORFs often show more extreme conservation patterns than their CDSs. Thousands of alternative proteins are detected in proteomic datasets by reanalysis using a database containing predicted alternative proteins. 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 genes are multicoding genes and code for a large protein and one or several small proteins.https://elifesciences.org/articles/27860small proteinsopen reading framestranslationalternative translationtranslation initiation sites |
| spellingShingle | 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 Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins eLife small proteins open reading frames translation alternative translation translation initiation sites |
| title | Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins |
| title_full | Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins |
| title_fullStr | Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins |
| title_full_unstemmed | Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins |
| title_short | Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins |
| title_sort | deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins |
| topic | small proteins open reading frames translation alternative translation translation initiation sites |
| url | https://elifesciences.org/articles/27860 |
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