Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome
| Autor: | Guillaume Tremblay, Jean-François Lucier, Xavier Roucou, Julie Motard, Maxence Wisztorski, Michel Salzet, Benoît Vanderperre, François-Michel Boisvert, Cyntia Bissonnette, Solène Vanderperre |
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| Rok vydání: | 2013 |
| Předmět: |
Proteomics
Proteome Reading frame Gene Expression lcsh:Medicine Protein Synthesis Biochemistry Molecular Cell Biology Databases Genetic Human proteome project Ribosome profiling Peptide Chain Initiation Translational lcsh:Science Genetics 0303 health sciences Spectrometric Identification of Proteins Multidisciplinary Proteomic Databases BRCA1 Protein 030302 biochemistry & molecular biology Protein Classes Information Technology Research Article Protein Binding Gene prediction Molecular Sequence Data Biology Transfection Cell Line Databases Open Reading Frames 03 medical and health sciences Humans Amino Acid Sequence 030304 developmental biology Plasma Proteins lcsh:R Alternative splicing Proteins Computational Biology Reproducibility of Results Alternative Splicing Open reading frame Protein Biosynthesis Computer Science Protein Translation lcsh:Q Sequence Alignment |
| Zdroj: | PLoS ONE, Vol 8, Iss 8, p e70698 (2013) PLoS ONE |
| ISSN: | 1932-6203 |
| Popis: | A fully mature mRNA is usually associated to a reference open reading frame encoding a single protein. Yet, mature mRNAs contain unconventional alternative open reading frames (AltORFs) located in untranslated regions (UTRs) or overlapping the reference ORFs (RefORFs) in non-canonical +2 and +3 reading frames. Although recent ribosome profiling and footprinting approaches have suggested the significant use of unconventional translation initiation sites in mammals, direct evidence of large-scale alternative protein expression at the proteome level is still lacking. To determine the contribution of alternative proteins to the human proteome, we generated a database of predicted human AltORFs revealing a new proteome mainly composed of small proteins with a median length of 57 amino acids, compared to 344 amino acids for the reference proteome. We experimentally detected a total of 1,259 alternative proteins by mass spectrometry analyses of human cell lines, tissues and fluids. In plasma and serum, alternative proteins represent up to 55% of the proteome and may be a potential unsuspected new source for biomarkers. We observed constitutive co-expression of RefORFs and AltORFs from endogenous genes and from transfected cDNAs, including tumor suppressor p53, and provide evidence that out-of-frame clones representing AltORFs are mistakenly rejected as false positive in cDNAs screening assays. Functional importance of alternative proteins is strongly supported by significant evolutionary conservation in vertebrates, invertebrates, and yeast. Our results imply that coding of multiple proteins in a single gene by the use of AltORFs may be a common feature in eukaryotes, and confirm that translation of unconventional ORFs generates an as yet unexplored proteome. |
| Databáze: | OpenAIRE |
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