PT  - JOURNAL ARTICLE
AU  - Sondos Samandi
AU  - Annie V. Roy
AU  - Vivian Delcourt
AU  - Jean-François Lucier
AU  - Jules Gagnon
AU  - Maxime C. Beaudoin
AU  - Benoît Vanderperre
AU  - Marc-André Breton
AU  - Julie Motard
AU  - Jean-François Jacques
AU  - Mylène Brunelle
AU  - Isabelle Gagnon-Arsenault
AU  - Isabelle Fournier
AU  - Aida Ouangraoua
AU  - Darel J. Hunting
AU  - Alan A. Cohen
AU  - Christian R. Landry
AU  - Michelle S. Scott
AU  - Xavier Roucou
TI  - Deep transcriptome annotation suggests that small and large proteins encoded in the same genes often cooperate
AID  - 10.1101/142992
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 142992
4099  - http://biorxiv.org/content/early/2017/09/22/142992.short
4100  - http://biorxiv.org/content/early/2017/09/22/142992.full
AB  - 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.