Figure 1
Scheme of the general method for the identification of smORFs in different related species. Based on primary data and schemes from Kessler et al. (2003)Kessler MM, Zeng Q, Hogan S, Cook R, Morales AJ and Cottarel G (2003) Systematic discovery of new genes in the Saccharomyces cerevisiae genome. Genome Res 13:264–271. and Ladoukakis et al. (2011)Ladoukakis E, Pereira V, Magny EG, Eyre-Walker A and Couso JP (2011) Hundreds of putatively functional small open reading frames in Drosophila. Genome Biol 12:R118.. smORF prediction is based on detection and filtering. The filtering process is important to reduce the false positive rate and increase the efficacy of functional smORFs estimation.
Figure 2
Schematic drawings of the generation of biologically active short peptides. A similar scheme was published by Hashimoto et al. (2008)Hashimoto Y, Kondo T and Kageyama Y (2008) Lilliputians get into the limelight: Novel class of small peptide genes in morphogenesis. Dev Growth Differ 50(Suppl 1):S269–276.. (A) Hormones and neuropeptides are generated via a large mRNA precursor (blue) in the nucleus, then translated by ribosomes (green) from a single initiation codon and finally processed in the ER and Golgi into small peptides, which are subsequently secreted by vesicles to act far from the production site. (B) Polycistronic smORFs (red) can be translated by several ribosomes (green) along a single mRNA, followed by cell secretion. Peptides from smORFs can also act far from the releasing cell.
Figure 3
Evolution and functional role of Mlpt/Tal/Pri in arthropods. Several arthropods display an ortholog of Mlpt/Tal/Pri (original alignments and phylogenetic trees from Galindo et al., 2007Galindo MI, Pueyo JI, Fouix S, Bishop SA and Couso JP (2007) Peptides encoded by short ORFs control development and define a new eukaryotic gene family. PLoS Biol 5:e106. and Savard et al., 2006Savard J, Marques-Souza H, Aranda M and Tautz D (2006) A segmentation gene in Tribolium produces a polycistronic mRNA that codes for multiple conserved peptides. Cell 126:559–569.). In the short-germ embryo of the beetle Tribolium castaneum, mlpt was shown to be expressed in the legs and trachea, where it acts as a gap gene during embryogenesis (Savard et al., 2006Savard J, Marques-Souza H, Aranda M and Tautz D (2006) A segmentation gene in Tribolium produces a polycistronic mRNA that codes for multiple conserved peptides. Cell 126:559–569.). In the long-germ embryo of the fly Drosophila melanogaster, Mlpt/Tal/Pri was shown to be involved in several processes, which are displayed in red (Chanut-Delalande et al., 2014Chanut-Delalande H, Hashimoto Y, Pelissier-Monier A, Spokony R, Dib A, Kondo T, Bohere J, Niimi K, Latapie Y, Inagaki S et al. (2014) Pri peptides are mediators of ecdysone for the temporal control of development. Nat Cell Biol 16:1035–1044.; Galindo et al., 2007Galindo MI, Pueyo JI, Fouix S, Bishop SA and Couso JP (2007) Peptides encoded by short ORFs control development and define a new eukaryotic gene family. PLoS Biol 5:e106.; Kondo et al., 2007Kondo T, Hashimoto Y, Kato K, Inagaki S, Hayashi S and Kageyama Y (2007) Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA. Nat Cell Biol 9:660–665., 2010Kondo T, Plaza S, Zanet J, Benrabah E, Valenti P, Hashimoto Y, Kobayashi S, Payre F and Kageyama Y (2010) Small peptides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis. Science 329:336–339.; Pueyo and Couso, 2008Pueyo JI and Couso JP (2008) The 11-aminoacid long Tarsal-less peptides trigger a cell signal in Drosophila leg development. Dev Biol 324:192–201., 2011Pueyo JI and Couso JP (2011) Tarsal-less peptides control Notch signalling through the Shavenbaby transcription factor. Dev Biol 355:183–193.). Notch, Svb and EcR are the known regulators of Mlpt/Tal/Pri (Chanut-Delalande et al., 2014Chanut-Delalande H, Hashimoto Y, Pelissier-Monier A, Spokony R, Dib A, Kondo T, Bohere J, Niimi K, Latapie Y, Inagaki S et al. (2014) Pri peptides are mediators of ecdysone for the temporal control of development. Nat Cell Biol 16:1035–1044.). Three unknown aspects of the evolution of Mlpt/Tal/Pri are highlighted in blue. These include the origin of the gene in arthropods, its ancestral function, and the loss of gap gene function after the split between the common ancestor of Coleoptera and Diptera. It is also possible that the gap gene function of Mlpt/Tal/Pri was independently acquired in Coleoptera.