Literature DB >> 26575237

Discovery and characterization of smORF-encoded bioactive polypeptides.

Alan Saghatelian1, Juan Pablo Couso2.   

Abstract

Analysis of genomes, transcriptomes and proteomes reveals the existence of hundreds to thousands of translated, yet non-annotated, short open reading frames (small ORFs or smORFs). The discovery of smORFs and their protein products, smORF-encoded polypeptides (SEPs), points to a fundamental gap in our knowledge of protein-coding genes. Various studies have identified central roles for smORFs in metabolism, apoptosis and development. The discovery of these bioactive SEPs emphasizes the functional potential of this unexplored class of biomolecules. Here, we provide an overview of this emerging field and highlight the opportunities for chemical biology to answer fundamental questions about these novel genes. Such studies will provide new insights into the protein-coding potential of genomes and identify functional genes with roles in biology and disease.

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Year:  2015        PMID: 26575237      PMCID: PMC4956473          DOI: 10.1038/nchembio.1964

Source DB:  PubMed          Journal:  Nat Chem Biol        ISSN: 1552-4450            Impact factor:   15.040


  82 in total

1.  Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA.

Authors:  Takefumi Kondo; Yoshiko Hashimoto; Kagayaki Kato; Sachi Inagaki; Shigeo Hayashi; Yuji Kageyama
Journal:  Nat Cell Biol       Date:  2007-05-07       Impact factor: 28.824

Review 2.  Small-molecule inhibitors of protein-protein interactions: progressing toward the reality.

Authors:  Michelle R Arkin; Yinyan Tang; James A Wells
Journal:  Chem Biol       Date:  2014-09-18

3.  Hundreds of putatively functional small open reading frames in Drosophila.

Authors:  Emmanuel Ladoukakis; Vini Pereira; Emile G Magny; Adam Eyre-Walker; Juan Pablo Couso
Journal:  Genome Biol       Date:  2011-11-25       Impact factor: 13.583

4.  Primary transcripts of microRNAs encode regulatory peptides.

Authors:  Dominique Lauressergues; Jean-Malo Couzigou; Hélène San Clemente; Yves Martinez; Christophe Dunand; Guillaume Bécard; Jean-Philippe Combier
Journal:  Nature       Date:  2015-03-25       Impact factor: 49.962

5.  Humanin peptide suppresses apoptosis by interfering with Bax activation.

Authors:  Bin Guo; Dayong Zhai; Edelmira Cabezas; Kate Welsh; Shahrzad Nouraini; Arnold C Satterthwait; John C Reed
Journal:  Nature       Date:  2003-05-04       Impact factor: 49.962

6.  Positional cloning of the mouse obese gene and its human homologue.

Authors:  Y Zhang; R Proenca; M Maffei; M Barone; L Leopold; J M Friedman
Journal:  Nature       Date:  1994-12-01       Impact factor: 49.962

7.  Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.

Authors:  Nicholas T Ingolia; Sina Ghaemmaghami; John R S Newman; Jonathan S Weissman
Journal:  Science       Date:  2009-02-12       Impact factor: 47.728

8.  HAltORF: a database of predicted out-of-frame alternative open reading frames in human.

Authors:  Benoît Vanderperre; Jean-François Lucier; Xavier Roucou
Journal:  Database (Oxford)       Date:  2012-05-20       Impact factor: 3.451

9.  Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.

Authors:  Maria Lluch-Senar; Javier Delgado; Wei-Hua Chen; Verónica Lloréns-Rico; Francis J O'Reilly; Judith Ah Wodke; E Besray Unal; Eva Yus; Sira Martínez; Robert J Nichols; Tony Ferrar; Ana Vivancos; Arne Schmeisky; Jörg Stülke; Vera van Noort; Anne-Claude Gavin; Peer Bork; Luis Serrano
Journal:  Mol Syst Biol       Date:  2015-01-21       Impact factor: 11.429

10.  Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs.

Authors:  Jeroen Crappé; Wim Van Criekinge; Geert Trooskens; Eisuke Hayakawa; Walter Luyten; Geert Baggerman; Gerben Menschaert
Journal:  BMC Genomics       Date:  2013-09-23       Impact factor: 3.969

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  75 in total

1.  Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins.

Authors:  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
Journal:  Elife       Date:  2017-10-30       Impact factor: 8.140

2.  MIEF1 Microprotein Regulates Mitochondrial Translation.

Authors:  Annie Rathore; Qian Chu; Dan Tan; Thomas F Martinez; Cynthia J Donaldson; Jolene K Diedrich; John R Yates; Alan Saghatelian
Journal:  Biochemistry       Date:  2018-09-14       Impact factor: 3.162

Review 3.  Small open reading frames and cellular stress responses.

Authors:  Alexandra Khitun; Travis J Ness; Sarah A Slavoff
Journal:  Mol Omics       Date:  2019-02-27

Review 4.  The role of micropeptides in biology.

Authors:  Rui Vitorino; Sofia Guedes; Francisco Amado; Manuel Santos; Nobuyoshi Akimitsu
Journal:  Cell Mol Life Sci       Date:  2021-01-28       Impact factor: 9.261

Review 5.  Roles of Long Noncoding RNAs and Circular RNAs in Translation.

Authors:  Marina Chekulaeva; Nikolaus Rajewsky
Journal:  Cold Spring Harb Perspect Biol       Date:  2019-06-03       Impact factor: 10.005

6.  Ribosome Footprint Profiling of Translation throughout the Genome.

Authors:  Nicholas T Ingolia
Journal:  Cell       Date:  2016-03-24       Impact factor: 41.582

7.  Starting too soon: upstream reading frames repress downstream translation.

Authors:  Anna M McGeachy; Nicholas T Ingolia
Journal:  EMBO J       Date:  2016-02-19       Impact factor: 11.598

Review 8.  Decoding sORF translation - from small proteins to gene regulation.

Authors:  Luis Enrique Cabrera-Quio; Sarah Herberg; Andrea Pauli
Journal:  RNA Biol       Date:  2016-08-12       Impact factor: 4.652

Review 9.  Encoding activities of non-coding RNAs.

Authors:  Yanan Pang; Chuanbin Mao; Shanrong Liu
Journal:  Theranostics       Date:  2018-03-28       Impact factor: 11.556

Review 10.  MOTS-c: A Mitochondrial-Encoded Regulator of the Nucleus.

Authors:  Bérénice A Benayoun; Changhan Lee
Journal:  Bioessays       Date:  2019-08-05       Impact factor: 4.345

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