title: Tinkering signaling pathways by gain and loss of protein isoforms: the case of the EDA pathway regulator EDARADD.
abstract: BACKGROUND
  Only a handful of signaling pathways are major actors of development and responsible for both the conservation and the diversification of animal morphologies. To explain this twofold nature, gene duplication and enhancer evolution were predominantly put forth as tinkering mechanisms whereas the evolution of alternative isoforms has been, so far, overlooked. We investigate here the role of gain and loss of isoforms using Edaradd, a gene of the Ecodysplasin pathway, implicated in morphological evolution. A previous study had suggested a scenario of isoform gain and loss with an alternative isoform (A) newly gained in mammals but secondarily lost in mouse lineage.
  
  
  RESULTS
  For a comprehensive view of A and B Edaradd isoforms history during mammal evolution, we obtained sequences for both isoforms in representative mammals and performed in vitro translations to support functional predictions. We showed that the ancestral B isoform is well conserved, whereas the mammal-specific A isoform was lost at least 7 times independently in terminal lineages throughout mammal phylogeny. Then, to gain insights into the functional relevance of this evolutionary pattern, we compared the biological function of these isoforms: i) In cellulo promoter assays showed that they are transcribed from two alternative promoters, only B exhibiting feedback regulation. ii) RT-PCR in various tissues and ENCODE data suggested that B isoform is systematically expressed whereas A isoform showed a more tissue-specific expression. iii) Both isoforms activated the NF-κB pathway in an in cellulo reporter assay, albeit at different levels and with different dynamics since A isoform exhibited feedback regulation at the protein level. Finally, only B isoform could rescue a zebrafish edaradd knockdown.
  
  
  CONCLUSIONS
  These results suggest that the newly evolved A isoform enables modulating EDA signaling in specific conditions and with different dynamics. We speculate that during mammal diversification, A isoform regulation may have evolved rapidly, accompanying and possibly supporting the diversity of ectodermal appendages, while B isoform may have ensured essential roles. This study makes the case to pay greater attention to mosaic loss of evolutionarily speaking "young" isoforms as an important mechanism underlying phenotypic diversity and not simply as a manifestation of neutral evolution.
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, UMR 5242 du CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, Cedex 07, France. alexa.sadier@ens-lyon.fr.
authors.forename: Alexa
authors.initials: A
authors.lastname: Sadier
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, UMR 5242 du CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, Cedex 07, France. elise.lambert@ens-lyon.fr.
authors.forename: Elise
authors.initials: E
authors.lastname: Lambert
authors.affiliation: Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR5558, Université de Lyon, Universite Claude Bernard Lyon 1, Villeurbanne, France. pascale.chevret@univ-lyon1.fr.
authors.forename: Pascale
authors.initials: P
authors.lastname: Chevret
authors.affiliation: CIRI, International Center for Infectiology Research, Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Lyon, France. Didier.Decimo@ens-lyon.fr.
authors.forename: Didier
authors.initials: D
authors.lastname: Décimo
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, UMR 5242 du CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, Cedex 07, France. marie.semon@ens-lyon.fr.
authors.forename: Marie
authors.initials: M
authors.lastname: Sémon
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, UMR 5242 du CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, Cedex 07, France. marie.tohme@ens-lyon.fr.
authors.forename: Marie
authors.initials: M
authors.lastname: Tohmé
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, UMR 5242 du CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, Cedex 07, France. florence.ruggiero@ens-lyon.fr.
authors.forename: Florence
authors.initials: F
authors.lastname: Ruggiero
authors.affiliation: CIRI, International Center for Infectiology Research, Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Lyon, France. tohlmann@ens-lyon.fr.
authors.forename: Théophile
authors.initials: T
authors.lastname: Ohlmann
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, UMR 5242 du CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, Cedex 07, France. sophie.pantalacci@ens-lyon.fr.
authors.forename: Sophie
authors.initials: S
authors.lastname: Pantalacci
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, UMR 5242 du CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, Cedex 07, France. vincent.laudet@ens-lyon.fr.
authors.forename: Vincent
authors.initials: V
authors.lastname: Laudet
mesh_terms: D000818:Animals; D053362:Edar-Associated Death Domain Protein / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D020440:Gene Duplication; D008322:Mammals / Q000145:classification / Q000235:genetics*; D051379:Mice; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D020033:Protein Isoforms / Q000235:genetics*; D051381:Rats; D015398:Signal Transduction; D015027:Zebrafish / Q000235:genetics / Q000378:metabolism
chemical_list: D053362:Edar-Associated Death Domain Protein; D020033:Protein Isoforms