title: Lineage-specific duplication of amphioxus retinoic acid degrading enzymes (CYP26) resulted in sub-functionalization of patterning and homeostatic roles.
abstract: During embryogenesis, tight regulation of retinoic acid (RA) availability is fundamental for normal development. In parallel to RA synthesis, a negative feedback loop controlled by RA catabolizing enzymes of the cytochrome P450 subfamily 26 (CYP26) is crucial. In vertebrates, the functions of the three CYP26 enzymes (CYP26A1, CYP26B1, and CYP26C1) have been well characterized. By contrast, outside vertebrates, little is known about CYP26 complements and their biological roles. In an effort to characterize the evolutionary diversification of RA catabolism, we studied the CYP26 genes of the cephalochordate amphioxus (Branchiostoma lanceolatum), a basal chordate with a vertebrate-like genome that has not undergone the massive, large-scale duplications of vertebrates.
  
  
  
  In the present study, we found that amphioxus also possess three CYP26 genes (CYP26-1, CYP26-2, and CYP26-3) that are clustered in the genome and originated by lineage-specific duplication. The amphioxus CYP26 cluster thus represents a useful model to assess adaptive evolutionary changes of the RA signaling system following gene duplication. The characterization of amphioxus CYP26 expression, function, and regulation by RA signaling demonstrated that, despite the independent origins of CYP26 duplicates in amphioxus and vertebrates, they convergently assume two main roles during development: RA-dependent patterning and protection against fluctuations of RA levels. Our analysis suggested that in amphioxus RA-dependent patterning is sustained by CYP26-2, while RA homeostasis is mediated by CYP26-1 and CYP26-3. Furthermore, comparisons of the regulatory regions of CYP26 genes of different bilaterian animals indicated that a CYP26-driven negative feedback system was present in the last common ancestor of deuterostomes, but not in that of bilaterians.
  
  
  
  Altogether, this work reveals the evolutionary origins of the RA-dependent regulation of CYP26 genes and highlights convergent functions for CYP26 enzymes that originated by independent duplication events, hence establishing a novel selective mechanism for the genomic retention of gene duplicates.
authors.affiliation: Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France.
authors.forename: João E
authors.initials: JE
authors.lastname: Carvalho
authors.affiliation: Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, Cedex 07, France.
authors.forename: Maria
authors.initials: M
authors.lastname: Theodosiou
authors.affiliation: Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, Cedex 07, France.|Present Address: Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Huchenghuan Road 999, Shanghai, 201306, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Chen
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, 43 Boulevard du 11 novembre 1918, 69622, Villeurbanne, France.
authors.forename: Pascale
authors.initials: P
authors.lastname: Chevret
authors.affiliation: Departamento de Química Organica, Facultad de Química, Universidade de Vigo, 36310, Vigo, Spain.
authors.forename: Susana
authors.initials: S
authors.lastname: Alvarez
authors.affiliation: Departamento de Química Organica, Facultad de Química, Universidade de Vigo, 36310, Vigo, Spain.
authors.forename: Angel R
authors.initials: AR
authors.lastname: De Lera
authors.affiliation: Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, Cedex 07, France.|Present Address: Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232, Université Pierre et Marie Curie Paris, 1 avenue du Fontaulé, 66650, Banyuls-sur-Mer, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Laudet
authors.affiliation: Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France.
authors.forename: Jenifer C
authors.initials: JC
authors.lastname: Croce
authors.affiliation: Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France. Michael.Schubert@obs-vlfr.fr.
authors.forename: Michael
authors.identifier: 0000-0002-2341-712X
authors.initials: M
authors.lastname: Schubert
mesh_terms: D000818:Animals; D000072500:Cytochrome P450 Family 26 / Q000235:genetics / Q000378:metabolism*; D047108:Embryonic Development; D019143:Evolution, Molecular; D020440:Gene Duplication; D016678:Genome; D064175:Lancelets / Q000201:enzymology / Q000235:genetics*; D015398:Signal Transduction; D014212:Tretinoin / Q000378:metabolism*
chemical_list: D014212:Tretinoin; D000072500:Cytochrome P450 Family 26
keywords: Branchiostoma lanceolatum; Cephalochordate; Duplication-Degeneration-Complementation (DDC) model; Lancelet; Retinoic acid (RA) signaling