title: The Cryptochrome/Photolyase Family in aquatic organisms.
abstract: The Cryptochrome/Photolyase Family (CPF) represents an ancient group of widely distributed UV-A/blue-light sensitive proteins sharing common structures and chromophores. During the course of evolution, different CPFs acquired distinct functions in DNA repair, light perception and circadian clock regulation. Previous phylogenetic analyses of the CPF have allowed reconstruction of the evolution and distribution of the different CPF super-classes in the tree of life. However, so far only limited information is available from the CPF orthologs in aquatic organisms that evolved in environments harboring great diversity of life forms and showing peculiar light distribution and rhythms. To gain new insights into the evolutionary and functional relationships within the CPF family, we performed a detailed study of CPF members from marine (diatoms, sea urchin and annelid) and freshwater organisms (teleost) that populate diverse habitats and exhibit different life strategies. In particular, we first extended the CPF family phylogeny by including genes from aquatic organisms representative of several branches of the tree of life. Our analysis identifies four major super-classes of CPF proteins and importantly singles out the presence of a plant-like CRY in diatoms and in metazoans. Moreover, we show a dynamic evolution of Cpf genes in eukaryotes with various events of gene duplication coupled to functional diversification and gene loss, which have shaped the complex array of Cpf genes in extant aquatic organisms. Second, we uncover clear rhythmic diurnal expression patterns and light-dependent regulation for the majority of the analyzed Cpf genes in our reference species. Our analyses reconstruct the molecular evolution of the CPF family in eukaryotes and provide a solid foundation for a systematic characterization of novel light activated proteins in aquatic environments.
authors.affiliation: Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK. Electronic address: p.oliveri@ucl.ac.uk.
authors.forename: Paola
authors.initials: P
authors.lastname: Oliveri
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France; CNRS, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France. Electronic address: antonio.fortunato@upmc.fr.
authors.forename: Antonio E
authors.initials: AE
authors.lastname: Fortunato
authors.affiliation: Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK; CoMPLEX/SysBio, UCL, Gower Street, London WC1E 6BT, UK.
authors.forename: Libero
authors.initials: L
authors.lastname: Petrone
authors.affiliation: Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University, B4, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Tomoko
authors.initials: T
authors.lastname: Ishikawa-Fujiwara
authors.affiliation: Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University, B4, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan; Radiation Biology Center, Kyoto University, Yoshida-konoe-cho, Sakyoku, Kyoto 606-8501, Japan.
authors.forename: Yuri
authors.initials: Y
authors.lastname: Kobayashi
authors.affiliation: Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University, B4, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Todo
authors.affiliation: Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria; Research Platform "Marine Rhythms of Life", Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria.
authors.forename: Olga
authors.initials: O
authors.lastname: Antonova
authors.affiliation: Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria; Research Platform "Marine Rhythms of Life", Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria.
authors.forename: Enrique
authors.initials: E
authors.lastname: Arboleda
authors.affiliation: Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria; Research Platform "Marine Rhythms of Life", Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria.
authors.forename: Juliane
authors.initials: J
authors.lastname: Zantke
authors.affiliation: Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria; Research Platform "Marine Rhythms of Life", Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria.
authors.forename: Kristin
authors.initials: K
authors.lastname: Tessmar-Raible
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France; CNRS, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France.
authors.forename: Angela
authors.initials: A
authors.lastname: Falciatore
mesh_terms: D000818:Animals; D000845:Annelida / Q000235:genetics*; D001483:Base Sequence; D016000:Cluster Analysis; D056931:Cryptochromes / Q000235:genetics*; D057225:Data Mining; D004255:Deoxyribodipyrimidine Photo-Lyase / Q000235:genetics*; D017377:Diatoms / Q000235:genetics*; D019143:Evolution, Molecular; D005399:Fishes / Q000235:genetics*; D020440:Gene Duplication / Q000235:genetics; D016013:Likelihood Functions; D008386:Marine Biology; D008957:Models, Genetic; D005810:Multigene Family / Q000235:genetics*; D010802:Phylogeny; D011506:Proteins / Q000235:genetics; D012617:Sea Urchins / Q000235:genetics*; D016415:Sequence Alignment; D059467:Transcriptome
chemical_list: D056931:Cryptochromes; D011506:Proteins; D004255:Deoxyribodipyrimidine Photo-Lyase
keywords: Aquatic environments; Cryptochrome; Eukaryota; Light; Photolyase; Rhythms