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.
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Molecular phylogenetic analyses show that Crys form multiple, evolutionarily conserved subgroups.
“Molecular phylogenetic analyses show that Crys form multiple, evolutionarily conserved subgroups (32–34).”
From An Overview of Monthly Rhythms and Clocks (2017) · cites this paper as [34]
Platynereis dumerilii possesses a complete set of animal Cry/photolyase genes, with one ortholog for each distinct subfamily.
“The bristle worm Platynereis dumerilii possesses a complete set of animal Cry/photolyase genes, with one ortholog for each distinct subfamily (34).”
From An Overview of Monthly Rhythms and Clocks (2017) · cites this paper as [34]
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Teschke, M., Wendt, S. L., Kawaguchi, S., Kramer, A., & Meyer, B. (2011) · PLoS ONE · doi:10.1371/journal.pone.0026090 · Cited by 80 · see citing works
Circadian variability in the photobiology of Phaeodactylum tricornutum: pigment content
Ragni, M., & d’Alcalà, M. R. (2007) · Journal of Plankton Research · doi:10.1093/plankt/fbm002 · Cited by 78 · see citing works
Castrillo, M., García–Martínez, J., & Ávalos, J. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.03110-12 · Cited by 76 · see citing works
Echinoderm Eggs and Embryos: Procurement and Culture
Foltz, K. R., Adams, N. L., & Runft, L. L. (2004) · Methods in cell biology · doi:10.1016/s0091-679x(04)74003-0 · Cited by 71 · see citing works
Common light signaling pathways controlling DNA repair and circadian clock entrainment in zebrafish
Hirayama, J., Miyamura, N., Uchida, Y., Asaoka, Y., Honda, R., Sawanobori, K., Todo, T., Yamamoto, T., Sassone‐Corsi, P., & Nishina, H. (2009) · Cell Cycle · doi:10.4161/cc.8.17.9447 · Cited by 66 · see citing works
Self-citationPlasticity and robustness of pattern formation in the model diatom Phaeodactylum tricornutum
Vartanian, M., Desclés, J., Quinet, M., Douady, S., & Lopez, P. J. (2009) · New Phytologist · doi:10.1111/j.1469-8137.2009.02769.x · Cited by 65 · see citing works
Annual and lunar reproductive rhythms of the sea urchin,Diadema antillarum(Philippi) in Bermuda
Iliffe, T. M., & Pearse, J. S. (1982) · International Journal of Invertebrate Reproduction · doi:10.1080/01651269.1982.10553463 · Cited by 63 · see citing works
High-resolution melting curve analysis for rapid detection of mutations in a Medaka TILLING library
Ishikawa, T., Kamei, Y., Otozai, S., Kim, J., Sato, A., Kuwahara, Y., Tanaka, M., Deguchi, T., Inohara, H., Tsujimura, T., et al. (2010) · BMC Molecular Biology · doi:10.1186/1471-2199-11-70 · Cited by 63 · see citing works
Self-citationExquisite Light Sensitivity of Drosophila melanogaster Cryptochrome
Vinayak, P., Coupar, J. F., Hughes, S. E., Fozdar, P., Kilby, J., Garren, E. J., Yoshii, T., & Hirsh, J. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003615 · Cited by 61 · see citing works
Lunar periodicities of diadematid echinoids breeding in Fiji
Coppard, S. E., & Campbell, A. (2005) · Coral Reefs · doi:10.1007/s00338-005-0491-5 · Cited by 54 · see citing works
The evolution of neurosecretory centers in bilaterian forebrains: insights from protostomes
Tessmar-Raible, K. (2007) · Seminars in Cell & Developmental Biology · doi:10.1016/j.semcdb.2007.04.007 · Cited by 53 · see citing works
Functional and Structural Analyses of Cryptochrome
Hirayama, J., Nakamura, H., Ishikawa, T., Kobayashi, Y., & Todo, T. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m305028200 · Cited by 53 · see citing works
Self-citationTheGonyaulaxClock at 50: Translational Control of Circadian ExpressionPreprint
Hastings, J. W. (2007) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2007.72.026 · Cited by 53 · see citing works
det1-1-induced UV-C hyposensitivity through UVR3 and PHR1 photolyase gene over-expression
Castells, E., Molinier, J., Drevensek, S., Genschik, P., Barnèche, F., & Bowler, C. (2010) · The Plant Journal · doi:10.1111/j.1365-313x.2010.04249.x · Cited by 50 · see citing works
Purification and Characterization of a Type III Photolyase from Caulobacter crescentus
Öztürk, N., Kao, Y., Selby, C. P., Kavaklı, İ. H., Partch, C. L., Zhong, D., & Sancar, A. (2008) · Biochemistry · doi:10.1021/bi801085a · Cited by 49 · see citing works
Bentley, M. G., Olive, P. J. W., & Last, K. (1999) · Earth Moon and Planets · doi:10.1023/a:1017039110161 · Cited by 47 · see citing works
A genome-wide survey of photoreceptor and circadian genes in the coral, Acropora digitifera
Shoguchi, E., Tanaka, M. R., Shinzato, C., Kawashima, T., & Satoh, N. (2012) · Gene · doi:10.1016/j.gene.2012.12.038 · Cited by 46 · see citing works
Cock, J. M., Coelho, S. M., Brownlee, C., & Taylor, A. R. (2010) · New Phytologist · doi:10.1111/j.1469-8137.2010.03454.x · Cited by 44 · see citing works
A cryptochrome‐based photosensory system in the siliceous sponge Suberites domuncula (Demospongiae)
Müller, W. E. G., Wang, X., Schröder, H. C., Korzhev, M., Grebenjuk, V. A., Markl, J. S., Jochum, K. P., Pisignano, D., & Wiens, M. (2010) · FEBS Journal · doi:10.1111/j.1742-4658.2009.07552.x · Cited by 44 · see citing works
The Potorous CPD Photolyase Rescues a Cryptochrome-Deficient Mammalian Circadian Clock
Chaves, I., Nijman, R., Biernat, M. A., Bajek, M. I., Brand, K., Silva, A. C., Saito, S., Yagita, K., Eker, A. P. M., & van der Horst, G. T. J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023447 · Cited by 31 · see citing works
Gene Regulatory Network Analysis in Sea Urchin Embryos
Oliveri, P., & Davidson, E. H. (2004) · Methods in cell biology · doi:10.1016/s0091-679x(04)74032-7 · Cited by 27 · see citing works
Self-citationIsely, N., Lamare, M. D., Marshall, C. J., & Barker, M. (2009) · Photochemistry and Photobiology · doi:10.1111/j.1751-1097.2009.00566.x · Cited by 24 · see citing works
Bentley, M. G., Olive, P. J. W., & Last, K. (2001) · Springer eBooks · doi:10.1007/978-94-010-0800-6_7 · Cited by 19 · see citing works
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Diatom Phytochromes Reveal the Existence of Far-Red-Light-Based Sensing in the Ocean
Fortunato, A. E., Jaubert, M. J., Enomoto, G., Bouly, J., Raniello, R., Thaler, M., Malviya, S., Bernardes, J., Rappaport, F., Gentili, B., et al. (2016) · The Plant Cell · doi:10.1105/tpc.15.00928 · Cited by 138 · see citing works
Self-citationEvolutionary History of the Photolyase/Cryptochrome Superfamily in Eukaryotes
Mei, Q., & Dvornyk, V. (2015) · PLoS ONE · doi:10.1371/journal.pone.0135940 · Cited by 125 · see citing works
“Recently, a plant-like Cry was identified in D. rerio (XP_009291670), which may act as a circadian photoreceptor [70] .”
BackgroundAn Overview of Monthly Rhythms and Clocks
Raible, F., Takekata, H., & Tessmar-Raible, K. (2017) · Frontiers in Neurology · doi:10.3389/fneur.2017.00189 · Cited by 121 · see citing works
“Their role outside of the plant phylum is currently unknown (34).”
BackgroundSelf-citationThe Still Dark Side of the Moon: Molecular Mechanisms of Lunar-Controlled Rhythms and Clocks
Andreatta, G., & Tessmar-Raible, K. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.03.009 · Cited by 111 · see citing works
Self-citationFortunato, A. E., Annunziata, R., Jaubert, M. J., Bouly, J., & Falciatore, A. (2014) · Journal of Plant Physiology · doi:10.1016/j.jplph.2014.06.011 · Cited by 94 · see citing works
Self-citationFungal cryptochrome with DNA repair activity reveals an early stage in cryptochrome evolution
Tagua, V. G., Pausch, M., Eckel, M., Gutiérrez, G., Miralles-Durán, A., Sanz, C., Eslava, A. P., Pokorny, R., Corrochano, L. M., & Batschauer, A. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1514637112 · Cited by 93 · see citing works
“This conclusion is fully consistent with recent phylogenetic studies of the CPF, indicating the presence of cry-DASH already in the last common ancestor of all eukaryotes (47).”
ResultDiatom frustules protect DNA from ultraviolet light
Aguirre, L. E., Ouyang, L., Elfwing, A., Hedblom, M., Wulff, A., & Inganäs, O. (2018) · Scientific Reports · doi:10.1038/s41598-018-21810-2 · Cited by 88 · see citing works
Biological rhythms in the deep-sea hydrothermal mussel Bathymodiolus azoricus
Mat, A. M., Sarrazin, J., Markov, G. V., Apremont, V., Dubreuil, C., Eché, C., Fabioux, C., Klopp, C., Sarradin, P., Tanguy, A., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17284-4 · Cited by 73 · see citing works
Cryptochrome photoreceptors in green algae: Unexpected versatility of mechanisms and functions
Kottke, T., Oldemeyer, S., Wenzel, S., Zou, Y., & Mittag, M. (2017) · Journal of Plant Physiology · doi:10.1016/j.jplph.2017.05.021 · Cited by 70 · see citing works
Lacombat, F., Espagne, A., Dozova, N., Plaza, P., Müller, P., Brettel, K., Franz-Badur, S., & Essen, L. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.9b03680 · Cited by 70 · see citing works
A gonad-expressed opsin mediates light-induced spawning in the jellyfish ClytiaPreprint
Quiroga-Artigas, G., Lapébie, P., Leclère, L., Takeda, N., Deguchi, R., Jékely, G., Momose, T., & Houliston, E. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/140210 · Cited by 61 · see citing works
“…used for animal non-visual photoreception: the evolutionarily ancient Cryptochrome/Photolyase family, which originated in unicellular eukaryotes (Oliveri et al., 2014), and the diverse, animal-specific opsin family of light-sensitive G Protein-Coupled Receptors (GPCRs) known best for…”
BackgroundBivalve mollusc circadian clock genes can run at tidal frequency
Tran, D., Perrigault, M., Ciret, P., & Payton, L. (2020) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2019.2440 · Cited by 56 · see citing works
“Finally, the weak diurnal Cgcry1 oscillations are consistent with its putative involvement in light synchronization of the clock [44] and consequently with the weak daily rhythm of VOA shown (figure 2).”
BackgroundThe World of Algae Reveals a Broad Variety of Cryptochrome Properties and Functions
Petersen, J., Rredhi, A., Szyttenholm, J., Oldemeyer, S., Kottke, T., & Mittag, M. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.766509 · Cited by 47 · see citing works
Yang, W., Zhou, L., Wang, J., Wang, L., Gao, S., & Wang, G. (2022) · Algal Research · doi:10.1016/j.algal.2022.102822 · Cited by 45 · see citing works
Coesel, S., Durham, B., Groussman, M., Hu, S. K., Caron, D., Morales, R., Ribalet, F., & Armbrust, E. (2021) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.2011038118 · Cited by 38 · see citing works
“Cryptochrome/photolyase, phytochrome, rhodopsin, and LOV protein se-quencesdescribedintheliterature(32,57,71,72,109)werealignedwithMultipleAlignmentusingFastFourierTransform(MAFFT)version7.”
Step in Time: Conservation of Circadian Clock Genes in Animal Evolution
Stanton, D., Justin, H. S., & Reitzel, A. M. (2022) · Integrative and Comparative Biology · doi:10.1093/icb/icac140 · Cited by 45 · see citing works
Modulation of DNA Repair Systems in Blind Cavefish during Evolution in Constant Darkness
Zhao, H., Mauro, G. D., Lungu-Mitea, S., Negrini, P., Guarino, A. M., Frigato, E., Braunbeck, T. A., Ma, H., Lamparter, T., Vallone, D., et al. (2018) · Current Biology · doi:10.1016/j.cub.2018.08.039 · Cited by 47 · see citing works
Zurl, M., Poehn, B., Rieger, D., Krishnan, S., Rokvić, D., Rajan, V. B. V., Gerrard, E. J., Schlichting, M., Orel, L., Ćorić, A., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2115725119 · Cited by 38 · see citing works
“In the common view based on the work in Drosophila melanogaster, the fly 1:1 ortholog of L-Cry—dCRY (14)—undergoes light-dependent binding to Timeless, which leads to the degradation of both Timeless and dCRY, thus resetting the flies’ circadian clock upon light input (reviewed in ref.”
BackgroundSelf-citationSay, T. E., & Degnan, S. M. (2019) · Molecular Ecology · doi:10.1111/mec.15318 · Cited by 42 · see citing works
“…Suberites domuncula (Müller et al., 2010), mollusc Crassostrea gigas (Mat, Perrigault, Massabuau, & Tran, 2016), annelid Platynereis dumerilii (Oliveri et al., 2014), and cnidarians Nematostella vectensis, Acropora millepora and Favia fragum (reviewed by Hoadley, Vize, Pyott, Goffredo, &…”
BackgroundResultEumetazoan Cryptochrome Phylogeny and Evolution
Haug, M. F., Gesemann, M., Lazović, V., & Neuhauss, S. C. F. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv010 · Cited by 40 · see citing works
Evolution of Proteins of the DNA Photolyase/Cryptochrome Family
Vechtomova, Y. L., Telegina, T. A., & Kritsky, M. S. (2020) · Biochemistry (Moscow) · doi:10.1134/s0006297920140072 · Cited by 41 · see citing works
Poehn, B., Krishnan, S., Zurl, M., Ćorić, A., Rokvić, D., Häfker, N. S., Jaenicke, E., Arboleda, E., Orel, L., Raible, F., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32562-z · Cited by 40 · see citing works
“dumerilii L-Cry (1-567) was heterologously expressed in Spodoptera frugiperda (Sf9) insect cells using the Bac-to-Bac baculovirus expression systemwith the pCoofy27 expression vector.”
MethodSelf-citationThe Gain and Loss of Cryptochrome/Photolyase Family Members during Evolution
Deppisch, P., Helfrich‐Förster, C., & Senthilan, P. R. (2022) · Genes · doi:10.3390/genes13091613 · Cited by 42 · see citing works
“In the diatom Phaeodactylum tricornutum and the zebrafish Danio rerio a role of PCRY-like in circadian rhythm regulation is quite likely, as its expression is cycling over the day [29].”
BackgroundIdentification of the Molecular Clockwork of the Oyster Crassostrea gigas
Perrigault, M., & Tran, D. (2017) · PLoS ONE · doi:10.1371/journal.pone.0169790 · Cited by 38 · see citing works
The cryptochrome—photolyase protein family in diatoms
König, S., Juhas, M., Jäger, S., Kottke, T., & Büchel, C. (2017) · Journal of Plant Physiology · doi:10.1016/j.jplph.2017.06.015 · Cited by 39 · see citing works
MacIntyre, H. L., Cullen, J. J., Whitsitt, T. J., & Petri, B. M. (2017) · Journal of Applied Phycology · doi:10.1007/s10811-017-1254-8 · Cited by 34 · see citing works
“Photorepair is catalyzed by light-sensitive flavoproteins, the cryptochrome/photolyase family, which are involved in light- sensing and signaling processes that both regulate protein synthesis and directly bind and repair DNA (reviewed by Oliveri et al. 2014; Lepetit and Dietzel 2015).”
BackgroundRomero‐Martínez, L., Moreno‐Andrés, J., Acevedo‐Merino, A., & Nebot, E. (2016) · Journal of Applied Phycology · doi:10.1007/s10811-016-0838-z · Cited by 33 · see citing works
“…effect of UV is limited by the lack of residual effect and the existence of cellular mechanisms to minimize the damage caused by the treatment, primarily based on DNA photorepair under photosynthetically active radiation (Fafanđel et al. 2002; Oliveri et al. 2014; Poepping et al. 2014).”
BackgroundLight signaling in photosynthetic eukaryotes with ‘green’ and ‘red’ chloroplasts
Bernard, L., & Dietzel, L. (2014) · Environmental and Experimental Botany · doi:10.1016/j.envexpbot.2014.07.007 · Cited by 32 · see citing works
Martin, R., Lacombat, F., Espagne, A., Dozova, N., Plaza, P., Yamamoto, J., Müller, P., Brettel, K., & de la Lande, A. (2017) · Physical Chemistry Chemical Physics · doi:10.1039/c7cp04555g · Cited by 29 · see citing works
Mat, A. M., Perrigault, M., Massabuau, J., & Tran, D. (2016) · Chronobiology International · doi:10.1080/07420528.2016.1181645 · Cited by 29 · see citing works
“However, Cgcry1 did not peak in the presence of light, like observed in drosophila (Emery et al., 1998) or larvae of the sea urchin Strongylocentrotus purpuratus (Oliveri et al., 2014), but peaked at the end of the night.”
BackgroundResultImmobilization strategies of photolyases: Challenges and perspectives for DNA repairing application
Ramírez, N., Serey, M., Illanes, A., Piumetti, M., & Ottone, C. (2020) · Journal of Photochemistry and Photobiology B Biology · doi:10.1016/j.jphotobiol.2020.112113 · Cited by 28 · see citing works
nig, S. K. ⁄., Eisenhut, M., utigam, A. B. ⁄., Kurz, S., Weber, A. P. M., & Büchel, C. (2017) · Plant and Cell Physiology · doi:10.1093/pcp/pcx127 · Cited by 25 · see citing works
Shikata, T., Takahashi, F., Nishide, H., Shigenobu, S., Kamei, Y., Sakamoto, S., 湯浅光貴, Nishiyama, Y., Yamasaki, Y., & Uchiyama, I. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01764 · Cited by 24 · see citing works
Marizcurrena, J. J., Acosta, S., Canclini, L., Hernández, P., Vallés, D., Lamparter, T., & Castro‐Sowinski, S. (2020) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-020-10734-5 · Cited by 24 · see citing works
Schneider, G., Figueroa, F. L., Vega, J., Avilés, A., Horta, P. A., Korbee, N., & Bonomi‐Barufi, J. (2022) · Algal Research · doi:10.1016/j.algal.2022.102702 · Cited by 22 · see citing works
Cohen, J. H., Last, K. S., Charpentier, C. L., Cottier, F. R., Daase, M., Hobbs, L., Johnsen, G. H., & Berge, J. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001413 · Cited by 21 · see citing works
Light-Harvesting Complexes of Diatoms: Fucoxanthin-Chlorophyll Proteins
Büchel, C. (2020) · Advances in Photosynthesis and Respiration · doi:10.1007/978-3-030-33397-3_16 · Cited by 20 · see citing works
Zhadan, P. M., Vaschenko, M. A., & Ryazanov, S. D. (2017) · Marine Ecology Progress Series · doi:10.3354/meps12436 · Cited by 20 · see citing works
“…phenomenon may be the genes belonging to the cryptochrome/photolyase family (Cpf), the products of which are involved in DNA repair, light perception and circadian clock regulation; Cpf genes have been found in the genomes of different aquatic organisms, including sea urchins (Oliveri et al. 2014).”
BackgroundBonadè, M., Ogura, A., Corre, E., Bassaglia, Y., & Bonnaud, L. (2020) · Frontiers in Physiology · doi:10.3389/fphys.2020.521989 · Cited by 19 · see citing works
CrusTome: a transcriptome database resource for large-scale analyses across Crustacea
Pérez‐Moreno, J. L., Kozma, M. T., DeLeo, D. M., Bracken‐Grissom, H. D., Durica, D. S., & Mykles, D. L. (2023) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkad098 · Cited by 19 · see citing works
Overview of the molecular defense systems used by sea urchin embryos to cope with UV radiation
Bonaventura, R., & Matranga, V. (2016) · Marine Environmental Research · doi:10.1016/j.marenvres.2016.05.019 · Cited by 19 · see citing works
All Light, Everywhere? Photoreceptors at Nonconventional Sites
Mat, A. M., Vu, H. H., Wolf, E., & Tessmar‐Raible, K. (2023) · Physiology · doi:10.1152/physiol.00017.2023 · Cited by 16 · see citing works
Self-citationMolluscan Genomes Reveal Extensive Differences in Photopigment Evolution Across the Phylum
McElroy, K. E., Audino, J. A., & Serb, J. M. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad263 · Cited by 15 · see citing works
“Other than evidence of rhythmic expression of this gene from zebrafish (Oliveri et al. 2014), virtually nothing else is known about the function of this protein.”
BackgroundResultInfluentialMadhuri, S., Bernard, L., Fürst, A. H., & Kroth, P. G. (2024) · Plants · doi:10.3390/plants13111465 · Cited by 14 · see citing works
“PtCPF1 transcription is induced at the beginning of the day (Day1 T8 and Day2 T8), with an mRNA peak one hour after dark to light transition in WT, which is consistent with results reported by [57,60].”
BackgroundResultGao, S., Yang, W., Li, X., Zhou, L., Liu, X., Wu, S., Wang, L., & Wang, G. (2024) · The ISME Journal · doi:10.1093/ismejo/wrad019 · Cited by 13 · see citing works
“S3B) [23].”
Hunsperger, H. M., Ford, C. J., Miller, J. S., & Cattolico, R. A. (2016) · PLoS ONE · doi:10.1371/journal.pone.0158614 · Cited by 13 · see citing works
“…especially intriguing given the universal roles played by blue-light receptors such as cryptochromes in the entrainment and maintenance of circadian rhythms [47,48] and the strict adherence to diurnal light cues we observe for P . tricornutum por 2 transcription as well as cellular POR2 abundance.”
Romero‐Martínez, L., Moreno‐Andrés, J., Acevedo‐Merino, A., & Nebot, E. (2018) · Journal of Applied Phycology · doi:10.1007/s10811-018-1687-8 · Cited by 13 · see citing works
Identification of medaka magnetoreceptor and cryptochromes
Wang, Y., Chen, J., Zhu, F., & Hong, Y. (2016) · Science China Life Sciences · doi:10.1007/s11427-016-0266-5 · Cited by 11 · see citing works
“Besides, cry5 appears to diverge earlier than cry1 and cry2 in the phylogenetic trees, and it has been reported to be clustered with 6-4 photolyases in previous phylogenetic studies (Oliveri et al., 2014), which can catalyze light-dependent DNA repair (Todo et al., 1993).”
BackgroundTranscriptome Profiling in the Marine Red Alga Neopyropia yezoensis Under Light/Dark Cycle
Kominami, S., Mizuta, H., & Uji, T. (2022) · Marine Biotechnology · doi:10.1007/s10126-022-10121-3 · Cited by 12 · see citing works
“The CPF constitutes a large group of UV-A/blue-light-activated proteins and is functionally divided into two types of proteins: the photolyases and cryptochromes (Oliveri et al. 2014; Fortunato et al. 2015; Mei and Dvornyk 2015).”
BackgroundSchneider, G., Figueroa, F. L., Vega, J., Avilés, A., Chaves, P., Horta, P. A., Korbee, N., & Bonomi‐Barufi, J. (2020) · Photochemical & Photobiological Sciences · doi:10.1039/d0pp00135j · Cited by 12 · see citing works
An, M., Qu, C., Miao, J., & Sha, Z. (2021) · Photochemistry and Photobiology · doi:10.1111/php.13478 · Cited by 11 · see citing works
Lacombat, F., Espagne, A., Dozova, N., Plaza, P., Ignatz, E., Kiontke, S., & Essen, L. (2018) · Physical Chemistry Chemical Physics · doi:10.1039/c8cp04548h · Cited by 11 · see citing works
A marine cryptochrome with an inverse photo-oligomerization mechanism
Vu, H. H., Behrmann, H., Hanić, M., Jeyasankar, G., Krishnan, S., Dannecker, D., Hammer, C., Gunkel, M., Solov’yov, I. A., Wolf, E., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42708-2 · Cited by 9 · see citing works
“Moreover,wefoundthatthe unique Tyr266 of the PBL, which in other animal and animal-like CRYs is usually replaced by a phenylalanine, is important for stabilizing the dimer (Fig.”
MethodInfluentialTranscriptome analysis of the harmful alga Heterosigma akashiwo under a 24-hour light-dark cycle
Ji, N., Wang, J., Huang, W., Huang, J., Cai, Y., Sun, S., Shen, X., & Liang, Y. (2024) · Harmful Algae · doi:10.1016/j.hal.2024.102601 · Cited by 8 · see citing works
An, M., Qu, C., Miao, J., & Sha, Z. (2021) · 3 Biotech · doi:10.1007/s13205-021-02927-0 · Cited by 8 · see citing works
Krischer, J., König, S., Weisheit, W., Mittag, M., & Büchel, C. (2022) · Journal of Experimental Botany · doi:10.1093/jxb/erac012 · Cited by 8 · see citing works
The role of photobehaviour in sponge larval dispersal and settlement
Whalan, S. (2023) · PLoS ONE · doi:10.1371/journal.pone.0287989 · Cited by 5 · see citing works
“More recent work has identified the capacity of larvae to respond to different wavelengths of light [29–32] with an increasing focus on sensory systems utilized to respond to light [30, 33, 34].”
BackgroundWulf, P. O., Häfker, N. S., Hofmann, K., & Tessmar‐Raible, K. (2025) · ZOOLOGICAL SCIENCE · doi:10.2108/zs240099 · Cited by 5 · see citing works
“This is consistent with the idea that cryptochromes are originally light-sensitive, given their evolutionary close relatedness to light-dependent DNA repair enzymes, the photolyases (Gehring and Rosbash, 2003; Oliveri et al., 2014).”
Self-citationNakagawa, M., Okano, K., Saratani, Y., Shoji, Y., & Okano, T. (2022) · Zoological Letters · doi:10.1186/s40851-022-00192-4 · Cited by 5 · see citing works
“In addition to Cry2 and Cry4, zebrafish have four Cry1 paralogs (Cry1aa/1ab/1ba/1bb [17], termed as zCry1a/1b/2a/2b in a previous report [18]) probably resulting from whole-genome duplications [19, 20].”
BackgroundBlue mussels’ valve behavior exhibits daily and lunar rhythms during the high Arctic polar day
Moal, A. L., Payton, L., Andrade, H., Camus, L., Ballantine, C., Ciret, P., & Tran, D. (2023) · Marine Biology · doi:10.1007/s00227-023-04257-6 · Cited by 4 · see citing works
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It's about time: Rhythms as a new dimension of molecular marine research
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“Oliveri et al. (2014) created a preliminary database of 254 CPF protein sequences.”
InfluentialCryptochrome 1 is involved in anti-bacterial immunity in Japanese flounder (Paralichthys olivaceus)
Zhang, P., & Sun, B.-G. (2022) · Aquaculture · doi:10.1016/j.aquaculture.2022.738675 · Cited by 2 · see citing works
Lunar cycle-mediated behaviours in animals, including humans
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The role of circadian rhythm and environmental factors in the regulation of sea urchin spawning
Zhadan, P. M., Vaschenko, M. A., & Ryazanov, S. D. (2017) · Doklady Biological Sciences · doi:10.1134/s0012496617050040 · Cited by 2 · see citing works
Annunziata, R., Ritter, A., Fortunato, A. E., Cheminant-Navarro, S., Agier, N., Huysman, M. J. J., Winge, P., Bones, A. M., Bouget, F., Lagomarsino, M. C., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/271445 · Cited by 2 · see citing works
Self-citationNon-visual photoreceptive brain specification in sea urchin larvae
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“The expression of cryptochrome-1 ( cry1 ), implicated in circadian rhythms in sea urchins 49 and in the relationship with Opsin5 in frog 50 , was also con fi rmed (Fig.”
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“To date, the mRNA expression pattern of vertebrate Cry6 has been examined only in fish cultured cells (Okano et al., 2017; Oliveri et al., 2014), and so we examined the expression level of XtCry6 mRNA in each tissue of X. tropicalis, using qRT-PCR.”
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Photosynthetic and Growth Responses of Planktonic Diatoms to Ocean Global Changes
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Light-induced oocyte maturation in the hydrozoan clytia hemisphaerica
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РОЛЬ ЦИРКАДНОГО РИТМА И ПРИРОДНЫХ ФАКТОРОВ В РЕГУЛЯЦИИ НЕРЕСТА МОРСКОГО ЕЖА
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Reproductive adaptations of sea urchins with planktotrophic larvae
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“Недавно эти гены обнаружены в геноме морских ежей [38].”
A gonad-expressed opsin mediates light-induced spawning in the jellyfish Clytia
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“Interestingly, echinoderms ( Strongylocentrotus pur-puratus ) represent the only class of deuterostomes that possess an orthologue of Drosophila Cry (Oliveri et al., 2014; Rubin et al., 2006; Yuan et al., 2007) supporting the idea that SpuCry may function as circadian photoreceptor in this phylum.”
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Wie erkennt der innere Monatskalender von Tieren die richtige Mondphase?
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“Cryptochromes, which mediate responses to UVA and blue light, play essential roles in DNA repair, pigment biosynthesis, and developmental regulation [60].”
Nagel, M., Steiner, M., Wenner, N. C. J., Büchel, C., & Kottke, T. (2026) · Biochemistry · doi:10.1021/acs.biochem.6c00479
- Authors
- Oliveri, P., Fortunato, A. E., Petrone, L., Ishikawa-Fujiwara, T., Kobayashi, Y., Todo, T., Antonova, O., Arboleda, E., Zantke, J., Tessmar-Raible, K., & Falciatore, A.
- Affiliations
- University College London (GB)
- Centre National de la Recherche Scientifique (FR)
- Kyoto University (JP)
- The University of Osaka (JP)
- University of Vienna (AT)
- Corresponding author
- Oliveri, Paola
- Fortunato, Antonio E.
- ORCID
- Venue
- Marine Genomics
- Publisher
- Elsevier BV
- Published
- 2014-04
- Volume
- 14
- Issue
- SI
- Pages
- 23-37
- ISSN
- 1874-7787 (ISSN-L)
- OpenAlex
- W2049327347
- Semantic Scholar
- 7df6bc632ce8397f69704ec3d30f715e9d637057
- Cited by
- 90
- References
- 116
- Citations by year
- 2026: 4 · 2025: 2 · 2024: 7 · 2023: 10 · 2022: 14 · 2021: 5 · 2020: 12 · 2019: 3 · 2018: 6 · 2017: 13 · 2016: 6 · 2015: 4 · 2014: 4
- FWCI
- 4.38
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Marine Genomics (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Funders
- HFSP (RGY0082/2010)
- Max F. Perutz Laboratories/University of Vienna
- FWF START (AY0041321)
- EU in the Marie-Curie ITN CALIPSO (ITN 2013 GA 607607)
- EU FP7 Research Infrastructure Initiative ASSEMBLE (227799)
- Topics
- Life Sciences › Neuroscience › Endocrine and Autonomic Systems › Circadian rhythm and melatonin
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Light effects on plants
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Photoreceptor and optogenetics research
- Keywords
- aquatic organisms, phylogenetic analysis, gene duplication, gene loss, functional diversification, diatoms, sea urchins, Annelida, teleosts, circadian clock, light perception, DNA repair, photolyase, diurnal gene expression, molecular evolution
- MeSH terms
- Animals, Annelida, Base Sequence, Deoxyribodipyrimidine Photo-Lyase, Fishes, Multigene Family, Marine Biology, Models, Genetic, Phylogeny, Proteins, Sea Urchins, Cluster Analysis, Likelihood Functions, Sequence Alignment, Diatoms, Evolution, Molecular, Gene Duplication, Cryptochromes, Data Mining, Transcriptome
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