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410 results on '"Falciatore A"'

51. The Evolution and Function of Blue and Red Light Photoreceptors

Author: Falciatore, Angela, primary and Bowler, Chris, additional
Published: 2005
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52. Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity

Author: Angela Falciatore, Jean-Pierre Bouly, Benjamin Bailleul, Marianne Jaubert, Thomas Mock, Biologie du chloroplaste et perception de la lumière chez les micro-algues, Institut de biologie physico-chimique (IBPC (FR_550)), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), School of Environmental Sciences [Norwich], and University of East Anglia [Norwich] (UEA)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Thalassiosira pseudonana, Biodiversity, Context (language use), Genomics, Plant Science, Review, 01 natural sciences, Models, Biological, 03 medical and health sciences, Algae, Phylogenetics, 14. Life underwater, Phaeodactylum tricornutum, Phylogeny, ComputingMilieux_MISCELLANEOUS, Diatoms, biology, Ecology, fungi, Cell Biology, biology.organism_classification, 030104 developmental biology, Diatom, Phytoplankton, 010606 plant biology & botany
Abstract: International audience; Diatoms are the world's most diverse group of algae, comprising at least 100,000 species. Contributing ;20% of annual global carbon fixation, they underpin major aquatic food webs and drive global biogeochemical cycles. Over the past two decades, Thalassiosira pseudonana and Phaeodactylum tricornutum have become the most important model systems for diatom molecular research, ranging from cell biology to ecophysiology, due to their rapid growth rates, small genomes, and the cumulative wealth of associated genetic resources. To explore the evolutionary divergence of diatoms, additional model species are emerging, such as Fragilariopsis cylindrus and Pseudo-nitzschia multistriata. Here, we describe how functional genomics and reverse genetics have contributed to our understanding of this important class of microalgae in the context of evolution, cell biology, and metabolic adaptations. Our review will also highlight promising areas of investigation into the diversity of these photosynthetic organisms, including the discovery of new molecular pathways governing the life of secondary plastid-bearing organisms in aquatic environments.
Published: 2020
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53. Genome-Scale Metabolic Reconstruction and in Silico Perturbation Analysis of the Polar Diatom Fragilariopsis cylindrus Predicts High Metabolic Robustness

Author: Simon Hardy, Michel Lavoie, Antoine Allard, Sébastien Guérin, Johann Lavaud, Angela Falciatore, Blanche Saint-Béat, Jan Strauss, Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), Universität Hamburg (UHH), Université Laval [Québec] (ULaval), Biologie du chloroplaste et perception de la lumière chez les micro-algues, Institut de biologie physico-chimique (IBPC (FR_550)), and Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Systems biology, In silico, flux balance analysis, Metabolic network, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, metabolic network, arctic, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, reaction deletion, Gene, lcsh:QH301-705.5, General Immunology and Microbiology, biology, gene deletion, Robustness (evolution), systems biology, Metabolism, biology.organism_classification, Flux balance analysis, 030104 developmental biology, Diatom, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, lcsh:Biology (General), Biophysics, General Agricultural and Biological Sciences, 010606 plant biology & botany
Abstract: International audience; Diatoms are major primary producers in polar environments where they can actively grow under extremely variable conditions. Integrative modeling using a genome-scale model (GSM) is a powerful approach to decipher the complex interactions between components of diatom metabolism and can provide insights into metabolic mechanisms underlying their evolutionary success in polar ecosystems. We developed the first GSM for a polar diatom, Fragilariopsis cylindrus, which enabled us to study its metabolic robustness using sensitivity analysis. We find that the predicted growth rate was robust to changes in all model parameters (i.e., cell biochemical composition) except the carbon uptake rate. Constraints on total cellular carbon buffer the effect of changes in the input parameters on reaction fluxes and growth rate. We also show that single reaction deletion of 20% to 32% of active (nonzero flux) reactions and single gene deletion of 44% to 55% of genes associated with active reactions affected the growth rate, as well as the production fluxes of total protein, lipid, carbohydrate, DNA, RNA, and pigments by less than 1%, which was due to the activation of compensatory reactions (e.g., analogous enzymes and alternative pathways) with more highly connected metabolites involved in the reactions that were robust to deletion. Interestingly, including highly divergent alleles unique for F. cylindrus increased its metabolic robustness to cellular perturbations even more. Overall, our results underscore the high robustness of metabolism in F. cylindrus, a feature that likely helps to maintain cell homeostasis under polar conditions.
Published: 2020
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54. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Author: Bowler, Chris, Allen, Andrew E., Badger, Jonathan H., Grimwood, Jane, Jabbari, Kamel, Kuo, Alan, Maheswari, Uma, Martens, Cindy, Maumus, Florian, Otillar, Robert P., Rayko, Edda, Salamov, Asaf, Vandepoele, Klaas, Beszteri, Bank, Gruber, Ansgar, Heijde, Marc, Katinka, Michael, Mock, Thomas, Valentin, Klaus, Verret, Fréderic, Berges, John A., Brownlee, Colin, Cadoret, Jean-Paul, Chiovitti, Anthony, Choi, Chang Jae, Coesel, Sacha, De Martino, Alessandra, Detter, J. Chris, Durkin, Colleen, Falciatore, Angela, Fournet, Jérome, Haruta, Miyoshi, Huysman, Marie J. J., Jenkins, Bethany D., Jiroutova, Katerina, Jorgensen, Richard E., Joubert, Yolaine, Kaplan, Aaron, Kröger, Nils, Kroth, Peter G., La Roche, Julie, Lindquist, Erica, Lommer, Markus, Martin-Jézéquel, Véronique, Lopez, Pascal J., Lucas, Susan, Mangogna, Manuela, McGinnis, Karen, Medlin, Linda K., Montsant, Anton, Secq, Marie-Pierre Oudot-Le, Napoli, Carolyn, Obornik, Miroslav, Parker, Micaela Schnitzler, Petit, Jean-Louis, Porcel, Betina M., Poulsen, Nicole, Robison, Matthew, Rychlewski, Leszek, Rynearson, Tatiana A., Schmutz, Jeremy, Shapiro, Harris, Siaut, Magali, Stanley, Michele, Sussman, Michael R., Taylor, Alison R., Vardi, Assaf, von Dassow, Peter, Vyverman, Wim, Willis, Anusuya, Wyrwicz, Lucjan S., Rokhsar, Daniel S., Weissenbach, Jean, Armbrust, E. Virginia, Green, Beverley R., Van de Peer, Yves, and Grigoriev, Igor V.
Published: 2008
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55. Lhcx proteins provide photoprotection via thermal dissipation of absorbed light in the diatom Phaeodactylum tricornutum

Author: Buck, Jochen M., Sherman, Jonathan, Bártulos, Carolina Río, Serif, Manuel, Halder, Marc, Henkel, Jan, Falciatore, Angela, Lavaud, Johann, Gorbunov, Maxim Y., Kroth, Peter G., Falkowski, Paul G., Lepetit, Bernard, University of Konstanz, Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Takuvik Joint International Laboratory ULAVAL-CNRS, Centre National de la Recherche Scientifique (CNRS)-Université Laval [Québec] (ULaval), Rutgers Center for Operations Research (RUTCOR), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), University of Bern, Université Laval [Québec] (ULaval), Lavaud, Johann, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Laval [Québec] (ULaval)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), and HAL-SU, Gestionnaire
Subjects: Diatoms, Light, Molecular biology, Physiology, Science, [SDV]Life Sciences [q-bio], Photosystem II Protein Complex, Xanthophylls, Article, [SDV] Life Sciences [q-bio], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, ddc:570, Non-photochemical quenching, lcsh:Q, Photosynthesis, lcsh:Science, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology
Abstract: Diatoms possess an impressive capacity for rapidly inducible thermal dissipation of excess absorbed energy (qE), provided by the xanthophyll diatoxanthin and Lhcx proteins. By knocking out the Lhcx1 and Lhcx2 genes individually in Phaeodactylum tricornutum strain 4 and complementing the knockout lines with different Lhcx proteins, multiple mutants with varying qE capacities are obtained, ranging from zero to high values. We demonstrate that qE is entirely dependent on the concerted action of diatoxanthin and Lhcx proteins, with Lhcx1, Lhcx2 and Lhcx3 having similar functions. Moreover, we establish a clear link between Lhcx1/2/3 mediated inducible thermal energy dissipation and a reduction in the functional absorption cross-section of photosystem II. This regulation of the functional absorption cross-section can be tuned by altered Lhcx protein expression in response to environmental conditions. Our results provide a holistic understanding of the rapidly inducible thermal energy dissipation process and its mechanistic implications in diatoms., Photosynthetic organisms can dissipate excess absorbed light energy as heat to avoid photodamage. Here the authors show that induced thermal dissipation in the diatom Phaeodactylum tricornutum Pt4 is Lhcx protein-dependent and correlates with a reduced functional absorption cross-section of photosystem II.
Published: 2019
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56. Multiple probabilistic models extract features from protein sequence data and resolve functional diversity of very different protein families

Author: Jean-Pierre Bouly, Riccardo Vicedomini, Angela Falciatore, Elodie Laine, and Alessandra Carbone
Subjects: 0303 health sciences, Sequence, Artificial neural network, Protein family, Computer science, Boltzmann machine, Probabilistic logic, Computational biology, 03 medical and health sciences, 0302 clinical medicine, Protein sequencing, Identification (biology), Time complexity, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: Sequence functional classification has become a critical bottleneck in understanding the myriad of protein sequences that accumulate in our databases. The great diversity of homologous sequences hides, in many cases, a variety of functional activities that cannot be anticipated. Their identification appears critical for a fundamental understanding of living organisms and for biotechnological applications.ProfileView is a sequence-based computational method, designed to functionally classify sets of homologous sequences. It relies on two main ideas: the use of multiple probabilistic models whose construction explores evolutionary information in available databases, and a new definition of a representation space where to look at sequences from the point of view of probabilistic models combined together. ProfileView classifies families of proteins for which functions should be discovered or characterised within known groups.We validate ProfileView on seven classes of widespread proteins, involved in the interaction with nucleic acids, amino acids and small molecules, and in a large variety of functions and enzymatic reactions. ProfileView agrees with the large set of functional data collected for these proteins from the literature regarding the organisation into functional subgroups and residues that characterize the functions. Furthermore, ProfileView resolves undefined functional classifications and extracts the molecular determinants underlying protein functional diversity, showing its potential to select sequences towards accurate experimental design and discovery of new biological functions.ProfileView proves to outperform three functional classification approaches, CUPP, PANTHER, and a recently developed neural network approach based on Restricted Boltzmann Machines. It overcomes time complexity limitations of the latter.
Published: 2019
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57. Phaeodactylum tricornutum

Author: Chris Bowler, Angela Falciatore, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris Seine (IBPS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Diatoms, 0303 health sciences, Genome, [SDV]Life Sciences [q-bio], DNA Methylation, 01 natural sciences, 03 medical and health sciences, Cytosine, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience
Published: 2019
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58. Genome-scale metabolic reconstruction and in silico perturbation analysis of the polar diatom fragilariopsis cylindrus predicts high metabolic robustness

Author: Lavoie, Michel, Saint-Béat, Blanche, Strauss, Jan, Guérin, Sébastien, Allard, Antoine, Hardy, Simon, Falciatore, Angela, Lavaud, Johann, Lavoie, Michel, Saint-Béat, Blanche, Strauss, Jan, Guérin, Sébastien, Allard, Antoine, Hardy, Simon, Falciatore, Angela, and Lavaud, Johann
Abstract: Diatoms are major primary producers in polar environments where they can actively grow under extremely variable conditions. Integrative modeling using a genome-scale model (GSM) is a powerful approach to decipher the complex interactions between components of diatom metabolism and can provide insights into metabolic mechanisms underlying their evolutionary success in polar ecosystems. We developed the first GSM for a polar diatom, Fragilariopsis cylindrus, which enabled us to study its metabolic robustness using sensitivity analysis. We find that the predicted growth rate was robust to changes in all model parameters (i.e., cell biochemical composition) except the carbon uptake rate. Constraints on total cellular carbon buffer the effect of changes in the input parameters on reaction fluxes and growth rate. We also show that single reaction deletion of 20% to 32% of active (nonzero flux) reactions and single gene deletion of 44% to 55% of genes associated with active reactions affected the growth rate, as well as the production fluxes of total protein, lipid, carbohydrate, DNA, RNA, and pigments by less than 1%, which was due to the activation of compensatory reactions (e.g., analogous enzymes and alternative pathways) with more highly connected metabolites involved in the reactions that were robust to deletion. Interestingly, including highly divergent alleles unique for F. cylindrus increased its metabolic robustness to cellular perturbations even more. Overall, our results underscore the high robustness of metabolism in F. cylindrus, a feature that likely helps to maintain cell homeostasis under polar conditions.
Published: 2020

59. Genome-scale metabolic reconstruction and in silico perturbation analysis of the polar diatom fragilariopsis cylindrus predicts high metabolic robustness

Author: Saint-Béat, Blanche, Strauss, Jan, Allard, Antoine, Guérin, Sébastien, Hardy, Simon, Lavaud, Johann, Falciatore, Angela, Lavoie, Michel, Saint-Béat, Blanche, Strauss, Jan, Allard, Antoine, Guérin, Sébastien, Hardy, Simon, Lavaud, Johann, Falciatore, Angela, and Lavoie, Michel
Abstract: Diatoms are major primary producers in polar environments where they can actively grow under extremely variable conditions. Integrative modeling using a genome-scale model (GSM) is a powerful approach to decipher the complex interactions between components of diatom metabolism and can provide insights into metabolic mechanisms underlying their evolutionary success in polar ecosystems. We developed the first GSM for a polar diatom, Fragilariopsis cylindrus, which enabled us to study its metabolic robustness using sensitivity analysis. We find that the predicted growth rate was robust to changes in all model parameters (i.e., cell biochemical composition) except the carbon uptake rate. Constraints on total cellular carbon buffer the effect of changes in the input parameters on reaction fluxes and growth rate. We also show that single reaction deletion of 20% to 32% of active (nonzero flux) reactions and single gene deletion of 44% to 55% of genes associated with active reactions affected the growth rate, as well as the production fluxes of total protein, lipid, carbohydrate, DNA, RNA, and pigments by less than 1%, which was due to the activation of compensatory reactions (e.g., analogous enzymes and alternative pathways) with more highly connected metabolites involved in the reactions that were robust to deletion. Interestingly, including highly divergent alleles unique for F. cylindrus increased its metabolic robustness to cellular perturbations even more. Overall, our results underscore the high robustness of metabolism in F. cylindrus, a feature that likely helps to maintain cell homeostasis under polar conditions.
Published: 2020

60. Proline biosynthesis in Streptococcus thermophilus: characterization of the proBA operon and its products

Author: Limauro, Danila, Falciatore, Angela, Basso, Anna L., Forlani, Giuseppe, and Felice, Maurilio De
Subjects: Streptococcus -- Genetic aspects, Operons -- Analysis, Genetic regulation -- Research, Genetic transcription -- Analysis, Microbial genetics -- Research, Biological sciences
Abstract: The proBA operon of Streptococcus thermopilus was isolated and analyzed to determine the genetic and biochemical mechanisms of microbial proline biosynthetic pathway. Cloning, sequencing and characterization of the proB and proA genes in the 2.408 kb region of Streptococcus thermophilus chromosome indicated the similarity of proline biosynthesis between the microbe and Escherichia coli. Furthermore, the proB and proA genes are organized by a single operon with a proBA transcription factor that is not affected by exogenous proline.
Published: 1996

61. Biochemical and molecular properties of LHCX1, the essential regulator of dynamic photoprotection in diatoms.

Author: Giovagnetti, Vasco, Jaubert, Marianne, Shukla, Mahendra K., Ungerer, Petra, Bouly, Jean-Pierre, Falciatore, Angela, and Ruban, Alexander V.
Published: 2022
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62. Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum

Author: Julien Pagliardini, Juliette Jouhet, Adeline Le Monnier, Melissa Conte, Toshihiro Obata, Giovanni Finazzi, Antonio Emidio Fortunato, Angela Falciatore, Eric Maréchal, Alisdair R. Fernie, Mark G. Poolman, Davide Dal Bo, Valeria Villanova, Dimitris Petroutsos, Gilles Curien, Dipali Singh, Fermentalg, Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Biological and Medical Sciences, Oxford Brookes University, Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Max-Planck-Gesellschaft, Marie Curie Initial Training Network Accliphot (FP7-PEPOPLE-2012-ITN, 316427), Region Rhone-Alpes (Cible project), Programme Investissement d’Avenir Oceanomics, ANR-12-BIME-0005,DiaDomOil,Domestication des diatomées pour la production de biocarburants(2012), ANR-10- LABX-49-01,Labex GRAL,Labex GRAL, Physiologie cellulaire et végétale [2016-2019] (LPCV [2016-2019]), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), UMR 1417 PCV Laboratoire de Physiologie Cellulaire Végétale, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de la Recherche Agronomique (INRA), Fermentalg SA, Department of Biological and Medical Sciences, Oxford Brookes University, Max Planck Institute of Molecular Plant Physiology (MPI-MP), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Pierre et Marie Curie - Paris 6 (UPMC), ANR (DiaDomOil) [ANR-12BIME-0005], CEA Bioenergies programme, Programme Investissement d'Avenir Oceanmics, CNRS Defi, HFSP [HFSP0052], Marie Curie Initial Training Network CALIPSO (ITN) [GA 607607], ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), European Project: 316427, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Grenoble Alpes (UGA), Université Pierre et Marie Curie (Paris 6), Villanova V., Fortunato A.E., Singh D., Bo D.D., Conte M., Obata T., Jouhet J., Fernie A.R., Marechal E., Falciatore A., Pagliardini J., Le Monnier A., Poolman M., Curien G., Petroutsos D., and Finazzi G.
Subjects: 0301 basic medicine, Glycerol, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Light, Metabolic flux, Biology, Settore BIO/19 - Microbiologia Generale, Photosynthesis, Phaeodactylum tricornutum, General Biochemistry, Genetics and Molecular Biology, Glycerolipid, 03 medical and health sciences, Nutrient, mixotrophy, Botany, Microalgae, Settore BIO/04 - Fisiologia Vegetale, Metabolomics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, photosynthèse, 14. Life underwater, Biomass, Transcriptomics, métabolisme, micro-algue, Diatoms, photosynthesis, Phototroph, marine diatoms, fungi, Carbon metabolism, Lipid metabolism, Articles, approche omique, biology.organism_classification, Carbon, Triacylglycerol biosynthesis, 030104 developmental biology, Diatom, Biomass production, Biochemistry, General Agricultural and Biological Sciences, Energy source, metabolism, Mixotroph, omics analyses
Abstract: Diatoms are prominent marine microalgae, interesting not only from an ecological point of view, but also for their possible use in biotechnology applications. They can be cultivated in phototrophic conditions, using sunlight as the sole energy source. Some diatoms, however, can also grow in a mixotrophic mode, wherein both light and external reduced carbon contribute to biomass accumulation. In this study, we investigated the consequences of mixotrophy on the growth and metabolism of the pennate diatom Phaeodactylum tricornutum , using glycerol as the source of reduced carbon. Transcriptomics, metabolomics, metabolic modelling and physiological data combine to indicate that glycerol affects the central-carbon, carbon-storage and lipid metabolism of the diatom. In particular, provision of glycerol mimics typical responses of nitrogen limitation on lipid metabolism at the level of triacylglycerol accumulation and fatty acid composition. The presence of glycerol, despite provoking features reminiscent of nutrient limitation, neither diminishes photosynthetic activity nor cell growth, revealing essential aspects of the metabolic flexibility of these microalgae and suggesting possible biotechnological applications of mixotrophy. This article is part of the themed issue ‘The peculiar carbon metabolism in diatoms'.
Published: 2017
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63. The diatom <scp>P</scp> haeodactylum tricornutum adjusts nonphotochemical fluorescence quenching capacity in response to dynamic light via fine‐tuned <scp>L</scp> hcx and xanthophyll cycle pigment synthesis

Author: Angela Falciatore, Bernard Lepetit, Sabine Sturm, Peter G. Kroth, Mariana Lepetit, Johann Lavaud, Gautier Gélin, Alessandra Rogato, and Sascha Vugrinec
Subjects: 0106 biological sciences, 0301 basic medicine, chemistry.chemical_classification, Quenching (fluorescence), biology, Physiology, Diadinoxanthin, Diatoxanthin, Plant Science, biology.organism_classification, 01 natural sciences, Acclimatization, 03 medical and health sciences, chemistry.chemical_compound, 030104 developmental biology, Diatom, chemistry, Photoprotection, Xanthophyll, Botany, Biophysics, Phaeodactylum tricornutum, 010606 plant biology & botany
Abstract: Summary Diatoms contain a highly flexible capacity to dissipate excessively absorbed light by nonphotochemical fluorescence quenching (NPQ) based on the light-induced conversion of diadinoxanthin (Dd) into diatoxanthin (Dt) and the presence of Lhcx proteins. Their NPQ fine regulation on the molecular level upon a shift to dynamic light conditions is unknown. We investigated the regulation of Dd + Dt amount, Lhcx gene and protein synthesis and NPQ capacity in the diatom Phaeodactylum tricornutum after a change from continuous low light to 3 d of sine (SL) or fluctuating (FL) light conditions. Four P. tricornutum strains with different NPQ capacities due to different expression of Lhcx1 were included. All strains responded to dynamic light comparably, independently of initial NPQ capacity. During SL, NPQ capacity was strongly enhanced due to a gradual increase of Lhcx2 and Dd + Dt amount. During FL, cells enhanced their NPQ capacity on the first day due to increased Dd + Dt, Lhcx2 and Lhcx3; already by the second day light acclimation was accomplished. While quenching efficiency of Dt was strongly lowered during SL conditions, it remained high throughout the whole FL exposure. Our results highlight a more balanced and cost-effective photoacclimation strategy of P. tricornutum under FL than under SL conditions.
Published: 2016
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64. Genome-Scale Metabolic Reconstruction and in Silico Perturbation Analysis of the Polar Diatom Fragilariopsis cylindrus Predicts High Metabolic Robustness

Author: Lavoie, Michel, primary, Saint-Béat, Blanche, additional, Strauss, Jan, additional, Guérin, Sébastien, additional, Allard, Antoine, additional, V. Hardy, Simon, additional, Falciatore, Angela, additional, and Lavaud, Johann, additional
Published: 2020
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65. Effect of Cromoglycate on Gas Changes, During Bronchial Challenge by UNCDW in Children with Asthma

Author: L. Mappa, S. Bavaro, G. Moramarco, D. Torio, D. Falciatore, G. Ciccarone, L. Cicciomessere, and N. Rigillo
Subjects: Pathology, RB1-214
Abstract: Eighteen asthmatic children were challenged with ultrasonically nebulized cold distilled water (UNCDW). Blood gas composition was monitored transcutaneously (tcpO2 and tcpCO2) during and after the challenge. Assuming as basal the response to this UNCDW test, nine children (Group A) were then chosen at random to inhale cromoglycate by aerosol delivery for 8 days. Nine children (Group B), acting as a control, inhaled saline for 8 days. At the end of this therapy, each child repeated the UNCDW test. Statistical analysis with t-test for paired data was used to compare the results of each child to both tests. Mean basal tcpO2 and tcpCO2 were all within the expected normal range. In all children, both mean tcpO2 and tcpCO2 were reduced during and after UNCDW inhalation. Mean tcpCO2 values during the challenge were significantly (p
Published: 1994
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66. Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity

Author: Falciatore, Angela, primary, Jaubert, Marianne, additional, Bouly, Jean-Pierre, additional, Bailleul, Benjamin, additional, and Mock, Thomas, additional
Published: 2019
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67. Multiple probabilistic models extract features from protein sequence data and resolve functional diversity of very different protein families

Author: Vicedomini, R., primary, Bouly, J.P., additional, Laine, E., additional, Falciatore, A., additional, and Carbone, A., additional
Published: 2019
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68. A systems-wide understanding of photosynthetic acclimation in algae and higher plants

Author: Roberto Bassi, Ioannis Dikaios, Brieuc Urbain, Michel Goldschmidt-Clermont, Oliver Ebenhöh, Anna Matuszyńska, Stephanie Spelberg, Julie Maguire, Kailash Adhikari, Adeline Le Monnier, Dipali Singh, Stefano Magni, Giulio Rocco Stella, Lucilla Taddei, Federica Cariti, Claudia Zabke, Fiona Wanjiku Moejes, Antonella Succurro, Kathrin Müller, Giovanni Finazzi, Mark G. Poolman, Valeria Villanova, Serena Flori, Guillaume Cogne, Angela Falciatore, Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Quantitative and Theoretical Biology, Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Bantry Marine Research Station, Department of Biological and Medical Sciences, Oxford Brookes University, Department of Biotechnology, University of Tehran-University College of Science, Department of Botany and Plant Biology, University of Geneva, Laboratoire de génie des procédés - environnement - agroalimentaire (GEPEA), Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN), Centre National de la Recherche Scientifique (CNRS), Ecole Nationale Vétérinaire Agroalimentaire et de l'Alimentation Nantes Atlantique (ONIRIS), PRES Université Nantes Angers Le Mans (UNAM), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC), Sorbonne Université (SU), UMR 1417 PCV Laboratoire de Physiologie Cellulaire Végétale., Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de la Recherche Agronomique (INRA), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Fermentalg SA, IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT), University of Aberdeen, Marie Curie Initial Training Network project, AccliPhot [PITN-GA-2012-316427], Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL), Heinrich-Heine-Universität Düsseldorf [Düsseldorf], Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, Université Grenoble Alpes (UGA), Ecole Nationale Supérieure des Mines de Nantes (Mines Nantes), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Nantes (UN)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique (IMT Atlantique), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), IMT Atlantique (IMT Atlantique), Moejes F.W., Matuszynska A., Adhikari K., Bassi R., Cariti F., Cogne G., Dikaios I., Falciatore A., Finazzi G., Flori S., Goldschmidt-Clermont M., Magni S., Maguire J., Le Monnier A., Muller K., Poolman M., Singh D., Spelberg S., Stella G.R., Succurro A., Taddei L., Urbain B., Villanova V., Zabke C., and Ebenhoh O.
Subjects: 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Physiology, Acclimatization, Context (language use), PhD training, interdisciplinary training, Plant Science, Biochemistry, biophysics & molecular biology [F05] [Life sciences], Biology, acclimation, Photosynthesis, Models, Biological, modelling, 03 medical and health sciences, Algae, Chlorophyta, application industrielle, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, mathematical modelling, Biochimie, biophysique & biologie moléculaire [F05] [Sciences du vivant], biodiversity, modélisation, micro-algue, Phototroph, photosynthetic system, Ecology, Non-photochemical quenching, Systems Biology, acclimatation photosynthétique, photosynthetic optimisation, Plankton, Plants, analyse rétrospective, biology.organism_classification, industrial application, European Training Network, 030104 developmental biology, Acclimation, microalgal cultivation, non-photochemical quenching, Photosynthetic acclimation, adaptation à la lumière, appareil photosynthétique, Biochemical engineering
Abstract: The ability of phototrophs to colonise different environments relies on robust protection against oxidative stress, a critical requirement for the successful evolutionary transition from water to land. Photosynthetic organisms have developed numerous strategies to adapt their photosynthetic apparatus to changing light conditions in order to optimise their photosynthetic yield, which is crucial for life on Earth to exist. Photosynthetic acclimation is an excellent example of the complexity of biological systems, where highly diverse processes, ranging from electron excitation over protein protonation to enzymatic processes coupling ion gradients with biosynthetic activity, interact on drastically different timescales from picoseconds to hours. Efficient functioning of the photosynthetic apparatus and its protection is paramount for efficient downstream processes, including metabolism and growth. Modern experimental techniques can be successfully integrated with theoretical and mathematical models to promote our understanding of underlying mechanisms and principles. This review aims to provide a retrospective analysis of multidisciplinary photosynthetic acclimation research carried out by members of the Marie Curie Initial Training Project, AccliPhot, placing the results in a wider context. The review also highlights the applicability of photosynthetic organisms for industry, particularly with regards to the cultivation of microalgae. It intends to demonstrate how theoretical concepts can successfully complement experimental studies broadening our knowledge of common principles in acclimation processes in photosynthetic organisms, as well as in the field of applied microalgal biotechnology.
Published: 2017
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69. Characterization of marine diatom-infecting virus promoters in the model diatom Phaeodactylum tricornutum

Author: Kadono, Takashi, Miyagawa-Yamaguchi, Arisa, Kira, Nozomu, Tomaru, Yuji, Okami, Takuma, Yoshimatsu, Takamichi, Hou, Liyuan, Ohama, Takeshi, Fukunaga, Kazunari, Okauchi, Masanori, Yamaguchi, Haruo, Ohnishi, Kohei, Falciatore, Angela, Adachi, Masao, Kadono, Takashi, Miyagawa-Yamaguchi, Arisa, Kira, Nozomu, Tomaru, Yuji, Okami, Takuma, Yoshimatsu, Takamichi, Hou, Liyuan, Ohama, Takeshi, Fukunaga, Kazunari, Okauchi, Masanori, Yamaguchi, Haruo, Ohnishi, Kohei, Falciatore, Angela, and Adachi, Masao
Abstract: Viruses are considered key players in phytoplankton population control in oceans. However, mechanisms that control viral gene expression in prominent microalgae such as diatoms remain largely unknown. In this study, potential promoter regions isolated from several marine diatom-infecting viruses (DIVs) were linked to the egfp reporter gene and transformed into the Pennales diatom Phaeodactylum tricornutum. We analysed their activity in cells grown under different conditions. Compared to diatom endogenous promoters, novel DIV promoter (ClP1) mediated a significantly higher degree of reporter transcription and translation. Stable expression levels were observed in transformants grown under both light and dark conditions, and high levels of expression were reported in cells in the stationary phase compared to the exponential phase of growth. Conserved motifs in the sequence of DIV promoters were also found. These results allow the identification of novel regulatory regions that drive DIV gene expression and further examinations of the mechanisms that control virus-mediated bloom control in diatoms. Moreover, the identified ClP1 promoter can serve as a novel tool for metabolic engineering of diatoms. This is the first report describing a promoter of DIVs that may be of use in basic and applied diatom research.
Published: 2019

70. A bHLH-PAS protein regulates light-dependent diurnal rhythmic processes in the marine diatomPhaeodactylum tricornutum

Author: Nicolas Agier, Soizic Cheminant-Navarro, Jean-Pierre Bouly, Andrés Ritter, François-Yves Bouget, Marie J. J. Huysman, Antonio Emidio Fortunato, Atle M. Bones, Marco Cosentino Lagomarsino, Angela Falciatore, Rossella Annunziata, and Per Winge
Subjects: 0106 biological sciences, 0303 health sciences, Cell division, biology, Period (gene), fungi, Cell, Cell cycle, biology.organism_classification, 01 natural sciences, Cell biology, 03 medical and health sciences, medicine.anatomical_structure, Diatom, Darkness, Gene expression, medicine, 14. Life underwater, Phaeodactylum tricornutum, 030304 developmental biology, 010606 plant biology & botany
Abstract: Periodic light-dark cycles govern the timing of basic biological processes in organisms inhabiting land as well as the sea, where life evolved. Although prominent marine phytoplanktonic organisms such as diatoms show robust diurnal rhythms in growth, cell cycle and gene expression, the molecular foundations controlling these processes are still obscure. By exploring the regulatory landscape of diatom diurnal rhythms, we unveil the function of aPhaeodactylum tricornutumbHLH-PAS protein,PtbHLH1a, in the regulation of light-dependent diurnal rhythms. Peak expression ofPtbHLH1amRNA occurs toward the end of the light period and it adjusts to photoperiod changes. Ectopic over-expression ofPtbHLH1a results in lines showing a phase shift in diurnal cell fluorescence, compared to the wild-type cells, and with altered cell cycle progression and gene expression. Reduced oscillations in gene expression are also observed in overexpression lines compared to wild-type in continuous darkness, showing that the regulation of rhythmicity byPtbHLH1a is not directly dependent on light inputs and cell division.PtbHLH1a homologs are widespread in diatom genomes which may indicate a common function in many species. This study adds new elements to understand diatom biology and ecology and offers new perspectives to elucidate timekeeping mechanisms in marine organisms belonging to a major, but underinvestigated branch of the tree of life.SIGNIFICANCE STATEMENTMost organisms experience diurnal light-dark changes and show rhythms of basic biological processes such that they occur at optimal times of the day. The ocean harbours a huge diversity of organisms showing light-dependent rhythms, but their molecular foundations are still largely unknown. In this study, we discover a novel protein,PtbHLH1a that regulates cell division, gene expression and the diurnal timing of these events in the marine diatomPhaedoactylum tricornutum. The identification ofPtbHLH1a-like genes in many diatom species suggests a conserved function in diurnal rhythm regulation in the most species-rich group of algae in the ocean. This study unveils critical features of diatom biology and advances the field of marine rhythms and their environmental regulation.
Published: 2018
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71. The diatom Phaeodactylum tricornutum adjusts NPQ capacity in response to dynamic light via fine-tuned Lhcx and xanthophyll cycle pigment synthesis

Author: Lepetit, Bernard, Gélin, Gautier, Lepetit, Mariana, Sturm, Sabine, Vugrinec, Sascha, Rogato, Alessandra, Kroth, Peter, Falciatore, Angela, Lavaud, Johann, Fachbereich Biologie [Konstanz], University of Konstanz, Stazione Zoologica Anton Dohrn (SZN), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), and Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2017
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72. Expression and RNA binding properties of the chloroplast ribosomal protein S1 from Chlamydomonas reinhardtii

Author: Merendino, Livia, Falciatore, Angela, Rochaix, Jean-David, Merendino, Livia, Falciatore, Angela, and Rochaix, Jean-David
Abstract: The gene encoding the chloroplast ribosomal protein S1 from Chlamydomonas reinhardtii, CreS1, was cloned and the RNA binding properties and the expression patterns were studied. Gel-shift analysis revealed that CreS1 binds AU-rich 5′-untranslated regions (5′-UTR) of chloroplast mRNAs with higher affinity than the corresponding sequence of a GC-rich nuclear transcript. The binding affinity of CreS1 for a mutant form of the psbD 5′-UTR with a deletion of a U-rich stretch that is required for translation decreases 4-fold as compared to the wild-type 5′-UTR. Our results suggest that CreS1 protein interacts with U-rich sequences. Most of CreS1 is bound to high-molecular-weight complexes which co-migrate with the 30S small ribosomal subunit, and only a small fraction of CreS1 exists in its free form. CreS1 is localized mainly to the chloroplast stroma albeit a significant fraction is associated with chloroplast membranes. The results suggest that most of CreS1 is associated with the 30S ribosomal subunit throughout the translation process. Upon a shift of cells from the dark to the light, the mRNA levels of CreS1 and Psrp-7, both components of the 30S ribosomal subunit, increase transiently and return to the dark levels after 8h. However, during this dark-to-light transition the levels of CreS1 and of other components of the 30S subunit remain the same suggesting that either protein synthesis or degradation is regulated. The possible implications of these findings are discussed
Published: 2018

73. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

Author: Beverley R. Green, Gernot Glöckner, Thomas Mock, Remo Sanges, James A. Raymond, Michael G. Janech, Barbara R. Lyon, Kerrie Barry, Florian Leese, Ansgar Gruber, Joel Martin, Erika Lindquist, Matthew D. Clark, Robert Otillar, Ben J. Ward, Alexandra Z. Worden, Christoph Mayer, Antonio Emidio Fortunato, Micaela S. Parker, Christopher L. Dupont, Maria Immacolata Ferrante, Stephan Frickenhaus, Klaus Valentin, Hadi Quesneville, Vincent Moulton, Rachel Hipkin, Angela Falciatore, Igor V. Grigoriev, Christiane Uhlig, Chris Bowler, Cock van Oosterhout, Ruben E. Valas, Asaf Salamov, Jeremy Schmutz, E. Virginia Armbrust, Andrew E. Allen, Alaguraj Veluchamy, Jan Strauss, Peter G. Kroth, Mark McMullan, Taoyang Wu, Andrew Toseland, Pirita Paajanen, Florian Maumus, School of Environmental Sciences [Norwich], University of East Anglia [Norwich] (UEA), Joint Genome Institute, United States Department of Energy, Hudson Alpha Institute, Sezione Ecologia Marina Integrata, Stazione Zoologica Anton Dohrn, School of Physics [NUI Galway], National University of Ireland [Galway] (NUI Galway), Infection et inflammation chronique (2I), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Technical University of Munich (TUM), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Genomics Institute for Biochemistry I, University of Cologne, University of Innsbruck, Laboratoire Genome Population & Interactions, Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-ORSTOM, Department of Biology, University of Konstanz, Animal Ecology, Evolution and Biodiversity, Ruhr-Universität Bochum [Bochum], Univ Reading, Sch Chem Pharm & Food Biosci, Reading RG6 6AD, Berks, England, Canadian Institute for Advanced Research (CIAR), Université de Montréal [Montréal], Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, University of California [Santa Cruz] (UCSC), University of California, School of Oceanography [Seattle], University of Washington [Seattle], Johns Hopkins University School of Medicine [Baltimore], Department of Computer Science, DOE Joint Genome Institute [Walnut Creek], Stazione Zoologica Anton Dohrn (SZN), Infection et inflammation (2I), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Leopold Franzens Universität Innsbruck - University of Innsbruck, Université Montpellier 2 - Sciences et Techniques (UM2)-ORSTOM-Centre National de la Recherche Scientifique (CNRS), Canadian Institute for Advanced Research (CIFAR), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC), ERC Advanced Grant ERC-2011-ADG (Diatomite) - Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 - NERC under grants NE/I001751/1, NE/K004530/1, MGF (NBAF) grant 197, The Royal Society grant RG090774 and the Earth & Life Systems Alliance in Norwich, European Project: 294823,EC:FP7:ERC,ERC-2011-ADG_20110310,DIATOMITE(2012), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut de Biologie Paris Seine (IBPS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Acclimatization, [SDV]Life Sciences [q-bio], 01 natural sciences, Mutation Rate, Settore BIO/13 - Biologia Applicata, Freezing, Alleles, Carbon Dioxide, Darkness, Diatoms, Gene Expression Profiling, Genetic Drift, Genome, Ice Cover, Iron, Oceans and Seas, Phylogeny, Recombination, Genetic, Transcriptome, Cold Temperature, Evolution, Molecular, Genomics, Multidisciplinary, biology, Ecology, Biologie, Biotechnology, Genome evolution, Evolution, General Science & Technology, 03 medical and health sciences, Genetic drift, Genetic, Cylindrus, Molecular evolution, ddc:570, Genetics, 14. Life underwater, Genome size, Human Genome, fungi, Molecular, biology.organism_classification, Recombination, 030104 developmental biology, Diatom, Adaptation, 010606 plant biology & botany
Abstract: The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-Adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2 . Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
Published: 2017
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74. Supplementary Fig. 1 Quantitative analysis of P. tricornutum glycerolipids from Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum

Author: Villanova, Valeria, Fortunato, Antonio Emidio, Dipali Singh, Bo, Davide Dal, Conte, Melissa, Obata, Toshihiro, Jouhet, Juliette, Fernie, Alisdair R., Marechal, Eric, Falciatore, Angela, Pagliardini, Julien, Monnier, Adeline Le, Poolman, Mark, Curien, Gilles, Petroutsos, Dimitris, and Finazzi, Giovanni
Abstract: TAG profile in a total lipid extract from cells grown in replete conditions (A) and deplete conditions (B) in both mixotrophic and phototrophic mode. Glycerolipids are expressed in nmol / mg of dry cells. Each result is the average of two biological replicates ± SD. PHOT: light in N-replete condition; PHOTO-N: light in N-deplete condi-tion; MIX: light+glycerol in N-replete condition; MIX-N: light+glycerol in N-deplete condition.
Published: 2017
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75. Supplementary Fig. 3 Quantification of intracellular pyruvate by a fluorescence-based method from Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum

Author: Villanova, Valeria, Fortunato, Antonio Emidio, Dipali Singh, Bo, Davide Dal, Conte, Melissa, Obata, Toshihiro, Jouhet, Juliette, Fernie, Alisdair R., Marechal, Eric, Falciatore, Angela, Pagliardini, Julien, Monnier, Adeline Le, Poolman, Mark, Curien, Gilles, Petroutsos, Dimitris, and Finazzi, Giovanni
Abstract: A. Pyruvate standard curve. B. Quantification of intracellular pyruvate in cells grown in phototrophy (PHOT) and mixotrophy (MIX).
Published: 2017
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76. Supplementary Fig. 2 Membrane lipid composition in P. tricornutum from Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum

Author: Villanova, Valeria, Fortunato, Antonio Emidio, Dipali Singh, Bo, Davide Dal, Conte, Melissa, Obata, Toshihiro, Jouhet, Juliette, Fernie, Alisdair R., Marechal, Eric, Falciatore, Angela, Pagliardini, Julien, Monnier, Adeline Le, Poolman, Mark, Curien, Gilles, Petroutsos, Dimitris, and Finazzi, Giovanni
Abstract: Lipid analysis of cells grow in N-replete conditions and N-deplete conditions in both mixotrophic and phototrophic mode. Each result is the average of two biological replicates ± SD. SQDG, sulfoquinovosyldiacylglycerol; DGDG, digalactosyldiacylglycerol; MGDG, monogalactosyldiacylglycerol; PC, phosphatidylcholine; PHOT: light in N-replete condition; PHOTO-N: light in N-deplete condition; MIX: light+glycerol in N-replete condition; MIX-N: light+glycerol in N-deplete condition.
Published: 2017
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77. Light sensing and responses in marine microalgae

Author: Marianne Jaubert, Jean-Pierre Bouly, Angela Falciatore, Maurizio Ribera d'Alcalà, OTERI, Francesco, Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Anton Dohrn (SZN), Institut de Biologie Paris Seine (IBPS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Photoreceptors, Plant, 0301 basic medicine, Light, Phototroph, Ecology, [SDV]Life Sciences [q-bio], fungi, Light sensing, Plant Science, Biology, Structure and function, [SDV] Life Sciences [q-bio], 03 medical and health sciences, 030104 developmental biology, Phytoplankton, Microalgae, 14. Life underwater, Plant metabolism, sense organs, Plant Proteins
Abstract: International audience; Marine eukaryotic phytoplankton are major contributors to global primary production. To adapt and thrive in the oceans, phytoplankton relies on a variety of light-regulated responses and light-acclimation capacities probably driven by sophisticated photoregulatory mechanisms. A plethora of photoreceptor-like sequences from marine microalgae have been identified in omics approaches. Initial studies have revealed that some algal photoreceptors are similar to those known in plants. In addition, new variants with different spectral tuning and algal-specific light sensors have also been found, changing current views and perspectives on how photoreceptor structure and function have diversified in phototrophs experiencing different environmental conditions.
Published: 2017

78. A role for the cell-wall protein silacidin in cell size of the diatom Thalassiosira pseudonana

Author: Kirkham, Amy R, Richthammer, Patrick, Schmidt, Katrin, Wustmann, Martin, Maeda, Yoshiaki, Hedrich, René, Brunner, Eike, Tanaka, Tsuyoshi, van Pée, Karl-Heinz, Falciatore, Angela, Mock, Thomas, University of East Anglia [Norwich] (UEA), Technische Universität Dresden = Dresden University of Technology (TU Dresden), Tokyo University of Agriculture and Technology (TUAT), Diatom Genomics [LCQB] (LCQB-DG), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Diatoms, Genome, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Gene Expression Regulation, Cell Wall, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], fungi, Proteins, Original Article, Cell Size
Abstract: International audience; Diatoms contribute 20% of global primary production and form the basis of many marine food webs. Although their species diversity correlates with broad diversity in cell size, there is also an intraspecific cell-size plasticity owing to sexual reproduction and varying environmental conditions. However, despite the ecological significance of the diatom cell size for food-web structure and global biogeochemical cycles, our knowledge about genes underpinning the size of diatom cells remains elusive. Here, a combination of reverse genetics, experimental evolution and comparative RNA-sequencing analyses enabled us to identify a previously unknown genetic control of cell size in the diatom Thalassiosira pseudonana. In particular, the targeted deregulation of the expression of the cell-wall protein silacidin caused a significant increase in valve diameter. Remarkably, the natural downregulation of the silacidin gene transcript due to experimental evolution under low temperature also correlated with cell-size increase. Our data give first evidence for a genetically controlled regulation of cell size in T. pseudonana and possibly other centric diatoms as they also encode the silacidin gene in their genomes.
Published: 2017
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79. Supplementary Fig. 4 A Respiration and photosynthesis in P. tricornutum cells from Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum

Author: Villanova, Valeria, Fortunato, Antonio Emidio, Dipali Singh, Bo, Davide Dal, Conte, Melissa, Obata, Toshihiro, Jouhet, Juliette, Fernie, Alisdair R., Marechal, Eric, Falciatore, Angela, Pagliardini, Julien, Monnier, Adeline Le, Poolman, Mark, Curien, Gilles, Petroutsos, Dimitris, and Finazzi, Giovanni
Abstract: Direct assessment of oxygen consumption by a polarographic approach in both phototrophy (black bar) and mix-otrophy (red bar). B. Fluorescent based-assay to monitoring the changes in respiration using the Redox Dye A in presence of the selected compounds (see methods).
Published: 2017
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80. Supplementary Fig. 5 Screening of mixotrophic efficiency by biolog and redox dye assay in P. tricornutum from Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum

Author: Villanova, Valeria, Fortunato, Antonio Emidio, Dipali Singh, Bo, Davide Dal, Conte, Melissa, Obata, Toshihiro, Jouhet, Juliette, Fernie, Alisdair R., Marechal, Eric, Falciatore, Angela, Pagliardini, Julien, Monnier, Adeline Le, Poolman, Mark, Curien, Gilles, Petroutsos, Dimitris, and Finazzi, Giovanni
Abstract: A. OD750 nm changes (relative to phototrophic growth) of P. tricornutum cells grown for 6 days in BiologTM plates P1 and PM2A that contains 190 carbon compounds (see methods). Each data point represents a different com-pound. B. Growth profile of P. tricornutum on few selected compounds (at 20 mM) and a phototrophic control in 100 mL flasks. C. Areas under the growth curves of Supplementary Fig. 5B normalized to the area of the curve of phototrophic growth.
Published: 2017
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81. Regulation of chain length in two diatoms as a growth-fragmentation process

Author: Marco Cosentino Lagomarsino, Daniele Iudicone, Soizic Cheminant, Jean-Pierre Bouly, Marco Gherardi, Maria Immacolata Ferrante, Maurizio Ribera d'Alcalà, Angela Falciatore, Alberto Amato, Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Università degli studi di Milano [Milano], I.N.F.N. Istituto Nazionale di Fisica Nucleare, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica di Napoli (SZN), Stazione Zoologica di Napoli, Stazione Zoologica Anton Dohrn, EC FP7-People COFUND [600407], MIUR Italian Flagship Project RITMARE (Ricerca Italiana per il MARE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Milano = University of Milan (UNIMI), Stazione Zoologica Anton Dohrn (SZN), and Università degli Studi di Milano [Milano] (UNIMI)
Subjects: Diatoms, 0301 basic medicine, [SDV]Life Sciences [q-bio], Biology, biology.organism_classification, Chaetoceros decipiens, Models, Biological, 03 medical and health sciences, Chain length, 030104 developmental biology, Chain formation, Ecosystem, Phaeodactylum tricornutum, Biological system
Abstract: International audience; Chain formation in diatoms is relevant because of several aspects of their adaptation to the ecosystem. However, the tools to quantify the regulation of their assemblage and infer specific mechanisms in a laboratory setting are scarce. To address this problem, we define an approach based on a statistical physics model of chain growth and separation in combination with experimental evaluation of chain-length distributions. Applying this combined analysis to data from Chaetoceros decipiens and Phaeodactylum tricornutum, we find that cells of the first species control chain separation, likely through a cell-to-cell communication process, while the second species only modulates the separation rate. These results promote quantitative methods for characterizing chain formation in several chain-forming species and in diatoms in particular.
Published: 2016
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82. The diatom Phaeodactylum tricornutum adjusts nonphotochemical fluorescence quenching capacity in response to dynamic light via fine-tuned Lhcx and xanthophyll cycle pigment synthesis

Author: Lepetit, Bernard, Gélin, Gautier, Lepetit, Mariana, Sturm, Sabine, Vugrinec, Sascha, Rogato, Alessandra, Kroth, Peter G., Falciatore, Angela, and Lavaud, Johann
Subjects: Chlorophyll, Diatoms, Light, ddc:570, Chlorophyll A, Protein Biosynthesis, Light-Harvesting Protein Complexes, Gene Expression Regulation, Bacterial, RNA, Messenger, Photosynthesis, Xanthophylls, Fluorescence
Abstract: Diatoms contain a highly flexible capacity to dissipate excessively absorbed light by nonphotochemical fluorescence quenching (NPQ) based on the light-induced conversion of diadinoxanthin (Dd) into diatoxanthin (Dt) and the presence of Lhcx proteins. Their NPQ fine regulation on the molecular level upon a shift to dynamic light conditions is unknown.We investigated the regulation of Dd + Dt amount, Lhcx gene and protein synthesis and NPQ capacity in the diatom Phaeodactylum tricornutum after a change from continuous low light to 3 d of sine (SL) or fluctuating (FL) light conditions. Four P. tricornutum strains with different NPQ capacities due to different expression of Lhcx1 were included.All strains responded to dynamic light comparably, independently of initial NPQ capacity. During SL, NPQ capacity was strongly enhanced due to a gradual increase of Lhcx2 and Dd + Dt amount. During FL, cells enhanced their NPQ capacity on the first day due to increased Dd + Dt, Lhcx2 and Lhcx3; already by the second day light acclimation was accomplished. While quenching efficiency of Dt was strongly lowered during SL conditions, it remained high throughout the whole FL exposure.Our results highlight a more balanced and cost-effective photoacclimation strategy of P. tricornutum under FL than under SL conditions. published
Published: 2016

83. Characterization of two members of the cryptochrome/photolyase family from Ostreococcus tauri provides insights into the origin and evolution of cryptochromes

Author: Marc Heijde, Takeshi Todo, François-Yves Bouget, Pascal Plaza, Tomoko Ishikawa, Anwar Usman, Florence Corellou, Johanna Brazard, Angela Falciatore, Frédéric Sanchez, Monique de Saint Martin, Chris Bowler, and Gérald Zabulon
Subjects: 0106 biological sciences, Genetics, 0303 health sciences, biology, Protein family, Physiology, Circadian clock, Plant Science, DNA photolyase, biology.organism_classification, 01 natural sciences, Ostreococcus tauri, Ostreococcus, ARNTL, 03 medical and health sciences, Cryptochrome, Botany, Photolyase, 030304 developmental biology, 010606 plant biology & botany
Abstract: Cryptochromes (Crys) are blue light receptors believed to have evolved from the DNA photolyase protein family, implying that light control and light protection share a common ancient origin. In this paper, we report the identification of five genes of the Cry/photolyase family (CPF) in two green algae of the Ostreococcus genus. Phylogenetic analyses were used to confidently assign three of these sequences to cyclobutane pyrimidine dimer (CPD) photolyases, one of them to a DASH-type Cry, and a third CPF gene has high homology with the recently described diatom CPF1 that displays a bifunctional activity. Both purified OtCPF1 and OtCPF2 proteins show non-covalent binding to flavin adenine dinucleotide (FAD), and additionally to 5,10-methenyl-tetrahydrofolate (MTHF) for OtCPF2. Expression analyses revealed that all five CPF members of Ostreococcus tauri are regulated by light. Furthermore, we show that OtCPF1 and OtCPF2 display photolyase activity and that OtCPF1 is able to interact with the CLOCK:BMAL heterodimer, transcription factors regulating circadian clock function in other organisms. Finally, we provide evidence for the involvement of OtCPF1 in the maintenance of the Ostreococcus circadian clock. This work improves our understanding of the evolutionary transition between photolyases and Crys.
Published: 2010
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84. A bHLH-PAS protein regulates light-dependent diurnal rhythmic processes in the marine diatomPhaeodactylum tricornutum

Author: Annunziata, Rossella, primary, Ritter, Andrés, additional, Fortunato, Antonio Emidio, additional, Cheminant-Navarro, Soizic, additional, Agier, Nicolas, additional, Huysman, Marie J. J., additional, Winge, Per, additional, Bones, Atle, additional, Bouget, François-Yves, additional, Lagomarsino, Marco Cosentino, additional, Bouly, Jean Pierre, additional, and Falciatore, Angela, additional
Published: 2018
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85. Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum

Author: Manuela Mangogna, Alessandro Manfredonia, Sacha Coesel, Magali Siaut, Anton Montsant, Angela Falciatore, Chris Bowler, Andrew E. Allen, and Marc Heijde
Subjects: 0106 biological sciences, Genetic Vectors, Thalassiosira pseudonana, Computational biology, 01 natural sciences, Genome, 03 medical and health sciences, 010608 biotechnology, Reference genes, Genetics, Animals, Phaeodactylum tricornutum, 030304 developmental biology, Diatoms, Expressed Sequence Tags, Recombination, Genetic, 0303 health sciences, Expressed sequence tag, biology, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, fungi, General Medicine, biology.organism_classification, Housekeeping gene, Gene expression profiling, Diatom
Abstract: Research into diatom biology has now entered the post-genomics era, following the recent completion of the Thalassiosira pseudonana and Phaeodactylum tricornutum whole genome sequences and the establishment of Expressed Sequence Tag (EST) databases. The thorough exploitation of these resources will require the development of molecular tools to analyze and modulate the function of diatom genes in vivo. Towards this objective, we report here the identification of several reference genes that can be used as internal standards for gene expression studies by quantitative real-time PCR (qRT-PCR) in P. tricornutum cells grown over a diel cycle. In addition, we describe a series of diatom expression vectors based on Invitrogen Gateway technology for high-throughput protein tagging and overexpression studies in P. tricornutum. We demonstrate the utility of the diatom Destination vectors for determining the subcellular localization of a protein of interest and for immunodetection. The availability of these new resources significantly enriches the molecular toolbox for P. tricornutum and provides the diatom research community with well defined high-throughput methods for the analysis of diatom genes and proteins in vivo.
Published: 2007
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86. IDENTIFICATION AND COMPARATIVE GENOMIC ANALYSIS OF SIGNALING AND REGULATORY COMPONENTS IN THE DIATOMTHALASSIOSIRA PSEUDONANA

Author: Micaela S. Parker, Mak A. Saito, Chris Bowler, Andrew E. Allen, Angela Falciatore, Sacha Coesel, Masood Z. Hadi, Kirk E. Apt, Marc Heijde, Assaf Vardi, Gregory J. Pazour, Kamel Jabbari, Edda Rayko, J. Casey Lippmeier, Uma Maheswari, Anthony Chiovitti, Anton Montsant, Daniel S. Rokhsar, Alessandra De Martino, Kimberlee Thamatrakoln, Diego Martinez, Aubrey K. Davis, Manuela Mangogna, Magali Siaut, E. Virginia Armbrust, John A. Berges, and Todd W. Lane
Subjects: Comparative genomics, biology, Endosymbiosis, Ecology, fungi, Thalassiosira pseudonana, Chlamydomonas reinhardtii, Plant Science, Aquatic Science, Flagellum, biology.organism_classification, Diatom, Evolutionary biology, Horizontal gene transfer, Phaeodactylum tricornutum
Abstract: Diatoms are unicellular brown algae that likely arose from the endocytobiosis of a red alga into a single-celled heterotroph and that constitute an algal class of major importance in phytoplankton communities around the globe. The first whole-genome sequence from a diatom species, Thalassiosira pseudonana Hasle et Heimdal, was recently reported, and features that are central to diatom physiology and ecology, such as silicon and nitrogen metabolism, iron uptake, and carbon concentration mechanisms, were described. Following this initial study, the basic cellular systems controlling cell signaling, gene expression, cytoskeletal structures, and response to stress have been cataloged in an attempt to obtain a global view of the molecular foundations that sustain such an ecologically successful group of organisms. Comparative analysis with several microbial, plant, and metazoan complete genome sequences allowed the identification of putative membrane receptors, signaling proteins, and other components of central interest to diatom ecophysiology and evolution. Thalassiosira pseudonana likely perceives light through a novel phytochrome and several cryptochrome photoreceptors; it may lack the conserved RHO small-GTPase subfamily of cell-polarity regulators, despite undergoing polarized cell-wall synthesis; and it possesses an unusually large number of heat-shock transcription factors, which may indicate the central importance of transcriptional responses to environmental stress. The availability of the complete gene repertoire will permit a detailed biochemical and genetic analysis of how diatoms prosper in aquatic environments and will contribute to the understanding of eukaryotic evolution.
Published: 2007
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87. Characterization of marine diatom-infecting virus promoters in the model diatom Phaeodactylum tricornutum

Author: Masanori Okauchi, Arisa Miyagawa-Yamaguchi, Yuji Tomaru, Nozomu Kira, Haruo Yamaguchi, Takuma Okami, Masao Adachi, Liyuan Hou, Takamichi Yoshimatsu, Takeshi Ohama, Takashi Kadono, Kohei Ohnishi, Kazunari Fukunaga, Angela Falciatore, Laboratory of Aquatic Environmental Science (LAQUES), The United Graduate School of Agricultural Sciences, Harmful Algal Bloom Division, National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, Kochi University of Technology (KUT), National Institute of Information and Communications Technology [Tokyo, Japan] (NICT), National Research Institute of Aquaculture, Research Institute of Molecular Genetics, Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Green Fluorescent Proteins, Article, Fluorescence, Transformation, Genetic, Botany, Gene expression, Computer Simulation, Seawater, Phaeodactylum tricornutum, RNA, Messenger, Promoter Regions, Genetic, Gene, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Diatoms, Reporter gene, Multidisciplinary, biology, fungi, Reproducibility of Results, Promoter, DNA, biology.organism_classification, Flow Cytometry, Pennales, Cell biology, Diatom, Genes, Regulatory sequence, Viruses
Abstract: Viruses are considered key players in phytoplankton population control in oceans. However, mechanisms that control viral gene expression in prominent microalgae such as diatoms remain largely unknown. In this study, potential promoter regions isolated from several marine diatom-infecting viruses (DIVs) were linked to the egfp reporter gene and transformed into the Pennales diatom Phaeodactylum tricornutum. We analysed their activity in cells grown under different conditions. Compared to diatom endogenous promoters, novel DIV promoter (ClP1) mediated a significantly higher degree of reporter transcription and translation. Stable expression levels were observed in transformants grown under both light and dark conditions and high levels of expression were reported in cells in the stationary phase compared to the exponential phase of growth. Conserved motifs in the sequence of DIV promoters were also found. These results allow the identification of novel regulatory regions that drive DIV gene expression and further examinations of the mechanisms that control virus-mediated bloom control in diatoms. Moreover, the identified ClP1 promoter can serve as a novel tool for metabolic engineering of diatoms. This is the first report describing a promoter of DIVs that may be of use in basic and applied diatom research.
Published: 2015
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88. Proline biosynthesis in Streptococcus thermophilus: characterization of the proBA operon and its products

Author: Danila Limauro, Angela Falciatore, Maurilio De Felice, A L Basso, Giuseppe Forlani, Limauro, Danila, Falciatore, A, Basso, A. L., Forlani, G., and DE FELICE, Maurilio
Subjects: DNA, Bacterial, Streptococcus thermophilus, Proline, Operon, Molecular Sequence Data, medicine.disease_cause, Microbiology, chemistry.chemical_compound, gamma-glutamyl kinase, Biosynthesis, medicine, Amino Acid Sequence, RNA, Messenger, Cloning, Molecular, Gene, Escherichia coli, Proa, Genetics, Base Sequence, biology, Nucleic acid sequence, Chromosome Mapping, Streptococcus, food and beverages, Phosphotransferases (Carboxyl Group Acceptor), biology.organism_classification, Aldehyde Oxidoreductases, Culture Media, RNA, Bacterial, gene structure and expression, gamma-glutamylphosphate reductase, Biochemistry, chemistry, Genes, Bacterial, Glutamate-5-Semialdehyde Dehydrogenase, proline biosynthesis, bacteria
Abstract: The presence of proline in the medium was not essential for growth of Streptococcus thermophilus, indicating that there is a proline biosynthetic pathway in this organism. Genetic and biochemical analysis identified and characterized this pathway. Two genes, designated proB and proA, were cloned, sequenced and characterized. Biochemical analysis of the proB- and proA-encoded enzymes showed that the proline biosynthetic pathway of S. thermophilus is similar to the one previously described in Escherichia coli. The deduced amino acid sequence of a 2-408 kb DNA region containing the genes revealed the similarity of the S. thermophilus gene products to ProB and ProA of E. coli and Serratia marcescens, and to the corresponding N- and C-terminal domains of the bifunctional plant enzyme delta 1-pyrroline-5-carboxylate synthetase of Vigna aconitifolia. Northern blot analysis showed that the two genes in S. thermophilus are organized in a single operon with proB proximal and proA distal to the promoter; primer extension analysis indicated that proBA transcription is not under repressive control by exogenously supplied proline.
Published: 1996
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89. Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity[OPEN].

Author: 1, Angela Falciatore, Jaubert, Marianne, Bouly, Jean-Pierre, Bailleul, Benjamin, and 1, Thomas Mock
Abstract: Diatoms are the world's most diverse group of algae, comprising at least 100,000 species. Contributing ~20% of annual global carbon fixation, they underpin major aquatic food webs and drive global biogeochemical cycles. Over the past two decades, Thalassiosira pseudonana and Phaeodactylum tricornutum have become the most important model systems for diatom molecular research, ranging from cell biology to ecophysiology, due to their rapid growth rates, small genomes, and the cumulative wealth of associated genetic resources. To explore the evolutionary divergence of diatoms, additional model species are emerging, such as Fragilariopsis cylindrus and Pseudo-nitzschia multistriata. Here, we describe how functional genomics and reverse genetics have contributed to our understanding of this important class of microalgae in the context of evolution, cell biology, and metabolic adaptations. Our review will also highlight promising areas of investigation into the diversity of these photosynthetic organisms, including the discovery of new molecular pathways governing the life of secondary plastid-bearing organisms in aquatic environments. [ABSTRACT FROM AUTHOR]
Published: 2020
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90. Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum

Author: Villanova, A, Fortunato, A, Singh, D, Dal Bo, D, Conte, M, Obata, T, Johuet, J, Fernie, AR, Marechal, E, Falciatore, A, Pagliardini, J, Le Monnier, A, Poolman, M, Curien, G, Petroutsos, D, Finazzi, G, Villanova, A, Fortunato, A, Singh, D, Dal Bo, D, Conte, M, Obata, T, Johuet, J, Fernie, AR, Marechal, E, Falciatore, A, Pagliardini, J, Le Monnier, A, Poolman, M, Curien, G, Petroutsos, D, and Finazzi, G
Abstract: Diatoms are prominent marine microalgae, interesting not only from an ecological point of view, but also for their possible use in biotechnology applications. They can be cultivated in phototrophic conditions, using sunlight as the sole energy source. Some diatoms, however, can also grow in a mixotrophic mode, wherein both light and external reduced carbon contribute to biomass accumulation. In this study, we investigated the consequences of mixotrophy on the growth and metabolism of the pennate diatom Phaeodactylum tricornutum, using glycerol as the source of reduced carbon. Transcriptomics, metabolomics, metabolic modelling and physiological data combine to indicate that glycerol affects the central-carbon, carbon-storage and lipid metabolism of the diatom. In particular, provision of glycerol mimics typical responses of nitrogen limitation on lipid metabolism at the level of TAG accumulation and fatty acid composition. The presence of glycerol, despite provoking features reminiscent of nutrient limitation, neither diminishes photosynthetic activity nor cell growth, revealing essential aspects of the metabolic flexibility of these microalgae and suggesting possible biotechnological applications of mixotrophy.
Published: 2017

91. A systems-wide understanding of photosynthetic acclimation in algae and higher plants

Author: Wanjiku Moejes, Fiona, Matuszyńska, Anna, Adhikari, Kailash, Bassi, Roberto, Cariti, Federica, Cogne, Guillaume, Dikaios, Joannis, Falciatore, Angela, Finazzi, Giovanni, Flori, Serena, Goldschmidt-Clermont, Michel, Magni, Stefano, Maguire, Julie, Le Monnier, Adeline, Müller, Kathrin, Poolman, Mark, Singh, Dipali, Spelberg, Stephanie, Stella, Giulio Rocco, Succurro, Antonella, Taddei, Lucilla, Urbain, Brieuc, Villanova, Valeria, Zabke, Claudia, Ebenhöh, Oliver, Wanjiku Moejes, Fiona, Matuszyńska, Anna, Adhikari, Kailash, Bassi, Roberto, Cariti, Federica, Cogne, Guillaume, Dikaios, Joannis, Falciatore, Angela, Finazzi, Giovanni, Flori, Serena, Goldschmidt-Clermont, Michel, Magni, Stefano, Maguire, Julie, Le Monnier, Adeline, Müller, Kathrin, Poolman, Mark, Singh, Dipali, Spelberg, Stephanie, Stella, Giulio Rocco, Succurro, Antonella, Taddei, Lucilla, Urbain, Brieuc, Villanova, Valeria, Zabke, Claudia, and Ebenhöh, Oliver
Abstract: The ability of phototrophs to colonise different environments relies on robust protection against oxidative stress, a critical requirement for the successful evolutionary transition from water to land. Photosynthetic organisms have developed numerous strategies to adapt their photosynthetic apparatus to changing light conditions in order to optimise their photosynthetic yield, which is crucial for life on Earth to exist. Photosynthetic acclimation is an excellent example of the complexity of biological systems, where highly diverse processes, ranging from electron excitation over protein protonation to enzymatic processes coupling ion gradients with biosynthetic activity, interact on drastically different timescales from picoseconds to hours. Efficient functioning of the photosynthetic apparatus and its protection is paramount for efficient downstream processes, including metabolism and growth. Modern experimental techniques can be successfully integrated with theoretical and mathematical models to promote our understanding of underlying mechanisms and principles. This review aims to provide a retrospective analysis of multidisciplinary photosynthetic acclimation research carried out by members of the Marie Curie Initial Training Project, AccliPhot, placing the results in a wider context. The review also highlights the applicability of photosynthetic organisms for industry, particularly with regards to the cultivation of microalgae. It intends to demonstrate how theoretical concepts can successfully complement experimental studies broadening our knowledge of common principles in acclimation processes in photosynthetic organisms, as well as in the field of applied microalgal biotechnology.
Published: 2017
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92. Evolutionary genomics of the cold-Adapted diatom Fragilariopsis cylindrus

Author: Mock, T., Otillar, R. P., Strauss, Jan, McMullan, M., Paajanen, P., Schmutz, J., Salamov, A., Sanges, R., Toseland, A., Ward, B. J., Allen, A. E., Dupont, C. L., Frickenhaus, S., Maumus, F., Veluchamy, A., Wu, T., Barry, K. W., Falciatore, A., Ferrante, M. I., Fortunato, A. E., Glöckner, G., Gruber, A., Hipkin, R., Janech, M. G., Kroth, P. G., Leese, F., Lindquist, E. A., Lyon, B. R., Martin, J., Mayer, C., Parker, M., Quesneville, H., Raymond, J. A., Uhlig, C., Valas, R. E., Valentin, K. U., Worden, Alexandra Z., Armbrust, E. V., Clark, M. D., Bowler, C., Green, B. R., Moulton, V., Van Oosterhout, C., Grigoriev, I. V., Mock, T., Otillar, R. P., Strauss, Jan, McMullan, M., Paajanen, P., Schmutz, J., Salamov, A., Sanges, R., Toseland, A., Ward, B. J., Allen, A. E., Dupont, C. L., Frickenhaus, S., Maumus, F., Veluchamy, A., Wu, T., Barry, K. W., Falciatore, A., Ferrante, M. I., Fortunato, A. E., Glöckner, G., Gruber, A., Hipkin, R., Janech, M. G., Kroth, P. G., Leese, F., Lindquist, E. A., Lyon, B. R., Martin, J., Mayer, C., Parker, M., Quesneville, H., Raymond, J. A., Uhlig, C., Valas, R. E., Valentin, K. U., Worden, Alexandra Z., Armbrust, E. V., Clark, M. D., Bowler, C., Green, B. R., Moulton, V., Van Oosterhout, C., and Grigoriev, I. V.
Abstract: The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-Adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2 . Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
Published: 2017
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93. A systems-wide understanding of photosynthetic acclimation in algae and higher plants

Author: Matuszy?ska, Anna, Moejes, Fiona Wanjiku, Adhikari, Kailash, Bassi, Roberto, Cariti, Federica, Cogne, Guillaume, Dikaios, Ioannis, Falciatore, Angela, Finazzi, Giovanni, Flori, Serena, Goldschmidt-Clermont, Michel, Magni, Stefano, Maguire, Julie, Le Monnier, Adeline, Müller, Kathrin, Poolman, Mark, Singh, Dipali, Spelberg, Stephanie, Stella, Giulio Rocco, Succurro, Antonello, Taddei, Lucilla, Urbain, Brieuc, Villanova, Valeria, Zabke, Claudia, Ebenhöh, Oliver, Matuszy?ska, Anna, Moejes, Fiona Wanjiku, Adhikari, Kailash, Bassi, Roberto, Cariti, Federica, Cogne, Guillaume, Dikaios, Ioannis, Falciatore, Angela, Finazzi, Giovanni, Flori, Serena, Goldschmidt-Clermont, Michel, Magni, Stefano, Maguire, Julie, Le Monnier, Adeline, Müller, Kathrin, Poolman, Mark, Singh, Dipali, Spelberg, Stephanie, Stella, Giulio Rocco, Succurro, Antonello, Taddei, Lucilla, Urbain, Brieuc, Villanova, Valeria, Zabke, Claudia, and Ebenhöh, Oliver
Abstract: The ability of phototrophs to colonise different environments relied on the robust protection against oxidative stress in phototrophs, a critical requirement for the successful evolutionary transition from water to land. Photosynthetic organisms have developed numerous strategies to adapt their photosynthetic apparatus to changing light conditions in order to optimise their photosynthetic yield, crucial for life to exist on Earth. Photosynthetic acclimation is an excellent example of the complexity of biological systems, in which highly diverse processes, ranging from electron excitation over protein protonation to enzymatic processes coupling ion gradients with biosynthetic activity interact on drastically different timescales, ranging from picoseconds to hours. An efficient functioning of the photosynthetic apparatus and its protection is paramount for efficient downstream processes including metabolism and growth. Modern experimental techniques can be successfully integrated with theoretical and mathematical models to promote our understanding of underlying mechanisms and principles. This Review aims to provide a retrospective analysis of multidisciplinary photosynthetic acclimation research carried out by members of the Marie Curie Initial Training Project “AccliPhot”, placing the results in a wider context. The Review also highlights the applicability of photosynthetic organisms for industry, particularly with regards to the cultivation of microalgae. It aims to demonstrate how theoretical concepts can successfully complement experimental studies broadening our knowledge of common principles in acclimation processes in photosynthetic organisms, as well as in the field of applied microalgal biotechnology.
Published: 2017

94. The circadian clock in the diatom Phaeodactylum tricornutum

Author: Annunziata, R., Fortunato, A., Navarro, S., Huysman, M.J.J., Petroutsos, D., Brembu, T., Winge, P., Atle, B., Finazzi, G., Lagomarsino, M., and Falciatore, A.
Published: 2015

95. The upstream regulatory sequence of the light harvesting complex Lhcf2 gene of the marine diatom Phaeodactylum tricornutum enhances transcription in an orientation- and distance-independent fashion

Author: Rossella Annunziata, Maria Immacolata Ferrante, Angela Falciatore, Monia Teresa Russo, Remo Sanges, Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Anton Dohrn (SZN), ASSEMBLE Project (Association of European Marine Biological Laboratories), European Union FP7 INFRASTRUCTURES [227799], Grand Emprunt Project-European Marine Biological Resource Centre-Trance (EMBRC), ANR ``DiaDomOil' PROGRAMME BIO-MATIERES ENERGIES [**ANR-12-BIME-0005], [BIOforIU PONa3\₀0025], Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Light-Harvesting Protein Complexes, GUS reporter system, Regulatory Sequences, Nucleic Acid, Aquatic Science, 01 natural sciences, Genome, 03 medical and health sciences, Settore BIO/13 - Biologia Applicata, Transcriptional regulation, Genetics, 14. Life underwater, Phaeodactylum tricornutum, Enhancer, Gene, 030304 developmental biology, Diatoms, 0303 health sciences, biology, Base Sequence, Nucleic Acid, Ecology, fungi, Promoter, Molecular Sequence Annotation, DNA, biology.organism_classification, Diatom, Gene Expression Regulation, Evolutionary biology, Regulatory sequence, Gene expression, Regulatory element, Regulatory Sequences, 010606 plant biology & botany
Abstract: International audience; Diatoms are a key phytoplankton group in the contemporary ocean, showing extraordinary adaptation capacities to rapidly changing environments. The recent availability of whole genome sequences from representative species has revealed distinct features in their genomes, like novel combinations of genes encoding distinct metabolisms and a significant number of diatom-specific genes. However, the regulatory mechanisms driving diatom gene expression are still largely uncharacterized. Considering the wide variety of fields of study orbiting diatoms, ranging from ecology, evolutionary biology to biotechnology, it is thus essential to increase our understanding of fundamental gene regulatory processes such as transcriptional regulation. To this aim, we explored the functional properties of the 5'-flanking region of the Phaeodatylum tricornutum Lhcf2 gene, encoding a member of the Light Harvesting Complex superfamily and we showed that this region enhances transcription of a GUS reporter gene in an orientation- and distance-independent fashion. This represents the first example of a cis-regulatory sequence with enhancer-like features discovered in diatoms and it is instrumental for the generation of novel genetic tools and diatom exploitation in different areas of study. (C) 2015 Elsevier B.V. All rights reserved.
Published: 2015
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96. Near-natural light stress conditions specifically regulate distinct NPQ compounds in phaeodactylum tricornutum

Author: Lepetit, Bernard, Lavaud, Johann, Falciatore, Angela, Kroth, Peter G., Fachbereich Biologie [Konstanz], University of Konstanz, LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract: International audience; no abstract
Published: 2015

97. R<scp>EVEALING THE</scp> M<scp>OLECULAR</scp> S<scp>ECRETS OF</scp> M<scp>ARINE</scp> D<scp>IATOMS</scp>

Author: Chris Bowler and Angela Falciatore
Subjects: Diatoms, Cellular basis, Marine biology, Physiology, Ecology, Marine Biology, Genomics, Cell Biology, Plant Science, Biology, biology.organism_classification, Microscopy, Electron, Molecular level, Diatom, Molecular Biology, Primary productivity
Abstract: ▪ Abstract Diatoms are unicellular photosynthetic eukaryotes that contribute close to one quarter of global primary productivity. In spite of their ecological success in the world's oceans, very little information is available at the molecular level about their biology. Their most well-known characteristic is the ability to generate a highly ornamented silica cell wall, which made them very popular study organisms for microscopists in the last century. Recent advances, such as the development of a range of molecular tools, are now allowing the dissection of diatom biology, e.g., for understanding the molecular and cellular basis of bioinorganic pattern formation of their cell walls and for elucidating key aspects of diatom ecophysiology. Making diatoms accessible to genomics technologies will potentiate greatly these efforts and may lead to the use of diatoms to construct submicrometer-scale silica structures for the nanotechnology industry.
Published: 2002
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98. The molecular life of diatoms

Author: Chris Bowler, Angela Falciatore, Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Transcriptome, Diatoms, Genome, Evolutionary biology, [SDV]Life Sciences [q-bio], Research, Publications, Genetics, Aquatic Science, Biology, ComputingMilieux_MISCELLANEOUS
Abstract: Diatoms are unicellular photosynthetic eukaryotes that are arguably the most species-rich group of algae, having conquered most aquatic habitats since their major diversification around 65millionyears ago (Bowler et al., 2010). They play a major role in the functioning of the global ecosystem, e.g., in silica and carbon biogeochemical cycles (Tréguer and De La Rocha, 2013andField et al., 1998). They have a complex evolutionary history, and like other chromalveolates are believed to be derived from a serial secondary endosymbiosis involving both green and red algae combining with a eukaryotic heterotrophic host cell (Moustafa et al., 2009). Their rigid cell wall has constrained them to acquire an unusual mode of cell division, with mitotically-derived daughter cells becoming progressively smaller until they reach a critical size threshold, following which they must undergo sexual reproduction for size restoration (Lewis, 1984andChepurnov et al., 2004). While many species are planktonic, the majority are benthic and can stick to virtually any surface. Many of these can move by gliding, a process mediated by the extrusion of polysaccharides from a slit in the cell wall known as the raphe (Edgar and Pickett-Heaps, 1984).
Published: 2014
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99. Genome engineering empowers the diatom Phaeodactylum tricornutum for biotechnology

Author: Christophe Perez-Michaut, Gwendoline Dubois, Alan Maréchal, Valérie Guyot, Angela Falciatore, Daniel F. Voytas, Sophie Leduc, Philippe Duchateau, Marine Beurdeley, Fayza Daboussi, Alexandre Juillerat, Alberto Amato, Laurent Cavarec, Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-IFR10, Département de pathologie [Mondor], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Cellectis, Cellectis SA, Total SA, Daboussi, Fayza, Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Genotype, [SDV]Life Sciences [q-bio], Molecular Sequence Data, General Physics and Astronomy, Mutagenesis (molecular biology technique), 7. Clean energy, 01 natural sciences, Genome, General Biochemistry, Genetics and Molecular Biology, Genome engineering, 03 medical and health sciences, Mutation Rate, Tandem Mass Spectrometry, Botany, DNA Breaks, Double-Stranded, Phaeodactylum tricornutum, Insertion, Gene, Selectable marker, Chromatography, High Pressure Liquid, Triglycerides, 030304 developmental biology, Diatoms, 0303 health sciences, Multidisciplinary, Vegetal Biology, biology, Base Sequence, fungi, General Chemistry, biology.organism_classification, Endonucleases, Flow Cytometry, Lipids, Diatom, Biochemistry, Mutagenesis, Trans-Activators, Genetic Engineering, Biologie végétale, 010606 plant biology & botany, Biotechnology
Abstract: Diatoms, a major group of photosynthetic microalgae, have a high biotechnological potential that has not been fully exploited because of the paucity of available genetic tools. Here we demonstrate targeted and stable modifications of the genome of the marine diatom Phaeodactylum tricornutum, using both meganucleases and TALE nucleases. When nuclease-encoding constructs are co-transformed with a selectable marker, high frequencies of genome modifications are readily attained with 56 and 27% of the colonies exhibiting targeted mutagenesis or targeted gene insertion, respectively. The generation of an enhanced lipid-producing strain (45-fold increase in triacylglycerol accumulation) through the disruption of the UDP-glucose pyrophosphorylase gene exemplifies the power of genome engineering to harness diatoms for biofuel production. Diatoms are photosynthetic microalgae with underutilized biotechnological potential. Here, the authors carry out targeted gene modifications of lipid metabolism genes in the diatom, Phaeodactylum tricornutum, resulting in a strain that exhibits a 45-fold increase in triacylglycerol accumulation.
Published: 2014
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100. The Cryptochrome/Photolyase Family in aquatic organisms

Author: Enrique Arboleda, Antonio Emidio Fortunato, Olga Antonova, Kristin Tessmar-Raible, Libero Petrone, Tomoko Ishikawa-Fujiwara, Takeshi Todo, Paola Oliveri, Yuri Kobayashi, Angela Falciatore, Juliane Zantke, Department of Radiation Biology and Medical Genetics, Osaka University [Osaka], Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), HFSP [RGY0082/2010], Max F. Perutz Laboratories/University of Vienna, research platform ``Marine Rhythms of Life' of University of Vienna, FWF START award [AY0041321], EU in the Marie-Curie ITN CALIPSO [ITN 2013 GA 607607], and EU FP7 Research Infrastructure Initiative ASSEMBLE [227799]
Subjects: Light, Aquatic environments, Annelida, [SDV]Life Sciences [q-bio], Circadian clock, Marine Biology, Aquatic Science, Biology, Evolution, Molecular, Cryptochrome, Phylogenetics, Molecular evolution, Gene Duplication, Gene duplication, Genetics, Animals, Cluster Analysis, Data Mining, Photolyase, Gene, Phylogeny, Diatoms, Likelihood Functions, Phylogenetic tree, Base Sequence, Models, Genetic, Fishes, Proteins, Eukaryota, Cryptochromes, Multigene Family, Sea Urchins, Transcriptome, Rhythms, Deoxyribodipyrimidine Photo-Lyase, Sequence Alignment
Abstract: International audience; 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. (C) 2014 Published by Elsevier B.V.
Published: 2014
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