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1. Light-independent regulation of algal photoprotection by CO2 availability

Author

M. Águila Ruiz-Sola, Serena Flori, Yizhong Yuan, Gaelle Villain, Emanuel Sanz-Luque, Petra Redekop, Ryutaro Tokutsu, Anika Küken, Angeliki Tsichla, Georgios Kepesidis, Guillaume Allorent, Marius Arend, Fabrizio Iacono, Giovanni Finazzi, Michael Hippler, Zoran Nikoloski, Jun Minagawa, Arthur R. Grossman, Dimitris Petroutsos, Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Light Photosynthesis & Metabolism (Photosynthesis), Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science, Universidad de Córdoba = University of Córdoba [Córdoba], National Institute for Basic Biology [Okazaki] (NIBB), Graduate University for Advanced Studies [Hayama] (SOKENDAI), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, University of Potsdam = Universität Potsdam, The Human Frontiers Science Program through the funding of the project RGP0046/2018, Prestige Marie-Curie co-financing grant PRESTIGE-2017-1-0028, The International Max Planck Research School 'Primary Metabolism and Plant Growth' at the Max Planck Institute of Molecular Plant Physiology, The program ‘Plan Propio UCO’ from University of Cordoba, The Carnegie Institution for Science and the Department of Energy, DE-SC0019417, The Marie Curie Initial Training Network Accliphot FP7-PEPOPLE-2012-ITN, The Japan Society for the Promotion of Science, JSPS, for the grants-in-Aid for Scientific Research, KAKENHI, 21H04778 and 21H05040, The German Research Foundation DFG HI 739/9.2, ANR-18-CE20-0006,MetaboLIGHT,Regulation de la photosynthèse par la Lumière et le métabolisme chez les algues(2018), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-15-IDEX-0002,UGA,IDEX UGA(2015), and European Project: 751039,UNREDE

Subjects
MESH: Chlamydomonas reinhardtii, Multidisciplinary, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Photosystem II Protein Complex, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], General Physics and Astronomy, MESH: Proteins, General Chemistry, MESH: Carbon Dioxide, General Biochemistry, Genetics and Molecular Biology, MESH: Photosynthesis
Abstract

Photosynthetic algae have evolved mechanisms to cope with suboptimal light and CO2 conditions. When light energy exceeds CO2 fixation capacity, Chlamydomonas reinhardtii activates photoprotection, mediated by LHCSR1/3 and PSBS, and the CO2 Concentrating Mechanism (CCM). How light and CO2 signals converge to regulate these processes remains unclear. Here, we show that excess light activates photoprotection- and CCM-related genes by altering intracellular CO2 concentrations and that depletion of CO2 drives these responses, even in total darkness. High CO2 levels, derived from respiration or impaired photosynthetic fixation, repress LHCSR3/CCM genes while stabilizing the LHCSR1 protein. Finally, we show that the CCM regulator CIA5 also regulates photoprotection, controlling LHCSR3 and PSBS transcript accumulation while inhibiting LHCSR1 protein accumulation. This work has allowed us to dissect the effect of CO2 and light on CCM and photoprotection, demonstrating that light often indirectly affects these processes by impacting intracellular CO2 levels.

Published
2023
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2. Leo1 is essential for the dynamic regulation of heterochromatin and gene expression during cellular quiescence

Author

Eriko Oya, Catherine Schurra, Ronit Weisman, Karl Ekwall, Mickaël Durand-Dubief, Adiel Cohen, Jun-ichi Nakayama, Vladimir Maksimov, Benoit Arcangioli, Department of Biosciences and Nutrition [Karolinska Insitutet, Sueden] (BioNut), Karolinska Institutet [Stockholm], Open University of Israël, Dynamique du Génome - Dynamics of the genome, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), National Institute for Basic Biology [Okazaki] (NIBB), Graduate University for Advanced Studies [Hayama] (SOKENDAI), Work in the K.E. laboratory was supported by grants from the Swedish Cancer Society (C.F.) and the Swedish Research Council (V.R.). K.E. was the recipient of a Wenner-Gren stipend for a sabbatical stay at the Pasteur Institute, France. E.O. was the recipient of a postdoctoral fellowship and travel support from the JSPS Program for Advancing Strategic International Networks to Accelerate the Circulation of Talented Researchers (S2704). Funding was provided by Cancerfonden, Vetenskapsrådet, Wenner-Gren Foundation and Japan Society for the Promotion of Science., We thank the BEA facility, particularly T. Damdimopoulos, for help in processing gene expression data., and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
lcsh:QH426-470, Heterochromatin, [SDV]Life Sciences [q-bio], Biology, Resting Phase, Cell Cycle, Epigenesis, Genetic, Histones, 03 medical and health sciences, 0302 clinical medicine, Downregulation and upregulation, Gene Expression Regulation, Fungal, Gene expression, Schizosaccharomyces, Genetics, Reversible differentiation, Epigenetics, Molecular Biology, Gene, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, Cellular quiescence, Research, Cell Cycle, Nuclear Proteins, RNA-Binding Proteins, Fission yeast, Chromatin, Cell biology, lcsh:Genetics, RNA Polymerase II, Schizosaccharomyces pombe Proteins, Paf1C, 030217 neurology & neurosurgery
Abstract

Background Cellular quiescence is a reversible differentiation state during which cells modify their gene expression program to inhibit metabolic functions and adapt to a new cellular environment. The epigenetic changes accompanying these alterations are not well understood. We used fission yeast cells as a model to study the regulation of quiescence. When these cells are starved for nitrogen, the cell cycle is arrested in G1, and the cells enter quiescence (G0). A gene regulatory program is initiated, including downregulation of thousands of genes—for example, those related to cell proliferation—and upregulation of specific genes—for example, autophagy genes—needed to adapt to the physiological challenge. These changes in gene expression are accompanied by a marked alteration of nuclear organization and chromatin structure. Results Here, we investigated the role of Leo1, a subunit of the conserved RNA polymerase-associated factor 1 (Paf1) complex, in the quiescence process using fission yeast as the model organism. Heterochromatic regions became very dynamic in fission yeast in G0 during nitrogen starvation. The reduction of heterochromatin in early G0 was correlated with reduced target of rapamycin complex 2 (TORC2) signaling. We demonstrated that cells lacking Leo1 show reduced survival in G0. In these cells, heterochromatic regions, including subtelomeres, were stabilized, and the expression of many genes, including membrane transport genes, was abrogated. TOR inhibition mimics the effect of nitrogen starvation, leading to the expression of subtelomeric genes, and this effect was suppressed by genetic deletion of leo1. Conclusions We identified a protein, Leo1, necessary for survival during quiescence. Leo1 is part of a conserved protein complex, Paf1C, linked to RNA polymerase II. We showed that Leo1, acting downstream of TOR, is crucial for the dynamic reorganization of chromosomes and the regulation of gene expression during cellular quiescence. Genes encoding membrane transporters are not expressed in quiescent leo1 mutant cells, and cells die after 2 weeks of nitrogen starvation. Taken together, our results suggest that Leo1 is essential for the dynamic regulation of heterochromatin and gene expression during cellular quiescence. Electronic supplementary material The online version of this article (10.1186/s13072-019-0292-7) contains supplementary material, which is available to authorized users.

Published
2019
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3. Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome

Author

Akifumi Sugiyama, Efraín De Luna, Hideya Fukuzawa, Yuki Hirakawa, Yoshihiro Yoshitake, Jeremy Schmutz, Minoru Kubo, Sabine Zachgo, Sumio Sugano, Satoshi Naramoto, Isabel Monte, Juan Caballero-Pérez, Takashi Okamoto, Feng Chen, Keita Kinose, Rui Sun, Bruno Catarino, Shin-ichiro Inoue, Tomokazu Kawashima, Yasukazu Nakamura, Masaaki Umeda, Masayuki Tsuzuki, Junko Kyozuka, John L. Bowman, Mitsuru Kakita, Chia-Wei Lu, Eduardo Flores-Sandoval, Takayuki Kohchi, Christian R. Boehm, Kimitsune Ishizaki, D. Magnus Eklund, Shih-Shun Lin, Makoto Shirakawa, Jim Haseloff, Moritz Rövekamp, Hirofumi Nakagami, Anna Lipzen, Yuichiro Watanabe, Kazuhiko Nishitani, Noriyuki Suetsugu, Keisuke Inoue, Marc W. Schmid, Yosuke Kawai, Hirokazu Tomogane, Robert A. Martienssen, Shengqiang Shu, Ryuichi Nishihama, Ulf Lagercrantz, Miya Mizutani, Liam Dolan, Tom Dierschke, Frédéric Berger, Felix Althoff, Kevin M. Davies, Ueli Grossniklaus, Bence Galik, Asao Fujiyama, Sureshkumar Balasubrmanian, Ryusuke Yokoyama, Takashi Ueda, Izumi Yotsui, Toshinori Kinoshita, Misato Ohtani, Eri Koide, Kazufumi Yazaki, Shinichiro Sawa, Jane Grimwood, Diane Bauer, Mario A. Arteaga-Vazquez, Sakiko Ishida, Takahiro Hamada, Roberto Solano, Alexander J. Hetherington, Daniel Grimanelli, Stevie N. Florent, Erika Lindquist, Ryosuke Sano, Kenji Komatsu, Catherine Adam, Asuka Higo, Sarah Kopischke, Hope Hundley, Rebecca A. Mosher, Jerry Jenkins, Naoki Minamino, Hideki Nagasaki, Mizuki Takenaka, Kerrie Barry, Takashi Araki, Nobuyoshi Mochizuki, Anke Reinders, Mihails Delmans, Yuji Kohara, Yoko Ikeda, Daisuke Takezawa, Mansi Chovatia, Ana E. Dorantes-Acosta, Taku Demura, Masaki Okumura, Qidong Jia, Takehiko Kanazawa, Yutaka Suzuki, Megan Kennedy, Jeremy Phillips, Bernardo Pollak, Liam N. Briginshaw, Shohei Yamaoka, Shota Chiyoda, Alexander Spunde, John M. Ward, Masaharu Mizutani, Katsuyuki T. Yamato, Shiori S Aki, Boehm, Christian [0000-0002-6633-7998], Haseloff, Jim [0000-0003-4793-8058], Pollak, Bernardo [0000-0003-2329-7401], Apollo - University of Cambridge Repository, Monash University [Clayton], Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Kobe University, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Nara Institute of Science and Technology, Monash University [Melbourne], The University of Tennessee [Knoxville], Osnabrück University of Applied Sciences (OS UAS), Hochschule Osnabrück, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Department of Earth Science and Astrononomy [Tokyo], The University of Tokyo (UTokyo), National Institute for Basic Biology [Okazaki] (NIBB), Graduate University for Advanced Studies [Hayama] (SOKENDAI), Cold Spring Harbor Laboratory (CSHL), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Max Planck Institute for Plant Breeding Research (MPIPZ), Tokyo Metropolitan University [Tokyo] (TMU), Kumamoto University, Biocomputing Unit [Madrid], Research Institute for Sustainable Humanosphere (RISH), Kyoto University [Kyoto], University of Ulm (UUlm), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Kyoto University

Subjects
inorganic chemicals, 0301 basic medicine, Flora, Transcription, Genetic, [SDV]Life Sciences [q-bio], Marchantia polymorpha, Adaptation, Biological, macromolecular substances, Genome, General Biochemistry, Genetics and Molecular Biology, Evolutionsbiologi, 03 medical and health sciences, Gene Expression Regulation, Plant, Botany, Marchantia, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, sex chromosome, Biological sciences, Plant evolution, Medical And Health Sciences, Evolutionary Biology, biology, Ecology, fungi, food and beverages, Molecular Sequence Annotation, Biological evolution, Biological Sciences, 15. Life on land, biology.organism_classification, charophycean algae, Biological Evolution, 030104 developmental biology, Embryophyta, Terrestrial ecosystem, land plant evolution, auxin, Genome, Plant, Developmental Biology, Signal Transduction
Abstract

The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant., 陸上植物の祖先の特徴をもつ苔類ゼニゴケの全ゲノム構造を解明. 京都大学プレスリリース. 2017-10-06.

Published
2017
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4. The rice LysM receptor-like kinase OsCERK1 is required for the perception of short-chain chitin oligomers in arbuscular mycorrhizal signaling

Author

Tomomi Nakagawa, Mireille Chabaud, Andrea Genre, Kana Miyata, Hanae Kaku, Naoya Takeda, David G. Barker, Martina Capozzi, Gennaro Carotenuto, Naoto Shibuya, Department of Life Sciences and Systems Biology, University of Turin, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Department of Life Sciences, School of Agriculture, Meiji University, National Institute for Basic Biology [Okazaki] (NIBB), Graduate University for Advanced Studies [Hayama] (SOKENDAI), Division of Biological Science, Graduate School of Science, Nagoya University, UNITO, French National Research Agency : ANR-12-BSV7-0007-02, 'TULIP' Laboratory of Excellence : ANR-10-LABX-41, Department of Life Sciences and Systems Biology [University of Turin], Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), and Meiji University [Tokyo]

Subjects
0106 biological sciences, 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Physiology, Mutant, plant-microbe interactions, Chitin, Plant Science, LysM receptor-like kinase (RLK), Biology, Protein Serine-Threonine Kinases, 01 natural sciences, Plant Roots, 03 medical and health sciences, chemistry.chemical_compound, Gene Knockout Techniques, Mycorrhizae, Botany, Receptor like kinase, Plant Proteins, Oryza sativa, Kinase, nuclear calcium spiking, chitin oligomer signaling, Oryza, Cameleon (protein), arbuscular mycorrhiza (AM), Cell biology, 030104 developmental biology, oryza sativa, chemistry, Mutation, biology.protein, Calcium, root symbiosis, Signal transduction, Arbuscular mycorrhizal, 010606 plant biology & botany, Signal Transduction
Abstract

The rice lysin-motif (LysM) receptor-like kinase OsCERK1 is now known to have a dual role in both pathogenic and symbiotic interactions. Following the recent discovery that the Oscerk1 mutant is unable to host arbuscular mycorrhizal (AM) fungi, we have examined whether OsCERK1 is directly involved in the perception of the short-chain chitin oligomers (Myc-COs) identified in AM fungal exudates and shown to activate nuclear calcium (Ca(2+) ) spiking in the rice root epidermis. An Oscerk1 knockout mutant expressing the cameleon NLS-YC2.60 was used to monitor nuclear Ca(2+) signaling following root treatment with either crude fungal exudates or purified Myc-COs. Compared with wild-type rice, Ca(2+) spiking responses to AM fungal elicitation were absent in root atrichoblasts of the Oscerk1 mutant. By contrast, rice lines mutated in OsCEBiP, encoding the LysM receptor-like protein which associates with OsCERK1 to perceive chitin elicitors of the host immune defense pathway, responded positively to Myc-COs. These findings provide direct evidence that the bi-functional OsCERK1 plays a central role in perceiving short-chain Myc-CO signals and activating the downstream conserved symbiotic signal transduction pathway.

Published
2017
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5. The Cytochrome b 6 f Complex: A Regulatory Hub Controlling Electron Flow and the Dynamics of Photosynthesis?

Author

Jun Minagawa, Giles N. Johnson, Giovanni Finazzi, Physiologie cellulaire et végétale (LPCV), 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), 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), Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Faculty of Life Sciences University of Manchester, University of Manchester [Manchester], Cramer, William A., Kallas, Toivo, Martin-Laffon, Jacqueline, Cramer, William A., Kallas, Toivo, 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), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), National Institute for Basic Biology [Okazaki] (NIBB), Graduate University for Advanced Studies [Hayama] (SOKENDAI), Faculty of Life Sciences, University of Vienna [Vienna], National Institute for Basic Biology, National Institute for Basic Biology (NIBB), Université Grenoble Alpes (UGA), and 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)

Subjects
0106 biological sciences, cytochrome, Bioenergetics, Photosynthesis, 01 natural sciences, 03 medical and health sciences, Carbon assimilation, Botany, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, photosynthèse, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, biology, Cytochrome b, Cytochrome b6f complex, oxydoréduction, Protein composition, Plant, oxidoreduction, Order (biology), Rieske protein, biology.protein, Biophysics, Electron flow, 010606 plant biology & botany
Abstract

Chapter 22; Photosynthetic organisms must respond to several external stimuli to adjust their photosynthetic performances in order to keep a high capacity of carbon assimilation and avoid photodamage. They do so integrating processes occurring at different time scales starting from very fast light harvesting, down to slow changes of electron flow and protein composition of the photosynthetic apparatus. Central to these regulatory mechanisms is the cytochrome b(6)f complex, which regulates intersystem electron flow via photosynthetic control and modulates light harvesting capacity by acting as a redox sensor to trigger an acclimation process named state transitions. In this chapter we describe how the cytochrome b(6)f complex performs to regulate these different functions in both plants and microalgae, proposing new mechanisms of regulation, and critically discussing how these processes are compatible with the existing literature on the structure and function of this complex.

Published
2016
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