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

Author

Ruiz-Sola, M. Águila, Flori, Serena, Yuan, Yizhong, Villain, Gaelle, Sanz-Luque, Emanuel, Redekop, Petra, Tokutsu, Ryutaro, Küken, Anika, Tsichla, Angeliki, Kepesidis, Georgios, Allorent, Guillaume, Arend, Marius, Iacono, Fabrizio, Finazzi, Giovanni, Hippler, Michael, Nikoloski, Zoran, Minagawa, Jun, Grossman, Arthur R., and Petroutsos, Dimitris

Published
2023
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2. Network analysis with quantum dynamics clarifies why photosystem II exploits both chlorophyll a and b

Author

Kim, Eunchul, Lee, Daekyung, Sakamoto, Souichi, Jo, Ju-Yeon, Vargas, Mauricio, Ishizaki, Akihito, Minagawa, Jun, and Kim, Heetae

Subjects
Physics - Data Analysis, Statistics and Probability, Physics - Biological Physics, Physics - Chemical Physics
Abstract

In green plants, chlorophyll-a and chlorophyll-b are the predominant pigments bound to light-harvesting proteins. While the individual characteristics of these chlorophylls are well understood, the advantages of their coexistence remain unclear. In this study, we establish a method to simulate excitation energy transfer within the entire photosystem II supercomplex by employing network analysis integrated with quantum dynamic calculations. We then investigate the effects of the coexistence of chlorophyll-a and chlorophyll-b by comparing various chlorophyll compositions. Our results reveal that the natural chlorophyll composition allows the excited energy to preferentially flow through specific domains that act as safety valves, preventing downstream overflow. Our findings suggest that the light-harvesting proteins in a photosystem II supercomplex achieve evolutionary advantages with the natural chlorophyll-a/b ratio, capturing light energy efficiently and safely across various light intensities. Using our framework, one can better understand how green plants harvest light energy and adapt to changing environmental conditions., Comment: 20 pages, 4 figures

Published
2021

5. Genetic tool development in marine protists: emerging model organisms for experimental cell biology

Author

Faktorová, Drahomíra, Nisbet, R Ellen R, Fernández Robledo, José A, Casacuberta, Elena, Sudek, Lisa, Allen, Andrew E, Ares, Manuel, Aresté, Cristina, Balestreri, Cecilia, Barbrook, Adrian C, Beardslee, Patrick, Bender, Sara, Booth, David S, Bouget, François-Yves, Bowler, Chris, Breglia, Susana A, Brownlee, Colin, Burger, Gertraud, Cerutti, Heriberto, Cesaroni, Rachele, Chiurillo, Miguel A, Clemente, Thomas, Coles, Duncan B, Collier, Jackie L, Cooney, Elizabeth C, Coyne, Kathryn, Docampo, Roberto, Dupont, Christopher L, Edgcomb, Virginia, Einarsson, Elin, Elustondo, Pía A, Federici, Fernan, Freire-Beneitez, Veronica, Freyria, Nastasia J, Fukuda, Kodai, García, Paulo A, Girguis, Peter R, Gomaa, Fatma, Gornik, Sebastian G, Guo, Jian, Hampl, Vladimír, Hanawa, Yutaka, Haro-Contreras, Esteban R, Hehenberger, Elisabeth, Highfield, Andrea, Hirakawa, Yoshihisa, Hopes, Amanda, Howe, Christopher J, Hu, Ian, Ibañez, Jorge, Irwin, Nicholas AT, Ishii, Yuu, Janowicz, Natalia Ewa, Jones, Adam C, Kachale, Ambar, Fujimura-Kamada, Konomi, Kaur, Binnypreet, Kaye, Jonathan Z, Kazana, Eleanna, Keeling, Patrick J, King, Nicole, Klobutcher, Lawrence A, Lander, Noelia, Lassadi, Imen, Li, Zhuhong, Lin, Senjie, Lozano, Jean-Claude, Luan, Fulei, Maruyama, Shinichiro, Matute, Tamara, Miceli, Cristina, Minagawa, Jun, Moosburner, Mark, Najle, Sebastián R, Nanjappa, Deepak, Nimmo, Isabel C, Noble, Luke, Novák Vanclová, Anna MG, Nowacki, Mariusz, Nuñez, Isaac, Pain, Arnab, Piersanti, Angela, Pucciarelli, Sandra, Pyrih, Jan, Rest, Joshua S, Rius, Mariana, Robertson, Deborah, Ruaud, Albane, Ruiz-Trillo, Iñaki, Sigg, Monika A, Silver, Pamela A, Slamovits, Claudio H, Jason Smith, G, Sprecher, Brittany N, Stern, Rowena, Swart, Estienne C, Tsaousis, Anastasios D, Tsypin, Lev, Turkewitz, Aaron, and Turnšek, Jernej

Subjects
Genetics, Biotechnology, Life Below Water, Biodiversity, DNA, Ecosystem, Environment, Eukaryota, Green Fluorescent Proteins, Marine Biology, Models, Biological, Species Specificity, Transformation, Genetic, Biological Sciences, Technology, Medical and Health Sciences, Developmental Biology
Abstract

Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.

Published
2020

6. Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology

Author

Faktorová, Drahomíra, Nisbet, R Ellen R, Fernández Robledo, José A, Casacuberta, Elena, Sudek, Lisa, Allen, Andrew E, Ares, Manuel, Aresté, Cristina, Balestreri, Cecilia, Barbrook, Adrian C, Beardslee, Patrick, Bender, Sara, Booth, David S, Bouget, François-Yves, Bowler, Chris, Breglia, Susana A, Brownlee, Colin, Burger, Gertraud, Cerutti, Heriberto, Cesaroni, Rachele, Chiurillo, Miguel A, Clemente, Thomas, Coles, Duncan B, Collier, Jackie L, Cooney, Elizabeth C, Coyne, Kathryn, Docampo, Roberto, Dupont, Christopher L, Edgcomb, Virginia, Einarsson, Elin, Elustondo, Pía A, Federici, Fernan, Freire-Beneitez, Veronica, Freyria, Nastasia J, Fukuda, Kodai, García, Paulo A, Girguis, Peter R, Gomaa, Fatma, Gornik, Sebastian G, Guo, Jian, Hampl, Vladimír, Hanawa, Yutaka, Haro-Contreras, Esteban R, Hehenberger, Elisabeth, Highfield, Andrea, Hirakawa, Yoshihisa, Hopes, Amanda, Howe, Christopher J, Hu, Ian, Ibañez, Jorge, Irwin, Nicholas AT, Ishii, Yuu, Janowicz, Natalia Ewa, Jones, Adam C, Kachale, Ambar, Fujimura-Kamada, Konomi, Kaur, Binnypreet, Kaye, Jonathan Z, Kazana, Eleanna, Keeling, Patrick J, King, Nicole, Klobutcher, Lawrence A, Lander, Noelia, Lassadi, Imen, Li, Zhuhong, Lin, Senjie, Lozano, Jean-Claude, Luan, Fulei, Maruyama, Shinichiro, Matute, Tamara, Miceli, Cristina, Minagawa, Jun, Moosburner, Mark, Najle, Sebastián R, Nanjappa, Deepak, Nimmo, Isabel C, Noble, Luke, Novák Vanclová, Anna MG, Nowacki, Mariusz, Nuñez, Isaac, Pain, Arnab, Piersanti, Angela, Pucciarelli, Sandra, Pyrih, Jan, Rest, Joshua S, Rius, Mariana, Robertson, Deborah, Ruaud, Albane, Ruiz-Trillo, Iñaki, Sigg, Monika A, Silver, Pamela A, Slamovits, Claudio H, Jason Smith, G, Sprecher, Brittany N, Stern, Rowena, Swart, Estienne C, Tsaousis, Anastasios D, Tsypin, Lev, Turkewitz, Aaron, and Turnšek, Jernej

Subjects
Biological Sciences, Technology, Medical and Health Sciences, Developmental Biology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

7. Characterization of the far-red light absorbing light-harvesting chlorophyll a/b binding complex, a derivative of the distinctive Lhca gene family in green algae

Author

Kosugi, Makiko, primary, Ohtani, Shuji, additional, Hara, Kojiro, additional, Toyoda, Atsushi, additional, Nishide, Hiroyo, additional, Ozawa, Shin-Ichiro, additional, Takahashi, Yuichiro, additional, Kashino, Yasuhiro, additional, Kudoh, Sakae, additional, Koike, Hiroyuki, additional, and Minagawa, Jun, additional

Published
2024
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8. Photosynthetic light harvesting and energy conversion.

Author

Fleming, Graham R., Minagawa, Jun, Renger, Thomas, and Schlau-Cohen, Gabriela S.

Subjects
*ENERGY harvesting, *ENERGY conversion, *XANTHOPHYLLS, *CHLOROPHYLL spectra, *QUANTUM Monte Carlo method, *NUCLEAR magnetic resonance spectroscopy, *OPTICAL polarization, *EXCITED state energies
Abstract

Pandit[1] provides a review on the application of magic angle spinning nuclear magnetic resonance (NMR) spectroscopy and related techniques, with which it is possible to access the motion of proteins, pigments, and lipids on sub-nanoseconds to millisecond timescales on very different length scales ranging from solubilized complexes to whole cells. Remarkably, the spectral density includes 50 high-frequency vibrational modes per pigment, besides a low-frequency part characterizing the pigment-protein coupling. Using this technique, excitation energy transfer between the bacteriochlorophyll a pigments of the LH2 complex of purple bacteria is studied. Two important points dealt with in the present Special Topic issue on "Photosynthetic Light-Harvesting and Energy Conversion" are the following: (i) Pigment-protein complexes undergo conformational transitions on many different timescales that include transitions between functionally relevant modes of light harvesting and photoprotection. [Extracted from the article]

Published
2023
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9. Red-edge position of habitable exoplanets around M-dwarfs

Author

Takizawa, Kenji, Minagawa, Jun, Tamura, Motohide, Kusakabe, Nobuhiko, and Narita, Norio

Subjects
Astrophysics - Earth and Planetary Astrophysics
Abstract

One of the possible signs of life on distant habitable exoplanets is the red-edge, which is a rise in the reflectivity of planets between visible and near-infrared (NIR) wavelengths. Previous studies suggested the possibility that the red-edge position for habitable exoplanets around M-dwarfs may be shifted to a longer wavelength than that for Earth. We investigated plausible red-edge position in terms of the light environment during the course of the evolution of phototrophs. We show that phototrophs on M-dwarf habitable exoplanets may use visible light when they first evolve in the ocean and when they first colonize the land. The adaptive evolution of oxygenic photosynthesis may eventually also use NIR radiation, by one of two photochemical reaction centers, with the other center continuing to use visible light. These "two-color" reaction centers can absorb more photons, but they will encounter difficulty in adapting to drastically changing light conditions at the boundary between land and water. NIR photosynthesis can be more productive on land, though its evolution would be preceded by the Earth-type vegetation. Thus, the red-edge position caused by photosynthetic organisms on habitable M-dwarf exoplanets could initially be similar to that on Earth and later move to a longer wavelength., Comment: Published in Scientific Reports, open access version is available from https://www.nature.com/articles/s41598-017-07948-5

Published
2017
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14. Contributors

Author

Battle, Martin, primary, Brienen, Roel, additional, Burgess, Alexandra J., additional, Cavanagh, Amanda P., additional, Dall’Osto, Luca, additional, Emmerson, Robyn, additional, Foyer, Christine H., additional, Galbraith, David, additional, Gloor, Emanuel, additional, Gomez, Rodrigo L., additional, Guardini, Zeno, additional, Hanke, Guy, additional, Harbinson, Jeremy, additional, Hofmann, Tanja A., additional, Kaiser, Elias, additional, Kirilovsky, Diana, additional, Krieger-Liszkay, Anja, additional, Lawson, Tracy, additional, McAusland, Lorna, additional, Minagawa, Jun, additional, Morales, Alejandro Sierra, additional, Mullineaux, Conrad W., additional, Murchie, Erik H., additional, Pullin, Jacob, additional, Raines, Christine A., additional, Simkin, Andrew J., additional, van Amerongen, Herbert, additional, Wall, Shellie, additional, and Wientjes, Emilie, additional

Published
2022
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18. Light-independent regulation of algal photoprotection by CO2 availability

Author

Agence Nationale de la Recherche (France), European Commission, International Max Planck Research Schools, Universidad de Córdoba (España), Carnegie Institution for Science, Japan Society for the Promotion of Science, German Research Foundation, Department of Energy (US), Ruiz-Sola, M Águila [0000-0002-2281-6700], Flori, Serena [0000-0003-3407-2785], Yuan, Yizhong [0000-0003-3386-983X], Sanz-Luque, Emanuel [0000-0002-7300-9730], Redekop, Petra [0000-0002-2281-633X], Tokutsu, Ryutaro [0000-0003-2037-255X], Küken, Anika [0000-0003-1367-0719], Kepesidis, Georgios [0000-0002-1194-1987], Arend, Marius [0000-0002-9608-4960], Iacono, Fabrizio [0000-0002-3931-1231], Finazzi, Giovanni [0000-0003-0597-7075], Hippler, Michael [0000-0001-9670-6101], Minagawa, Jun [0000-0002-3028-3203], Grossman, Arthur R [0000-0002-3747-5881], Petroutsos, Dimitris [0000-0002-9656-661X], Ruiz-Sola, M Águila, Flori, Serena, Yuan, Yizhong, Villain, Gaelle, Sanz-Luque, Emanuel, Redekop, Petra, Tokutsu, Ryutaro, Küken, Anika, Tsichla, Angeliki, Kepesidis, Georgios, Allorent, Guillaume, Arend, Marius, Iacono, Fabrizio, Finazzi, Giovanni, Hippler, Michael, Nikoloski, Zoran, Minagawa, Jun, Grossman, Arthur R, Petroutsos, Dimitris, Agence Nationale de la Recherche (France), European Commission, International Max Planck Research Schools, Universidad de Córdoba (España), Carnegie Institution for Science, Japan Society for the Promotion of Science, German Research Foundation, Department of Energy (US), Ruiz-Sola, M Águila [0000-0002-2281-6700], Flori, Serena [0000-0003-3407-2785], Yuan, Yizhong [0000-0003-3386-983X], Sanz-Luque, Emanuel [0000-0002-7300-9730], Redekop, Petra [0000-0002-2281-633X], Tokutsu, Ryutaro [0000-0003-2037-255X], Küken, Anika [0000-0003-1367-0719], Kepesidis, Georgios [0000-0002-1194-1987], Arend, Marius [0000-0002-9608-4960], Iacono, Fabrizio [0000-0002-3931-1231], Finazzi, Giovanni [0000-0003-0597-7075], Hippler, Michael [0000-0001-9670-6101], Minagawa, Jun [0000-0002-3028-3203], Grossman, Arthur R [0000-0002-3747-5881], Petroutsos, Dimitris [0000-0002-9656-661X], Ruiz-Sola, M Águila, Flori, Serena, Yuan, Yizhong, Villain, Gaelle, Sanz-Luque, Emanuel, Redekop, Petra, Tokutsu, Ryutaro, Küken, Anika, Tsichla, Angeliki, Kepesidis, Georgios, Allorent, Guillaume, Arend, Marius, Iacono, Fabrizio, Finazzi, Giovanni, Hippler, Michael, Nikoloski, Zoran, Minagawa, Jun, Grossman, Arthur R, and Petroutsos, Dimitris

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

21. Field Report: UAV-Based Volcano Observation System for Debris Flow Evacuation Alarm

Author

Nagatani, Keiji, Yajima, Ryosuke, Kiribayashi, Seiga, Izu, Tomoaki, Kanai, Hiromichi, Kanasaki, Hiroyuki, Minagawa, Jun, Moriyama, Yuji, Siciliano, Bruno, Series editor, Khatib, Oussama, Series editor, Antonelli, Gianluca, Advisory editor, Fox, Dieter, Advisory editor, Harada, Kensuke, Advisory editor, Hsieh, M. Ani, Advisory editor, Kröger, Torsten, Advisory editor, Kulic, Dana, Advisory editor, Hutter, Marco, editor, and Siegwart, Roland, editor

Published
2018
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31. The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions

Author

Merchant, Sabeeha S., Prochnik, Simon E., Vallon, Olivier, Harris, Elizabeth H., Karpowicz, Steven J., Witman, George B., Terry, Astrid, Salamov, Asaf, Fritz-Laylin, Lillian K., Maréchal-Drouard, Laurence, Marshal, Wallace F., Qu, Liang-Hu, Nelson, David R., Sanderfoot, Anton A., Spalding, Martin H., Kapitonov, Vladimir V., Ren, Qinghu, Ferris, Patrick, Lindquist, Erika, Shapiro, Harris, Lucas, Susan M., Grimwood, Jane, Schmutz, Jeremy, Cardol, Pierre, Cerutti, Heriberto, Chanfreau, Guillaume, Chen, Chun-Long, Cognat, Valérie, Croft, Martin T., Dent, Rachel, Dutcher, Susan, Fernández, Emilio, Fukuzawa, Hideya, González-Ballester, David, González-Halphen, Diego, Hallmann, Armin, Hanikenne, Marc, Hippler, Michael, Inwood, William, Jabbari, Kamel, Kalanon, Ming, Kuras, Richard, Lefebvre, Paul A., Lemaire, Stéphane D., Loba, Alexey V., Lohr, Martin, Manuell, Andrea, Meier, Iris, Mets, Laurens, Mittag, Maria, Mittelmeier, Telsa, Moroney, James V., Moseley, Jeffrey, Napoli, Carolyn, Nedelcu, Aurora M., Niyogi, Krishna, Novoselov, Sergey V., Paulsen, Ian T., Pazour, Greg, Purton, Saul, Ral, Jean-Philippe, Riano-Pachon, Diego Mauricio, Riekhof, Wayne, Rymarquis, Linda, Schroda, Michael, Stern, David, Umen, James, Willows, Robert, Wilson, Nedra, Zimmer, Sara Lana, Allmer, Jens, Balk, Janneke, Bisova, Katerina, Chen, Chong-Jian, Elias, Marek, Gendler, Karla, Hauser, Charles, Lamb, Mary Rose, Ledford, Heidi, Long, Joanne C., Minagawa, Jun, Page, M. Dudley, Pan, Junmin, Pootakham, Wirulda, Roje, Sanja, Rose, Annkatrin, Stahlberg, Eric, Terauchi, Aimee M., Yang, Pinfen, Ball, Steven, Bowler, Chris, Dieckmann, Carol L., Gladyshev, Vadim N., Green, Pamela, Jorgensen, Richard, Mayfield, Stephen, Mueller-Roeber, Bernd, Rajamani, Sathish, and Sayre, Richard T.

Abstract

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.

Published
2007

32. Text Data Mining of English Interviews

Author

Ban, Hiromi, Kimura, Haruhiko, Oyabu, Takashi, Minagawa, Jun, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Saeed, Khalid, editor, and Homenda, Wladyslaw, editor

Published
2015
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33. Factors to Affect Descriptions on Intra-Concept Relation in Introductory Concept Mapping

Author

Minagawa, Jun, Ban, Hiromi, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Saeed, Khalid, editor, and Homenda, Wladyslaw, editor

Published
2015
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