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Wang G, Huang L, Zhuang S, Han F, Huang Q, Hao M, Lin G, Chen L, Shen B, Li F, Li X, Chen C, Gao Y, Mock T, Liang J. Resting cell formation in the marine diatom Thalassiosira pseudonana. New Phytol 2024. [PMID: 38402560 DOI: 10.1111/nph.19646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/08/2024] [Indexed: 02/26/2024]
Abstract
Resting cells represent a survival strategy employed by diatoms to endure prolonged periods of unfavourable conditions. In the oceans, many diatoms sink at the end of their blooming season and therefore need to endure cold and dark conditions in the deeper layers of the water column. How they survive these conditions is largely unknown. We conducted an integrative analysis encompassing methods from histology, physiology, biochemistry, and genetics to reveal the biological mechanism of resting-cell formation in the model diatom Thalassiosira pseudonana. Resting-cell formation was triggered by a decrease in light and temperature with subsequent catabolism of storage compounds. Resting cells were characterised by an acidic and viscous cytoplasm and altered morphology of the chloroplast ultrastructure. The formation of resting cells in T. pseudonana is an energy demanding process required for a biophysical alteration of the cytosol and chloroplasts to endure the unfavourable conditions of the deeper ocean as photosynthetic organisms. However, most resting cells (> 90%) germinate upon return to favorable growth conditions.
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Affiliation(s)
- Guangning Wang
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Lu Huang
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Shanshan Zhuang
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Fang Han
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Qianqian Huang
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Mengyuan Hao
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Guifang Lin
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Longnan Chen
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Biying Shen
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Feng Li
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Xuesong Li
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Changping Chen
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yahui Gao
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
- State Key Laboratory of Marine Environment Science, Xiamen University, Xiamen, 361102, Fujian, China
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia (UEA), Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Junrong Liang
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
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2
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Jin H, Zhang C, Meng S, Wang Q, Ding X, Meng L, Zhuang Y, Yao X, Gao Y, Shi F, Mock T, Gao H. Atmospheric deposition and river runoff stimulate the utilization of dissolved organic phosphorus in coastal seas. Nat Commun 2024; 15:658. [PMID: 38291022 PMCID: PMC10828365 DOI: 10.1038/s41467-024-44838-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024] Open
Abstract
In coastal seas, the role of atmospheric deposition and river runoff in dissolved organic phosphorus (DOP) utilization is not well understood. Here, we address this knowledge gap by combining microcosm experiments with a global approach considering the relationship between the activity of alkaline phosphatases and changes in phytoplankton biomass in relation to the concentration of dissolved inorganic phosphorus (DIP). Our results suggest that the addition of aerosols and riverine water stimulate the biological utilization of DOP in coastal seas primarily by depleting DIP due to increasing nitrogen concentrations, which enhances phytoplankton growth. This "Anthropogenic Nitrogen Pump" was therefore identified to make DOP an important source of phosphorus for phytoplankton in coastal seas but only when the ratio of chlorophyll a to DIP [Log10 (Chl a / DIP)] is larger than 1.20. Our study therefore suggests that anthropogenic nitrogen input might contribute to the phosphorus cycle in coastal seas.
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Affiliation(s)
- Haoyu Jin
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Environment and Ecology, Ministry of Education of China, Ocean University of China, Qingdao, 266100, China
- Marine Ecology and Environmental Science Laboratory, Laoshan Laboratory, Qingdao, 266071, China
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Chao Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Environment and Ecology, Ministry of Education of China, Ocean University of China, Qingdao, 266100, China.
- Marine Ecology and Environmental Science Laboratory, Laoshan Laboratory, Qingdao, 266071, China.
| | - Siyu Meng
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Environment and Ecology, Ministry of Education of China, Ocean University of China, Qingdao, 266100, China
- Marine Ecology and Environmental Science Laboratory, Laoshan Laboratory, Qingdao, 266071, China
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Qin Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Environment and Ecology, Ministry of Education of China, Ocean University of China, Qingdao, 266100, China
- Marine Ecology and Environmental Science Laboratory, Laoshan Laboratory, Qingdao, 266071, China
| | - Xiaokun Ding
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Ling Meng
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunyun Zhuang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Environment and Ecology, Ministry of Education of China, Ocean University of China, Qingdao, 266100, China
- Marine Ecology and Environmental Science Laboratory, Laoshan Laboratory, Qingdao, 266071, China
| | - Xiaohong Yao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Environment and Ecology, Ministry of Education of China, Ocean University of China, Qingdao, 266100, China
- Marine Ecology and Environmental Science Laboratory, Laoshan Laboratory, Qingdao, 266071, China
| | - Yang Gao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Environment and Ecology, Ministry of Education of China, Ocean University of China, Qingdao, 266100, China
- Marine Ecology and Environmental Science Laboratory, Laoshan Laboratory, Qingdao, 266071, China
| | - Feng Shi
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Environment and Ecology, Ministry of Education of China, Ocean University of China, Qingdao, 266100, China
- Marine Ecology and Environmental Science Laboratory, Laoshan Laboratory, Qingdao, 266071, China
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Huiwang Gao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Environment and Ecology, Ministry of Education of China, Ocean University of China, Qingdao, 266100, China.
- Marine Ecology and Environmental Science Laboratory, Laoshan Laboratory, Qingdao, 266071, China.
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3
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Clark MS, Hoffman JI, Peck LS, Bargelloni L, Gande D, Havermans C, Meyer B, Patarnello T, Phillips T, Stoof-Leichsenring KR, Vendrami DLJ, Beck A, Collins G, Friedrich MW, Halanych KM, Masello JF, Nagel R, Norén K, Printzen C, Ruiz MB, Wohlrab S, Becker B, Dumack K, Ghaderiardakani F, Glaser K, Heesch S, Held C, John U, Karsten U, Kempf S, Lucassen M, Paijmans A, Schimani K, Wallberg A, Wunder LC, Mock T. Multi-omics for studying and understanding polar life. Nat Commun 2023; 14:7451. [PMID: 37978186 PMCID: PMC10656552 DOI: 10.1038/s41467-023-43209-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Polar ecosystems are experiencing amongst the most rapid rates of regional warming on Earth. Here, we discuss 'omics' approaches to investigate polar biodiversity, including the current state of the art, future perspectives and recommendations. We propose a community road map to generate and more fully exploit multi-omics data from polar organisms. These data are needed for the comprehensive evaluation of polar biodiversity and to reveal how life evolved and adapted to permanently cold environments with extreme seasonality. We argue that concerted action is required to mitigate the impact of warming on polar ecosystems via conservation efforts, to sustainably manage these unique habitats and their ecosystem services, and for the sustainable bioprospecting of novel genes and compounds for societal gain.
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Affiliation(s)
- M S Clark
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
| | - J I Hoffman
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany.
| | - L S Peck
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, Università degli Studi di Padova, Viale dell'Università 16, I-35020, Legnaro, Italy
| | - D Gande
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry & MARUM, University of Bremen, Leobener Straße 3, 28359, Bremen, Germany
| | - C Havermans
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - B Meyer
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 23129, Oldenburg, Germany
| | - T Patarnello
- Department of Comparative Biomedicine and Food Science, Università degli Studi di Padova, Viale dell'Università 16, I-35020, Legnaro, Italy
| | - T Phillips
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - K R Stoof-Leichsenring
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, 14473, Potsdam, Germany
| | - D L J Vendrami
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
| | - A Beck
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, Botanische Staatssammlung München (SNSB-BSM), Menzinger Str. 67, 80638, München, Germany
| | - G Collins
- Senckenberg Biodiversity and Climate Research Centre & Loewe-Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Manaaki Whenua-Landcare Research, 231 Morrin Road St Johns, Auckland, 1072, New Zealand
| | - M W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry & MARUM, University of Bremen, Leobener Straße 3, 28359, Bremen, Germany
| | - K M Halanych
- Center for Marine Science, University of North Carolina, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
| | - J F Masello
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
- Justus-Liebig-Universität Gießen, Giessen, Germany
| | - R Nagel
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK
| | - K Norén
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - C Printzen
- Senckenberg Biodiversity and Climate Research Centre & Loewe-Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Natural History Museum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - M B Ruiz
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Universität Duisburg-Essen, Universitätstrasse 5, 45151, Essen, Germany
| | - S Wohlrab
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 23129, Oldenburg, Germany
| | - B Becker
- Universität zu Köln, Institut für Pflanzenwissenschaften, Zülpicher Str. 47b, 60674, Köln, Germany
| | - K Dumack
- Universität zu Köln, Terrestrische Ökologie, Zülpicher Str. 47b, 60674, Köln, Germany
| | - F Ghaderiardakani
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany
| | - K Glaser
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - S Heesch
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - C Held
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - U John
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - U Karsten
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - S Kempf
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - M Lucassen
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - A Paijmans
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
| | - K Schimani
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195, Berlin, Germany
| | - A Wallberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
| | - L C Wunder
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry & MARUM, University of Bremen, Leobener Straße 3, 28359, Bremen, Germany
| | - T Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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4
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Strauss J, Deng L, Gao S, Toseland A, Bachy C, Zhang C, Kirkham A, Hopes A, Utting R, Joest EF, Tagliabue A, Löw C, Worden AZ, Nagel G, Mock T. Plastid-localized xanthorhodopsin increases diatom biomass and ecosystem productivity in iron-limited surface oceans. Nat Microbiol 2023; 8:2050-2066. [PMID: 37845316 PMCID: PMC10627834 DOI: 10.1038/s41564-023-01498-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Microbial rhodopsins are photoreceptor proteins that convert light into biological signals or energy. Proteins of the xanthorhodopsin family are common in eukaryotic photosynthetic plankton including diatoms. However, their biological role in these organisms remains elusive. Here we report on a xanthorhodopsin variant (FcR1) isolated from the polar diatom Fragilariopsis cylindrus. Applying a combination of biophysical, biochemical and reverse genetics approaches, we demonstrate that FcR1 is a plastid-localized proton pump which binds the chromophore retinal and is activated by green light. Enhanced growth of a Thalassiora pseudonana gain-of-function mutant expressing FcR1 under iron limitation shows that the xanthorhodopsin proton pump supports growth when chlorophyll-based photosynthesis is iron-limited. The abundance of xanthorhodopsin transcripts in natural diatom communities of the surface oceans is anticorrelated with the availability of dissolved iron. Thus, we propose that these proton pumps convey a fitness advantage in regions where phytoplankton growth is limited by the availability of dissolved iron.
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Affiliation(s)
- Jan Strauss
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany.
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany.
- German Maritime Centre, Hamburg, Germany.
| | - Longji Deng
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Shiqiang Gao
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, Wuerzburg, Germany
| | - Andrew Toseland
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Charles Bachy
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Sorbonne Université, CNRS, FR2424, Station biologique de Roscoff, Roscoff, France
| | - Chong Zhang
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, Wuerzburg, Germany
| | - Amy Kirkham
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Robert Utting
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Eike F Joest
- Department of Biology, Biocenter, University of Würzburg, Wuerzburg, Germany
| | | | - Christian Löw
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Marine Biological Laboratory, Woods Hole, MA, USA
| | - Georg Nagel
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, Wuerzburg, Germany
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
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5
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Priest T, von Appen WJ, Oldenburg E, Popa O, Torres-Valdés S, Bienhold C, Metfies K, Boulton W, Mock T, Fuchs BM, Amann R, Boetius A, Wietz M. Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities. ISME J 2023; 17:1612-1625. [PMID: 37422598 PMCID: PMC10504371 DOI: 10.1038/s41396-023-01461-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 07/10/2023]
Abstract
The Arctic Ocean is experiencing unprecedented changes because of climate warming, necessitating detailed analyses on the ecology and dynamics of biological communities to understand current and future ecosystem shifts. Here, we generated a four-year, high-resolution amplicon dataset along with one annual cycle of PacBio HiFi read metagenomes from the East Greenland Current (EGC), and combined this with datasets spanning different spatiotemporal scales (Tara Arctic and MOSAiC) to assess the impact of Atlantic water influx and sea-ice cover on bacterial communities in the Arctic Ocean. Densely ice-covered polar waters harboured a temporally stable, resident microbiome. Atlantic water influx and reduced sea-ice cover resulted in the dominance of seasonally fluctuating populations, resembling a process of "replacement" through advection, mixing and environmental sorting. We identified bacterial signature populations of distinct environmental regimes, including polar night and high-ice cover, and assessed their ecological roles. Dynamics of signature populations were consistent across the wider Arctic; e.g. those associated with dense ice cover and winter in the EGC were abundant in the central Arctic Ocean in winter. Population- and community-level analyses revealed metabolic distinctions between bacteria affiliated with Arctic and Atlantic conditions; the former with increased potential to use bacterial- and terrestrial-derived substrates or inorganic compounds. Our evidence on bacterial dynamics over spatiotemporal scales provides novel insights into Arctic ecology and indicates a progressing Biological Atlantification of the warming Arctic Ocean, with consequences for food webs and biogeochemical cycles.
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Affiliation(s)
- Taylor Priest
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany.
| | - Wilken-Jon von Appen
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - Ellen Oldenburg
- Institute for Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Ovidiu Popa
- Institute for Quantitative and Theoretical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Sinhué Torres-Valdés
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - Christina Bienhold
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - William Boulton
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, 28359, Germany
| | - Matthias Wietz
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany.
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, 27570, Germany.
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6
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Pichler M, Meindl A, Romberger M, Eckes-Shephard A, Nyberg-Brodda CF, Buhigas C, Llaneza-Lago S, Lehmann G, Hopes A, Meister G, Medenbach J, Mock T. Ribosome Profiling in the Model Diatom Thalassiosira pseudonana. Curr Protoc 2023; 3:e843. [PMID: 37439534 DOI: 10.1002/cpz1.843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Diatoms are an important group of eukaryotic microalgae, which play key roles in marine biochemical cycling and possess significant biotechnological potential. Despite the importance of diatoms, their regulatory mechanisms of protein synthesis at the translational level remain largely unexplored. Here, we describe the detailed development of a ribosome profiling protocol to study translation in the model diatom Thalassiosira pseudonana, which can easily be adopted for other diatom species. To isolate and sequence ribosome-protected mRNA, total RNA was digested, and the ribosome-protected fragments were obtained by a combination of sucrose-cushion ultracentrifugation and polyacrylamide gel electrophoresis for size selection. To minimize rRNA contamination, a subtractive hybridization step using biotinylated oligos was employed. Subsequently, fragments were converted into sequencing libraries, enabling the global quantification and analysis of changes in protein synthesis in diatoms. The development of this novel ribosome profiling protocol represents a major expansion of the molecular toolbox available for diatoms and therefore has the potential to advance our understanding of the translational regulation in this important group of phytoplankton. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Ribosome profiling in Thalassiosira pseudonana Alternate Protocol: Ribosome profiling protocol for diatoms using sucrose gradient fractionation.
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Affiliation(s)
- Monica Pichler
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
- These authors contributed equally to this work
| | - Andreas Meindl
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
- These authors contributed equally to this work
| | - Markus Romberger
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Annemarie Eckes-Shephard
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
- Department of Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
- Current affiliation: Department of Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | | | - Claudia Buhigas
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | | | - Gerhard Lehmann
- Biochemistry I, University of Regensburg, Regensburg, Germany
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Gunter Meister
- Biochemistry I, University of Regensburg, Regensburg, Germany
| | - Jan Medenbach
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
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7
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Duncan A, Barry K, Daum C, Eloe-Fadrosh E, Roux S, Schmidt K, Tringe SG, Valentin KU, Varghese N, Salamov A, Grigoriev IV, Leggett RM, Moulton V, Mock T. Dataset of 143 metagenome-assembled genomes from the Arctic and Atlantic Oceans, including 21 for eukaryotic organisms. Data Brief 2023; 47:108990. [PMID: 36879606 PMCID: PMC9984783 DOI: 10.1016/j.dib.2023.108990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 01/18/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
This article presents metagenome-assembled genomes (MAGs) for both eukaryotic and prokaryotic organisms originating from the Arctic and Atlantic oceans, along with gene prediction and functional annotation for MAGs from both domains. Eleven samples from the chlorophyll-a maximum layer of the surface ocean were collected during two cruises in 2012; six from the Arctic in June-July on ARK-XXVII/1 (PS80), and five from the Atlantic in November on ANT-XXIX/1 (PS81). Sequencing and assembly was carried out by the Joint Genome Institute (JGI), who provide annotation of the assembled sequences, and 122 MAGs for prokaryotic organisms. A subsequent binning process identified 21 MAGs for eukaryotic organisms, mostly identified as Mamiellophyceae or Bacillariophyceae. The data for each MAG includes sequences in FASTA format, and tables of functional annotation of genes. For eukaryotic MAGs, transcript and protein sequences for predicted genes are available. A spreadsheet is provided summarising quality measures and taxonomic classifications for each MAG. These data provide draft genomes for uncultured marine microbes, including some of the first MAGs for polar eukaryotes, and can provide reference genetic data for these environments, or used in genomics-based comparison between environments.
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Affiliation(s)
- Anthony Duncan
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Chris Daum
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Emiley Eloe-Fadrosh
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Simon Roux
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Katrin Schmidt
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK
| | - Susannah G Tringe
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Klaus U Valentin
- Alfred-Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Neha Varghese
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | | | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK
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8
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Belshaw N, Grouneva I, Aram L, Gal A, Hopes A, Mock T. Efficient gene replacement by CRISPR/Cas-mediated homologous recombination in the model diatom Thalassiosira pseudonana. New Phytol 2023; 238:438-452. [PMID: 36307966 DOI: 10.1111/nph.18587] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
CRISPR/Cas enables targeted genome editing in many different plant and algal species including the model diatom Thalassiosira pseudonana. However, efficient gene targeting by homologous recombination (HR) to date is only reported for photosynthetic organisms in their haploid life-cycle phase. Here, a CRISPR/Cas construct, assembled using Golden Gate cloning, enabled highly efficient HR in a diploid photosynthetic organism. Homologous recombination was induced in T. pseudonana using sequence-specific CRISPR/Cas, paired with a dsDNA donor matrix, generating substitution of the silacidin, nitrate reductase and urease genes by a resistance cassette (FCP:NAT). Up to c. 85% of NAT-resistant T. pseudonana colonies screened positive for HR by nested PCR. Precise integration of FCP:NAT at each locus was confirmed using an inverse PCR approach. The knockout of the nitrate reductase and urease genes impacted growth on nitrate and urea, respectively, while the knockout of the silacidin gene in T. pseudonana caused a significant increase in cell size, confirming the role of this gene for cell-size regulation in centric diatoms. Highly efficient gene targeting by HR makes T. pseudonana as genetically tractable as Nannochloropsis and Physcomitrella, hence rapidly advancing functional diatom biology, bionanotechnology and biotechnological applications targeted on harnessing the metabolic potential of diatoms.
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Affiliation(s)
- Nigel Belshaw
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Irina Grouneva
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Lior Aram
- Department of Plant and Environmental Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Assaf Gal
- Department of Plant and Environmental Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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9
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Otte A, Winder JC, Deng L, Schmutz J, Jenkins J, Grigoriev IV, Hopes A, Mock T. The diatom Fragilariopsis cylindrus: A model alga to understand cold-adapted life. J Phycol 2023; 59:301-306. [PMID: 36856453 DOI: 10.1111/jpy.13325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 02/24/2023] [Accepted: 02/24/2023] [Indexed: 05/28/2023]
Abstract
Diatoms are significant primary producers especially in cold, turbulent, and nutrient-rich surface oceans. Hence, they are abundant in polar oceans, but also underpin most of the polar food webs and related biogeochemical cycles. The cold-adapted pennate diatom Fragilariopsis cylindrus is considered a keystone species in polar oceans and sea ice because it can thrive under different environmental conditions if temperatures are low. In this perspective paper, we provide insights into the latest molecular work that has been done on F. cylindrus and discuss its role as a model alga to understand cold-adapted life.
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Affiliation(s)
- Antonia Otte
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Johanna C Winder
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Longji Deng
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Igor V Grigoriev
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, UK
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10
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Mock T. Algal model species for advancing biological sciences. J Phycol 2023; 59:1-3. [PMID: 36779558 DOI: 10.1111/jpy.13312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Affiliation(s)
- Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ, Norwich, UK
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11
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Kleiner FH, Helliwell KE, Chrachri A, Hopes A, Parry-Wilson H, Gaikwad T, Mieszkowska N, Mock T, Wheeler GL, Brownlee C. Cold-induced [Ca2+]cyt elevations function to support osmoregulation in marine diatoms. Plant Physiol 2022; 190:1384-1399. [PMID: 35894667 PMCID: PMC9516774 DOI: 10.1093/plphys/kiac324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Diatoms are a group of microalgae that are important primary producers in a range of open ocean, freshwater, and intertidal environments. The latter can experience substantial long- and short-term variability in temperature, from seasonal variations to rapid temperature shifts caused by tidal immersion and emersion. As temperature is a major determinant in the distribution of diatom species, their temperature sensory and response mechanisms likely have important roles in their ecological success. We examined the mechanisms diatoms use to sense rapid changes in temperature, such as those experienced in the intertidal zone. We found that the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana exhibit a transient cytosolic Ca2+ ([Ca2+]cyt) elevation in response to rapid cooling, similar to those observed in plant and animal cells. However, [Ca2+]cyt elevations were not observed in response to rapid warming. The kinetics and magnitude of cold-induced [Ca2+]cyt elevations corresponded with the rate of temperature decrease. We did not find a role for the [Ca2+]cyt elevations in enhancing cold tolerance but showed that cold shock induces a Ca2+-dependent K+ efflux and reduces mortality of P. tricornutum during a simultaneous hypo-osmotic shock. As intertidal diatom species may routinely encounter simultaneous cold and hypo-osmotic shocks during tidal cycles, we propose that cold-induced Ca2+ signaling interacts with osmotic signaling pathways to aid in the regulation of cell volume. Our findings provide insight into the nature of temperature perception in diatoms and highlight that cross-talk between signaling pathways may play an important role in their cellular responses to multiple simultaneous stressors.
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Affiliation(s)
- Friedrich H Kleiner
- The Marine Biological Association of the United Kingdom, The Laboratory, Plymouth PL1 2PB, UK
- School of Ocean and Earth Science, University of Southampton, Southampton SO14 3ZH, UK
| | - Katherine E Helliwell
- The Marine Biological Association of the United Kingdom, The Laboratory, Plymouth PL1 2PB, UK
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Abdul Chrachri
- The Marine Biological Association of the United Kingdom, The Laboratory, Plymouth PL1 2PB, UK
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Hannah Parry-Wilson
- The Marine Biological Association of the United Kingdom, The Laboratory, Plymouth PL1 2PB, UK
- School of Ocean and Earth Science, University of Southampton, Southampton SO14 3ZH, UK
| | - Trupti Gaikwad
- The Marine Biological Association of the United Kingdom, The Laboratory, Plymouth PL1 2PB, UK
| | - Nova Mieszkowska
- The Marine Biological Association of the United Kingdom, The Laboratory, Plymouth PL1 2PB, UK
- School of Environmental Sciences, University of Liverpool, Liverpool, L69 3GP, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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12
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Kamikawa R, Mochizuki T, Sakamoto M, Tanizawa Y, Nakayama T, Onuma R, Cenci U, Moog D, Speak S, Sarkozi K, Toseland A, van Oosterhout C, Oyama K, Kato M, Kume K, Kayama M, Azuma T, Ishii KI, Miyashita H, Henrissat B, Lombard V, Win J, Kamoun S, Kashiyama Y, Mayama S, Miyagishima SY, Tanifuji G, Mock T, Nakamura Y. Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida. Sci Adv 2022; 8:eabi5075. [PMID: 35486731 PMCID: PMC9054022 DOI: 10.1126/sciadv.abi5075] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Secondary loss of photosynthesis is observed across almost all plastid-bearing branches of the eukaryotic tree of life. However, genome-based insights into the transition from a phototroph into a secondary heterotroph have so far only been revealed for parasitic species. Free-living organisms can yield unique insights into the evolutionary consequence of the loss of photosynthesis, as the parasitic lifestyle requires specific adaptations to host environments. Here, we report on the diploid genome of the free-living diatom Nitzschia putrida (35 Mbp), a nonphotosynthetic osmotroph whose photosynthetic relatives contribute ca. 40% of net oceanic primary production. Comparative analyses with photosynthetic diatoms and heterotrophic algae with parasitic lifestyle revealed that a combination of gene loss, the accumulation of genes involved in organic carbon degradation, a unique secretome, and the rapid divergence of conserved gene families involved in cell wall and extracellular metabolism appear to have facilitated the lifestyle of a free-living secondary heterotroph.
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Affiliation(s)
- Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takako Mochizuki
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Mika Sakamoto
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Takuro Nakayama
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Ryo Onuma
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Ugo Cenci
- Université de Lille, CNRS, UMR 8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Daniel Moog
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8
- SYNMIKRO Research Center, Hans-Meerwein-Str. 6, 35032, Marburg, Germany
| | - Samuel Speak
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Krisztina Sarkozi
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew Toseland
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Kaori Oyama
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Misako Kato
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Keitaro Kume
- Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Motoki Kayama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Tomonori Azuma
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Ken-ichiro Ishii
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Hideaki Miyashita
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yuichiro Kashiyama
- Graduate School of Engineering, Fukui University of Technology, Fukui, Japan
| | - Shigeki Mayama
- Advanced Support Center for Science Teachers, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Shin-ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Goro Tanifuji
- Department of Zoology, National Museum of Nature and Science, Tsukuba 305-0005, Japan
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
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13
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Duncan A, Barry K, Daum C, Eloe-Fadrosh E, Roux S, Schmidt K, Tringe SG, Valentin KU, Varghese N, Salamov A, Grigoriev IV, Leggett RM, Moulton V, Mock T. Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans. Microbiome 2022; 10:67. [PMID: 35484634 PMCID: PMC9047304 DOI: 10.1186/s40168-022-01254-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Phytoplankton communities significantly contribute to global biogeochemical cycles of elements and underpin marine food webs. Although their uncultured genomic diversity has been estimated by planetary-scale metagenome sequencing and subsequent reconstruction of metagenome-assembled genomes (MAGs), this approach has yet to be applied for complex phytoplankton microbiomes from polar and non-polar oceans consisting of microbial eukaryotes and their associated prokaryotes. RESULTS Here, we have assembled MAGs from chlorophyll a maximum layers in the surface of the Arctic and Atlantic Oceans enriched for species associations (microbiomes) with a focus on pico- and nanophytoplankton and their associated heterotrophic prokaryotes. From 679 Gbp and estimated 50 million genes in total, we recovered 143 MAGs of medium to high quality. Although there was a strict demarcation between Arctic and Atlantic MAGs, adjacent sampling stations in each ocean had 51-88% MAGs in common with most species associations between Prasinophytes and Proteobacteria. Phylogenetic placement revealed eukaryotic MAGs to be more diverse in the Arctic whereas prokaryotic MAGs were more diverse in the Atlantic Ocean. Approximately 70% of protein families were shared between Arctic and Atlantic MAGs for both prokaryotes and eukaryotes. However, eukaryotic MAGs had more protein families unique to the Arctic whereas prokaryotic MAGs had more families unique to the Atlantic. CONCLUSION Our study provides a genomic context to complex phytoplankton microbiomes to reveal that their community structure was likely driven by significant differences in environmental conditions between the polar Arctic and warm surface waters of the tropical and subtropical Atlantic Ocean. Video Abstract.
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Affiliation(s)
- Anthony Duncan
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Chris Daum
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Emiley Eloe-Fadrosh
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Simon Roux
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Katrin Schmidt
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK
| | - Susannah G Tringe
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Klaus U Valentin
- Alfred-Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Neha Varghese
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | | | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK.
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14
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Abstract
Diatoms, a key group of polar marine microbes, support highly productive ocean ecosystems. Like all life on earth, diatoms do not live in isolation, and they are therefore under constant biotic and abiotic pressures which directly influence their evolution through natural selection. Despite their importance in polar ecosystems, polar diatoms are understudied compared to temperate species. The observed rapid change in the polar climate, especially warming, has created increased research interest to discover the underlying causes and potential consequences on single species to entire ecosystems. Next-Generation Sequencing (NGS) technologies have greatly expanded our knowledge by revealing the molecular underpinnings of physiological adaptations to polar environmental conditions. Their genomes, transcriptomes, and proteomes together with the first eukaryotic meta-omics data of surface ocean polar microbiomes reflect the environmental pressures through adaptive responses such as the expansion of protein families over time as a consequence of selection. Polar regions and their microbiomes are inherently connected to climate cycles and their feedback loops. An integrated understanding built on “omics” resources centered around diatoms as key primary producers will enable us to reveal unifying concepts of microbial co-evolution and adaptation in polar oceans. This knowledge, which aims to relate past environmental changes to specific adaptations, will be required to improve climate prediction models for polar ecosystems because it provides a unifying framework of how interacting and co-evolving biological communities might respond to future environmental change.
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Affiliation(s)
- Reuben Gilbertson
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Emma Langan
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.,The Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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15
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Laundon D, Chrismas N, Bird K, Thomas S, Mock T, Cunliffe M. A cellular and molecular atlas reveals the basis of chytrid development. eLife 2022; 11:73933. [PMID: 35227375 PMCID: PMC8887899 DOI: 10.7554/elife.73933] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/01/2022] [Indexed: 12/26/2022] Open
Abstract
The chytrids (phylum Chytridiomycota) are a major fungal lineage of ecological and evolutionary importance. Despite their importance, many fundamental aspects of chytrid developmental and cell biology remain poorly understood. To address these knowledge gaps, we combined quantitative volume electron microscopy and comparative transcriptome profiling to create an 'atlas' of the cellular and molecular basis of the chytrid life cycle, using the model chytrid Rhizoclosmatium globosum. From our developmental atlas, we describe the transition from the transcriptionally inactive free-swimming zoospore to the more biologically complex germling, and show that lipid processing is multifaceted and dynamic throughout the life cycle. We demonstrate that the chytrid apophysis is a compartmentalised site of high intracellular trafficking, linking the feeding/attaching rhizoids to the reproductive zoosporangium, and constituting division of labour in the chytrid cell plan. We provide evidence that during zoosporogenesis, zoospores display amoeboid morphologies and exhibit endocytotic cargo transport from the interstitial maternal cytoplasm. Taken together, our results reveal insights into chytrid developmental biology and provide a basis for future investigations into non-dikaryan fungal cell biology.
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Affiliation(s)
- Davis Laundon
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom.,School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Nathan Chrismas
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom
| | - Kimberley Bird
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom
| | - Seth Thomas
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Michael Cunliffe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, United Kingdom.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom
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16
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Mao X, Chen J, van Oosterhout C, Zhang H, Liu G, Zhuang Y, Mock T. Diversity, prevalence, and expression of cyanase genes (cynS) in planktonic marine microorganisms. ISME J 2022; 16:602-605. [PMID: 34408267 PMCID: PMC8776842 DOI: 10.1038/s41396-021-01081-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023]
Abstract
Cyanate is utilized by many microbes as an organic nitrogen source. The key enzyme for cyanate metabolism is cyanase, converting cyanate to ammonium and carbon dioxide. Although the cyanase gene cynS has been identified in many species, the diversity, prevalence, and expression of cynS in marine microbial communities remains poorly understood. Here, based on the full-length cDNA sequence of a dinoflagellate cynS and 260 homologs across the tree of life, we extend the conserved nature of cyanases by the identification of additional ultra-conserved residues as part of the modeled holoenzyme structure. Our phylogenetic analysis showed that horizontal gene transfer of cynS appears to be more prominent than previously reported for bacteria, archaea, chlorophytes, and metazoans. Quantitative analyses of marine planktonic metagenomes revealed that cynS is as prevalent as ureC (urease subunit alpha), suggesting that cyanate plays an important role in nitrogen metabolism of marine microbes. Highly abundant cynS transcripts from phytoplankton and nitrite-oxidizing bacteria identified in global ocean metatranscriptomes indicate that cyanases potentially occupy a key position in the marine nitrogen cycle by facilitating photosynthetic assimilation of organic N and its remineralisation to NO3 by the activity of nitrifying bacteria.
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Affiliation(s)
- Xuewei Mao
- grid.4422.00000 0001 2152 3263Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100 China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China ,grid.8273.e0000 0001 1092 7967School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
| | - Jianwei Chen
- grid.21155.320000 0001 2034 1839BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China ,grid.21155.320000 0001 2034 1839Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555 China
| | - Cock van Oosterhout
- grid.8273.e0000 0001 1092 7967School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
| | - Huan Zhang
- grid.63054.340000 0001 0860 4915Department of Marine Sciences, University of Connecticut, Groton, CT 06340 USA
| | - Guangxing Liu
- grid.4422.00000 0001 2152 3263Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100 China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Yunyun Zhuang
- grid.4422.00000 0001 2152 3263Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100 China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Thomas Mock
- grid.8273.e0000 0001 1092 7967School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
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17
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Martin K, Schmidt K, Toseland A, Boulton CA, Barry K, Beszteri B, Brussaard CPD, Clum A, Daum CG, Eloe-Fadrosh E, Fong A, Foster B, Foster B, Ginzburg M, Huntemann M, Ivanova NN, Kyrpides NC, Lindquist E, Mukherjee S, Palaniappan K, Reddy TBK, Rizkallah MR, Roux S, Timmermans K, Tringe SG, van de Poll WH, Varghese N, Valentin KU, Lenton TM, Grigoriev IV, Leggett RM, Moulton V, Mock T. The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole. Nat Commun 2021; 12:5483. [PMID: 34531387 PMCID: PMC8446083 DOI: 10.1038/s41467-021-25646-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023] Open
Abstract
Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although differences in their local species diversity have been estimated, we still have a limited understanding of environmental conditions responsible for compositional differences between local species communities on a large scale from pole to pole. Here, we show, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNA sequencing, that environmental differences between polar and non-polar upper oceans most strongly impact the large-scale spatial pattern of biodiversity and gene activity in algal microbiomes. The geographic differentiation of co-occurring microbes in algal microbiomes can be well explained by the latitudinal temperature gradient and associated break points in their beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warm upper oceans. As global warming impacts upper ocean temperatures, we project that break points of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algal microbiomes could be caused by anthropogenic climate change.
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Affiliation(s)
- Kara Martin
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Katrin Schmidt
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew Toseland
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bánk Beszteri
- Department of Biology, University of Duisburg-Essen, Essen, Essen, Germany
| | | | - Alicia Clum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris G Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Emiley Eloe-Fadrosh
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Allison Fong
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Brian Foster
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bryce Foster
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael Ginzburg
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Marcel Huntemann
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia N Ivanova
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikos C Kyrpides
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Erika Lindquist
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Supratim Mukherjee
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Krishnaveni Palaniappan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - T B K Reddy
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mariam R Rizkallah
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Simon Roux
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Klaas Timmermans
- Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Susannah G Tringe
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Willem H van de Poll
- Centre for Isotope Research - Oceans, Energy and Sustainability Research Institute Groningen, Faculty of Science and Engineering, University of Groningen, AG Groningen, The Netherlands
| | - Neha Varghese
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Klaus U Valentin
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | | | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Plant and Microbial Biology Department, University of California, Berkeley, CA, USA
| | | | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
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18
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Graff van Creveld S, Ben-Dor S, Mizrachi A, Alcolombri U, Hopes A, Mock T, Rosenwasser S, Vardi A. Biochemical Characterization of a Novel Redox-Regulated Metacaspase in a Marine Diatom. Front Microbiol 2021; 12:688199. [PMID: 34566902 PMCID: PMC8455989 DOI: 10.3389/fmicb.2021.688199] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/16/2021] [Indexed: 11/24/2022] Open
Abstract
Programmed cell death (PCD) in marine microalgae was suggested to be one of the mechanisms that facilitates bloom demise, yet its molecular components in phytoplankton are unknown. Phytoplankton are completely lacking any of the canonical components of PCD, such as caspases, but possess metacaspases. Metacaspases were shown to regulate PCD in plants and some protists, but their roles in algae and other organisms are still elusive. Here, we identified and biochemically characterized a type III metacaspase from the model diatom Phaeodactylum tricornutum, termed PtMCA-IIIc. Through expression of recombinant PtMCA-IIIc in E. coli, we revealed that PtMCA-IIIc exhibits a calcium-dependent protease activity, including auto-processing and cleavage after arginine. Similar metacaspase activity was detected in P. tricornutum cell extracts. PtMCA-IIIc overexpressing cells exhibited higher metacaspase activity, while CRISPR/Cas9-mediated knockout cells had decreased metacaspase activity compared to WT cells. Site-directed mutagenesis of cysteines that were predicted to form a disulfide bond decreased recombinant PtMCA-IIIc activity, suggesting its enhancement under oxidizing conditions. One of those cysteines was oxidized, detected in redox proteomics, specifically in response to lethal concentrations of hydrogen peroxide and a diatom derived aldehyde. Phylogenetic analysis revealed that this cysteine-pair is unique and widespread among diatom type III metacaspases. The characterization of a cell death associated protein in diatoms provides insights into the evolutionary origins of PCD and its ecological significance in algal bloom dynamics.
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Affiliation(s)
- Shiri Graff van Creveld
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Avia Mizrachi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Uria Alcolombri
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Civil, Environmental and Geomatic Engineering, Institute for Environmental Engineering, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Shilo Rosenwasser
- Robert H. Smith Faculty of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
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19
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Mock T. Silicon drives the evolution of complex crystal morphology in calcifying algae. New Phytol 2021; 231:1663-1666. [PMID: 34165808 DOI: 10.1111/nph.17507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/19/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR47TJ, UK
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20
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Bulankova P, Sekulić M, Jallet D, Nef C, van Oosterhout C, Delmont TO, Vercauteren I, Osuna-Cruz CM, Vancaester E, Mock T, Sabbe K, Daboussi F, Bowler C, Vyverman W, Vandepoele K, De Veylder L. Mitotic recombination between homologous chromosomes drives genomic diversity in diatoms. Curr Biol 2021; 31:3221-3232.e9. [PMID: 34102110 DOI: 10.1016/j.cub.2021.05.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/17/2021] [Accepted: 05/06/2021] [Indexed: 01/31/2023]
Abstract
Diatoms, an evolutionarily successful group of microalgae, display high levels of intraspecific genetic variability in natural populations. However, the contribution of various mechanisms generating such diversity is unknown. Here we estimated the genetic micro-diversity within a natural diatom population and mapped the genomic changes arising within clonally propagated diatom cell cultures. Through quantification of haplotype diversity by next-generation sequencing and amplicon re-sequencing of selected loci, we documented a rapid accumulation of multiple haplotypes accompanied by the appearance of novel protein variants in cell cultures initiated from a single founder cell. Comparison of the genomic changes between mother and daughter cells revealed copy number variation and copy-neutral loss of heterozygosity leading to the fixation of alleles within individual daughter cells. The loss of heterozygosity can be accomplished by recombination between homologous chromosomes. To test this hypothesis, we established an endogenous readout system and estimated that the frequency of interhomolog mitotic recombination was under standard growth conditions 4.2 events per 100 cell divisions. This frequency is increased under environmental stress conditions, including treatment with hydrogen peroxide and cadmium. These data demonstrate that copy number variation and mitotic recombination between homologous chromosomes underlie clonal variability in diatom populations. We discuss the potential adaptive evolutionary benefits of the plastic response in the interhomolog mitotic recombination rate, and we propose that this may have contributed to the ecological success of diatoms.
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Affiliation(s)
- Petra Bulankova
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.
| | - Mirna Sekulić
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Denis Jallet
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 135 Avenue de Rangueil, 31077 Toulouse, France
| | - Charlotte Nef
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Tom O Delmont
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
| | - Ilse Vercauteren
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Cristina Maria Osuna-Cruz
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Emmelien Vancaester
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Koen Sabbe
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Fayza Daboussi
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 135 Avenue de Rangueil, 31077 Toulouse, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Wim Vyverman
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Klaas Vandepoele
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
| | - Lieven De Veylder
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.
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21
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Teng L, Han W, Fan X, Zhang X, Xu D, Wang Y, Rahman S, Pellegrini M, Mock T, Ye N. Integrative analysis of chloroplast DNA methylation in a marine alga-Saccharina japonica. Plant Mol Biol 2021; 105:611-623. [PMID: 33528753 DOI: 10.1007/s11103-020-01113-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 12/30/2020] [Indexed: 05/17/2023]
Abstract
KEY MESSAGE We applied an integrative approach using multiple methods to verify cytosine methylation in the chloroplast DNA of the multicellular brown alga Saccharina japonica. Cytosine DNA methylation is a heritable process which plays important roles in regulating development throughout the life cycle of an organism. Although methylation of nuclear DNA has been studied extensively, little is known about the state and role of DNA methylation in chloroplast genomes, especially in marine algae. Here, we have applied an integrated approach encompassing whole-genome bisulfite sequencing, methylated DNA immunoprecipitation, gene co-expression networks and photophysiological analyses to provide evidence for the role of chloroplast DNA methylation in a marine alga, the multicellular brown alga Saccharina japonica. Although the overall methylation level was relatively low in the chloroplast genome of S. japonica, gametophytes exhibited higher methylation levels than sporophytes. Gene-specific bisulfite-cloning sequencing provided additional evidence for the methylation of key photosynthetic genes. Many of them were highly expressed in sporophytes whereas genes involved in transcription, translation and biosynthesis were strongly expressed in gametophytes. Nucleus-encoded photosynthesis genes were co-expressed with their chloroplast-encoded counterparts potentially contributing to the higher photosynthetic performance in sporophytes compared to gametophytes where these co-expression networks were less pronounced. A nucleus-encoded DNA methyltransferase of the DNMT2 family is assumed to be responsible for the methylation of the chloroplast genome because it is predicted to possess a plastid transit peptide.
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Affiliation(s)
- Linhong Teng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Life Science, Dezhou University, Dezhou, 253023, China
| | - Wentao Han
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Yitao Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Sadequr Rahman
- Tropical Medicine and Biology Platform and School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, Institute for Genomics and Proteomics, University of California, Los Angeles, CA, 90095, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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22
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Osuna-Cruz CM, Bilcke G, Vancaester E, De Decker S, Bones AM, Winge P, Poulsen N, Bulankova P, Verhelst B, Audoor S, Belisova D, Pargana A, Russo M, Stock F, Cirri E, Brembu T, Pohnert G, Piganeau G, Ferrante MI, Mock T, Sterck L, Sabbe K, De Veylder L, Vyverman W, Vandepoele K. Author Correction: The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms. Nat Commun 2020; 11:5331. [PMID: 33067470 PMCID: PMC7567852 DOI: 10.1038/s41467-020-19222-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Cristina Maria Osuna-Cruz
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Gust Bilcke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.,Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000, Ghent, Belgium
| | - Emmelien Vancaester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Sam De Decker
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Atle M Bones
- Cell Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Per Winge
- Cell Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Nicole Poulsen
- B CUBE Center for Molecular Bioengineering, Technical University of Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Petra Bulankova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Bram Verhelst
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Sien Audoor
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Darja Belisova
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Aikaterini Pargana
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Monia Russo
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | - Frederike Stock
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Emilio Cirri
- Friedrich Schiller University Jena, Institute of Inorganic and Analytical Chemistry, Lessingstrasse 8, 07745, Jena, Germany
| | - Tore Brembu
- Cell Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Georg Pohnert
- Friedrich Schiller University Jena, Institute of Inorganic and Analytical Chemistry, Lessingstrasse 8, 07745, Jena, Germany
| | - Gwenael Piganeau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins BIOM, Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | | | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Koen Sabbe
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Wim Vyverman
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium. .,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium. .,Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.
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23
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Postel U, Glemser B, Salazar Alekseyeva K, Eggers SL, Groth M, Glöckner G, John U, Mock T, Klemm K, Valentin K, Beszteri B. Adaptive divergence across Southern Ocean gradients in the pelagic diatom
Fragilariopsis kerguelensis. Mol Ecol 2020; 29:4913-4924. [DOI: 10.1111/mec.15554] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/20/2020] [Accepted: 07/08/2020] [Indexed: 01/16/2023]
Affiliation(s)
- Ute Postel
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
- Institute for Biochemistry I University Cologne Cologne Germany
- University of Duisburg‐Essen Essen Germany
| | - Barbara Glemser
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
| | - Katherine Salazar Alekseyeva
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
- Department of Functional and Evolutionary Ecology University of Vienna Vienna Austria
| | - Sarah Lena Eggers
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
| | - Marco Groth
- Leibniz Institute on Aging ‐ Fritz Lipmann Institute (FLI) Jena Germany
| | - Gernot Glöckner
- Institute for Biochemistry I University Cologne Cologne Germany
| | - Uwe John
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg Oldenburg Germany
| | - Thomas Mock
- University of East AngliaNorwich Research Park Norwich UK
| | - Kerstin Klemm
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
| | - Klaus Valentin
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
| | - Bánk Beszteri
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
- University of Duisburg‐Essen Essen Germany
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24
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Osuna-Cruz CM, Bilcke G, Vancaester E, De Decker S, Bones AM, Winge P, Poulsen N, Bulankova P, Verhelst B, Audoor S, Belisova D, Pargana A, Russo M, Stock F, Cirri E, Brembu T, Pohnert G, Piganeau G, Ferrante MI, Mock T, Sterck L, Sabbe K, De Veylder L, Vyverman W, Vandepoele K. The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms. Nat Commun 2020; 11:3320. [PMID: 32620776 PMCID: PMC7335047 DOI: 10.1038/s41467-020-17191-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/12/2020] [Indexed: 12/15/2022] Open
Abstract
Benthic diatoms are the main primary producers in shallow freshwater and coastal environments, fulfilling important ecological functions such as nutrient cycling and sediment stabilization. However, little is known about their evolutionary adaptations to these highly structured but heterogeneous environments. Here, we report a reference genome for the marine biofilm-forming diatom Seminavis robusta, showing that gene family expansions are responsible for a quarter of all 36,254 protein-coding genes. Tandem duplications play a key role in extending the repertoire of specific gene functions, including light and oxygen sensing, which are probably central for its adaptation to benthic habitats. Genes differentially expressed during interactions with bacteria are strongly conserved in other benthic diatoms while many species-specific genes are strongly upregulated during sexual reproduction. Combined with re-sequencing data from 48 strains, our results offer insights into the genetic diversity and gene functions in benthic diatoms.
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Affiliation(s)
- Cristina Maria Osuna-Cruz
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Gust Bilcke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000, Ghent, Belgium
| | - Emmelien Vancaester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Sam De Decker
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Atle M Bones
- Cell Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Per Winge
- Cell Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Nicole Poulsen
- B CUBE Center for Molecular Bioengineering, Technical University of Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Petra Bulankova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Bram Verhelst
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Sien Audoor
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Darja Belisova
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Aikaterini Pargana
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Monia Russo
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | - Frederike Stock
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Emilio Cirri
- Friedrich Schiller University Jena, Institute of Inorganic and Analytical Chemistry, Lessingstrasse 8, 07745, Jena, Germany
| | - Tore Brembu
- Cell Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Georg Pohnert
- Friedrich Schiller University Jena, Institute of Inorganic and Analytical Chemistry, Lessingstrasse 8, 07745, Jena, Germany
| | - Gwenael Piganeau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins BIOM, Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | | | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Koen Sabbe
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Wim Vyverman
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.
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25
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Mahato B, Kaya KD, Fan Y, Sumien N, Shetty RA, Zhang W, Davis D, Mock T, Batabyal S, Ni A, Mohanty S, Han Z, Farjo R, Forster MJ, Swaroop A, Chavala SH. Pharmacologic fibroblast reprogramming into photoreceptors restores vision. Nature 2020; 581:83-88. [PMID: 32376950 PMCID: PMC7469946 DOI: 10.1038/s41586-020-2201-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/10/2020] [Indexed: 12/14/2022]
Abstract
Photoreceptor loss is the final common endpoint in most retinopathies that lead to irreversible blindness, and there are no effective treatments to restore vision1,2. Chemical reprogramming of fibroblasts offers an opportunity to reverse vision loss; however, the generation of sensory neuronal subtypes such as photoreceptors remains a challenge. Here we report that the administration of a set of five small molecules can chemically induce the transformation of fibroblasts into rod photoreceptor-like cells. The transplantation of these chemically induced photoreceptor-like cells (CiPCs) into the subretinal space of rod degeneration mice (homozygous for rd1, also known as Pde6b) leads to partial restoration of the pupil reflex and visual function. We show that mitonuclear communication is a key determining factor for the reprogramming of fibroblasts into CiPCs. Specifically, treatment with these five compounds leads to the translocation of AXIN2 to the mitochondria, which results in the production of reactive oxygen species, the activation of NF-κB and the upregulation of Ascl1. We anticipate that CiPCs could have therapeutic potential for restoring vision.
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Affiliation(s)
- Biraj Mahato
- Department of Pharmacology and Neuroscience, Laboratory for Retinal Rehabilitation, North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Koray Dogan Kaya
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yan Fan
- Department of Pharmacology and Neuroscience, Laboratory for Retinal Rehabilitation, North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Nathalie Sumien
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Ritu A Shetty
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Wei Zhang
- Department of Pharmacology and Neuroscience, Laboratory for Retinal Rehabilitation, North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Delaney Davis
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Thomas Mock
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA
| | | | - Aiguo Ni
- Department of Pharmacology and Neuroscience, Laboratory for Retinal Rehabilitation, North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX, USA
| | | | - Zongchao Han
- Department of Ophthalmology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Michael J Forster
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sai H Chavala
- Department of Pharmacology and Neuroscience, Laboratory for Retinal Rehabilitation, North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX, USA.
- CIRC Therapeutics, Inc., Dallas, TX, USA.
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26
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Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J. Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nat Methods 2020; 17:551. [PMID: 32296171 PMCID: PMC7200595 DOI: 10.1038/s41592-020-0828-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
| | - R Ellen R Nisbet
- Department of Biochemistry, University of Cambridge, Cambridge, UK.,School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | | | - Elena Casacuberta
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Lisa Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Andrew E Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.,Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Manuel Ares
- Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Cristina Aresté
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Cecilia Balestreri
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | | | - Patrick Beardslee
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Sara Bender
- Gordon and Betty Moore Foundation, Palo Alto, CA, USA
| | - David S Booth
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - François-Yves Bouget
- Sorbonne Université, CNRS UMR7621, Observatoire Océanologique, Banyuls sur Mer, France
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Susana A Breglia
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Colin Brownlee
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Heriberto Cerutti
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Rachele Cesaroni
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Miguel A Chiurillo
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Thomas Clemente
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Duncan B Coles
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Jackie L Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Elizabeth C Cooney
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathryn Coyne
- University of Delaware College of Earth, Ocean and Environment, Lewes, DE, USA
| | - Roberto Docampo
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Christopher L Dupont
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | | | - Elin Einarsson
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Pía A Elustondo
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada.,AGADA Biosciences Inc., Halifax, Nova Scotia, Canada
| | - Fernan Federici
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Veronica Freire-Beneitez
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Laboratory of Molecular and Evolutionary Parasitology, University of Kent, Kent, UK
| | | | - Kodai Fukuda
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Paulo A García
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Boston, MA, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Fatma Gomaa
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Sebastian G Gornik
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Jian Guo
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Yutaka Hanawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Esteban R Haro-Contreras
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Elisabeth Hehenberger
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrea Highfield
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Yoshihisa Hirakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | | | - Ian Hu
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jorge Ibañez
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yuu Ishii
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Natalia Ewa Janowicz
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Adam C Jones
- Gordon and Betty Moore Foundation, Palo Alto, CA, USA
| | - Ambar Kachale
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | - Konomi Fujimura-Kamada
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Binnypreet Kaur
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | | | - Eleanna Kazana
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Laboratory of Molecular and Evolutionary Parasitology, University of Kent, Kent, UK
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicole King
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Noelia Lander
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Zhuhong Li
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Jean-Claude Lozano
- Sorbonne Université, CNRS UMR7621, Observatoire Océanologique, Banyuls sur Mer, France
| | - Fulei Luan
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | | | - Tamara Matute
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Aichi, Japan.,Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki, Aichi, Japan
| | - Mark Moosburner
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.,Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Sebastián R Najle
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.,Instituto de Biología Molecular y Celular, CONICET, and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Deepak Nanjappa
- University of Delaware College of Earth, Ocean and Environment, Lewes, DE, USA
| | - Isabel C Nimmo
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Luke Noble
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.,Institute de Biologie de l'ENS, Département de biologie, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Anna M G Novák Vanclová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Isaac Nuñez
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Arnab Pain
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Center for Zoonosis Control, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Angela Piersanti
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Jan Pyrih
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Joshua S Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Mariana Rius
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | | | - Albane Ruaud
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.,Departament de Genètica Microbiologia i Estadıśtica, Universitat de Barcelona, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Monika A Sigg
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Claudio H Slamovits
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - G Jason Smith
- Department of Environmental Biotechnology, Moss Landing Marine Laboratories, Moss Landing, CA, USA
| | | | - Rowena Stern
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Estienne C Swart
- Institute of Cell Biology, University of Bern, Bern, Switzerland.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Anastasios D Tsaousis
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Laboratory of Molecular and Evolutionary Parasitology, University of Kent, Kent, UK
| | - Lev Tsypin
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA.,Department of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Aaron Turkewitz
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Jernej Turnšek
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.,Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Valérie Vergé
- Sorbonne Université, CNRS UMR7621, Observatoire Océanologique, Banyuls sur Mer, France
| | - Peter von Dassow
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile.,Instituto Milenio de Oceanografia de Chile, Concepción, Chile
| | | | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Lu Wang
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Xiaoxue Wen
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Glen Wheeler
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - April Woods
- Department of Environmental Biotechnology, Moss Landing Marine Laboratories, Moss Landing, CA, USA
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, UK.
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA. .,Ocean EcoSystems Biology Unit, Marine Ecology Division, Helmholtz Centre for Ocean Research, Kiel, Germany.
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
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27
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Falciatore A, Jaubert M, Bouly JP, Bailleul B, Mock T. Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity. Plant Cell 2020; 32:547-572. [PMID: 31852772 PMCID: PMC7054031 DOI: 10.1105/tpc.19.00158] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/18/2019] [Accepted: 12/13/2019] [Indexed: 05/08/2023]
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.
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Affiliation(s)
- Angela Falciatore
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Marianne Jaubert
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Jean-Pierre Bouly
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Benjamin Bailleul
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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Waldvogel AM, Feldmeyer B, Rolshausen G, Exposito-Alonso M, Rellstab C, Kofler R, Mock T, Schmid K, Schmitt I, Bataillon T, Savolainen O, Bergland A, Flatt T, Guillaume F, Pfenninger M. Evolutionary genomics can improve prediction of species' responses to climate change. Evol Lett 2020; 4:4-18. [PMID: 32055407 PMCID: PMC7006467 DOI: 10.1002/evl3.154] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/31/2019] [Accepted: 11/26/2019] [Indexed: 01/08/2023] Open
Abstract
Global climate change (GCC) increasingly threatens biodiversity through the loss of species, and the transformation of entire ecosystems. Many species are challenged by the pace of GCC because they might not be able to respond fast enough to changing biotic and abiotic conditions. Species can respond either by shifting their range, or by persisting in their local habitat. If populations persist, they can tolerate climatic changes through phenotypic plasticity, or genetically adapt to changing conditions depending on their genetic variability and census population size to allow for de novo mutations. Otherwise, populations will experience demographic collapses and species may go extinct. Current approaches to predicting species responses to GCC begin to combine ecological and evolutionary information for species distribution modelling. Including an evolutionary dimension will substantially improve species distribution projections which have not accounted for key processes such as dispersal, adaptive genetic change, demography, or species interactions. However, eco‐evolutionary models require new data and methods for the estimation of a species' adaptive potential, which have so far only been available for a small number of model species. To represent global biodiversity, we need to devise large‐scale data collection strategies to define the ecology and evolutionary potential of a broad range of species, especially of keystone species of ecosystems. We also need standardized and replicable modelling approaches that integrate these new data to account for eco‐evolutionary processes when predicting the impact of GCC on species' survival. Here, we discuss different genomic approaches that can be used to investigate and predict species responses to GCC. This can serve as guidance for researchers looking for the appropriate experimental setup for their particular system. We furthermore highlight future directions for moving forward in the field and allocating available resources more effectively, to implement mitigation measures before species go extinct and ecosystems lose important functions.
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Affiliation(s)
- Ann-Marie Waldvogel
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany
| | | | | | - Robert Kofler
- Institute of Population Genetics Vetmeduni Vienna Austria
| | - Thomas Mock
- School of Environmental Sciences University of East Anglia Norwich United Kingdom
| | - Karl Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics University of Hohenheim Stuttgart Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany.,Institute of Ecology, Evolution and Diversity Goethe-University Frankfurt am Main Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) Frankfurt am Main Germany
| | | | - Outi Savolainen
- Department of Ecology and Genetics University of Oulu Finland
| | - Alan Bergland
- Department of Biology University of Virginia Charlottesville Virginia
| | - Thomas Flatt
- Department of Biology University of Fribourg Fribourg Switzerland
| | - Frederic Guillaume
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zürich Switzerland
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre Frankfurt am Main Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) Frankfurt am Main Germany.,Institute for Organismic and Molecular Evolution Johannes Gutenberg University Mainz Germany
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Fan X, Han W, Teng L, Jiang P, Zhang X, Xu D, Li C, Pellegrini M, Wu C, Wang Y, Kaczurowski MJS, Lin X, Tirichine L, Mock T, Ye N. Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants. New Phytol 2020; 225:234-249. [PMID: 31419316 PMCID: PMC6916402 DOI: 10.1111/nph.16125] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 08/06/2019] [Indexed: 05/28/2023]
Abstract
Brown algae have convergently evolved plant-like body plans and reproductive cycles, which in plants are controlled by differential DNA methylation. This contribution provides the first single-base methylome profiles of haploid gametophytes and diploid sporophytes of a multicellular alga. Although only c. 1.4% of cytosines in Saccharina japonica were methylated mainly at CHH sites and characterized by 5-methylcytosine (5mC), there were significant differences between life-cycle stages. DNA methyltransferase 2 (DNMT2), known to efficiently catalyze tRNA methylation, is assumed to methylate the genome of S. japonica in the structural context of tRNAs as the genome does not encode any other DNA methyltransferases. Circular and long noncoding RNA genes were the most strongly methylated regulatory elements in S. japonica. Differential expression of genes was negatively correlated with DNA methylation with the highest methylation levels measured in both haploid gametophytes. Hypomethylated and highly expressed genes in diploid sporophytes included genes involved in morphogenesis and halogen metabolism. The data herein provide evidence that cytosine methylation, although occurring at a low level, is significantly contributing to the formation of different life-cycle stages, tissue differentiation and metabolism in brown algae.
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Affiliation(s)
- Xiao Fan
- Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoChina
- Function Laboratory for Marine Fisheries Science and Food Production ProcessesQingdaoChina
- Key Laboratory of Exploration and Utilization of Aquatic Genetic ResourcesMinistry of EducationShanghai Ocean UniversityShanghai201306China
| | - Wentao Han
- Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoChina
| | - Linhong Teng
- Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoChina
- College of Life ScienceDezhou UniversityDezhou253023China
- Shandong Key Laboratory of BiophysicsDezhou UniversityDezhou253023China
| | - Peng Jiang
- Institute of OceanologyChinese Academy of SciencesQingdao266071China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoChina
| | - Dong Xu
- Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoChina
| | - Chang Li
- University of Chinese Academy of SciencesShenzhenChina
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental BiologyInstitute for Genomics and ProteomicsUniversity of CaliforniaLos AngelesCA90095USA
| | - Chunhui Wu
- Institute of OceanologyChinese Academy of SciencesQingdao266071China
| | - Yitao Wang
- Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoChina
| | | | - Xin Lin
- State Key Laboratory of Marine Environmental ScienceCollege of Ocean & Earth SciencesXiamen UniversityXiamenChina
| | - Leila Tirichine
- CNRS UMR 6286Faculté des Sciences et des TechniquesUniversité de Nantes2 rue de la Houssinière44322NantesFrance
| | - Thomas Mock
- School of Environmental SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Naihao Ye
- Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoChina
- Function Laboratory for Marine Fisheries Science and Food Production ProcessesQingdaoChina
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Häfliger IM, Hofstetter S, Mock T, Stettler MH, Meylan M, Mehinagic K, Stokar-Regenscheit N, Drögemüller C. APOB-associated cholesterol deficiency in Holstein cattle is not a simple recessive disease. Anim Genet 2019; 50:372-375. [PMID: 31215050 PMCID: PMC7159454 DOI: 10.1111/age.12801] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2019] [Indexed: 11/27/2022]
Abstract
In 2015, cholesterol deficiency (CD) was reported for the first time as a new recessive defect in Holstein cattle. After GWAS mapping and identification of a disease-associated haplotype, a causative loss-of-function variant in APOB was identified. CD-clinically affected APOB homozygotes showed poor development, intermittent diarrhea and hypocholesterolemia and, consequently, a limited life expectation. Herein, we present a collection of 18 cases clinically diagnosed as CD-affected APOB heterozygotes. CD-clinically affected heterozygotes show reduced cholesterol and triglyceride blood concentrations. The differences in total blood cholesterol and triglycerides between nine CD-clinically affected and 36 non-affected heterozygotes were significant. As only some APOB heterozygotes show the clinical CD phenotype, we assume that the penetrance is reduced in heterozygotes compared to the fully penetrant effect observed in homozygotes. We conclude that APOB-associated CD represents most likely an incomplete dominant inherited metabolic disease with incomplete penetrance in heterozygotes.
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Affiliation(s)
- Irene Monika Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Sonja Hofstetter
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Thomas Mock
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | | | - Mireille Meylan
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Kemal Mehinagic
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
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Laundon D, Wheeler G, Mock T, Cunliffe M. Shining new lights on chytrid cell biology: quantitative live cell imaging of rhizoid development in an early-diverging fungus. Access Microbiol 2019. [DOI: 10.1099/acmi.ac2019.po0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Davis Laundon
- 1The Marine Biological Association, Plymouth, United Kingdom
- 2University of East Anglia, Norwich, United Kingdom
| | - Glen Wheeler
- 1The Marine Biological Association, Plymouth, United Kingdom
| | - Thomas Mock
- 2University of East Anglia, Norwich, United Kingdom
| | - Michael Cunliffe
- 3Plymouth University, Plymouth, United Kingdom
- 1The Marine Biological Association, Plymouth, United Kingdom
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32
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Xu D, Brennan G, Xu L, Zhang XW, Fan X, Han WT, Mock T, McMinn A, Hutchins DA, Ye N. Ocean acidification increases iodine accumulation in kelp-based coastal food webs. Glob Chang Biol 2019; 25:629-639. [PMID: 30295390 DOI: 10.1111/gcb.14467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
Kelp are main iodine accumulators in the ocean, and their growth and photosynthesis are likely to benefit from elevated seawater CO2 levels due to ocean acidification. However, there are currently no data on the effects of ocean acidification on iodine metabolism in kelp. As key primary producers in coastal ecosystems worldwide, any change in their iodine metabolism caused by climate change will potentially have important consequences for global geochemical cycles of iodine, including iodine levels of coastal food webs that underpin the nutrition of billions of humans around the world. Here, we found that elevated pCO2 enhanced growth and increased iodine accumulation not only in the model kelp Saccharina japonica using both short-term laboratory experiment and long-term in situ mesocosms, but also in several other edible and ecologically significant seaweeds using long-term in situ mesocosms. Transcriptomic and proteomic analysis of S. japonica revealed that most vanadium-dependent haloperoxidase genes involved in iodine efflux during oxidative stress are down-regulated under increasing pCO2 , suggesting that ocean acidification alleviates oxidative stress in kelp, which might contribute to their enhanced growth. When consumed by abalone (Haliotis discus), elevated iodine concentrations in S. japonica caused increased iodine accumulation in abalone, accompanied by reduced synthesis of thyroid hormones. Thus, our results suggest that kelp will benefit from ocean acidification by a reduction in environmental stress however; iodine levels, in kelp-based coastal food webs will increase, with potential impacts on biogeochemical cycles of iodine in coastal ecosystems.
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Affiliation(s)
- Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Georgina Brennan
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, UK
| | - Le Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiao W Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Wen T Han
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Andrew McMinn
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
- Fisheries College, Ocean University of China, Qingdao, China
| | - David A Hutchins
- Department of Biological Sciences, University of Southern California, Los Angeles, California
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Hopes A, Nekrasov V, Belshaw N, Grouneva I, Kamoun S, Mock T. Genome Editing in Diatoms Using CRISPR-Cas to Induce Precise Bi-allelic Deletions. Bio Protoc 2017; 7:e2625. [PMID: 34595293 PMCID: PMC8438374 DOI: 10.21769/bioprotoc.2625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/21/2017] [Accepted: 11/01/2017] [Indexed: 11/02/2022] Open
Abstract
Genome editing in diatoms has recently been established for the model species Phaeodactylum tricornutum and Thalassiosira pseudonana. The present protocol, although developed for T. pseudonana, can be modified to edit any diatom genome as we utilize the flexible, modular Golden Gate cloning system. The main steps include how to design a construct using Golden Gate cloning for targeting two sites, allowing a precise deletion to be introduced into the target gene. The transformation protocol is explained, as are the methods for screening using band shift assay and/or restriction site loss.
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Affiliation(s)
- Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Nigel Belshaw
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Irina Grouneva
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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Brodie J, Ball SG, Bouget FY, Chan CX, De Clerck O, Cock JM, Gachon C, Grossman AR, Mock T, Raven JA, Saha M, Smith AG, Vardi A, Yoon HS, Bhattacharya D. Biotic interactions as drivers of algal origin and evolution. New Phytol 2017; 216:670-681. [PMID: 28857164 DOI: 10.1111/nph.14760] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/10/2017] [Indexed: 05/07/2023]
Abstract
Contents 670 I. 671 II. 671 III. 676 IV. 678 678 References 678 SUMMARY: Biotic interactions underlie life's diversity and are the lynchpin to understanding its complexity and resilience within an ecological niche. Algal biologists have embraced this paradigm, and studies building on the explosive growth in omics and cell biology methods have facilitated the in-depth analysis of nonmodel organisms and communities from a variety of ecosystems. In turn, these advances have enabled a major revision of our understanding of the origin and evolution of photosynthesis in eukaryotes, bacterial-algal interactions, control of massive algal blooms in the ocean, and the maintenance and degradation of coral reefs. Here, we review some of the most exciting developments in the field of algal biotic interactions and identify challenges for scientists in the coming years. We foresee the development of an algal knowledgebase that integrates ecosystem-wide omics data and the development of molecular tools/resources to perform functional analyses of individuals in isolation and in populations. These assets will allow us to move beyond mechanistic studies of a single species towards understanding the interactions amongst algae and other organisms in both the laboratory and the field.
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Affiliation(s)
- Juliet Brodie
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Steven G Ball
- UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille CNRS, F 59000, Lille, France
| | - François-Yves Bouget
- Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, University Pierre et Marie Curie, University of Paris VI, CNRS, F-66650, Banyuls-sur-Mer, France
| | - Cheong Xin Chan
- Institute for Molecular Bioscience and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Olivier De Clerck
- Phycology Research Group, Ghent University, Krijgslaan 281, S8, 9000, Gent, Belgium
| | - J Mark Cock
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, F-29688, France
| | | | - Arthur R Grossman
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
| | - Mahasweta Saha
- Helmholtz Center for Ocean Research, Kiel, 24105, Germany
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
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Kirkham AR, Richthammer P, Schmidt K, Wustmann M, Maeda Y, Hedrich R, Brunner E, Tanaka T, van Pée KH, Falciatore A, Mock T. A role for the cell-wall protein silacidin in cell size of the diatom Thalassiosira pseudonana. ISME J 2017; 11:2452-2464. [PMID: 28731468 PMCID: PMC5649158 DOI: 10.1038/ismej.2017.100] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/28/2017] [Accepted: 05/19/2017] [Indexed: 01/06/2023]
Abstract
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.
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Affiliation(s)
- Amy R Kirkham
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Katrin Schmidt
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Yoshiaki Maeda
- Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - René Hedrich
- Allgemeine Biochemie, TU Dresden, Dresden, Germany
| | - Eike Brunner
- Allgemeine Biochemie, TU Dresden, Dresden, Germany
| | - Tsuyoshi Tanaka
- Tokyo University of Agriculture and Technology, Tokyo, Japan
| | | | - Angela Falciatore
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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Paajanen P, Strauss J, van Oosterhout C, McMullan M, Clark MD, Mock T. Building a locally diploid genome and transcriptome of the diatom Fragilariopsis cylindrus. Sci Data 2017; 4:170149. [PMID: 28994819 PMCID: PMC5634323 DOI: 10.1038/sdata.2017.149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/22/2017] [Indexed: 11/30/2022] Open
Abstract
The genome of the cold-adapted diatom Fragilariopsis cylindrus is characterized by highly diverged haplotypes that intersperse its homozygous genome. Here, we describe how a combination of PacBio DNA and Illumina RNA sequencing can be used to resolve this complex genomic landscape locally into the highly diverged haplotypes, and how to map various environmentally controlled transcripts onto individual haplotypes. We assembled PacBio sequence data with the FALCON assembler and created a haplotype resolved annotation of the assembly using annotations of a Sanger sequenced F. cylindrus genome. RNA-seq datasets from six different growth conditions were used to resolve allele-specifc gene expression in F. cylindrus. This approach enables to study differential expression of alleles in a complex genomic landscape and provides a useful tool to study how diverged haplotypes in diploid organisms are used for adaptation and evolution to highly variable environments.
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Affiliation(s)
- Pirita Paajanen
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jan Strauss
- European Molecular Biology Laboratory (EMBL) Hamburg, c/o German Electron Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Mark McMullan
- Earlham Institute, Norwich Research Park, Norwich NR4 7HU, UK
| | - Matthew D. Clark
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- Earlham Institute, Norwich Research Park, Norwich NR4 7HU, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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Singh AK, Sharma N, Farooqi H, Abdin MZ, Mock T, Kumar S. Phycoremediation of municipal wastewater by microalgae to produce biofuel. Int J Phytoremediation 2017; 19:805-812. [PMID: 28156133 DOI: 10.1080/15226514.2017.1284758] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Municipal wastewater (WW), if not properly remediated, poses a threat to the environment and human health by carrying significant loads of nutrients and pathogens. These contaminants pollute rivers, lakes, and natural reservoirs where they cause eutrophication and pathogen-mediated diseases. However, the high nutrient content of WW makes it an ideal environment for remediation with microalgae that require high nutrient concentrations for growth and are not susceptible to toxins and pathogens. Given that an appropriate algal strain is used for remediation, the incurred biomass can be refined for the production of biofuel. Four microalgal species (Chlamydomonas reinhardtii, Chlorella sp., Parachlorella kessleri-I, and Nannochloropsis gaditana) were screened for efficient phycoremediation of municipal WW and potential use for biodiesel production. Among the four strains tested, P. kessleri-I showed the highest growth rate and biomass production in 100% WW. It efficiently removed all major nutrients with a removal rate of up to 98% for phosphate after 10 days of growth in 100% municipal WW collected from Delhi. The growth of P. kessleri-I in WW resulted in a 50% increase of biomass and a 115% increase of lipid yield in comparison to growth in control media. The Fatty acid methyl ester (FAME), and fuel properties of lipids isolated from cells grown in WW complied with international standards. The present study provides evidence that the green alga P. kessleri-I effectively remediates municipal WW and can be used to produce biodiesel.
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Affiliation(s)
- Amit Kumar Singh
- a International Centre for Genetic Engineering and Biotechnology , New Delhi , India
| | - Nikunj Sharma
- a International Centre for Genetic Engineering and Biotechnology , New Delhi , India
| | - Humaira Farooqi
- b Department of Biotechnology , Jamia Hamdard University , New Delhi , India
| | - Malik Zainul Abdin
- b Department of Biotechnology , Jamia Hamdard University , New Delhi , India
| | - Thomas Mock
- c School of Environmental Sciences , University of East Anglia , Norwich Research Park, Norwich , United Kingdom
| | - Shashi Kumar
- a International Centre for Genetic Engineering and Biotechnology , New Delhi , India
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Brodie J, Chan CX, De Clerck O, Cock JM, Coelho SM, Gachon C, Grossman AR, Mock T, Raven JA, Smith AG, Yoon HS, Bhattacharya D. The Algal Revolution. Trends Plant Sci 2017; 22:726-738. [PMID: 28610890 DOI: 10.1016/j.tplants.2017.05.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/04/2017] [Accepted: 05/16/2017] [Indexed: 05/28/2023]
Abstract
Algae are (mostly) photosynthetic eukaryotes that occupy multiple branches of the tree of life, and are vital for planet function and health. In this review, we highlight a transformative period in studies of the evolution and functioning of this extraordinary group of organisms and their potential for novel applications, wrought by high-throughput 'omic' and reverse genetic methods. We cover the origin and diversification of algal groups, explore advances in understanding the link between phenotype and genotype, consider algal sex determination, and review progress in understanding the roots of algal multicellularity. Experimental evolution studies to determine how algae evolve in changing environments are highlighted, as is their potential as production platforms for compounds of commercial interest, such as biofuel precursors, nutraceuticals, or therapeutics.
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Affiliation(s)
- Juliet Brodie
- Natural History Museum, Department of Life Sciences, London SW7 5BD, UK
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Olivier De Clerck
- Research Group Phycology, Ghent University, Krijgslaan 281, S8, 9000 Ghent, Belgium
| | - J Mark Cock
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Susana M Coelho
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Claire Gachon
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, PA37 1QA, UK
| | - Arthur R Grossman
- Department of Plant Biology, The Carnegie Institution, Stanford, CA 94305, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - John A Raven
- Permanent address: Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, UK; School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA.
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Hofstetter S, Welle M, Gorgas D, Balmer P, Roosje P, Mock T, Meylan M, Jagannathan V, Drögemüller C. A de novo germline mutation of DLX3 in a Brown Swiss calf with tricho-dento-osseus-like syndrome. Vet Dermatol 2017; 28:616-e150. [PMID: 28670783 DOI: 10.1111/vde.12462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2017] [Indexed: 11/30/2022]
Abstract
OBJECTIVE A novel congenital disorder affecting a calf was observed, and its phenotype and genetic mutation identified. ANIMAL A six-month-old female Brown Swiss calf. METHODS Diagnostic investigation and whole genome sequencing of a case parent trio was performed. RESULTS The calf had a dull kinky coat with mild hypotrichosis, and teeth with brown staining and enamel defects. Histological examination of skin biopsies was compatible with a follicular dysplasia. Radiography and computed tomography revealed thickening of the skull bones and large pulp cavities with a marked thinning of enamel affecting all teeth. A de novo germline mutation affecting the distal-less homeobox gene (DLX3) was identified. The 10 bp frameshift mutation in exon 3 of the bovine DLX3 gene is predicted to replace the second C-terminal transactivation domain of the wild-type protein by a recoded peptide of 99 amino acids without any sequence similarity. CONCLUSION AND CLINICAL IMPORTANCE A causative mutation for a sporadic phenotype resembling human tricho-dento-osseous syndrome was identified after detection of a de novo germline mutation in the DLX3 gene.
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Affiliation(s)
- Sonja Hofstetter
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
| | - Monika Welle
- Vetsuisse Faculty, Institute of Animal Pathology, University of Bern, Länggassstrasse 122, Bern, 3001, Switzerland.,DermFocus, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
| | - Daniela Gorgas
- Vetsuisse Faculty, Division of Radiology, Department of Clinical Veterinary Medicine, University of Bern, Länggassstrasse 128, Bern, 3001, Switzerland
| | - Pierre Balmer
- DermFocus, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland.,Vetsuisse Faculty, Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, University of Bern, Länggassstrasse 128, Bern, 3001, Switzerland
| | - Petra Roosje
- DermFocus, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland.,Vetsuisse Faculty, Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, University of Bern, Länggassstrasse 128, Bern, 3001, Switzerland
| | - Thomas Mock
- Vetsuisse Faculty, Clinic for Ruminants, University of Bern, Bremgartenstrasse 109a, Bern, 3012, Switzerland
| | - Mireille Meylan
- Vetsuisse Faculty, Clinic for Ruminants, University of Bern, Bremgartenstrasse 109a, Bern, 3012, Switzerland
| | - Vidhya Jagannathan
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
| | - Cord Drögemüller
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bremgartenstrasse 109a, Bern, 3001, Switzerland
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40
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Basu S, Patil S, Mapleson D, Russo MT, Vitale L, Fevola C, Maumus F, Casotti R, Mock T, Caccamo M, Montresor M, Sanges R, Ferrante MI. Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom. New Phytol 2017; 215:140-156. [PMID: 28429538 PMCID: PMC5485032 DOI: 10.1111/nph.14557] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 02/25/2017] [Indexed: 05/03/2023]
Abstract
Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process in phytoplankton is poorly defined. Using the marine planktonic diatom Pseudo-nitzschia multistriata, we investigated the cell response to cues released during sexual reproduction, an event that demands strong regulatory mechanisms and impacts on population dynamics. We sequenced the genome of P. multistriata and performed phylogenomic and transcriptomic analyses, which allowed the definition of gene gains and losses, horizontal gene transfers, conservation and evolutionary rate of sex-related genes. We also identified a small number of conserved noncoding elements. Sexual reproduction impacted on cell cycle progression and induced an asymmetric response of the opposite mating types. G protein-coupled receptors and cyclic guanosine monophosphate (cGMP) are implicated in the response to sexual cues, which overall entails a modulation of cell cycle, meiosis-related and nutrient transporter genes, suggesting a fine control of nutrient uptake even under nutrient-replete conditions. The controllable life cycle and the genome sequence of P. multistriata allow the reconstruction of changes occurring in diatoms in a key phase of their life cycle, providing hints on the evolution and putative function of their genes and empowering studies on sexual reproduction.
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Affiliation(s)
- Swaraj Basu
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Shrikant Patil
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | | | - Monia Teresa Russo
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Laura Vitale
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Cristina Fevola
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | | | - Raffaella Casotti
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Thomas Mock
- School of Environmental SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Mario Caccamo
- Earlham InstituteNorwich Research ParkNorwichNR4 7UGUK
| | - Marina Montresor
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Remo Sanges
- Biology and Evolution of Marine OrganismsStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
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Bao F, Whitehurst M, Slusher AL, Maharaj A, Mock T, Huang CJ. An Exploratory Investigation of Inflammation-Associated Circulating MicroRNAs Following Acute High-Intensity Interval Exercise. Med Sci Sports Exerc 2017. [DOI: 10.1249/01.mss.0000518242.47506.79] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bentkowski P, van Oosterhout C, Ashby B, Mock T. The effect of extrinsic mortality on genome size evolution in prokaryotes. ISME J 2017; 11:1011-1018. [PMID: 27922601 PMCID: PMC5364348 DOI: 10.1038/ismej.2016.165] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 10/06/2016] [Accepted: 10/20/2016] [Indexed: 01/13/2023]
Abstract
Mortality has a significant role in prokaryotic ecology and evolution, yet the impact of variations in extrinsic mortality on prokaryotic genome evolution has received little attention. We used both mathematical and agent-based models to reveal how variations in extrinsic mortality affect prokaryotic genome evolution. Our results suggest that the genome size of bacteria increases with increased mortality. A high extrinsic mortality increases the pool of free resources and shortens life expectancy, which selects for faster reproduction, a phenotype we called 'scramblers'. This phenotype is realised by the expansion of gene families involved in nutrient acquisition and metabolism. In contrast, a low mortality rate increases an individual's life expectancy, which results in natural selection favouring tolerance to starvation when conditions are unfavourable. This leads to the evolution of small, streamlined genomes ('stayers'). Our models predict that large genomes, gene family expansion and horizontal gene transfer should be observed in prokaryotes occupying ecosystems exposed to high abiotic stress, as well as those under strong predator- and/or pathogen-mediated selection. A comparison of genome size of cyanobacteria in relatively stable marine versus more turbulent freshwater environments corroborates our predictions, although other factors between these environments could also be responsible.
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Affiliation(s)
- Piotr Bentkowski
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ben Ashby
- Department of Mathematical Sciences, University of Bath, Bath, UK
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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Teng L, Fan X, Xu D, Zhang X, Mock T, Ye N. Identification of Genes under Positive Selection Reveals Differences in Evolutionary Adaptation between Brown-Algal Species. Front Plant Sci 2017; 8:1429. [PMID: 28861104 PMCID: PMC5559719 DOI: 10.3389/fpls.2017.01429] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/03/2017] [Indexed: 05/07/2023]
Abstract
Brown algae are an important taxonomic group in coastal ecosystems. The model brown algal species Ectocarpus siliculosus and Saccharina japonica are closely related lineages. Despite their close phylogenetic relationship, they vary greatly in morphology and physiology. To obtain further insights into the evolutionary forces driving divergence in brown algae, we analyzed 3,909 orthologs from both species to identify Genes Under Positive Selection (GUPS). About 12% of the orthologs in each species were considered to be under positive selection. Many GUPS are involved in membrane transport, regulation of homeostasis, and sexual reproduction in the small sporophyte of E. siliculosus, which is known to have a complex life cycle and to occupy a wide range of habitats. Genes involved in photosynthesis and cell division dominated the group of GUPS in the large kelp of S. japonica, which might explain why this alga has evolved the ability to grow very rapidly and to form some of the largest sporophytes. A significant number of molecular chaperones (e.g., heat-shock proteins) involved in stress responses were identified to be under positive selection in both species, potentially indicating their important roles for macroalgae to cope with the relatively variable environment of coastal ecosystems. Moreover, analysis of previously published microarray data of E. siliculosus showed that many GUPS in E. siliculosus were responsive to stress conditions, such as oxidative and hyposaline stress, whereas our RNA-seq data of S. japonica showed that GUPS in this species were most highly expressed in large sporophytes, which supports the suggestion that selection largely acts on different sets of genes in both marcoalgal species, potentially reflecting their adaptation to different ecological niches.
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Affiliation(s)
- Linhong Teng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesQingdao, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesQingdao, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesQingdao, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesQingdao, China
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research ParkNorwich, United Kingdom
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesQingdao, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
- *Correspondence: Naihao Ye
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Mock T, Mehinagic K, Menzi F, Studer E, Oevermann A, Stoffel MH, Drögemüller C, Meylan M, Regenscheit N. Clinicopathological Phenotype of Autosomal Recessive Cholesterol Deficiency in Holstein Cattle. J Vet Intern Med 2016; 30:1369-75. [PMID: 27279263 PMCID: PMC5089636 DOI: 10.1111/jvim.13976] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/14/2016] [Accepted: 04/28/2016] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Cholesterol deficiency (CD), a newly identified autosomal recessive genetic defect in Holstein cattle, is associated with clinical signs of diarrhea, failure to thrive, and hypocholesterolemia. HYPOTHESIS/OBJECTIVES The objective is to describe the clinicopathological phenotype of affected Holstein cattle homozygous for the causative apolipoprotein B gene (APOB) mutation. ANIMALS Six Holstein cattle, 5 calves with a clinical history of chronic diarrhea, and 1 heifer with erosions in the buccal cavity and neurologic symptoms were admitted to the Clinic for Ruminants. METHODS This case review included a full clinical examination, a complete blood count, blood chemistry, and measurements of cholesterol and triglycerides. The animals were euthanized and necropsied. A PCR-based direct gene test was applied to determine the APOB genotype. RESULTS All 6 animals were inbred, could be traced back to the sire Maughlin Storm, and were confirmed homozygous for the APOB mutation. The clinical phenotype included poor development, underweight, and intermittent diarrhea in the calves, and neurologic signs in the heifer included hypermetria and pacing. Hypocholesterolemia and low triglycerides concentrations were present in all animals. The pathological phenotype of all animals was steatorrhea with enterocytes of the small intestine containing intracytoplasmic lipid vacuoles. The peripheral nervous system of the heifer displayed degenerative changes. CONCLUSIONS AND CLINICAL IMPORTANCE Suspicion of CD in Holstein cattle is based on the presence of chronic diarrhea with no evidence of primary infections. Confirmation of the associated APOB gene mutation is needed. Additionally, the heifer demonstrated primarily signs of neurologic disease providing an unexpected phenotype of CD.
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Affiliation(s)
- T Mock
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - K Mehinagic
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - F Menzi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - E Studer
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - A Oevermann
- Division of Neurological Sciences, DCR-VPH, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - M H Stoffel
- Division of Veterinary Anatomy, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - M Meylan
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - N Regenscheit
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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Zhang X, Gamarra J, Castro S, Carrasco E, Hernandez A, Mock T, Hadaegh AR, Read BA. Characterization of the Small RNA Transcriptome of the Marine Coccolithophorid, Emiliania huxleyi. PLoS One 2016; 11:e0154279. [PMID: 27101007 PMCID: PMC4839659 DOI: 10.1371/journal.pone.0154279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/11/2016] [Indexed: 12/31/2022] Open
Abstract
Small RNAs (smRNAs) control a variety of cellular processes by silencing target genes at the transcriptional or post-transcription level. While extensively studied in plants, relatively little is known about smRNAs and their targets in marine phytoplankton, such as Emiliania huxleyi (E. huxleyi). Deep sequencing was performed of smRNAs extracted at different time points as E. huxleyi cells transition from logarithmic to stationary phase growth in batch culture. Computational analyses predicted 18 E. huxleyi specific miRNAs. The 18 miRNA candidates and their precursors vary in length (18–24 nt and 71–252 nt, respectively), genome copy number (3–1,459), and the number of genes targeted (2–107). Stem-loop real time reverse transcriptase (RT) PCR was used to validate miRNA expression which varied by nearly three orders of magnitude when growth slows and cells enter stationary phase. Stem-loop RT PCR was also used to examine the expression profiles of miRNA in calcifying and non-calcifying cultures, and a small subset was found to be differentially expressed when nutrients become limiting and calcification is enhanced. In addition to miRNAs, endogenous small RNAs such as ra-siRNAs, ta-siRNAs, nat-siRNAs, and piwiRNAs were predicted along with the machinery for the biogenesis and processing of si-RNAs. This study is the first genome-wide investigation smRNAs pathways in E. huxleyi. Results provide new insights into the importance of smRNAs in regulating aspects of physiological growth and adaptation in marine phytoplankton and further challenge the notion that smRNAs evolved with multicellularity, expanding our perspective of these ancient regulatory pathways.
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Affiliation(s)
- Xiaoyu Zhang
- Department of Computer Science and Information Systems, California State University, San Marcos, CA, 92096, United States of America
| | - Jaime Gamarra
- Department of Computer Science and Information Systems, California State University, San Marcos, CA, 92096, United States of America
| | - Steven Castro
- Department of Biological Sciences, California State University, San Marcos, CA, 92096, United States of America
| | - Estela Carrasco
- Department of Biological Sciences, California State University, San Marcos, CA, 92096, United States of America
| | - Aaron Hernandez
- Department of Biological Sciences, California State University, San Marcos, CA, 92096, United States of America
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, United Kingdom
| | - Ahmad R. Hadaegh
- Department of Computer Science and Information Systems, California State University, San Marcos, CA, 92096, United States of America
| | - Betsy A. Read
- Department of Biological Sciences, California State University, San Marcos, CA, 92096, United States of America
- * E-mail:
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Menzi F, Besuchet-Schmutz N, Fragnière M, Hofstetter S, Jagannathan V, Mock T, Raemy A, Studer E, Mehinagic K, Regenscheit N, Meylan M, Schmitz-Hsu F, Drögemüller C. A transposable element insertion in APOB causes cholesterol deficiency in Holstein cattle. Anim Genet 2016; 47:253-7. [PMID: 26763170 PMCID: PMC4849205 DOI: 10.1111/age.12410] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2015] [Indexed: 11/29/2022]
Abstract
Cholesterol deficiency, a new autosomal recessive inherited genetic defect in Holstein cattle, has been recently reported to have an influence on the rearing success of calves. The affected animals show unresponsive diarrhea accompanied by hypocholesterolemia and usually die within the first weeks or months of life. Here, we show that whole genome sequencing combined with the knowledge about the pedigree and inbreeding status of a livestock population facilitates the identification of the causative mutation. We resequenced the entire genomes of an affected calf and a healthy partially inbred male carrying one copy of the critical 2.24‐Mb chromosome 11 segment in its ancestral state and one copy of the same segment with the cholesterol deficiency mutation. We detected a single structural variant, homozygous in the affected case and heterozygous in the non‐affected carrier male. The genetic makeup of this key animal provides extremely strong support for the causality of this mutation. The mutation represents a 1.3kb insertion of a transposable LTR element (ERV2‐1) in the coding sequence of the APOB gene, which leads to truncated transcripts and aberrant splicing. This finding was further supported by RNA sequencing of the liver transcriptome of an affected calf. The encoded apolipoprotein B is an essential apolipoprotein on chylomicrons and low‐density lipoproteins, and therefore, the mutation represents a loss of function mutation similar to autosomal recessive inherited familial hypobetalipoproteinemia‐1 (FHBL1) in humans. Our findings provide a direct gene test to improve selection against this deleterious mutation in Holstein cattle.
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Affiliation(s)
- F Menzi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - N Besuchet-Schmutz
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - M Fragnière
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - S Hofstetter
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - T Mock
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - A Raemy
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - E Studer
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - K Mehinagic
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122 CH-3001, Bern, Switzerland
| | - N Regenscheit
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122 CH-3001, Bern, Switzerland
| | - M Meylan
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
| | - F Schmitz-Hsu
- Swissgenetics, Meielenfeldweg 12 CH-3052, Zollikofen, Switzerland
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a CH-3001, Bern, Switzerland
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Hopes A, Nekrasov V, Kamoun S, Mock T. Editing of the urease gene by CRISPR-Cas in the diatom Thalassiosira pseudonana. Plant Methods 2016; 12:49. [PMID: 27904648 PMCID: PMC5121945 DOI: 10.1186/s13007-016-0148-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 11/10/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND CRISPR-Cas is a recent and powerful addition to the molecular toolbox which allows programmable genome editing. It has been used to modify genes in a wide variety of organisms, but only two alga to date. Here we present a methodology to edit the genome of Thalassiosira pseudonana, a model centric diatom with both ecological significance and high biotechnological potential, using CRISPR-Cas. RESULTS A single construct was assembled using Golden Gate cloning. Two sgRNAs were used to introduce a precise 37 nt deletion early in the coding region of the urease gene. A high percentage of bi-allelic mutations (≤61.5%) were observed in clones with the CRISPR-Cas construct. Growth of bi-allelic mutants in urea led to a significant reduction in growth rate and cell size compared to growth in nitrate. CONCLUSIONS CRISPR-Cas can precisely and efficiently edit the genome of T. pseudonana. The use of Golden Gate cloning to assemble CRISPR-Cas constructs gives additional flexibility to the CRISPR-Cas method and facilitates modifications to target alternative genes or species.
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Affiliation(s)
- Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Vladimir Nekrasov
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
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Mock T, Daines SJ, Geider R, Collins S, Metodiev M, Millar AJ, Moulton V, Lenton TM. Bridging the gap between omics and earth system science to better understand how environmental change impacts marine microbes. Glob Chang Biol 2016; 22:61-75. [PMID: 25988950 PMCID: PMC4949645 DOI: 10.1111/gcb.12983] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/05/2015] [Accepted: 05/12/2015] [Indexed: 05/17/2023]
Abstract
The advent of genomic-, transcriptomic- and proteomic-based approaches has revolutionized our ability to describe marine microbial communities, including biogeography, metabolic potential and diversity, mechanisms of adaptation, and phylogeny and evolutionary history. New interdisciplinary approaches are needed to move from this descriptive level to improved quantitative, process-level understanding of the roles of marine microbes in biogeochemical cycles and of the impact of environmental change on the marine microbial ecosystem. Linking studies at levels from the genome to the organism, to ecological strategies and organism and ecosystem response, requires new modelling approaches. Key to this will be a fundamental shift in modelling scale that represents micro-organisms from the level of their macromolecular components. This will enable contact with omics data sets and allow acclimation and adaptive response at the phenotype level (i.e. traits) to be simulated as a combination of fitness maximization and evolutionary constraints. This way forward will build on ecological approaches that identify key organism traits and systems biology approaches that integrate traditional physiological measurements with new insights from omics. It will rely on developing an improved understanding of ecophysiology to understand quantitatively environmental controls on microbial growth strategies. It will also incorporate results from experimental evolution studies in the representation of adaptation. The resulting ecosystem-level models can then evaluate our level of understanding of controls on ecosystem structure and function, highlight major gaps in understanding and help prioritize areas for future research programs. Ultimately, this grand synthesis should improve predictive capability of the ecosystem response to multiple environmental drivers.
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Affiliation(s)
- Thomas Mock
- School of Environmental SciencesUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Stuart J. Daines
- College of Life and Environmental SciencesUniversity of ExeterEX4 4QEExeterUK
| | - Richard Geider
- School of Biological SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
| | - Sinead Collins
- Ashworth LaboratoriesEdinburgh UniversityEH9 3JFEdinburghUK
| | - Metodi Metodiev
- School of Biological SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
| | - Andrew J. Millar
- SynthSys and School of Biological SciencesEdinburgh UniversityEH9 3BFEdinburghUK
| | - Vincent Moulton
- School of Computing SciencesUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Timothy M. Lenton
- College of Life and Environmental SciencesUniversity of ExeterEX4 4QEExeterUK
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49
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Abstract
Temporal variability in ecosystems significantly impacts species diversity and ecosystem productivity and therefore the evolution of organisms. Different levels of environmental perturbations such as seasonal fluctuations, natural disasters, and global change have different impacts on organisms and therefore their ability to acclimatize and adapt. Thus, to understand how organisms evolve under different perturbations is a key for predicting how environmental change will impact species diversity and ecosystem productivity. Here, we developed a computer simulation utilizing the individual-based model approach to investigate genome size evolution of a haploid, clonal and free-living prokaryotic population across different levels of environmental perturbations. Our results show that a greater variability of the environment resulted in genomes with a larger number of genes. Environmental perturbations were more effectively buffered by populations of individuals with relatively large genomes. Unpredictable changes of the environment led to a series of population bottlenecks followed by adaptive radiations. Our model shows that the evolution of genome size is indirectly driven by the temporal variability of the environment. This complements the effects of natural selection directly acting on genome optimization. Furthermore, species that have evolved in relatively stable environments may face the greatest risk of extinction under global change as genome streamlining genetically constrains their ability to acclimatize to the new environmental conditions, unless mechanisms of genetic diversification such as horizontal gene transfer will enrich their gene pool and therefore their potential to adapt.
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Affiliation(s)
- Piotr Bentkowski
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom Present address: Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Cock Van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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50
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Kiss A, Posner M, Mock T. Seasonally Induced Hepatotranscriptomic Changes in the Freeze Tolerant North American Wood Frog
Rana sylvatica. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.981.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Andor Kiss
- Center for Bioinformatics and Functional Genomics Miami UniversityOxfordOhioUnited States
| | - Mason Posner
- Department of Biology and Toxicology Ashland UniversityAshlandOhioUnited States
| | - Thomas Mock
- School of Environmental Sciences University of East AngliaNorwichNorfolkUnited Kingdom
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