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Ritter A, Tessmar-Raible K. Time me by the moon : The evolution and function of lunar timing systems. EMBO Rep 2024:10.1038/s44319-024-00196-5. [PMID: 39014253 DOI: 10.1038/s44319-024-00196-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 06/24/2024] [Indexed: 07/18/2024] Open
Affiliation(s)
- Andrés Ritter
- Laboratory of Integrative Biology of Marine Models, UMR8227 Sorbonne Université-CNRS, Station Biologique de Roscoff, 29688, Roscoff, CEDEX, France.
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030, Vienna, Austria.
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany.
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Ammerländer Heerstraße 114-118, 26129, Oldenburg, Germany.
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Foresi N, De Marco MA, Del Castello F, Ramirez L, Nejamkin A, Calo G, Grimsley N, Correa-Aragunde N, Martínez-Noël GMA. The tiny giant of the sea, Ostreococcus's unique adaptations. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108661. [PMID: 38735153 DOI: 10.1016/j.plaphy.2024.108661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 04/14/2024] [Accepted: 04/23/2024] [Indexed: 05/14/2024]
Abstract
Ostreococcus spp. are unicellular organisms with one of the simplest cellular organizations. The sequencing of the genomes of different Ostreococcus species has reinforced this status since Ostreococcus tauri has one most compact nuclear genomes among eukaryotic organisms. Despite this, it has retained a number of genes, setting it apart from other organisms with similar small genomes. Ostreococcus spp. feature a substantial number of selenocysteine-containing proteins, which, due to their higher catalytic activity compared to their selenium-lacking counterparts, may require a reduced quantity of proteins. Notably, O. tauri encodes several ammonium transporter genes, that may provide it with a competitive edge for acquiring nitrogen (N). This characteristic makes it an intriguing model for studying the efficient use of N in eukaryotes. Under conditions of low N availability, O. tauri utilizes N from abundant proteins or amino acids, such as L-arginine, similar to higher plants. However, the presence of a nitric oxide synthase (L-arg substrate) sheds light on a new metabolic pathway for L-arg in algae. The metabolic adaptations of O. tauri to day and night cycles offer valuable insights into carbon and iron metabolic configuration. O. tauri has evolved novel strategies to optimize iron uptake, lacking the classic components of the iron absorption mechanism. Overall, the cellular and genetic characteristics of Ostreococcus contribute to its evolutionary success, making it an excellent model for studying the physiological and genetic aspects of how green algae have adapted to the marine environment. Furthermore, given its potential for lipid accumulation and its marine habitat, it may represent a promising avenue for third-generation biofuels.
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Affiliation(s)
- Noelia Foresi
- Instituto de Investigaciones Biológicas-UNMdP-CONICET, Mar del Plata, Argentina.
| | - María Agustina De Marco
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC)-CONICET-FIBA, Mar del Plata, Argentina
| | | | - Leonor Ramirez
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-901 87, Umeå, Sweden
| | - Andres Nejamkin
- Instituto de Investigaciones Biológicas-UNMdP-CONICET, Mar del Plata, Argentina
| | - Gonzalo Calo
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC)-CONICET-FIBA, Mar del Plata, Argentina
| | - Nigel Grimsley
- CNRS, LBBM, Sorbonne Université OOB, 1 Avenue de Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | | | - Giselle M A Martínez-Noël
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC)-CONICET-FIBA, Mar del Plata, Argentina.
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3
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Im SH, Lepetit B, Mosesso N, Shrestha S, Weiss L, Nymark M, Roellig R, Wilhelm C, Isono E, Kroth PG. Identification of promoter targets by Aureochrome 1a in the diatom Phaeodactylum tricornutum. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1834-1851. [PMID: 38066674 DOI: 10.1093/jxb/erad478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 12/04/2023] [Indexed: 03/28/2024]
Abstract
Aureochromes (AUREOs) are unique blue light receptors and transcription factors found only in stramenopile algae. While each of the four AUREOs identified in the diatom Phaeodactylum tricornutum may have a specific function, PtAUREO1a has been shown to have a strong impact on overall gene regulation, when light changes from red to blue light conditions. Despite its significance, the molecular mechanism of PtAUREO1a is largely unexplored. To comprehend the overall process of gene regulation by PtAUREO1a, we conducted a series of in vitro and in vivo experiments, including pull-down assays, yeast one-hybrid experiments, and phenotypical characterization using recombinant PtAUREOs and diatom mutant lines expressing a modified PtAureo1a gene. We describe the distinct light absorption properties of four PtAUREOs and the formation of all combinations of their potential dimers. We demonstrate the capability of PtAUREO1a and 1b to activate the genes, diatom-specific cyclin 2, PtAureo1a, and PtAureo1c under both light and dark conditions. Using mutant lines expressing a modified PtAUREO1a protein with a considerably reduced light absorption, we found novel evidence that PtAUREO1a regulates the expression of PtLHCF15, which is essential for red light acclimation. Based on current knowledge, we present a working model of PtAUREO1a gene regulation properties.
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Affiliation(s)
- Soo Hyun Im
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Bernard Lepetit
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
- Molecular Stress Physiology, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany
| | - Niccolò Mosesso
- Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Sandeep Shrestha
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Laura Weiss
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Marianne Nymark
- Department of Biology, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Robert Roellig
- Institute of Biology, Department of Plant Physiology, University of Leipzig, D-04103 Leipzig, Germany
| | - Christian Wilhelm
- Institute of Biology, Department of Plant Physiology, University of Leipzig, D-04103 Leipzig, Germany
| | - Erika Isono
- Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Peter G Kroth
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
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4
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Hong Y, Yang L, You X, Zhang H, Xin X, Zhang Y, Zhou X. Effects of light quality on microalgae cultivation: bibliometric analysis, mini-review, and regulation approaches. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-31192-2. [PMID: 38015404 DOI: 10.1007/s11356-023-31192-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/19/2023] [Indexed: 11/29/2023]
Abstract
The ever-increasing concern for energy shortages and greenhouse effect has triggered the development of sustainable green technologies. Microalgae have received more attention due to the characteristics of biofuel production and CO2 fixation. From the perspective of autotrophic growth, the optimization of light quality has the potential to promote biomass production and bio-component accumulation in microalgae at low cost. In this study, bibliometric analysis was used to describe the basic features, identify the hotspots, and predict future trends of the research related to the light quality on microalgae cultivation. In addition, a mini-review referring to regulation methods of light quality was provided to optimize the framework of research. Results demonstrated that China has the greatest interest in this area. The destination of most research was to obtain biofuels and high-value-added products. Both blue and red lights were identified as the crucial spectrums for microalgae cultivation. However, sunlight is the most affordable light resource, which could not be fully utilized by microalgae through the photosynthetic process. Hence, some regulation approaches (e.g., dyes, plasmonic scattering, and carbon-based quantum dots) are proposed to increase the proportion of beneficial spectrum for enhancement of photosynthetic efficiency. In summary, this review introduces state-of-the-art research and provides theoretical guidance for light quality optimization in microalgae cultivation to obtain more benefits.
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Affiliation(s)
- Yongyuan Hong
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Libin Yang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China.
| | - Xiaogang You
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Haigeng Zhang
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200092, China
| | - Xiaying Xin
- Department of Civil Engineering, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Yalei Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Xuefei Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
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Sands E, Davies S, Puxty RJ, Vergé V, Bouget FY, Scanlan DJ, Carré IA. Genetic and physiological responses to light quality in a deep ocean ecotype of Ostreococcus, an ecologically important photosynthetic picoeukaryote. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6773-6789. [PMID: 37658791 PMCID: PMC10662239 DOI: 10.1093/jxb/erad347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/31/2023] [Indexed: 09/05/2023]
Abstract
Phytoplankton are exposed to dramatic variations in light quality when cells are carried by upwelling or downwelling currents or encounter sediment. We investigated the potential impact of light quality changes in Ostreococcus, a key marine photosynthetic picoeukaryote, by analysing changes in its transcriptome, pigment content, and photophysiology after acclimation to monochromatic red, green, or blue light. The clade B species RCC809, isolated from the deep euphotic zone of the tropical Atlantic Ocean, responded to blue light by accelerating cell division at the expense of storage reserves and by increasing the relative level of blue-light-absorbing pigments. It responded to red and green light by increasing its potential for photoprotection. In contrast, the clade A species OTTH0595, which originated from a shallow water environment, showed no difference in photosynthetic properties and minor differences in carotenoid contents between light qualities. This was associated with the loss of candidate light-quality responsive promoter motifs identified in RCC809 genes. These results demonstrate that light quality can have a major influence on the physiology of eukaryotic phytoplankton and suggest that different light quality environments can drive selection for diverse patterns of responsiveness and environmental niche partitioning.
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Affiliation(s)
- Elizabeth Sands
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Sian Davies
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Valerie Vergé
- Université Pierre et Marie Curie, Paris 06, UMR 7621, Laboratoire d’Océanographie Microbienne, Observatoire Océanologique, Banyuls sur Mer, France
| | - François-Yves Bouget
- Université Pierre et Marie Curie, Paris 06, UMR 7621, Laboratoire d’Océanographie Microbienne, Observatoire Océanologique, Banyuls sur Mer, France
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Xin Z, Zhang M, Cui H, Ding X, Zhang T, Wu L, Cui H, Xue Q, Chen C, Gao J. Algae: A Robust Living Material Against Cancer. Int J Nanomedicine 2023; 18:5243-5264. [PMID: 37727650 PMCID: PMC10506609 DOI: 10.2147/ijn.s423412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
Cancer is the second leading cause of death worldwide. Its incidence has been increasing in recent years, and it is becoming a major threat to human health. Conventional cancer treatment strategies, including surgery, chemotherapy, and radiotherapy, have faced problems such as drug resistance, toxic side effects and unsatisfactory therapeutic efficacy. Therefore, better development and utilization of biomaterials can improve the specificity and efficacy of tumor therapy. Algae, as a novel living material, possesses good biocompatibility. Although some reviews have elucidated several algae-based biomaterials for cancer treatment, the majority of the literature has focused on a limited number of algae. As a result, there is currently a lack of comprehensive reviews on the subject of anticancer algae. This review aims to address this gap by conducting a thorough examination of algal species that show potential for anticancer activity. Furthermore, our review will also elucidate the engineering strategies of algae and discuss the challenges and prospects associated with their implementation.
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Affiliation(s)
- Zhongyuan Xin
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, People’s Republic of China
- Changhai Clinical Research Unit, Shanghai Changhai Hospital, Naval Medical University, Shanghai, People’s Republic of China
| | - Mengya Zhang
- Changhai Clinical Research Unit, Shanghai Changhai Hospital, Naval Medical University, Shanghai, People’s Republic of China
| | - Hengqing Cui
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Xiuwen Ding
- Changhai Clinical Research Unit, Shanghai Changhai Hospital, Naval Medical University, Shanghai, People’s Republic of China
| | - Tinglin Zhang
- Changhai Clinical Research Unit, Shanghai Changhai Hospital, Naval Medical University, Shanghai, People’s Republic of China
| | - Lili Wu
- Changhai Clinical Research Unit, Shanghai Changhai Hospital, Naval Medical University, Shanghai, People’s Republic of China
| | - Haipo Cui
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, People’s Republic of China
| | - Qian Xue
- Changhai Clinical Research Unit, Shanghai Changhai Hospital, Naval Medical University, Shanghai, People’s Republic of China
| | - Cuimin Chen
- Changhai Clinical Research Unit, Shanghai Changhai Hospital, Naval Medical University, Shanghai, People’s Republic of China
| | - Jie Gao
- Changhai Clinical Research Unit, Shanghai Changhai Hospital, Naval Medical University, Shanghai, People’s Republic of China
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Decelle A, Seoane B, Rosset L. Unsupervised hierarchical clustering using the learning dynamics of restricted Boltzmann machines. Phys Rev E 2023; 108:014110. [PMID: 37583157 DOI: 10.1103/physreve.108.014110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/09/2023] [Indexed: 08/17/2023]
Abstract
Data sets in the real world are often complex and to some degree hierarchical, with groups and subgroups of data sharing common characteristics at different levels of abstraction. Understanding and uncovering the hidden structure of these data sets is an important task that has many practical applications. To address this challenge, we present a general method for building relational data trees by exploiting the learning dynamics of the restricted Boltzmann machine. Our method is based on the mean-field approach, derived from the Plefka expansion, and developed in the context of disordered systems. It is designed to be easily interpretable. We tested our method in an artificially created hierarchical data set and on three different real-world data sets (images of digits, mutations in the human genome, and a homologous family of proteins). The method is able to automatically identify the hierarchical structure of the data. This could be useful in the study of homologous protein sequences, where the relationships between proteins are critical for understanding their function and evolution.
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Affiliation(s)
- Aurélien Decelle
- Departamento de Física Teórica, Universidad Complutense de Madrid, 28040 Madrid, Spain and Université Paris-Saclay, CNRS, INRIA Tau team, LISN, 91190 Gif-sur-Yvette, France
| | | | - Lorenzo Rosset
- Departamento de Física Teórica, Universidad Complutense de Madrid, 28040 Madrid, Spain
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8
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Ren H, Zhou D, Lu J, Show PL, Sun FF. Mapping the field of microalgae CO 2 sequestration: a bibliometric analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27850-0. [PMID: 37311860 DOI: 10.1007/s11356-023-27850-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/19/2023] [Indexed: 06/15/2023]
Abstract
Microalgae CO2 sequestration has gained considerable attention in the last three decades as a promising technology to slow global warming caused by CO2 emissions. To provide a comprehensive and objective analysis of the research status, hot spots, and frontiers of CO2 fixation by microalgae, a bibliometric approach was recently chosen for review. In this study, 1561 articles (1991-2022) from the Web of Science (WOS) on microalgae CO2 sequestration were screened. A knowledge map of the domain was presented using VOSviewer and CiteSpace. It visually demonstrates the most productive journals (Bioresource Technology), countries (China and USA), funding sources, and top contributors (Cheng J, Chang JS, and their team) in the field of CO2 sequestration by microalgae. The analysis also revealed that research hotspots changed over time and that recent research has focused heavily on improving carbon sequestration efficiency. Finally, commercialization of carbon fixation by microalgae is a key hurdle, and supports from other disciplines could improve carbon sequestration efficiency.
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Affiliation(s)
- Hongyan Ren
- School of Environment Science and Civil Engineering, Jiangnan University, Wuxi, 214122, China.
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi, 214122, China.
| | - Duan Zhou
- School of Environment Science and Civil Engineering, Jiangnan University, Wuxi, 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi, 214122, China
| | - Jiawen Lu
- School of Environment Science and Civil Engineering, Jiangnan University, Wuxi, 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi, 214122, China
| | - Pau Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham Malaysia, 43500, Semenyih, Malaysia
| | - Fubao Fuelbiol Sun
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
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The antioxidant, wound healing properties and proteomic analysis of water extracts from the tropical cyanobacteria, Nostoc NIES-2111_MUM004. 3 Biotech 2023; 13:71. [PMID: 36742448 PMCID: PMC9895726 DOI: 10.1007/s13205-022-03448-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 12/23/2022] [Indexed: 02/05/2023] Open
Abstract
Cyanobacteria bioactive compounds are chemical treasure troves for product discovery and development. The wound healing effects and antioxidant capacities of water extracts from Nostoc NIES-2111_MUM004 were evaluated via in vitro wound scratch assay and three antioxidant assays respectively. Results showed that the water extracts were protein-rich and exhibited good antioxidant properties in ABTS radical scavenging (11.27 ± 0.205 mg TAE g-1 extract), Ferric reducing antioxidant power (1652.71 ± 110.71 mg TAE g-1 extract) and β-carotene bleaching assay (354.90 ± 31.80 mg TAE g-1 extract). Also, extracts were non-cytotoxic in concentrations up to 250 µg/mL as reflected in cytotoxicity assay. Importantly, water extracts showed considerable proliferation and migration activity at 125 µg/mL with wound closure rate as high as 42.67%. Statistical correlation revealed no significant relationship (p > 0.05) between protein fraction and the wound healing properties, confirming that phycobiliproteins were not solely responsible for wound healing activities. Subsequent Q-TOF-LCMS analysis identified six protein families involved in enhancing the proliferation and migration of epithelial cells. These findings are antecedent in the uncovering of continuous supplies of bioactive compounds from new and sustainable sources. Ultimately, enriching the microalgae menu for applications in pharmaceutical, nutraceutical and cosmeceuticals.
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Falciatore A, Bailleul B, Boulouis A, Bouly JP, Bujaldon S, Cheminant-Navarro S, Choquet Y, de Vitry C, Eberhard S, Jaubert M, Kuras R, Lafontaine I, Landier S, Selles J, Vallon O, Wostrikoff K. Light-driven processes: key players of the functional biodiversity in microalgae. C R Biol 2022; 345:15-38. [PMID: 36847462 DOI: 10.5802/crbiol.80] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/11/2022] [Indexed: 11/24/2022]
Abstract
Microalgae are prominent aquatic organisms, responsible for about half of the photosynthetic activity on Earth. Over the past two decades, breakthroughs in genomics and ecosystem biology, as well as the development of genetic resources in model species, have redrawn the boundaries of our knowledge on the relevance of these microbes in global ecosystems. However, considering their vast biodiversity and complex evolutionary history, our comprehension of algal biology remains limited. As algae rely on light, both as their main source of energy and for information about their environment, we focus here on photosynthesis, photoperception, and chloroplast biogenesis in the green alga Chlamydomonas reinhardtii and marine diatoms. We describe how the studies of light-driven processes are key to assessing functional biodiversity in evolutionary distant microalgae. We also emphasize that integration of laboratory and environmental studies, and dialogues between different scientific communities are both timely and essential to understand the life of phototrophs in complex ecosystems and to properly assess the consequences of environmental changes on aquatic environments globally.
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Genome-Wide Identification and Analysis of the Aureochrome Gene Family in Saccharina japonica and a Comparative Analysis with Six Other Algae. PLANTS 2022; 11:plants11162088. [PMID: 36015392 PMCID: PMC9416419 DOI: 10.3390/plants11162088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022]
Abstract
Aureochrome (AUREO) is a kind of blue light photoreceptor with both LOV and bZIP structural domains, identified only in Stramenopiles. It functions as a transcription factor that responds to blue light, playing diverse roles in the growth, development, and reproduction of Stramenopiles. Most of its functions are currently unknown, especially in the economically important alga S. japonica farmed on a large scale. This study provided a comprehensive analysis of the characteristics of AUREO gene families in seven algae, focusing on the AUREOs of S. japonica. AUREO genes were strictly identified from seven algal genomes. Then AUREO phylogenetic tree was constructed from 44 conserved AUREO genes collected. These AUREO genes were divided into five groups based on phylogenetic relationships. A total of 28 genes unnamed previously were named according to the phylogenetic tree. A large number of different cis-acting elements, especially bZIP transcription factors, were discovered upstream of AUREO genes in brown algae. Different intron/exon structural patterns were identified among all AUREOs. Transcriptomic data indicated that the expression of Sj AUREO varied significantly during the different development stages of S. japonica gametophytes. Periodic rhythms of light induction experiments indicate that Sj AUREO existed in a light-dependent circadian expression pattern, differing from other similar studies in the past. This may indicate that blue light affects gametophyte development through AUREO as a light signal receptor. This study systematically identified and analyzed the AUREO gene family in seven representative brown algae, which lay a good foundation for further study and understanding of AUERO functions in agal growth and development.
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Vicedomini R, Bouly JP, Laine E, Falciatore A, Carbone A. Multiple profile models extract features from protein sequence data and resolve functional diversity of very different protein families. Mol Biol Evol 2022; 39:6556147. [PMID: 35353898 PMCID: PMC9016551 DOI: 10.1093/molbev/msac070] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Functional classification of proteins from sequences alone has become a critical bottleneck in understanding the myriad of protein sequences that accumulate in our databases. The great diversity of homologous sequences hides, in many cases, a variety of functional activities that cannot be anticipated. Their identification appears critical for a fundamental understanding of the evolution of living organisms and for biotechnological applications. ProfileView is a sequence-based computational method, designed to functionally classify sets of homologous sequences. It relies on two main ideas: the use of multiple profile models whose construction explores evolutionary information in available databases, and a novel definition of a representation space in which to analyse sequences with multiple profile models combined together. ProfileView classifies protein families by enriching known functional groups with new sequences and discovering new groups and subgroups. We validate ProfileView on seven classes of widespread proteins involved in the interaction with nucleic acids, amino acids and small molecules, and in a large variety of functions and enzymatic reactions. Profile-View agrees with the large set of functional data collected for these proteins from the literature regarding the organisation into functional subgroups and residues that characterise the functions. In addition, ProfileView resolves undefined functional classifications and extracts the molecular determinants underlying protein functional diversity, showing its potential to select sequences towards accurate experimental design and discovery of novel biological functions. On protein families with complex domain architecture, ProfileView functional classification reconciles domain combinations, unlike phylogenetic reconstruction. ProfileView proves to outperform the functional classification approach PANTHER, the two k-mer based methods CUPP and eCAMI and a neural network approach based on Restricted Boltzmann Machines. It overcomes time complexity limitations of the latter.
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Affiliation(s)
- R Vicedomini
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 place Jussieu, 75005 Paris, France.,Sorbonne Université, Institut des Sciences du Calcul et des Données
| | - J P Bouly
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 place Jussieu, 75005 Paris, France.,CNRS, Sorbonne Université Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae - UMR7141, Paris, France
| | - E Laine
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 place Jussieu, 75005 Paris, France
| | - A Falciatore
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 place Jussieu, 75005 Paris, France.,CNRS, Sorbonne Université Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae - UMR7141, Paris, France
| | - A Carbone
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 place Jussieu, 75005 Paris, France.,Institut Universitaire de France, Paris 75005, France
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13
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Font-Muñoz JS, Sourisseau M, Cohen-Sánchez A, Tuval I, Basterretxea G. Pelagic diatoms communicate through synchronized beacon natural fluorescence signaling. SCIENCE ADVANCES 2021; 7:eabj5230. [PMID: 34910521 PMCID: PMC8673755 DOI: 10.1126/sciadv.abj5230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
Communication between conspecific individuals is an essential part of life both in terrestrial and marine realms. Until recently, social behavior in marine phytoplankton was assumed to rely mainly on the secretion of a variety of infochemicals that allowed population-scale collective responses. Here, we demonstrate that pelagic diatoms also use Sun-stimulated fluorescence signals for synchronizing their behavior. These unicellular microorganisms, playing a key biogeochemical role in the ocean, use photoreceptor proteins and red–far-red fluorescent radiation to communicate. A characteristic beaconing signal is generated by rhythmic organelle displacement within the cell cytoplasm, triggering coordinated population behavior. These light-based communication networks could critically determine major facets of diatom ecology and fitness and regulate the dynamics of larger-scale ocean processes.
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Affiliation(s)
- Joan S. Font-Muñoz
- IFREMER, French Institute for Sea Research, DYNECO PELAGOS, 29280 Plouzané, France
- Université de Brest-UBO/CNRS/IFREMER/IRD, 29238 Brest, France
| | - Marc Sourisseau
- IFREMER, French Institute for Sea Research, DYNECO PELAGOS, 29280 Plouzané, France
| | - Amanda Cohen-Sánchez
- Mediterranean Institute for Advanced Studies, IMEDEA (UIB-CSIC), Miquel Marques 21, 07190 Esporles, Balearic Islands, Spain
| | - Idan Tuval
- Mediterranean Institute for Advanced Studies, IMEDEA (UIB-CSIC), Miquel Marques 21, 07190 Esporles, Balearic Islands, Spain
- Department of Physics, University of the Balearic Islands, Ctra. Valldemossa Km. 7.5, 07122 Palma, Balearic Islands, Spain
| | - Gotzon Basterretxea
- Mediterranean Institute for Advanced Studies, IMEDEA (UIB-CSIC), Miquel Marques 21, 07190 Esporles, Balearic Islands, Spain
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14
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Liu X, Xie X, Gao S, Wang L, Zhou L, Liu Y, Hu Q, Gu W, Wang G. Chlorophyll fluorescence as a light signal enhances iron uptake by the marine diatom Phaeodactylum tricornutum under high-cell density conditions. BMC Biol 2021; 19:249. [PMID: 34814917 PMCID: PMC8609858 DOI: 10.1186/s12915-021-01177-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
Background Diatoms usually dominate phytoplankton blooms in open oceans, exhibiting extremely high population densities. Although the iron uptake rate of diatoms largely determines the magnitude and longevity of diatom blooms, the underlying mechanisms regulating iron uptake remain unclear. Results The transcription of two iron uptake proteins, ISIP2a and ISIP1, in the marine diatom Phaeodactylum tricornutum was enhanced with increasing cell density, whereas the cellular iron content showed the opposite trend. When compared with the wild-type strain, knockdown of ISIP2a resulted in 43% decrease in cellular iron content, implying the involvement of ISIP2a in iron uptake under high-cell density conditions. Incubation of the diatom cells with sonicated cell lysate conditioned by different cell densities did not affect ISIP2a and ISIP1 expression, ruling out regulation via chemical cues. In contrast, ISIP2a and ISIP1 transcription were strongly induced by red light. Besides, chlorophyll fluorescence excited from the blue light was also positively correlated with population density. Subsequently, a “sandwich” illumination incubator was designed to filter out stray light and ensure that the inner layer cells only receive the emitted chlorophyll fluorescence from outer layers, and the results showed that the increase in outer cell density significantly elevated ISIP2a and ISIP1 transcription in inner layer cells. In situ evidence from Tara oceans also showed positively correlated between diatom ISIP transcripts and chlorophyll content. Conclusions This study shows that chlorophyll fluorescence derived from neighboring cells is able to upregulate ISIP2a and ISIP1 expression to facilitate iron assimilation under high-cell density. These results provide novel insights into biotic signal sensing in phytoplankton, which can help to elucidate the underlying mechanisms of marine diatom blooms. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01177-z.
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Affiliation(s)
- Xuehua Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiujun Xie
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shan Gao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lepu Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lu Zhou
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yao Liu
- Public Technology Service Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Qiang Hu
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Wenhui Gu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Guangce Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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15
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Petersen J, Rredhi A, Szyttenholm J, Oldemeyer S, Kottke T, Mittag M. The World of Algae Reveals a Broad Variety of Cryptochrome Properties and Functions. FRONTIERS IN PLANT SCIENCE 2021; 12:766509. [PMID: 34790217 PMCID: PMC8591175 DOI: 10.3389/fpls.2021.766509] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/11/2021] [Indexed: 05/25/2023]
Abstract
Algae are photosynthetic eukaryotic (micro-)organisms, lacking roots, leaves, and other organs that are typical for land plants. They live in freshwater, marine, or terrestrial habitats. Together with the cyanobacteria they contribute to about half of global carbon fixation. As primary producers, they are at the basis of many food webs and they are involved in biogeochemical processes. Algae are evolutionarily distinct and are derived either by primary (e.g., green and red algae) or secondary endosymbiosis (e.g., diatoms, dinoflagellates, and brown algae). Light is a key abiotic factor needed to maintain the fitness of algae as it delivers energy for photosynthesis, regulates algal cell- and life cycles, and entrains their biological clocks. However, excess light can also be harmful, especially in the ultraviolet range. Among the variety of receptors perceiving light information, the cryptochromes originally evolved as UV-A and blue-light receptors and have been found in all studied algal genomes so far. Yet, the classification, biophysical properties, wavelength range of absorbance, and biological functions of cryptochromes are remarkably diverse among algal species, especially when compared to cryptochromes from land plants or animals.
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Affiliation(s)
- Jan Petersen
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, Germany
| | - Anxhela Rredhi
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, Germany
| | - Julie Szyttenholm
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, Germany
| | - Sabine Oldemeyer
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Tilman Kottke
- Department of Chemistry, Bielefeld University, Bielefeld, Germany
- Biophysical Chemistry and Diagnostics, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, Germany
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16
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Michel-Rodriguez M, Lefebvre S, Crouvoisier M, Mériaux X, Lizon F. Underwater light climate and wavelength dependence of microalgae photosynthetic parameters in a temperate sea. PeerJ 2021; 9:e12101. [PMID: 34707925 PMCID: PMC8496463 DOI: 10.7717/peerj.12101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 08/11/2021] [Indexed: 11/20/2022] Open
Abstract
Studying how natural phytoplankton adjust their photosynthetic properties to the quantity and quality of underwater light (i.e. light climate) is essential to understand primary production. A wavelength-dependent photoacclimation strategy was assessed using a multi-color pulse-amplitude-modulation chlorophyll fluorometer for phytoplankton samples collected in the spring at 19 locations across the English Channel. The functional absorption cross section of photosystem II, photosynthetic electron transport (PETλ) parameters and non-photochemical quenching were analyzed using an original approach with a sequence of three statistical analyses. Linear mixed-effects models using wavelength as a longitudinal variable were first applied to distinguish the fixed effect of the population from the random effect of individuals. Population and individual trends of wavelength-dependent PETλ parameters were consistent with photosynthesis and photoacclimation theories. The natural phytoplankton communities studied were in a photoprotective state for blue wavelengths (440 and 480 nm), but not for other wavelengths (green (540 nm), amber (590 nm) and light red (625 nm)). Population-detrended PETλ values were then used in multivariate analyses (partial triadic analysis and redundancy analysis) to study ecological implications of PETλ dynamics among water masses. Two wavelength ratios based on the microalgae saturation parameter Ek (in relative and absolute units), related to the hydrodynamic regime and underwater light climate, clearly confirmed the physiological state of microalgae. They also illustrate more accurately that natural phytoplankton communities can implement photoacclimation processes that are influenced by in situ light quality during the daylight cycle in temporarily and weakly stratified water. Ecological implications and consequences of PETλ are discussed in the context of turbulent coastal ecosystems.
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Affiliation(s)
- Monica Michel-Rodriguez
- Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, UMR 8187 LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
| | - Sebastien Lefebvre
- Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, UMR 8187 LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
| | - Muriel Crouvoisier
- Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, UMR 8187 LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
| | - Xavier Mériaux
- Univ. Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187-LOG-Laboratoire d'Océanologie et de Géosciences, Wimereux, France
| | - Fabrice Lizon
- Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, UMR 8187 LOG, Laboratoire d'Océanologie et de Géosciences, Lille, France
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17
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Bioluminescence and Photoreception in Unicellular Organisms: Light-Signalling in a Bio-Communication Perspective. Int J Mol Sci 2021; 22:ijms222111311. [PMID: 34768741 PMCID: PMC8582858 DOI: 10.3390/ijms222111311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
Bioluminescence, the emission of light catalysed by luciferases, has evolved in many taxa from bacteria to vertebrates and is predominant in the marine environment. It is now well established that in animals possessing a nervous system capable of integrating light stimuli, bioluminescence triggers various behavioural responses and plays a role in intra- or interspecific visual communication. The function of light emission in unicellular organisms is less clear and it is currently thought that it has evolved in an ecological framework, to be perceived by visual animals. For example, while it is thought that bioluminescence allows bacteria to be ingested by zooplankton or fish, providing them with favourable conditions for growth and dispersal, the luminous flashes emitted by dinoflagellates may have evolved as an anti-predation system against copepods. In this short review, we re-examine this paradigm in light of recent findings in microorganism photoreception, signal integration and complex behaviours. Numerous studies show that on the one hand, bacteria and protists, whether autotrophs or heterotrophs, possess a variety of photoreceptors capable of perceiving and integrating light stimuli of different wavelengths. Single-cell light-perception produces responses ranging from phototaxis to more complex behaviours. On the other hand, there is growing evidence that unicellular prokaryotes and eukaryotes can perform complex tasks ranging from habituation and decision-making to associative learning, despite lacking a nervous system. Here, we focus our analysis on two taxa, bacteria and dinoflagellates, whose bioluminescence is well studied. We propose the hypothesis that similar to visual animals, the interplay between light-emission and reception could play multiple roles in intra- and interspecific communication and participate in complex behaviour in the unicellular world.
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18
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Rredhi A, Petersen J, Schubert M, Li W, Oldemeyer S, Li W, Westermann M, Wagner V, Kottke T, Mittag M. DASH cryptochrome 1, a UV-A receptor, balances the photosynthetic machinery of Chlamydomonas reinhardtii. THE NEW PHYTOLOGIST 2021; 232:610-624. [PMID: 34235760 DOI: 10.1111/nph.17603] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Drosophila, Arabidopsis, Synechocystis, Homo (DASH) cryptochromes belong to the cryptochrome/photolyase family and can act as DNA repair enzymes. In bacteria and fungi, they also can play regulatory roles, but in plants their biological functions remain elusive. Here, we characterize CRY-DASH1 from the green alga Chlamydomonas reinhardtii. We perform biochemical and in vitro photochemical analysis. For functional characterization, a knock-out mutant of cry-dash1 is used. CRY-DASH1 protein is localized in the chloroplast and accumulates at midday. Although the photoautotrophic growth of the mutant is significantly reduced compared to the wild-type (WT), the mutant has increased levels of photosynthetic pigments and a higher maximum photochemical efficiency of photosystem II (PS II). Hyper-stacking of thylakoid membranes occurs together with an increase in proteins of the PS II reaction center, D1 and its antenna CP43, but not of their transcripts. CRY-DASH1 binds fully reduced flavin adenine dinucleotide and the antenna 5,10-methenyltetrahydrofolate, leading to an absorption peak in the UV-A range. Supplementation of white light with UV-A increases photoautotrophic growth of the WT but not of the cry-dash1 mutant. These results suggest a balancing function of CRY-DASH1 in the photosynthetic machinery and point to its role as a photoreceptor for the UV-A range separated from the absorption of photosynthetic pigments.
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Affiliation(s)
- Anxhela Rredhi
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, 07743, Germany
| | - Jan Petersen
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, 07743, Germany
| | - Melvin Schubert
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, 07743, Germany
| | - Wei Li
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, 07743, Germany
| | - Sabine Oldemeyer
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, 33615, Germany
| | - Wenshuang Li
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, 07743, Germany
| | - Martin Westermann
- Electron Microscopy Center, Jena University Hospital, Jena, 07743, Germany
| | - Volker Wagner
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, 07743, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Bielefeld, 33615, Germany
- Medical School OWL, Bielefeld University, Bielefeld, 33615, Germany
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena, 07743, Germany
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19
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Milito A, Castellano I, Damiani E. From Sea to Skin: Is There a Future for Natural Photoprotectants? Mar Drugs 2021; 19:md19070379. [PMID: 34209059 PMCID: PMC8303403 DOI: 10.3390/md19070379] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 12/20/2022] Open
Abstract
In the last few decades, the thinning of the ozone layer due to increased atmospheric pollution has exacerbated the negative effects of excessive exposure to solar ultraviolet radiation (UVR), and skin cancer has become a major public health concern. In order to prevent skin damage, public health advice mainly focuses on the use of sunscreens, along with wearing protective clothing and avoiding sun exposure during peak hours. Sunscreens present on the market are topical formulations that contain a number of different synthetic, organic, and inorganic UVR filters with different absorbance profiles, which, when combined, provide broad UVR spectrum protection. However, increased evidence suggests that some of these compounds cause subtle damage to marine ecosystems. One alternative may be the use of natural products that are produced in a wide range of marine species and are mainly thought to act as a defense against UVR-mediated damage. However, their potential for human photoprotection is largely under-investigated. In this review, attention has been placed on the molecular strategies adopted by marine organisms to counteract UVR-induced negative effects and we provide a broad portrayal of the recent literature concerning marine-derived natural products having potential as natural sunscreens/photoprotectants for human skin. Their chemical structure, UVR absorption properties, and their pleiotropic role as bioactive molecules are discussed. Most studies strongly suggest that these natural products could be promising for use in biocompatible sunscreens and may represent an alternative eco-friendly approach to protect humans against UV-induced skin damage.
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Affiliation(s)
- Alfonsina Milito
- Centre for Research in Agricultural Genomics, Department of Molecular Genetics, Cerdanyola, 08193 Barcelona, Spain;
| | - Immacolata Castellano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80131 Napoli, Italy
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
- Correspondence: (I.C.); (E.D.)
| | - Elisabetta Damiani
- Department of Life and Environmental Sciences, Polytechnic University of the Marche, Via Brecce Bianche, 60131 Ancona, Italy
- Correspondence: (I.C.); (E.D.)
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20
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Diamantopoulou C, Christoforou E, Dominoni DM, Kaiserli E, Czyzewski J, Mirzai N, Spatharis S. Wavelength-dependent effects of artificial light at night on phytoplankton growth and community structure. Proc Biol Sci 2021; 288:20210525. [PMID: 34157871 DOI: 10.1098/rspb.2021.0525] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Artificial light at night (ALAN) is a disruptive form of pollution, impacting physiological and behavioural processes that may scale up to population and community levels. Evidence from terrestrial habitats show that the severity and type of impact depend on the wavelength and intensity of ALAN; however, research on marine organisms is still limited. Here, we experimentally investigated the effect of different ALAN colours on marine primary producers. We tested the effect of green (525 nm), red (624 nm) and broad-spectrum white LED ALAN, compared to a dark control, on the green microalgae Tetraselmis suesica and a diatom assemblage. We show that green ALAN boosted chlorophyll production and abundance in T. suesica. All ALAN wavelengths affected assemblage biomass and diversity, with red and green ALAN having the strongest effects, leading to higher overall abundance and selective dominance of specific diatom species, some known to cause harmful algal blooms. Our findings show that green and red ALAN should be used with caution as alternative LED colours in coastal areas, where there might be a need to strike a balance between the effects of green and red light on marine primary producers with the benefit they appear to bring to other organisms.
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Affiliation(s)
- Christina Diamantopoulou
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece.,School of Life Sciences, University of Glasgow, Glasgow G128QQ, UK
| | - Eleni Christoforou
- School of Life Sciences, University of Glasgow, Glasgow G128QQ, UK.,Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G128QQ, UK
| | - Davide M Dominoni
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G128QQ, UK
| | - Eirini Kaiserli
- Molecular Cell and Systems Biology, University of Glasgow, Glasgow G128QQ, UK
| | - Jakub Czyzewski
- College of Medical, Veterinary and Life Sciences (MVLS), Bioelectronics Unit, University of Glasgow, Glasgow G128QQ, UK
| | - Nosrat Mirzai
- College of Medical, Veterinary and Life Sciences (MVLS), Bioelectronics Unit, University of Glasgow, Glasgow G128QQ, UK
| | - Sofie Spatharis
- School of Life Sciences, University of Glasgow, Glasgow G128QQ, UK.,Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G128QQ, UK
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21
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Huang Z, Zhong C, Dai J, Li S, Zheng M, He Y, Wang M, Chen B. Simultaneous enhancement on renewable bioactive compounds from Porphyridium cruentum via a novel two-stage cultivation. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102270] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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22
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Yang X, Wang X, Yao J, Li W, Duan D. MiR8181 is involved in the cell growth regulation of Saccharina japonica. JOURNAL OF PLANT PHYSIOLOGY 2021; 260:153394. [PMID: 33676110 DOI: 10.1016/j.jplph.2021.153394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
Aureochrome, a blue-light receptor specifically found in photosynthetic stramenopiles, plays an important role in algal growth and development. It holds a reversed effector-sensor topology for the reception of blue light, acting as a candidate of optogenetic tool in transcriptional regulation. However, the inner regulatory mechanism of aureochrome is still unclear. In this study, we explored the potential regulatory relationship between microRNAs (miRNAs) and mRNAs by small RNA, transcriptome and degradome sequencing in Saccharina japonica. Through screening miRNA-mRNA interaction networks at the whole-genome level, we found that 18 miRNAs perfectly paired with aureochrome. Among these screened miRNAs, miR8181 was negatively correlated with aureochrome5 with high credibility, exhibiting tissue-specific expression in sporophyte of S. japonica. Degradome analysis further revealed the exact cleavage site of miR8181 on aureochrome5, confirming their targeting relationship. For the 54 target genes of miR8181, nine genes that exhibited similar expression to that of aureochrome5 competed for the same binding site, thus establishing a competing endogenous RNA network. Functional enrichment of the target genes revealed that miR8181 was involved in the regulation of cell differentiation and development in S. japonica. Moreover, overexpression of miR8181 resulted in significant decreases in the cell growth rates of Phaeodactylum tricornutum, suggesting negative roles of miR8181 in regulating cell growth. Our study revealed that miR8181, the targeting miRNA of aureochrome5, played negative roles in cell growth and development.
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Affiliation(s)
- Xiaoqi Yang
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuliang Wang
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jianting Yao
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Wei Li
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Delin Duan
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
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23
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Goett-Zink L, Klocke JL, Kottke T. Resolving Structural Changes of Photoreceptors in Living Escherichia coli via In-cell Infrared Difference Spectroscopy. Bio Protoc 2021; 11:e3909. [PMID: 33732796 DOI: 10.21769/bioprotoc.3909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 11/02/2022] Open
Abstract
Several in-cell spectroscopic techniques have been developed recently to investigate the structure and mechanism of proteins in their native environment. Conditions in vivo differ dramatically from those selected for in vitro experiments. Accordingly, the cellular environment can affect the protein mechanism for example by molecular crowding or binding of small molecules. Fourier transform infrared (FTIR) difference spectroscopy is a well-suited method to study the light-induced structural responses of photoreceptors including changes in cofactor, side chains and secondary structure. Here, we describe a protocol to study the response of cofactor and protein in living E. coli cells via in-cell infrared difference (ICIRD) spectroscopy using the attenuated total reflection (ATR) configuration. Proteins are overexpressed in E. coli, the cells are transferred into saline solution and the copy number per cell is determined using fluorescence spectroscopy. The suspension is centrifuged and the concentrated cells transferred onto the ATR cell inside the FTIR spectrometer. The thermostatted cell is sealed and illuminated from the top with an LED. Intensity spectra are recorded before and after illumination to generate the difference spectrum of the receptor inside the living cell. With ICIRD spectroscopy, structural changes of soluble photoreceptors are resolved in a near-native environment. The approach works in H2O at ambient conditions, is label free, without any limitations in protein size and does not require any purification step. Graphic abstract: In-cell infrared difference spectroscopy on photoreceptors in living E. coli using attenuated total reflection.
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Affiliation(s)
- Lukas Goett-Zink
- Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Jessica L Klocke
- Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Tilman Kottke
- Department of Chemistry, Bielefeld University, Bielefeld, Germany.,Medical School OWL, Bielefeld University, Bielefeld, Germany
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Hikosaka-Katayama T, Watanuki N, Niiho S, Hikosaka A. Geographical Distribution and Genetic Diversity of Praesagittifera naikaiensis (Acoelomorpha) in the Seto Inland Sea, Japan. Zoolog Sci 2021; 37:314-322. [PMID: 32729709 DOI: 10.2108/zs190119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/25/2020] [Indexed: 11/17/2022]
Abstract
Acoel flatworms are simple bilaterians that lack digestive lumens and coelomic cavities. Although they are a significant taxon for evaluating the evolution of metazoans, suitable species for biological experiments are not available in Japan. We recently focused on Praesagittifera naikaiensis, which inhabits the sandy shores of intertidal zones in the Seto Inland Sea in Japan, as a candidate for a representative acoel species to be used in experiments. However, reports on its distribution range remain limited. Here, we surveyed the habitats of P. naikaiensis on 108 beaches along the Seto Inland Sea. Praesagittifera naikaiensis is reported here from 37 sites (six previously known and 31 newly discovered sites) spread over a wide area of the Seto Inland Sea, from Awaji Island in Hyogo Prefecture to Fukuoka Prefecture (364 km direct distance). Based on the mitochondrial cytochrome oxidase subunit I (COI) gene haplotypes, we evaluated the genetic diversity of 145 individuals collected from 33 sites. Out of 42 COI haplotypes, 13 haplotypes were shared by multiple individuals. The most frequent haplotype was observed in 67 individuals collected from 31 sites. Eight other haplotypes were detected at geographically distant locations (maximum of 299 km direct distance). Multiple haplotypes were found at 32 sites. These results demonstrate that sufficient genetic flow exists among P. naikaiensis populations throughout the Seto Inland Sea. Molecular phylogenetic analysis of the COI haplotypes of P. naikaiensis revealed that all specimens were grouped into one clade. The genetic homogeneity of the animals in this area favors their use as an experimental animal.
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Affiliation(s)
- Tomoe Hikosaka-Katayama
- Center for Gene Science, Hiroshima University, 1-4-2 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Nanami Watanuki
- Faculty of Integrated Arts and Sciences, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Saki Niiho
- Faculty of Integrated Arts and Sciences, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Akira Hikosaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan,
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Annunziata R, Balestra C, Marotta P, Ruggiero A, Manfellotto F, Benvenuto G, Biffali E, Ferrante MI. An optimised method for intact nuclei isolation from diatoms. Sci Rep 2021; 11:1681. [PMID: 33462289 PMCID: PMC7813820 DOI: 10.1038/s41598-021-81238-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 12/22/2020] [Indexed: 01/21/2023] Open
Abstract
Due to their abundance in the oceans, their extraordinary biodiversity and the increasing use for biotech applications, the study of diatom biology is receiving more and more attention in the recent years. One of the limitations in developing molecular tools for diatoms lies in the peculiar nature of their cell wall, that is made of silica and organic molecules and that hinders the application of standard methods for cell lysis required, for example, to extract organelles. In this study we present a protocol for intact nuclei isolation from diatoms that was successfully applied to three different species: two pennates, Pseudo-nitzschia multistriata and Phaeodactylum tricornutum, and one centric diatom species, Chaetoceros diadema. Intact nuclei were extracted by treatment with acidified NH4F solution combined to low intensity sonication pulses and separated from cell debris via FAC-sorting upon incubation with SYBR Green. Microscopy observations confirmed the integrity of isolated nuclei and high sensitivity DNA electrophoresis showed that genomic DNA extracted from isolated nuclei has low degree of fragmentation. This protocol has proved to be a flexible and versatile method to obtain intact nuclei preparations from different diatom species and it has the potential to speed up applications such as epigenetic explorations as well as single cell ("single nuclei") genomics, transcriptomics and proteomics in different diatom species.
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Affiliation(s)
| | | | - Pina Marotta
- Stazione Zoologica Anton Dohrn, 80121, Napoli, Italy
| | | | | | | | - Elio Biffali
- Stazione Zoologica Anton Dohrn, 80121, Napoli, Italy
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Falcón J, Torriglia A, Attia D, Viénot F, Gronfier C, Behar-Cohen F, Martinsons C, Hicks D. Exposure to Artificial Light at Night and the Consequences for Flora, Fauna, and Ecosystems. Front Neurosci 2020; 14:602796. [PMID: 33304237 PMCID: PMC7701298 DOI: 10.3389/fnins.2020.602796] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/22/2020] [Indexed: 12/22/2022] Open
Abstract
The present review draws together wide-ranging studies performed over the last decades that catalogue the effects of artificial-light-at-night (ALAN) upon living species and their environment. We provide an overview of the tremendous variety of light-detection strategies which have evolved in living organisms - unicellular, plants and animals, covering chloroplasts (plants), and the plethora of ocular and extra-ocular organs (animals). We describe the visual pigments which permit photo-detection, paying attention to their spectral characteristics, which extend from the ultraviolet into infrared. We discuss how organisms use light information in a way crucial for their development, growth and survival: phototropism, phototaxis, photoperiodism, and synchronization of circadian clocks. These aspects are treated in depth, as their perturbation underlies much of the disruptive effects of ALAN. The review goes into detail on circadian networks in living organisms, since these fundamental features are of critical importance in regulating the interface between environment and body. Especially, hormonal synthesis and secretion are often under circadian and circannual control, hence perturbation of the clock will lead to hormonal imbalance. The review addresses how the ubiquitous introduction of light-emitting diode technology may exacerbate, or in some cases reduce, the generalized ever-increasing light pollution. Numerous examples are given of how widespread exposure to ALAN is perturbing many aspects of plant and animal behaviour and survival: foraging, orientation, migration, seasonal reproduction, colonization and more. We examine the potential problems at the level of individual species and populations and extend the debate to the consequences for ecosystems. We stress, through a few examples, the synergistic harmful effects resulting from the impacts of ALAN combined with other anthropogenic pressures, which often impact the neuroendocrine loops in vertebrates. The article concludes by debating how these anthropogenic changes could be mitigated by more reasonable use of available technology - for example by restricting illumination to more essential areas and hours, directing lighting to avoid wasteful radiation and selecting spectral emissions, to reduce impact on circadian clocks. We end by discussing how society should take into account the potentially major consequences that ALAN has on the natural world and the repercussions for ongoing human health and welfare.
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Affiliation(s)
- Jack Falcón
- Laboratoire Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), MNHN, CNRS FRE 2030, SU, IRD 207, UCN, UA, Paris, France
| | - Alicia Torriglia
- Centre de Recherche des Cordeliers, INSERM U 1138, Ophtalmopole Hôpital Cochin, Assistance Publique - Hôpitaux de Paris, Université de Paris - SU, Paris, France
| | - Dina Attia
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Maisons-Alfort, France
| | | | - Claude Gronfier
- Lyon Neuroscience Research Center (CRNL), Waking Team, Inserm UMRS 1028, CNRS UMR 5292, Université Claude Bernard Lyon 1, Lyon, France
| | - Francine Behar-Cohen
- Centre de Recherche des Cordeliers, INSERM U 1138, Ophtalmopole Hôpital Cochin, Assistance Publique - Hôpitaux de Paris, Université de Paris - SU, Paris, France
| | | | - David Hicks
- Inserm, CNRS, Institut des Neurosciences Cellulaires et Intégratives, Université de Strasbourg, Strasbourg, France
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Deka D, Marwein R, Chikkaputtaiah C, Kaki SS, Azmeera T, Boruah HPD, Velmurugan N. Strain improvement of long-chain fatty acids producing Micractinium sp. by flow cytometry. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Resilience and self-regulation processes of microalgae under UV radiation stress. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C: PHOTOCHEMISTRY REVIEWS 2020. [DOI: 10.1016/j.jphotochemrev.2019.100322] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Trench-Fiol S, Fink P. Metatranscriptomics From a Small Aquatic System: Microeukaryotic Community Functions Through the Diurnal Cycle. Front Microbiol 2020; 11:1006. [PMID: 32523568 PMCID: PMC7261829 DOI: 10.3389/fmicb.2020.01006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/24/2020] [Indexed: 11/13/2022] Open
Abstract
Light is an important factor for the growth of planktonic organisms, and many of them depend on the diurnal light/dark cycle to regulate key metabolic processes. So far, most of the diel responses were only studied in single species or marine and large lake communities. Yet, we lack information on whether these processes are regulated similarly in small aquatic systems such as ponds. Here, we investigated the activity of a microeukaryotic community from a temperate, small freshwater pond in response to the diurnal cycle. For this, we took samples at midday and night during the Central European summer. We extracted pigments and RNA from samples and the sequencing of eukaryotic transcripts allowed us to obtain day and night metatranscriptomes. Differentially expressed transcripts primarily corresponded to photosynthesis-related and translational processes, and were found to be upregulated at midday with high light conditions compared to darkness. Unique gene ontology classes were found at each respective condition. During the day, ontology classes including photoreception for photosynthesis, defense, and stress mechanisms dominated, while motility, ribosomal assembly and other large, energy-consuming processes were restricted to the night. Euglenophyta and Chlorophyta dominated the active phototrophic community, as shown by the pigment composition analysis. Regarding the gene expression patterns, we could confirm that the pond community appears to follow similar diurnal dynamics as those described for larger aquatic ecosystems. Overall, combining pigment analyses, metatranscriptomics, and data on physicochemical factors yielded considerably more insight into the metabolic processes performed by the microeukaryotic community of a small freshwater ecosystem.
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Affiliation(s)
- Stephanie Trench-Fiol
- Workgroup Aquatic Chemical Ecology, Institute for Zoology, University of Cologne, Cologne, Germany
| | - Patrick Fink
- Workgroup Aquatic Chemical Ecology, Institute for Zoology, University of Cologne, Cologne, Germany
- Department of Aquatic Ecosystem Analysis and Management, Helmholtz Centre for Environmental Research – UFZ, Magdeburg, Germany
- Department River Ecology, Helmholtz Centre for Environmental Research – UFZ, Magdeburg, Germany
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Shikata T, Takahashi F, Nishide H, Shigenobu S, Kamei Y, Sakamoto S, Yuasa K, Nishiyama Y, Yamasaki Y, Uchiyama I. RNA-Seq Analysis Reveals Genes Related to Photoreception, Nutrient Uptake, and Toxicity in a Noxious Red-Tide Raphidophyte Chattonella antiqua. Front Microbiol 2019; 10:1764. [PMID: 31417538 PMCID: PMC6685483 DOI: 10.3389/fmicb.2019.01764] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/16/2019] [Indexed: 11/13/2022] Open
Abstract
Aquaculture industries are under threat from noxious red tides, but harm can be mitigated by precautions such as early harvesting and restricting fish feeding to just before the outbreak of a red tide. Therefore, accurate techniques for forecasting red-tide outbreaks are strongly needed. Omics analyses have the potential to expand our understanding of the eco-physiology of these organisms at the molecular level, and to facilitate identification of molecular markers for forecasting their population dynamics and occurrence of damages to fisheries. Red tides of marine raphidophytes, especially Chattonella species, often extensively harm aquaculture industries in regions with a temperate climate around the world. A red tide of Chattonella tends to develop just after an input of nutrients along the coast. Chattonella displays diurnal vertical migration regulated by a weak blue light, so it photosynthesizes in the surface layer during the daytime and takes up nutrients in the bottom layer during the nighttime. Superoxide produced by Chattonella cells is a strong candidate for the cause of its toxicity to bacteria and fishes. Here we conducted mRNA-seq of Chattonella antiqua to identify genes with functions closely related to the dynamics of the noxious red tide, such as photosynthesis, photoreception, nutrient uptake, and superoxide production. The genes related to photosynthetic pigment biosynthesis and nutrient uptake had high similarity with those of model organisms of plants and algae and other red-tide microalgae. We identified orthologous genes of photoreceptors such as aureochrome (newly five genes), the cryptochrome/photolyase (CRY/PHR) family (6-4PHR, plant CRY or cyclobutane pyrimidine dimer [CPD] Class III, CPD Class II, and CRY-DASH), and phytochrome (four genes), which regulate various physiological processes such as flagellar motion and cell cycle in model organisms. Six orthologous genes of NADPH oxidase, which produces superoxide on the cell membrane, were found and divided into two types: one with 5-6 transmembrane domains and another with 11 transmembrane domains. The present study should open the way for analyzing the eco-physiological features of marine raphidophytes at the molecular level.
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Affiliation(s)
- Tomoyuki Shikata
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research and Education Agency, Hatsukaiti, Japan
| | - Fumio Takahashi
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Kawaguchi, Japan
| | - Hiroyo Nishide
- Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
| | - Shuji Shigenobu
- Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Yasuhiro Kamei
- Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Setsuko Sakamoto
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research and Education Agency, Hatsukaiti, Japan
| | - Kouki Yuasa
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Japan
| | - Yoshitaka Nishiyama
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Sakura-ku, Japan
| | - Yasuhiro Yamasaki
- Laboratory of Environmental Biology, Department of Applied Aquabiology, National Fisheries University, Fisheries Research and Education Agency, Yamaguchi, Japan
| | - Ikuo Uchiyama
- Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
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Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. ISME JOURNAL 2019; 13:2817-2833. [PMID: 31320727 PMCID: PMC6794264 DOI: 10.1038/s41396-019-0472-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 06/11/2019] [Accepted: 06/15/2019] [Indexed: 01/06/2023]
Abstract
Phytoplankton and associated microbial communities provide organic carbon to oceanic food webs and drive ecosystem dynamics. However, capturing those dynamics is challenging. Here, an in situ, semi-Lagrangian, robotic sampler profiled pelagic microbes at 4 h intervals over ~2.6 days in North Pacific high-nutrient, low-chlorophyll waters. We report on the community structure and transcriptional dynamics of microbes in an operationally large size class (>5 μm) predominantly populated by dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria (chiefly Synechococcus), prasinophytes (chiefly Ostreococcus), fungi, archaea, and proteobacteria. Apart from fungi and archaea, all groups exhibited 24-h periodicity in some transcripts, but larger portions of the transcriptome oscillated in phototrophs. Periodic photosynthesis-related transcripts exhibited a temporal cascade across the morning hours, conserved across diverse phototrophic lineages. Pronounced silica:nitrate drawdown, a high flavodoxin to ferredoxin transcript ratio, and elevated expression of other Fe-stress markers indicated Fe-limitation. Fe-stress markers peaked during a photoperiodically adaptive time window that could modulate phytoplankton response to seasonal Fe-limitation. Remarkably, we observed viruses that infect the majority of abundant taxa, often with total transcriptional activity synchronized with putative hosts. Taken together, these data reveal a microbial plankton community that is shaped by recycled production and tightly controlled by Fe-limitation and viral activity.
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Cepas V, López Y, Gabasa Y, Martins CB, Ferreira JD, Correia MJ, Santos LMA, Oliveira F, Ramos V, Reis M, Castelo-Branco R, Morais J, Vasconcelos V, Probert I, Guilloud E, Mehiri M, Soto SM. Inhibition of Bacterial and Fungal Biofilm Formation by 675 Extracts from Microalgae and Cyanobacteria. Antibiotics (Basel) 2019; 8:antibiotics8020077. [PMID: 31212792 PMCID: PMC6628188 DOI: 10.3390/antibiotics8020077] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 11/17/2022] Open
Abstract
Bacterial biofilms are complex biological systems that are difficult to eradicate at a medical, industrial, or environmental level. Biofilms confer bacteria protection against external factors and antimicrobial treatments. Taking into account that about 80% of human infections are caused by bacterial biofilms, the eradication of these structures is a great priority. Biofilms are resistant to old-generation antibiotics, which has led to the search for new antimicrobials from different sources, including deep oceans/seas. In this study, 675 extracts obtained from 225 cyanobacteria and microalgae species (11 phyla and 6 samples belonging to unknown group) were obtained from different culture collections: The Blue Biotechnology and Ecotoxicology Culture Collection (LEGE-CC), the Coimbra Collection of Algae (ACOI) from Portugal, and the Roscoff Culture Collection (RCC) from France. The largest number of samples was made up of the microalgae phylum Chlorophyta (270) followed by Cyanobacteria (261). To obtain a large range of new bioactive compounds, a method involving three consecutive extractions (hexane, ethyl acetate, and methanol) was used. The antibiofilm activity of extracts was determined against seven different bacterial species and two Candida strains in terms of minimal biofilm inhibitory concentration (MBIC). The highest biofilm inhibition rates (%) were achieved against Candida albicans and Enterobacter cloacae. Charophyta, Chlorophyta, and Cyanobacteria were the most effective against all microorganisms. In particular, extracts of Cercozoa phylum presented the lowest MBIC50 and MBIC90 values for all the strains except C. albicans.
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Affiliation(s)
- Virginio Cepas
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Spain.
| | - Yuly López
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Spain.
| | - Yaiza Gabasa
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Spain.
| | - Clara B Martins
- Coimbra Collection of Algae (ACOI), Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal.
| | - Joana D Ferreira
- Coimbra Collection of Algae (ACOI), Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal.
| | - Maria J Correia
- Coimbra Collection of Algae (ACOI), Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal.
| | - Lília M A Santos
- Coimbra Collection of Algae (ACOI), Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal.
| | - Flávio Oliveira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), 4450-208 Porto, Portugal.
| | - Vitor Ramos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), 4450-208 Porto, Portugal.
| | - Mariana Reis
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), 4450-208 Porto, Portugal.
| | - Raquel Castelo-Branco
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), 4450-208 Porto, Portugal.
| | - João Morais
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), 4450-208 Porto, Portugal.
| | - Vitor Vasconcelos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), 4450-208 Porto, Portugal.
- Faculty of Sciences, University of Porto, 4450-208 Porto, Portugal.
| | - Ian Probert
- Roscoff Culture Collection, Sorbonne University/CNRS, Roscoff Biological Station, 29680 Roscoff, France.
| | - Emilie Guilloud
- Roscoff Culture Collection, Sorbonne University/CNRS, Roscoff Biological Station, 29680 Roscoff, France.
| | - Mohamed Mehiri
- Marine Natural Products Team, Nice Institute of Chemistry, UMR 7272 University Nice Côte d'Azur/CNRS, 60103 Nice, France.
| | - Sara M Soto
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036 Barcelona, Spain.
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bHLH-PAS protein RITMO1 regulates diel biological rhythms in the marine diatom Phaeodactylum tricornutum. Proc Natl Acad Sci U S A 2019; 116:13137-13142. [PMID: 31171659 PMCID: PMC6600994 DOI: 10.1073/pnas.1819660116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Periodic light-dark cycles govern the timing of basic biological processes in organisms inhabiting land as well as the sea, where life evolved. Although prominent marine phytoplanktonic organisms such as diatoms show robust diel rhythms, the mechanisms regulating these processes are still obscure. By characterizing a Phaeodactylum tricornutum bHLH-PAS nuclear protein, hereby named RITMO1, we shed light on the regulation of the daily life of diatoms. Alteration of RITMO1 expression levels and timing by ectopic overexpression results in lines with deregulated diurnal gene expression profiles compared with the wild-type cells. Reduced gene expression oscillations are also observed in these lines in continuous darkness, showing that the regulation of rhythmicity by RITMO1 is not directly dependent on light inputs. We also describe strong diurnal rhythms of cellular fluorescence in wild-type cells, which persist in continuous light conditions, indicating the existence of an endogenous circadian clock in diatoms. The altered rhythmicity observed in RITMO1 overexpression lines in continuous light supports the involvement of this protein in circadian rhythm regulation. Phylogenetic analysis reveals a wide distribution of RITMO1-like proteins in the genomes of diatoms as well as in other marine algae, which may indicate a common function in these phototrophs. This study adds elements to our understanding of diatom biology and offers perspectives to elucidate timekeeping mechanisms in marine organisms belonging to a major, but under-investigated, branch of the tree of life.
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Ribera d’Alcalà M. Similarities, differences and mechanisms of climate impact on terrestrial vs. marine ecosystems. NATURE CONSERVATION 2019. [DOI: 10.3897/natureconservation.34.30923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Comparisons between terrestrial and marine ecosystems are generally not in the main stream of scientific literature even though Webb (2012) listed several points for which the transfer of knowledge and concepts related to one or to the other system would benefit our understanding of both. Even sharing this view, the leading hypothesis behind this contribution is that the pelagic system, where the dominant biotic component by number and biomass is microscopic, has specific features which strongly differentiate it from the above-the-surface terrestrial systems. Due to this, climate change, i.e. changes in temperature, precipitation and most importantly in the dynamics of the two fluid media, atmosphere and ocean, act with different mechanisms which prevents proceeding with analogies in many cases. In addition, the non-linearity of most of the processes and responses to perturbations requires, in order to obtain reliable forecasts or hindcasts, a detailed analysis of the path followed by the system which is normally overlooked in the step-change simulations or projections.
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Baldisserotto C, Sabia A, Ferroni L, Pancaldi S. Biological aspects and biotechnological potential of marine diatoms in relation to different light regimens. World J Microbiol Biotechnol 2019; 35:35. [PMID: 30712106 DOI: 10.1007/s11274-019-2607-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/27/2019] [Indexed: 11/25/2022]
Abstract
As major primary producers in marine environments, diatoms are considered a valuable feedstock of biologically active compounds for application in several biotechnological fields. Due to their metabolic plasticity, especially for light perception and use and in order to make microalgal production more environmentally sustainable, marine diatoms are considered good candidates for the large-scale cultivation. Among physical parameters, light plays a primary role. Even if sunlight is cost-effective, the employment of artificial light becomes a winning strategy if a high-value microalgal biomass is produced. Several researches on marine diatoms are designed to study the influence of different light regimens to increase biomass production enriched in biotechnologically high-value compounds (lipids, carotenoids, proteins, polysaccharides), or with emphasised photonic properties of the frustule.
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Affiliation(s)
- Costanza Baldisserotto
- Department of Life Sciences and Biotechnology, University of Ferrara, C.so Ercole I d'Este, 32, 44121, Ferrara, Italy
| | - Alessandra Sabia
- Department of Life Sciences and Biotechnology, University of Ferrara, C.so Ercole I d'Este, 32, 44121, Ferrara, Italy
| | - Lorenzo Ferroni
- Department of Life Sciences and Biotechnology, University of Ferrara, C.so Ercole I d'Este, 32, 44121, Ferrara, Italy
| | - Simonetta Pancaldi
- Department of Life Sciences and Biotechnology, University of Ferrara, C.so Ercole I d'Este, 32, 44121, Ferrara, Italy.
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Arboleda E, Hartenstein V, Martinez P, Reichert H, Sen S, Sprecher S, Bailly X. An Emerging System to Study Photosymbiosis, Brain Regeneration, Chronobiology, and Behavior: The Marine Acoel Symsagittifera roscoffensis. Bioessays 2018; 40:e1800107. [PMID: 30151860 DOI: 10.1002/bies.201800107] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/23/2018] [Indexed: 01/23/2023]
Abstract
The acoel worm Symsagittifera roscoffensis, an early offshoot of the Bilateria and the only well-studied marine acoel that lives in a photosymbiotic relationship, exhibits a centralized nervous system, brain regeneration, and a wide repertoire of complex behaviors such as circatidal rhythmicity, photo/geotaxis, and social interactions. While this animal can be collected by the thousands and is studied historically, significant progress is made over the last decade to develop it as an emerging marine model. The authors here present the feasibility of culturing it in the laboratory and describe the progress made on different areas, including genomic and tissue architectures, highlighting the associated challenges. In light of these developments, and on the ability to access abundant synchronized embryos, the authors put forward S. roscoffensis as a marine system to revisit questions in the areas of photosymbiosis, regeneration, chronobiology, and the study of complex behaviors from a molecular and evolutionary perspective.
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Affiliation(s)
- Enrique Arboleda
- Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | | | - Pedro Martinez
- Institut Català de Recerca i EstudisAvancats (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
| | - Heinrich Reichert
- Departement de Biologie Universite de Fribourg, 1700 Fribourg, Switzerland
| | - Sonia Sen
- Institute of Neuroscience, Institute of Molecular Biology, Howard Hughes Medical Institute, Eugene, OR 97403
| | | | - Xavier Bailly
- CNRS, Station Biologique de Roscoff, 29680 Roscoff, France
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Niyogi KK. Editorial overview: Physiology and metabolism: Light responses from photoreceptors to photosynthesis and photoprotection. CURRENT OPINION IN PLANT BIOLOGY 2017; 37:iv-vi. [PMID: 28606394 DOI: 10.1016/j.pbi.2017.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Krishna K Niyogi
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720-3102, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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