1
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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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2
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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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3
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Noordally ZB, Hindle MM, Martin SF, Seaton DD, Simpson TI, Le Bihan T, Millar AJ. A phospho-dawn of protein modification anticipates light onset in the picoeukaryote Ostreococcus tauri. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5514-5531. [PMID: 37481465 PMCID: PMC10540734 DOI: 10.1093/jxb/erad290] [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: 12/15/2022] [Accepted: 07/20/2023] [Indexed: 07/24/2023]
Abstract
Diel regulation of protein levels and protein modification had been less studied than transcript rhythms. Here, we compare transcriptome data under light-dark cycles with partial proteome and phosphoproteome data, assayed using shotgun MS, from the alga Ostreococcus tauri, the smallest free-living eukaryote. A total of 10% of quantified proteins but two-thirds of phosphoproteins were rhythmic. Mathematical modelling showed that light-stimulated protein synthesis can account for the observed clustering of protein peaks in the daytime. Prompted by night-peaking and apparently dark-stable proteins, we also tested cultures under prolonged darkness, where the proteome changed less than under the diel cycle. Among the dark-stable proteins were prasinophyte-specific sequences that were also reported to accumulate when O. tauri formed lipid droplets. In the phosphoproteome, 39% of rhythmic phospho-sites reached peak levels just before dawn. This anticipatory phosphorylation suggests that a clock-regulated phospho-dawn prepares green cells for daytime functions. Acid-directed and proline-directed protein phosphorylation sites were regulated in antiphase, implicating the clock-related casein kinases 1 and 2 in phase-specific regulation, alternating with the CMGC protein kinase family. Understanding the dynamic phosphoprotein network should be facilitated by the minimal kinome and proteome of O. tauri. The data are available from ProteomeXchange, with identifiers PXD001734, PXD001735, and PXD002909.
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Affiliation(s)
- Zeenat B Noordally
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Matthew M Hindle
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Sarah F Martin
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Daniel D Seaton
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - T Ian Simpson
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK
| | - Thierry Le Bihan
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
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4
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Gururaj M, Ohmura A, Ozawa M, Yamano T, Fukuzawa H, Matsuo T. A potential EARLY FLOWERING 3 homolog in Chlamydomonas is involved in the red/violet and blue light signaling pathways for the degradation of RHYTHM OF CHLOROPLAST 15. PLoS Genet 2022; 18:e1010449. [PMID: 36251728 PMCID: PMC9612821 DOI: 10.1371/journal.pgen.1010449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 10/27/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022] Open
Abstract
Light plays a major role in resetting the circadian clock, allowing the organism to synchronize with the environmental day and night cycle. In Chlamydomonas the light-induced degradation of the circadian clock protein, RHYTHM OF CHLOROPLAST 15 (ROC15), is considered one of the key events in resetting the circadian clock. Red/violet and blue light signals have been shown to reach the clock via different molecular pathways; however, many of the participating components of these pathways are yet to be elucidated. Here, we used a forward genetics approach using a reporter strain that expresses a ROC15-luciferase fusion protein. We isolated a mutant that showed impaired ROC15 degradation in response to a wide range of visible wavelengths and impaired light-induced phosphorylation of ROC15. These results suggest that the effects of different wavelengths converge before acting on ROC15 or at ROC15 phosphorylation. Furthermore, the mutant showed a weakened phase resetting in response to light, but its circadian rhythmicity remained largely unaffected under constant light and constant dark conditions. Surprisingly, the gene disrupted in this mutant was found to encode a protein that possessed a very weak similarity to the Arabidopsis thaliana EARLY FLOWERING 3 (ELF3). Our results suggest that this protein is involved in the many different light signaling pathways to the Chlamydomonas circadian clock. However, it may not influence the transcriptional oscillator of Chlamydomonas to a great extent. This study provides an opportunity to further understand the mechanisms underlying light-induced clock resetting and explore the evolution of the circadian clock architecture in Viridiplantae. Resetting of the circadian clock is crucial for an organism, as it allows the synchronization of its internal processes with the day/night cycle. Environmental signals—such as light and temperature—contribute to this event. In plants, the molecular mechanisms underlying the light-induced resetting of the circadian clock have been well-studied in the streptophyte, Arabidopsis thaliana, and has been explored in some chlorophyte algae such as Ostreococcus tauri and Chlamydomonas reinhardtii. Here, we used a forward genetics approach to examine the light signaling pathway of a process considered critical for the light resetting of the Chlamydomonas clock—light-induced degradation of the circadian clock protein ROC15. We explored various aspects of the isolated mutant, such as the degradation of ROC15 in response to a range of visible wavelengths, the circadian rhythm, and the phase resetting of the rhythm. We show that the effects of different wavelengths of light converge before acting on ROC15 or at ROC15 phosphorylation with the aid of a potential homolog of the Arabidopsis thaliana ELF3. Our findings contradict the existing view that there is no known homolog of ELF3 in chlorophyte algae. This study, therefore, sheds light on the evolutionary aspects of the Viridiplantae circadian clocks and their light resetting.
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Affiliation(s)
- Malavika Gururaj
- Center for Gene Research, Nagoya University, Nagoya, Japan
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Ayumi Ohmura
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Mariko Ozawa
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Takashi Yamano
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Hideya Fukuzawa
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takuya Matsuo
- Center for Gene Research, Nagoya University, Nagoya, Japan
- Graduate School of Science, Nagoya University, Nagoya, Japan
- * E-mail:
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5
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Petersen J, Rredhi A, Szyttenholm J, Mittag M. Evolution of circadian clocks along the green lineage. PLANT PHYSIOLOGY 2022; 190:924-937. [PMID: 35325228 PMCID: PMC9516769 DOI: 10.1093/plphys/kiac141] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/04/2022] [Indexed: 05/10/2023]
Abstract
Circadian clocks govern temporal programs in the green lineage (Chloroplastida) as they do in other photosynthetic pro- and eukaryotes, bacteria, fungi, animals, and humans. Their physiological properties, including entrainment, phase responses, and temperature compensation, are well conserved. The involvement of transcriptional/translational feedback loops in the oscillatory machinery and reversible phosphorylation events are also maintained. Circadian clocks control a large variety of output rhythms in green algae and terrestrial plants, adjusting their metabolism and behavior to the day-night cycle. The angiosperm Arabidopsis (Arabidopsis thaliana) represents a well-studied circadian clock model. Several molecular components of its oscillatory machinery are conserved in other Chloroplastida, but their functions may differ. Conserved clock components include at least one member of the CIRCADIAN CLOCK ASSOCIATED1/REVEILLE and one of the PSEUDO RESPONSE REGULATOR family. The Arabidopsis evening complex members EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRHYTHMO are found in the moss Physcomitrium patens and in the liverwort Marchantia polymorpha. In the flagellate chlorophyte alga Chlamydomonas reinhardtii, only homologs of ELF4 and LUX (named RHYTHM OF CHLOROPLAST ROC75) are present. Temporal ROC75 expression in C. reinhardtii is opposite to that of the angiosperm LUX, suggesting different clock mechanisms. In the picoalga Ostreococcus tauri, both ELF genes are missing, suggesting that it has a progenitor circadian "green" clock. Clock-relevant photoreceptors and thermosensors vary within the green lineage, except for the CRYPTOCHROMEs, whose variety and functions may differ. More genetically tractable models of Chloroplastida are needed to draw final conclusions about the gradual evolution of circadian clocks within the green lineage.
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Affiliation(s)
- Jan Petersen
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Anxhela Rredhi
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Julie Szyttenholm
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Jena 07743, Germany
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6
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Sharma S, Sanyal SK, Sushmita K, Chauhan M, Sharma A, Anirudhan G, Veetil SK, Kateriya S. Modulation of Phototropin Signalosome with Artificial Illumination Holds Great Potential in the Development of Climate-Smart Crops. Curr Genomics 2021; 22:181-213. [PMID: 34975290 PMCID: PMC8640849 DOI: 10.2174/1389202922666210412104817] [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: 09/17/2020] [Revised: 01/21/2021] [Accepted: 03/01/2021] [Indexed: 11/22/2022] Open
Abstract
Changes in environmental conditions like temperature and light critically influence crop production. To deal with these changes, plants possess various photoreceptors such as Phototropin (PHOT), Phytochrome (PHY), Cryptochrome (CRY), and UVR8 that work synergistically as sensor and stress sensing receptors to different external cues. PHOTs are capable of regulating several functions like growth and development, chloroplast relocation, thermomorphogenesis, metabolite accumulation, stomatal opening, and phototropism in plants. PHOT plays a pivotal role in overcoming the damage caused by excess light and other environmental stresses (heat, cold, and salinity) and biotic stress. The crosstalk between photoreceptors and phytohormones contributes to plant growth, seed germination, photo-protection, flowering, phototropism, and stomatal opening. Molecular genetic studies using gene targeting and synthetic biology approaches have revealed the potential role of different photoreceptor genes in the manipulation of various beneficial agronomic traits. Overexpression of PHOT2 in Fragaria ananassa leads to the increase in anthocyanin content in its leaves and fruits. Artificial illumination with blue light alone and in combination with red light influence the growth, yield, and secondary metabolite production in many plants, while in algal species, it affects growth, chlorophyll content, lipid production and also increases its bioremediation efficiency. Artificial illumination alters the morphological, developmental, and physiological characteristics of agronomic crops and algal species. This review focuses on PHOT modulated signalosome and artificial illumination-based photo-biotechnological approaches for the development of climate-smart crops.
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Affiliation(s)
- Sunita Sharma
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sibaji K Sanyal
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Kumari Sushmita
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manisha Chauhan
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi-110025, India
| | - Amit Sharma
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi-110025, India
| | - Gireesh Anirudhan
- Integrated Science Education and Research Centre (ISERC), Institute of Science (Siksha Bhavana), Visva Bharati (A Central University), Santiniketan (PO), West Bengal, 731235, India
| | - Sindhu K Veetil
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suneel Kateriya
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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7
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Kay H, Grünewald E, Feord HK, Gil S, Peak-Chew SY, Stangherlin A, O'Neill JS, van Ooijen G. Deep-coverage spatiotemporal proteome of the picoeukaryote Ostreococcus tauri reveals differential effects of environmental and endogenous 24-hour rhythms. Commun Biol 2021; 4:1147. [PMID: 34593975 PMCID: PMC8484446 DOI: 10.1038/s42003-021-02680-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 09/07/2021] [Indexed: 11/18/2022] Open
Abstract
The cellular landscape changes dramatically over the course of a 24 h day. The proteome responds directly to daily environmental cycles and is additionally regulated by the circadian clock. To quantify the relative contribution of diurnal versus circadian regulation, we mapped proteome dynamics under light:dark cycles compared with constant light. Using Ostreococcus tauri, a prototypical eukaryotic cell, we achieved 85% coverage, which allowed an unprecedented insight into the identity of proteins that facilitate rhythmic cellular functions. The overlap between diurnally- and circadian-regulated proteins was modest and these proteins exhibited different phases of oscillation between the two conditions. Transcript oscillations were generally poorly predictive of protein oscillations, in which a far lower relative amplitude was observed. We observed coordination between the rhythmic regulation of organelle-encoded proteins with the nuclear-encoded proteins that are targeted to organelles. Rhythmic transmembrane proteins showed a different phase distribution compared with rhythmic soluble proteins, indicating the existence of a circadian regulatory process specific to the biogenesis and/or degradation of membrane proteins. Our observations argue that the cellular spatiotemporal proteome is shaped by a complex interaction between intrinsic and extrinsic regulatory factors through rhythmic regulation at the transcriptional as well as post-transcriptional, translational, and post-translational levels. Holly Kay, Ellen Grünewald, et al. provide an in-depth examination of the proteome in the eukaryotic green alga, Ostreococcus tauri, under circadian constant light or cycling diurnal light-dark conditions. They observe that there is little overlap between mRNA and protein expression rhythms, or the diurnal and circadian proteome, suggesting that the cellular spatiotemporal proteome is shaped through rhythmic regulation at multiple stages of transcription and translation.
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Affiliation(s)
- Holly Kay
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Ellen Grünewald
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Helen K Feord
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Sergio Gil
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Sew Y Peak-Chew
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - John S O'Neill
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Gerben van Ooijen
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK.
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8
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Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. Proc Natl Acad Sci U S A 2021; 118:2011038118. [PMID: 33547239 PMCID: PMC8017926 DOI: 10.1073/pnas.2011038118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Most organisms coordinate key biological events to coincide with the day/night cycle. These diel oscillations are entrained through the activity of light-sensitive photoreceptors that allow organisms to respond rapidly to changes in light exposure. In the ocean, the plankton community must additionally contend with dramatic changes in the quantity and quality of light over depth. Here, we show that the predominantly blue-light field in the open-ocean environment may have driven expansion of blue light-sensitive regulatory elements in open-ocean eukaryotic plankton derived from secondary and tertiary endosymbiosis. The diel transcription of genes encoding light-sensitive elements indicate that photosynthetic and heterotrophic marine protists respond to and anticipate fluctuating light conditions in the dynamic marine environment. The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular photoreceptors sense specific wavelengths of light that can reset the internal circadian clock and/or elicit distinct phenotypic responses. In the surface ocean, microbial communities additionally modulate nonrhythmic changes in light quality and quantity as they are mixed to different depths. Here, we show that eukaryotic plankton in the North Pacific Subtropical Gyre transcribe genes encoding light-sensitive proteins that may serve as light-activated transcription factors, elicit light-driven electrical/chemical cascades, or initiate secondary messenger-signaling cascades. Overall, the protistan community relies on blue light-sensitive photoreceptors of the cryptochrome/photolyase family, and proteins containing the Light-Oxygen-Voltage (LOV) domain. The greatest diversification occurred within Haptophyta and photosynthetic stramenopiles where the LOV domain was combined with different DNA-binding domains and secondary signal-transduction motifs. Flagellated protists utilize green-light sensory rhodopsins and blue-light helmchromes, potentially underlying phototactic/photophobic and other behaviors toward specific wavelengths of light. Photoreceptors such as phytochromes appear to play minor roles in the North Pacific Subtropical Gyre. Transcript abundance of environmental light-sensitive protein-encoding genes that display diel patterns are found to primarily peak at dawn. The exceptions are the LOV-domain transcription factors with peaks in transcript abundances at different times and putative phototaxis photoreceptors transcribed throughout the day. Together, these data illustrate the diversity of light-sensitive proteins that may allow disparate groups of protists to respond to light and potentially synchronize patterns of growth, division, and mortality within the dynamic ocean environment.
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9
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Yu C, Li X, Han B, Zhao Y, Geng S, Ning D, Ma T, Yu X. Simultaneous improvement of astaxanthin and lipid production of Haematococcus pluvialis by using walnut shell extracts. ALGAL RES 2021. [DOI: 10.1016/j.algal.2020.102171] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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10
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Matsuo T, Iida T, Ohmura A, Gururaj M, Kato D, Mutoh R, Ihara K, Ishiura M. The role of ROC75 as a daytime component of the circadian oscillator in Chlamydomonas reinhardtii. PLoS Genet 2020; 16:e1008814. [PMID: 32555650 PMCID: PMC7299327 DOI: 10.1371/journal.pgen.1008814] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 04/29/2020] [Indexed: 01/20/2023] Open
Abstract
The circadian clocks in chlorophyte algae have been studied in two model organisms, Chlamydomonas reinhardtii and Ostreococcus tauri. These studies revealed that the chlorophyte clocks include some genes that are homologous to those of the angiosperm circadian clock. However, the genetic network architectures of the chlorophyte clocks are largely unknown, especially in C. reinhardtii. In this study, using C. reinhardtii as a model, we characterized RHYTHM OF CHLOROPLAST (ROC) 75, a clock gene encoding a putative GARP DNA-binding transcription factor similar to the clock proteins LUX ARRHYTHMO (LUX, also called PHYTOCLOCK 1 [PCL1]) and BROTHER OF LUX ARRHYTHMO (BOA, also called NOX) of the angiosperm Arabidopsis thaliana. We observed that ROC75 is a day/subjective day-phase-expressed nuclear-localized protein that associates with some night-phased clock genes and represses their expression. This repression may be essential for the gating of reaccumulation of the other clock-related GARP protein, ROC15, after its light-dependent degradation. The restoration of ROC75 function in an arrhythmic roc75 mutant under constant darkness leads to the resumption of circadian oscillation from the subjective dawn, suggesting that the ROC75 restoration acts as a morning cue for the C. reinhardtii clock. Our study reveals a part of the genetic network of C. reinhardtii clock that could be considerably different from that of A. thaliana.
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Affiliation(s)
- Takuya Matsuo
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- * E-mail:
| | - Takahiro Iida
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Ayumi Ohmura
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Malavika Gururaj
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Daisaku Kato
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Risa Mutoh
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Masahiro Ishiura
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
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11
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Brandoli C, Petri C, Egea-Cortines M, Weiss J. The clock gene Gigantea 1 from Petunia hybrida coordinates vegetative growth and inflorescence architecture. Sci Rep 2020; 10:275. [PMID: 31937847 PMCID: PMC6959227 DOI: 10.1038/s41598-019-57145-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/18/2019] [Indexed: 12/20/2022] Open
Abstract
The gene GIGANTEA (GI) appeared early in land plants. It is a single copy gene in most plants and is found in two to three copies in Solanaceae. We analyzed the silencing of one GI copy, Petunia hybrida GI1 (PhGI1), by hairpin RNAs in Petunia in order to gain knowledge about its range of functions. Decreased transcript levels of PhGI1 were accompanied also by a reduction of PhGI2. They were further associated with increased time period between two consecutive peaks for PhGI1 and CHANEL (PhCHL), the orthologue of the blue light receptor gene ZEITLUPE (ZTL), confirming its role in maintaining circadian rhythmicity. Silenced plants were bigger with modified internode length and increased leaf size while flowering time was not altered. We uncovered a new function for PhGI1 as silenced plants showed reduction of flower bud number and the appearance of two flower buds in the bifurcation point, were normally one flower bud and the inflorescence meristem separate. Furthermore, one of the flower buds consistently showed premature flower abortion. Flowers that developed fully were significantly smaller as a result of decreased cell size. Even so the circadian pattern of volatile emission was unchanged in the silenced lines, flowers emitted 20% less volatiles on fresh weight basis over 24 hours and showed changes in the scent profile. Our results indicate a novel role of PhGI1 in the development of reproductive organs in Petunia. PhGI1 therefore represses growth in vegetative plant parts, maintains the typical cymose inflorescence structure, and inhibits premature flower abortion.
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Affiliation(s)
- Claudio Brandoli
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain
| | - César Petri
- Instituto de Hortofruticultura Subtropical y Mediterránea-UMA-CSIC, Departamento de Fruticultura Subtropical y Mediterránea, 29750, Algarrobo-costa, Málaga, Spain
| | - Marcos Egea-Cortines
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain
| | - Julia Weiss
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain.
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12
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Transcriptional Structure of Petunia Clock in Leaves and Petals. Genes (Basel) 2019; 10:genes10110860. [PMID: 31671570 PMCID: PMC6895785 DOI: 10.3390/genes10110860] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 01/20/2023] Open
Abstract
The plant circadian clock coordinates environmental signals with internal processes including secondary metabolism, growth, flowering, and volatile emission. Plant tissues are specialized in different functions, and petals conceal the sexual organs while attracting pollinators. Here we analyzed the transcriptional structure of the petunia (Petunia x hybrida) circadian clock in leaves and petals. We recorded the expression of 13 clock genes in petunia under light:dark (LD) and constant darkness (DD). Under light:dark conditions, clock genes reached maximum expression during the light phase in leaves and the dark period in petals. Under free running conditions of constant darkness, maximum expression was delayed, especially in petals. Interestingly, the rhythmic expression pattern of PhLHY persisted in leaves and petals in LD and DD. Gene expression variability differed among leaves and petals, time of day and photoperiod. The transcriptional noise was higher especially in leaves under constant darkness. We found that PhPRR7, PhPRR5, and PhGI paralogs showed changes in gene structure including exon number and deletions of CCT domain of the PRR family. Our results revealed that petunia petals presented a specialized clock.
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13
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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: 42] [Impact Index Per Article: 8.4] [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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14
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Luck M, Velázquez Escobar F, Glass K, Sabotke MI, Hagedorn R, Corellou F, Siebert F, Hildebrandt P, Hegemann P. Photoreactions of the Histidine Kinase Rhodopsin Ot-HKR from the Marine Picoalga Ostreococcus tauri. Biochemistry 2019; 58:1878-1891. [PMID: 30768260 DOI: 10.1021/acs.biochem.8b01200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The tiny picoalga, Ostreococcus tauri, originating from the Thau Lagoon is a member of the marine phytoplankton. Because of its highly reduced genome and small cell size, while retaining the fundamental requirements of a eukaryotic photosynthetic cell, it became a popular model organism for studying photosynthesis or circadian clock-related processes. We analyzed the spectroscopic properties of the photoreceptor domain of the histidine kinase rhodopsin Ot-HKR that is suggested to be involved in the light-induced entrainment of the Ostreococcus circadian clock. We found that the rhodopsin, Ot-Rh, dark state absorbs maximally at 505 nm. Exposure to green-orange light led to the accumulation of a blue-shifted M-state-like absorbance form with a deprotonated Schiff base. This Ot-Rh P400 state had an unusually long lifetime of several minutes. A second long-living photoproduct with a red-shifted absorbance, P560, accumulated upon illumination with blue/UVA light. The resulting photochromicity of the rhodopsin is expected to be advantageous to its function as a molecular control element of the signal transducing HKR domains. The light intensity and the ratio of blue vs green light are reflected by the ratio of rhodopsin molecules in the long-living absorbance forms. Furthermore, dark-state absorbance and the photocycle kinetics vary with the salt content of the environment substantially. This observation is attributed to anion binding in the dark state and a transient anion release during the photocycle, indicating that the salinity affects the photoinduced processes.
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Affiliation(s)
- Meike Luck
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Berlin 10115 , Germany
| | | | - Kathrin Glass
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Berlin 10115 , Germany
| | - Mareike-Isabel Sabotke
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Berlin 10115 , Germany
| | - Rolf Hagedorn
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Berlin 10115 , Germany
| | - Florence Corellou
- Laboratoire d'Oceanographie Microbienne , Université Pierre et Marie Curie (Paris 6), Centre National de la Recherche Scientifique, Unité Mixte de Recherche , 7621 , Observatoire Oceanologique, Banyuls/mer , France
| | - Friedrich Siebert
- Institute of Chemistry, Technische Universität Berlin , Berlin 10623 , Germany.,Institut für Molekulare Medizin und Zellforschung, Sektion Biophysik , Albert-Ludwigs-Universität Freiburg , Freiburg 79104 , Germany
| | - Peter Hildebrandt
- Institute of Chemistry, Technische Universität Berlin , Berlin 10623 , Germany
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Berlin 10115 , Germany
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15
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Ryo M, Yamashino T, Nomoto Y, Goto Y, Ichinose M, Sato K, Sugita M, Aoki S. Light-regulated PAS-containing histidine kinases delay gametophore formation in the moss Physcomitrella patens. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4839-4851. [PMID: 29992239 PMCID: PMC6137987 DOI: 10.1093/jxb/ery257] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 07/04/2018] [Indexed: 05/07/2023]
Abstract
Two-component systems (TCSs) are signal transduction mechanisms for responding to various environmental stimuli. In angiosperms, TCSs involved in phytohormone signaling have been intensively studied, whereas there are only a few reports on TCSs in basal land plants. The moss Physcomitrella patens possesses several histidine kinases (HKs) that are lacking in seed plant genomes. Here, we studied two of these unique HKs, PAS-histidine kinase 1 (PHK1) and its paralog PHK2, both of which have PAS (Per-Arnt-Sim) domains, which are known to show versatile functions such as sensing light or molecular oxygen. We found homologs of PHK1 and PHK2 only in early diverged clades such as bryophytes and lycophytes, but not in seed plants. The PAS sequences of PHK1 and PHK2 are more similar to a subset of bacterial PAS sequences than to any angiosperm PAS sequences. Gene disruption lines that lack either PHK1 or PHK2 or both formed gametophores earlier than the wild-type, and consistently, more caulonema side branches were induced in response to light in the disruption lines. Therefore, PHK1 and PHK2 delay the timing of gametophore development, probably by suppressing light-induced caulonema branching. This study provides new insights into the evolution of TCSs in plants.
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Affiliation(s)
- Masashi Ryo
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Takafumi Yamashino
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Correspondence: or
| | - Yuji Nomoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Yuki Goto
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Mizuho Ichinose
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Kensuke Sato
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Mamoru Sugita
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Setsuyuki Aoki
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Correspondence: or
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16
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Santamaría-Hernando S, Rodríguez-Herva JJ, Martínez-García PM, Río-Álvarez I, González-Melendi P, Zamorano J, Tapia C, Rodríguez-Palenzuela P, López-Solanilla E. Pseudomonas syringae pv. tomato exploits light signals to optimize virulence and colonization of leaves. Environ Microbiol 2018; 20:4261-4280. [PMID: 30058114 DOI: 10.1111/1462-2920.14331] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/13/2018] [Accepted: 06/17/2018] [Indexed: 11/30/2022]
Abstract
Light is pervasive in the leaf environment, creating opportunities for both plants and pathogens to cue into light as a signal to regulate plant-microbe interactions. Light enhances plant defences and regulates opening of stomata, an entry point for foliar bacterial pathogens such as Pseudomonas syringae pv. tomato DC3000 (PsPto). The effect of light perception on gene expression and virulence was investigated in PsPto. Light induced genetic reprogramming in PsPto that entailed significant changes in stress tolerance and virulence. Blue light-mediated up-regulation of type three secretion system genes and red light-mediated down-regulation of coronatine biosynthesis genes. Cells exposed to white light, blue light or darkness before inoculation were more virulent when inoculated at dawn than dusk probably due to an enhanced entry through open stomata. Exposure to red light repressed coronatine biosynthesis genes which could lead to a reduced stomatal re-opening and PsPto entry. Photoreceptor were required for the greater virulence of light-treated and dark-treated PsPto inoculated at dawn as compared to dusk, indicating that these proteins sense the absence of light and contribute to priming of virulence in the dark. These results support a model in which PsPto exploits light changes to maximize survival, entry and virulence on plants.
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Affiliation(s)
- Saray Santamaría-Hernando
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Campus Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - José J Rodríguez-Herva
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Campus Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain.,Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, Madrid, Spain
| | - Pedro M Martínez-García
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Campus Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Isabel Río-Álvarez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Campus Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Pablo González-Melendi
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Campus Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain.,Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, Madrid, Spain
| | - Jaime Zamorano
- Departamento de Astrofísica y CC. de la Atmósfera, Universidad Complutense, Madrid, Spain
| | - Carlos Tapia
- Departamento de Astrofísica y CC. de la Atmósfera, Universidad Complutense, Madrid, Spain
| | - Pablo Rodríguez-Palenzuela
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Campus Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain.,Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, Madrid, Spain
| | - Emilia López-Solanilla
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Campus Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain.,Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, Madrid, Spain
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17
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Kottke T, Oldemeyer S, Wenzel S, Zou Y, Mittag M. Cryptochrome photoreceptors in green algae: Unexpected versatility of mechanisms and functions. JOURNAL OF PLANT PHYSIOLOGY 2017; 217:4-14. [PMID: 28619534 DOI: 10.1016/j.jplph.2017.05.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/29/2017] [Accepted: 05/29/2017] [Indexed: 06/07/2023]
Abstract
Green algae have a highly complex and diverse set of cryptochrome photoreceptor candidates including members of the following subfamilies: plant, plant-like, animal-like, DASH and cryptochrome photolyase family 1 (CPF1). While some green algae encode most or all of them, others lack certain members. Here we present an overview about functional analyses of so far investigated cryptochrome photoreceptors from the green algae Chlamydomonas reinhardtii (plant and animal-like cryptochromes) and Ostreococcus tauri (CPF1) with regard to their biological significance and spectroscopic properties. Cryptochromes of both algae have been demonstrated recently to be involved to various extents in circadian clock regulation and in Chlamydomonas additionally in life cycle control. Moreover, CPF1 even performs light-driven DNA repair. The plant cryptochrome and CPF1 are UVA/blue light receptors, whereas the animal-like cryptochrome responds to almost the whole visible spectrum including red light. Accordingly, plant cryptochrome, animal-like cryptochrome and CPF1 differ fundamentally in their structural response to light as revealed by their visible and infrared spectroscopic signatures, and in the role of the flavin neutral radical acting as dark form or signaling state.
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Affiliation(s)
- Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.
| | - Sabine Oldemeyer
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Sandra Wenzel
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Yong Zou
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Maria Mittag
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, 07743 Jena, Germany.
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18
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Serrano-Bueno G, Romero-Campero FJ, Lucas-Reina E, Romero JM, Valverde F. Evolution of photoperiod sensing in plants and algae. CURRENT OPINION IN PLANT BIOLOGY 2017; 37:10-17. [PMID: 28391047 DOI: 10.1016/j.pbi.2017.03.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 05/21/2023]
Abstract
Measuring day length confers a strong fitness improvement to photosynthetic organisms as it allows them to anticipate light phases and take the best decisions preceding diurnal transitions. In close association with signals from the circadian clock and the photoreceptors, photoperiodic sensing constitutes also a precise way to determine the passing of the seasons and to take annual decisions such as the best time to flower or the beginning of dormancy. Photoperiodic sensing in photosynthetic organisms is ancient and two major stages in its evolution could be identified, the cyanobacterial time sensing and the evolutionary tool kit that arose in green algae and developed into the photoperiodic system of modern plants. The most recent discoveries about the evolution of the perception of light, measurement of day length and relationship with the circadian clock along the evolution of the eukaryotic green lineage will be discussed in this review.
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Affiliation(s)
- Gloria Serrano-Bueno
- Plant Development Unit, Institute for Plan Biochemistry and Photosynthesis, CSIC-Universidad de Sevilla, 49th, Americo Vespucio Av., 41092 Sevilla, Spain
| | - Francisco J Romero-Campero
- Plant Development Unit, Institute for Plan Biochemistry and Photosynthesis, CSIC-Universidad de Sevilla, 49th, Americo Vespucio Av., 41092 Sevilla, Spain
| | - Eva Lucas-Reina
- Plant Development Unit, Institute for Plan Biochemistry and Photosynthesis, CSIC-Universidad de Sevilla, 49th, Americo Vespucio Av., 41092 Sevilla, Spain
| | - Jose M Romero
- Plant Development Unit, Institute for Plan Biochemistry and Photosynthesis, CSIC-Universidad de Sevilla, 49th, Americo Vespucio Av., 41092 Sevilla, Spain
| | - Federico Valverde
- Plant Development Unit, Institute for Plan Biochemistry and Photosynthesis, CSIC-Universidad de Sevilla, 49th, Americo Vespucio Av., 41092 Sevilla, Spain.
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19
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Jaubert M, Bouly JP, Ribera d'Alcalà M, Falciatore A. Light sensing and responses in marine microalgae. CURRENT OPINION IN PLANT BIOLOGY 2017; 37:70-77. [PMID: 28456112 DOI: 10.1016/j.pbi.2017.03.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/13/2017] [Indexed: 06/07/2023]
Abstract
Marine eukaryotic phytoplankton are major contributors to global primary production. To adapt and thrive in the oceans, phytoplankton relies on a variety of light-regulated responses and light-acclimation capacities probably driven by sophisticated photoregulatory mechanisms. A plethora of photoreceptor-like sequences from marine microalgae have been identified in omics approaches. Initial studies have revealed that some algal photoreceptors are similar to those known in plants. In addition, new variants with different spectral tuning and algal-specific light sensors have also been found, changing current views and perspectives on how photoreceptor structure and function have diversified in phototrophs experiencing different environmental conditions.
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Affiliation(s)
- Marianne Jaubert
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 4, Place de Jussieu, 75005 Paris, France
| | - Jean-Pierre Bouly
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 4, Place de Jussieu, 75005 Paris, France
| | - Maurizio Ribera d'Alcalà
- Stazione Zoologica Anton Dohrn, Laboratory of Ecology and Evolution of Plankton, Villa Comunale, 80121 Naples, Italy.
| | - Angela Falciatore
- Sorbonne Universités, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative, 4, Place de Jussieu, 75005 Paris, France.
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20
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de los Reyes P, Romero-Campero FJ, Ruiz MT, Romero JM, Valverde F. Evolution of Daily Gene Co-expression Patterns from Algae to Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1217. [PMID: 28751903 PMCID: PMC5508029 DOI: 10.3389/fpls.2017.01217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 06/28/2017] [Indexed: 05/04/2023]
Abstract
Daily rhythms play a key role in transcriptome regulation in plants and microalgae orchestrating responses that, among other processes, anticipate light transitions that are essential for their metabolism and development. The recent accumulation of genome-wide transcriptomic data generated under alternating light:dark periods from plants and microalgae has made possible integrative and comparative analysis that could contribute to shed light on the evolution of daily rhythms in the green lineage. In this work, RNA-seq and microarray data generated over 24 h periods in different light regimes from the eudicot Arabidopsis thaliana and the microalgae Chlamydomonas reinhardtii and Ostreococcus tauri have been integrated and analyzed using gene co-expression networks. This analysis revealed a reduction in the size of the daily rhythmic transcriptome from around 90% in Ostreococcus, being heavily influenced by light transitions, to around 40% in Arabidopsis, where a certain independence from light transitions can be observed. A novel Multiple Bidirectional Best Hit (MBBH) algorithm was applied to associate single genes with a family of potential orthologues from evolutionary distant species. Gene duplication, amplification and divergence of rhythmic expression profiles seems to have played a central role in the evolution of gene families in the green lineage such as Pseudo Response Regulators (PRRs), CONSTANS-Likes (COLs), and DNA-binding with One Finger (DOFs). Gene clustering and functional enrichment have been used to identify groups of genes with similar rhythmic gene expression patterns. The comparison of gene clusters between species based on potential orthologous relationships has unveiled a low to moderate level of conservation of daily rhythmic expression patterns. However, a strikingly high conservation was found for the gene clusters exhibiting their highest and/or lowest expression value during the light transitions.
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Affiliation(s)
- Pedro de los Reyes
- Plant Development Unit, Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de SevillaSeville, Spain
| | - Francisco J. Romero-Campero
- Plant Development Unit, Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de SevillaSeville, Spain
- Department of Computer Science and Artificial Intelligence, Universidad de SevillaSeville, Spain
| | - M. Teresa Ruiz
- Plant Development Unit, Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de SevillaSeville, Spain
| | - José M. Romero
- Plant Development Unit, Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de SevillaSeville, Spain
| | - Federico Valverde
- Plant Development Unit, Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de SevillaSeville, Spain
- *Correspondence: Federico Valverde
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21
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Hirth M, Liverani S, Mahlow S, Bouget FY, Pohnert G, Sasso S. Metabolic profiling identifies trehalose as an abundant and diurnally fluctuating metabolite in the microalga Ostreococcus tauri. Metabolomics 2017; 13:68. [PMID: 28473745 PMCID: PMC5392535 DOI: 10.1007/s11306-017-1203-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/31/2017] [Indexed: 12/18/2022]
Abstract
INTRODUCTION The picoeukaryotic alga Ostreococcus tauri (Chlorophyta) belongs to the widespread group of marine prasinophytes. Despite its ecological importance, little is known about the metabolism of this alga. OBJECTIVES In this work, changes in the metabolome were quantified when O. tauri was grown under alternating cycles of 12 h light and 12 h darkness. METHODS Algal metabolism was analyzed by gas chromatography-mass spectrometry. Using fluorescence-activated cell sorting, the bacteria associated with O. tauri were depleted to below 0.1% of total cells at the time of metabolic profiling. RESULTS Of 111 metabolites quantified over light-dark cycles, 20 (18%) showed clear diurnal variations. The strongest fluctuations were found for trehalose. With an intracellular concentration of 1.6 mM in the dark, this disaccharide was six times more abundant at night than during the day. This fluctuation pattern of trehalose may be a consequence of starch degradation or of the synchronized cell cycle. On the other hand, maltose (and also sucrose) was below the detection limit (~10 μM). Accumulation of glycine in the light is in agreement with the presence of a classical glycolate pathway of photorespiration. We also provide evidence for the presence of fatty acid methyl and ethyl esters in O. tauri. CONCLUSIONS This study shows how the metabolism of O. tauri adapts to day and night and gives new insights into the configuration of the carbon metabolism. In addition, several less common metabolites were identified.
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Affiliation(s)
- Matthias Hirth
- 0000 0001 1939 2794grid.9613.dInstitute of General Botany and Plant Physiology, Friedrich Schiller University, Jena, Germany
| | - Silvia Liverani
- 0000 0001 0724 6933grid.7728.aDepartment of Mathematics, Brunel University London, Uxbridge, UK
| | - Sebastian Mahlow
- 0000 0001 1939 2794grid.9613.dInstitute of General Botany and Plant Physiology, Friedrich Schiller University, Jena, Germany
| | - François-Yves Bouget
- 0000 0001 2369 4306grid.463752.1Sorbonne Universités, UPMC Univ Paris 06 & Centre National pour la Recherche Scientifique CNRS, UMR 7621, Laboratoire d’Océanographie Microbienne, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Georg Pohnert
- 0000 0001 1939 2794grid.9613.dInstitute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- 0000 0004 0491 7131grid.418160.aMax Planck Institute for Chemical Ecology, Jena, Germany
| | - Severin Sasso
- 0000 0001 1939 2794grid.9613.dInstitute of General Botany and Plant Physiology, Friedrich Schiller University, Jena, Germany
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Ryo M, Matsuo T, Yamashino T, Ichinose M, Sugita M, Aoki S. Diversity of plant circadian clocks: Insights from studies of Chlamydomonas reinhardtii and Physcomitrella patens. PLANT SIGNALING & BEHAVIOR 2016; 11:e1116661. [PMID: 26645746 PMCID: PMC4871632 DOI: 10.1080/15592324.2015.1116661] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Arabidopsis thaliana has long been the model plant of choice for elucidating the mechanisms of the circadian clock. Recently, relevant results have accumulated in other species of green plant lineages, including green algae. This mini-review describes a comparison of the mechanism of the A. thaliana clock to those of the green alga Chlamydomonas reinhardtii and the moss Physcomitrella patens, focusing on commonalities and divergences of subsystems of the clock. The potential of such an approach from an evolutionary viewpoint is discussed.
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Affiliation(s)
- Masashi Ryo
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Takuya Matsuo
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Takafumi Yamashino
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Mizuho Ichinose
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Mamoru Sugita
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Setsuyuki Aoki
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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Thommen Q, Pfeuty B, Schatt P, Bijoux A, Bouget FY, Lefranc M. Probing entrainment of Ostreococcus tauri circadian clock by green and blue light through a mathematical modeling approach. Front Genet 2015; 6:65. [PMID: 25774167 PMCID: PMC4343026 DOI: 10.3389/fgene.2015.00065] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 02/09/2015] [Indexed: 12/22/2022] Open
Abstract
Most organisms anticipate daily environmental variations and orchestrate cellular functions thanks to a circadian clock which entrains robustly to the day/night cycle, despite fluctuations in light intensity due to weather or seasonal variations. Marine organisms are also subjected to fluctuations in light spectral composition as their depth varies, due to differential absorption of different wavelengths by sea water. Studying how light input pathways contribute to circadian clock robustness is therefore important. Ostreococcus tauri, a unicellular picoplanktonic marine green alga with low genomic complexity and simple cellular organization, has become a promising model organism for systems biology. Functional and modeling approaches have shown that a core circadian oscillator based on orthologs of Arabidopsis TOC1 and CCA1 clock genes accounts for most experimental data acquired under a wide range of conditions. Some evidence points at putative light input pathway(s) consisting of a two-component signaling system (TCS) controlled by the only two histidine kinases (HK) of O. tauri. LOV-HK is a blue light photoreceptor under circadian control, that is required for circadian clock function. An involvement of Rhodopsin-HK (Rhod-HK) is also conceivable since rhodopsin photoreceptors mediate blue to green light input in animal circadian clocks. Here, we probe the role of LOV-HK and Rhod-HK in mediating light input to the TOC1-CCA1 oscillator using a mathematical model incorporating the TCS hypothesis. This model agrees with clock gene expression time series representative of multiple environmental conditions in blue or green light, characterizing entrainment by light/dark cycles, free-running in constant light, and resetting. Experimental and theoretical results indicate that both blue and green light can reset O. tauri circadian clock. Moreover, our mathematical analysis suggests that Rhod-HK is a blue-green light receptor and drives the clock together with LOV-HK.
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Affiliation(s)
- Quentin Thommen
- Laboratoire de Physique, Lasers, Atomes, Molécules, Université Lille 1 Sciences et Technologies, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8523 Villeneuve d'Ascq, France
| | - Benjamin Pfeuty
- Laboratoire de Physique, Lasers, Atomes, Molécules, Université Lille 1 Sciences et Technologies, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8523 Villeneuve d'Ascq, France
| | - Philippe Schatt
- Unité Mixte de Recherche 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités Banyuls sur Mer, France
| | - Amandine Bijoux
- Unité Mixte de Recherche 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités Banyuls sur Mer, France
| | - François-Yves Bouget
- Unité Mixte de Recherche 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités Banyuls sur Mer, France
| | - Marc Lefranc
- Laboratoire de Physique, Lasers, Atomes, Molécules, Université Lille 1 Sciences et Technologies, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8523 Villeneuve d'Ascq, France
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Hisatomi O, Furuya K. A light-regulated bZIP module, photozipper, induces the binding of fused proteins to the target DNA sequence in a blue light-dependent manner. Photochem Photobiol Sci 2015; 14:1998-2006. [DOI: 10.1039/c5pp00178a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Yellow fluorescent protein or mCherry protein fused with the Photozipper underwent blue light-induced dimerization, which enhanced their affinities for the target DNA.
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Affiliation(s)
- Osamu Hisatomi
- Department of Earth and Space Science
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Keigo Furuya
- Department of Earth and Space Science
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
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25
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Abstract
As major contributors to global oxygen levels and producers of fatty acids, carotenoids, sterols, and phycocolloids, algae have significant ecological and commercial roles. Early algal models have contributed much to our understanding of circadian clocks at physiological and biochemical levels. The genetic and molecular approaches that identified clock components in other taxa have not been as widely applied to algae. We review results from seven species: the chlorophytes Chlamydomonas reinhardtii, Ostreococcus tauri, and Acetabularia spp.; the dinoflagellates Lingulodinium polyedrum and Symbiodinium spp.; the euglenozoa Euglena gracilis; and the red alga Cyanidioschyzon merolae. The relative simplicity, experimental tractability, and ecological and evolutionary diversity of algal systems may now make them particularly useful in integrating quantitative data from "omic" technologies (e.g., genomics, transcriptomics, metabolomics, and proteomics) with computational and mathematical methods.
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Affiliation(s)
- Zeenat B Noordally
- SynthSys and School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3BF, United Kingdom
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26
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Lozano JC, Schatt P, Botebol H, Vergé V, Lesuisse E, Blain S, Carré IA, Bouget FY. Efficient gene targeting and removal of foreign DNA by homologous recombination in the picoeukaryote Ostreococcus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:1073-83. [PMID: 24698018 DOI: 10.1111/tpj.12530] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 02/14/2014] [Accepted: 03/31/2014] [Indexed: 05/03/2023]
Abstract
With fewer than 8000 genes and a minimalist cellular organization, the green picoalga Ostreococcus tauri is one of the simplest photosynthetic eukaryotes. Ostreococcus tauri contains many plant-specific genes but exhibits a very low gene redundancy. The haploid genome is extremely dense with few repeated sequences and rare transposons. Thanks to the implementation of genetic transformation and vectors for inducible overexpression/knockdown this picoeukaryotic alga has emerged in recent years as a model organism for functional genomics analyses and systems biology. Here we report the development of an efficient gene targeting technique which we use to knock out the nitrate reductase and ferritin genes and to knock in a luciferase reporter in frame to the ferritin native protein. Furthermore, we show that the frequency of insertion by homologous recombination is greatly enhanced when the transgene is designed to replace an existing genomic insertion. We propose that a natural mechanism based on homologous recombination may operate to remove inserted DNA sequences from the genome.
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Affiliation(s)
- Jean-Claude Lozano
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls/mer, France; CNRS, UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls/mer, France
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27
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Bouget FY, Lefranc M, Thommen Q, Pfeuty B, Lozano JC, Schatt P, Botebol H, Vergé V. Transcriptional versus non-transcriptional clocks: A case study in Ostreococcus. Mar Genomics 2014; 14:17-22. [DOI: 10.1016/j.margen.2014.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 01/06/2014] [Accepted: 01/23/2014] [Indexed: 12/20/2022]
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28
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Raffelberg S, Gutt A, Gärtner W, Mandalari C, Abbruzzetti S, Viappiani C, Losi A. The amino acids surrounding the flavin 7a-methyl group determine the UVA spectral features of a LOV protein. Biol Chem 2014; 394:1517-28. [PMID: 23828427 DOI: 10.1515/hsz-2013-0163] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 07/01/2013] [Indexed: 11/15/2022]
Abstract
Flavin-binding light, oxygen, and voltage (LOV) domains are UVA/blue-light-sensing protein units that form a reversible flavin mononucleotide-cysteine adduct upon light induction. In their dark-adapted state, LOV domains exhibit the typical spectral features of fully oxidized riboflavin derivatives. A survey on the absorption spectra of various LOV domains revealed that the UVA spectral range is the most variable region (whereas the absorption band at 450 nm is virtually unchanged), showing essentially two distinct patterns found in plant phototropin LOV1 and LOV2 domains, respectively. In this work, we have identified a residue directly interacting with the isoalloxazine methyl group at C(7a) as the major UVA spectral tuner. In YtvA from Bacillus subtilis, this amino acid is threonine 30, and its mutation into apolar residues converts the LOV2-like spectrum of native YtvA into a LOV1-like pattern. Mutation T30A also accelerates the photocycle ca. 4-fold. Together with control mutations at different positions, our results experimentally confirm the previously calculated direction of the transition dipole moment for the UVA ππ* state and identify the mechanisms underlying spectral tuning in the LOV domains.
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29
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McClung CR. Beyond Arabidopsis: the circadian clock in non-model plant species. Semin Cell Dev Biol 2013; 24:430-6. [PMID: 23466287 DOI: 10.1016/j.semcdb.2013.02.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 02/13/2013] [Accepted: 02/15/2013] [Indexed: 01/26/2023]
Abstract
Circadian clocks allow plants to temporally coordinate many aspects of their biology with the diurnal cycle derived from the rotation of Earth on its axis. Although there is a rich history of the study of clocks in many plant species, in recent years much progress in elucidating the architecture and function of the plant clock has emerged from studies of the model plant, Arabidopsis thaliana. There is considerable interest in extending this knowledge of the circadian clock into diverse plant species in order to address its role in topics as varied as agricultural productivity and the responses of individual species and plant communities to global climate change and environmental degradation. The analysis of circadian clocks in the green lineage provides insight into evolutionary processes in plants and throughout the eukaryotes.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Class of 1978 Life Sciences Center, Hanover, NH 03755, USA.
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30
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Beel B, Müller N, Kottke T, Mittag M. News about cryptochrome photoreceptors in algae. PLANT SIGNALING & BEHAVIOR 2013; 8:e22870. [PMID: 23154511 PMCID: PMC3656988 DOI: 10.4161/psb.22870] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Cryptochromes (CRYs) are flavoproteins that are known as blue light photoreceptors in many organisms. Recently, genome sequences from a variety of algae became available. Functional characterizations of animal-like CRYs from Oestreococcus tauri, Chlamydomonas reinhardtii and Phaeodactylum tricornutum highlighted novel functions and properties. As arising from studies in fungi, certain algal CRYs of the "cryptochrome photolyase family" (PtCPF1, OtCPF1) have dual or even triple functions. They are involved in blue light perception and/or in the circadian clock and are able to repair DNA damages. On the other hand, the animal-like aCRY from C. reinhardtii is not only acting as sensory blue light- but also as sensory red light receptor thus expanding our current view of flavoproteins in general and CRYs in particular. The observed broad spectral response points to the neutral radical state of flavin, which is assumed to be the dark form in aCRY in contrast to the plant CRYs.
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Affiliation(s)
- Benedikt Beel
- Institute of General Botany and Plant Physiology; Friedrich Schiller University Jena; Jena, Germany
| | - Nico Müller
- Institute of General Botany and Plant Physiology; Friedrich Schiller University Jena; Jena, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry; Department of Chemistry; Bielefeld University; Bielefeld, Germany
| | - Maria Mittag
- Institute of General Botany and Plant Physiology; Friedrich Schiller University Jena; Jena, Germany
- Correspondence to: Maria Mittag,
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31
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Hisatomi O, Takeuchi K, Zikihara K, Ookubo Y, Nakatani Y, Takahashi F, Tokutomi S, Kataoka H. Blue Light-Induced Conformational Changes in a Light-Regulated Transcription Factor, Aureochrome-1. ACTA ACUST UNITED AC 2012; 54:93-106. [DOI: 10.1093/pcp/pcs160] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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32
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A new, sensitive marine microalgal recombinant biosensor using luminescence monitoring for toxicity testing of antifouling biocides. Appl Environ Microbiol 2012; 79:631-8. [PMID: 23144143 DOI: 10.1128/aem.02688-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we propose the use of the marine green alga Ostreococcus tauri, the smallest free-living eukaryotic cell known to date, as a new luminescent biosensor for toxicity testing in the environment. Diuron and Irgarol 1051, two antifouling biocides commonly encountered in coastal waters, were chosen to test this new biosensor along with two degradation products of diuron. The effects of various concentrations of the antifoulants on four genetic constructs of O. tauri (based on genes involved in photosynthesis, cell cycle, and circadian clock) were compared using 96-well culture microplates and a luminometer to automatically measure luminescence over 3 days. This was compared to growth inhibition of O. tauri wild type under the same conditions. Luminescence appeared to be more sensitive than growth inhibition as an indicator of toxicity. Cyclin-dependent kinase (CDKA), a protein involved in the cell cycle, fused to luciferase (CDKA-Luc) was found to be the most sensitive of the biosensors, allowing an accurate determination of the 50% effective concentration (EC(50)) after only 2 days (diuron, 5.65 ± 0.44 μg/liter; Irgarol 1015, 0.76 ± 0.10 μg/liter). The effects of the antifoulants on the CDKA-Luc biosensor were then compared to growth inhibition in natural marine phytoplankton. The effective concentrations of diuron and Irgarol 1051 were found to be similar, indicating that this biosensor would be suitable as a reliable ecotoxicological test. The advantage of this biosensor over cell growth inhibition testing is that the process can be easily automated and could provide a high-throughput laboratory approach to perform short-term toxicity tests. The ability to genetically transform and culture recombinant O. tauri gives it huge potential for screening many other toxic compounds.
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Pfeuty B, Thommen Q, Corellou F, Djouani-Tahri EB, Bouget FY, Lefranc M. Circadian clocks in changing weather and seasons: Lessons from the picoalgaOstreococcus tauri. Bioessays 2012; 34:781-90. [DOI: 10.1002/bies.201200012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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34
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Thommen Q, Pfeuty B, Corellou F, Bouget FY, Lefranc M. Robust and flexible response of theOstreococcus tauricircadian clock to light/dark cycles of varying photoperiod. FEBS J 2012; 279:3432-48. [DOI: 10.1111/j.1742-4658.2012.08666.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Christie JM, Gawthorne J, Young G, Fraser NJ, Roe AJ. LOV to BLUF: flavoprotein contributions to the optogenetic toolkit. MOLECULAR PLANT 2012; 5:533-44. [PMID: 22431563 DOI: 10.1093/mp/sss020] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Optogenetics is an emerging field that combines optical and genetic approaches to non-invasively interfere with cellular events with exquisite spatiotemporal control. Although it arose originally from neuroscience, optogenetics is widely applicable to the study of many different biological systems and the range of applications arising from this technology continues to increase. Moreover, the repertoire of light-sensitive proteins used for devising new optogenetic tools is rapidly expanding. Light, Oxygen, or Voltage sensing (LOV) and Blue-Light-Utilizing flavin adenine dinucleotide (FAD) (BLUF) domains represent new contributors to the optogenetic toolkit. These small (100-140-amino acids) flavoprotein modules are derived from plant and bacterial photoreceptors that respond to UV-A/blue light. In recent years, considerable progress has been made in uncovering the photoactivation mechanisms of both LOV and BLUF domains. This knowledge has been applied in the design of synthetic photoswitches and fluorescent reporters with applications in cell biology and biotechnology. In this review, we summarize the photochemical properties of LOV and BLUF photosensors and highlight some of the recent advances in how these flavoproteins are being employed to artificially regulate and image a variety of biological processes.
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Affiliation(s)
- John M Christie
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK.
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36
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Circolone F, Granzin J, Jentzsch K, Drepper T, Jaeger KE, Willbold D, Krauss U, Batra-Safferling R. Structural basis for the slow dark recovery of a full-length LOV protein from Pseudomonas putida. J Mol Biol 2012; 417:362-74. [PMID: 22326872 DOI: 10.1016/j.jmb.2012.01.056] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 12/15/2011] [Accepted: 01/31/2012] [Indexed: 10/14/2022]
Abstract
Blue-light photoreceptors containing light–oxygen–voltage (LOV) domains regulate a myriad of different physiological responses in both eukaryotes and prokaryotes. Their light sensitivity is intricately linked to the photochemistry of the non-covalently bound flavin mononucleotide (FMN) chromophore that forms a covalent adduct with a conserved cysteine residue in the LOV domain upon illumination with blue light. All LOV domains undergo the same primary photochemistry leading to adduct formation; however, considerable variation is found in the lifetime of the adduct state that varies from seconds to several hours. The molecular mechanism underlying this variation among the structurally conserved LOV protein family is not well understood. Here, we describe the structural characterization of PpSB1-LOV, a very slow cycling full-length LOV protein from the Gram-negative bacterium Pseudomonas putida KT2440. Its crystal structure reveals a novel dimer interface that is mediated by N- and C-terminal auxiliary structural elements and a unique cluster of four arginine residues coordinating with the FMN-phosphate moiety. Site-directed mutagenesis of two arginines (R61 and R66) in PpSB1-LOV resulted in acceleration of the dark recovery reaction approximately by a factor of 280. The presented structural and biochemical data suggest a direct link between structural features and the slow dark recovery observed for PpSB1-LOV. The overall structural arrangement of PpSB1-LOV, together with a complementary phylogenetic analysis, highlights a common ancestry of bacterial LOV photoreceptors and Per-ARNT-Sim chemosensors.
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Affiliation(s)
- Franco Circolone
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, D-52426 Jülich, Germany
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37
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Depauw FA, Rogato A, Ribera d'Alcalá M, Falciatore A. Exploring the molecular basis of responses to light in marine diatoms. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:1575-91. [PMID: 22328904 DOI: 10.1093/jxb/ers005] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Light is an essential source of energy for life on Earth and is one of the most important signals that organisms use to obtain information from the surrounding environment, on land and in the oceans. Prominent marine microalgae, such as diatoms, display a suite of sophisticated responses (physiological, biochemical, and behavioural) to optimize their photosynthesis and growth under changing light conditions. However, the molecular mechanisms controlling diatom responses to light are still largely unknown. Recent progress in marine diatom genomics and genetics, combined with well-established (eco) physiological and biophysical approaches, now offers novel opportunities to address these issues. This review provides a description of the molecular components identified in diatom genomes that are involved in light perception and acclimation mechanisms. How the initial functional characterizations of specific light regulators provide the basis to investigate the conservation or diversification of light-mediated processes in diatoms is also discussed. Hypotheses on the role of the identified factors in determining the growth, distribution, and adaptation of diatoms in different marine environments are reported.
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Affiliation(s)
- Frauke Angelique Depauw
- Université Pierre et Marie Curie, Paris 06, Centre National de la Recherche Scientifique, UMR7238, Laboratoire de Génomique des Microorganismes, 75006 Paris, France
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Losi A, Gärtner W. The evolution of flavin-binding photoreceptors: an ancient chromophore serving trendy blue-light sensors. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:49-72. [PMID: 22136567 DOI: 10.1146/annurev-arplant-042811-105538] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Photoreceptor flavoproteins of the LOV, BLUF, and cryptochrome families are ubiquitous among the three domains of life and are configured as UVA/blue-light systems not only in plants-their original arena-but also in prokaryotes and microscopic algae. Here, we review these proteins' structure and function, their biological roles, and their evolution and impact in the living world, and underline their growing application in biotechnologies. We present novel developments such as the interplay of light and redox stimuli, emerging enzymatic and biological functions, lessons on evolution from picoalgae, metagenomics analysis, and optogenetics applications.
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Affiliation(s)
- Aba Losi
- Department of Physics, University of Parma, Parma, Italy.
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Djouani-Tahri EB, Sanchez F, Lozano JC, Bouget FY. A phosphate-regulated promoter for fine-tuned and reversible overexpression in Ostreococcus: application to circadian clock functional analysis. PLoS One 2011; 6:e28471. [PMID: 22174815 PMCID: PMC3236181 DOI: 10.1371/journal.pone.0028471] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 11/08/2011] [Indexed: 11/23/2022] Open
Abstract
Background The green picoalga Ostreococcus tauri (Prasinophyceae), which has been described as the smallest free-living eukaryotic organism, has minimal cellular ultra-structure and a very small genome. In recent years, O. tauri has emerged as a novel model organism for systems biology approaches that combine functional genomics and mathematical modeling, with a strong emphasis on light regulated processes and circadian clock. These approaches were made possible through the implementation of a minimal molecular toolbox for gene functional analysis including overexpression and knockdown strategies. We have previously shown that the promoter of the High Affinity Phosphate Transporter (HAPT) gene drives the expression of a luciferase reporter at high and constitutive levels under constant light. Methodology/Principal Findings Here we report, using a luciferase reporter construct, that the HAPT promoter can be finely and reversibly tuned by modulating the level and nature of phosphate in culture medium. This HAPT regulation was additionally used to analyze the circadian clock gene Time of Cab expression 1 (TOC1). The phenotype of a TOC1ox/CCA1:Luc line was reverted from arrhythmic to rhythmic simply by adding phosphate to the culture medium. Furthermore, since the time of phosphate injection had no effect on the phase of CCA1:Luc expression, this study suggests further that TOC1 is a central clock gene in Ostreococcus. Conclusions/Perspectives We have developed a phosphate-regulated expression system that allows fine gene function analysis in Ostreococcus. Recently, there has been a growing interest in microalgae as cell factories. This non-toxic phosphate-regulated system may prove useful in tuning protein expression levels quantitatively and temporally for biotechnological applications.
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Affiliation(s)
- El Batoul Djouani-Tahri
- Universite Pierre et Marie Curie (Paris 06), Observatoire Océanologique, Banyuls/mer, France
- Centre national de la Recherche Scientifique, Unité Mixte de Recherche, UMR7621, LOMIC, Laboratoire d'océanographie microbienne, Banyuls/mer, France
| | - Frédéric Sanchez
- Universite Pierre et Marie Curie (Paris 06), Observatoire Océanologique, Banyuls/mer, France
- Centre national de la Recherche Scientifique, Unité Mixte de Recherche, UMR7621, LOMIC, Laboratoire d'océanographie microbienne, Banyuls/mer, France
| | - Jean-Claude Lozano
- Universite Pierre et Marie Curie (Paris 06), Observatoire Océanologique, Banyuls/mer, France
- Centre national de la Recherche Scientifique, Unité Mixte de Recherche, UMR7621, LOMIC, Laboratoire d'océanographie microbienne, Banyuls/mer, France
| | - François-Yves Bouget
- Universite Pierre et Marie Curie (Paris 06), Observatoire Océanologique, Banyuls/mer, France
- Centre national de la Recherche Scientifique, Unité Mixte de Recherche, UMR7621, LOMIC, Laboratoire d'océanographie microbienne, Banyuls/mer, France
- * E-mail:
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Abstract
The rotation of the earth on its axis confers the property of dramatic, recurrent, rhythmic environmental change. The rhythmicity of this change from day to night and again to day imparts predictability. As a consequence, most organisms have acquired the capacity to measure time to use this time information to temporally regulate their biology to coordinate with their environment in anticipation of coming change. Circadian rhythms, endogenous rhythms with periods of ∼24h, are driven by an internal circadian clock. This clock integrates temporal information and coordinates of many aspects of biology, including basic metabolism, hormone signaling and responses, and responses to biotic and abiotic stress, making clocks central to "systems biology." This review will first address the extent to which the clock regulates many biological processes. The architecture and mechanisms of the plant circadian oscillator, emphasizing what has been learned from intensive study of the circadian clock in the model plant, Arabidopsis thaliana, will be considered. The conservation of clock components in other species will address the extent to which the Arabidopsis model will inform our consideration of plants in general. Finally, studies addressing the role of clocks in fitness will be discussed. Accumulating evidence indicates that the consonance of the endogenous circadian clock with environmental cycles enhances fitness, including both biomass accumulation and reproductive performance. Thus, increased understanding of plant responses to environmental input and to endogenous temporal cues has ecological and agricultural importance.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
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