1
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Prasetyaningrum P, Litthauer S, Vegliani F, Battle MW, Wood MW, Liu X, Dickson C, Jones MA. Inhibition of RNA degradation integrates the metabolic signals induced by osmotic stress into the Arabidopsis circadian system. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5805-5819. [PMID: 37453132 PMCID: PMC10540740 DOI: 10.1093/jxb/erad274] [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: 02/05/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
The circadian clock system acts as an endogenous timing reference that coordinates many metabolic and physiological processes in plants. Previous studies have shown that the application of osmotic stress delays circadian rhythms via 3'-phospho-adenosine 5'-phosphate (PAP), a retrograde signalling metabolite that is produced in response to redox stress within organelles. PAP accumulation leads to the inhibition of exoribonucleases (XRNs), which are responsible for RNA degradation. Interestingly, we are now able to demonstrate that post-transcriptional processing is crucial for the circadian response to osmotic stress. Our data show that osmotic stress increases the stability of specific circadian RNAs, suggesting that RNA metabolism plays a vital role in circadian clock coordination during drought. Inactivation of XRN4 is sufficient to extend circadian rhythms as part of this response, with PRR7 and LWD1 identified as transcripts that are post-transcriptionally regulated to delay circadian progression.
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Affiliation(s)
| | | | - Franco Vegliani
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | | | | | - Xinmeng Liu
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Cathryn Dickson
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Matthew Alan Jones
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK
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2
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Watanabe E, Muranaka T, Nakamura S, Isoda M, Horikawa Y, Aiso T, Ito S, Oyama T. A non-cell-autonomous circadian rhythm of bioluminescence reporter activities in individual duckweed cells. PLANT PHYSIOLOGY 2023; 193:677-688. [PMID: 37042358 DOI: 10.1093/plphys/kiad218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
The circadian clock is responsible for the temporal regulation of various physiological processes in plants. Individual cells contain a circadian oscillator consisting of a clock gene circuit that coordinates physiological rhythms within the plant body in an orderly manner. The coordination of time information has been studied from the perspective of cell-cell local coupling and long-distance communication between tissues based on the view that the behavior of circadian oscillators represents physiological rhythms. Here, we report the cellular circadian rhythm of bioluminescence reporters that are not governed by the clock gene circuit in expressing cells. We detected cellular bioluminescence rhythms with different free-running periods in the same cells using a dual-color bioluminescence monitoring system in duckweed (Lemna minor) transfected with Arabidopsis CIRCADIAN CLOCK ASSOCIATED 1::luciferace+ (AtCCA1::LUC+) and Cauliflower mosaic virus 35S::modified click-beetle red-color luciferase (CaMV35S::PtRLUC) reporters. Co-transfection experiments with the two reporters and a clock gene-overexpressing effector revealed that the AtCCA1::LUC+ rhythm, but not the CaMV35S::PtRLUC rhythm, was altered in cells with a dysfunctional clock gene circuit. This indicated that the AtCCA1::LUC+ rhythm is a direct output of the cellular circadian oscillator, whereas the CaMV35S::PtRLUC rhythm is not. After plasmolysis, the CaMV35S::PtRLUC rhythm disappeared, whereas the AtCCA1::LUC+ rhythm persisted. This suggests that the CaMV35S::PtRLUC bioluminescence has a symplast/apoplast-mediated circadian rhythm generated at the organismal level. The CaMV35S::PtRLUC-type bioluminescence rhythm was also observed when other bioluminescence reporters were expressed. These results reveal that the plant circadian system consists of both cell-autonomous and noncell-autonomous rhythms that are unaffected by cellular oscillators.
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Affiliation(s)
- Emiri Watanabe
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Tomoaki Muranaka
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Shunji Nakamura
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Minako Isoda
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yu Horikawa
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tsuyoshi Aiso
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Shogo Ito
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tokitaka Oyama
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
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3
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Rees H, Rusholme-Pilcher R, Bailey P, Colmer J, White B, Reynolds C, Ward SJ, Coombes B, Graham CA, de Barros Dantas LL, Dodd AN, Hall A. Circadian regulation of the transcriptome in a complex polyploid crop. PLoS Biol 2022; 20:e3001802. [PMID: 36227835 PMCID: PMC9560141 DOI: 10.1371/journal.pbio.3001802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/18/2022] [Indexed: 11/07/2022] Open
Abstract
The circadian clock is a finely balanced timekeeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolution time-course dataset to investigate the circadian balance between sets of 3 homoeologous genes (triads) from hexaploid bread wheat. We find a large proportion of circadian triads exhibit imbalanced rhythmic expression patterns, with no specific subgenome favoured. In wheat, period lengths of rhythmic transcripts are found to be longer and have a higher level of variance than in other plant species. Expression of transcripts associated with circadian controlled biological processes is largely conserved between wheat and Arabidopsis; however, striking differences are seen in agriculturally critical processes such as starch metabolism. Together, this work highlights the ongoing selection for balance versus diversification in circadian homoeologs and identifies clock-controlled pathways that might provide important targets for future wheat breeding.
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Affiliation(s)
- Hannah Rees
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Paul Bailey
- Royal Botanic Gardens Kew, Richmond, Surrey, United Kingdom
| | - Joshua Colmer
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Benjamen White
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Connor Reynolds
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Benedict Coombes
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Calum A. Graham
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | | - Antony N. Dodd
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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4
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Watanabe E, Isoda M, Muranaka T, Ito S, Oyama T. Detection of Uncoupled Circadian Rhythms in Individual Cells of Lemna minor using a Dual-Color Bioluminescence Monitoring System. PLANT & CELL PHYSIOLOGY 2021; 62:815-826. [PMID: 33693842 DOI: 10.1093/pcp/pcab037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
The plant circadian oscillation system is based on the circadian clock of individual cells. Circadian behavior of cells has been observed by monitoring the circadian reporter activity, such as bioluminescence of AtCCA1::LUC+. To deeply analyze different circadian behaviors in individual cells, we developed the dual-color bioluminescence monitoring system that automatically measured the luminescence of two luciferase reporters simultaneously at a single-cell level. We selected a yellow-green-emitting firefly luciferase (LUC+) and a red-emitting luciferase (PtRLUC) that is a mutant form of Brazilian click beetle ELUC. We used AtCCA1::LUC+ and CaMV35S::PtRLUC. CaMV35S::LUC+ was previously reported as a circadian reporter with a low-amplitude rhythm. These bioluminescent reporters were introduced into the cells of a duckweed, Lemna minor, by particle bombardment. Time series of the bioluminescence of individual cells in a frond were obtained using a dual-color bioluminescence monitoring system with a green-pass- and red-pass filter. Luminescence intensities from the LUC+ and PtRLUC of each cell were calculated from the filtered luminescence intensities. We succeeded in reconstructing the bioluminescence behaviors of AtCCA1::LUC+ and CaMV35S::PtRLUC in the same cells. Under prolonged constant light conditions, AtCCA1::LUC+ showed a robust circadian rhythm in individual cells in an asynchronous state in the frond, as previously reported. By contrast, CaMV35S::PtRLUC stochastically showed circadian rhythms in a synchronous state. These results strongly suggested the uncoupling of cellular behavior between these circadian reporters. This dual-color bioluminescence monitoring system is a powerful tool to analyze various stochastic phenomena accompanying large cell-to-cell variation in gene expression.
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Affiliation(s)
- Emiri Watanabe
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Minako Isoda
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Tomoaki Muranaka
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
- Faculty of Agriculture, Kagoshima University, Kohrimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Shogo Ito
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Tokitaka Oyama
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
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5
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Balcerowicz M, Mahjoub M, Nguyen D, Lan H, Stoeckle D, Conde S, Jaeger KE, Wigge PA, Ezer D. An early-morning gene network controlled by phytochromes and cryptochromes regulates photomorphogenesis pathways in Arabidopsis. MOLECULAR PLANT 2021; 14:983-996. [PMID: 33766657 DOI: 10.1016/j.molp.2021.03.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/04/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Light perception at dawn plays a key role in coordinating multiple molecular processes and in entraining the plant circadian clock. The Arabidopsis mutant lacking the main photoreceptors, however, still shows clock entrainment, indicating that the integration of light into the morning transcriptome is not well understood. In this study, we performed a high-resolution RNA-sequencing time-series experiment, sampling every 2 min beginning at dawn. In parallel experiments, we perturbed temperature, the circadian clock, photoreceptor signaling, and chloroplast-derived light signaling. We used these data to infer a gene network that describes the gene expression dynamics after light stimulus in the morning, and then validated key edges. By sampling time points at high density, we are able to identify three light- and temperature-sensitive bursts of transcription factor activity, one of which lasts for only about 8 min. Phytochrome and cryptochrome mutants cause a delay in the transcriptional bursts at dawn, and completely remove a burst of expression in key photomorphogenesis genes (HY5 and BBX family). Our complete network is available online (http://www-users.york.ac.uk/∼de656/dawnBurst/dawnBurst.html). Taken together, our results show that phytochrome and cryptochrome signaling is required for fine-tuning the dawn transcriptional response to light, but separate pathways can robustly activate much of the program in their absence.
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Affiliation(s)
| | - Mahiar Mahjoub
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Duy Nguyen
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Hui Lan
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | | | - Susana Conde
- Department of Statistics, University of Warwick, Coventry, UK; Alan Turing Institute, London, UK
| | - Katja E Jaeger
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany
| | - Philip A Wigge
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany; Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Daphne Ezer
- Alan Turing Institute, London, UK; Department of Biology, University of York, York YO10 5DD, UK.
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6
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Spatial Organization and Coordination of the Plant Circadian System. Genes (Basel) 2021; 12:genes12030442. [PMID: 33804638 PMCID: PMC8003751 DOI: 10.3390/genes12030442] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/21/2022] Open
Abstract
The plant circadian clock has a pervasive influence on many aspects of plant biology and is proposed to function as a developmental manager. To do so, the circadian oscillator needs to be able to integrate a multiplicity of environmental signals and coordinate an extensive and diverse repertoire of endogenous rhythms accordingly. Recent studies on tissue-specific characteristics and spatial structure of the plant circadian clock suggest that such plasticity may be achieved through the function of distinct oscillators, which sense the environment locally and are then coordinated across the plant through both intercellular coupling and long-distance communication. This review summarizes the current knowledge on tissue-specific features of the clock in plants and their spatial organization and synchronization at the organismal level.
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7
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Li Y, Lu Y, Zhou Y, Wei X, Peng Y, Dai Y, Zhang L, Zhu Z. Diurnal transcriptomics analysis reveals the regulatory role of the circadian rhythm in super-hybrid rice LY2186. Genomics 2021; 113:1281-1290. [PMID: 33705889 DOI: 10.1016/j.ygeno.2020.12.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/23/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022]
Abstract
Heterosis, an important biological phenomenon wherein F1 hybrids exhibit better performance than any of their parents, has been widely applied; however, its underlying mechanism remains largely unknown. Here, we studied and compared the dynamic transcriptional profiles of super-hybrid rice LY2186 and its parents at 17 time points during 2 day/night cycles and identified 1552 rhythmic differentially expressed genes (RDGs). Cluster and functional enrichment analyses revealed that the day- and night-phased RDGs were mainly enriched in the photosynthesis and stress response categories, respectively. Regulatory network analysis indicated that circadian-related RDGs are core components in both the day and night phases and extensively regulate downstream genes involved in photosynthesis, starch synthesis, plant hormone signal transduction, and other pathways. Furthermore, among the 282 RDGs mapped onto the quantitative tract loci of small intervals (≤100 genes), 72.3% were significantly enriched in the yield, vigor, and anatomy categories. These findings provide valuable information for exploring heterosis mechanisms further and guiding breeding practices.
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Affiliation(s)
- Yue Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yufei Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoli Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yonggang Peng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Dai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Lei Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zhen Zhu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
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8
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Sanchez SE, Rugnone ML, Kay SA. Light Perception: A Matter of Time. MOLECULAR PLANT 2020; 13:363-385. [PMID: 32068156 PMCID: PMC7056494 DOI: 10.1016/j.molp.2020.02.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 05/02/2023]
Abstract
Optimizing the perception of external cues and regulating physiology accordingly help plants to cope with the constantly changing environmental conditions to which they are exposed. An array of photoreceptors and intricate signaling pathways allow plants to convey the surrounding light information and synchronize an endogenous timekeeping system known as the circadian clock. This biological clock integrates multiple cues to modulate a myriad of downstream responses, timing them to occur at the best moment of the day and the year. Notably, the mechanism underlying entrainment of the light-mediated clock is not clear. This review addresses known interactions between the light-signaling and circadian-clock networks, focusing on the role of light in clock entrainment and known molecular players in this process.
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Affiliation(s)
- Sabrina E Sanchez
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Matias L Rugnone
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Steve A Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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9
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Philippou K, Ronald J, Sánchez-Villarreal A, Davis AM, Davis SJ. Physiological and Genetic Dissection of Sucrose Inputs to the Arabidopsis thaliana Circadian System. Genes (Basel) 2019; 10:genes10050334. [PMID: 31052578 PMCID: PMC6563356 DOI: 10.3390/genes10050334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 11/21/2022] Open
Abstract
Circadian rhythms allow an organism to synchronize internal physiological responses to the external environment. Perception of external signals such as light and temperature are critical in the entrainment of the oscillator. However, sugar can also act as an entraining signal. In this work, we have confirmed that sucrose accelerates the circadian period, but this observed effect is dependent on the reporter gene used. This observed response was dependent on sucrose being available during free-running conditions. If sucrose was applied during entrainment, the circadian period was only temporally accelerated, if any effect was observed at all. We also found that sucrose acts to stabilize the robustness of the circadian period under red light or blue light, in addition to its previously described role in stabilizing the robustness of rhythms in the dark. Finally, we also found that CCA1 is required for both a short- and long-term response of the circadian oscillator to sucrose, while LHY acts to attenuate the effects of sucrose on circadian period. Together, this work highlights new pathways for how sucrose could be signaling to the oscillator and reveals further functional separation of CCA1 and LHY.
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Affiliation(s)
- Koumis Philippou
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Cologne D50829, Germany.
| | - James Ronald
- Department of Biology, University of York, York, YO10 5DD, UK.
| | - Alfredo Sánchez-Villarreal
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Cologne D50829, Germany.
- Colegio de Postgraduados campus Campeche, Campeche, CP 24450, México.
| | - Amanda M Davis
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Cologne D50829, Germany.
- Department of Biology, University of York, York, YO10 5DD, UK.
| | - Seth J Davis
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Cologne D50829, Germany.
- Department of Biology, University of York, York, YO10 5DD, UK.
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10
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McClung CR. The Plant Circadian Oscillator. BIOLOGY 2019; 8:E14. [PMID: 30870980 PMCID: PMC6466001 DOI: 10.3390/biology8010014] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/17/2019] [Accepted: 03/09/2019] [Indexed: 12/20/2022]
Abstract
It has been nearly 300 years since the first scientific demonstration of a self-sustaining circadian clock in plants. It has become clear that plants are richly rhythmic, and many aspects of plant biology, including photosynthetic light harvesting and carbon assimilation, resistance to abiotic stresses, pathogens, and pests, photoperiodic flower induction, petal movement, and floral fragrance emission, exhibit circadian rhythmicity in one or more plant species. Much experimental effort, primarily, but not exclusively in Arabidopsis thaliana, has been expended to characterize and understand the plant circadian oscillator, which has been revealed to be a highly complex network of interlocked transcriptional feedback loops. In addition, the plant circadian oscillator has employed a panoply of post-transcriptional regulatory mechanisms, including alternative splicing, adjustable rates of translation, and regulated protein activity and stability. This review focuses on our present understanding of the regulatory network that comprises the plant circadian oscillator. The complexity of this oscillatory network facilitates the maintenance of robust rhythmicity in response to environmental extremes and permits nuanced control of multiple clock outputs. Consistent with this view, the clock is emerging as a target of domestication and presents multiple targets for targeted breeding to improve crop performance.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
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11
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Inoue K, Araki T, Endo M. Oscillator networks with tissue-specific circadian clocks in plants. Semin Cell Dev Biol 2018; 83:78-85. [DOI: 10.1016/j.semcdb.2017.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 12/31/2022]
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12
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Rubin MJ, Brock MT, Davis AM, German ZM, Knapp M, Welch SM, Harmer SL, Maloof JN, Davis SJ, Weinig C. Circadian rhythms vary over the growing season and correlate with fitness components. Mol Ecol 2017; 26:5528-5540. [PMID: 28792639 DOI: 10.1111/mec.14287] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 06/15/2017] [Accepted: 06/29/2017] [Indexed: 12/21/2022]
Abstract
Circadian clocks have evolved independently in all three domains of life, suggesting that internal mechanisms of time-keeping are adaptive in contemporary populations. However, the performance consequences of either discrete or quantitative clock variation have rarely been tested in field settings. Clock sensitivity of diverse segregating lines to the environment remains uncharacterized as do the statistical genetic parameters that determine evolutionary potential. In field studies with Arabidopsis thaliana, we found that major perturbations to circadian cycle length (referred to as clock period) via mutation reduce both survival and fecundity. Subtler adjustments via genomic introgression of naturally occurring alleles indicated that clock periods slightly >24 hr were adaptive, consistent with prior models describing how well the timing of biological processes is adjusted within a diurnal cycle (referred to as phase). In segregating recombinant inbred lines (RILs), circadian phase varied up to 2 hr across months of the growing season, and both period and phase expressed significant genetic variances. Performance metrics including developmental rate, size and fruit set were described by principal components (PC) analyses and circadian parameters correlated with the first PC, such that period lengths slightly >24 hr were associated with improved performance in multiple RIL sets. These experiments translate functional analyses of clock behaviour performed in controlled settings to natural ones, demonstrating that quantitative variation in circadian phase is highly responsive to seasonally variable abiotic factors. The results expand upon prior studies in controlled settings, showing that discrete and quantitative variation in clock phenotypes correlates with performance in nature.
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Affiliation(s)
- Matthew J Rubin
- Department of Botany, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, WY, USA
| | - Amanda M Davis
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Biology, University of York, Heslington, York, UK
| | - Zachary M German
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Mary Knapp
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Stephen M Welch
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Stacey L Harmer
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Seth J Davis
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Biology, University of York, Heslington, York, UK
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA.,Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
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13
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Liu H, Gu F, Dong S, Liu W, Wang H, Chen Z, Wang J. CONSTANS-like 9 (COL9) delays the flowering time in Oryza sativa by repressing the Ehd1 pathway. Biochem Biophys Res Commun 2016; 479:173-178. [PMID: 27620492 DOI: 10.1016/j.bbrc.2016.09.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 12/15/2022]
Abstract
Flowering or heading is one of most important agronomic traits in rice. It has been characterized that CONSTANS (CO) and CONSTANS-like (COL) proteins are critical flowering regulators in response to photoperiodic stress in plants. We have previously identified that the COL family member OsCOL9 can positively enhance the rice blast resistance. In the present study, we aimed to explore the functional role of OsCOL9 in modulating the photoperiodic flowering. Our data showed that overexpression of OsCOL9 delayed the flowering time under both short-day (SD) and long-day (LD) conditions, leading to suppressed expressions of EHd1, RFT and Hd3a at the mRNA Level. OsCOL9 expression exhibited two types of circadian patterns under different daylight conditions, and it could delay the heading date by suppressing the Ehd1 photoperiodic flowering pathway. In contrast, the expressions of previously reported flowering regulators were not significantly changed in OsCOL9 transgenic plants, indicating that OsCOL9 functioned independently of other flowering pathways. In addition, OsCOL9 served as a potential yield gene, and its deficiency reduced the grain number of main panicle in plants. Furthermore, yeast two-hybrid assay indicated that OsCOL9 physically interacted with Receptor for Activated C-kinase 1 (OsRACK1). Rhythmic pattern analysis suggested that OsRACK1 responded to the change of daylight, which was regulated by the circadian clock. Taken together, our results revealed that OsCOL9 could delay the flowering time in rice by repressing the Ehd1 pathway.
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Affiliation(s)
- Hao Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Fengwei Gu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Shuangyu Dong
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Wei Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Jiafeng Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
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14
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Endo M. Tissue-specific circadian clocks in plants. CURRENT OPINION IN PLANT BIOLOGY 2016; 29:44-9. [PMID: 26723003 DOI: 10.1016/j.pbi.2015.11.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/30/2015] [Accepted: 11/05/2015] [Indexed: 05/28/2023]
Abstract
Circadian clocks affect a large proportion of differentially expressed genes in many organisms. Tissue-specific hierarchies in circadian networks in mammals have been contentiously debated, whereas little attention has been devoted to the concept in plants, owing to technical difficulties. Recently, several studies have demonstrated tissue-specific circadian clocks and their coupling in plants, suggesting that plants possess a hierarchical network of circadian clocks. The following review summarizes recent studies describing the tissue-specific functions and properties of these circadian clocks and discusses the network structure and potential messengers that might share temporal information on such a network.
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Affiliation(s)
- Motomu Endo
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto 606-8501, Japan; Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan.
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15
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Hajdu A, Ádám É, Sheerin DJ, Dobos O, Bernula P, Hiltbrunner A, Kozma-Bognár L, Nagy F. High-level expression and phosphorylation of phytochrome B modulates flowering time in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:794-805. [PMID: 26120968 DOI: 10.1111/tpj.12926] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 06/16/2015] [Accepted: 06/23/2015] [Indexed: 06/04/2023]
Abstract
Optimal timing of flowering in higher plants is crucial for successful reproduction and is coordinated by external and internal factors, including light and the circadian clock. In Arabidopsis, light-dependent stabilization of the rhythmically expressed CONSTANS (CO) is required for the activation of FLOWERING LOCUS T (FT), resulting in the initiation of flowering. Phytochrome A and cryptochrome photoreceptors stabilize CO in the evening by attenuating the activity of the CONSTITUTIVE PHOTOMORPHOGENIC 1-SUPPRESSOR OF PHYA-105 1 (COP1-SPA1) ubiquitin ligase complex, which promotes turnover of CO. In contrast, phytochrome B (phyB) facilitates degradation of CO in the morning and delays flowering. Accordingly, flowering is accelerated in phyB mutants. Paradoxically, plants overexpressing phyB also show early flowering, which may arise from an early phase of rhythmic CO expression. Here we demonstrate that overexpression of phyB induces FT transcription at dusk and in the night without affecting the phase or level of CO transcription. This response depends on the light-activated Pfr form of phyB that inhibits the function of the COP1-SPA1 complex by direct interactions. Our data suggest that attenuation of COP1 activity results in the accumulation of CO protein and subsequent induction of FT. We show that phosphorylation of Ser-86 inhibits this function of phyB by accelerating dark reversion and thus depletion of Pfr forms in the night. Our results explain the early flowering phenotype of phyB overexpression and reveal additional features of the molecular machinery by which photoreceptors mediate photoperiodism.
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Affiliation(s)
- Anita Hajdu
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Éva Ádám
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - David J Sheerin
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Orsolya Dobos
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Péter Bernula
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Andreas Hiltbrunner
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, 79104, Germany
| | - László Kozma-Bognár
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JR, UK
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16
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Song MF, Zhang S, Hou P, Shang HZ, Gu HK, Li JJ, Xiao Y, Guo L, Su L, Gao JW, Yang JP. Ectopic expression of a phytochrome B gene from Chinese cabbage (Brassica rapa L. ssp. pekinensis) in Arabidopsis thaliana promotes seedling de-etiolation, dwarfing in mature plants, and delayed flowering. PLANT MOLECULAR BIOLOGY 2015; 87:633-43. [PMID: 25724426 DOI: 10.1007/s11103-015-0302-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 02/18/2015] [Indexed: 05/22/2023]
Abstract
Phytochrome B (phyB) is an essential red light receptor that predominantly mediates seedling de-etiolation, shade-avoidance response, and flowering time. In this study, we isolate a full-length cDNA of PHYB, designated BrPHYB, from Chinese cabbage (Brassica rapa L. ssp. pekinensis), and we find that BrphyB protein has high amino acid sequence similarity and the closest evolutionary relationship to Arabidopsis thaliana phyB (i.e., AtphyB). Quantitative reverse transcription (RT)-PCR results indicate that the BrPHYB gene is ubiquitously expressed in different tissues under all light conditions. Constitutive expression of the BrPHYB gene in A. thaliana significantly enhances seedling de-etiolation under red- and white-light conditions, and causes dwarf stature in mature plants. Unexpectedly, overexpression of BrPHYB in transgenic A. thaliana resulted in reduced expression of gibberellins biosynthesis genes and delayed flowering under short-day conditions, whereas AtPHYB overexpression caused enhanced expression of FLOWERING LOCUS T and earlier flowering. Our results suggest that BrphyB might play an important role in regulating the development of Chinese cabbage. BrphyB and AtphyB have conserved functions during de-etiolation and vegetative plant growth and divergent functions in the regulation of flowering time.
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Affiliation(s)
- Mei-Fang Song
- Beijing Radiation Center, Beijing, 100875, People's Republic of China
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17
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Kusakina J, Gould PD, Hall A. A fast circadian clock at high temperatures is a conserved feature across Arabidopsis accessions and likely to be important for vegetative yield. PLANT, CELL & ENVIRONMENT 2014; 37:327-40. [PMID: 23777196 PMCID: PMC4280891 DOI: 10.1111/pce.12152] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 05/29/2013] [Accepted: 05/30/2013] [Indexed: 05/03/2023]
Abstract
The circadian clock is an endogenous 24 h oscillator regulating many critical biological processes in plants. One of the key characteristics of the circadian clock is that it is buffered against temperature, maintaining an approximately 24 h rhythm over a broad physiological temperature range. Here, we tested temperature-buffering capacity of the circadian clock across a number of Arabidopsis accessions using several circadian clock reporters: leaf movement, CCA1:LUC and LHY:LUC. We found that leaf movement was the best temperature buffered circadian output. On the other hand, when temperature increases, circadian rhythms of CCA1 and LHY transcription shorten considerably across all accessions, indicating that the clock driving expression of CCA1 and LHY is not perfectly buffered. This feature might be crucial to plants growing in a constantly changing environment, and here, we provide insight into the importance of period shortening to plant growth performance and the benefits of a flexible clock.
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Affiliation(s)
- Jelena Kusakina
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK; School of Biological Sciences, University of Bristol, Bristol, BS8 1UG, UK
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18
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Salomé PA, Oliva M, Weigel D, Krämer U. Circadian clock adjustment to plant iron status depends on chloroplast and phytochrome function. EMBO J 2012; 32:511-23. [PMID: 23241948 PMCID: PMC3579136 DOI: 10.1038/emboj.2012.330] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 11/22/2012] [Indexed: 01/21/2023] Open
Abstract
Plant chloroplasts are not only the main cellular location for storage of elemental iron (Fe), but also the main site for Fe, which is incorporated into chlorophyll, haem and the photosynthetic machinery. How plants measure internal Fe levels is unknown. We describe here a new Fe-dependent response, a change in the period of the circadian clock. In Arabidopsis, the period lengthens when Fe becomes limiting, and gradually shortens as external Fe levels increase. Etiolated seedlings or light-grown plants treated with plastid translation inhibitors do not respond to changes in Fe supply, pointing to developed chloroplasts as central hubs for circadian Fe sensing. Phytochrome-deficient mutants maintain a short period even under Fe deficiency, stressing the role of early light signalling in coupling the clock to Fe responses. Further mutant and pharmacological analyses suggest that known players in plastid-to-nucleus signalling do not directly participate in Fe sensing. We propose that the sensor governing circadian Fe responses defines a new retrograde pathway that involves a plastid-encoded protein that depends on phytochromes and the functional state of chloroplasts. The circadian clock of Arabidopsis is found to be hardwired to cellular iron levels, with chloroplasts playing a central role in iron sensing.
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Affiliation(s)
- Patrice A Salomé
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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19
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Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf. Proc Natl Acad Sci U S A 2012; 109:6757-62. [PMID: 22496591 DOI: 10.1073/pnas.1118814109] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The circadian clocks that drive daily rhythms in animals are tightly coupled among the cells of some tissues. The coupling profoundly affects cellular rhythmicity and is central to contemporary understanding of circadian physiology and behavior. In contrast, studies of the clock in plant cells have largely ignored intercellular coupling, which is reported to be very weak or absent. We used luciferase reporter gene imaging to monitor circadian rhythms in leaves of Arabidopsis thaliana plants, achieving resolution close to the cellular level. Leaves grown without environmental cycles for up to 3 wk reproducibly showed spatiotemporal waves of gene expression consistent with intercellular coupling, using several reporter genes. Within individual leaves, different regions differed in phase by up to 17 h. A broad range of patterns was observed among leaves, rather than a common spatial distribution of circadian properties. Leaves exposed to light-dark cycles always had fully synchronized rhythms, which could desynchronize rapidly. After 4 d in constant light, some leaves were as desynchronized as leaves grown without any rhythmic input. Applying light-dark cycles to such a leaf resulted in full synchronization within 2-4 d. Thus, the rhythms of all cells were coupled to external light-dark cycles far more strongly than the cellular clocks were coupled to each other. Spontaneous desynchronization under constant conditions was limited, consistent with weak intercellular coupling among heterogeneous clocks. Both the weakness of coupling and the heterogeneity among cells are relevant to interpret molecular studies and to understand the physiological functions of the plant circadian clock.
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20
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Kolmos E, Herrero E, Bujdoso N, Millar AJ, Tóth R, Gyula P, Nagy F, Davis SJ. A reduced-function allele reveals that EARLY FLOWERING3 repressive action on the circadian clock is modulated by phytochrome signals in Arabidopsis. THE PLANT CELL 2011; 23:3230-46. [PMID: 21908721 PMCID: PMC3203447 DOI: 10.1105/tpc.111.088195] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 07/31/2011] [Accepted: 08/16/2011] [Indexed: 05/18/2023]
Abstract
Arabidopsis thaliana EARLY FLOWERING3 (ELF3) is essential for the generation of circadian rhythms. ELF3 has been proposed to restrict light signals to the oscillator through phytochrome photoreceptors, but that has not been explicitly shown. Furthermore, the genetic action of ELF3 within the clock had remained elusive. Here, we report a functional characterization of ELF3 through the analysis of the elf3-12 allele, which encodes an amino acid replacement in a conserved domain. Circadian oscillations persisted, and unlike elf3 null alleles, elf3-12 resulted in a short circadian period only under ambient light. The period shortening effect of elf3-12 was enhanced by the overexpression of phytochromes phyA and phyB. We found that elf3-12 was only modestly perturbed in resetting of the oscillator and in gating light-regulated gene expression. Furthermore, elf3-12 essentially displayed wild-type development. We identified targets of ELF3 transcriptional repression in the oscillator, highlighting the action at the morning gene PSEUDO-RESPONSE REGULATOR9. Taken together, we identified two separable roles for ELF3, one affecting the circadian network and the other affecting light input to the oscillator. This is consistent with a dual function of ELF3 as both an integrator of phytochrome signals and a repressor component of the core oscillator.
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Affiliation(s)
- Elsebeth Kolmos
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Eva Herrero
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Nora Bujdoso
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Andrew J. Millar
- Centre for Systems Biology at Edinburgh, University of Edinburgh, Edinburgh EH9 3JD, United Kingdom
| | - Réka Tóth
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Peter Gyula
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Ferenc Nagy
- Centre for Systems Biology at Edinburgh, University of Edinburgh, Edinburgh EH9 3JD, United Kingdom
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Seth J. Davis
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Address correspondence to
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21
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Wang X, Roig-Villanova I, Khan S, Shanahan H, Quail PH, Martinez-Garcia JF, Devlin PF. A novel high-throughput in vivo molecular screen for shade avoidance mutants identifies a novel phyA mutation. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:2973-87. [PMID: 21398429 PMCID: PMC3202935 DOI: 10.1093/jxb/err062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The shade avoidance syndrome (SAS) allows plants to anticipate and avoid shading by neighbouring plants by initiating an elongation growth response. The phytochrome photoreceptors are able to detect a reduction in the red:far red ratio in incident light, the result of selective absorption of red and blue wavelengths by proximal vegetation. A shade-responsive luciferase reporter line (PHYB::LUC) was used to carry out a high-throughput screen to identify novel SAS mutants. The dracula 1 (dra1) mutant, that showed no avoidance of shade for the PHYB::LUC response, was the result of a mutation in the PHYA gene. Like previously characterized phyA mutants, dra1 showed a long hypocotyl in far red light and an enhanced hypocotyl elongation response to shade. However, dra1 additionally showed a long hypocotyl in red light. Since phyB levels are relatively unaffected in dra1, this gain-of-function red light phenotype strongly suggests a disruption of phyB signalling. The dra1 mutation, G773E within the phyA PAS2 domain, occurs at a residue absolutely conserved among phyA sequences. The equivalent residue in phyB is absolutely conserved as a threonine. PAS domains are structurally conserved domains involved in molecular interaction. Structural modelling of the dra1 mutation within the phyA PAS2 domain shows some similarity with the structure of the phyB PAS2 domain, suggesting that the interference with phyB signalling may be the result of non-functional mimicry. Hence, it was hypothesized that this PAS2 residue forms a key distinction between the phyA and phyB phytochrome species.
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Affiliation(s)
- Xuewen Wang
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Irma Roig-Villanova
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB, 08034 Barcelona, Spain
| | - Safina Khan
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Hugh Shanahan
- Department of Computer Science, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Peter H. Quail
- Department of Plant and Microbial Biology, UC Berkeley, Albany, CA 94710, USA
| | - Jaime F. Martinez-Garcia
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB, 08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Ps. Lluís Companys 23, 08010 Barcelona, Spain
| | - Paul F. Devlin
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
- To whom correspondence should be addressed. E-mail:
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22
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Wenden B, Kozma-Bognár L, Edwards KD, Hall AJW, Locke JCW, Millar AJ. Light inputs shape the Arabidopsis circadian system. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 66:480-91. [PMID: 21255161 DOI: 10.1111/j.1365-313x.2011.04505.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The circadian clock is a fundamental feature of eukaryotic gene regulation that is emerging as an exemplar genetic sub-network for systems biology. The circadian system in Arabidopsis plants is complex, in part due to its phototransduction pathways, which are themselves under circadian control. We therefore analysed two simpler experimental systems. Etiolated seedlings entrained by temperature cycles showed circadian rhythms in the expression of genes that are important for the clock mechanism, but only a restricted set of downstream target genes were rhythmic in microarray assays. Clock control of phototransduction pathways remained robust across a range of light inputs, despite the arrhythmic transcription of light-signalling genes. Circadian interactions with light signalling were then analysed using a single active photoreceptor. Phytochrome A (phyA) is expected to be the only active photoreceptor that can mediate far-red (FR) light input to the circadian clock. Surprisingly, rhythmic gene expression was profoundly altered under constant FR light, in a phyA-dependent manner, resulting in high expression of evening genes and low expression of morning genes. Dark intervals were required to allow high-amplitude rhythms across the transcriptome. Clock genes involved in this response were identified by mutant analysis, showing that the EARLY FLOWERING 4 gene is a likely target and mediator of the FR effects. Both experimental systems illustrate how profoundly the light input pathways affect the plant circadian clock, and provide strong experimental manipulations to understand critical steps in the plant clock mechanism.
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Affiliation(s)
- Bénédicte Wenden
- School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH93JH, UK
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23
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McWatters HG, Devlin PF. Timing in plants - A rhythmic arrangement. FEBS Lett 2011; 585:1474-84. [DOI: 10.1016/j.febslet.2011.03.051] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 03/14/2011] [Accepted: 03/23/2011] [Indexed: 12/16/2022]
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24
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Palágyi A, Terecskei K, Ádám É, Kevei É, Kircher S, Mérai Z, Schäfer E, Nagy F, Kozma-Bognár L. Functional analysis of amino-terminal domains of the photoreceptor phytochrome B. PLANT PHYSIOLOGY 2010; 153:1834-45. [PMID: 20530216 PMCID: PMC2923874 DOI: 10.1104/pp.110.153031] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 06/06/2010] [Indexed: 05/18/2023]
Abstract
At the core of the circadian network in Arabidopsis (Arabidopsis thaliana), clock genes/proteins form multiple transcriptional/translational negative feedback loops and generate a basic approximately 24-h oscillation, which provides daily regulation for a wide range of processes. This temporal organization enhances the fitness of plants only if it corresponds to the natural day/night cycles. Light, absorbed by photoreceptors, is the most effective signal in synchronizing the oscillator to environmental cycles. Phytochrome B (PHYB) is the major red/far-red light-absorbing phytochrome receptor in light-grown plants. Besides modulating the pace and phase of the circadian clock, PHYB controls photomorphogenesis and delays flowering. It has been demonstrated that the nuclear-localized amino-terminal domain of PHYB is capable of controlling photomorphogenesis and, partly, flowering. Here, we show (1) that PHYB derivatives containing 651 or 450 amino acid residues of the amino-terminal domains are functional in mediating red light signaling to the clock, (2) that circadian entrainment is a nuclear function of PHYB, and (3) that a 410-amino acid amino-terminal fragment does not possess any functions of PHYB due to impaired chromophore binding. However, we provide evidence that the carboxyl-terminal domain is required to mediate entrainment in white light, suggesting a role for this domain in integrating red and blue light signaling to the clock. Moreover, careful analysis of the circadian phenotype of phyB-9 indicates that PHYB provides light signaling for different regulatory loops of the circadian oscillator in a different manner, which results in an apparent decoupling of the loops in the absence of PHYB under specific light conditions.
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25
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Más P, Yanovsky MJ. Time for circadian rhythms: plants get synchronized. CURRENT OPINION IN PLANT BIOLOGY 2009; 12:574-9. [PMID: 19709921 DOI: 10.1016/j.pbi.2009.07.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 06/04/2009] [Accepted: 07/21/2009] [Indexed: 05/22/2023]
Abstract
Most organisms adjust their physiology and metabolism in synchronization with the diurnal and seasonal time by using an endogenous mechanism known as circadian clock. In plants, light and temperature signals interact with the circadian system to regulate the circadian rhythmicity of physiological and developmental processes including flowering time. Recent studies in Arabidopsis thaliana now reveal that the circadian clock orchestrates not only the expression of protein coding genes but also the rhythmic oscillation of introns, intergenic regions, and noncoding RNAs. Furthermore, recent evidence showing the existence of different oscillators at separate parts of the plant has placed the spotlight on the diverse mechanisms and communicating channels that regulate circadian synchronization in plants.
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Affiliation(s)
- Paloma Más
- Centre for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB, C/Jordi Girona 18-26, 08034 Barcelona, Spain.
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26
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Gould PD, Diaz P, Hogben C, Kusakina J, Salem R, Hartwell J, Hall A. Delayed fluorescence as a universal tool for the measurement of circadian rhythms in higher plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 58:893-901. [PMID: 19638147 DOI: 10.1111/j.1365-313x.2009.03819.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The plant circadian clock plays an important role in enhancing performance and increasing vegetative yield. Much of our current understanding of the mechanism and function of the plant clock has come from the development of Arabidopsis thaliana as a model circadian organism. Key to this rapid progress has been the development of robust circadian markers, specifically circadian-regulated luciferase reporter genes. Studies of the clock in crop species and non-model organisms are currently hindered by the absence of a simple high-throughput universal assay for clock function, accuracy and robustness. Delayed fluorescence (DF) is a fundamental process occurring in all photosynthetic organisms. It is luminescence-produced post-illumination due to charge recombination in photosystem II (PSII) leading to excitation of P680 and the subsequent emission of a photon. Here we report that the amount of DF oscillates with an approximately 24-h period and is under the control of the circadian clock in a diverse selection of plants. Thus, DF provides a simple clock output that may allow the clock to be assayed in vivo in any photosynthetic organism. Furthermore, our data provide direct evidence that the nucleus-encoded, three-loop circadian oscillator underlies rhythms of PSII activity in the chloroplast. This simple, high-throughput and non-transgenic assay could be integrated into crop breeding programmes, the assay allows the selection of plants that have robust and accurate clocks, and possibly enhanced performance and vegetative yield. This assay could also be used to characterize rapidly the role and function of any novel Arabidopsis circadian mutant.
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Affiliation(s)
- Peter D Gould
- School of Biological Sciences, University of Liverpool, Crown Street, Liverpool, UK
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27
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28
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Xu X, Hotta CT, Dodd AN, Love J, Sharrock R, Lee YW, Xie Q, Johnson CH, Webb AAR. Distinct light and clock modulation of cytosolic free Ca2+ oscillations and rhythmic CHLOROPHYLL A/B BINDING PROTEIN2 promoter activity in Arabidopsis. THE PLANT CELL 2007; 19:3474-90. [PMID: 17982000 PMCID: PMC2174886 DOI: 10.1105/tpc.106.046011] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 09/30/2007] [Accepted: 10/15/2007] [Indexed: 05/17/2023]
Abstract
Plants have circadian oscillations in the concentration of cytosolic free calcium ([Ca(2+)](cyt)). To dissect the circadian Ca(2+)-signaling network, we monitored circadian [Ca(2+)](cyt) oscillations under various light/dark conditions (including different spectra) in Arabidopsis thaliana wild type and photoreceptor and circadian clock mutants. Both red and blue light regulate circadian oscillations of [Ca(2+)](cyt). Red light signaling is mediated by PHYTOCHROME B (PHYB). Blue light signaling occurs through the redundant action of CRYPTOCHROME1 (CRY1) and CRY2. Blue light also increases the basal level of [Ca(2+)](cyt), and this response requires PHYB, CRY1, and CRY2. Light input into the oscillator controlling [Ca(2+)](cyt) rhythms is gated by EARLY FLOWERING3. Signals generated in the dark also regulate the circadian behavior of [Ca(2+)](cyt). Oscillations of [Ca(2+)](cyt) and CHLOROPHYLL A/B BINDING PROTEIN2 (CAB2) promoter activity are dependent on the rhythmic expression of LATE ELONGATED HYPOCOTYL and CIRCADIAN CLOCK-ASSOCIATED1, but [Ca(2+)](cyt) and CAB2 promoter activity are uncoupled in the timing of cab1 (toc1-1) mutant but not in toc1-2. We suggest that the circadian oscillations of [Ca(2+)](cyt) and CAB2 promoter activity are regulated by distinct oscillators with similar components that are used in a different manner and that these oscillators may be located in different cell types in Arabidopsis.
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Affiliation(s)
- Xiaodong Xu
- Department of Biological Sciences, Vanderbilt University, Nashville, Tenessee 37235, USA
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Hall A, Brown P. Monitoring circadian rhythms in Arabidopsis thaliana using luciferase reporter genes. Methods Mol Biol 2007; 362:143-52. [PMID: 17417007 DOI: 10.1007/978-1-59745-257-1_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Arabidopsis thaliana is internationally adopted as the model plant species for molecular genetics. As such a huge range of resources are available for its study. Arabidopsis does not display any obvious circadian rhythms; however, rhythms in gene expression can be readily detected. For this reason the promoters of rhythmically expressed genes have been fused to the firefly luciferase gene. Using this reporter gene we have developed a number of automated techniques for monitoring luciferase activity in vivo in plants. This provides us with a robust and high-throughput assay for the circadian clock in Arabidopsis.
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Affiliation(s)
- Anthony Hall
- School of Biological Sciences, University of Liverpool, UK
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McWatters HG, Kolmos E, Hall A, Doyle MR, Amasino RM, Gyula P, Nagy F, Millar AJ, Davis SJ. ELF4 is required for oscillatory properties of the circadian clock. PLANT PHYSIOLOGY 2007; 144:391-401. [PMID: 17384164 PMCID: PMC1913775 DOI: 10.1104/pp.107.096206] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Circadian clocks are required to coordinate metabolism and physiology with daily changes in the environment. Such clocks have several distinctive features, including a free-running rhythm of approximately 24 h and the ability to entrain to both light or temperature cycles (zeitgebers). We have previously characterized the EARLY FLOWERING4 (ELF4) locus of Arabidopsis (Arabidopsis thaliana) as being important for robust rhythms. Here, it is shown that ELF4 is necessary for at least two core clock functions: entrainment to an environmental cycle and rhythm sustainability under constant conditions. We show that elf4 demonstrates clock input defects in light responsiveness and in circadian gating. Rhythmicity in elf4 could be driven by an environmental cycle, but an increased sensitivity to light means the circadian system of elf4 plants does not entrain normally. Expression of putative core clock genes and outputs were characterized in various ELF4 backgrounds to establish the molecular network of action. ELF4 was found to be intimately associated with the CIRCADIAN CLOCK-ASSOCIATED1 (CCA1)/LONG ELONGATED HYPOCOTYL (LHY)-TIMING OF CAB EXPRESSION1 (TOC1) feedback loop because, under free run, ELF4 is required to regulate the expression of CCA1 and TOC1 and, further, elf4 is locked in the evening phase of this feedback loop. ELF4, therefore, can be considered a component of the central CCA1/LHY-TOC1 feedback loop in the plant circadian clock.
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Affiliation(s)
- Harriet G McWatters
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
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31
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Schöning JC, Streitner C, Staiger D. Clockwork green—the circadian oscillator inArabidopsis. BIOL RHYTHM RES 2007. [DOI: 10.1080/09291010600804577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Locke JCW, Kozma-Bognár L, Gould PD, Fehér B, Kevei É, Nagy F, Turner MS, Hall A, Millar AJ. Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. Mol Syst Biol 2006; 2:59. [PMID: 17102804 PMCID: PMC1682024 DOI: 10.1038/msb4100102] [Citation(s) in RCA: 349] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Accepted: 08/14/2006] [Indexed: 01/20/2023] Open
Abstract
Our computational model of the circadian clock comprised the feedback loop between LATE ELONGATED HYPOCOTYL (LHY), CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and TIMING OF CAB EXPRESSION 1 (TOC1), and a predicted, interlocking feedback loop involving TOC1 and a hypothetical component Y. Experiments based on model predictions suggested GIGANTEA (GI) as a candidate for Y. We now extend the model to include a recently demonstrated feedback loop between the TOC1 homologues PSEUDO-RESPONSE REGULATOR 7 (PRR7), PRR9 and LHY and CCA1. This three-loop network explains the rhythmic phenotype of toc1 mutant alleles. Model predictions fit closely to new data on the gi;lhy;cca1 mutant, which confirm that GI is a major contributor to Y function. Analysis of the three-loop network suggests that the plant clock consists of morning and evening oscillators, coupled intracellularly, which may be analogous to coupled, morning and evening clock cells in Drosophila and the mouse.
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Affiliation(s)
- James C W Locke
- Department of Biological Sciences, University of Warwick, Coventry, UK
- Department of Physics, University of Warwick, Coventry, UK
- Interdisciplinary Programme for Cellular Regulation, University of Warwick, Coventry, UK
| | - László Kozma-Bognár
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, UK
| | - Peter D Gould
- School of Biological Sciences, University of Liverpool, Liverpool, UK
| | - Balázs Fehér
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary
| | - Éva Kevei
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary
| | - Matthew S Turner
- Department of Physics, University of Warwick, Coventry, UK
- Interdisciplinary Programme for Cellular Regulation, University of Warwick, Coventry, UK
| | - Anthony Hall
- School of Biological Sciences, University of Liverpool, Liverpool, UK
- School of Biological Sciences, University of Liverpool, Crown Street, Liverpool, UK. Tel.: +44 151 795 4565; Fax: +44 151 795 4403;
| | - Andrew J Millar
- Interdisciplinary Programme for Cellular Regulation, University of Warwick, Coventry, UK
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, UK
- Institute of Molecular Plant Sciences, University of Edinburgh, Rutherford Building, Mayfield Road, Edinburgh EH9 3JH, UK. Tel.: +44 131 651 3325; Fax: +44 131 650 5392;
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Gardner M, Hubbard K, Hotta C, Dodd A, Webb A. How plants tell the time. Biochem J 2006; 397:15-24. [PMID: 16761955 PMCID: PMC1479754 DOI: 10.1042/bj20060484] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Accepted: 05/08/2006] [Indexed: 01/16/2023]
Abstract
Plants, like all eukaryotes and most prokaryotes, have evolved sophisticated mechanisms for anticipating predictable environmental changes that arise due to the rotation of the Earth on its axis. These mechanisms are collectively termed the circadian clock. Many aspects of plant physiology, metabolism and development are under circadian control and a large proportion of the transcriptome exhibits circadian regulation. In the present review, we describe the advances in determining the molecular nature of the circadian oscillator and propose an architecture of several interlocking negative-feedback loops. The adaptive advantages of circadian control, with particular reference to the regulation of metabolism, are also considered. We review the evidence for the presence of multiple circadian oscillator types located in within individual cells and in different tissues.
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Key Words
- biological rhythm
- circadian clock
- photoperiodism
- plant
- temperature regulation
- timekeeping
- arna, antisense rna
- cab, chlorophyll a/b-binding protein
- cat3, catalase 3
- cbs, cca1-binding site
- cca1, circadian clock associated 1
- chs, chalcone synthase
- cop1, constitutively photomorphogenic 1
- co, constans
- cry, cryptochrome
- [ca2+]cyt, cytosolic free ca2+ concentration
- det1, de-etiolated 1
- elf, early flowering
- ft, flowering locus t
- frq, frequency
- grp, glycine-rich protein
- gi, gigantea
- lhy, late elongated hypocotyl
- lkp2, light oxygen or voltage/kelch protein 2
- lov, light oxygen or voltage
- luc, luciferase
- lux, lux arrhythmo
- nr, nitrate reductase
- per, period
- phot, phototropin
- phy, phytochrome
- prr, pseudo response regulator
- skp1, s-phase kinase-associated protein 1
- scf, skp1/cullin/f-box
- scn, suprachiasmatic nucleus
- spy, spindly
- toc1, timing of cab expression 1
- ztl, zeitlupe
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Affiliation(s)
- Michael J. Gardner
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Katharine E. Hubbard
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Carlos T. Hotta
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Antony N. Dodd
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
| | - Alex A. R. Webb
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, U.K
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Gould PD, Locke JCW, Larue C, Southern MM, Davis SJ, Hanano S, Moyle R, Milich R, Putterill J, Millar AJ, Hall A. The molecular basis of temperature compensation in the Arabidopsis circadian clock. THE PLANT CELL 2006; 18:1177-87. [PMID: 16617099 PMCID: PMC1456873 DOI: 10.1105/tpc.105.039990] [Citation(s) in RCA: 256] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Circadian clocks maintain robust and accurate timing over a broad range of physiological temperatures, a characteristic termed temperature compensation. In Arabidopsis thaliana, ambient temperature affects the rhythmic accumulation of transcripts encoding the clock components TIMING OF CAB EXPRESSION1 (TOC1), GIGANTEA (GI), and the partially redundant genes CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY). The amplitude and peak levels increase for TOC1 and GI RNA rhythms as the temperature increases (from 17 to 27 degrees C), whereas they decrease for LHY. However, as temperatures decrease (from 17 to 12 degrees C), CCA1 and LHY RNA rhythms increase in amplitude and peak expression level. At 27 degrees C, a dynamic balance between GI and LHY allows temperature compensation in wild-type plants, but circadian function is impaired in lhy and gi mutant plants. However, at 12 degrees C, CCA1 has more effect on the buffering mechanism than LHY, as the cca1 and gi mutations impair circadian rhythms more than lhy at the lower temperature. At 17 degrees C, GI is apparently dispensable for free-running circadian rhythms, although partial GI function can affect circadian period. Numerical simulations using the interlocking-loop model show that balancing LHY/CCA1 function against GI and other evening-expressed genes can largely account for temperature compensation in wild-type plants and the temperature-specific phenotypes of gi mutants.
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Affiliation(s)
- Peter D Gould
- School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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37
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Darrah C, Taylor BL, Edwards KD, Brown PE, Hall A, McWatters HG. Analysis of phase of LUCIFERASE expression reveals novel circadian quantitative trait loci in Arabidopsis. PLANT PHYSIOLOGY 2006; 140:1464-74. [PMID: 16461388 PMCID: PMC1435814 DOI: 10.1104/pp.105.074518] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In response to exogenous rhythms of light and temperature, most organisms exhibit endogenous circadian rhythms (i.e. cycles of behavior and gene expression with a periodicity of approximately 24 h). One of the defining characteristics of the circadian clock is its ability to synchronize (entrain) to an environmental rhythm. Entrainment is arguably the most salient feature of the clock in evolutionary terms. Previous quantitative trait studies of circadian characteristics in Arabidopsis (Arabidopsis thaliana) considered leaf movement under constant (free-running) conditions. This study, however, addressed the important circadian parameter of phase, which reflects the entrained relationship between the clock and the external cycle. Here it is shown that, when exposed to the same photoperiod, Arabidopsis accessions differ dramatically in phase. Variation in the timing of circadian LUCIFERASE expression was used to map loci affecting the entrained phase of the clock in a recombinant population derived from two geographically distant accessions, Landsberg erecta and Cape Verde Islands. Four quantitative trait loci (QTL) were found with major effects on circadian phase. A QTL on chromosome 5 contained SIGNALING IN RED LIGHT REDUCED 1 and PSEUDORESPONSE REGULATOR 3, both genes known to affect the circadian clock. Previously unknown polymorphisms were found in both genes, making them candidates for the effect on phase. Fine mapping of two other QTL highlighted genomic regions not previously identified in any circadian screens, indicating their effects are likely due to genes not hitherto considered part of the circadian system.
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Affiliation(s)
- Chiarina Darrah
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
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38
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Salomé PA, To JPC, Kieber JJ, McClung CR. Arabidopsis response regulators ARR3 and ARR4 play cytokinin-independent roles in the control of circadian period. THE PLANT CELL 2006; 18:55-69. [PMID: 16326927 PMCID: PMC1323484 DOI: 10.1105/tpc.105.037994] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Light and temperature are potent environmental signals used to synchronize the circadian oscillator with external time and photoperiod. Phytochrome and cryptochrome photoreceptors integrate light quantity and quality to modulate the pace and phase of the clock. PHYTOCHROME B (phyB) controls period length in red light as well as the phase of the clock in white light. phyB interacts with ARABIDOPSIS RESPONSE REGULATOR4 (ARR4) in a light-dependent manner. Accordingly, we tested ARR4 and other members of the type-A ARR family for roles in clock function and show that ARR4 and its closest relative, ARR3, act redundantly in the Arabidopsis thaliana circadian system. Loss of ARR3 and ARR4 lengthens the period of the clock even in the absence of light, demonstrating that they do so independently of active phyB. In addition, in white light, arr3,4 mutants show a leading phase similar to phyB mutants, suggesting that circadian light input is modulated by the interaction of phyB with ARR4. Although type-A ARRs are involved in cytokinin signaling, the circadian defects appear to be independent of cytokinin, as exogenous cytokinin affects the phase but not the period of the clock. Therefore, ARR3 and ARR4 are critical for proper circadian period and define an additional level of regulation of the circadian clock in Arabidopsis.
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Affiliation(s)
- Patrice A Salomé
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755-3576, USA
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39
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Quantitative inference of dynamic regulatory pathways via microarray data. BMC Bioinformatics 2005; 6:44. [PMID: 15748298 PMCID: PMC555938 DOI: 10.1186/1471-2105-6-44] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Accepted: 03/07/2005] [Indexed: 01/10/2023] Open
Abstract
Background The cellular signaling pathway (network) is one of the main topics of organismic investigations. The intracellular interactions between genes in a signaling pathway are considered as the foundation of functional genomics. Thus, what genes and how much they influence each other through transcriptional binding or physical interactions are essential problems. Under the synchronous measures of gene expression via a microarray chip, an amount of dynamic information is embedded and remains to be discovered. Using a systematically dynamic modeling approach, we explore the causal relationship among genes in cellular signaling pathways from the system biology approach. Results In this study, a second-order dynamic model is developed to describe the regulatory mechanism of a target gene from the upstream causality point of view. From the expression profile and dynamic model of a target gene, we can estimate its upstream regulatory function. According to this upstream regulatory function, we would deduce the upstream regulatory genes with their regulatory abilities and activation delays, and then link up a regulatory pathway. Iteratively, these regulatory genes are considered as target genes to trace back their upstream regulatory genes. Then we could construct the regulatory pathway (or network) to the genome wide. In short, we can infer the genetic regulatory pathways from gene-expression profiles quantitatively, which can confirm some doubted paths or seek some unknown paths in a regulatory pathway (network). Finally, the proposed approach is validated by randomly reshuffling the time order of microarray data. Conclusion We focus our algorithm on the inference of regulatory abilities of the identified causal genes, and how much delay before they regulate the downstream genes. With this information, a regulatory pathway would be built up using microarray data. In the present study, two signaling pathways, i.e. circadian regulatory pathway in Arabidopsis thaliana and metabolic shift pathway from fermentation to respiration in yeast Saccharomyces cerevisiae, are reconstructed using microarray data to evaluate the performance of our proposed method. In the circadian regulatory pathway, we identified mainly the interactions between the biological clock and the photoperiodic genes consistent with the known regulatory mechanisms. We also discovered the now less-known regulations between crytochrome and phytochrome. In the metabolic shift pathway, the casual relationship of enzymatic genes could be detected properly.
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40
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Abstract
A combination of forward and reverse genetic approaches together with transcriptome-scale gene expression analyses have allowed the elaboration of a model for the Arabidopsis thaliana circadian clock. The working model largely conforms to the expected negative feedback loop model that has emerged from studies in other model systems. Although a core loop has emerged, it is clear that additional components remain to be identified and that the workings of the Arabidopsis clock have been established only in outline. Similarly, the details of resetting by light and temperature are only incompletely known. In contrast, the mechanism of photoperiodic induction of flowering is known in considerable detail and is consistent with the external coincidence model.
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Affiliation(s)
- Patrice A Salomé
- Department of Biological Sciences, 6044 Gilman Laboratories, Dartmouth College, Hanover, NH 03755-3576, USA
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41
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Somers DE, Kim WY, Geng R. The F-box protein ZEITLUPE confers dosage-dependent control on the circadian clock, photomorphogenesis, and flowering time. THE PLANT CELL 2004; 16:769-82. [PMID: 14973171 PMCID: PMC385287 DOI: 10.1105/tpc.016808] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2003] [Accepted: 01/08/2004] [Indexed: 05/18/2023]
Abstract
As an F-box protein, ZEITLUPE (ZTL) is involved in targeting one or more substrates for ubiquitination and degradation via the proteasome. The initial characterization of ZTL suggested a function limited largely to the regulation of the circadian clock. Here, we show a considerably broader role for ZTL in the control of circadian period and photomorphogenesis. Using a ZTL-specific antibody, we quantitated and characterized a ZTL dosage series that ranges from a null mutation to a strong ZTL overexpressor. In the dark, ztl null mutations lengthen circadian period, and overexpression causes arrhythmicity, suggesting a more comprehensive role for this protein in the clock than previously suspected. In the light, circadian period becomes increasingly shorter at higher levels of ZTL, to the point of arrhythmicity. By contrast, hypocotyl length increases and flowering time is delayed in direct proportion to the level of ZTL. We propose a novel testable mechanism by which circadian period and amplitude may act together to gate phytochrome B-mediated suppression of hypocotyl. We also demonstrate that ZTL-dependent delay of flowering is mediated through decreases in CONSTANS and FLOWERING LOCUS T message levels, thus directly linking proteasome-dependent proteolysis to flowering.
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Affiliation(s)
- David E Somers
- Department of Plant Biology/Plant Biotechnology Center, Ohio State University, Columbus, Ohio 43210, USA.
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42
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Devlin PF, Yanovsky MJ, Kay SA. A genomic analysis of the shade avoidance response in Arabidopsis. PLANT PHYSIOLOGY 2003; 133:1617-29. [PMID: 14645734 PMCID: PMC300718 DOI: 10.1104/pp.103.034397] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2003] [Revised: 10/13/2003] [Accepted: 10/15/2003] [Indexed: 05/18/2023]
Abstract
Plants respond to the proximity of neighboring vegetation by elongating to prevent shading. Red-depleted light reflected from neighboring vegetation triggers a shade avoidance response leading to a dramatic change in plant architecture. These changes in light quality are detected by the phytochrome family of photoreceptors. We analyzed global changes in gene expression over time in wild-type, phyB mutant, and phyA phyB double mutant seedlings of Arabidopsis in response to simulated shade. Using pattern fitting software, we identified 301 genes as shade responsive with patterns of expression corresponding to one of various physiological response modes. A requirement for a consistent pattern of expression across 12 chips in this way allowed more subtle changes in gene expression to be considered meaningful. A number of previously characterized genes involved in light and hormone signaling were identified as shade responsive, as well as several putative, novel shade-specific signal transduction factors. In addition, changes in expression of genes in a range of pathways associated with elongation growth and stress responses were observed. The majority of shade-responsive genes demonstrated antagonistic regulation by phyA and phyB in response to shade following the pattern of many physiological responses. An analysis of promoter elements of genes regulated in this way identified conserved promoter motifs potentially important in shade regulation.
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Affiliation(s)
- Paul Francis Devlin
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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43
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Hall A, Bastow RM, Davis SJ, Hanano S, McWatters HG, Hibberd V, Doyle MR, Sung S, Halliday KJ, Amasino RM, Millar AJ. The TIME FOR COFFEE gene maintains the amplitude and timing of Arabidopsis circadian clocks. THE PLANT CELL 2003; 15:2719-29. [PMID: 14555691 PMCID: PMC280574 DOI: 10.1105/tpc.013730] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2003] [Accepted: 09/03/2003] [Indexed: 05/18/2023]
Abstract
Plants synchronize developmental and metabolic processes with the earth's 24-h rotation through the integration of circadian rhythms and responses to light. We characterize the time for coffee (tic) mutant that disrupts circadian gating, photoperiodism, and multiple circadian rhythms, with differential effects among rhythms. TIC is distinct in physiological functions and genetic map position from other rhythm mutants and their homologous loci. Detailed rhythm analysis shows that the chlorophyll a/b-binding protein gene expression rhythm requires TIC function in the mid to late subjective night, when human activity may require coffee, in contrast to the function of EARLY-FLOWERING3 (ELF3) in the late day to early night. tic mutants misexpress genes that are thought to be critical for circadian timing, consistent with our functional analysis. Thus, we identify TIC as a regulator of the clock gene circuit. In contrast to tic and elf3 single mutants, tic elf3 double mutants are completely arrhythmic. Even the robust circadian clock of plants cannot function with defects at two different phases.
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Affiliation(s)
- Anthony Hall
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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Abstract
Circadian rhythms regulate many aspects of plant physiology including leaf, organ and stomatal movements, growth and signalling. The genetic identity of some of the components of the core circadian oscillator has recently become known. Similarly, the photoperception and phototransduction pathways that entrain the oscillator to the day and night cycle are being determined. Less clear are the pathways by which the circadian oscillator regulates cellular physiology. Circadian oscillations in cytosolic free calcium might act to transduce the temporal outputs of the circadian oscillator. This hypothesis requires rigorous testing using novel noninvasive technologies. Plants might gain advantage from the circadian clock by being able to predict changes in the environment and coordinate physiological processes, presumably increasing survival and hence, reproductive fitness. Technical advances coupled with cell-specific measurement techniques will allow the advantages of the circadian regulation of physiology to be quantified. Summary 281 I. Introduction 282 II. The circadian clock 283 III. The regulation of cellular physiology by circadian oscillations in cytosolic free Ca2+ 286 IV. The circadian regulation of physiology 292 V. The benefits of the circadian regulation of physiology 298 VI. Future prospects 299 VIII. Conclusions 300 Acknowledgements 300 References 300.
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Affiliation(s)
- Alex A R Webb
- Department of Plant Sciences, University of Cambridge, Downing Street, CAMBRIDGE, CB2 3EA, UK
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45
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Abstract
Circadian rhythms in plants are relatively robust, as they are maintained both in constant light of high fluence rates and in darkness. Plant circadian clocks exhibit the expected modes of photoentrainment, including period modulation by ambient light and phase resetting by brief light pulses. Several of the phytochrome and cryptochrome photoreceptors responsible have been studied in detail. This review concentrates on the resulting patterns of entrainment and on the multiple proposed mechanisms of light input to the circadian oscillator components.
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Affiliation(s)
- Andrew J Millar
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.
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46
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Eriksson ME, Millar AJ. The circadian clock. A plant's best friend in a spinning world. PLANT PHYSIOLOGY 2003; 132:732-8. [PMID: 12805602 PMCID: PMC523864 DOI: 10.1104/pp.103.022343] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2003] [Revised: 02/21/2003] [Accepted: 02/21/2003] [Indexed: 05/18/2023]
Affiliation(s)
- Maria E Eriksson
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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Michael TP, Salome PA, McClung CR. Two Arabidopsis circadian oscillators can be distinguished by differential temperature sensitivity. Proc Natl Acad Sci U S A 2003; 100:6878-83. [PMID: 12736379 PMCID: PMC164540 DOI: 10.1073/pnas.1131995100] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Circadian rhythms are widespread in nature and reflect the activity of an endogenous biological clock. In metazoans, the circadian system includes a central circadian clock in the brain as well as distinct clocks in peripheral tissues such as the retina or liver. Similarly, plants have distinct clocks in different cell layers and tissues. Here, we show that two different circadian clocks, distinguishable by their sensitivity to environmental temperature signals, regulate the transcription of genes that are expressed in the Arabidopsis thaliana cotyledon. One oscillator, which regulates CAB2 expression, responds preferentially to light-dark versus temperature cycles and fails to respond to the temperature step associated with release from stratification. The second oscillator, which regulates CAT3 expression, responds preferentially to temperature versus light-dark cycles and entrains to the release from stratification. Finally, the phase response curves of these two oscillators to cold pulses are distinct. The phase response curve of the oscillator component TOC1 to cold pulses is similar to that of CAB2, indicating that CAB2 is regulated by a TOC1-containing clock. The existence of two clocks, distinguishable on the basis of their sensitivity to temperature, provides an additional means by which plants may integrate both photoperiodic and temperature signals to respond to the changing seasons.
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Affiliation(s)
- Todd P Michael
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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Abstract
Reproductive processes in plants and animals are usually synchronized with favourable seasons of the year. It has been known for 80 years that organisms anticipate seasonal changes by adjusting developmental programmes in response to daylength. Recent studies indicate that plants perceive daylength through the degree of coincidence of light with the expression of CONSTANS, which encodes a clock-regulated transcription factor that controls the expression of floral-inductive genes in a light-dependent manner.
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Affiliation(s)
- Marcelo J Yanovsky
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037 USA
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Staiger D, Allenbach L, Salathia N, Fiechter V, Davis SJ, Millar AJ, Chory J, Fankhauser C. The Arabidopsis SRR1 gene mediates phyB signaling and is required for normal circadian clock function. Genes Dev 2003; 17:256-68. [PMID: 12533513 PMCID: PMC195977 DOI: 10.1101/gad.244103] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Plants possess several photoreceptors to sense the light environment. In Arabidopsis cryptochromes and phytochromes play roles in photomorphogenesis and in the light input pathways that synchronize the circadian clock with the external world. We have identified SRR1 (sensitivity to red light reduced), a gene that plays an important role in phytochrome B (phyB)-mediated light signaling. The recessive srr1 null allele and phyB mutants display a number of similar phenotypes indicating that SRR1 is required for normal phyB signaling. Genetic analysis suggests that SRR1 works both in the phyB pathway but also independently of phyB. srr1 mutants are affected in multiple outputs of the circadian clock in continuous light conditions, including leaf movement and expression of the clock components, CCA1 and TOC1. Clock-regulated gene expression is also impaired during day-night cycles and in constant darkness. The circadian phenotypes of srr1 mutants in all three conditions suggest that SRR1 activity is required for normal oscillator function. The SRR1 gene was identified and shown to code for a protein conserved in numerous eukaryotes including mammals and flies, implicating a conserved role for this protein in both the animal and plant kingdoms.
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Affiliation(s)
- Dorothee Staiger
- Institute for Plant Sciences, Swiss Federal Institute of Technology, ETH Center, Zurich, Switzerland
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