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Singh SK, Srivastava A. Decoding the plant clock: a review of mathematical models for the circadian regulatory network. PLANT MOLECULAR BIOLOGY 2024; 114:93. [PMID: 39207587 DOI: 10.1007/s11103-024-01493-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
Most organisms have evolved specific mechanisms to respond to changes in environmental conditions such as light and temperature over the course of day. These periodic changes in the physiology and behaviour of organisms, referred to as circadian rhythms, are a consequence of intricate molecular mechanisms in the form of transcription and translational feedback loops. The plant circadian regulatory network is a complex web of interconnected feedback loops involving various transcription factors such as CCA1, LHY, PRRs, TOC1, LUX, ELF3, ELF4, RVE8, and more. This network enables plants to adapt and thrive in diverse environmental conditions. It responds to entrainment signals, including light, temperature, and nutrient concentrations and interacts with most of the physiological functions such as flowering, growth and stress response. Mathematical modelling of these gene regulatory networks enables a deeper understanding of not only the function but also the perturbations that may affect the plant growth and function with changing climate. Over the years, numerous mathematical models have been developed to understand the diverse aspects of plant circadian regulation. In this review, we have delved into the systematic development of these models, outlining the model components and refinements over time. We have also highlighted strengths and limitations of each of the models developed so far. Finally, we conclude the review by describing the prospects for investigation and advancement of these models for better understanding of plant circadian regulation.
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Affiliation(s)
- Shashank Kumar Singh
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, India
| | - Ashutosh Srivastava
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, India.
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2
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Schmal C. The seasons within: a theoretical perspective on photoperiodic entrainment and encoding. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2024; 210:549-564. [PMID: 37659985 PMCID: PMC11226496 DOI: 10.1007/s00359-023-01669-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 09/04/2023]
Abstract
Circadian clocks are internal timing devices that have evolved as an adaption to the omnipresent natural 24 h rhythmicity of daylight intensity. Properties of the circadian system are photoperiod dependent. The phase of entrainment varies systematically with season. Plastic photoperiod-dependent re-arrangements in the mammalian circadian core pacemaker yield an internal representation of season. Output pathways of the circadian clock regulate photoperiodic responses such as flowering time in plants or hibernation in mammals. Here, we review the concepts of seasonal entrainment and photoperiodic encoding. We introduce conceptual phase oscillator models as their high level of abstraction, but, yet, intuitive interpretation of underlying parameters allows for a straightforward analysis of principles that determine entrainment characteristics. Results from this class of models are related and discussed in the context of more complex conceptual amplitude-phase oscillators as well as contextual molecular models that take into account organism, tissue, and cell-type-specific details.
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Affiliation(s)
- Christoph Schmal
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115, Berlin, Germany.
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3
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Yuan L, Avello P, Zhu Z, Lock SCL, McCarthy K, Redmond EJ, Davis AM, Song Y, Ezer D, Pitchford JW, Quint M, Xie Q, Xu X, Davis SJ, Ronald J. Complex epistatic interactions between ELF3, PRR9, and PRR7 regulate the circadian clock and plant physiology. Genetics 2024; 226:iyad217. [PMID: 38142447 PMCID: PMC10917503 DOI: 10.1093/genetics/iyad217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/07/2023] [Accepted: 12/05/2023] [Indexed: 12/26/2023] Open
Abstract
Circadian clocks are endogenous timekeeping mechanisms that coordinate internal physiological responses with the external environment. EARLY FLOWERING3 (ELF3), PSEUDO RESPONSE REGULATOR (PRR9), and PRR7 are essential components of the plant circadian clock and facilitate entrainment of the clock to internal and external stimuli. Previous studies have highlighted a critical role for ELF3 in repressing the expression of PRR9 and PRR7. However, the functional significance of activity in regulating circadian clock dynamics and plant development is unknown. To explore this regulatory dynamic further, we first employed mathematical modeling to simulate the effect of the prr9/prr7 mutation on the elf3 circadian phenotype. These simulations suggested that simultaneous mutations in prr9/prr7 could rescue the elf3 circadian arrhythmia. Following these simulations, we generated all Arabidopsis elf3/prr9/prr7 mutant combinations and investigated their circadian and developmental phenotypes. Although these assays could not replicate the results from the mathematical modeling, our results have revealed a complex epistatic relationship between ELF3 and PRR9/7 in regulating different aspects of plant development. ELF3 was essential for hypocotyl development under ambient and warm temperatures, while PRR9 was critical for root thermomorphogenesis. Finally, mutations in prr9 and prr7 rescued the photoperiod-insensitive flowering phenotype of the elf3 mutant. Together, our results highlight the importance of investigating the genetic relationship among plant circadian genes.
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Affiliation(s)
- Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Paula Avello
- Department of Mathematics, University of York, York, YO10 5DD, UK
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Zihao Zhu
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale) 06108, Germany
| | - Sarah C L Lock
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Kayla McCarthy
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Ethan J Redmond
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Amanda M Davis
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Yang Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Daphne Ezer
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Jonathan W Pitchford
- Department of Mathematics, University of York, York, YO10 5DD, UK
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale) 06108, Germany
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Seth J Davis
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - James Ronald
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, University Avenue, Glasgow G12 8QQ, UK
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4
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Lee J, Yang JH, Weber APM, Bhattacharya D, Kim WY, Yoon HS. Diurnal Rhythms in the Red Seaweed Gracilariopsis chorda are Characterized by Unique Regulatory Networks of Carbon Metabolism. Mol Biol Evol 2024; 41:msae012. [PMID: 38267085 PMCID: PMC10853006 DOI: 10.1093/molbev/msae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 01/01/2024] [Accepted: 01/08/2024] [Indexed: 01/26/2024] Open
Abstract
Cellular and physiological cycles are driven by endogenous pacemakers, the diurnal and circadian rhythms. Key functions such as cell cycle progression and cellular metabolism are under rhythmic regulation, thereby maintaining physiological homeostasis. The photoreceptors phytochrome and cryptochrome, in response to light cues, are central input pathways for physiological cycles in most photosynthetic organisms. However, among Archaeplastida, red algae are the only taxa that lack phytochromes. Current knowledge about oscillatory rhythms is primarily derived from model species such as Arabidopsis thaliana and Chlamydomonas reinhardtii in the Viridiplantae, whereas little is known about these processes in other clades of the Archaeplastida, such as the red algae (Rhodophyta). We used genome-wide expression profiling of the red seaweed Gracilariopsis chorda and identified 3,098 rhythmic genes. Here, we characterized possible cryptochrome-based regulation and photosynthetic/cytosolic carbon metabolism in this species. We found a large family of cryptochrome genes in G. chorda that display rhythmic expression over the diurnal cycle and may compensate for the lack of phytochromes in this species. The input pathway gates regulatory networks of carbon metabolism which results in a compact and efficient energy metabolism during daylight hours. The system in G. chorda is distinct from energy metabolism in most plants, which activates in the dark. The green lineage, in particular, land plants, balance water loss and CO2 capture in terrestrial environments. In contrast, red seaweeds maintain a reduced set of photoreceptors and a compact cytosolic carbon metabolism to thrive in the harsh abiotic conditions typical of intertidal zones.
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Affiliation(s)
- JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu 41566, Korea
- Kyungpook Institute of Oceanography, Kyungpook National University, Daegu 41566, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 four), Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
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5
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Rodriguez-Maroto G, Catalán P, Nieto C, Prat S, Ares S. Mathematical Modeling of Photo- and Thermomorphogenesis in Plants. Methods Mol Biol 2024; 2795:247-261. [PMID: 38594544 DOI: 10.1007/978-1-0716-3814-9_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Increased day lengths and warm conditions inversely affect plant growth by directly modulating nuclear phyB, ELF3, and COP1 levels. Quantitative measures of the hypocotyl length have been key to gaining a deeper understanding of this complex regulatory network, while similar quantitative data are the foundation for many studies in plant biology. Here, we explore the application of mathematical modeling, specifically ordinary differential equations (ODEs), to understand plant responses to these environmental cues. We provide a comprehensive guide to constructing, simulating, and fitting these models to data, using the law of mass action to study the evolution of molecular species. The fundamental principles of these models are introduced, highlighting their utility in deciphering complex plant physiological interactions and testing hypotheses. This brief introduction will not allow experimentalists without a mathematical background to run their own simulations overnight, but it will help them grasp modeling principles and communicate with more theory-inclined colleagues.
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Affiliation(s)
- Gabriel Rodriguez-Maroto
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
- Department of Mathematics, Universidad Carlos III de Madrid, Madrid, Spain
| | - Pablo Catalán
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
- Department of Mathematics, Universidad Carlos III de Madrid, Madrid, Spain.
| | - Cristina Nieto
- Centro Nacional de Biotecnologia (CNB), CSIC, Madrid, Spain
- Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), CSIC, Madrid, Spain
| | - Salomé Prat
- Centro Nacional de Biotecnologia (CNB), CSIC, Madrid, Spain
- Centro de Investigación en Agrigenomica (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Saúl Ares
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
- Centro Nacional de Biotecnologia (CNB), CSIC, Madrid, Spain.
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6
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Huang T, Liu H, Tao JP, Zhang JQ, Zhao TM, Hou XL, Xiong AS, You X. Low light intensity elongates period and defers peak time of photosynthesis: a computational approach to circadian-clock-controlled photosynthesis in tomato. HORTICULTURE RESEARCH 2023; 10:uhad077. [PMID: 37323229 PMCID: PMC10261901 DOI: 10.1093/hr/uhad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 04/09/2023] [Indexed: 06/17/2023]
Abstract
Photosynthesis is involved in the essential process of transforming light energy into chemical energy. Although the interaction between photosynthesis and the circadian clock has been confirmed, the mechanism of how light intensity affects photosynthesis through the circadian clock remains unclear. Here, we propose a first computational model for circadian-clock-controlled photosynthesis, which consists of the light-sensitive protein P, the core oscillator, photosynthetic genes, and parameters involved in the process of photosynthesis. The model parameters were determined by minimizing the cost function ( [Formula: see text]), which is defined by the errors of expression levels, periods, and phases of the clock genes (CCA1, PRR9, TOC1, ELF4, GI, and RVE8). The model recapitulates the expression pattern of the core oscillator under moderate light intensity (100 μmol m -2 s-1). Further simulation validated the dynamic behaviors of the circadian clock and photosynthetic outputs under low (62.5 μmol m-2 s-1) and normal (187.5 μmol m-2 s-1) intensities. When exposed to low light intensity, the peak times of clock and photosynthetic genes were shifted backward by 1-2 hours, the period was elongated by approximately the same length, and the photosynthetic parameters attained low values and showed delayed peak times, which confirmed our model predictions. Our study reveals a potential mechanism underlying the circadian regulation of photosynthesis by the clock under different light intensities in tomato.
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Affiliation(s)
- Ting Huang
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
| | - Hui Liu
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
| | - Jian-Ping Tao
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
- The Institute of Agricultural Information, Jiangsu Province Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
| | - Jia-Qi Zhang
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
| | - Tong-Min Zhao
- Laboratory for Genetic Improvement of High Efficiency Horticultural Crops in Jiangsu Province, Institute of Vegetable Crop, Jiangsu Province Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
| | - Xi-Lin Hou
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
| | - Ai-Sheng Xiong
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
| | - Xiong You
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu China
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7
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Red Light Resets the Expression Pattern, Phase, and Period of the Circadian Clock in Plants: A Computational Approach. BIOLOGY 2022; 11:biology11101479. [PMID: 36290383 PMCID: PMC9598827 DOI: 10.3390/biology11101479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/02/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Simple Summary Progress in computational biology has provided a comprehensive understanding of the dynamics of the plant circadian clock. Previously proposed models of the plant circadian clock have intended to model its entrainment using white-light/dark cycles. However, these models have failed to take into account the effect of light quality on circadian rhythms, which has been experimentally observed. In this work, we developed a computational approach to characterizing the effects of light quality on plant circadian rhythms. The results demonstrated that red light can reset the expression patterns, phases, and periods of clock component genes. The circadian period, amplitude, and phase can be co-optimized for high-quality and efficient breeding. Abstract Recent research in the fields of biochemistry and molecular biology has shown that different light qualities have extremely different effects on plant development, and optimizing light quality conditions can speed up plant growth. Clock-regulated red-light signaling, can enhance hypocotyl elongation, and increase seedling height and flower and fruit productivity. In order to investigate the effect of red light on circadian clocks in plants, a novel computational model was established. The expression profiles of the circadian element CCA1 from previous related studies were used to fit the model. The simulation results were validated by the expression patterns of CCA1 in Arabidopsis, including wild types and mutants, and by the phase shifts of CCA1 after red-light pulse. The model was used to further explore the complex responses to various photoperiods, such as the natural white-light/dark cycles, red/white/dark cycles, and extreme 24 h photoperiods. These results demonstrated that red light can reset the expression pattern, period, and phase of the circadian clock. Finally, we identified the dependence of phase shifts on the length of red-light pulse and the minimum red-light pulse length required for producing an observable phase shift. This work provides a promising computational approach to investigating the response of the circadian clock to other light qualities.
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Okada M, Yang Z, Mas P. Circadian autonomy and rhythmic precision of the Arabidopsis female reproductive organ. Dev Cell 2022; 57:2168-2180.e4. [PMID: 36115345 DOI: 10.1016/j.devcel.2022.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/12/2022] [Accepted: 08/26/2022] [Indexed: 11/03/2022]
Abstract
The plant circadian clock regulates essential biological processes including flowering time or petal movement. However, little is known about how the clock functions in flowers. Here, we identified the circadian components and transcriptional networks contributing to the generation of rhythms in pistils, the female reproductive organ. When detached from the rest of the flower, pistils sustain highly precise rhythms, indicating organ-specific circadian autonomy. Analyses of clock mutants and chromatin immunoprecipitation assays showed distinct expression patterns and specific regulatory functions for clock activators and repressors in pistils. Genetic interaction studies also suggested a hierarchy of the repressing activities that provide robustness and precision to the pistil clock. Globally, the circadian function in pistils primarily governs responses to environmental stimuli and photosynthesis and controls pistil growth and seed weight and production. Understanding the circadian intricacies in reproductive organs may prove useful for optimizing plant reproduction and productivity.
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Affiliation(s)
- Masaaki Okada
- Centre for Research in Agricultural Genomics (CRAG), CSIC, IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Zhiyuan Yang
- Centre for Research in Agricultural Genomics (CRAG), CSIC, IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Paloma Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC, IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain; Consejo Superior de Investigaciones Científicas (CSIC), 08028 Barcelona, Spain.
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Nieto C, Catalán P, Luengo LM, Legris M, López-Salmerón V, Davière JM, Casal JJ, Ares S, Prat S. COP1 dynamics integrate conflicting seasonal light and thermal cues in the control of Arabidopsis elongation. SCIENCE ADVANCES 2022; 8:eabp8412. [PMID: 35984876 PMCID: PMC9390991 DOI: 10.1126/sciadv.abp8412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/07/2022] [Indexed: 05/19/2023]
Abstract
As the summer approaches, plants experience enhanced light inputs and warm temperatures, two environmental cues with an opposite morphogenic impact. Key components of this response are PHYTOCHROME B (phyB), EARLY FLOWERING 3 (ELF3), and CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). Here, we used single and double mutant/overexpression lines to fit a mathematical model incorporating known interactions of these regulators. The fitted model recapitulates thermal growth of all lines used and correctly predicts thermal behavior of others not used in the fit. While thermal COP1 function is accepted to be independent of diurnal timing, our model shows that it acts at temperature signaling only during daytime. Defective response of cop1-4 mutants is epistatic to phyB-9 and elf3-8, indicating that COP1 activity is essential to transduce phyB and ELF3 thermosensory function. Our thermal model provides a unique toolbox to identify best allelic combinations enhancing climate change resilience of crops adapted to different latitudes.
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Affiliation(s)
- Cristina Nieto
- Centro Nacional de Biotecnologia (CNB), CSIC, Darwin 3, 28049 Madrid, Spain
- Centro de Recursos Fitogeneticos y Agricultura Sostenible (CRF-INIA), CSIC, Autovia A2, km 32, 28805 Alcala de Henares, Madrid, Spain
| | - Pablo Catalán
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
- Department of Mathematics, Universidad Carlos III de Madrid, Avenida de la Universidad 30, 28911 Leganes, Madrid, Spain
| | - Luis Miguel Luengo
- Centro Nacional de Biotecnologia (CNB), CSIC, Darwin 3, 28049 Madrid, Spain
- Centro de Investigación en Agrigenomica (CRAG), CSIC-IRTA-UAB-UB, 08193 Cerdanyola, Barcelona, Spain
| | - Martina Legris
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, 1405 Buenos Aires, Argentina
| | | | | | - Jorge J. Casal
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, 1405 Buenos Aires, Argentina
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, 1417 Buenos Aires, Argentina
| | - Saúl Ares
- Centro Nacional de Biotecnologia (CNB), CSIC, Darwin 3, 28049 Madrid, Spain
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
- Corresponding author. (S.A.); (S.P.)
| | - Salomé Prat
- Centro Nacional de Biotecnologia (CNB), CSIC, Darwin 3, 28049 Madrid, Spain
- Centro de Investigación en Agrigenomica (CRAG), CSIC-IRTA-UAB-UB, 08193 Cerdanyola, Barcelona, Spain
- Corresponding author. (S.A.); (S.P.)
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10
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Foo M, Dony L, He F. Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: A comparative analysis. Biosystems 2022; 219:104732. [PMID: 35781035 DOI: 10.1016/j.biosystems.2022.104732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/30/2022] [Accepted: 06/22/2022] [Indexed: 11/02/2022]
Abstract
Recent advances in synthetic biology have enabled the design of genetic feedback control circuits that could be implemented to build resilient plants against pathogen attacks. To facilitate the proper design of these genetic feedback control circuits, an accurate model that is able to capture the vital dynamical behaviour of the pathogen-infected plant is required. In this study, using a data-driven modelling approach, we develop and compare four dynamical models (i.e. linear, Michaelis-Menten with Hill coefficient (Hill Function), standard S-System and extended S-System) of a pathogen-infected plant gene regulatory network (GRN). These models are then assessed across several criteria, i.e. ease of identifying the type of gene regulation, the predictive capability, Akaike Information Criterion (AIC) and the robustness to parameter uncertainty to determine its viability of balancing between biological complexity and accuracy when modelling the pathogen-infected plant GRN. Using our defined ranking score, we obtain the following insights to the modelling of GRN. Our analyses show that despite commonly used and provide biological relevance, the Hill Function model ranks the lowest while the extended S-System model ranks highest in the overall comparison. Interestingly, the performance of the linear model is more consistent throughout the comparison, making it the preferred model for this pathogen-infected plant GRN when considering data-driven modelling approach.
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Affiliation(s)
- Mathias Foo
- School of Engineering, University of Warwick, CV4 7AL, Coventry, UK.
| | - Leander Dony
- Institute of Computational Biology, Helmholtz Munich, 85764, Neuherberg, Germany; Department of Translational Psychiatry, Max Planck Institute of Psychiatry, International Max Planck Research School for Translational Psychiatry (IMPRS-TP), 80804, Munich, Germany; TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany.
| | - Fei He
- Centre for Computational Science and Mathematical Modelling, Coventry University, CV1 2JH, Coventry, UK.
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11
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Nie YM, Han FX, Ma JJ, Chen X, Song YT, Niu SH, Wu HX. Genome-wide TCP transcription factors analysis provides insight into their new functions in seasonal and diurnal growth rhythm in Pinus tabuliformis. BMC PLANT BIOLOGY 2022; 22:167. [PMID: 35366809 PMCID: PMC8976390 DOI: 10.1186/s12870-022-03554-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/23/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND Pinus tabuliformis adapts to cold climate with dry winter in northern China, serving as important commercial tree species. The TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTOR family(TCP)transcription factors were found to play a role in the circadian clock system in Arabidopsis. However, the role of TCP transcription factors in P. tabuliformis remains little understood. RESULTS In the present study, 43 TCP genes were identified from P. tabuliformis genome database. Based on the phylogeny tree and sequence similarity, the 43 TCP genes were classified into four groups. The motif results showed that different subfamilies indeed contained different motifs. Clade II genes contain motif 1, clade I genes contain motif 1, 8, 10 and clade III and IV contain more motifs, which is consistent with our grouping results. The structural analysis of PtTCP genes showed that most PtTCPs lacked introns. The distribution of clade I and clade II on the chromosome is relatively scattered, while clade III and clade IV is relatively concentrated. Co-expression network indicated that PtTCP2, PtTCP12, PtTCP36, PtTCP37, PtTCP38, PtTCP41 and PtTCP43 were co-expressed with clock genes in annual cycle and their annual cycle expression profiles both showed obvious seasonal oscillations. PtTCP2, PtTCP12, PtTCP37, PtTCP38, PtTCP40, PtTCP41, PtTCP42 and PtTCP43 were co-expressed with clock genes in diurnal cycle. Only the expression of PtTCP42 showed diurnal oscillation. CONCLUSIONS The TCP gene family, especially clade II, may play an important role in the regulation of the season and circadian rhythm of P. tabuliformis. In addition, the low temperature in winter may affect the diurnal oscillations.
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Affiliation(s)
- Yu-meng Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Fang-xu Han
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Jing-jing Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Xi Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Yi-tong Song
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Shi-Hui Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, PR China
| | - Harry X. Wu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Linnaeus väg 6, SE-901 83 Umeå, Sweden
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12
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Greenwood M, Tokuda IT, Locke JCW. A spatial model of the plant circadian clock reveals design principles for coordinated timing. Mol Syst Biol 2022; 18:e10140. [PMID: 35312157 PMCID: PMC8935279 DOI: 10.15252/msb.202010140] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 11/28/2022] Open
Abstract
Individual plant cells possess a genetic network, the circadian clock, that times internal processes to the day-night cycle. Mathematical models of the clock are typically either "whole-plant" that ignore tissue or cell type-specific clock behavior, or "phase-only" that do not include molecular components. To address the complex spatial coordination observed in experiments, here we implemented a clock network model on a template of a seedling. In our model, the sensitivity to light varies across the plant, and cells communicate their timing via local or long-distance sharing of clock components, causing their rhythms to couple. We found that both varied light sensitivity and long-distance coupling could generate period differences between organs, while local coupling was required to generate the spatial waves of clock gene expression observed experimentally. We then examined our model under noisy light-dark cycles and found that local coupling minimized timing errors caused by the noise while allowing each plant region to maintain a different clock phase. Thus, local sensitivity to environmental inputs combined with local coupling enables flexible yet robust circadian timing.
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Affiliation(s)
- Mark Greenwood
- Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Present address:
Whitehead Institute for Biomedical ResearchCambridgeMAUSA
| | - Isao T Tokuda
- Department of Mechanical EngineeringRitsumeikan UniversityKusatsuJapan
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13
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Pay ML, Kim DW, Somers DE, Kim JK, Foo M. Modelling of plant circadian clock for characterizing hypocotyl growth under different light quality conditions. IN SILICO PLANTS 2022; 4:diac001. [PMID: 35369361 PMCID: PMC8963510 DOI: 10.1093/insilicoplants/diac001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
To meet the ever-increasing global food demand, the food production rate needs to be increased significantly in the near future. Speed breeding is considered as a promising agricultural technology solution to achieve the zero-hunger vision as specified in the United Nations Sustainable Development Goal 2. In speed breeding, the photoperiod of the artificial light has been manipulated to enhance crop productivity. In particular, regulating the photoperiod of different light qualities rather than solely white light can further improve speed breading. However, identifying the optimal light quality and the associated photoperiod simultaneously remains a challenging open problem due to complex interactions between multiple photoreceptors and proteins controlling plant growth. To tackle this, we develop a first comprehensive model describing the profound effect of multiple light qualities with different photoperiods on plant growth (i.e. hypocotyl growth). The model predicts that hypocotyls elongated more under red light compared to both red and blue light. Drawing similar findings from previous related studies, we propose that this might result from the competitive binding of red and blue light receptors, primarily Phytochrome B (phyB) and Cryptochrome 1 (cry1) for the core photomorphogenic regulator, CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). This prediction is validated through an experimental study on Arabidopsis thaliana. Our work proposes a potential molecular mechanism underlying plant growth under different light qualities and ultimately suggests an optimal breeding protocol that takes into account light quality.
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Affiliation(s)
- Miao Lin Pay
- Institute for Future Transport and Cities, Coventry University, Coventry CV1 2TE, UK
| | - Dae Wook Kim
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Biomedical Mathematics Group, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - David E Somers
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Jae Kyoung Kim
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Biomedical Mathematics Group, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Mathias Foo
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK
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14
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Chen P, Liu P, Zhang Q, Zhao L, Hao X, Liu L, Bu C, Pan Y, Zhang D, Song Y. Dynamic physiological and transcriptome changes reveal a potential relationship between the circadian clock and salt stress response in Ulmus pumila. Mol Genet Genomics 2022; 297:303-317. [PMID: 35089426 DOI: 10.1007/s00438-021-01838-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 11/13/2021] [Indexed: 11/26/2022]
Abstract
Despite the important role the circadian clock plays in numerous critical physiological responses in plants, such as hypocotyl elongation, leaf movement, stomatal opening, flowering, and stress responses, there have been no investigations into the effect of the circadian clock on physiological and transcriptional networks under salt stress. Ulmus pumila L. has been reported to tolerate 100-150 mM NaCl treatment. We measured the diurnal variation in photosynthesis and chlorophyll fluorescence parameters and performed a time-course transcriptome analysis of 2-years-old U. pumila seedlings under salt treatment to dissect the physiological regulation and potential relationship between the circadian network and the salt stress response. Seedlings in 150 mM NaCl treatment exhibited salt-induced physiological enhancement compared to the control group. A total of 7009 differentially expressed unigenes (DEGs) were identified under salt stress, of which 16 DEGs were identified as circadian rhythm-related DEGs (crDEGs). Further analysis of dynamic expression changes revealed that DEGs involved in four crucial pathways-photosynthesis, thiamine metabolism, abscisic acid synthesis and metabolism, and the hormone-MAPK signal crosstalk pathway-are closely related to the circadian clock. Finally, we constructed a co-expression network between the circadian clock and these four crucial pathways. Our results help shed light on the molecular link between the circadian network and salt stress tolerance in U. pumila.
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Affiliation(s)
- Panfei Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, 102300, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Peng Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Quanfeng Zhang
- Hebei Academy of Forestry Sciences, No. 75, Xuefu Road, Hebei, 050072, People's Republic of China
| | - Lei Zhao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Xuri Hao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Lei Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Chenhao Bu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Yanjun Pan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China
| | - Yuepeng Song
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, People's Republic of China.
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15
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Singh G, Singh V, Singh V. Systems scale characterization of circadian rhythm pathway in Camellia sinensis. Comput Struct Biotechnol J 2022; 20:598-607. [PMID: 35116135 PMCID: PMC8790616 DOI: 10.1016/j.csbj.2021.12.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 12/14/2021] [Accepted: 12/18/2021] [Indexed: 11/29/2022] Open
Abstract
Tea (Camellia sinensis) is among the most valuable commercial crops being a non-alcoholic beverage having antioxidant properties. Like in other plants, circadian oscillator in tea modulates several biological processes according to earth's revolution dependent variations in environmental cues like light and temperature. In the present study, we report genome wide identification and characterization of circadian oscillator (CO) proteins in tea. We first mined the genes (24, in total) involved in circadian rhythm pathway in the 56 plant species having available genomic information and then built their hidden Markov models (HMMs). Using these HMMs, 24 proteins were identified in tea and were further assessed for their functional annotation. Expression analysis of all these 24 CO proteins was then performed in 3 abiotic (A) and 3 biotic conditions (B) stress conditions and co-expressed as well as differentially expressed genes in the selected 6 stress conditions were elaborated. A methodology to identify the differentially expressed genes in specific types of stresses (A or B) is proposed and novel markers among CO proteins are presented. By mapping the identified CO proteins against the recently reported genome wide interologous protein-protein interaction network of tea (TeaGPIN), an interaction sub-network of tea CO proteins (TeaCO-PIN) is developed and analysed. Out of 24 CO proteins, structures of 4 proteins could be successfully predicted and validated using consensus of three structure prediction algorithms and their stability was further assessed using molecular dynamic simulations at 100 ns. Phylogenetic analysis of these proteins is performed to examine their molecular evolution.
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Affiliation(s)
| | | | - Vikram Singh
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Dharamshala 176206, India
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16
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Pitchford JW, Avello P. ODE (Ordinary Differential Equation) Models for Plant Circadian Networks: What the Models Are and How They Should Be Used. Methods Mol Biol 2022; 2398:75-88. [PMID: 34674169 DOI: 10.1007/978-1-0716-1912-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
ODE models have been used for decades to help circadian biologists understand the rhythmic phenomena they observe and to predict the behavior of plant circadian rhythms under changed conditions such as genetic mutations or novel environments. The models vary in complexity, and for good reasons, but they share the same mathematical ingredients in their construction and the same computational methods in their solution. Here we explain the fundamental concepts which define ODE models. We sketch how ODE models can be understood, how they can be solved mathematically and computationally, and the important distinction between autonomous and non-autonomous phenomena. The concepts are illustrated with examples which illustrate the basic concepts and which may help to describe the strengths and limitations of these models and the computational investigations of their properties.
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Affiliation(s)
- Jonathan W Pitchford
- Department of Biology, University of York, York, UK.
- Department of Mathematics, University of York, York, UK.
| | - Paula Avello
- Department of Mathematics, University of York, York, UK
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, UK
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17
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A framework of artificial light management for optimal plant development for smart greenhouse application. PLoS One 2021; 16:e0261281. [PMID: 34898651 PMCID: PMC8668093 DOI: 10.1371/journal.pone.0261281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/25/2021] [Indexed: 11/19/2022] Open
Abstract
Smart greenhouse farming has emerged as one of the solutions to global food security, where farming productivity can be managed and improved in an automated manner. While it is known that plant development is highly dependent on the quantity and quality of light exposure, the specific impact of the different light properties is yet to be fully understood. In this study, using the model plant Arabidopsis, we systematically investigate how six different light properties (i.e., photoperiod, light offset, intensity, phase of dawn, duration of twilight and period) would affect plant development i.e., flowering time and hypocotyl (seedling stem) elongation using an established mathematical model of the plant circadian system relating light input to flowering time and hypocotyl elongation outputs for smart greenhouse application. We vary each of the light properties individually and then collectively to understand their effect on plant development. Our analyses show in comparison to the nominal value, the photoperiod of 18 hours, period of 24 hours, no light offset, phase of dawn of 0 hour, duration of twilight of 0.05 hour and a reduced light intensity of 1% are able to improve by at least 30% in days to flower (from 32.52 days to 20.61 days) and hypocotyl length (from 1.90 mm to 1.19mm) with the added benefit of reducing energy consumption by at least 15% (from 4.27 MWh/year to 3.62 MWh/year). These findings could provide beneficial solutions to the smart greenhouse farming industries in terms of achieving enhanced productivity while consuming less energy.
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18
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Xu Y, Asadi-Zeydabadi M, Tagg R, Shindell O. Universality in kinetic models of circadian rhythms in [Formula: see text]. J Math Biol 2021; 83:51. [PMID: 34657966 DOI: 10.1007/s00285-021-01677-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 07/20/2021] [Accepted: 10/06/2021] [Indexed: 11/26/2022]
Abstract
Biological evolution has endowed the plant Arabidopsis thaliana with genetically regulated circadian rhythms. A number of authors have published kinetic models for these oscillating chemical reactions based on a network of interacting genes. To investigate the hypothesis that the Arabidopsis circadian dynamical system is poised near a Hopf bifurcation like some other biological oscillators, we varied the kinetic parameters in the models and searched for bifurcations. Finding that each model does exhibit a supercritical Hopf bifurcation, we performed a weakly nonlinear analysis near the bifurcation points to derive the Stuart-Landau amplitude equation. To illustrate a common dynamical structure, we scaled the numerical solutions to the models with the asymptotic solutions to the Stuart-Landau equation to collapse the circadian oscillations onto two universal curves-one for amplitude, and one for frequency. However, some models are close to bifurcation while others are far, some models are post-bifurcation while others are pre-bifurcation, and kinetic parameters that lead to a bifurcation in some models do not lead to a bifurcation in others. Future kinetic modeling can make use of our analysis to ensure models are consistent with each other and with the dynamics of the Arabidopsis circadian rhythm.
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Affiliation(s)
- Yian Xu
- Physics and Astronomy, Trinity University, San Antonio, TX, 78212, USA
| | | | - Randall Tagg
- Physics, University of Colorado Denver, Denver, CO, 80203, USA
| | - Orrin Shindell
- Physics and Astronomy, Trinity University, San Antonio, TX, 78212, USA.
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19
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Lagercrantz U, Billhardt A, Rousku SN, Leso M, Reza SH, Eklund DM. DE-ETIOLATED1 has a role in the circadian clock of the liverwort Marchantia polymorpha. THE NEW PHYTOLOGIST 2021; 232:595-609. [PMID: 34320227 DOI: 10.1111/nph.17653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Previous studies of plant circadian clock evolution have often relied on clock models and genes defined in Arabidopsis. These studies identified homologues with seemingly conserved function, as well as frequent gene loss. In the present study, we aimed to identify candidate clock genes in the liverwort Marchantia polymorpha using a more unbiased approach. To identify genes with circadian rhythm we sequenced the transcriptomes of gemmalings in a time series in constant light conditions. Subsequently, we performed functional studies using loss-of-function mutants and gene expression reporters. Among the genes displaying circadian rhythm, a homologue to the transcriptional co-repressor Arabidopsis DE-ETIOLATED1 showed high amplitude and morning phase. Because AtDET1 is arrhythmic and associated with the morning gene function of AtCCA1/LHY, that lack a homologue in liverworts, we functionally studied DET1 in M. polymorpha. We found that the circadian rhythm of MpDET1 expression is disrupted in loss-of-function mutants of core clock genes and putative evening-complex genes. MpDET1 knock-down in turn results in altered circadian rhythm of nyctinastic thallus movement and clock gene expression. We could not detect any effect of MpDET1 knock-down on circadian response to light, suggesting that MpDET1 has a yet unknown function in the M. polymorpha circadian clock.
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Affiliation(s)
- Ulf Lagercrantz
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Anja Billhardt
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Sabine N Rousku
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Martina Leso
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Salim Hossain Reza
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - D Magnus Eklund
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
- Physiological Botany, Department of Organismal Biology, Linnean Centre for Plant Biology in Uppsala, Uppsala University, Ulls Väg 24E, SE-756 51, Uppsala, Sweden
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20
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Palm D, Uzoni A, Simon F, Fischer M, Coogan A, Tucha O, Thome J, Faltraco F. Evolutionary conservations, changes of circadian rhythms and their effect on circadian disturbances and therapeutic approaches. Neurosci Biobehav Rev 2021; 128:21-34. [PMID: 34102148 DOI: 10.1016/j.neubiorev.2021.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 02/04/2021] [Accepted: 06/01/2021] [Indexed: 12/21/2022]
Abstract
The circadian rhythm is essential for the interaction of all living organisms with their environments. Several processes, such as thermoregulation, metabolism, cognition and memory, are regulated by the internal clock. Disturbances in the circadian rhythm have been shown to lead to the development of neuropsychiatric disorders, including attention-deficit hyperactivity disorder (ADHD). Interestingly, the mechanism of the circadian rhythms has been conserved in many different species, and misalignment between circadian rhythms and the environment results in evolutionary regression and lifespan reduction. This review summarises the conserved mechanism of the internal clock and its major interspecies differences. In addition, it focuses on effects the circadian rhythm disturbances, especially in cases of ADHD, and describes the possibility of recombinant proteins generated by eukaryotic expression systems as therapeutic agents as well as CRISPR/Cas9 technology as a potential tool for research and therapy. The aim is to give an overview about the evolutionary conserved mechanism as well as the changes of the circadian clock. Furthermore, current knowledge about circadian rhythm disturbances and therapeutic approaches is discussed.
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Affiliation(s)
- Denise Palm
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Adriana Uzoni
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Frederick Simon
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Matthias Fischer
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Andrew Coogan
- Department of Psychology, Maynooth University, National University of Ireland, Ireland
| | - Oliver Tucha
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Johannes Thome
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Frank Faltraco
- Department of Psychiatry and Psychotherapy, University Medical Center Rostock, Rostock, Gehlsheimer Str. 20, 18147, Rostock, Germany.
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21
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Zhang R, Gonze D. Stochastic simulation of a model for circadian rhythms in plants. J Theor Biol 2021; 527:110790. [PMID: 34087270 DOI: 10.1016/j.jtbi.2021.110790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/09/2021] [Accepted: 05/27/2021] [Indexed: 11/29/2022]
Abstract
Circadian clocks allow living organisms to anticipate and adapt to the daily variations of the environment. The interlocked feedback loops of the transcription factors network in the plant clock generate oscillations with expression peaks at specific times of the day. In this work, we explore the effect of molecular noise on the behavior of the plant circadian clock through numerical simulations. The influence of system size, photoperiod, and mutations of clock genes on the robustness of the oscillations are discussed. Our simulations show that the oscillations remain robust when the mRNA and protein levels are in the range of a few hundreds molecules. Entrainment by light-dark cycles enhances the robustness compared to constant conditions. Multiple light inputs and inter-cellular coupling also contribute to the robustness of the oscillations. The comparison between deterministic and stochastic simulations of single and double mutants shows that stochasticity does not qualitatively affect the behaviour of mutants but that they do not have the same robustness to noise. Finally, the model shows that noise can induce transitions between two limit cycles in a birhythmic clock mutant.
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Affiliation(s)
- Ruqiang Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Didier Gonze
- Unité de Chronobiologie Théorique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium.
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22
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Paajanen P, Lane de Barros Dantas L, Dodd AN. Layers of crosstalk between circadian regulation and environmental signalling in plants. Curr Biol 2021; 31:R399-R413. [PMID: 33905701 DOI: 10.1016/j.cub.2021.03.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Circadian regulation has a pervasive influence upon plant development, physiology and metabolism, impacting upon components of fitness and traits of agricultural importance. Circadian regulation is inextricably connected to the responses of plants to their abiotic environments, from the cellular to whole plant scales. Here, we review the crosstalk that occurs between circadian regulation and responses to the abiotic environment from the intracellular scale through to naturally fluctuating environments. We examine the spatial crosstalk that forms part of plant circadian regulation, at the subcellular, tissue, organ and whole-plant scales. This includes a focus on chloroplast and mitochondrial signalling, alternative splicing, long-distance circadian signalling and circadian regulation within natural environments. We also consider mathematical models for plant circadian regulation, to suggest future areas for advancing understanding of roles for circadian regulation in plant responses to environmental cues.
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Affiliation(s)
- Pirita Paajanen
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Antony N Dodd
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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23
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de Melo JRF, Gutsch A, Caluwé TD, Leloup JC, Gonze D, Hermans C, Webb AAR, Verbruggen N. Magnesium maintains the length of the circadian period in Arabidopsis. PLANT PHYSIOLOGY 2021; 185:519-532. [PMID: 33721908 PMCID: PMC8133681 DOI: 10.1093/plphys/kiaa042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/05/2020] [Indexed: 05/14/2023]
Abstract
The circadian clock coordinates the physiological responses of a biological system to day and night rhythms through complex loops of transcriptional/translational regulation. It can respond to external stimuli and adjust generated circadian oscillations accordingly to maintain an endogenous period close to 24 h. However, the interaction between nutritional status and circadian rhythms in plants is poorly understood. Magnesium (Mg) is essential for numerous biological processes in plants, and its homeostasis is crucial to maintain optimal development and growth. Magnesium deficiency in young Arabidopsis thaliana seedlings increased the period of circadian oscillations of the CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) promoter (pCCA1:LUC) activity and dampened their amplitude under constant light in a dose-dependent manner. Although the circadian period increase caused by Mg deficiency was light dependent, it did not depend on active photosynthesis. Mathematical modeling of the Mg input into the circadian clock reproduced the experimental increase of the circadian period and suggested that Mg is likely to affect global transcription/translation levels rather than a single component of the circadian oscillator. Upon addition of a low dose of cycloheximide to perturb translation, the circadian period increased further under Mg deficiency, which was rescued when sufficient Mg was supplied, supporting the model's prediction. These findings suggest that sufficient Mg supply is required to support proper timekeeping in plants.
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Affiliation(s)
- J Romário F de Melo
- Laboratory of Plant Physiology and Molecular Genetics, Université libre de Bruxelles, 1050 Brussels, Belgium
| | - Annelie Gutsch
- Laboratory of Plant Physiology and Molecular Genetics, Université libre de Bruxelles, 1050 Brussels, Belgium
- Department of Plant Sciences, University of Cambridge, CB2 3EA Cambridge, UK
| | - Thomas De Caluwé
- Unité de Chronobiologie Théorique, Université libre de Bruxelles, 1050 Brussels, Belgium
| | - Jean-Christophe Leloup
- Unité de Chronobiologie Théorique, Université libre de Bruxelles, 1050 Brussels, Belgium
| | - Didier Gonze
- Unité de Chronobiologie Théorique, Université libre de Bruxelles, 1050 Brussels, Belgium
| | - Christian Hermans
- Crop Production and Biostimulation Laboratory, Université libre de Bruxelles, 1050 Brussels, Belgium
| | - Alex A R Webb
- Department of Plant Sciences, University of Cambridge, CB2 3EA Cambridge, UK
| | - Nathalie Verbruggen
- Laboratory of Plant Physiology and Molecular Genetics, Université libre de Bruxelles, 1050 Brussels, Belgium
- Author to communication:
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Zhang R, Gonze D, Hou X, You X, Goldbeter A. A Computational Model for the Cold Response Pathway in Plants. Front Physiol 2020; 11:591073. [PMID: 33250782 PMCID: PMC7674828 DOI: 10.3389/fphys.2020.591073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/16/2020] [Indexed: 01/27/2023] Open
Abstract
Understanding the mechanism by which plants respond to cold stress and strengthen their tolerance to low temperatures is an important and challenging task in plant sciences. Experiments have established that the first step in the perception and transduction of the cold stress signal consists of a transient influx of Ca2+. This Ca2+ influx triggers the activation of a cascade of phosphorylation-dephosphorylation reactions that eventually affects the expression of C-repeat-binding factors (CBFs, notably CBF3), which were shown in many plants to control resistance to cold stress by regulating the expression of cold-regulated (COR) genes. Based on experimental observations mostly made on Arabidopsis thaliana, we build a computational model for the cold response pathway in plants, from the transduction of the cold signal via the transient influx of Ca2+ to the activation of the phosphorylation cascade leading to CBF3 expression. We explore the dynamics of this regulatory network by means of numerical simulations and compare the results with experimental observations on the dynamics of the cold response, both for the wild type and for mutants. The simulations show how, in response to cold stress, a brief Ca2+ influx, which is over in minutes, is transduced along the successive steps of the network to trigger the expression of cold response genes such as CBF3 within hours. Sometimes, instead of a single Ca2+ spike the decrease in temperature brings about a train of high-frequency Ca2+ oscillations. The model is applied to both types of Ca2+ signaling. We determine the dynamics of the network in response to a series of identical cold stresses, to account for the observation of desensitization and resensitization. The analysis of the model predicts the possibility of an oscillatory expression of CBF3 originating from the negative feedback exerted by ZAT12, a factor itself controlled by CBF3. Finally, we extend the model to incorporate the circadian control of CBF3 expression, to account for the gating of the response to cold stress by the plant circadian clock.
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Affiliation(s)
- Ruqiang Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Didier Gonze
- Unité de Chronobiologie Théorique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Xilin Hou
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xiong You
- College of Sciences, Nanjing Agricultural University, Nanjing, China
| | - Albert Goldbeter
- Unité de Chronobiologie Théorique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium
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Panchy N, von Arnim AG, Hong T. Early Detection of Daylengths with a Feedforward Circuit Coregulated by Circadian and Diurnal Cycles. Biophys J 2020; 119:1878-1895. [PMID: 33086045 PMCID: PMC7677250 DOI: 10.1016/j.bpj.2020.09.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/31/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
Light-entrained circadian clocks confer rhythmic dynamics of cellular and molecular activities to animals and plants. These intrinsic clocks allow stable anticipations to light-dark (diel) cycles. Many genes in the model plant Arabidopsis thaliana are regulated by diel cycles via pathways independent of the clock, suggesting that the integration of circadian and light signals is important for the fitness of plants. Previous studies of light-clock signal integrations have focused on moderate phase adjustment of the two signals. However, dynamical features of integrations across a broad range of phases remain elusive. Phosphorylation of ribosomal protein of the small subunit 6 (eS6), a ubiquitous post-translational modification across kingdoms, is influenced by the circadian clock and the light-dark (diel) cycle in an opposite manner. To understand this striking phenomenon and its underlying information processing capabilities, we built a mathematical model for the eS6 phosphorylation (eS6-P) control circuit. We found that the dynamics of eS6-P can be explained by a feedforward circuit with inputs from both circadian and diel cycles. Furthermore, the early day response of this circuit with dual rhythmic inputs is sensitive to the changes in daylength, including both transient and gradual changes observed in realistic light intervals across a year, because of weather and seasons. By analyzing published gene expression data, we found that the dynamics produced by the eS6-P control circuit can be observed in the expression profiles of a large number of genes. Our work provides mechanistic insights into the complex dynamics of a ribosomal protein, and it proposes a previously underappreciated function of the circadian clock, which not only prepares organisms for normal diel cycles but also helps to detect both transient and seasonal changes with a predictive power.
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Affiliation(s)
- Nicholas Panchy
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Knoxville, Tennessee; National Institute for Mathematical and Biological Synthesis, Knoxville, Tennessee
| | - Albrecht G von Arnim
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Knoxville, Tennessee
| | - Tian Hong
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Knoxville, Tennessee; National Institute for Mathematical and Biological Synthesis, Knoxville, Tennessee.
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Wang J, Du Z, Huo X, Zhou J, Chen Y, Zhang J, Pan A, Wang X, Wang F, Zhang J. Genome-wide analysis of PRR gene family uncovers their roles in circadian rhythmic changes and response to drought stress in Gossypium hirsutum L. PeerJ 2020; 8:e9936. [PMID: 33033660 PMCID: PMC7521341 DOI: 10.7717/peerj.9936] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/24/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The circadian clock not only participates in regulating various stages of plant growth, development and metabolism, but confers plant environmental adaptability to stress such as drought. Pseudo-Response Regulators (PRRs) are important component of the central oscillator (the core of circadian clock) and play a significant role in plant photoperiod pathway. However, no systematical study about this gene family has been performed in cotton. METHODS PRR genes were identified in diploid and tetraploid cotton using bioinformatics methods to investigate their homology, duplication and evolution relationship. Differential gene expression, KEGG enrichment analysis and qRT-PCR were conducted to analyze PRR gene expression patterns under diurnal changes and their response to drought stress. RESULTS A total of 44 PRR family members were identified in four Gossypium species, with 16 in G. hirsutum, 10 in G. raimondii, and nine in G. barbadense as well as in G. arboreum. Phylogenetic analysis indicated that PRR proteins were divided into five subfamilies and whole genome duplication or segmental duplication contributed to the expansion of Gossypium PRR gene family. Gene structure analysis revealed that members in the same clade are similar, and multiple cis-elements related to light and drought stress response were enriched in the promoters of GhPRR genes. qRT-PCR results showed that GhPRR genes transcripts presented four expression peaks (6 h, 9 h, 12 h, 15 h) during 24 h and form obvious rhythmic expression trend. Transcriptome data with PEG treatment, along with qRT-PCR verification suggested that members of clade III (GhPRR5a, b, d) and clade V (GhPRR3a and GhPRR3c) may be involved in drought response. This study provides an insight into understanding the function of PRR genes in circadian rhythm and in response to drought stress in cotton.
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Affiliation(s)
- Jingjing Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- College of Life Sciences, Shandong Normal University, Jinan, P. R. China
| | - Zhaohai Du
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Xuehan Huo
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- College of Life Sciences, Shandong Normal University, Jinan, P. R. China
| | - Juan Zhou
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Jingxia Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Ao Pan
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
| | - Xiaoyang Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, P. R. China
| | - Furong Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- College of Life Sciences, Shandong Normal University, Jinan, P. R. China
| | - Jun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, P. R. China
- College of Life Sciences, Shandong Normal University, Jinan, P. R. China
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27
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Avello P, Davis SJ, Pitchford JW. Temperature robustness in Arabidopsis circadian clock models is facilitated by repressive interactions, autoregulation, and three-node feedbacks. J Theor Biol 2020; 509:110495. [PMID: 32966827 DOI: 10.1016/j.jtbi.2020.110495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 09/13/2020] [Accepted: 09/14/2020] [Indexed: 11/26/2022]
Abstract
The biological interactions underpinning the Arabidopsis circadian clock have been systematically uncovered and explored by biological experiments and mathematical models. This is captured by a series of published ordinary differential equation (ODE) models, which describe plant clock dynamics in response to light/dark conditions. However, understanding the role of temperature in resetting the clock (entrainment) and the mechanisms by which circadian rhythms maintain a near-24 h period over a range of temperatures (temperature compensation) is still unclear. Understanding entrainment and temperature compensation may elucidate the principles governing the structure of the circadian clock network. Here we explore the design principles of the Arabidopsis clock and its responses to changes in temperature. We analyse published clock models of Arabidopsis, spanning a range of complexity, and incorporate temperature-dependent dynamics into the parameters of translation rates in these models, to discern which regulatory patterns may best explain clock function and temperature compensation. We additionally construct three minimal clock models and explore what key features govern their rhythmicity and temperature robustness via a series of random parameterisations. Results show that the highly repressive interactions between the components of the plant clock, together with autoregulation patterns and three-node feedback loops, are associated with circadian function of the clock in general, and enhance its robustness to temperature variation in particular. However, because the networks governing clock function vary with time due to light and temperature conditions, we emphasise the importance of studying plant clock functionality in its entirety rather than as a set of discrete regulation patterns.
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Affiliation(s)
- Paula Avello
- Department of Mathematics, University of York, Heslington, York YO10 5DD, United Kingdom.
| | - Seth J Davis
- Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom; Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jonathan W Pitchford
- Department of Mathematics, University of York, Heslington, York YO10 5DD, United Kingdom; Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
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Joanito I, Yan CCS, Chu JW, Wu SH, Hsu CP. Basal leakage in oscillation: Coupled transcriptional and translational control using feed-forward loops. PLoS Comput Biol 2020; 16:e1007740. [PMID: 32881861 PMCID: PMC7494099 DOI: 10.1371/journal.pcbi.1007740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 09/16/2020] [Accepted: 06/26/2020] [Indexed: 11/19/2022] Open
Abstract
The circadian clock is a complex system that plays many important roles in most organisms. Previously, many mathematical models have been used to sharpen our understanding of the Arabidopsis clock, which brought to light the roles of each transcriptional and post-translational regulations. However, the presence of both regulations, instead of either transcription or post-translation, raised curiosity of whether the combination of these two regulations is important for the clock’s system. In this study, we built a series of simplified oscillators with different regulations to study the importance of post-translational regulation (specifically, 26S proteasome degradation) in the clock system. We found that a simple transcriptional-based oscillator can already generate sustained oscillation, but the oscillation can be easily destroyed in the presence of transcriptional leakage. Coupling post-translational control with transcriptional-based oscillator in a feed-forward loop will greatly improve the robustness of the oscillator in the presence of basal leakage. Using these general models, we were able to replicate the increased variability observed in the E3 ligase mutant for both plant and mammalian clocks. With this insight, we also predict a plausible regulator of several E3 ligase genes in the plant’s clock. Thus, our results provide insights into and the plausible importance in coupling transcription and post-translation controls in the clock system. For circadian clocks, several current models had successfully captured the essential dynamic behavior of the clock system mainly with transcriptional regulation. Previous studies have shown that the 26S proteasome degradation controls are important in maintaining the stability of circadian rhythms. However, how the loss-of-function or over-expression mutant of this targeted degradations lead to unstable oscillation is still unclear. In this work, we investigate the importance of coupled transcriptional and post-translational feedback loop in the circadian oscillator. With general models our study indicate that the unstable behavior of degradation mutants could be caused by the increase in the basal level of the clock genes. We found that coupling a non-linear degradation control into this transcriptional based oscillator using feed-forward loop improves the robustness of the oscillator. Using this finding, we further predict some plausible regulators of Arabidopsis’s E3 ligase protein such as COP1 and SINAT5. Hence, our results provide insights on the importance of coupling transcription and post-translation controls in the clock system.
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Affiliation(s)
- Ignasius Joanito
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan and Institute of Bioinformatics and System Biology, National Chiao Tung University, Hsinchu, Taiwan
| | | | - Jhih-Wei Chu
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan and Institute of Bioinformatics and System Biology, National Chiao Tung University, Hsinchu, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
| | - Chao-Ping Hsu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
- * E-mail:
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Kebrom TH, McKinley BA, Mullet JE. Shade signals alter the expression of circadian clock genes in newly-formed bioenergy sorghum internodes. PLANT DIRECT 2020; 4:e00235. [PMID: 32607464 PMCID: PMC7315773 DOI: 10.1002/pld3.235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
Stem internodes of bioenergy sorghum inbred R.07020 are longer at high plant density (shade) than at low plant density (control). Initially, the youngest newly-formed subapical stem internodes of shade-treated and control plants are comparable in length. However, full-length internodes of shade-treated plants are three times longer than the internodes of the control plants. To identify the early molecular events associated with internode elongation in response to shade, we analyzed the transcriptome of the newly-formed internodes of shade-treated and control plants sampled between 4 and 6 hr after the start of the light period (14 hr light/10 hr dark). Sorghum genes homologous to the Arabidopsis shade marker genes ATHB2 and PIL1 were not differentially expressed. The results indicate that shade signals promote internode elongation indirectly because sorghum internodes are not illuminated and grow while enclosed with leaf sheaths. Sorghum genes homologous to the Arabidopsis morning-phased circadian clock genes LHY, RVE, and LNK were downregulated and evening-phased genes such as TOC1, PRR5, and GI were upregulated in young internodes in response to shade. We hypothesize that a change in the function or patterns of expression of the circadian clock genes is the earliest molecular event associated with internode elongation in response to shade in bioenergy sorghum. Increased expression of CycD1, which promotes cell division, and decreased expression of cell wall-loosening and MBF1-like genes, which promote cell expansion, suggest that shade signals promote internode elongation in bioenergy sorghum in part through increasing cell number by delaying transition from cell division to cell expansion.
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Affiliation(s)
- Tesfamichael H. Kebrom
- Cooperative Agricultural Research CenterCollege of Agriculture and Human SciencesPrairie View A&M UniversityPrairie ViewTXUSA
- Center for Computational Systems BiologyCollege of EngineeringPrairie View A&M UniversityPrairie ViewTXUSA
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Brian A. McKinley
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - John E. Mullet
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
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30
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A simplified modelling framework facilitates more complex representations of plant circadian clocks. PLoS Comput Biol 2020; 16:e1007671. [PMID: 32176683 PMCID: PMC7098658 DOI: 10.1371/journal.pcbi.1007671] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 03/26/2020] [Accepted: 01/21/2020] [Indexed: 11/19/2022] Open
Abstract
The circadian clock orchestrates biological processes so that they occur at specific times of the day, thereby facilitating adaptation to diurnal and seasonal environmental changes. In plants, mathematical modelling has been comprehensively integrated with experimental studies to gain a better mechanistic understanding of the complex genetic regulatory network comprising the clock. However, with an increasing number of circadian genes being discovered, there is a pressing need for methods facilitating the expansion of computational models to incorporate these newly-discovered components. Conventionally, plant clock models have comprised differential equation systems based on Michaelis-Menten kinetics. However, the difficulties associated with modifying interactions using this approach-and the concomitant problem of robustly identifying regulation types-has contributed to a complexity bottleneck, with quantitative fits to experimental data rapidly becoming computationally intractable for models possessing more than ≈50 parameters. Here, we address these issues by constructing the first plant clock models based on the S-System formalism originally developed by Savageau for analysing biochemical networks. We show that despite its relative simplicity, this approach yields clock models with comparable accuracy to the conventional Michaelis-Menten formalism. The S-System formulation also confers several key advantages in terms of model construction and expansion. In particular, it simplifies the inclusion of new interactions, whilst also facilitating the modification of regulation types, thereby making it well-suited to network inference. Furthermore, S-System models mitigate the issue of parameter identifiability. Finally, by applying linear systems theory to the models considered, we provide some justification for the increased use of aggregated protein equations in recent plant clock modelling, replacing the separate cytoplasmic/nuclear protein compartments that were characteristic of the earlier models. We conclude that as well as providing a simplified framework for model development, the S-System formalism also possesses significant potential as a robust modelling method for designing synthetic gene circuits.
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31
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Schmal C, Ono D, Myung J, Pett JP, Honma S, Honma KI, Herzel H, Tokuda IT. Weak coupling between intracellular feedback loops explains dissociation of clock gene dynamics. PLoS Comput Biol 2019; 15:e1007330. [PMID: 31513579 PMCID: PMC6759184 DOI: 10.1371/journal.pcbi.1007330] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 09/24/2019] [Accepted: 08/12/2019] [Indexed: 01/11/2023] Open
Abstract
Circadian rhythms are generated by interlocked transcriptional-translational negative feedback loops (TTFLs), the molecular process implemented within a cell. The contributions, weighting and balancing between the multiple feedback loops remain debated. Dissociated, free-running dynamics in the expression of distinct clock genes has been described in recent experimental studies that applied various perturbations such as slice preparations, light pulses, jet-lag, and culture medium exchange. In this paper, we provide evidence that this "presumably transient" dissociation of circadian gene expression oscillations may occur at the single-cell level. Conceptual and detailed mechanistic mathematical modeling suggests that such dissociation is due to a weak interaction between multiple feedback loops present within a single cell. The dissociable loops provide insights into underlying mechanisms and general design principles of the molecular circadian clock.
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Affiliation(s)
- Christoph Schmal
- Department of Mechanical Engineering, Ritsumeikan University, Kusatsu, Japan
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Daisuke Ono
- Department of Neuroscience II, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Jihwan Myung
- Laboratory of Braintime, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
- Graduate Institute of Mind, Brain, and Consciousness, Taipei Medical University, Taipei, Taiwan
- Graduate Institute of Medical Sciences, Taipei Medical University, Taipei, Taiwan
- TMU Research Center of Brain and Consciousness, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
- Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - J. Patrick Pett
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Sato Honma
- Department of Chronomedicine, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Ken-Ichi Honma
- Department of Chronomedicine, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Isao T. Tokuda
- Department of Mechanical Engineering, Ritsumeikan University, Kusatsu, Japan
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32
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Abstract
The circadian clock is a biological mechanism that permits some organisms to anticipate daily environmental variations. This clock generates biological rhythms, which can be reset by environmental cues such as cycles of light or temperature, a process known as entrainment. After entrainment, circadian rhythms typically persist with approximately 24 hours periodicity in free-running conditions, i.e. in the absence of environmental cues. Experimental evidence also shows that a free-running period close to 24 hours is maintained across a range of temperatures, a process known as temperature compensation. In the plant Arabidopsis, the effect of light on the circadian system has been widely studied and successfully modelled mathematically. However, the role of temperature in periodicity, and the relationship between entrainment and compensation, are not fully understood. Here we adapt recent models to incorporate temperature dependence by applying Arrhenius equations to the parameters of the models that characterize transcription, translation, and degradation rates. We show that the resulting models can exhibit thermal entrainment and temperature compensation, but that these phenomena emerge from physiologically different sets of processes. Further simulations combining thermal and photic forcing in more realistic scenarios clearly distinguish between the processes of entrainment and compensation, and reveal temperature compensation as an emergent property which can arise as a result of multiple temperature-dependent interactions. Our results consistently point to the thermal sensitivity of degradation rates as driving compensation and entrainment across a range of conditions.
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Abstract
Gaussian process dynamical systems (GPDS) represent Bayesian nonparametric approaches to inference of nonlinear dynamical systems, and provide a principled framework for the learning of biological networks from multiple perturbed time series measurements of gene or protein expression. Such approaches are able to capture the full richness of complex ODE models, and can be scaled for inference in moderately large systems containing hundreds of genes. Related hierarchical approaches allow for inference from multiple datasets in which the underlying generative networks are assumed to have been rewired, either by context-dependent changes in network structure, evolutionary processes, or synthetic manipulation. These approaches can also be used to leverage experimentally determined network structures from one species into another where the network structure is unknown. Collectively, these methods provide a comprehensive and flexible platform for inference from a diverse range of data, with applications in systems and synthetic biology, as well as spatiotemporal modelling of embryo development. In this chapter we provide an overview of GPDS approaches and highlight their applications in the biological sciences, with accompanying tutorials available as a Jupyter notebook from https://github.com/cap76/GPDS .
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Affiliation(s)
| | - Iulia Gherman
- Warwick Integrative Synthetic Biology Centre, School of Engineering, University of Warwick, Coventry, UK
| | - Anastasiya Sybirna
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Wellcome/MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, UK
| | - David L Wild
- Department of Statistics and Systems Biology Centre, University of Warwick, Coventry, UK
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Tokuda IT, Akman OE, Locke JCW. Reducing the complexity of mathematical models for the plant circadian clock by distributed delays. J Theor Biol 2018; 463:155-166. [PMID: 30550861 DOI: 10.1016/j.jtbi.2018.12.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 12/04/2018] [Accepted: 12/11/2018] [Indexed: 11/29/2022]
Abstract
A major bottleneck in the modelling of biological networks is the parameter explosion problem - the exponential increase in the number of parameters that need to be optimised to data as the size of the model increases. Here, we address this problem in the context of the plant circadian clock by applying the method of distributed delays. We show that using this approach, the system architecture can be simplified efficiently - reducing the number of parameters - whilst still preserving the core mechanistic dynamics of the gene regulatory network. Compared to models with discrete time-delays, which are governed by functional differential equations, the distributed delay models can be converted into sets of equivalent ordinary differential equations, enabling the use of standard methods for numerical integration, and for stability and bifurcation analyses. We demonstrate the efficiency of our modelling approach by applying it to three exemplar mathematical models of the Arabidopsis circadian clock of varying complexity, obtaining significant reductions in complexity in each case. Moreover, we revise one of the most up-to-date Arabidopsis models, updating the regulation of the PRR9 and PRR7 genes by LHY in accordance with recent experimental data. The revised model more accurately reproduces the LHY-induction experiments of core clock genes, compared with the original model. Our work thus shows that the method of distributed delays facilitates the optimisation and reformulation of genetic network models.
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Affiliation(s)
- Isao T Tokuda
- Graduate School of Science and Engineering, Ritsumeikan University, Noji-higashi, Kusatsu, Shiga 525-8577, Japan.
| | - Ozgur E Akman
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, EX4 4QD, UK.
| | - James C W Locke
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK.
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35
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Hajdu A, Dobos O, Domijan M, Bálint B, Nagy I, Nagy F, Kozma-Bognár L. ELONGATED HYPOCOTYL 5 mediates blue light signalling to the Arabidopsis circadian clock. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:1242-1254. [PMID: 30256479 DOI: 10.1111/tpj.14106] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 05/21/2023]
Abstract
Circadian clocks are gene networks producing 24-h oscillations at the level of clock gene expression that are synchronized to environmental cycles via light signals. The ELONGATED HYPOCOTYL 5 (HY5) transcription factor is a signalling hub acting downstream of several photoreceptors and is a key mediator of photomorphogenesis. Here we describe a mechanism by which light quality could modulate the pace of the circadian clock through governing abundance of HY5. We show that hy5 mutants display remarkably shorter period rhythms in blue but not in red light or darkness, and blue light is more efficient than red to induce accumulation of HY5 at transcriptional and post-transcriptional levels. We demonstrate that the pattern and level of HY5 accumulation modulates its binding to specific promoter elements of the majority of clock genes, but only a few of these show altered transcription in the hy5 mutant. Mathematical modelling suggests that the direct effect of HY5 on the apparently non-responsive clock genes could be masked by feedback from the clock gene network. We conclude that the information on the ratio of blue and red components of the white light spectrum is decoded and relayed to the circadian oscillator, at least partially, by HY5.
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Affiliation(s)
- Anita Hajdu
- Institute of Plant Biology, Biological Research Centre, Szeged, H-6726, Hungary
| | - Orsolya Dobos
- Institute of Plant Biology, Biological Research Centre, Szeged, H-6726, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, H-6726, Hungary
| | - Mirela Domijan
- Department of Mathematical Sciences, University of Liverpool, Liverpool, L69 7ZL, UK
| | | | - István Nagy
- SeqOmics Ltd, Mórahalom, H-6782, Hungary
- Institute of Biochemistry, Biological Research Centre, Szeged, H-6726, Hungary
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre, Szeged, H-6726, Hungary
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - László Kozma-Bognár
- Institute of Plant Biology, Biological Research Centre, Szeged, H-6726, Hungary
- Department of Genetics, Faculty of Sciences and Informatics, University of Szeged, Szeged, H-6726, Hungary
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36
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Joanito I, Chu JW, Wu SH, Hsu CP. An incoherent feed-forward loop switches the Arabidopsis clock rapidly between two hysteretic states. Sci Rep 2018; 8:13944. [PMID: 30224713 PMCID: PMC6141573 DOI: 10.1038/s41598-018-32030-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/24/2018] [Indexed: 12/02/2022] Open
Abstract
In higher plants (e.g., Arabidopsis thaliana), the core structure of the circadian clock is mostly governed by a repression process with very few direct activators. With a series of simplified models, we studied the underlying mechanism and found that the Arabidopsis clock consists of type-2 incoherent feed-forward loops (IFFLs), one of them creating a pulse-like expression in PRR9/7. The double-negative feedback loop between CCA1/LHY and PRR5/TOC1 generates a bistable, hysteretic behavior in the Arabidopsis circadian clock. We found that the IFFL involving PRR9/7 breaks the bistability and moves the system forward with a rapid pulse in the daytime, and the evening complex (EC) breaks it in the evening. With this illustration, we can intuitively explain the behavior of the clock under mutant conditions. Thus, our results provide new insights into the underlying network structures of the Arabidopsis core oscillator.
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Affiliation(s)
- Ignasius Joanito
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Bioinformatics and System Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Jhih-Wei Chu
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Bioinformatics and System Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan
| | - Chao-Ping Hsu
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan.
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan.
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37
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Gene regulatory network models in response to sugars in the plant circadian system. J Theor Biol 2018; 457:137-151. [PMID: 30125577 DOI: 10.1016/j.jtbi.2018.08.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 08/01/2018] [Accepted: 08/16/2018] [Indexed: 01/15/2023]
Abstract
Circadian entrainment is the process by which internal circadian oscillators staying in synchronization with the local environmental rhythms. Circadian clocks are entrained by adjusting phase and period in response to environmental and metabolic signals. In Arabidopsis thaliana, light and sugar signals differentially affect the circadian phase; the former advances the phase in the late of the subjective night and delays around dusk, while the latter advances the phase mainly in the morning, which is optimal to maintain sucrose homeostasis. We have proposed that the phase adjustment of the A. thaliana circadian oscillator by sugar signals contributes to the realization of carbon homeostasis and the increase of plant growth under fluctuating day-night cycles. However, which genes in the circadian oscillator are targets of sucrose signals and how the potential target genes should be regulated by sucrose to realize sucrose homeostasis has not been studied from the theoretical perspective. Here we investigate the effect of sugar on the phase response property of the plant circadian oscillator using clock gene-regulatory network models. We simulated phase response curves (PRCs) to sucrose pulses, which were compared with an experimental PRC. Our analyses of the gene-regulatory network model demonstrated that target genes of the sugar signal could be members of the PSEUDO-RESPONSE REGULATOR gene family and the evening complex components. We also examined the phase response property using a single feedback-loop model and elucidated how phase advance is induced in the subjective morning under certain conditions of a target clock gene of sucrose and its regulatory property.
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38
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Guadagno CR, Ewers BE, Weinig C. Circadian Rhythms and Redox State in Plants: Till Stress Do Us Part. FRONTIERS IN PLANT SCIENCE 2018; 9:247. [PMID: 29556244 PMCID: PMC5844964 DOI: 10.3389/fpls.2018.00247] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/12/2018] [Indexed: 05/22/2023]
Abstract
A growing body of evidence demonstrates a significant relationship between cellular redox state and circadian rhythms. Each day these two vital components of plant biology influence one another, dictating the pace for metabolism and physiology. Diverse environmental stressors can disrupt this condition and, although plant scientists have made significant progress in re-constructing functional networks of plant stress responses, stress impacts on the clock-redox crosstalk is poorly understood. Inter-connected phenomena such as redox state and metabolism, internal and external environments, cellular homeostasis and rhythms can impede predictive understanding of coordinated regulation of plant stress response. The integration of circadian clock effects into predictive network models is likely to increase final yield and better predict plant responses to stress. To achieve such integrated understanding, it is necessary to consider the internal clock not only as a gatekeeper of environmental responses but also as a target of stress syndromes. Using chlorophyll fluorescence as a reliable and high-throughput probe of stress coupled to functional genomics and metabolomics will provide insights on the crosstalk across a wide range of stress severity and duration, including potential insights into oxidative stress response and signaling. We suggest the efficiency of photosystem II in light conditions (Fv'/Fm') to be the most dynamic of the fluorescence variables and therefore the most reliable parameter to follow the stress response from early sensing to mortality.
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Affiliation(s)
| | - Brent E. Ewers
- Department of Botany, University of Wyoming, Laramie, WY, United States
- Program in Ecology, University of Wyoming, Laramie, WY, United States
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, United States
- Program in Ecology, University of Wyoming, Laramie, WY, United States
- Department of Molecular and Cellular Life Sciences, University of Wyoming, Laramie, WY, United States
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Ohara T, Satake A. Photosynthetic Entrainment of the Circadian Clock Facilitates Plant Growth under Environmental Fluctuations: Perspectives from an Integrated Model of Phase Oscillator and Phloem Transportation. FRONTIERS IN PLANT SCIENCE 2017; 8:1859. [PMID: 29163586 PMCID: PMC5670358 DOI: 10.3389/fpls.2017.01859] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/11/2017] [Indexed: 05/22/2023]
Abstract
Plants need to avoid carbon starvation and resultant growth inhibition under fluctuating light environments to ensure optimal growth and reproduction. As diel patterns of carbon metabolism are influenced by the circadian clock, appropriate regulation of the clock is essential for plants to properly manage their carbon resources. For proper adjustment of the circadian phase, higher plants utilize environmental signals such as light or temperature and metabolic signals such as photosynthetic products; the importance of the latter as phase regulators has been recently elucidated. A mutant of Arabidopsis thaliana that is deficient in phase response to sugar has been shown, under fluctuating light conditions, to be unable to adjust starch turnover and to realize carbon homeostasis. Whereas, the effects of light entrainment on growth and survival of higher plants are well studied, the impact of phase regulation by sugar remains unknown. Here we show that endogenous sugar entrainment facilitates plant growth. We integrated two mathematical models, one describing the dynamics of carbon metabolism in A. thaliana source leaves and the other growth of sink tissues dependent on sucrose translocation from the source. The integrated model predicted that sugar-sensitive plants grow faster than sugar-insensitive plants under constant as well as changing photoperiod conditions. We found that sugar entrainment enables efficient carbon investment for growth by stabilizing sucrose supply to sink tissues. Our results highlight the importance of clock entrainment by both exogenous and endogenous signals for optimizing growth and increasing fitness.
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Affiliation(s)
- Takayuki Ohara
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Akiko Satake
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
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40
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Simak M, Yeang CH, Lu HHS. Exploring candidate biological functions by Boolean Function Networks for Saccharomyces cerevisiae. PLoS One 2017; 12:e0185475. [PMID: 28981547 PMCID: PMC5628832 DOI: 10.1371/journal.pone.0185475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 09/13/2017] [Indexed: 01/26/2023] Open
Abstract
The great amount of gene expression data has brought a big challenge for the discovery of Gene Regulatory Network (GRN). For network reconstruction and the investigation of regulatory relations, it is desirable to ensure directness of links between genes on a map, infer their directionality and explore candidate biological functions from high-throughput transcriptomic data. To address these problems, we introduce a Boolean Function Network (BFN) model based on techniques of hidden Markov model (HMM), likelihood ratio test and Boolean logic functions. BFN consists of two consecutive tests to establish links between pairs of genes and check their directness. We evaluate the performance of BFN through the application to S. cerevisiae time course data. BFN produces regulatory relations which show consistency with succession of cell cycle phases. Furthermore, it also improves sensitivity and specificity when compared with alternative methods of genetic network reverse engineering. Moreover, we demonstrate that BFN can provide proper resolution for GO enrichment of gene sets. Finally, the Boolean functions discovered by BFN can provide useful insights for the identification of control mechanisms of regulatory processes, which is the special advantage of the proposed approach. In combination with low computational complexity, BFN can serve as an efficient screening tool to reconstruct genes relations on the whole genome level. In addition, the BFN approach is also feasible to a wide range of time course datasets.
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Affiliation(s)
- Maria Simak
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan
- Institute of Statistics, National Chiao Tung University, Hsinchu, Taiwan
| | | | - Henry Horng-Shing Lu
- Institute of Statistics, National Chiao Tung University, Hsinchu, Taiwan
- Big Data Research Center, National Chiao Tung University, Hsinchu, Taiwan
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41
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Linde A, Eklund DM, Kubota A, Pederson ERA, Holm K, Gyllenstrand N, Nishihama R, Cronberg N, Muranaka T, Oyama T, Kohchi T, Lagercrantz U. Early evolution of the land plant circadian clock. THE NEW PHYTOLOGIST 2017; 216:576-590. [PMID: 28244104 PMCID: PMC5638080 DOI: 10.1111/nph.14487] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/18/2017] [Indexed: 05/21/2023]
Abstract
While angiosperm clocks can be described as an intricate network of interlocked transcriptional feedback loops, clocks of green algae have been modelled as a loop of only two genes. To investigate the transition from a simple clock in algae to a complex one in angiosperms, we performed an inventory of circadian clock genes in bryophytes and charophytes. Additionally, we performed functional characterization of putative core clock genes in the liverwort Marchantia polymorpha and the hornwort Anthoceros agrestis. Phylogenetic construction was combined with studies of spatiotemporal expression patterns and analysis of M. polymorpha clock gene mutants. Homologues to core clock genes identified in Arabidopsis were found not only in bryophytes but also in charophytes, albeit in fewer copies. Circadian rhythms were detected for most identified genes in M. polymorpha and A. agrestis, and mutant analysis supports a role for putative clock genes in M. polymorpha. Our data are in line with a recent hypothesis that adaptation to terrestrial life occurred earlier than previously expected in the evolutionary history of charophyte algae. Both gene duplication and acquisition of new genes was important in the evolution of the plant circadian clock, but gene loss has also contributed to shaping the clock of bryophytes.
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Affiliation(s)
- Anna‐Malin Linde
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | - D. Magnus Eklund
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | - Akane Kubota
- Graduate School of BiostudiesKyoto UniversityKyoto606‐8502Japan
| | - Eric R. A. Pederson
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | - Karl Holm
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | - Niclas Gyllenstrand
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
| | | | - Nils Cronberg
- Department of BiologyLund UniversityEcology BuildingSE‐22362LundSweden
| | | | - Tokitaka Oyama
- Graduate School of ScienceKyoto UniversityKyoto606‐8502Japan
| | - Takayuki Kohchi
- Graduate School of BiostudiesKyoto UniversityKyoto606‐8502Japan
| | - Ulf Lagercrantz
- Department of Plant Ecology and EvolutionEvolutionary Biology CentreUppsala UniversityNorbyvägen 18DSE‐75236UppsalaSweden
- The Linnean Centre for Plant Biology in UppsalaUppsalaSweden
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42
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Abstract
Sustained oscillations abound in biological systems. They occur at all levels of biological organization over a wide range of periods, from a fraction of a second to years, and with a variety of underlying mechanisms. They control major physiological functions, and their dysfunction is associated with a variety of physiological disorders. The goal of this review is (i) to give an overview of the main rhythms observed at the cellular and supracellular levels, (ii) to briefly describe how the study of biological rhythms unfolded in the course of time, in parallel with studies on chemical oscillations, (iii) to present the major roles of biological rhythms in the control of physiological functions, and (iv) the pathologies associated with the alteration, disappearance, or spurious occurrence of biological rhythms. Two tables present the main examples of cellular and supracellular rhythms ordered according to their period, and their role in physiology and pathophysiology. Among the rhythms discussed are neural and cardiac rhythms, metabolic oscillations such as those occurring in glycolysis in yeast, intracellular Ca++ oscillations, cyclic AMP oscillations in Dictyostelium amoebae, the segmentation clock that controls somitogenesis, pulsatile hormone secretion, circadian rhythms which occur in all eukaryotes and some bacteria with a period close to 24 h, the oscillatory dynamics of the enzymatic network driving the cell cycle, and oscillations in transcription factors such as NF-ΚB and tumor suppressors such as p53. Ilya Prigogine's concept of dissipative structures applies to temporal oscillations and allows us to unify within a common framework the various rhythms observed at different levels of biological organization, regardless of their period and underlying mechanism.
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Affiliation(s)
- Albert Goldbeter
- Unité de Chronobiologie théorique, Service de Chimie physique et Biologie théorique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus Plaine, CP 231, B-1050 Brussels, Belgium
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43
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Modeling the photoperiodic entrainment of the plant circadian clock. J Theor Biol 2017; 420:220-231. [DOI: 10.1016/j.jtbi.2017.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 01/12/2017] [Accepted: 03/07/2017] [Indexed: 11/21/2022]
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44
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Pudasaini A, Shim JS, Song YH, Shi H, Kiba T, Somers DE, Imaizumi T, Zoltowski BD. Kinetics of the LOV domain of ZEITLUPE determine its circadian function in Arabidopsis. eLife 2017; 6. [PMID: 28244872 PMCID: PMC5370183 DOI: 10.7554/elife.21646] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 02/26/2017] [Indexed: 11/13/2022] Open
Abstract
A LOV (Light, Oxygen, or Voltage) domain containing blue-light photoreceptor ZEITLUPE (ZTL) directs circadian timing by degrading clock proteins in plants. Functions hinge upon allosteric differences coupled to the ZTL photocycle; however, structural and kinetic information was unavailable. Herein, we tune the ZTL photocycle over two orders of magnitude. These variants reveal that ZTL complexes with targets independent of light, but dictates enhanced protein degradation in the dark. In vivo experiments definitively show photocycle kinetics dictate the rate of clock component degradation, thereby impacting circadian period. Structural studies demonstrate that photocycle dependent activation of ZTL depends on an unusual dark-state conformation of ZTL. Crystal structures of ZTL LOV domain confirm delineation of structural and kinetic mechanisms and identify an evolutionarily selected allosteric hinge differentiating modes of PAS/LOV signal transduction. The combined biochemical, genetic and structural studies provide new mechanisms indicating how PAS/LOV proteins integrate environmental variables in complex networks.
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Affiliation(s)
- Ashutosh Pudasaini
- Department of Chemistry, Southern Methodist University, Dallas, United States.,Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, United States
| | - Jae Sung Shim
- Department of Biology, University of Washington, Seattle, United States
| | - Young Hun Song
- Department of Biology, University of Washington, Seattle, United States.,Department of Life Sciences, Ajou University, Suwon, Korea
| | - Hua Shi
- Department of Molecular Genetics, Ohio State University, Columbus, United States
| | - Takatoshi Kiba
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - David E Somers
- Department of Molecular Genetics, Ohio State University, Columbus, United States
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, United States
| | - Brian D Zoltowski
- Department of Chemistry, Southern Methodist University, Dallas, United States.,Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, United States
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45
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Koda S, Onda Y, Matsui H, Takahagi K, Uehara-Yamaguchi Y, Shimizu M, Inoue K, Yoshida T, Sakurai T, Honda H, Eguchi S, Nishii R, Mochida K. Diurnal Transcriptome and Gene Network Represented through Sparse Modeling in Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2017; 8:2055. [PMID: 29234348 PMCID: PMC5712366 DOI: 10.3389/fpls.2017.02055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/16/2017] [Indexed: 05/08/2023]
Abstract
We report the comprehensive identification of periodic genes and their network inference, based on a gene co-expression analysis and an Auto-Regressive eXogenous (ARX) model with a group smoothly clipped absolute deviation (SCAD) method using a time-series transcriptome dataset in a model grass, Brachypodium distachyon. To reveal the diurnal changes in the transcriptome in B. distachyon, we performed RNA-seq analysis of its leaves sampled through a diurnal cycle of over 48 h at 4 h intervals using three biological replications, and identified 3,621 periodic genes through our wavelet analysis. The expression data are feasible to infer network sparsity based on ARX models. We found that genes involved in biological processes such as transcriptional regulation, protein degradation, and post-transcriptional modification and photosynthesis are significantly enriched in the periodic genes, suggesting that these processes might be regulated by circadian rhythm in B. distachyon. On the basis of the time-series expression patterns of the periodic genes, we constructed a chronological gene co-expression network and identified putative transcription factors encoding genes that might be involved in the time-specific regulatory transcriptional network. Moreover, we inferred a transcriptional network composed of the periodic genes in B. distachyon, aiming to identify genes associated with other genes through variable selection by grouping time points for each gene. Based on the ARX model with the group SCAD regularization using our time-series expression datasets of the periodic genes, we constructed gene networks and found that the networks represent typical scale-free structure. Our findings demonstrate that the diurnal changes in the transcriptome in B. distachyon leaves have a sparse network structure, demonstrating the spatiotemporal gene regulatory network over the cyclic phase transitions in B. distachyon diurnal growth.
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Affiliation(s)
- Satoru Koda
- Graduate School of Mathematics, Kyushu University, Fukuoka, Japan
| | - Yoshihiko Onda
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | | | - Kotaro Takahagi
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
| | - Yukiko Uehara-Yamaguchi
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Minami Shimizu
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Komaki Inoue
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Takuhiro Yoshida
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Tetsuya Sakurai
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
- Research and Education Faculty, Multidisciplinary Science Cluster, Interdisciplinary Science Unit, Kochi University, Kochi, Japan
| | - Hiroshi Honda
- Graduate School of Mathematics, Kyushu University, Fukuoka, Japan
| | - Shinto Eguchi
- The Institute of Statistical Mathematics, Tokyo, Japan
| | - Ryuei Nishii
- Institute of Mathematics for Industry, Kyushu University, Fukuoka, Japan
- *Correspondence: Keiichi Mochida, Ryuei Nishii,
| | - Keiichi Mochida
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
- *Correspondence: Keiichi Mochida, Ryuei Nishii,
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