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Rovira A, Veciana N, Basté-Miquel A, Quevedo M, Locascio A, Yenush L, Toledo-Ortiz G, Leivar P, Monte E. PIF transcriptional regulators are required for rhythmic stomatal movements. Nat Commun 2024; 15:4540. [PMID: 38811542 DOI: 10.1038/s41467-024-48669-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/07/2024] [Indexed: 05/31/2024] Open
Abstract
Stomata govern the gaseous exchange between the leaf and the external atmosphere, and their function is essential for photosynthesis and the global carbon and oxygen cycles. Rhythmic stomata movements in daily dark/light cycles prevent water loss at night and allow CO2 uptake during the day. How the actors involved are transcriptionally regulated and how this might contribute to rhythmicity is largely unknown. Here, we show that morning stomata opening depends on the previous night period. The transcription factors PHYTOCHROME-INTERACTING FACTORS (PIFs) accumulate at the end of the night and directly induce the guard cell-specific K+ channel KAT1. Remarkably, PIFs and KAT1 are required for blue light-induced stomata opening. Together, our data establish a molecular framework for daily rhythmic stomatal movements under well-watered conditions, whereby PIFs are required for accumulation of KAT1 at night, which upon activation by blue light in the morning leads to the K+ intake driving stomata opening.
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Affiliation(s)
- Arnau Rovira
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Nil Veciana
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Aina Basté-Miquel
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Martí Quevedo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Antonella Locascio
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
- Department of biomedical science, Faculty of Health Sciences, Universidad CEU Cardenal Herrera, Alfara del Patriarca (Valencia), Spain
| | - Lynne Yenush
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Gabriela Toledo-Ortiz
- James Hutton Institute, Cell and Molecular Sciences, Errol Road Invergowrie, Dundee, UK
| | - Pablo Leivar
- Laboratory of Biochemistry, Institut Químic de Sarrià (IQS), Universitat Ramon Llull, Barcelona, Spain
| | - Elena Monte
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain.
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.
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2
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Li T, Fang K, Tie Y, Lu Y, Lei Y, Li W, Zheng T, Yao X. NAC transcription factor ATAF1 negatively modulates the PIF-regulated hypocotyl elongation under a short-day photoperiod. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38736429 DOI: 10.1111/pce.14944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 04/17/2024] [Accepted: 04/28/2024] [Indexed: 05/14/2024]
Abstract
Day length modulates hypocotyl elongation in seedlings to optimize their overall fitness. Variations in cell growth-associated genes are regulated by several transcription factors. However, the specific transcription factors through which the plant clock increases plant fitness are still being elucidated. In this study, we identified the no apical meristem, Arabidopsis thaliana-activating factor (ATAF-1/2), and cup-shaped cotyledon (NAC) family transcription factor ATAF1 as a novel repressor of hypocotyl elongation under a short-day (SD) photoperiod. Variations in day length profoundly affected the transcriptional and protein levels of ATAF1. ATAF1-deficient mutant exhibited increased hypocotyl length and cell growth-promoting gene expression under SD conditions. Moreover, ATAF1 directly targeted and repressed the expression of the cycling Dof factor 1/5 (CDF1/5), two key transcription factors involved in hypocotyl elongation under SD conditions. Additionally, ATAF1 interacted with and negatively modulated the effects of phytochrome-interacting factor (PIF), thus inhibiting PIF-promoted gene expression and hypocotyl elongation. Taken together, our results revealed ATAF1-PIF as a crucial pair modulating the expression of key transcription factors to facilitate plant growth during day/night cycles under fluctuating light conditions.
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Affiliation(s)
- Taotao Li
- School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
- Solid-State Fermentation Resource Utilization Key Laboratory of Sichuan Province, Department of Agriculture Forestry and Food Engineering, Yibin University, Yibin, China
| | - Ke Fang
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Yu Tie
- Solid-State Fermentation Resource Utilization Key Laboratory of Sichuan Province, Department of Agriculture Forestry and Food Engineering, Yibin University, Yibin, China
| | - Yuxin Lu
- Solid-State Fermentation Resource Utilization Key Laboratory of Sichuan Province, Department of Agriculture Forestry and Food Engineering, Yibin University, Yibin, China
| | - Yuxin Lei
- Solid-State Fermentation Resource Utilization Key Laboratory of Sichuan Province, Department of Agriculture Forestry and Food Engineering, Yibin University, Yibin, China
| | - Weijian Li
- Solid-State Fermentation Resource Utilization Key Laboratory of Sichuan Province, Department of Agriculture Forestry and Food Engineering, Yibin University, Yibin, China
| | - Ting Zheng
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Xiuhong Yao
- Solid-State Fermentation Resource Utilization Key Laboratory of Sichuan Province, Department of Agriculture Forestry and Food Engineering, Yibin University, Yibin, China
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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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Tiwari LD, Bdolach E, Prusty MR, Bodenheimer S, Be'ery A, Faigenboim-Doron A, Yamamoto E, Panzarová K, Kashkush K, Shental N, Fridman E. Cytonuclear interactions modulate the plasticity of photosynthetic rhythmicity and growth in wild barley. PHYSIOLOGIA PLANTARUM 2024; 176:e14192. [PMID: 38351880 DOI: 10.1111/ppl.14192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
In plants, the contribution of the plasmotype (mitochondria and chloroplast) in controlling the circadian clock plasticity and possible consequences on cytonuclear genetic makeup have yet to be fully elucidated. A genome-wide association study in the wild barley (Hordeum vulgare ssp. spontaneum) B1K collection identified overlap with our previously mapped DRIVERS OF CLOCKS (DOCs) loci in wild-cultivated interspecific population. Moreover, we identified non-random segregation and epistatic interactions between nuclear DOCs loci and the chloroplastic RpoC1 gene, indicating an adaptive value for specific cytonuclear gene combinations. Furthermore, we show that DOC1.1, which harbours the candidate SIGMA FACTOR-B (SIG-B) gene, is linked with the differential expression of SIG-B and CCA1 genes and contributes to the circadian gating response to heat. High-resolution temporal growth and photosynthesis measurements of B1K also link the DOCs loci to differential growth, Chl content and quantum yield. To validate the involvement of the Plastid encoded polymerase (PEP) complex, we over-expressed the two barley chloroplastic RpoC1 alleles in Arabidopsis and identified significant differential plasticity under elevated temperatures. Finally, enhanced clock plasticity of de novo ENU (N-Ethyl-N-nitrosourea) -induced barley rpoB1 mutant further implicates the PEP complex as a key player in regulating the circadian clock output. Overall, this study highlights the contribution of specific cytonuclear interaction between rpoC1 (PEP gene) and SIG-B with distinct circadian timing regulation under heat, and their pleiotropic effects on growth implicate an adaptive value.
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Affiliation(s)
- Lalit Dev Tiwari
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| | - Eyal Bdolach
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Manas Ranjan Prusty
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| | - Schewach Bodenheimer
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Avital Be'ery
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| | - Adi Faigenboim-Doron
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| | - Eiji Yamamoto
- Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | | | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Noam Shental
- Department of Mathematics and Computer Science, The Open University of Israel, Raanana, Israel
| | - Eyal Fridman
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
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5
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Zhang Y, Ma Y, Zhang H, Xu J, Gao X, Zhang T, Liu X, Guo L, Zhao D. Environmental F actors coordinate circadian clock function and rhythm to regulate plant development. PLANT SIGNALING & BEHAVIOR 2023; 18:2231202. [PMID: 37481743 PMCID: PMC10364662 DOI: 10.1080/15592324.2023.2231202] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 07/25/2023]
Abstract
Changes in the external environment necessitate plant growth plasticity, with environmental signals such as light, temperature, and humidity regulating growth and development. The plant circadian clock is a biological time keeper that can be "reset" to adjust internal time to changes in the external environment. Exploring the regulatory mechanisms behind plant acclimation to environmental factors is important for understanding how plant growth and development are shaped and for boosting agricultural production. In this review, we summarize recent insights into the coordinated regulation of plant growth and development by environmental signals and the circadian clock, further discussing the potential of this knowledge.
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Affiliation(s)
- Ying Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Yuru Ma
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Hao Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Jiahui Xu
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Xiaokuan Gao
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
| | - Tengteng Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Xigang Liu
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Lin Guo
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Dan Zhao
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
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6
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Ikeda H, Uchikawa T, Kondo Y, Takahashi N, Shishikui T, Watahiki MK, Kubota A, Endo M. Circadian Clock Controls Root Hair Elongation through Long-Distance Communication. PLANT & CELL PHYSIOLOGY 2023; 64:1289-1300. [PMID: 37552691 DOI: 10.1093/pcp/pcad076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/06/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023]
Abstract
Plants adapt to periodic environmental changes, such as day and night, by using circadian clocks. Cell division and elongation are primary steps to adjust plant development according to their environments. In Arabidopsis, hypocotyl elongation has been studied as a representative model to understand how the circadian clock regulates cell elongation. However, it remains unknown whether similar phenomena exist in other organs, such as roots, where circadian clocks regulate physiological responses. Here, we show that root hair elongation is controlled by both light and the circadian clock. By developing machine-learning models to automatically analyze the images of root hairs, we found that genes encoding major components of the central oscillator, such as TIMING OF CAB EXPRESSION1 (TOC1) or CIRCADIAN CLOCK ASSOCIATED1 (CCA1), regulate the rhythmicity of root hair length. The partial illumination of light to either shoots or roots suggested that light received in shoots is mainly responsible for the generation of root hair rhythmicity. Furthermore, grafting experiments between wild-type (WT) and toc1 plants demonstrated that TOC1 in shoots is responsible for the generation of root hair rhythmicity. Our results illustrate the combinational effects of long-distance signaling and the circadian clock on the regulation of root hair length.
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Affiliation(s)
- Hikari Ikeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
| | - Taiga Uchikawa
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
| | - Yohei Kondo
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, 444-8787 Japan
| | - Nozomu Takahashi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012 Japan
| | - Takuma Shishikui
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
| | - Masaaki K Watahiki
- Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810 Japan
- Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Akane Kubota
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
| | - Motomu Endo
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan
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7
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Wei Z, Zhang H, Fang M, Lin S, Zhu M, Li Y, Jiang L, Cui T, Cui Y, Kui H, Peng L, Gou X, Li J. The Dof transcription factor COG1 acts as a key regulator of plant biomass by promoting photosynthesis and starch accumulation. MOLECULAR PLANT 2023; 16:1759-1772. [PMID: 37742075 DOI: 10.1016/j.molp.2023.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 07/14/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
Photosynthetic efficiency is the primary determinant of crop yield, including vegetative biomass and grain yield. Manipulation of key transcription factors known to directly control photosynthetic machinery can be an effective strategy to improve photosynthetic traits. In this study, we identified an Arabidopsis gain-of-function mutant, cogwheel1-3D, that shows a significantly enlarged rosette and increased biomass compared with wild-type plants. Overexpression of COG1, a Dof transcription factor, recapitulated the phenotype of cogwheel1-3D, whereas knocking out COG1 and its six paralogs resulted in a reduced rosette size and decreased biomass. Transcriptomic and quantitative reverse transcription polymerase chain reaction analyses demonstrated that COG1 and its paralogs were required for light-induced expression of genes involved in photosynthesis. Further chromatin immunoprecipitation and electrophoretic mobility shift assays indicated that COG1 can directly bind to the promoter regions of multiple genes encoding light-harvesting antenna proteins. Physiological, biochemical, and microscopy analyses revealed that COG1 enhances photosynthetic capacity and starch accumulation in Arabidopsis rosette leaves. Furthermore, combined results of bioinformatic, genetic, and molecular experiments suggested that the functions of COG1 in increasing biomass are conserved in different plant species. These results collectively demonstrated that COG1 acts as a key regulator of plant biomass by promoting photosynthesis and starch accumulation. Manipulating COG1 to optimize photosynthetic capacity would create new strategies for future crop yield improvement.
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Affiliation(s)
- Zhuoyun Wei
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; Gansu Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Haoyong Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Meng Fang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Shuyuan Lin
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Mingsong Zhu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yuxiu Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Limin Jiang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Tianliang Cui
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yanwei Cui
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; Gansu Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Hong Kui
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; Gansu Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Liang Peng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; Gansu Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaoping Gou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; Gansu Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; Gansu Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
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8
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Gao G, Chen M, Mo R, Li N, Xu Y, Lu Y. Linking New Alleles at the Oscillator Loci to Flowering and Expansion of Asian Rice. Genes (Basel) 2023; 14:2027. [PMID: 38002970 PMCID: PMC10671530 DOI: 10.3390/genes14112027] [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: 09/10/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
The central oscillator is believed to be the key mechanism by which plants adapt to new environments. However, impacts from hybridization, the natural environment, and human selection have rarely been assessed on the oscillator of a crop. Here, from clearly identified alleles at oscillator loci (OsCCA1/LHY, OsPRR95, OsPRR37, OsPRR59, and OsPRR1) in ten diverse genomes of Oryza sativa, additional accessions, and functional analysis, we show that rice's oscillator was rebuilt primarily by new alleles from recombining parental sequences and subsequent 5' or/and coding mutations. New alleles may exhibit altered transcript levels from that of a parental allele and are transcribed variably among genetic backgrounds and natural environments in RIL lines. Plants carrying more expressed OsCCA1_a and less transcribed OsPRR1_e flower early in the paddy field. 5' mutations are instrumental in varied transcription, as shown by EMSA tests on one deletion at the 5' region of highly transcribed OsPRR1_a. Compared to relatively balanced mutations at oscillator loci of Arabidopsis thaliana, 5' mutations of OsPRR37 (and OsCCA1 to a less degree) were under negative selection while those of OsPRR1 alleles were under strong positive selection. Together, range expansion of Asian rice can be elucidated by human selection on OsPRR1 alleles via local flowering time-yield relationships.
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Affiliation(s)
- Guangtong Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maoxian Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Mo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunzhang Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Yingqing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Hughes CL, Harmer SL. Myb-like transcription factors have epistatic effects on circadian clock function but additive effects on plant growth. PLANT DIRECT 2023; 7:e533. [PMID: 37811362 PMCID: PMC10557472 DOI: 10.1002/pld3.533] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/23/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023]
Abstract
The functions of closely related Myb-like repressor and Myb-like activator proteins within the plant circadian oscillator have been well-studied as separate groups, but the genetic interactions between them are less clear. We hypothesized that these repressors and activators would interact additively to regulate both circadian and growth phenotypes. We used CRISPR-Cas9 to generate new mutant alleles and performed physiological and molecular characterization of plant mutants for five of these core Myb-like clock factors compared with a repressor mutant and an activator mutant. We first examined circadian clock function in plants likely null for both the repressor proteins, CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), and the activator proteins, REVEILLE 4 (RVE4), REVEILLE (RVE6), and REVEILLE (RVE8). The rve468 triple mutant has a long period and flowers late, while cca1 lhy rve468 quintuple mutants, similarly to cca1 lhy mutants, have poor circadian rhythms and flower early. This suggests that CCA1 and LHY are epistatic to RVE4, RVE6, and RVE8 for circadian clock and flowering time function. We next examined hypocotyl elongation and rosette leaf size in these mutants. The cca1 lhy rve468 mutants have growth phenotypes intermediate between cca1 lhy and rve468 mutants, suggesting that CCA1, LHY, RVE4, RVE6, and RVE8 interact additively to regulate growth. Together, our data suggest that these five Myb-like factors interact differently in regulation of the circadian clock versus growth. More generally, the near-norm al seedling phenotypes observed in the largely arrhythmic quintuple mutant demonstrate that circadian-regulated output processes, like control of hypocotyl elongation, do not always depend upon rhythmic oscillator function.
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Affiliation(s)
| | - Stacey L. Harmer
- Department of Plant BiologyUniversity of CaliforniaDavisCaliforniaUSA
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10
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Li J, Qiu JX, Zeng QH, Zhang N, Xu SX, Jin J, Dong ZC, Chen L, Huang W. OsTOC1 plays dual roles in the regulation of plant circadian clock by functioning as a direct transcription activator or repressor. Cell Rep 2023; 42:112765. [PMID: 37421622 DOI: 10.1016/j.celrep.2023.112765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/28/2023] [Accepted: 06/22/2023] [Indexed: 07/10/2023] Open
Abstract
Plant clock function relies on precise timing of gene expression through complex regulatory networks consisting of activators and repressors at the core of oscillators. Although TIMING OF CAB EXPRESSION 1 (TOC1) has been recognized as a repressor involved in shaping oscillations and regulating clock-driven processes, its potential to directly activate gene expression remains unclear. In this study, we find that OsTOC1 primarily acts as a transcriptional repressor for core clock components, including OsLHY and OsGI. Here, we show that OsTOC1 possesses the ability to directly activate the expression of circadian target genes. Through binding to the promoters of OsTGAL3a/b, transient activation of OsTOC1 induces the expression of OsTGAL3a/b, indicating its role as an activator contributing to pathogen resistance. Moreover, TOC1 participates in regulating multiple yield-related traits in rice. These findings suggest that TOC1's function as a transcriptional repressor is not inherent, providing flexibility to circadian regulations, particularly in outputs.
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Affiliation(s)
- Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Jia-Xin Qiu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Qing-Hua Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Ning Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Shu-Xuan Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Jian Jin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Zhi-Cheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
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11
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Gendron JM, Staiger D. New Horizons in Plant Photoperiodism. ANNUAL REVIEW OF PLANT BIOLOGY 2023; 74:481-509. [PMID: 36854481 PMCID: PMC11114106 DOI: 10.1146/annurev-arplant-070522-055628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Photoperiod-measuring mechanisms allow organisms to anticipate seasonal changes to align reproduction and growth with appropriate times of the year. This review provides historical and modern context to studies of plant photoperiodism. We describe how studies of photoperiodic flowering in plants led to the first theoretical models of photoperiod-measuring mechanisms in any organism. We discuss how more recent molecular genetic studies in Arabidopsis and rice have revisited these concepts. We then discuss how photoperiod transcriptomics provides new lessons about photoperiodic gene regulatory networks and the discovery of noncanonical photoperiod-measuring systems housed in metabolic networks of plants. This leads to an examination of nonflowering developmental processes controlled by photoperiod, including metabolism and growth. Finally, we highlight the importance of understanding photoperiodism in the context of climate change, delving into the rapid latitudinal migration of plant species and the potential role of photoperiod-measuring systems in generating photic barriers during migration.
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Affiliation(s)
- Joshua M Gendron
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA;
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany;
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12
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Cano-Ramirez DL, Panter PE, Takemura T, de Fraine TS, de Barros Dantas LL, Dekeya R, Barros-Galvão T, Paajanen P, Bellandi A, Batstone T, Manley BF, Tanaka K, Imamura S, Franklin KA, Knight H, Dodd AN. Low-temperature and circadian signals are integrated by the sigma factor SIG5. NATURE PLANTS 2023; 9:661-672. [PMID: 36997687 PMCID: PMC10119024 DOI: 10.1038/s41477-023-01377-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Chloroplasts are a common feature of plant cells and aspects of their metabolism, including photosynthesis, are influenced by low-temperature conditions. Chloroplasts contain a small circular genome that encodes essential components of the photosynthetic apparatus and chloroplast transcription/translation machinery. Here, we show that in Arabidopsis, a nuclear-encoded sigma factor that controls chloroplast transcription (SIGMA FACTOR5) contributes to adaptation to low-temperature conditions. This process involves the regulation of SIGMA FACTOR5 expression in response to cold by the bZIP transcription factors ELONGATED HYPOCOTYL5 and ELONGATED HYPOCOTYL5 HOMOLOG. The response of this pathway to cold is gated by the circadian clock, and it enhances photosynthetic efficiency during long-term cold and freezing exposure. We identify a process that integrates low-temperature and circadian signals, and modulates the response of chloroplasts to low-temperature conditions.
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Affiliation(s)
- Dora L Cano-Ramirez
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Tokiaki Takemura
- Laboratory for Chemistry and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | | | | | | | | | | | - Annalisa Bellandi
- John Innes Centre, Norwich, UK
- Laboratoire de Reproduction et Développement des Plantes, ENS de Lyon, Université de Lyon, UCBL, INRAE, CNRS, Lyon, France
| | - Tom Batstone
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Bethan F Manley
- School of Biological Sciences, University of Bristol, Bristol, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Sousuke Imamura
- Laboratory for Chemistry and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- Space Environment and Energy Laboratories, Nippon Telegraph and Telephone Corporation, Musashino-shi, Japan
| | - Keara A Franklin
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Heather Knight
- Department of Biosciences, Durham University, Durham, UK
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13
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Kim H, Kim J, Choi G. Epidermal phyB requires RRC1 to promote light responses by activating the circadian rhythm. THE NEW PHYTOLOGIST 2023; 238:705-723. [PMID: 36651061 DOI: 10.1111/nph.18746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Phytochrome B (phyB) expressed in the epidermis is sufficient to promote red light responses, including the inhibition of hypocotyl elongation and hypocotyl negative gravitropism. Nonetheless, the downstream mechanism of epidermal phyB in promoting light responses had been elusive. Here, we mutagenized the epidermis-specific phyB-expressing line (MLB) using ethyl methanesulfonate (EMS) and characterized a novel mutant allele of RRC1 (rrc1-689), which causes reduced epidermal phyB-mediated red light responses. The rrc1-689 mutation increases the alternative splicing of major clock gene transcripts, including PRR7 and TOC1, disrupting the rhythmic expression of the entire clock and clock-controlled genes. Combined with the result that MLB/prr7 exhibits the same red-hyposensitive phenotypes as MLB/rrc1-689, our data support that the circadian clock is required for the ability of epidermal phyB to promote light responses. We also found that, unlike phyB, RRC1 preferentially acts in the endodermis to maintain the circadian rhythm by suppressing the alternative splicing of core clock genes. Together, our results suggest that epidermal phyB requires RRC1 to promote light responses by activating the circadian rhythm in Arabidopsis thaliana.
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Affiliation(s)
- Hanim Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Jaewook Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
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14
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Zhao X, Niu Y, Hossain Z, Zhao B, Bai X, Mao T. New insights into light spectral quality inhibits the plasticity elongation of maize mesocotyl and coleoptile during seed germination. FRONTIERS IN PLANT SCIENCE 2023; 14:1152399. [PMID: 37008499 PMCID: PMC10050570 DOI: 10.3389/fpls.2023.1152399] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
The plastic elongation of mesocotyl (MES) and coleoptile (COL), which can be repressed by light exposure, plays a vital role in maize seedling emergence and establishment under adverse environmental conditions. Understanding the molecular mechanisms of light-mediated repression of MES and COL elongation in maize will allow us to develop new strategies for genetic improvement of these two crucial traits in maize. A maize variety, Zheng58, was used to monitor the transcriptome and physiological changes in MES and COL in response to darkness, as well as red, blue, and white light. The elongation of MES and COL was significantly inhibited by light spectral quality in this order: blue light > red light > white light. Physiological analyses revealed that light-mediated inhibition of maize MES and COL elongation was closely related to the dynamics of phytohormones accumulation and lignin deposition in these tissues. In response to light exposure, the levels of indole-3-acetic acid, trans-zeatin, gibberellin 3, and abscisic acid levels significantly decreased in MES and COL; by contrast, the levels of jasmonic acid, salicylic acid, lignin, phenylalanine ammonia-lyase, and peroxidase enzyme activity significantly increased. Transcriptome analysis revealed multiple differentially expressed genes (DEGs) involved in circadian rhythm, phytohormone biosynthesis and signal transduction, cytoskeleton and cell wall organization, lignin biosynthesis, and starch and sucrose metabolism. These DEGs exhibited synergistic and antagonistic interactions, forming a complex network that regulated the light-mediated inhibition of MES and COL elongation. Additionally, gene co-expression network analysis revealed that 49 hub genes in one and 19 hub genes in two modules were significantly associated with the elongation plasticity of COL and MES, respectively. These findings enhance our knowledge of the light-regulated elongation mechanisms of MES and COL, and provide a theoretical foundation for developing elite maize varieties with improved abiotic stress resistance.
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Affiliation(s)
- Xiaoqiang Zhao
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Yining Niu
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zakir Hossain
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Bingyu Zhao
- School of Plant and Environmental Sciences, College of Agriculture and Life Sciences, Blacksburg, VA, United States
| | - Xiaodong Bai
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Taotao Mao
- State Key Laboratory of Aridland Crop Science/College of Agronomy, Gansu Agricultural University, Lanzhou, China
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15
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Ji M, Wang G, Liu X, Li X, Xue Y, Amombo E, Fu J. The extended day length promotes earlier flowering of bermudagrass. PeerJ 2022; 10:e14326. [PMID: 36411836 PMCID: PMC9675341 DOI: 10.7717/peerj.14326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 10/11/2022] [Indexed: 11/17/2022] Open
Abstract
Day length is a very critical environmental factor affecting plant growth and development. The extension of light application time has been shown to promote flowering in the long-day plant and to shorten breeding time in some crops. However, previous research on the regulation of bermudagrass flowering by light application time is scarce. Therefore, this study investigated the effect of day length on the growth and flowering of bermudagrass by prolonging the light application time in a controlled greenhouse. Three different light application times were set up in the experiment: 22/2 h (22 hours light/2 hours dark), 18/6 h (18 hours light/6 hours dark), 14/10 h (14 hours light/10 hours dark). Results showed that extending the light application time not only promoted the growth of bermudagrass (plant height, fresh weight, dry weight) but also its nutrient uptake (nitrogen (N) and phosphorous (P) content). In addition, daily light integrals were different when flowering under different light application times. Most importantly, under the 22/2 h condition, flowering time was successfully reduced to 44 days for common bermudagrass (Cynodon dactylon [L.] pers) genotype A12359 and 36 days for African bermudagrass (Cynodon transvaalensis Burtt-Davy) genotype ABD11. This study demonstrated a successful method of bermudagrass flowering earlier than usual time by manipulating light application time which may provide useful insights for bermudagrass breeding.
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16
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Urrea-Castellanos R, Caldana C, Henriques R. Growing at the right time: interconnecting the TOR pathway with photoperiod and circadian regulation. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7006-7015. [PMID: 35738873 PMCID: PMC9664226 DOI: 10.1093/jxb/erac279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Plants can adjust their growth to specific times of the day and season. Different photoperiods result in distinct growth patterns, which correlate with specific carbon-partitioning strategies in source (leaves) and sink (roots) organs. Therefore, external cues such as light, day length, and temperature need to be integrated with intracellular processes controlling overall carbon availability and anabolism. The target of rapamycin (TOR) pathway is a signalling hub where environmental signals, circadian information, and metabolic processes converge to regulate plant growth. TOR complex mutants display altered patterns of root growth and starch levels. Moreover, depletion of TOR or reduction in cellular energy levels affect the pace of the clock by extending the period length, suggesting that this pathway could participate in circadian metabolic entrainment. However, this seems to be a mutual interaction, since the TOR pathway components are also under circadian regulation. These results strengthen the role of this signalling pathway as a master sensor of metabolic status, integrating day length and circadian cues to control anabolic processes in the cell, thus promoting plant growth and development. Expanding this knowledge from Arabidopsis thaliana to crops will improve our understanding of the molecular links connecting environmental perception and growth regulation under field conditions.
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Affiliation(s)
| | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
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17
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Calderon RH, Dalton J, Zhang Y, Quail PH. Shade triggers posttranscriptional PHYTOCHROME-INTERACTING FACTOR-dependent increases in H3K4 trimethylation. PLANT PHYSIOLOGY 2022; 190:1915-1926. [PMID: 35674379 PMCID: PMC9614472 DOI: 10.1093/plphys/kiac282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
The phytochrome (phy)-PHYTOCHROME-INTERACTING FACTOR (PIF) sensory module perceives and transduces light signals to direct target genes (DTGs), which then drive the adaptational responses in plant growth and development appropriate to the prevailing environment. These signals include the first exposure of etiolated seedlings to sunlight upon emergence from subterranean darkness and the change in color of the light that is filtered through, or reflected from, neighboring vegetation ("shade"). Previously, we identified three broad categories of rapidly signal-responsive genes: those repressed by light and conversely induced by shade; those repressed by light, but subsequently unresponsive to shade; and those responsive to shade only. Here, we investigate the potential role of epigenetic chromatin modifications in regulating these contrasting patterns of phy-PIF module-induced expression of DTGs in Arabidopsis (Arabidopsis thaliana). Using RNA-seq and ChIP-seq to determine time-resolved profiling of transcript and histone 3 lysine 4 trimethylation (H3K4me3) levels, respectively, we show that, whereas the initial dark-to-light transition triggers a rapid, apparently temporally coincident decline of both parameters, the light-to-shade transition induces similarly rapid increases in transcript levels that precede increases in H3K4me3 levels. Together with other recent findings, these data raise the possibility that, rather than being causal in the shade-induced expression changes, H3K4me3 may function to buffer the rapidly fluctuating shade/light switching that is intrinsic to vegetational canopies under natural sunlight conditions.
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Affiliation(s)
- Robert H Calderon
- Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720, USA
- Plant Gene Expression Center, Agriculture Research Service, US Department of Agriculture, Albany, California, 94710, USA
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, 901 87, Sweden
| | - Jutta Dalton
- Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720, USA
- Plant Gene Expression Center, Agriculture Research Service, US Department of Agriculture, Albany, California, 94710, USA
| | - Yu Zhang
- Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720, USA
- Plant Gene Expression Center, Agriculture Research Service, US Department of Agriculture, Albany, California, 94710, USA
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Peter H Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720, USA
- Plant Gene Expression Center, Agriculture Research Service, US Department of Agriculture, Albany, California, 94710, USA
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18
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He Y, Yu Y, Wang X, Qin Y, Su C, Wang L. Aschoff's rule on circadian rhythms orchestrated by blue light sensor CRY2 and clock component PRR9. Nat Commun 2022; 13:5869. [PMID: 36198686 PMCID: PMC9535003 DOI: 10.1038/s41467-022-33568-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 09/22/2022] [Indexed: 11/09/2022] Open
Abstract
Circadian pace is modulated by light intensity, known as the Aschoff’s rule, with largely unrevealed mechanisms. Here we report that photoreceptor CRY2 mediates blue light input to the circadian clock by directly interacting with clock core component PRR9 in blue light dependent manner. This physical interaction dually blocks the accessibility of PRR9 protein to its co-repressor TPL/TPRs and the resulting kinase PPKs. Notably, phosphorylation of PRR9 by PPKs is critical for its DNA binding and repressive activity, hence to ensure proper circadian speed. Given the labile nature of CRY2 in strong blue light, our findings provide a mechanistic explanation for Aschoff’s rule in plants, i.e., blue light triggers CRY2 turnover in proportional to its intensity, which accordingly releasing PRR9 to fine tune circadian speed. Our findings not only reveal a network mediating light input into the circadian clock, but also unmask a mechanism by which the Arabidopsis circadian clock senses light intensity. Circadian pace is modulated by light intensity. Here the authors show that CRY2 interacts with PRR9 to mediate blue light input to the circadian clock and is degraded at higher light intensity offering a mechanistic explanation as to how intensity can modify clock place.
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Affiliation(s)
- Yuqing He
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingjun Yu
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiling Wang
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yumei Qin
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Su
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Wang
- Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Davis W, Endo M, Locke JCW. Spatially specific mechanisms and functions of the plant circadian clock. PLANT PHYSIOLOGY 2022; 190:938-951. [PMID: 35640123 PMCID: PMC9516738 DOI: 10.1093/plphys/kiac236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Like many organisms, plants have evolved a genetic network, the circadian clock, to coordinate processes with day/night cycles. In plants, the clock is a pervasive regulator of development and modulates many aspects of physiology. Clock-regulated processes range from the correct timing of growth and cell division to interactions with the root microbiome. Recently developed techniques, such as single-cell time-lapse microscopy and single-cell RNA-seq, are beginning to revolutionize our understanding of this clock regulation, revealing a surprising degree of organ, tissue, and cell-type specificity. In this review, we highlight recent advances in our spatial view of the clock across the plant, both in terms of how it is regulated and how it regulates a diversity of output processes. We outline how understanding these spatially specific functions will help reveal the range of ways that the clock provides a fitness benefit for the plant.
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Affiliation(s)
- William Davis
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Motomu Endo
- Authors for correspondence: (M.E.); (J.C.W.L.)
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20
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Michael TP. Core circadian clock and light signaling genes brought into genetic linkage across the green lineage. PLANT PHYSIOLOGY 2022; 190:1037-1056. [PMID: 35674369 PMCID: PMC9516744 DOI: 10.1093/plphys/kiac276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The circadian clock is conserved at both the level of transcriptional networks as well as core genes in plants, ensuring that biological processes are phased to the correct time of day. In the model plant Arabidopsis (Arabidopsis thaliana), the core circadian SHAQKYF-type-MYB (sMYB) genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and REVEILLE (RVE4) show genetic linkage with PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7, respectively. Leveraging chromosome-resolved plant genomes and syntenic ortholog analysis enabled tracing this genetic linkage back to Amborella trichopoda, a sister lineage to the angiosperm, and identifying an additional evolutionarily conserved genetic linkage in light signaling genes. The LHY/CCA1-PRR5/9, RVE4/8-PRR3/7, and PIF3-PHYA genetic linkages emerged in the bryophyte lineage and progressively moved within several genes of each other across an array of angiosperm families representing distinct whole-genome duplication and fractionation events. Soybean (Glycine max) maintained all but two genetic linkages, and expression analysis revealed the PIF3-PHYA linkage overlapping with the E4 maturity group locus was the only pair to robustly cycle with an evening phase, in contrast to the sMYB-PRR morning and midday phase. While most monocots maintain the genetic linkages, they have been lost in the economically important grasses (Poaceae), such as maize (Zea mays), where the genes have been fractionated to separate chromosomes and presence/absence variation results in the segregation of PRR7 paralogs across heterotic groups. The environmental robustness model is put forward, suggesting that evolutionarily conserved genetic linkages ensure superior microhabitat pollinator synchrony, while wide-hybrids or unlinking the genes, as seen in the grasses, result in heterosis, adaptation, and colonization of new ecological niches.
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21
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Wang S, Steed G, Webb AAR. Circadian entrainment in Arabidopsis. PLANT PHYSIOLOGY 2022; 190:981-993. [PMID: 35512209 PMCID: PMC9516740 DOI: 10.1093/plphys/kiac204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Circadian clocks coordinate physiology and development as an adaption to the oscillating day/night cycle caused by the rotation of Earth on its axis and the changing length of day and night away from the equator caused by orbiting the sun. Circadian clocks confer advantages by entraining to rhythmic environmental cycles to ensure that internal events within the plant occur at the correct time with respect to the cyclic external environment. Advances in determining the structure of circadian oscillators and the pathways that allow them to respond to light, temperature, and metabolic signals have begun to provide a mechanistic insight to the process of entrainment in Arabidopsis (Arabidopsis thaliana). We describe the concepts of entrainment and how it occurs. It is likely that a thorough mechanistic understanding of the genetic and physiological basis of circadian entrainment will provide opportunities for crop improvement.
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Affiliation(s)
- Shouming Wang
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
- School of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Gareth Steed
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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22
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Hotta CT. The evolution and function of the PSEUDO RESPONSE REGULATOR gene family in the plant circadian clock. Genet Mol Biol 2022; 45:e20220137. [PMID: 36125163 PMCID: PMC9486492 DOI: 10.1590/1678-4685-gmb-2022-0137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/12/2022] [Indexed: 11/22/2022] Open
Abstract
PSEUDO-RESPONSE PROTEINS (PRRs) are a gene
family vital for the generation of rhythms by the circadian clock. Plants have
circadian clocks, or circadian oscillators, to adapt to a rhythmic environment.
The circadian clock system can be divided into three parts: the core oscillator,
the input pathways, and the output pathways. The PRRs have a role in all three
parts. These nuclear proteins have an N-terminal pseudo receiver domain and a
C-terminal CONSTANS, CONSTANS-LIKE, and TOC1 (CCT) domain. The PRRs can be
identified from green algae to monocots, ranging from one to >5 genes per
species. Arabidopsis thaliana, for example, has five genes:
PRR9, PRR7, PRR5,
PRR3 and TOC1/PRR1. The
PRR genes can be divided into three clades using protein
homology: TOC1/PRR1, PRR7/3, and PRR9/5 expanded independently in eudicots and
monocots. The PRRs can make protein complexes and bind to DNA, and the wide
variety of protein-protein interactions are essential for the multiple roles in
the circadian clock. In this review, the history of PRR research is briefly
recapitulated, and the diversity of PRR genes in green and recent works about
their role in the circadian clock are discussed.
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Affiliation(s)
- Carlos Takeshi Hotta
- Universidade de São Paulo, Instituto de Química, Departamento de Bioquímica, São Paulo, SP, Brazil
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23
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Li T, Li H, Lian H, Song P, Wang Y, Duan J, Song Z, Cao Y, Xu D, Li J, Zhang H. SICKLE represses photomorphogenic development of Arabidopsis seedlings via HY5- and PIF4-mediated signaling. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1706-1723. [PMID: 35848532 DOI: 10.1111/jipb.13329] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Arabidopsis CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) and PHYTOCHROME INTERACTING FACTORs (PIFs) are negative regulators, and ELONGATED HYPOCOTYL5 (HY5) is a positive regulator of seedling photomorphogenic development. Here, we report that SICKLE (SIC), a proline rich protein, acts as a novel negative regulator of photomorphogenesis. HY5 directly binds the SIC promoter and activates SIC expression in response to light. In turn, SIC physically interacts with HY5 and interferes with its transcriptional regulation of downstream target genes. Moreover, SIC interacts with PIF4 and promotes PIF4-activated transcription of itself. Interestingly, SIC is targeted by COP1 for 26S proteasome-mediated degradation in the dark. Collectively, our data demonstrate that light-induced SIC functions as a brake to prevent exaggerated light response via mediating HY5 and PIF4 signaling, and its degradation by COP1 in the dark avoid too strong inhibition on photomorphogenesis at the beginning of light exposure.
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Affiliation(s)
- Tao Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Haojie Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongmei Lian
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Pengyu Song
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yulong Wang
- School of Life Sciences, Westlake University, Hangzhou, 310024, China
| | - Jie Duan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhaoqing Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Huiyong Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
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24
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Gao H, Song W, Severing E, Vayssières A, Huettel B, Franzen R, Richter R, Chai J, Coupland G. PIF4 enhances DNA binding of CDF2 to co-regulate target gene expression and promote Arabidopsis hypocotyl cell elongation. NATURE PLANTS 2022; 8:1082-1093. [PMID: 35970973 PMCID: PMC9477738 DOI: 10.1038/s41477-022-01213-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 07/04/2022] [Indexed: 05/19/2023]
Abstract
How specificity is conferred within gene regulatory networks is an important problem in biology. The basic helix-loop-helix PHYTOCHROME-INTERACTING FACTORs (PIFs) and single zinc-finger CYCLING DOF FACTORs (CDFs) mediate growth responses of Arabidopsis to light and temperature. We show that these two classes of transcription factor (TF) act cooperatively. CDF2 and PIF4 are temporally and spatially co-expressed, they interact to form a protein complex and act in the same genetic pathway to promote hypocotyl cell elongation. Furthermore, PIF4 substantially strengthens genome-wide occupancy of CDF2 at a subset of its target genes. One of these, YUCCA8, encodes an auxin biosynthesis enzyme whose transcription is increased by PIF4 and CDF2 to contribute to hypocotyl elongation. The binding sites of PIF4 and CDF2 in YUCCA8 are closely spaced, and in vitro PIF4 enhances binding of CDF2. We propose that this occurs by direct protein interaction and because PIF4 binding alters DNA conformation. Thus, we define mechanisms by which PIF and CDF TFs cooperate to achieve regulatory specificity and promote cell elongation in response to light.
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Affiliation(s)
- He Gao
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Wen Song
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Edouard Severing
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Alice Vayssières
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bruno Huettel
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Rainer Franzen
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - René Richter
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jijie Chai
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - George Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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25
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Jacques CN, Favero DS, Kawamura A, Suzuki T, Sugimoto K, Neff MM. SUPPRESSOR OF PHYTOCHROME B-4 #3 reduces the expression of PIF-activated genes and increases expression of growth repressors to regulate hypocotyl elongation in short days. BMC PLANT BIOLOGY 2022; 22:399. [PMID: 35965321 PMCID: PMC9377115 DOI: 10.1186/s12870-022-03737-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
SUPPRESSOR OF PHYTOCHROME B-4 #3 (SOB3) is a member of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family of transcription factors that are involved in light-mediated growth in Arabidopsis thaliana, affecting processes such as hypocotyl elongation. The majority of the research on the AHLs has been conducted in continuous light. However, there are unique molecular events that promote growth in short days (SD) compared to constant light conditions. Therefore, we investigated how AHLs affect hypocotyl elongation in SD. Firstly, we observed that AHLs inhibit hypocotyl growth in SD, similar to their effect in constant light. Next, we identified AHL-regulated genes in SD-grown seedlings by performing RNA-seq in two sob3 mutants at different time points. Our transcriptomic data indicate that PHYTOCHROME INTERACTING FACTORS (PIFs) 4, 5, 7, and 8 along with PIF-target genes are repressed by SOB3 and/or other AHLs. We also identified PIF target genes that are repressed and have not been previously described as AHL-regulated, including PRE1, PIL1, HFR1, CDF5, and XTR7. Interestingly, our RNA-seq data also suggest that AHLs activate the expression of growth repressors to control hypocotyl elongation, such as HY5 and IAA17. Notably, many growth-regulating and other genes identified from the RNA-seq experiment were differentially regulated between these two sob3 mutants at the time points tested. Surprisingly, our ChIP-seq data suggest that SOB3 mostly binds to similar genes throughout the day. Collectively, these data suggest that AHLs affect gene expression in a time point-specific manner irrespective of changes in binding to DNA throughout SD.
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Affiliation(s)
- Caitlin N Jacques
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Department of Crops and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, 99164, USA
| | - David S Favero
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
| | - Ayako Kawamura
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Biosciences and Biotechnology, Chubu University, Kasugai, Aichi, 487-8501, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biological Sciences, The University of Tokyo, Tokyo, 119-0033, Japan
| | - Michael M Neff
- Department of Crops and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, 99164, USA.
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26
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Blair EJ, Goralogia GS, Lincoln MJ, Imaizumi T, Nagel DH. Clock-Controlled and Cold-Induced CYCLING DOF FACTOR6 Alters Growth and Development in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:919676. [PMID: 35958204 PMCID: PMC9361860 DOI: 10.3389/fpls.2022.919676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
The circadian clock represents a critical regulatory network, which allows plants to anticipate environmental changes as inputs and promote plant survival by regulating various physiological outputs. Here, we examine the function of the clock-regulated transcription factor, CYCLING DOF FACTOR 6 (CDF6), during cold stress in Arabidopsis thaliana. We found that the clock gates CDF6 transcript accumulation in the vasculature during cold stress. CDF6 mis-expression results in an altered flowering phenotype during both ambient and cold stress. A genome-wide transcriptome analysis links CDF6 to genes associated with flowering and seed germination during cold and ambient temperatures, respectively. Analysis of key floral regulators indicates that CDF6 alters flowering during cold stress by repressing photoperiodic flowering components, FLOWERING LOCUS T (FT), CONSTANS (CO), and BROTHER OF FT (BFT). Gene ontology enrichment further suggests that CDF6 regulates circadian and developmental-associated genes. These results provide insights into how the clock-controlled CDF6 modulates plant development during moderate cold stress.
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Affiliation(s)
- Emily J. Blair
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Greg S. Goralogia
- Department of Biology, University of Washington, Seattle, WA, United States
| | - Matthew J. Lincoln
- Department of Biology, University of Washington, Seattle, WA, United States
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA, United States
| | - Dawn H. Nagel
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
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27
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Lee HG, Jeong YY, Lee H, Seo PJ. Arabidopsis HISTONE DEACETYLASE 9 Stimulates Hypocotyl Cell Elongation by Repressing GIGANTEA Expression Under Short Day Photoperiod. FRONTIERS IN PLANT SCIENCE 2022; 13:950378. [PMID: 35923878 PMCID: PMC9341324 DOI: 10.3389/fpls.2022.950378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Developmental plasticity contributes to plant adaptation and fitness in a given condition. Hypocotyl elongation is under the tight control of complex genetic networks encompassing light, circadian, and photoperiod signaling. In this study, we demonstrate that HISTONE DEACETYLASE 9 (HDA9) mediates day length-dependent hypocotyl cell elongation. HDA9 binds to the GIGANTEA (GI) locus involved in photoperiodic hypocotyl elongation. The short day (SD)-accumulated HDA9 protein promotes histone H3 deacetylation at the GI locus during the dark period, promoting hypocotyl elongation. Consistently, HDA9-deficient mutants display reduced hypocotyl length, along with an increase in GI gene expression, only under SD conditions. Taken together, our study reveals the genetic basis of day length-dependent cell elongation in plants.
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Affiliation(s)
- Hong Gil Lee
- Department of Chemistry, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Yeong Yeop Jeong
- Research Institute of Basic Sciences, Seoul National University, Seoul, South Korea
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Hongwoo Lee
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
- Research Institute of Basic Sciences, Seoul National University, Seoul, South Korea
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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28
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Veciana N, Martín G, Leivar P, Monte E. BBX16 mediates the repression of seedling photomorphogenesis downstream of the GUN1/GLK1 module during retrograde signalling. THE NEW PHYTOLOGIST 2022; 234:93-106. [PMID: 35043407 PMCID: PMC9305768 DOI: 10.1111/nph.17975] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/05/2022] [Indexed: 05/03/2023]
Abstract
Plastid-to-nucleus retrograde signalling (RS) initiated by dysfunctional chloroplasts impact photomorphogenic development. We have previously shown that the transcription factor GLK1 acts downstream of the RS regulator GUN1 in photodamaging conditions to regulate not only the well established expression of photosynthesis-associated nuclear genes (PhANGs) but also to regulate seedling morphogenesis. Specifically, the GUN1/GLK1 module inhibits the light-induced phytochrome-interacting factor (PIF)-repressed transcriptional network to suppress cotyledon development when chloroplast integrity is compromised, modulating the area exposed to potentially damaging high light. However, how the GUN1/GLK1 module inhibits photomorphogenesis upon chloroplast damage remained undefined. Here, we report the identification of BBX16 as a novel direct target of GLK1. BBX16 is induced and promotes photomorphogenesis in moderate light and is repressed via GUN1/GLK1 after chloroplast damage. Additionally, we showed that BBX16 represents a regulatory branching point downstream of GUN1/GLK1 in the regulation of PhANG expression and seedling development upon RS activation. The gun1 phenotype in lincomycin and the gun1-like phenotype of GLK1OX are markedly suppressed in gun1bbx16 and GLK1OXbbx16. This study identified BBX16 as the first member of the BBX family involved in RS, and defines a molecular bifurcation mechanism operated by GLK1/BBX16 to optimise seedling de-etiolation, and to ensure photoprotection in unfavourable light conditions.
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Affiliation(s)
- Nil Veciana
- Centre for Research in Agricultural Genomics (CRAG) CSIC‐IRTA‐UAB‐UBCampus UAB, Bellaterra08193BarcelonaSpain
| | - Guiomar Martín
- Centre for Research in Agricultural Genomics (CRAG) CSIC‐IRTA‐UAB‐UBCampus UAB, Bellaterra08193BarcelonaSpain
| | - Pablo Leivar
- Laboratory of BiochemistryInstitut Químic de SarriàUniversitat Ramon Llull08017BarcelonaSpain
| | - Elena Monte
- Centre for Research in Agricultural Genomics (CRAG) CSIC‐IRTA‐UAB‐UBCampus UAB, Bellaterra08193BarcelonaSpain
- Consejo Superior de Investigaciones Científicas (CSIC)08028BarcelonaSpain
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29
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Xu X, Yuan L, Xie Q. The circadian clock ticks in plant stress responses. STRESS BIOLOGY 2022; 2:15. [PMID: 37676516 PMCID: PMC10441891 DOI: 10.1007/s44154-022-00040-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/15/2022] [Indexed: 09/08/2023]
Abstract
The circadian clock, a time-keeping mechanism, drives nearly 24-h self-sustaining rhythms at the physiological, cellular, and molecular levels, keeping them synchronized with the cyclic changes of environmental signals. The plant clock is sensitive to external and internal stress signals that act as timing cues to influence the circadian rhythms through input pathways of the circadian clock system. In order to cope with environmental stresses, many core oscillators are involved in defense while maintaining daily growth in various ways. Recent studies have shown that a hierarchical multi-oscillator network orchestrates the defense through rhythmic accumulation of gene transcripts, alternative splicing of mRNA precursors, modification and turnover of proteins, subcellular localization, stimuli-induced phase separation, and long-distance transport of proteins. This review summarizes the essential role of circadian core oscillators in response to stresses in Arabidopsis thaliana and crops, including daily and seasonal abiotic stresses (low or high temperature, drought, high salinity, and nutrition deficiency) and biotic stresses (pathogens and herbivorous insects). By integrating time-keeping mechanisms, circadian rhythms and stress resistance, we provide a temporal perspective for scientists to better understand plant environmental adaptation and breed high-quality crop germplasm for agricultural production.
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Affiliation(s)
- Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
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30
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Liu R, Gao Y, Fan Z, Guan C, Zhang Q. Effects of different photoperiods on flower opening, flower closing and circadian expression of clock-related genes in Iris domestica and I. dichotoma. JOURNAL OF PLANT RESEARCH 2022; 135:351-360. [PMID: 35157159 DOI: 10.1007/s10265-022-01374-z] [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: 06/26/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
The circadian clock can entrain to forced light-dark cycles by adjusting the phases and periods of flower opening and closing in ephemeral flowers. The responses of circadian rhythms to the same light conditions differ from species. However, the differences in internal genetic mechanisms underlying the different responses between species remain unclear. Iris domestica and I. dichotoma have ephemeral flowers and significantly divergent flower opening and closing times. The effects of different photoperiods (continuous darkness, 4L20D, 8L16D, 12L12D, 16L8D, 20L4D and continuous white light) on flower opening and closing, and expression patterns of seven genes (CRYPTOCHROME 1, PHYTOCHROME B, LATE ELONGATED HYPOCOTYL, PSEUDO RESPONSE REGULATOR 95, PHYTOCHROME INTERACTING FACTOR 4-like, SMUX AUXIN UP RNA 64-like and senescence-associated gene 39-like) involved in the circadian regulation of flower opening and closing were compared between I. domestica and I. dichotoma. Flower opening and closing in the two species exhibited circadian rhythms under continuous darkness (DD), but showed arrhythmia in continuous white light (LL). In the two species, keeping robust rhythms, strong synchronicity, rapid progressions of flower opening and closing and reaching full opening stage required a dark period longer than 4 h. In light-dark cycles with dark periods longer than 4 h, flower opening and closing times of the two species delayed with the delay of dawn, and the degree to which flower opening time varies with the time of dawn was greater in I. dichotoma than in I. domestica. The arrhythmia of flower opening and closing under 20L4D and LL would result from the arrhythmic output signals rather than arrhythmia of oscillators and photoreceptors. The different responses of the two species to the change of photoperiods would be caused by the transcriptional differences of genes in the output pathway of circadian clock system rather than in the input pathway or oscillators.
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Affiliation(s)
- Rong Liu
- Department of Landscape Architecture, Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, China
| | - Yike Gao
- Department of Landscape Architecture, Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, China.
| | - Zhuping Fan
- Department of Landscape Architecture, Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, China
| | - Chunjing Guan
- Department of Landscape Architecture, Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, China
| | - Qixiang Zhang
- Department of Landscape Architecture, Beijing Forestry University, No. 35 Tsinghua East Road, Haidian District, Beijing, China
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31
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Xu H, Chen P, Tao Y. Understanding the Shade Tolerance Responses Through Hints From Phytochrome A-Mediated Negative Feedback Regulation in Shade Avoiding Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:813092. [PMID: 35003197 PMCID: PMC8727698 DOI: 10.3389/fpls.2021.813092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Based on how plants respond to shade, we typically classify them into two groups: shade avoiding and shade tolerance plants. Under vegetative shade, the shade avoiding species induce a series of shade avoidance responses (SARs) to outgrow their competitors, while the shade tolerance species induce shade tolerance responses (STRs) to increase their survival rates under dense canopy. The molecular mechanism underlying the SARs has been extensively studied using the shade avoiding model plant Arabidopsis thaliana, while little is known about STRs. In Aarabidopsis, there is a PHYA-mediated negative feedback regulation that suppresses exaggerated SARs. Recent studies revealed that in shade tolerance Cardamine hirsuta plants, a hyperactive PHYA was responsible for suppressing shade-induced elongation growth. We propose that similar signaling components may be used by shade avoiding and shade tolerance plants, and different phenotypic outputs may result from differential regulation or altered dynamic properties of these signaling components. In this review, we summarized the role of PHYA and its downstream components in shade responses, which may provide insights into understanding how both types of plants respond to shade.
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Affiliation(s)
| | | | - Yi Tao
- Key Laboratory of Xiamen Plant Genetics and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
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32
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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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33
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Yan J, Li S, Kim YJ, Zeng Q, Radziejwoski A, Wang L, Nomura Y, Nakagami H, Somers DE. TOC1 clock protein phosphorylation controls complex formation with NF-YB/C to repress hypocotyl growth. EMBO J 2021; 40:e108684. [PMID: 34726281 DOI: 10.15252/embj.2021108684] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/09/2022] Open
Abstract
Plant photoperiodic growth is coordinated by interactions between circadian clock and light signaling networks. How post-translational modifications of clock proteins affect these interactions to mediate rhythmic growth remains unclear. Here, we identify five phosphorylation sites in the Arabidopsis core clock protein TIMING OF CAB EXPRESSION 1 (TOC1) which when mutated to alanine eliminate detectable phosphorylation. The TOC1 phospho-mutant fails to fully rescue the clock, growth, and flowering phenotypes of the toc1 mutant. Further, the TOC1 phospho-mutant shows advanced phase, a faster degradation rate, reduced interactions with PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) and HISTONE DEACETYLASE 15 (HDA15), and poor binding at pre-dawn hypocotyl growth-related genes (PHGs), leading to a net de-repression of hypocotyl growth. NUCLEAR FACTOR Y subunits B and C (NF-YB/C) stabilize TOC1 at target promoters, and this novel trimeric complex (NF-TOC1) acts as a transcriptional co-repressor with HDA15 to inhibit PIF-mediated hypocotyl elongation. Collectively, we identify a molecular mechanism suggesting how phosphorylation of TOC1 alters its phase, stability, and physical interactions with co-regulators to precisely phase PHG expression to control photoperiodic hypocotyl growth.
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Affiliation(s)
- Jiapei Yan
- Molecular Genetics, Ohio State University, Columbus, OH, USA
| | - Shibai Li
- Molecular Genetics, Ohio State University, Columbus, OH, USA.,Memorial Sloan Kettering Cancer Center, Molecular Biology Program, New York, NY, USA
| | - Yeon Jeong Kim
- Molecular Genetics, Ohio State University, Columbus, OH, USA
| | - Qingning Zeng
- Molecular Genetics, Ohio State University, Columbus, OH, USA
| | | | - Lei Wang
- Molecular Genetics, Ohio State University, Columbus, OH, USA.,The Chinese Academy of Sciences, Institute of Botany, Beijing, China
| | - Yuko Nomura
- RIKEN Center for Sustainable Resource Science (CSRS), Plant Proteomics Research Unit, Yokohama, Japan
| | - Hirofumi Nakagami
- RIKEN Center for Sustainable Resource Science (CSRS), Plant Proteomics Research Unit, Yokohama, Japan.,Max Planck Institute for Plant Breeding Research, Protein Mass Spectrometry, Cologne, Germany
| | - David E Somers
- Molecular Genetics, Ohio State University, Columbus, OH, USA.,POSTECH, Division of Integrative Biosciences and Biotechnology, Pohang, South Korea
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Viana AJC, Matiolli CC, Newman DW, Vieira JGP, Duarte GT, Martins MCM, Gilbault E, Hotta CT, Caldana C, Vincentz M. The sugar-responsive circadian clock regulator bZIP63 modulates plant growth. THE NEW PHYTOLOGIST 2021; 231:1875-1889. [PMID: 34053087 PMCID: PMC9292441 DOI: 10.1111/nph.17518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/18/2021] [Indexed: 05/02/2023]
Abstract
Adjustment to energy starvation is crucial to ensure growth and survival. In Arabidopsis thaliana (Arabidopsis), this process relies in part on the phosphorylation of the circadian clock regulator bZIP63 by SUCROSE non-fermenting RELATED KINASE1 (SnRK1), a key mediator of responses to low energy. We investigated the effects of mutations in bZIP63 on plant carbon (C) metabolism and growth. Results from phenotypic, transcriptomic and metabolomic analysis of bZIP63 mutants prompted us to investigate the starch accumulation pattern and the expression of genes involved in starch degradation and in the circadian oscillator. bZIP63 mutation impairs growth under light-dark cycles, but not under constant light. The reduced growth likely results from the accentuated C depletion towards the end of the night, which is caused by the accelerated starch degradation of bZIP63 mutants. The diel expression pattern of bZIP63 is dictated by both the circadian clock and energy levels, which could determine the changes in the circadian expression of clock and starch metabolic genes observed in bZIP63 mutants. We conclude that bZIP63 composes a regulatory interface between the metabolic and circadian control of starch breakdown to optimize C usage and plant growth.
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Affiliation(s)
- Américo J. C. Viana
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
| | - Cleverson C. Matiolli
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
| | - David W. Newman
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
| | - João G. P. Vieira
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
| | - Gustavo T. Duarte
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
| | - Marina C. M. Martins
- Brazilian Bioethanol Science and Technology Laboratory (CTBE/CNPEM)Rua Giuseppe Máximo Scolfaro 10000CampinasSPCEP 13083‐970Brazil
- Max‐Planck Partner GroupBrazilian Bioethanol Science and Technology Laboratory (CTBE/CNPEM)Campinas, SPBrazil
- Laboratory of Plant Physiological EcologyDepartment of BotanyInstitute of BiosciencesUniversity of São PauloSão Paulo, SPCEP 05508‐090Brazil
| | - Elodie Gilbault
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersailles78000France
| | - Carlos T. Hotta
- Departamento de BioquímicaInstituto de QuímicaUniversidade de São PauloSão Paulo, SPCEP 05508‐000Brazil
| | - Camila Caldana
- Brazilian Bioethanol Science and Technology Laboratory (CTBE/CNPEM)Rua Giuseppe Máximo Scolfaro 10000CampinasSPCEP 13083‐970Brazil
- Max‐Planck Partner GroupBrazilian Bioethanol Science and Technology Laboratory (CTBE/CNPEM)Campinas, SPBrazil
- Max Planck Institute of Molecular Plant PhysiologyAm Mühlenberg 114476 PotsdamGolmGermany
| | - Michel Vincentz
- Centro de Biologia Molecular e Engenharia GenéticaDepartamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de CampinasCEP 13083‐875, CP 6010CampinasSPBrazil
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Yuan L, Yu Y, Liu M, Song Y, Li H, Sun J, Wang Q, Xie Q, Wang L, Xu X. BBX19 fine-tunes the circadian rhythm by interacting with PSEUDO-RESPONSE REGULATOR proteins to facilitate their repressive effect on morning-phased clock genes. THE PLANT CELL 2021; 33:2602-2617. [PMID: 34164694 PMCID: PMC8408442 DOI: 10.1093/plcell/koab133] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/11/2021] [Indexed: 05/19/2023]
Abstract
The core plant circadian oscillator is composed of multiple interlocked transcriptional-translational feedback loops, which synchronize endogenous diel physiological rhythms to the cyclic changes of environmental cues. PSEUDO-RESPONSE REGULATORS (PRRs) have been identified as negative components in the circadian clock, though their underlying molecular mechanisms remain largely unknown. Here, we found that a subfamily of zinc finger transcription factors, B-box (BBX)-containing proteins, have a critical role in fine-tuning circadian rhythm. We demonstrated that overexpressing Arabidopsis thaliana BBX19 and BBX18 significantly lengthened the circadian period, while the null mutation of BBX19 accelerated the circadian speed. Moreover, BBX19 and BBX18, which are expressed during the day, physically interacted with PRR9, PRR7, and PRR5 in the nucleus in precise temporal ordering from dawn to dusk, consistent with the respective protein accumulation pattern of PRRs. Our transcriptomic and genetic analysis indicated that BBX19 and PRR9, PRR7, and PRR5 cooperatively inhibited the expression of morning-phased clock genes. PRR proteins affected BBX19 recruitment to the CCA1, LHY, and RVE8 promoters. Collectively, our findings show that BBX19 interacts with PRRs to orchestrate circadian rhythms, and suggest the indispensable role of transcriptional regulators in fine-tuning the circadian clock.
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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
| | - Yingjun Yu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingming Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yang Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Hongmin Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Junqiu Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Qiao Wang
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Authors for correspondence: (X.X.), (L.W.), (Q.X.)
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Authors for correspondence: (X.X.), (L.W.), (Q.X.)
| | - Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Authors for correspondence: (X.X.), (L.W.), (Q.X.)
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36
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Phytochrome A elevates plant circadian-clock components to suppress shade avoidance in deep-canopy shade. Proc Natl Acad Sci U S A 2021; 118:2108176118. [PMID: 34187900 DOI: 10.1073/pnas.2108176118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Shade-avoiding plants can detect the presence of neighboring vegetation and evoke escape responses before canopy cover limits photosynthesis. Rapid stem elongation facilitates light foraging and enables plants to overtop competitors. A major regulator of this response is the phytochrome B photoreceptor, which becomes inactivated in light environments with a low ratio of red to far-red light (low R:FR), characteristic of vegetational shade. Although shade avoidance can provide plants with a competitive advantage in fast-growing stands, excessive stem elongation can be detrimental to plant survival. As such, plants have evolved multiple feedback mechanisms to attenuate shade-avoidance signaling. The very low R:FR and reduced levels of photosynthetically active radiation (PAR) present in deep canopy shade can, together, trigger phytochrome A (phyA) signaling, inhibiting shade avoidance and promoting plant survival when resources are severely limited. The molecular mechanisms underlying this response have not been fully elucidated. Here, we show that Arabidopsis thaliana phyA elevates early-evening expression of the central circadian-clock components TIMING OF CAB EXPRESSION 1 (TOC1), PSEUDO RESPONSE REGULATOR 7 (PRR7), EARLY FLOWERING 3 (ELF3), and ELF4 in photocycles of low R:FR and low PAR. These collectively suppress stem elongation, antagonizing shade avoidance in deep canopy shade.
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37
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Balcerowicz M, Mahjoub M, Nguyen D, Lan H, Stoeckle D, Conde S, Jaeger KE, Wigge PA, Ezer D. An early-morning gene network controlled by phytochromes and cryptochromes regulates photomorphogenesis pathways in Arabidopsis. MOLECULAR PLANT 2021; 14:983-996. [PMID: 33766657 DOI: 10.1016/j.molp.2021.03.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/04/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Light perception at dawn plays a key role in coordinating multiple molecular processes and in entraining the plant circadian clock. The Arabidopsis mutant lacking the main photoreceptors, however, still shows clock entrainment, indicating that the integration of light into the morning transcriptome is not well understood. In this study, we performed a high-resolution RNA-sequencing time-series experiment, sampling every 2 min beginning at dawn. In parallel experiments, we perturbed temperature, the circadian clock, photoreceptor signaling, and chloroplast-derived light signaling. We used these data to infer a gene network that describes the gene expression dynamics after light stimulus in the morning, and then validated key edges. By sampling time points at high density, we are able to identify three light- and temperature-sensitive bursts of transcription factor activity, one of which lasts for only about 8 min. Phytochrome and cryptochrome mutants cause a delay in the transcriptional bursts at dawn, and completely remove a burst of expression in key photomorphogenesis genes (HY5 and BBX family). Our complete network is available online (http://www-users.york.ac.uk/∼de656/dawnBurst/dawnBurst.html). Taken together, our results show that phytochrome and cryptochrome signaling is required for fine-tuning the dawn transcriptional response to light, but separate pathways can robustly activate much of the program in their absence.
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Affiliation(s)
| | - Mahiar Mahjoub
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Duy Nguyen
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Hui Lan
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | | | - Susana Conde
- Department of Statistics, University of Warwick, Coventry, UK; Alan Turing Institute, London, UK
| | - Katja E Jaeger
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany
| | - Philip A Wigge
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany; Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Daphne Ezer
- Alan Turing Institute, London, UK; Department of Biology, University of York, York YO10 5DD, UK.
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38
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Coordinative regulation of plants growth and development by light and circadian clock. ABIOTECH 2021; 2:176-189. [PMID: 36304756 PMCID: PMC9590570 DOI: 10.1007/s42994-021-00041-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/13/2021] [Indexed: 11/30/2022]
Abstract
The circadian clock, known as an endogenous timekeeping system, can integrate various cues to regulate plant physiological functions for adapting to the changing environment and thus ensure optimal plant growth. The synchronization of internal clock with external environmental information needs a process termed entrainment, and light is one of the predominant entraining signals for the plant circadian clock. Photoreceptors can detect and transmit light information to the clock core oscillator through transcriptional or post-transcriptional interactions with core-clock components to sustain circadian rhythms and regulate a myriad of downstream responses, including photomorphogenesis and photoperiodic flowering which are key links in the process of growth and development. Here we summarize the current understanding of the molecular network of the circadian clock and how light information is integrated into the circadian system, especially focus on how the circadian clock and light signals coordinately regulate the common downstream outputs. We discuss the functions of the clock and light signals in regulating photoperiodic flowering among various crop species.
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39
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Tian W, Wang R, Bo C, Yu Y, Zhang Y, Shin GI, Kim WY, Wang L. SDC mediates DNA methylation-controlled clock pace by interacting with ZTL in Arabidopsis. Nucleic Acids Res 2021; 49:3764-3780. [PMID: 33675668 PMCID: PMC8053106 DOI: 10.1093/nar/gkab128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 12/29/2022] Open
Abstract
Molecular bases of eukaryotic circadian clocks mainly rely on transcriptional-translational feedback loops (TTFLs), while epigenetic codes also play critical roles in fine-tuning circadian rhythms. However, unlike histone modification codes that play extensive and well-known roles in the regulation of circadian clocks, whether DNA methylation (5mC) can affect the circadian clock, and the associated underlying molecular mechanisms, remains largely unexplored in many organisms. Here we demonstrate that global genome DNA hypomethylation can significantly lengthen the circadian period of Arabidopsis. Transcriptomic and genetic evidence demonstrate that SUPPRESSOR OF drm1 drm2 cmt3 (SDC), encoding an F-box containing protein, is required for the DNA hypomethylation-tuned circadian clock. Moreover, SDC can physically interact with another F-box containing protein ZEITLUPE (ZTL) to diminish its accumulation. Genetic analysis further revealed that ZTL and its substrate TIMING OF CAB EXPRESSION 1 (TOC1) likely act downstream of DNA methyltransferases to control circadian rhythm. Together, our findings support the notion that DNA methylation is important to maintain proper circadian pace in Arabidopsis, and further established that SDC links DNA hypomethylation with a proteolytic cascade to assist in tuning the circadian clock.
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Affiliation(s)
- Wenwen Tian
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Ruyi Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Cunpei Bo
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yingjun Yu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuanyuan Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21Plus), Research Institute of Life Sciences (RILS) and Institute of Agricultural and Life Science(IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), Research Institute of Life Sciences (RILS) and Institute of Agricultural and Life Science(IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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40
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Singh RK, Bhalerao RP, Eriksson ME. Growing in time: exploring the molecular mechanisms of tree growth. TREE PHYSIOLOGY 2021; 41:657-678. [PMID: 32470114 PMCID: PMC8033248 DOI: 10.1093/treephys/tpaa065] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/31/2020] [Accepted: 05/27/2020] [Indexed: 05/31/2023]
Abstract
Trees cover vast areas of the Earth's landmasses. They mitigate erosion, capture carbon dioxide, produce oxygen and support biodiversity, and also are a source of food, raw materials and energy for human populations. Understanding the growth cycles of trees is fundamental for many areas of research. Trees, like most other organisms, have evolved a circadian clock to synchronize their growth and development with the daily and seasonal cycles of the environment. These regular changes in light, daylength and temperature are perceived via a range of dedicated receptors and cause resetting of the circadian clock to local time. This allows anticipation of daily and seasonal fluctuations and enables trees to co-ordinate their metabolism and physiology to ensure vital processes occur at the optimal times. In this review, we explore the current state of knowledge concerning the regulation of growth and seasonal dormancy in trees, using information drawn from model systems such as Populus spp.
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Affiliation(s)
- Rajesh Kumar Singh
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå SE-901 87, Sweden
| | - Rishikesh P Bhalerao
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå SE-901 82, Sweden
| | - Maria E Eriksson
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå SE-901 87, Sweden
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41
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Li W, Liu Y, Wang W, Liu J, Yao M, Guan M, Guan C, He X. Phytochrome-interacting factor (PIF) in rapeseed (Brassica napus L.): Genome-wide identification, evolution and expression analyses during abiotic stress, light quality and vernalization. Int J Biol Macromol 2021; 180:14-27. [PMID: 33722620 DOI: 10.1016/j.ijbiomac.2021.03.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 03/07/2021] [Accepted: 03/10/2021] [Indexed: 10/21/2022]
Abstract
Phytochrome-interacting factors (PIFs) are members of basic helix-loop-helix (bHLH) transcription factors and the primary partners of phytochromes (PHY) in light signaling. PIFs interact with the Pfr forms of phytochrome to play an important role in the pathways of response to light and temperature in plants. In this study, 30, 12, and 16 potential PIF genes were identified in Brassica napus, Brassica rapa, Brassica oleracea, respectively, which could be divided into three subgroups. The Br/Bo/BnaPIF genes are intron-rich and similar to the PIF genes in Arabidopsis. However, unlike the AtPIFs that exist in multiple alternative-splicing forms, the majority of Br/Bo/BnaPIF genes have no alternative-splicing forms. A total of 52 Br/Bo/BnaPIF proteins have both the conserved active PHYB binding (APB) and bHLH domains. The Ka/Ks ratio revealed that most BnaPIFs underwent purifying selection. A promoter analysis found that light-related, abscisic acid-related and MYB-binding sites were the most abundant in the promoters of BnaPIFs. BnaPIF genes displayed different spatiotemporal patterns of expression and were regulated by light quality, circadian rhythms, cold, heat, and vernalization. Our results are useful for understanding the biological functions of PIF proteins in rapeseed.
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Affiliation(s)
- Wenqian Li
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Yan Liu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Weiping Wang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Juncen Liu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Mingyao Yao
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Mei Guan
- Oil Crops Research, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan 410128, China
| | - Chunyun Guan
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China; Oil Crops Research, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan 410128, China
| | - Xin He
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China; Oil Crops Research, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan 410128, China.
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42
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Rovira A, Sentandreu M, Nagatani A, Leivar P, Monte E. The Sequential Action of MIDA9/PP2C.D1, PP2C.D2, and PP2C.D5 Is Necessary to Form and Maintain the Hook After Germination in the Dark. FRONTIERS IN PLANT SCIENCE 2021; 12:636098. [PMID: 33767720 PMCID: PMC7985339 DOI: 10.3389/fpls.2021.636098] [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: 11/30/2020] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
During seedling etiolation after germination in the dark, seedlings have closed cotyledons and form an apical hook to protect the meristem as they break through the soil to reach the surface. Once in contact with light, the hook opens and cotyledons are oriented upward and separate. Hook development in the dark after seedling emergence from the seed follows three distinctly timed and sequential phases: formation, maintenance, and eventual opening. We previously identified MISREGULATED IN DARK9 (MIDA9) as a phytochrome interacting factor (PIF)-repressed gene in the dark necessary for hook development during etiolated growth. MIDA9 encodes the type 2C phosphatase PP2C.D1, and pp2c-d1/mida9 mutants exhibit open hooks in the dark. Recent evidence has described that PP2C.D1 and other PP2C.D members negatively regulate SMALL AUXIN UP RNA (SAUR)-mediated cell elongation. However, the fundamental question of the timing of PP2C.D1 action (and possibly other members of the PP2C.D family) during hook development remains to be addressed. Here, we show that PP2C.D1 is required immediately after germination to form the hook. pp2c.d1/mida9 shows reduced cell expansion in the outer layer of the hook and, therefore, does not establish the differential cell growth necessary for hook formation, indicating that PP2C.D1 is necessary to promote cell elongation during this early stage. Additionally, genetic analyses of single and high order mutants in PP2C.D1, PP2C.D2, and PP2C.D5 demonstrate that the three PP2C.Ds act collectively and sequentially during etiolation: whereas PP2C.D1 dominates hook formation, PP2C.D2 is necessary during the maintenance phase, and PP2C.D5 acts to prevent opening during the third phase together with PP2C.D1 and PP2C.D2. Finally, we uncover a possible connection of PP2C.D1 levels with ethylene physiology, which could help optimize hook formation during post-germinative growth in the dark.
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Affiliation(s)
- Arnau Rovira
- Plant Development and Signal Transduction Program, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Maria Sentandreu
- Plant Development and Signal Transduction Program, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Akira Nagatani
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Pablo Leivar
- Plant Development and Signal Transduction Program, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain
| | - Elena Monte
- Plant Development and Signal Transduction Program, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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43
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van Hoogdalem M, Shapulatov U, Sergeeva L, Busscher-Lange J, Schreuder M, Jamar D, van der Krol AR. A temperature regime that disrupts clock-controlled starch mobilization induces transient carbohydrate starvation, resulting in compact growth. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab075. [PMID: 33617638 DOI: 10.1093/jxb/erab075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Indexed: 06/12/2023]
Abstract
In nature plants are usually subjected to a light/temperature regime of warm day and cold night (referred to as +DIF). Compared to growth under +DIF, Arabidopsis plants show compact growth under the same photoperiod, but with an inverse temperature regime (cold day and warm night: -DIF). Here we show that -DIF differentially affects the phase and amplitude of core clock gene expression. Under -DIF the phase of the morning clock gene CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) is delayed, similar to that of plants grown on low sucrose. Indeed, under -DIF carbohydrate (CHO) starvation marker genes are specifically upregulated at the End of the Night (EN) in Arabidopsis rosettes. However, only in inner-rosette tissue (small sink leaves and petioles of older leaves) sucrose levels are lower under -DIF compared to under +DIF, suggesting that sucrose in source leaf blades is not sensed for CHO status and that sucrose transport from source to sink may be impaired at EN. CHO-starvation under -DIF correlated with increased starch breakdown during the night and decreased starch accumulation during the day. Moreover, we demonstrate that different ways of inducing CHO-starvation all link to reduced growth of sink leaves. Practical implications for control of plant growth in horticulture are discussed.
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Affiliation(s)
- Mark van Hoogdalem
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg, Wageningen, The Netherlands
- Current Business Unit Greenhouse Horticulture, Wageningen University & Research, Droevendaalsesteeg, Wageningen, The Netherlands
| | - Umidjon Shapulatov
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg, Wageningen, The Netherlands
- Current Department of Botany and Plant Physiology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Lidiya Sergeeva
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg, Wageningen, The Netherlands
| | - Jacqueline Busscher-Lange
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg, Wageningen, The Netherlands
- Business Unit Bioscience, Wageningen Plant Research, Droevendaalsesteeg, Wageningen, The Netherlands
| | - Mariëlle Schreuder
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg, Wageningen, The Netherlands
| | - Diaan Jamar
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg, Wageningen, The Netherlands
| | - Alexander R van der Krol
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg, Wageningen, The Netherlands
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Ke Q, Tao W, Li T, Pan W, Chen X, Wu X, Nie X, Cui L. Genome-wide Identification, Evolution and Expression Analysis of Basic Helix-loop-helix (bHLH) Gene Family in Barley ( Hordeum vulgare L.). Curr Genomics 2021; 21:621-644. [PMID: 33414683 PMCID: PMC7770637 DOI: 10.2174/1389202921999201102165537] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/17/2020] [Accepted: 10/05/2020] [Indexed: 11/22/2022] Open
Abstract
Background The basic helix-loop-helix (bHLH) transcription factor is one of the most important gene families in plants, playing a key role in diverse metabolic, physiological, and developmental processes. Although it has been well characterized in many plants, the significance of the bHLH family in barley is not well understood at present. Methods Through a genome-wide search against the updated barley reference genome, the genomic organization, evolution and expression of the bHLH family in barley were systematically analyzed. Results We identified 141 bHLHs in the barley genome (HvbHLHs) and further classified them into 24 subfamilies based on phylogenetic analysis. It was found that HvbHLHs in the same subfamily shared a similar conserved motif composition and exon-intron structures. Chromosome distribution and gene duplication analysis revealed that segmental duplication mainly contributed to the expansion of HvbHLHs and the duplicated genes were subjected to strong purifying selection. Furthermore, expression analysis revealed that HvbHLHs were widely expressed in different tissues and also involved in response to diverse abiotic stresses. The co-expression network was further analyzed to underpin the regulatory function of HvbHLHs. Finally, 25 genes were selected for qRT-PCR validation, the expression profiles of HvbHLHs showed diverse patterns, demonstrating their potential roles in relation to stress tolerance regulation. Conclusion This study reported the genome organization, evolutionary characteristics and expression profile of the bHLH family in barley, which not only provide the targets for further functional analysis, but also facilitate better understanding of the regulatory network bHLH genes involved in stress tolerance in barley.
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Affiliation(s)
- Qinglin Ke
- 1College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang330045, Jiangxi, China; 2State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wenjing Tao
- 1College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang330045, Jiangxi, China; 2State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Tingting Li
- 1College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang330045, Jiangxi, China; 2State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wenqiu Pan
- 1College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang330045, Jiangxi, China; 2State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiaoyun Chen
- 1College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang330045, Jiangxi, China; 2State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiaoyu Wu
- 1College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang330045, Jiangxi, China; 2State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiaojun Nie
- 1College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang330045, Jiangxi, China; 2State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Licao Cui
- 1College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang330045, Jiangxi, China; 2State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
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Favero DS, Lambolez A, Sugimoto K. Molecular pathways regulating elongation of aerial plant organs: a focus on light, the circadian clock, and temperature. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:392-420. [PMID: 32986276 DOI: 10.1111/tpj.14996] [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: 07/16/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Organs such as hypocotyls and petioles rapidly elongate in response to shade and temperature cues, contributing to adaptive responses that improve plant fitness. Growth plasticity in these organs is achieved through a complex network of molecular signals. Besides conveying information from the environment, this signaling network also transduces internal signals, such as those associated with the circadian clock. A number of studies performed in Arabidopsis hypocotyls, and to a lesser degree in petioles, have been informative for understanding the signaling networks that regulate elongation of aerial plant organs. In particular, substantial progress has been made towards understanding the molecular mechanisms that regulate responses to light, the circadian clock, and temperature. Signals derived from these three stimuli converge on the BAP module, a set of three different types of transcription factors that interdependently promote gene transcription and growth. Additional key positive regulators of growth that are also affected by environmental cues include the CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and SUPPRESSOR OF PHYA-105 (SPA) E3 ubiquitin ligase proteins. In this review we summarize the key signaling pathways that regulate the growth of hypocotyls and petioles, focusing specifically on molecular mechanisms important for transducing signals derived from light, the circadian clock, and temperature. While it is clear that similarities abound between the signaling networks at play in these two organs, there are also important differences between the mechanisms regulating growth in hypocotyls and petioles.
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Affiliation(s)
- David S Favero
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Alice Lambolez
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biological Sciences, The University of Tokyo, Tokyo, 119-0033, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biological Sciences, The University of Tokyo, Tokyo, 119-0033, Japan
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Osnato M, Cota I, Nebhnani P, Cereijo U, Pelaz S. Photoperiod Control of Plant Growth: Flowering Time Genes Beyond Flowering. FRONTIERS IN PLANT SCIENCE 2021; 12:805635. [PMID: 35222453 PMCID: PMC8864088 DOI: 10.3389/fpls.2021.805635] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/23/2021] [Indexed: 05/02/2023]
Abstract
Fluctuations in environmental conditions greatly influence life on earth. Plants, as sessile organisms, have developed molecular mechanisms to adapt their development to changes in daylength, or photoperiod. One of the first plant features that comes to mind as affected by the duration of the day is flowering time; we all bring up a clear image of spring blossom. However, for many plants flowering happens at other times of the year, and many other developmental aspects are also affected by changes in daylength, which range from hypocotyl elongation in Arabidopsis thaliana to tuberization in potato or autumn growth cessation in trees. Strikingly, many of the processes affected by photoperiod employ similar gene networks to respond to changes in the length of light/dark cycles. In this review, we have focused on developmental processes affected by photoperiod that share similar genes and gene regulatory networks.
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Affiliation(s)
- Michela Osnato
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institute of Environmental Science and Technology of the Universitat Autònoma de Barcelona, Barcelona, Spain
- *Correspondence: Michela Osnato,
| | - Ignacio Cota
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Poonam Nebhnani
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Unai Cereijo
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Soraya Pelaz
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Soraya Pelaz,
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47
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Kahle N, Sheerin DJ, Fischbach P, Koch LA, Schwenk P, Lambert D, Rodriguez R, Kerner K, Hoecker U, Zurbriggen MD, Hiltbrunner A. COLD REGULATED 27 and 28 are targets of CONSTITUTIVELY PHOTOMORPHOGENIC 1 and negatively affect phytochrome B signalling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1038-1053. [PMID: 32890447 DOI: 10.1111/tpj.14979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 05/23/2023]
Abstract
Phytochromes are red/far-red light receptors in plants involved in the regulation of growth and development. Phytochromes can sense the light environment and contribute to measuring day length; thereby, they allow plants to respond and adapt to changes in the ambient environment. Two well-characterized signalling pathways act downstream of phytochromes and link light perception to the regulation of gene expression. The CONSTITUTIVELY PHOTOMORPHOGENIC 1/SUPPRESSOR OF PHYA-105 (COP1/SPA) E3 ubiquitin ligase complex and the PHYTOCHROME INTERACTING FACTORs (PIFs) are key components of these pathways and repress light responses in the dark. In light-grown seedlings, phytochromes inhibit COP1/SPA and PIF activity and thereby promote light signalling. In a yeast-two-hybrid screen for proteins binding to light-activated phytochromes, we identified COLD-REGULATED GENE 27 (COR27). COR27 and its homologue COR28 bind to phyA and phyB, the two primary phytochromes in seed plants. COR27 and COR28 have been described previously with regard to a function in the regulation of freezing tolerance, flowering and the circadian clock. Here, we show that COR27 and COR28 repress early seedling development in blue, far-red and in particular red light. COR27 and COR28 contain a conserved Val-Pro (VP)-peptide motif, which mediates binding to the COP1/SPA complex. COR27 and COR28 are targeted for degradation by COP1/SPA and mutant versions with a VP to AA amino acid substitution in the VP-peptide motif are stabilized. Overall, our data suggest that COR27 and COR28 accumulate in light but act as negative regulators of light signalling during early seedling development, thereby preventing an exaggerated response to light.
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Affiliation(s)
- Nikolai Kahle
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - David J Sheerin
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Patrick Fischbach
- Institute of Synthetic Biology and CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Leonie-Alexa Koch
- Institute of Synthetic Biology and CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Philipp Schwenk
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, 79104, Germany
| | - Dorothee Lambert
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Ryan Rodriguez
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Konstantin Kerner
- Institute for Plant Sciences, University of Cologne, Cologne, 50674, Germany
| | - Ute Hoecker
- Institute for Plant Sciences, University of Cologne, Cologne, 50674, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
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The Transcriptional Network in the Arabidopsis Circadian Clock System. Genes (Basel) 2020; 11:genes11111284. [PMID: 33138078 PMCID: PMC7692566 DOI: 10.3390/genes11111284] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 12/18/2022] Open
Abstract
The circadian clock is the biological timekeeping system that governs the approximately 24-h rhythms of genetic, metabolic, physiological and behavioral processes in most organisms. This oscillation allows organisms to anticipate and adapt to day–night changes in the environment. Molecular studies have indicated that a transcription–translation feedback loop (TTFL), consisting of transcriptional repressors and activators, is essential for clock function in Arabidopsis thaliana (Arabidopsis). Omics studies using next-generation sequencers have further revealed that transcription factors in the TTFL directly regulate key genes implicated in clock-output pathways. In this review, the target genes of the Arabidopsis clock-associated transcription factors are summarized. The Arabidopsis clock transcriptional network is partly conserved among angiosperms. In addition, the clock-dependent transcriptional network structure is discussed in the context of plant behaviors for adapting to day–night cycles.
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Bursch K, Toledo-Ortiz G, Pireyre M, Lohr M, Braatz C, Johansson H. Identification of BBX proteins as rate-limiting cofactors of HY5. NATURE PLANTS 2020; 6:921-928. [PMID: 32661279 DOI: 10.1038/s41477-020-0725-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 06/11/2020] [Indexed: 05/04/2023]
Abstract
As a source of both energy and environmental information, monitoring of incoming light is crucial for plants to optimize growth throughout development1. Concordantly, the light signalling pathways in plants are highly integrated with numerous other regulatory pathways2,3. One of these signal integrators is the basic leucine zipper domain (bZIP) transcription factor LONG HYPOCOTYL 5 (HY5), which has a key role as a positive regulator of light signalling in plants4,5. Although HY5 is thought to act as a DNA-binding transcriptional regulator6,7, the lack of any apparent transactivation domain8 makes it unclear how HY5 is able to accomplish its many functions. Here we describe the identification of three B-box containing proteins (BBX20, BBX21 and BBX22) as essential partners for HY5-dependent modulation of hypocotyl elongation, anthocyanin accumulation and transcriptional regulation. The bbx20 bbx21 bbx22 (bbx202122) triple mutant mimics the phenotypes of hy5 in the light and its ability to suppress the cop1 mutant phenotype in darkness. Furthermore, 84% of genes that exhibit differential expression in bbx202122 are also regulated by HY5, and we provide evidence that HY5 requires the B-box proteins for transcriptional regulation. Finally, expression of a truncated dark-stable version of HY5 (HY5(ΔN77)) together with BBX21 mutated in its VP motif strongly promoted de-etiolation in dark-grown seedlings, demonstrating the functional interdependence of these factors. In sum, this work clarifies long-standing questions regarding HY5 action and provides an example of how a master regulator might gain both specificity and dynamicity through the obligate dependence of cofactors.
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Affiliation(s)
- Katharina Bursch
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Berlin, Germany
| | | | - Marie Pireyre
- Department of Botany and Plant Biology, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Miriam Lohr
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Berlin, Germany
| | - Cordula Braatz
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Berlin, Germany
| | - Henrik Johansson
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Berlin, Germany.
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50
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Martín G, Veciana N, Boix M, Rovira A, Henriques R, Monte E. The photoperiodic response of hypocotyl elongation involves regulation of CDF1 and CDF5 activity. PHYSIOLOGIA PLANTARUM 2020; 169:480-490. [PMID: 32379360 DOI: 10.1111/ppl.13119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/23/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
Hypocotyl elongation relies on directional cell expansion, a process under light and circadian clock control. Under short photoperiods (SD), hypocotyl elongation in Arabidopsis thaliana follows a rhythmic pattern, a process in which circadian morning-to-midnight waves of the transcriptional repressors PSEUDO-RESPONSE REGULATORS (PRRs) jointly gate PHYTOCHROME-INTERACTING FACTOR (PIF) activity to dawn. Previously, we described CYCLING DOF FACTOR 5 (CDF5) as a target of this antagonistic PRR/PIF dynamic interplay. Under SD, PIFs induce CDF5 accumulation specifically at dawn, when it promotes the expression of positive cell elongation regulators such as YUCCA8 to induce growth. In contrast to SD, hypocotyl elongation under long days (LD) is largely reduced. Here, we examine whether CDF5 is an actor in this photoperiod specific regulation. We report that transcription of CDF5 is robustly induced in SD compared to LD, in accordance with PIFs accumulating to higher levels in SD, and in contrast to other members of the CDF family, whose expression is mainly clock regulated and have similar waveforms in SD and LD. Notably, when CDF5 was constitutively expressed under LD, CDF5 protein accumulated to levels comparable to SD but was inactive in promoting cell elongation. Similar results were observed for CDF1. Our findings indicate that both CDFs can promote cell elongation specifically in shorter photoperiods, however, their activity in LD is inhibited at the post-translational level. These data not only expand our understanding of the biological role of CDF transcription factors, but also identify a previously unrecognized regulatory layer in the photoperiodic response of hypocotyl elongation.
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Affiliation(s)
- Guiomar Martín
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
- Instituto Gulbenkian de Ciência (IGC), Oeiras, 2780-156, Portugal
| | - Nil Veciana
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
| | - Marc Boix
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
| | - Arnau Rovira
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
| | - Rossana Henriques
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, T23 TK30, Ireland
- Environmental Research Institute, University College Cork, Cork, T23 XE10, Ireland
| | - Elena Monte
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08028, Spain
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