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James AB, Sharples C, Laird J, Armstrong EM, Guo W, Tzioutziou N, Zhang R, Brown JWS, Nimmo HG, Jones MA. REVEILLE2 thermosensitive splicing: a molecular basis for the integration of nocturnal temperature information by the Arabidopsis circadian clock. THE NEW PHYTOLOGIST 2024; 241:283-297. [PMID: 37897048 DOI: 10.1111/nph.19339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023]
Abstract
Cold stress is one of the major environmental factors that limit growth and yield of plants. However, it is still not fully understood how plants account for daily temperature fluctuations, nor how these temperature changes are integrated with other regulatory systems such as the circadian clock. We demonstrate that REVEILLE2 undergoes alternative splicing after chilling that increases accumulation of a transcript isoform encoding a MYB-like transcription factor. We explore the biological function of REVEILLE2 in Arabidopsis thaliana using a combination of molecular genetics, transcriptomics, and physiology. Disruption of REVEILLE2 alternative splicing alters regulatory gene expression, impairs circadian timing, and improves photosynthetic capacity. Changes in nuclear gene expression are particularly apparent in the initial hours following chilling, with chloroplast gene expression subsequently upregulated. The response of REVEILLE2 to chilling extends our understanding of plants immediate response to cooling. We propose that the circadian component REVEILLE2 restricts plants responses to nocturnal reductions in temperature, thereby enabling appropriate responses to daily environmental changes.
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Affiliation(s)
- Allan B James
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Chantal Sharples
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany
| | - Janet Laird
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Emily May Armstrong
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Wenbin Guo
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Nikoleta Tzioutziou
- Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee, DD2 5DA, UK
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - John W S Brown
- Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee, DD2 5DA, UK
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Hugh G Nimmo
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Matthew A Jones
- School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ, UK
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2
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Kidokoro S, Konoura I, Soma F, Suzuki T, Miyakawa T, Tanokura M, Shinozaki K, Yamaguchi-Shinozaki K. Clock-regulated coactivators selectively control gene expression in response to different temperature stress conditions in Arabidopsis. Proc Natl Acad Sci U S A 2023; 120:e2216183120. [PMID: 37036986 PMCID: PMC10120023 DOI: 10.1073/pnas.2216183120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/12/2023] [Indexed: 04/12/2023] Open
Abstract
Plants respond to severe temperature changes by inducing the expression of numerous genes whose products enhance stress tolerance and responses. Dehydration-responsive element (DRE)-binding protein 1/C-repeat binding factor (DREB1/CBF) transcription factors act as master switches in cold-inducible gene expression. Since DREB1 genes are rapidly and strongly induced by cold stress, the elucidation of the molecular mechanisms of DREB1 expression is vital for the recognition of the initial responses to cold stress in plants. A previous study indicated that the circadian clock-related MYB-like transcription factors REVEILLE4/LHY-CCA1-Like1 (RVE4/LCL1) and RVE8/LCL5 directly activate DREB1 expression under cold stress conditions. These RVEs function in the regulation of circadian clock-related gene expression under normal temperature conditions. They also activate the expression of HSF-independent heat-inducible genes under high-temperature conditions. Thus, there are thought to be specific regulatory mechanisms whereby the target genes of these transcription factors are switched when temperature changes are sensed. We revealed that NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED (LNK) proteins act as coactivators of RVEs in cold and heat stress responses in addition to regulating circadian-regulated genes at normal temperatures. We found that among the four Arabidopsis LNKs, LNK1 and LNK2 function under normal and high-temperature conditions, and LNK3 and LNK4 function under cold conditions. Thus, these LNK proteins play important roles in inducing specific genes under different temperature conditions. Furthermore, LNK3 and LNK4 are specifically phosphorylated under cold conditions, suggesting that phosphorylation is involved in their activation.
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Affiliation(s)
- Satoshi Kidokoro
- Laboratory of Plant Molecular Physiology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo113-8657, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa226-8502, Japan
| | - Izumi Konoura
- Laboratory of Plant Molecular Physiology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo113-8657, Japan
| | - Fumiyuki Soma
- Laboratory of Plant Molecular Physiology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo113-8657, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Matsumoto-cho, Kasugai, Aichi487-8501, Japan
| | - Takuya Miyakawa
- Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo113-8657, Japan
| | - Masaru Tanokura
- Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo113-8657, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki305-0074, Japan
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo113-8657, Japan
- Research Institute for Agricultural and Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo156-8502, Japan
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Noordally Z, Land L, Trichtinger C, Dalvit I, de Meyer M, Wang K, Fitzpatrick TB. Clock and riboswitch control of THIC in tandem are essential for appropriate gauging of TDP levels under light/dark cycles in Arabidopsis. iScience 2023; 26:106134. [PMID: 36866249 PMCID: PMC9972560 DOI: 10.1016/j.isci.2023.106134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/03/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Metabolic homeostasis is regulated by enzyme activities, but the importance of regulating their corresponding coenzyme levels is unexplored. The organic coenzyme thiamine diphosphate (TDP) is suggested to be supplied as needed and controlled by a riboswitch-sensing mechanism in plants through the circadian-regulated THIC gene. Riboswitch disruption negatively impacts plant fitness. A comparison of riboswitch-disrupted lines to those engineered for enhanced TDP levels suggests that time-of-day regulation of THIC expression particularly under light/dark cycles is crucial. Altering the phase of THIC expression to be synchronous with TDP transporters disrupts the precision of the riboswitch implying that temporal separation of these processes by the circadian clock is important for gauging its response. All defects are bypassed by growing plants under continuous light conditions, highlighting the need to control levels of this coenzyme under light/dark cycles. Thus, consideration of coenzyme homeostasis within the well-studied domain of metabolic homeostasis is highlighted.
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Affiliation(s)
- Zeenat Noordally
- Vitamins and Environmental Stress Responses in Plants, Department of Plant Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Lara Land
- Vitamins and Environmental Stress Responses in Plants, Department of Plant Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Celso Trichtinger
- Vitamins and Environmental Stress Responses in Plants, Department of Plant Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Ivan Dalvit
- Vitamins and Environmental Stress Responses in Plants, Department of Plant Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Mireille de Meyer
- Vitamins and Environmental Stress Responses in Plants, Department of Plant Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Kai Wang
- Vitamins and Environmental Stress Responses in Plants, Department of Plant Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Teresa B. Fitzpatrick
- Vitamins and Environmental Stress Responses in Plants, Department of Plant Sciences, University of Geneva, 1211 Geneva, Switzerland,Corresponding author
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Ghosh S, Majee M. Protein l-isoAspartyl Methyltransferase (PIMT) and antioxidants in plants. VITAMINS AND HORMONES 2022; 121:413-432. [PMID: 36707142 DOI: 10.1016/bs.vh.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
All life forms, including plants, accumulate reactive oxygen species (ROS) as a byproduct of metabolism; however, environmental stresses, including abiotic stresses and pathogen attacks, cause enhanced accumulation of ROS in plants. The increased accumulation of ROS often causes oxidative damage to cells. Organisms are able to maintain levels of ROS below permissible limits by several mechanisms, including efficient antioxidant systems. In addition to antioxidant systems, recent studies suggest that protein l-isoaspartyl methyltransferase (PIMT), a highly conserved protein repair enzyme across evolutionary diverse organisms, plays a critical role in maintaining ROS homeostasis by repairing isoaspartyl-mediated damage to antioxidants in plants. Under stress conditions, antioxidant proteins undergo spontaneous isoaspartyl (isoAsp) modification which is often detrimental to protein structure and function. This reduces the catalytic action of antioxidants and disturbs the ROS homeostasis of cells. This chapter focuses on PIMT and its interaction with antioxidants in plants, where PIMT constitutes a secondary level of protection by shielding a primary level of antioxidants from dysfunction and permitting them to guard during unfavorable situations.
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Affiliation(s)
- Shraboni Ghosh
- National Institute of Plant Genome Research, New Delhi, India
| | - Manoj Majee
- National Institute of Plant Genome Research, New Delhi, India.
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5
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Yeh CW, Zhong HQ, Ho YF, Tian ZH, Yeh KW. The diurnal emission of floral scent in Oncidium hybrid orchid is controlled by CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) through the direct regulation on terpene synthase. BMC PLANT BIOLOGY 2022; 22:472. [PMID: 36195835 PMCID: PMC9531428 DOI: 10.1186/s12870-022-03850-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: 06/03/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND To adapt the periodic fluctuation of environmental factors, plants are subtle to monitor the natural variation for the growth and development. The daily activities and physiological functions in coordination with the natural variation are regulated by circadian clock genes. The circadian emission of floral scents is one of the rhythmic physiological activities controlled by circadian clock genes. Here, we study the molecular mechanism of circadian emission pattern of ocimene and linalool compounds in Oncidium Sharry Baby (Onc. SB) orchid. RESULTS GC-Mass analysis revealed that Onc. SB periodically emitted ocimene and linalool during 6 to 14 o'clock daily. Terpene synthase, one of the key gene in the terpenoid biosynthetic pathway is expressed in coordination with scent emission. The promoter structure of terpene synthase revealed a circadian binding sequence (CBS), 5'-AGATTTTT-3' for CIRCADIAN CLOCK ASSOCIATED1 (CCA1) transcription factor. EMSA data confirms the binding affinity of CCA1. Transactivation assay further verified that TPS expression is regulated by CCA1. It suggests that the emission of floral scents is controlled by CCA1. CONCLUSIONS The work validates that the mechanism of circadian emission of floral scents in Onc. Sharry Baby is controlled by the oscillator gene, CCA1(CIRCADIAN CLOCK ASSOCIATED 1) under light condition. CCA1 transcription factor up-regulates terpene synthase (TPS) by binding on CBS motif, 5'-AGATTTTT-3' of promoter region to affect the circadian emission of floral scents in Onc. SB.
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Affiliation(s)
- Chao-Wei Yeh
- Institute of Plant Biology, College of Life Science, National Taiwan University, No 1, Sect. 4, Roosevelt Road, 106, Taipei, Taiwan
| | - Hui-Qin Zhong
- Fujian Engineering Research Center for Characteristic Floriculture, Crop Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian Province, China
| | - Yung-Feng Ho
- Institute of Plant Biology, College of Life Science, National Taiwan University, No 1, Sect. 4, Roosevelt Road, 106, Taipei, Taiwan
| | - Zhi-Hong Tian
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, College of Life Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Kai-Wun Yeh
- Institute of Plant Biology, College of Life Science, National Taiwan University, No 1, Sect. 4, Roosevelt Road, 106, Taipei, Taiwan.
- Center for Weather Climate and Disaster Research, National Taiwan University, Taipei, 106, Taiwan.
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6
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Xin H, Wang Y, Li Q, Wan T, Hou Y, Liu Y, Gichuki DK, Zhou H, Zhu Z, Xu C, Zhou Y, Liu Z, Li R, Liu B, Lu L, Jiang H, Zhang J, Wan J, Aryal R, Hu G, Chen Z, Gituru RW, Liang Z, Wen J, Wang Q. A genome for Cissus illustrates features underlying its evolutionary success in dry savannas. HORTICULTURE RESEARCH 2022; 9:uhac208. [PMID: 36467268 PMCID: PMC9715578 DOI: 10.1093/hr/uhac208] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/08/2022] [Indexed: 06/17/2023]
Abstract
Cissus is the largest genus in Vitaceae and is mainly distributed in the tropics and subtropics. Crassulacean acid metabolism (CAM), a photosynthetic adaptation to the occurrence of succulent leaves or stems, indicates that convergent evolution occurred in response to drought stress during species radiation. Here we provide the chromosomal level assembly of Cissus rotundifolia (an endemic species in Eastern Africa) and a genome-wide comparison with grape to understand genome divergence within an ancient eudicot family. Extensive transcriptome data were produced to illustrate the genetics underpinning C. rotundifolia's ecological adaption to seasonal aridity. The modern karyotype and smaller genome of C. rotundifolia (n = 12, 350.69 Mb/1C), which lack further whole-genome duplication, were mainly derived from gross chromosomal rearrangements such as fusions and segmental duplications, and were sculpted by a very recent burst of retrotransposon activity. Bias in local gene amplification contributed to its remarkable functional divergence from grape, and the specific proliferated genes associated with abiotic and biotic responses (e.g. HSP-20, NBS-LRR) enabled C. rotundifolia to survive in a hostile environment. Reorganization of existing enzymes of CAM characterized as diurnal expression patterns of relevant genes further confer the ability to thrive in dry savannas.
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Affiliation(s)
| | | | | | | | - Yujun Hou
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanshuang Liu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Duncan Kiragu Gichuki
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huimin Zhou
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenfei Zhu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Xu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Yadong Zhou
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Zhiming Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen 518004, China
| | - Rongjun Li
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Bing Liu
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Limin Lu
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Hongsheng Jiang
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Junnan Wan
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Rishi Aryal
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Guangwan Hu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Zhiduan Chen
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Robert Wahiti Gituru
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, 62000-00200, Nairobi, Kenya
| | | | - Jun Wen
- Corresponding authors. E-mail: ; ;
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7
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Watanabe E, Isoda M, Muranaka T, Ito S, Oyama T. Detection of Uncoupled Circadian Rhythms in Individual Cells of Lemna minor using a Dual-Color Bioluminescence Monitoring System. PLANT & CELL PHYSIOLOGY 2021; 62:815-826. [PMID: 33693842 DOI: 10.1093/pcp/pcab037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
The plant circadian oscillation system is based on the circadian clock of individual cells. Circadian behavior of cells has been observed by monitoring the circadian reporter activity, such as bioluminescence of AtCCA1::LUC+. To deeply analyze different circadian behaviors in individual cells, we developed the dual-color bioluminescence monitoring system that automatically measured the luminescence of two luciferase reporters simultaneously at a single-cell level. We selected a yellow-green-emitting firefly luciferase (LUC+) and a red-emitting luciferase (PtRLUC) that is a mutant form of Brazilian click beetle ELUC. We used AtCCA1::LUC+ and CaMV35S::PtRLUC. CaMV35S::LUC+ was previously reported as a circadian reporter with a low-amplitude rhythm. These bioluminescent reporters were introduced into the cells of a duckweed, Lemna minor, by particle bombardment. Time series of the bioluminescence of individual cells in a frond were obtained using a dual-color bioluminescence monitoring system with a green-pass- and red-pass filter. Luminescence intensities from the LUC+ and PtRLUC of each cell were calculated from the filtered luminescence intensities. We succeeded in reconstructing the bioluminescence behaviors of AtCCA1::LUC+ and CaMV35S::PtRLUC in the same cells. Under prolonged constant light conditions, AtCCA1::LUC+ showed a robust circadian rhythm in individual cells in an asynchronous state in the frond, as previously reported. By contrast, CaMV35S::PtRLUC stochastically showed circadian rhythms in a synchronous state. These results strongly suggested the uncoupling of cellular behavior between these circadian reporters. This dual-color bioluminescence monitoring system is a powerful tool to analyze various stochastic phenomena accompanying large cell-to-cell variation in gene expression.
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Affiliation(s)
- Emiri Watanabe
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Minako Isoda
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Tomoaki Muranaka
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
- Faculty of Agriculture, Kagoshima University, Kohrimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Shogo Ito
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Tokitaka Oyama
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
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Peng H, Neff MM. Two ATAF transcription factors ANAC102 and ATAF1 contribute to the suppression of cytochrome P450-mediated brassinosteroid catabolism in Arabidopsis. PHYSIOLOGIA PLANTARUM 2021; 172:1493-1505. [PMID: 33491178 DOI: 10.1111/ppl.13339] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/16/2020] [Accepted: 01/17/2021] [Indexed: 06/12/2023]
Abstract
PHYB ACTIVATION TAGGED SUPPRESSOR 1 (BAS1) and SUPPRESSOR OF PHYB-4 7 (SOB7) are two cytochrome P450 enzymes that inactivate brassinosteroids (BRs) in Arabidopsis. The NAC transcription factor (TF) ATAF2 (ANAC081) and the core circadian clock regulator CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) both suppress the expression of BAS1 and SOB7 via direct promoter binding. Additionally, BRs cause feedback suppression on ATAF2 expression. Here, we report that two ATAF-subgroup TFs, ANAC102 and ATAF1 (ANAC002), also contribute to the transcriptional suppression of BAS1 and SOB7. ANAC102 and ATAF1 gene-knockout mutants exhibit elevated expression of both BAS1 and SOB7, expanded tissue-level accumulation of their protein products and reduced hypocotyl growth in response to exogenous BR treatments. Similar to ATAF2, both ANAC102 and ATAF1 are transcriptionally suppressed by BRs and white light. Neither BAS1 nor SOB7 expression is further elevated in ATAF double or triple mutants, suggesting that the suppression effect of these three ATAFs is not additive. In addition, ATAF single, double, and triple mutants have similar levels of BR responsiveness with regard to hypocotyl elongation. ATAF2, ANAC102, ATAF1, and CCA1 physically interact with itself and each other, suggesting that they may coordinately suppress BAS1 and SOB7 expression via protein-protein interactions. Despite the absence of CCA1-binding elements in their promoters, ANAC102 and ATAF1 have similar transcript circadian oscillation patterns as that of CCA1, suggesting that these two ATAF genes may be indirectly regulated by the circadian clock.
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Affiliation(s)
- Hao Peng
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
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9
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Abstract
Crassulacean acid metabolism (CAM) has evolved from a C3 ground state to increase water use efficiency of photosynthesis. During CAM evolution, selective pressures altered the abundance and expression patterns of C3 genes and their regulators to enable the trait. The circadian pattern of CO2 fixation and the stomatal opening pattern observed in CAM can be explained largely with a regulatory architecture already present in C3 plants. The metabolic CAM cycle relies on enzymes and transporters that exist in C3 plants and requires tight regulatory control to avoid futile cycles between carboxylation and decarboxylation. Ecological observations and modeling point to mesophyll conductance as a major factor during CAM evolution. The present state of knowledge enables suggestions for genes for a minimal CAM cycle for proof-of-concept engineering, assuming altered regulation of starch synthesis and degradation are not critical elements of CAM photosynthesis and sufficient malic acid export from the vacuole is possible.
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Affiliation(s)
- Katharina Schiller
- Computational Biology, Faculty of Biology, CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; ,
| | - Andrea Bräutigam
- Computational Biology, Faculty of Biology, CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; ,
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10
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Posttranslational regulation of multiple clock-related transcription factors triggers cold-inducible gene expression in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2021048118. [PMID: 33649234 DOI: 10.1073/pnas.2021048118] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cold stress is an adverse environmental condition that affects plant growth, development, and crop productivity. Under cold stress conditions, the expression of numerous genes that function in the stress response and tolerance is induced in various plant species, and the dehydration-responsive element (DRE) binding protein 1/C-repeat binding factor (DREB1/CBF) transcription factors function as master switches for cold-inducible gene expression. Cold stress strongly induces these DREB1 genes. Therefore, it is important to elucidate the mechanisms of DREB1 expression in response to cold stress to clarify the perception and response of cold stress in plants. Previous studies indicated that the central oscillator components of the circadian clock, CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), are involved in cold-inducible DREB1 expression, but the underlying mechanisms are not clear. We revealed that the clock-related MYB proteins REVEILLE4/LHY-CCA1-Like1 (RVE4/LCL1) and RVE8/LCL5 are quickly and reversibly transferred from the cytoplasm to the nucleus under cold stress conditions and function as direct transcriptional activators of DREB1 expression. We found that CCA1 and LHY suppressed the expression of DREB1s under unstressed conditions and were rapidly degraded specifically in response to cold stress, which suggests that they act as transcriptional repressors and indirectly regulate the cold-inducible expression of DREB1s We concluded that posttranslational regulation of multiple clock-related transcription factors triggers cold-inducible gene expression. Our findings clarify the complex relationship between the plant circadian clock and the regulatory mechanisms of cold-inducible gene expression.
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11
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Djerrab D, Bertrand B, Breitler JC, Léran S, Dechamp E, Campa C, Barrachina C, Conejero G, Etienne H, Sulpice R. Photoperiod-dependent transcriptional modifications in key metabolic pathways in Coffea arabica. TREE PHYSIOLOGY 2021; 41:302-316. [PMID: 33080620 PMCID: PMC7874067 DOI: 10.1093/treephys/tpaa130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/20/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
Photoperiod length induces in temperate plants major changes in growth rates, morphology and metabolism with, for example, modifications in the partitioning of photosynthates to avoid starvation at the end of long nights. However, this has never been studied for a tropical perennial species adapted to grow in a natural photoperiod close to 12 h/12 h all year long. We grew Coffea arabica L., an understorey perennial evergreen tropical species in its natural 12 h/12 h and in a short 8 h/16 h photoperiod, and we investigated its responses at the physiological, metabolic and transcriptomic levels. The expression pattern of rhythmic genes, including core clock genes, was affected by changes in photoperiod. Overall, we identified 2859 rhythmic genes, of which 89% were also rhythmic in Arabidopsis thaliana L. Under short-days, plant growth was reduced, and leaves were thinner with lower chlorophyll content. In addition, secondary metabolism was also affected with chlorogenic acid and epicatechin levels decreasing, and in agreement, the genes involved in lignin synthesis were overexpressed and those involved in the flavanol pathway were underexpressed. Our results show that the 8 h/16 h photoperiod induces drastic changes in morphology, metabolites and gene expression, and the responses for gene expression are similar to those observed in the temperate annual A. thaliana species. Short photoperiod induces drastic changes in gene expression, metabolites and leaf structure, some of these responses being similar to those observed in A. thaliana.
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Affiliation(s)
- Doâa Djerrab
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), UMR IPME, F-34398 Montpellier, France
- UMR IPME, Université de Montpellier, CIRAD, IRD, F-34398 Montpellier, France
| | | | - Jean-Christophe Breitler
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), UMR IPME, F-34398 Montpellier, France
- UMR IPME, Université de Montpellier, CIRAD, IRD, F-34398 Montpellier, France
| | - Sophie Léran
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), UMR IPME, F-34398 Montpellier, France
- UMR IPME, Université de Montpellier, CIRAD, IRD, F-34398 Montpellier, France
| | - Eveline Dechamp
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), UMR IPME, F-34398 Montpellier, France
- UMR IPME, Université de Montpellier, CIRAD, IRD, F-34398 Montpellier, France
| | - Claudine Campa
- UMR IPME, Université de Montpellier, CIRAD, IRD, F-34398 Montpellier, France
- IRD, UMR IPME, F-34394 Montpellier, France
| | - Célia Barrachina
- MGX, Biocampus Montpellier, CNRS, INSERM, University of Montpellier, 34000 Montpellier, France
| | - Geneviève Conejero
- BPMP, University of Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Hervé Etienne
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), UMR IPME, F-34398 Montpellier, France
- UMR IPME, Université de Montpellier, CIRAD, IRD, F-34398 Montpellier, France
| | - Ronan Sulpice
- National University of Ireland, Plant Systems Biology Lab, Ryan Institute, School of Natural Sciences, University Road, Galway H91 TK33, Ireland
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12
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Michael TP, Ernst E, Hartwick N, Chu P, Bryant D, Gilbert S, Ortleb S, Baggs EL, Sree KS, Appenroth KJ, Fuchs J, Jupe F, Sandoval JP, Krasileva KV, Borisjuk L, Mockler TC, Ecker JR, Martienssen RA, Lam E. Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control. Genome Res 2021; 31:225-238. [PMID: 33361111 PMCID: PMC7849404 DOI: 10.1101/gr.266429.120] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/16/2020] [Indexed: 11/24/2022]
Abstract
Rootless plants in the genus Wolffia are some of the fastest growing known plants on Earth. Wolffia have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for Wolffia australiana (Benth.) Hartog & Plas, which has the smallest genome size in the genus at 357 Mb and has a reduced set of predicted protein-coding genes at about 15,000. Comparison between multiple high-quality draft genome sequences from W. australiana clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. Wolffia has also lost most of the conserved nucleotide-binding leucine-rich repeat (NLR) genes that are known to be involved in innate immunity, as well as those involved in terpene biosynthesis, while having a significant overrepresentation of genes in the sphingolipid pathways that may signify an alternative defense system. Diurnal expression analysis revealed that only 13% of Wolffia genes are expressed in a time-of-day (TOD) fashion, which is less than the typical ∼40% found in several model plants under the same condition. In contrast to the model plants Arabidopsis and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in W. australiana, where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The Wolffia genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.
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Affiliation(s)
- Todd P Michael
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Evan Ernst
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Nolan Hartwick
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Philomena Chu
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Douglas Bryant
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Sarah Gilbert
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Stefan Ortleb
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Erin L Baggs
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye, Kerala 671316, India
| | | | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Florian Jupe
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Justin P Sandoval
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Ljudmylla Borisjuk
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Joseph R Ecker
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Robert A Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Eric Lam
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
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13
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Peng H, Phung J, Zhai Y, Neff MM. Self-transcriptional repression of the Arabidopsis NAC transcription factor ATAF2 and its genetic interaction with phytochrome A in modulating seedling photomorphogenesis. PLANTA 2020; 252:48. [PMID: 32892254 DOI: 10.1007/s00425-020-03456-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
The NAC transcription factor ATAF2 suppresses its own transcription via self-promoter binding. ATAF2 genetically interacts with the circadian regulator CCA1 and phytochrome A to modulate seedling photomorphogenesis in Arabidopsis thaliana. ATAF2 (ANAC081) is a NAC (NAM, ATAF and CUC) transcription factor (TF) that participates in the regulation of disease resistance, stress tolerance and hormone metabolism in Arabidopsis thaliana. We previously reported that ATAF2 promotes Arabidopsis hypocotyl growth in a light-dependent manner via transcriptionally suppressing the brassinosteroid (BR)-inactivating cytochrome P450 genes BAS1 (CYP734A1, formerly CYP72B1) and SOB7 (CYP72C1). Assays using low light intensities suggest that the photoreceptor phytochrome A (PHYA) may play a more critical role in ATAF2-regulated photomorphogenesis than phytochrome B (PHYB) and cryptochrome 1 (CRY1). In addition, ATAF2 is also regulated by the circadian clock. The core circadian TF CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) physically interacts with ATAF2 at the DNA-protein and protein-protein levels, and both differentially suppress BAS1- and SOB7-mediated BR catabolism. In this research, we show that ATAF2 can bind its own promoter as a transcriptional self-repressor. This self-feedback-suppression loop is a typical feature of multiple circadian-regulated genes. Additionally, ATAF2 and CCA1 synergistically suppress seedling photomorphogenesis as reflected by the light-dependent hypocotyl growth analysis of their single and double gene knock-out mutants. Similar fluence-rate response assays using ATAF2 and photoreceptor (PHYB, CRY1 and PHYA) knock-out mutants demonstrate that PHYA is required for ATAF2-regulated photomorphogenesis in a wide range of light intensities. Furthermore, disruption of PHYA can suppress the BR-insensitive hypocotyl-growth phenotype of ATAF2 loss-of-function seedlings in the light, but not in darkness. Collectively, our results provide a genetic interaction synopsis of the circadian-clock-photomorphogenesis-BR integration node involving ATAF2, CCA1 and PHYA.
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Affiliation(s)
- Hao Peng
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Jessica Phung
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Ying Zhai
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
| | - Michael M Neff
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
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14
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Zhai Y, Peng H, Neff MM, Pappu HR. Emerging Molecular Links Between Plant Photomorphogenesis and Virus Resistance. FRONTIERS IN PLANT SCIENCE 2020; 11:920. [PMID: 32695129 PMCID: PMC7338571 DOI: 10.3389/fpls.2020.00920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/05/2020] [Indexed: 05/25/2023]
Abstract
Photomorphogenesis refers to photoreceptor-mediated morphological changes in plant development that are triggered by light. Multiple photoreceptors and transcription factors (TFs) are involved in the molecular regulation of photomorphogenesis. Likewise, light can also modulate the outcome of plant-virus interactions since both photosynthesis and many viral infection events occur in the chloroplast. Despite the apparent association between photosynthesis and virus infection, little is known about whether there are also interplays between photomorphogenesis and plant virus resistance. Recent research suggests that plant-virus interactions are potentially regulated by several photoreceptors and photomorphogenesis regulators, including phytochromes A and B (PHYA and PHYB), cryptochromes 2 (CRY2), phototropin 2 (PHOT2), the photomorphogenesis repressor constitutive photomorphogenesis 1 (COP1), the NAM, ATAF, and CUC (NAC)-family TF ATAF2, the Aux/IAA protein phytochrome-associated protein 1 (PAP1), the homeodomain-leucine zipper (HD-Zip) TF HAT1, and the core circadian clock component circadian clock associated 1 (CCA1). Particularly, the plant growth promoting brassinosteroid (BR) hormones play critical roles in integrating the regulatory pathways of plant photomorphogenesis and viral defense. Here, we summarize the current understanding of molecular mechanisms linking plant photomorphogenesis and defense against viruses, which represents an emerging interdisciplinary research topic in both molecular plant biology and virology.
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Affiliation(s)
- Ying Zhai
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Hao Peng
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Michael M. Neff
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Hanu R. Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
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15
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Lai X, Bendix C, Yan L, Zhang Y, Schnable JC, Harmon FG. Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs. BMC Genomics 2020; 21:428. [PMID: 32586356 PMCID: PMC7315539 DOI: 10.1186/s12864-020-06824-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/12/2020] [Indexed: 11/17/2022] Open
Abstract
Background The circadian clock drives endogenous 24-h rhythms that allow organisms to adapt and prepare for predictable and repeated changes in their environment throughout the day-night (diurnal) cycle. Many components of the circadian clock in Arabidopsis thaliana have been functionally characterized, but comparatively little is known about circadian clocks in grass species including major crops like maize and sorghum. Results Comparative research based on protein homology and diurnal gene expression patterns suggests the function of some predicted clock components in grasses is conserved with their Arabidopsis counterparts, while others have diverged in function. Our analysis of diurnal gene expression in three panicoid grasses sorghum, maize, and foxtail millet revealed conserved and divergent evolution of expression for core circadian clock genes and for the overall transcriptome. We find that several classes of core circadian clock genes in these grasses differ in copy number compared to Arabidopsis, but mostly exhibit conservation of both protein sequence and diurnal expression pattern with the notable exception of maize paralogous genes. We predict conserved cis-regulatory motifs shared between maize, sorghum, and foxtail millet through identification of diurnal co-expression clusters for a subset of 27,196 orthologous syntenic genes. In this analysis, a Cochran–Mantel–Haenszel based method to control for background variation identified significant enrichment for both expected and novel 6–8 nucleotide motifs in the promoter regions of genes with shared diurnal regulation predicted to function in common physiological activities. Conclusions This study illustrates the divergence and conservation of circadian clocks and diurnal regulatory networks across syntenic orthologous genes in panacoid grass species. Further, conserved local regulatory sequences contribute to the architecture of these diurnal regulatory networks that produce conserved patterns of diurnal gene expression.
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Affiliation(s)
- Xianjun Lai
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA.,College of Agricultural Sciences, Xichang University, Liangshan, Xichang, 615000, China
| | - Claire Bendix
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, 94710, USA
| | - Lang Yan
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA.,College of Agricultural Sciences, Xichang University, Liangshan, Xichang, 615000, China
| | - Yang Zhang
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA
| | - James C Schnable
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, USA.
| | - Frank G Harmon
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA. .,Plant Gene Expression Center, USDA-ARS, Albany, CA, 94710, USA.
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16
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Dong MY, Lei L, Fan XW, Li YZ. Dark response genes: a group of endogenous pendulum/timing players in maize? PLANTA 2020; 252:1. [PMID: 32504137 DOI: 10.1007/s00425-020-03403-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/18/2020] [Indexed: 05/21/2023]
Abstract
MAIN CONCLUSION Maize has a set of dark response genes, expression of which is influenced by multiple factor and varies with maize inbred lines but without germplasm specificity. The response to photoperiod is a common biological issue across the species kingdoms. Dark is as important as light in photoperiod. However, further in-depth understanding of responses of maize (Zea mays) to light and dark transition under photoperiod is hindered due to the lack of understanding of dark response genes. With multiple public "-omic" datasets of temperate and tropical/subtropical maize, 16 maize dark response genes, ZmDRGs, were found and had rhythmic expression under dark and light-dark cycle. ZmDRGs 6-8 were tandemly duplicated. ZmDRGs 2, 13, and 14 had a chromosomal collinearity with other maize genes. ZmDRGs 1-11 and 13-16 had copy-number variations. ZmDRGs 2, 9, and 16 showed 5'-end sequence deletion mutations. Some ZmDRGs had chromatin interactions and underwent DNA methylation and/or m6A mRNA methylation. Chromosomal histones associated with 15 ZmDRGs were methylated and acetylated. ZmDRGs 1, 2, 4, 9, and 13 involved photoperiodic phenotypes. ZmDRG16 was within flowering-related QTLs. ZmDRGs 1, 3, and 6-11 were present in cis-acting expression QTLs (eQTLs). ZmDRGs 1, 4, 6-9, 11, 12, and 14-16 showed co-expression with other maize genes. Some of ZmDRG-encoded ZmDRGs showed obvious differences in abundance and phosphorylation. CONCLUSION Sixteen ZmDRGs 1-16 are associated with the dark response of maize. In the process of post-domestication and/or breeding, the ZmDRGs undergo the changes without germplasm specificity, including epigenetic modifications, gene copy numbers, chromatin interactions, and deletion mutations. In addition to effects by these factors, ZmDRG expression is influenced by promoter elements, cis-acting eQTLs, and co-expression networks.
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Affiliation(s)
- Ming-You Dong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, China
| | - Ling Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, China
| | - Xian-Wei Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, China
| | - You-Zhi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, China.
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17
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Peng H, Neff MM. CIRCADIAN CLOCK ASSOCIATED 1 and ATAF2 differentially suppress cytochrome P450-mediated brassinosteroid inactivation. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:970-985. [PMID: 31639820 PMCID: PMC6977193 DOI: 10.1093/jxb/erz468] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 10/15/2019] [Indexed: 05/20/2023]
Abstract
Brassinosteroids (BRs) are a group of steroid hormones regulating plant growth and development. Since BRs do not undergo transport among plant tissues, their metabolism is tightly regulated by transcription factors (TFs) and feedback loops. BAS1 (CYP734A1, formerly CYP72B1) and SOB7 (CYP72C1) are two BR-inactivating cytochrome P450s identified in Arabidopsis thaliana. We previously found that a TF ATAF2 (ANAC081) suppresses BAS1 and SOB7 expression by binding to the Evening Element (EE) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1)-binding site (CBS) on their promoters. Both the EE and CBS are known binding targets of the circadian regulatory protein CCA1. Here, we confirm that CCA1 binds the EE and CBS motifs on BAS1 and SOB7 promoters, respectively. Elevated accumulations of BAS1 and SOB7 transcripts in the CCA1 null mutant cca1-1 indicate that CCA1 is a repressor of their expression. When compared with either cca1-1 or the ATAF2 null mutant ataf2-2, the cca1-1 ataf2-2 double mutant shows higher SOB7 transcript accumulations and a stronger BR-insensitive phenotype of hypocotyl elongation in white light. CCA1 interacts with ATAF2 at both DNA-protein and protein-protein levels. ATAF2, BAS1, and SOB7 are all circadian regulated with distinct expression patterns. These results demonstrate that CCA1 and ATAF2 differentially suppress BAS1- and SOB7-mediated BR inactivation.
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Affiliation(s)
- Hao Peng
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Michael M Neff
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
- Correspondence:
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18
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Wai CM, Weise SE, Ozersky P, Mockler TC, Michael TP, VanBuren R. Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album. PLoS Genet 2019; 15:e1008209. [PMID: 31199791 PMCID: PMC6594660 DOI: 10.1371/journal.pgen.1008209] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/26/2019] [Accepted: 05/24/2019] [Indexed: 12/22/2022] Open
Abstract
Plants with facultative crassulacean acid metabolism (CAM) maximize performance through utilizing C3 or C4 photosynthesis under ideal conditions while temporally switching to CAM under water stress (drought). While genome-scale analyses of constitutive CAM plants suggest that time of day networks are shifted, or phased to the evening compared to C3, little is known for how the shift from C3 to CAM networks is modulated in drought induced CAM. Here we generate a draft genome for the drought-induced CAM-cycling species Sedum album. Through parallel sampling in well-watered (C3) and drought (CAM) conditions, we uncover a massive rewiring of time of day expression and a CAM and stress-specific network. The core circadian genes are expanded in S. album and under CAM induction, core clock genes either change phase or amplitude. While the core clock cis-elements are conserved in S. album, we uncover a set of novel CAM and stress specific cis-elements consistent with our finding of rewired co-expression networks. We identified shared elements between constitutive CAM and CAM-cycling species and expression patterns unique to CAM-cycling S. album. Together these results demonstrate that drought induced CAM-cycling photosynthesis evolved through the mobilization of a stress-specific, time of day network, and not solely the phasing of existing C3 networks. These results will inform efforts to engineer water use efficiency into crop plants for growth on marginal land.
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Affiliation(s)
- Ching Man Wai
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Sean E. Weise
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Philip Ozersky
- Donald Danforth Plant Science Center, St. Louis MO, United States of America
| | - Todd C. Mockler
- Donald Danforth Plant Science Center, St. Louis MO, United States of America
| | - Todd P. Michael
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
- Plant Resilience Institute, Michigan State University, East Lansing, MI, United States of America
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19
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Lee K, Mas P, Seo PJ. The EC-HDA9 complex rhythmically regulates histone acetylation at the TOC1 promoter in Arabidopsis. Commun Biol 2019; 2:143. [PMID: 31044168 PMCID: PMC6478914 DOI: 10.1038/s42003-019-0377-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 03/06/2019] [Indexed: 12/13/2022] Open
Abstract
Circadian clocks are conserved time-keeper mechanisms in some prokaryotes and higher eukaryotes. Chromatin modification is emerging as key regulatory mechanism for refining core clock gene expression. Rhythmic changes in histone marks are closely associated to the TIMING OF CAB EXPRESSION 1 (TOC1) Arabidopsis clock gene. However, the chromatin-related modifiers responsible for these marks remain largely unknown. Here, we uncover that the chromatin modifier HISTONE DEACETYLASE 9 (HDA9) and the Evening complex (EC) component EARLY FLOWERING 3 (ELF3) directly interact to regulate the declining phase of TOC1 after its peak expression. We found that HDA9 specifically binds to the TOC1 promoter through the interaction with ELF3. The EC-HDA9 complex promotes H3 deacetylation at the TOC1 locus, contributing to suppressing TOC1 expression during the night, the time of EC function. Therefore, we have identified the mechanism by which the circadian clock intertwines with chromatin-related components to shape the circadian waveforms of gene expression in Arabidopsis.
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Affiliation(s)
- Kyounghee Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419 Republic of Korea
| | - Paloma Mas
- Center for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Parc de Recerca Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419 Republic of Korea
- Department of Chemistry, Seoul National University, Seoul, 08826 Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
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20
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Del Prete S, Molitor A, Charif D, Bessoltane N, Soubigou-Taconnat L, Guichard C, Brunaud V, Granier F, Fransz P, Gaudin V. Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction. BMC PLANT BIOLOGY 2019; 19:135. [PMID: 30971226 PMCID: PMC6458719 DOI: 10.1186/s12870-019-1738-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/24/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND The floral transition is a complex developmental event, fine-tuned by various environmental and endogenous cues to ensure the success of offspring production. Leaves are key organs in sensing floral inductive signals, such as a change in light regime, and in the production of the mobile florigen. CONSTANS and FLOWERING LOCUS T are major players in leaves in response to photoperiod. Morphological and molecular events during the floral transition have been intensively studied in the shoot apical meristem. To better understand the concomitant processes in leaves, which are less described, we investigated the nuclear changes in fully developed leaves during the time course of the floral transition. RESULTS We highlighted new putative regulatory candidates of flowering in leaves. We observed differential expression profiles of genes related to cellular, hormonal and metabolic actions, but also of genes encoding long non-coding RNAs and new natural antisense transcripts. In addition, we detected a significant increase in ploidy level during the floral transition, indicating endoreduplication. CONCLUSIONS Our data indicate that differentiated mature leaves, possess physiological plasticity and undergo extensive nuclear reprogramming during the floral transition. The dynamic events point at functionally related networks of transcription factors and novel regulatory motifs, but also complex hormonal and metabolic changes.
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Affiliation(s)
- Stefania Del Prete
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Anne Molitor
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Delphine Charif
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Nadia Bessoltane
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, 91405 Orsay, France
| | - Cécile Guichard
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, 91405 Orsay, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, 91405 Orsay, France
| | - Fabienne Granier
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Paul Fransz
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
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21
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Gil KE, Park CM. Thermal adaptation and plasticity of the plant circadian clock. THE NEW PHYTOLOGIST 2019; 221:1215-1229. [PMID: 30289568 DOI: 10.1111/nph.15518] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/11/2018] [Indexed: 05/20/2023]
Abstract
Contents Summary 1215 I. Introduction 1215 II. Molecular organization of the plant circadian clock 1216 III. Temperature compensation 1219 IV. Temperature regulation of circadian behaviors 1220 V. Thermal adaptation of the clock: evolutionary considerations 1223 VI. Light and temperature information for the clock function - synergic or individual? 1224 VII. Concluding remarks and future prospects 1225 Acknowledgements 1225 References 1225 SUMMARY: Plant growth and development is widely affected by diverse temperature conditions. Although studies have been focused mainly on the effects of stressful temperature extremes in recent decades, nonstressful ambient temperatures also influence an array of plant growth and morphogenic aspects, a process termed thermomorphogenesis. Notably, accumulating evidence indicates that both stressful and nonstressful temperatures modulate the functional process of the circadian clock, a molecular timer of biological rhythms in higher eukaryotes and photosynthetic prokaryotes. The circadian clock can sustain robust and precise timing over a range of physiological temperatures. Genes and molecular mechanisms governing the temperature compensation process have been explored in different plant species. In addition, a ZEITLUPE/HSP90-mediated protein quality control mechanism helps plants maintain the thermal stability of the clock under heat stress. The thermal adaptation capability and plasticity of the clock are of particular interest in view of the growing concern about global climate changes. Considering these circumstances in the field, we believe that it is timely to provide a provoking discussion on the current knowledge of temperature regulation of the clock function. The review also will discuss stimulating ideas on this topic along with ecosystem management and future agricultural innovation.
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Affiliation(s)
- Kyung-Eun Gil
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
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22
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Beyond Transcription: Fine-Tuning of Circadian Timekeeping by Post-Transcriptional Regulation. Genes (Basel) 2018; 9:genes9120616. [PMID: 30544736 PMCID: PMC6315869 DOI: 10.3390/genes9120616] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/28/2022] Open
Abstract
The circadian clock is an important endogenous timekeeper, helping plants to prepare for the periodic changes of light and darkness in their environment. The clockwork of this molecular timer is made up of clock proteins that regulate transcription of their own genes with a 24 h rhythm. Furthermore, the rhythmically expressed clock proteins regulate time-of-day dependent transcription of downstream genes, causing messenger RNA (mRNA) oscillations of a large part of the transcriptome. On top of the transcriptional regulation by the clock, circadian rhythms in mRNAs rely in large parts on post-transcriptional regulation, including alternative pre-mRNA splicing, mRNA degradation, and translational control. Here, we present recent insights into the contribution of post-transcriptional regulation to core clock function and to regulation of circadian gene expression in Arabidopsis thaliana.
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23
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Mwimba M, Karapetyan S, Liu L, Marqués J, McGinnis EM, Buchler NE, Dong X. Daily humidity oscillation regulates the circadian clock to influence plant physiology. Nat Commun 2018; 9:4290. [PMID: 30327472 PMCID: PMC6191426 DOI: 10.1038/s41467-018-06692-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/20/2018] [Indexed: 01/27/2023] Open
Abstract
Early circadian studies in plants by de Mairan and de Candolle alluded to a regulation of circadian clocks by humidity. However, this regulation has not been described in detail, nor has its influence on physiology been demonstrated. Here we report that, under constant light, circadian humidity oscillation can entrain the plant circadian clock to a period of 24 h probably through the induction of clock genes such as CIRCADIAN CLOCK ASSOCIATED 1. Under simulated natural light and humidity cycles, humidity oscillation increases the amplitude of the circadian clock and further improves plant fitness-related traits. In addition, humidity oscillation enhances effector-triggered immunity at night possibly to counter increased pathogen virulence under high humidity. These results indicate that the humidity oscillation regulates specific circadian outputs besides those co-regulated with the light-dark cycle.
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Affiliation(s)
- Musoki Mwimba
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA.,Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA
| | - Sargis Karapetyan
- Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA.,Department of Physics, Duke University, Durham, NC, 27708, USA
| | - Lijing Liu
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA.,Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA
| | - Jorge Marqués
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA.,Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA
| | - Erin M McGinnis
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA.,Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA
| | - Nicolas E Buchler
- Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA.,Department of Physics, Duke University, Durham, NC, 27708, USA.,Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, 27606, USA
| | - Xinnian Dong
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA. .,Department of Biology, Duke University, PO Box 90338, Durham, NC, 27708, USA.
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24
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Buzduga IM, Volkov RA, Panchuk II. Metabolic compensation in Arabidopsis thaliana catalase-deficient mutants. CYTOL GENET+ 2018. [DOI: 10.3103/s0095452718010036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Alam NB, Ghosh A. Comprehensive analysis and transcript profiling of Arabidopsis thaliana and Oryza sativa catalase gene family suggests their specific roles in development and stress responses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 123:54-64. [PMID: 29223068 DOI: 10.1016/j.plaphy.2017.11.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 11/12/2017] [Accepted: 11/27/2017] [Indexed: 05/05/2023]
Abstract
Stress induces the generation of Reactive Oxygen Species (ROS) that ultimately hampers the growth, development, and productivity of the plant. As an antioxidant enzyme, catalase converts hydrogen peroxide to water and keeps ROS level down to protect cells from stress-induced apoptosis. Here, a genome-wide analysis of catalase gene family has been performed in two model plants- Arabidopsis thaliana and Oryza sativa. Both Arabidopsis and rice has a small family of three and four genes, respectively; that code for seven proteins each. Detailed analysis of these members in terms of their structure, duplication, chromosomal position and proteins subcellular localization, as well as expression profiling under various developmental and environmental cues, was performed. Catalase proteins were mostly found to be localized in the cytoplasm, followed by peroxisome and mitochondria. Phylogenetically plant catalases showed strong divergence from their non-plant counterparts. Expression profiling revealed that AtCAT3 and OsCATA are the constitutively expressive member; while AtCAT2, OsCATA, and OsCATC are the stress-responsive members. Moreover, an altered level of total rice catalase enzyme activity and H2O2 level was observed under various abiotic stress conditions. This indicates the stress-responsive transcriptome as well as proteome alteration of catalase in the plant.
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Affiliation(s)
- Nazmir Binta Alam
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
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26
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Golubov A, Byeon B, Woycicki R, Laing C, Gannon V, Kovalchuk I. Transcriptomic profiling of Arabidopsis thaliana plants exposed to the human pathogen Escherichia coli O157-H7. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2016. [DOI: 10.1016/j.bcab.2016.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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27
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Laxa M, Müller K, Lange N, Doering L, Pruscha JT, Peterhänsel C. The 5'UTR Intron of Arabidopsis GGT1 Aminotransferase Enhances Promoter Activity by Recruiting RNA Polymerase II. PLANT PHYSIOLOGY 2016; 172:313-27. [PMID: 27418588 PMCID: PMC5074633 DOI: 10.1104/pp.16.00881] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/07/2016] [Indexed: 05/19/2023]
Abstract
Photorespiration is essential for the detoxification of glycolate and recycling of carbon to the Calvin Benson Bassham cycle. Enzymes participating in the pathway have been identified, and investigations now focus on the regulation of photorespiration by transporters and metabolites. However, regulation of photorespiration on the gene level has not been intensively studied. Here, we show that maximum transcript abundance of Glu:glyoxylate aminotransferase 1 (GGT1) is regulated by intron-mediated enhancement (IME) of the 5' leader intron rather than by regulatory elements in the 5' upstream region. The intron is rich in CT-stretches and contains the motif TGTGATTTG that is highly similar to the IME-related motif TTNGATYTG. The GGT1 intron also confers leaf-specific expression of foreign promoters. Quantitative PCR analysis and GUS activity measurements revealed that IME of the GGT1 5'UTR intron is controlled on the transcriptional level. IME by the GGT1 5'UTR intron was at least 2-fold. Chromatin immunoprecipitation experiments showed that the abundance of RNA polymerase II binding to the intron-less construct is reduced.
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Affiliation(s)
- Miriam Laxa
- Leibniz University Hannover, Institute of Botany, 30419 Hannover, Germany
| | - Kristin Müller
- Leibniz University Hannover, Institute of Botany, 30419 Hannover, Germany
| | - Natalie Lange
- Leibniz University Hannover, Institute of Botany, 30419 Hannover, Germany
| | - Lennart Doering
- Leibniz University Hannover, Institute of Botany, 30419 Hannover, Germany
| | - Jan Thomas Pruscha
- Leibniz University Hannover, Institute of Botany, 30419 Hannover, Germany
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28
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Kong SL, Abdullah SNA, Ho CL, Amiruddin MD. Molecular cloning, gene expression profiling and in silico sequence analysis of vitamin E biosynthetic genes from the oil palm. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.plgene.2016.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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29
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Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang ML, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo HB, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck FJ, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Qin Y, Wang K, Chen LY, Shirley N, Lin YR, Liu LY, Hernandez AG, Wright CL, Bulone V, Tuskan GA, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X, Yang X, Smith JAC, Cushman JC, Paull RE, Yu Q. The pineapple genome and the evolution of CAM photosynthesis. Nat Genet 2015; 47:1435-42. [PMID: 26523774 PMCID: PMC4867222 DOI: 10.1038/ng.3435] [Citation(s) in RCA: 313] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/05/2015] [Indexed: 12/21/2022]
Abstract
Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5. The pineapple genome has one fewer ancient whole-genome duplication event than sequenced grass genomes and a conserved karyotype with seven chromosomes from before the ρ duplication event. The pineapple lineage has transitioned from C3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues. CAM pathway genes were enriched with cis-regulatory elements associated with the regulation of circadian clock genes, providing the first cis-regulatory link between CAM and circadian clock regulation. Pineapple CAM photosynthesis evolved by the reconfiguration of pathways in C3 plants, through the regulatory neofunctionalization of preexisting genes and not through the acquisition of neofunctionalized genes via whole-genome or tandem gene duplication.
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Affiliation(s)
- Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Robert VanBuren
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Ching Man Wai
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Haibao Tang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- iPlant Collaborative/University of Arizona, Tuscon, AZ 85719, USA
| | | | - John E. Bowers
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Eric Lyons
- iPlant Collaborative/University of Arizona, Tuscon, AZ 85719, USA
| | - Ming-Li Wang
- Hawaii Agriculture Research Center, Kunia, HI 96759, USA
| | - Jung Chen
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Eric Biggers
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724, USA
| | - Jisen Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Lixian Huang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Lingmao Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Wenjing Miao
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jian Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Zhangyao Ye
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Chenyong Miao
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Zhicong Lin
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Hao Wang
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Hongye Zhou
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Won C. Yim
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557-0330, USA
| | | | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada K1N 6N5
| | - Margaret Woodhouse
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Patrick P. Edger
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Romain Guyot
- IRD, UMR DIADE, EVODYN, BP 64501, 34394 Montpellier Cedex 5, France
| | - Hao-Bo Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Hong Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Guangyong Zheng
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ratnesh Singh
- Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, Dallas, TX 75252, USA
| | - Anupma Sharma
- Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, Dallas, TX 75252, USA
| | - Xiangjia Min
- Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA
| | - Yun Zheng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Hayan Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724, USA
| | - James Gurtowski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724, USA
| | | | - Alex Harkess
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | | | - Zhenyang Liao
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jingping Fang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Juan Liu
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiaodan Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Qing Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Weichang Hu
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Yuan Qin
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Kai Wang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Li-Yu Chen
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Neil Shirley
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus Urrbrae, South Australia 5064, Australia
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, Taipei 10617, Taiwan
| | - Li-Yu Liu
- Department of Agronomy, National Taiwan University, Taipei 10617, Taiwan
| | - Alvaro G. Hernandez
- W.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chris L. Wright
- W.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Vincent Bulone
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus Urrbrae, South Australia 5064, Australia
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Katy Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Francis Zee
- USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI 96720, USA
| | - Paul H. Moore
- Hawaii Agriculture Research Center, Kunia, HI 96759, USA
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK 74078, USA
| | | | - Todd Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada K1N 6N5
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Xinguang Zhu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - J. Andrew C. Smith
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - John C. Cushman
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557-0330, USA
| | - Robert E. Paull
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, Dallas, TX 75252, USA
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Circadian Control of Global Transcription. BIOMED RESEARCH INTERNATIONAL 2015; 2015:187809. [PMID: 26682214 PMCID: PMC4670846 DOI: 10.1155/2015/187809] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/04/2015] [Indexed: 01/10/2023]
Abstract
Circadian rhythms exist in most if not all organisms on the Earth and manifest in various aspects of physiology and behavior. These rhythmic processes are believed to be driven by endogenous molecular clocks that regulate rhythmic expression of clock-controlled genes (CCGs). CCGs consist of a significant portion of the genome and are involved in diverse biological pathways. The transcription of CCGs is tuned by rhythmic actions of transcription factors and circadian alterations in chromatin. Here, we review the circadian control of CCG transcription in five model organisms that are widely used, including cyanobacterium, fungus, plant, fruit fly, and mouse. Comparing the similarity and differences in the five organisms could help us better understand the function of the circadian clock, as well as its output mechanisms adapted to meet the demands of diverse environmental conditions.
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31
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Peng H, Zhao J, Neff MM. ATAF2 integrates Arabidopsis brassinosteroid inactivation and seedling photomorphogenesis. Development 2015; 142:4129-38. [PMID: 26493403 DOI: 10.1242/dev.124347] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 10/12/2015] [Indexed: 01/24/2023]
Abstract
The Arabidopsis thaliana hypocotyl is a robust system for studying the interplay of light and plant hormones, such as brassinosteroids (BRs), in the regulation of plant growth and development. Since BRs cannot be transported between plant tissues, their cellular levels must be appropriate for given developmental fates. BR homeostasis is maintained in part by transcriptional feedback regulation loops that control the expression of key metabolic enzymes, including the BR-inactivating enzymes BAS1 (CYP734A1, formerly CYP72B1) and SOB7 (CYP72C1). Here, we find that the NAC transcription factor (TF) ATAF2 binds the promoters of BAS1 and SOB7 to suppress their expression. ATAF2 restricts the tissue-specific expression of BAS1 and SOB7 in planta. ATAF2 loss- and gain-of-function seedlings have opposite BR-response phenotypes for hypocotyl elongation. ATAF2 modulates hypocotyl growth in a light-dependent manner, with the photoreceptor phytochrome A playing a major role. The photomorphogenic phenotypes of ATAF2 loss- and gain-of-function seedlings are suppressed by treatment with the BR biosynthesis inhibitor brassinazole. Moreover, the disruption of BAS1 and SOB7 abolishes the short-hypocotyl phenotype of ATAF2 loss-of-function seedlings in low fluence rate white light, demonstrating an ATAF2-mediated connection between BR catabolism and photomorphogenesis. ATAF2 expression is suppressed by both BRs and light, which demonstrates the existence of an ATAF2-BAS1/SOB7-BR-ATAF2 feedback regulation loop, as well as a light-ATAF2-BAS1/SOB7-BR-photomorphogenesis pathway. ATAF2 also modulates root growth by regulating BR catabolism. As it is known to regulate plant defense and auxin biosynthesis, ATAF2 therefore acts as a central regulator of plant defense, hormone metabolism and light-mediated seedling development.
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Affiliation(s)
- Hao Peng
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - Jianfei Zhao
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA Molecular Plant Science Graduate Program, Washington State University, Pullman, WA 99164, USA
| | - Michael M Neff
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA Molecular Plant Science Graduate Program, Washington State University, Pullman, WA 99164, USA
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Miller M, Song Q, Shi X, Juenger TE, Chen ZJ. Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of Arabidopsis. Nat Commun 2015; 6:7453. [PMID: 26154604 DOI: 10.1038/ncomms8453] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 05/11/2015] [Indexed: 11/09/2022] Open
Abstract
The genetic distance between hybridizing parents affects heterosis; however, the mechanisms for this remain unclear. Here we report that this genetic distance correlates with natural variation and epigenetic regulation of circadian clock-mediated stress responses. In intraspecific hybrids of Arabidopsis thaliana, genome-wide expression of many biotic and abiotic stress-responsive genes is diurnally repressed and this correlates with biomass heterosis and biomass quantitative trait loci. Expression differences of selected stress-responsive genes among diverse ecotypes are predictive of heterosis in their hybrids. Stress-responsive genes are repressed in the hybrids under normal conditions but are induced to mid-parent or higher levels under stress at certain times of the day, potentially balancing the tradeoff between stress responses and growth. Consistent with this hypothesis, repression of two candidate stress-responsive genes increases growth vigour. Our findings may therefore provide new criteria for effectively selecting parents to produce high- or low-yield hybrids.
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Affiliation(s)
- Marisa Miller
- Departments of Molecular Biosciences and of Integrative Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Qingxin Song
- Departments of Molecular Biosciences and of Integrative Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Xiaoli Shi
- Departments of Molecular Biosciences and of Integrative Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Thomas E Juenger
- Departments of Molecular Biosciences and of Integrative Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Z Jeffrey Chen
- 1] Departments of Molecular Biosciences and of Integrative Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA [2] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
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Miller M, Song Q, Shi X, Juenger TE, Chen ZJ. Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of Arabidopsis. Nat Commun 2015. [PMID: 26154604 DOI: 10.1038/ncomms845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
The genetic distance between hybridizing parents affects heterosis; however, the mechanisms for this remain unclear. Here we report that this genetic distance correlates with natural variation and epigenetic regulation of circadian clock-mediated stress responses. In intraspecific hybrids of Arabidopsis thaliana, genome-wide expression of many biotic and abiotic stress-responsive genes is diurnally repressed and this correlates with biomass heterosis and biomass quantitative trait loci. Expression differences of selected stress-responsive genes among diverse ecotypes are predictive of heterosis in their hybrids. Stress-responsive genes are repressed in the hybrids under normal conditions but are induced to mid-parent or higher levels under stress at certain times of the day, potentially balancing the tradeoff between stress responses and growth. Consistent with this hypothesis, repression of two candidate stress-responsive genes increases growth vigour. Our findings may therefore provide new criteria for effectively selecting parents to produce high- or low-yield hybrids.
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Affiliation(s)
- Marisa Miller
- Departments of Molecular Biosciences and of Integrative Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Qingxin Song
- Departments of Molecular Biosciences and of Integrative Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Xiaoli Shi
- Departments of Molecular Biosciences and of Integrative Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Thomas E Juenger
- Departments of Molecular Biosciences and of Integrative Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Z Jeffrey Chen
- 1] Departments of Molecular Biosciences and of Integrative Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA [2] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
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Seaton DD, Smith RW, Song YH, MacGregor DR, Stewart K, Steel G, Foreman J, Penfield S, Imaizumi T, Millar AJ, Halliday KJ. Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature. Mol Syst Biol 2015; 11:776. [PMID: 25600997 PMCID: PMC4332151 DOI: 10.15252/msb.20145766] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Clock-regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best-understood clock output pathways in Arabidopsis, which control key regulators of flowering and elongation growth. In flowering, the model predicted regulatory links from the clock to CYCLING DOF FACTOR 1 (CDF1) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) transcription. Physical interaction data support these links, which create threefold feed-forward motifs from two clock components to the floral regulator FT. In hypocotyl growth, the model described clock-regulated transcription of PHYTOCHROME-INTERACTING FACTOR 4 and 5 (PIF4, PIF5), interacting with post-translational regulation of PIF proteins by phytochrome B (phyB) and other light-activated pathways. The model predicted bimodal and end-of-day PIF activity profiles that are observed across hundreds of PIF-regulated target genes. In the response to temperature, warmth-enhanced PIF4 activity explained the observed hypocotyl growth dynamics but additional, temperature-dependent regulators were implicated in the flowering response. Integrating these two pathways with the clock model highlights the molecular mechanisms that coordinate plant development across changing conditions.
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Affiliation(s)
- Daniel D Seaton
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Robert W Smith
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Young Hun Song
- Department of Biology, University of Washington, Seattle, WA, USA
| | | | - Kelly Stewart
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Gavin Steel
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Julia Foreman
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Karen J Halliday
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Nolte C, Staiger D. RNA around the clock - regulation at the RNA level in biological timing. FRONTIERS IN PLANT SCIENCE 2015; 6:311. [PMID: 25999975 PMCID: PMC4419606 DOI: 10.3389/fpls.2015.00311] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/19/2015] [Indexed: 05/21/2023]
Abstract
The circadian timing system in plants synchronizes their physiological functions with the environment. This is achieved by a global control of gene expression programs with a considerable part of the transcriptome undergoing 24-h oscillations in steady-state abundance. These circadian oscillations are driven by a set of core clock proteins that generate their own 24-h rhythm through periodic feedback on their own transcription. Additionally, post-transcriptional events are instrumental for oscillations of core clock genes and genes in clock output. Here we provide an update on molecular events at the RNA level that contribute to the 24-h rhythm of the core clock proteins and shape the circadian transcriptome. We focus on the circadian system of the model plant Arabidopsis thaliana but also discuss selected regulatory principles in other organisms.
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Affiliation(s)
| | - Dorothee Staiger
- *Correspondence: Dorothee Staiger, Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Universitaetsstrasse 25, Bielefeld D-33615, Germany
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Prevalence, evolution, and cis-regulation of diel transcription in Chlamydomonas reinhardtii. G3-GENES GENOMES GENETICS 2014; 4:2461-71. [PMID: 25354782 PMCID: PMC4267941 DOI: 10.1534/g3.114.015032] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Endogenous (circadian) and exogenous (e.g., diel) biological rhythms are a prominent feature of many living systems. In green algal species, knowledge of the extent of diel rhythmicity of genome-wide gene expression, its evolution, and its cis-regulatory mechanism is limited. In this study, we identified cyclically expressed genes under diel conditions in Chlamydomonas reinhardtii and found that ~50% of the 17,114 annotated genes exhibited cyclic expression. These cyclic expression patterns indicate a clear succession of biological processes during the course of a day. Among 237 functional categories enriched in cyclically expressed genes, >90% were phase-specific, including photosynthesis, cell division, and motility-related processes. By contrasting cyclic expression between C. reinhardtii and Arabidopsis thaliana putative orthologs, we found significant but weak conservation in cyclic gene expression patterns. On the other hand, within C. reinhardtii cyclic expression was preferentially maintained between duplicates, and the evolution of phase between paralogs is limited to relatively minor time shifts. Finally, to better understand the cis regulatory basis of diel expression, putative cis-regulatory elements were identified that could predict the expression phase of a subset of the cyclic transcriptome. Our findings demonstrate both the prevalence of cycling genes as well as the complex regulatory circuitry required to control cyclic expression in a green algal model, highlighting the need to consider diel expression in studying algal molecular networks and in future biotechnological applications.
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Nozoye T, Nagasaka S, Bashir K, Takahashi M, Kobayashi T, Nakanishi H, Nishizawa NK. Nicotianamine synthase 2 localizes to the vesicles of iron-deficient rice roots, and its mutation in the YXXφ or LL motif causes the disruption of vesicle formation or movement in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:246-60. [PMID: 24251791 DOI: 10.1111/tpj.12383] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 11/07/2013] [Accepted: 11/12/2013] [Indexed: 05/03/2023]
Abstract
Graminaceous plants release mugineic acid family phytosiderophores (MAs) to acquire iron from the soil. Here, we show that deoxymugineic acid (DMA) secretion from rice roots fluctuates throughout the day, and that vesicles accumulate in roots before MAs secretion. We developed transgenic rice plants that express rice nicotianamine (NA) synthase (NAS) 2 (OsNAS2) fused to synthetic green fluorescent protein (sGFP) under the control of its own promoter. In root cells, OsNAS2-sGFP fluorescence was observed in a dot-like pattern, moving dynamically within the cell. This suggests that these vesicles are involved in NA and DMA biosynthesis. A tyrosine motif and a di-leucine motif, which have been reported to be involved in cellular transport, are conserved in all identified NAS proteins in plants. OsNAS2 mutated in the tyrosine motif showed NAS activity and was localized to the vesicles; however, these vesicles stuck together and did not move. On the other hand, OsNAS2 mutated in the di-leucine motif lost NAS activity and did not localize to these vesicles. The amounts of NA and DMA produced and the amount of DMA secreted by OsNAS2-sGFP plants were significantly higher than in non-transformants and domain-mutated lines, suggesting that OsNAS2-sGFP, but not the mutated forms, was functional in vivo. Overall, the localization of NAS to vesicles and the transport of these vesicles are crucial steps in NA synthesis, leading to DMA synthesis and secretion in rice.
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Affiliation(s)
- Tomoko Nozoye
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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38
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McClung CR, Xie Q. Measurement of luciferase rhythms. Methods Mol Biol 2014; 1158:1-11. [PMID: 24792041 DOI: 10.1007/978-1-4939-0700-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Firefly luciferase (LUC) is a sensitive and versatile reporter for the analysis of gene expression. Transgenic plants carrying CLOCK GENE promoter:LUC fusions can be assayed with high temporal resolution. LUC measurement is sensitive, noninvasive, and nondestructive and can be readily automated, greatly facilitating genetic studies. For these reasons, LUC fusion analysis is a mainstay in the study of plant circadian clocks.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA,
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39
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Wang G, Zhang C, Battle S, Lu H. The phosphate transporter PHT4;1 is a salicylic acid regulator likely controlled by the circadian clock protein CCA1. FRONTIERS IN PLANT SCIENCE 2014; 5:701. [PMID: 25566276 PMCID: PMC4267192 DOI: 10.3389/fpls.2014.00701] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 11/25/2014] [Indexed: 05/08/2023]
Abstract
The small phenolic compound salicylic acid (SA) plays a critical role in plant defense against broad-spectrum of pathogens. The phosphate transporter gene PHT4;1 was previously shown to affect SA-mediated defense and its expression is regulated by the circadian clock. To further understand how PHT4;1 affects SA accumulation, here we analyzed the genetic interactions between the gain-of-function mutant pht4;1-1 and several known SA mutants, including sid2-1, ald1-1, eds5-3, and pad4-1. The genetic analysis was conducted in the acd6-1 background since the change of acd6-1 dwarfism can be used as a convenient readout for the change of defense levels caused by impairments in some SA genes. We found that compared with the corresponding double mutants, the triple mutants acd6-1pht4;1-1ald1-1, acd6-1pht4;1-1eds5-3, and acd6-1pht4;1-1pad4-1 accumulated lower levels of SA and PR1 transcripts, suggesting that PHT4;1 contributes to acd6-1-conferred defense phenotypes independently of these known SA regulators. Although some triple mutants had wild type (wt)-like levels of SA and PR1 transcripts, these plants were smaller than wt and displayed minor cell death, suggesting that additional regulatory pathways contribute to acd6-1-conferred dwarfism and cell death. Our data further showed that circadian expression of PHT4;1 was dependent on CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), a central oscillator component of Arabidopsis circadian clock. Recombinant CCA1 protein was demonstrated to bind to the PHT4;1 promoter in electrophoretic mobility shift assays, suggesting a direct transcriptional regulation of PHT4;1 by CCA1. Together these results indicate that PHT4;1 is a SA regulator acting independently of several known SA genes and they also implicate a role of the circadian clock mediated by CCA1 in regulating phosphate transport and/or innate immunity in Arabidopsis.
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Affiliation(s)
| | | | | | - Hua Lu
- *Correspondence: Hua Lu, Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA e-mail:
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40
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Emerging roles for post-transcriptional regulation in circadian clocks. Nat Neurosci 2013; 16:1544-50. [PMID: 24165681 DOI: 10.1038/nn.3543] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 09/12/2013] [Indexed: 12/13/2022]
Abstract
Circadian clocks temporally organize behavior and physiology across the 24-h day. Great progress has been made in understanding the molecular basis of timekeeping, with a focus on transcriptional feedback networks that are post-translationally modulated. Yet emerging evidence indicates an important role for post-transcriptional regulation, from splicing, polyadenylation and mRNA stability to translation and non-coding functions exemplified by microRNAs. This level of regulation affects virtually all aspects of circadian systems, from the core timing mechanism and input pathways that synchronize clocks to the environment and output pathways that control overt rhythmicity. We hypothesize that post-transcriptional control confers on circadian clocks enhanced robustness as well as the ability to adapt to different environments. As much of what is known derives from nonneural cells or tissues, future work will be required to investigate the role of post-transcriptional regulation in neural clocks.
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41
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Abstract
Large-scale biology among plant species, as well as comparative genomics of circadian clock architecture and clock-regulated output processes, have greatly advanced our understanding of the endogenous timing system in plants.
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Hong S, Kim SA, Guerinot ML, McClung CR. Reciprocal interaction of the circadian clock with the iron homeostasis network in Arabidopsis. PLANT PHYSIOLOGY 2013; 161:893-903. [PMID: 23250624 PMCID: PMC3561027 DOI: 10.1104/pp.112.208603] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 12/17/2012] [Indexed: 05/18/2023]
Abstract
In plants, iron (Fe) uptake and homeostasis are critical for survival, and these processes are tightly regulated at the transcriptional and posttranscriptional levels. Circadian clocks are endogenous oscillating mechanisms that allow an organism to anticipate environmental changes to coordinate biological processes both with one another and with the environmental day/night cycle. The plant circadian clock controls many physiological processes through rhythmic expression of transcripts. In this study, we examined the expression of three Fe homeostasis genes (IRON REGULATED TRANSPORTER1 [IRT1], BASIC HELIX LOOP HELIX39, and FERRITIN1) in Arabidopsis (Arabidopsis thaliana) using promoter:LUCIFERASE transgenic lines. Each of these promoters showed circadian regulation of transcription. The circadian clock monitors a number of clock outputs and uses these outputs as inputs to modulate clock function. We show that this is also true for Fe status. Fe deficiency results in a lengthened circadian period. We interrogated mutants impaired in the Fe homeostasis response, including irt1-1, which lacks the major high-affinity Fe transporter, and fit-2, which lacks Fe deficiency-induced TRANSCRIPTION FACTOR1, a basic helix-loop-helix transcription factor necessary for induction of the Fe deficiency response. Both mutants exhibit symptoms of Fe deficiency, including lengthened circadian period. To determine which components are involved in this cross talk between the circadian and Fe homeostasis networks, we tested clock- or Fe homeostasis-related mutants. Mutants defective in specific clock gene components were resistant to the change in period length under different Fe conditions observed in the wild type, suggesting that these mutants are impaired in cross talk between Fe homeostasis and the circadian clock.
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Thellier M, Lüttge U. Plant memory: a tentative model. PLANT BIOLOGY (STUTTGART, GERMANY) 2013; 15:1-12. [PMID: 23121044 DOI: 10.1111/j.1438-8677.2012.00674.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 08/09/2012] [Indexed: 05/20/2023]
Abstract
All memory functions have molecular bases, namely in signal reception and transduction, and in storage and recall of information. Thus, at all levels of organisation living organisms have some kind of memory. In plants one may distinguish two types. There are linear pathways from reception of signals and propagation of effectors to a type of memory that may be described by terms such as learning, habituation or priming. There is a storage and recall memory based on a complex network of elements with a high degree of integration and feedback. The most important elements envisaged are calcium waves, epigenetic modifications of DNA and histones, and regulation of timing via a biological clock. Experiments are described that document the occurrence of the two sorts of memory and which show how they can be distinguished. A schematic model of plant memory is derived as emergent from integration of the various modules. Possessing the two forms of memory supports the fitness of plants in response to environmental stimuli and stress.
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44
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Salomé PA, Oliva M, Weigel D, Krämer U. Circadian clock adjustment to plant iron status depends on chloroplast and phytochrome function. EMBO J 2012; 32:511-23. [PMID: 23241948 PMCID: PMC3579136 DOI: 10.1038/emboj.2012.330] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 11/22/2012] [Indexed: 01/21/2023] Open
Abstract
Plant chloroplasts are not only the main cellular location for storage of elemental iron (Fe), but also the main site for Fe, which is incorporated into chlorophyll, haem and the photosynthetic machinery. How plants measure internal Fe levels is unknown. We describe here a new Fe-dependent response, a change in the period of the circadian clock. In Arabidopsis, the period lengthens when Fe becomes limiting, and gradually shortens as external Fe levels increase. Etiolated seedlings or light-grown plants treated with plastid translation inhibitors do not respond to changes in Fe supply, pointing to developed chloroplasts as central hubs for circadian Fe sensing. Phytochrome-deficient mutants maintain a short period even under Fe deficiency, stressing the role of early light signalling in coupling the clock to Fe responses. Further mutant and pharmacological analyses suggest that known players in plastid-to-nucleus signalling do not directly participate in Fe sensing. We propose that the sensor governing circadian Fe responses defines a new retrograde pathway that involves a plastid-encoded protein that depends on phytochromes and the functional state of chloroplasts. The circadian clock of Arabidopsis is found to be hardwired to cellular iron levels, with chloroplasts playing a central role in iron sensing.
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Affiliation(s)
- Patrice A Salomé
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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45
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CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses. Proc Natl Acad Sci U S A 2012; 109:17129-34. [PMID: 23027948 DOI: 10.1073/pnas.1209148109] [Citation(s) in RCA: 244] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Organisms have evolved endogenous biological clocks as internal timekeepers to coordinate metabolic processes with the external environment. Here, we seek to understand the mechanism of synchrony between the oscillator and products of metabolism known as Reactive Oxygen Species (ROS) in Arabidopsis thaliana. ROS-responsive genes exhibit a time-of-day-specific phase of expression under diurnal and circadian conditions, implying a role of the circadian clock in transcriptional regulation of these genes. Hydrogen peroxide production and scavenging also display time-of-day phases. Mutations in the core-clock regulator, CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), affect the transcriptional regulation of ROS-responsive genes, ROS homeostasis, and tolerance to oxidative stress. Mis-expression of EARLY FLOWERING 3, LUX ARRHYTHMO, and TIMING OF CAB EXPRESSION 1 affect ROS production and transcription, indicating a global effect of the clock on the ROS network. We propose CCA1 as a master regulator of ROS homeostasis through association with the Evening Element in promoters of ROS genes in vivo to coordinate time-dependent responses to oxidative stress. We also find that ROS functions as an input signal that affects the transcriptional output of the clock, revealing an important link between ROS signaling and circadian output. Temporal coordination of ROS signaling by CCA1 and the reciprocal control of circadian output by ROS reveal a mechanistic link that allows plants to master oxidative stress responses.
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46
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Park MJ, Seo PJ, Park CM. CCA1 alternative splicing as a way of linking the circadian clock to temperature response in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2012; 7:1194-6. [PMID: 22899064 PMCID: PMC3489659 DOI: 10.4161/psb.21300] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Most living organisms on the earth have the circadian clock to synchronize their biochemical processes and physiological activities with environmental changes to optimize their propagation and survival. CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) is one of the core clock components in Arabidopsis. Notably, it is also associated with cold acclimation. However, it is largely unknown how CCA1 activity is modulated by low temperatures. We found that the CCA1 activity is self-regulated by a splice variant CCA1β and the CCA1β production is modulated by low temperatures, linking the circadian clock with cold acclimation. CCA1β competitively inhibits the activities of functional CCA1α and LATE ELONGATED HYPOCOTYL (LHY) transcription factors by forming nonfunctional CCA1α-CCA1β and LHY-CCA1β heterodimers. Consequently, CCA1β-overexpressing plants (35S:CCA1β) exhibit shortened circadian periods as observed in cca1 lhy double mutants. In addition, elongated hypocotyls and petioles and delayed flowering of CCA1α-overexpressing plants (35S:CCA1α) were rescued by coexpression of CCA1β. Interestingly, low temperatures suppress CCA1 alternative splicing and thus derepress the CCA1α activity in inducing cold tolerance. These observations indicate that a cold-responsive self-regulatory circuit of CCA1 plays a role in plant responses to low temperatures.
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Affiliation(s)
- Mi-Jeong Park
- Department of Chemistry; Seoul National University; Seoul, Korea
| | - Pil Joon Seo
- Department of Chemistry; Seoul National University; Seoul, Korea
| | - Chung-Mo Park
- Department of Chemistry; Seoul National University; Seoul, Korea
- Plant Genomics and Breeding Institute; Seoul National University; Seoul, Korea
- Correspondence to: Chung-Mo Park,
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47
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Abstract
Endogenous circadian rhythms regulate many aspects of an organism's behavior, physiology and development. These daily oscillations synchronize with the environment to generate robust rhythms, resulting in enhanced fitness and growth vigor in plants. Collective studies over the years have focused on understanding the transcription-based oscillator in Arabidopsis. Recent advances combining mechanistic data with genome-wide approaches have contributed significantly to a more comprehensive understanding of the molecular interactions within the oscillator, and with clock-controlled pathways. This review focuses on the regulatory mechanisms within the oscillator, highlighting key connections between new and existing components, and direct mechanistic links to downstream pathways that control overt rhythms in the whole plant.
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Affiliation(s)
- Dawn H. Nagel
- Section of Cell and Developmental Biology, Division of Biological Sciences; University of California San Diego, La Jolla, CA 92093, USA
- Center for Chronobiology; University of California San Diego, La Jolla, CA 92093, USA
| | - Steve A. Kay
- Section of Cell and Developmental Biology, Division of Biological Sciences; University of California San Diego, La Jolla, CA 92093, USA
- Center for Chronobiology; University of California San Diego, La Jolla, CA 92093, USA
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48
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Hua W, Li RJ, Zhan GM, Liu J, Li J, Wang XF, Liu GH, Wang HZ. Maternal control of seed oil content in Brassica napus: the role of silique wall photosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:432-44. [PMID: 21954986 DOI: 10.1111/j.1365-313x.2011.04802.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Seed oil content is an important agronomic trait in rapeseed. However, our understanding of the regulatory processes controlling oil accumulation is still limited. Using two rapeseed lines (zy036 and 51070) with contrasting oil content, we found that maternal genotype greatly affects seed oil content. Genetic and physiological evidence indicated that difference in the local and tissue-specific photosynthetic activity in the silique wall (a maternal tissue) was responsible for the different seed oil contents. This effect was mimicked by in planta manipulation of silique wall photosynthesis. Furthermore, the starch content and expression of the important lipid synthesis regulatory gene WRINKLED1 in developing seeds were linked with silique wall photosynthetic activity. 454 pyrosequencing was performed to explore the possible molecular mechanism for the difference in silique wall photosynthesis between zy036 and 51070. Interestingly, the results suggested that photosynthesis-related genes were over-represented in both total silique wall expressed genes and genes that were differentially expressed between genotypes. A potential regulatory mechanism for elevated photosynthesis in the zy036 silique wall is proposed on the basis of knowledge from Arabidopsis. Differentially expressed ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)-related genes were used for further investigations. Oil content correlated closely with BnRBCS1A expression levels and Rubisco activities in the silique wall, but not in the leaf. Taken together, our results highlight an important role of silique wall photosynthesis in the regulation of seed oil content in terms of maternal effects.
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Affiliation(s)
- Wei Hua
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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49
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Staiger D, Green R. RNA-based regulation in the plant circadian clock. TRENDS IN PLANT SCIENCE 2011; 16:517-523. [PMID: 21782493 DOI: 10.1016/j.tplants.2011.06.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 06/03/2011] [Accepted: 06/14/2011] [Indexed: 05/31/2023]
Abstract
The circadian clock is an endogenous, approximately 24-h timer that enables plants to anticipate daily changes in their environment and regulates a considerable fraction of the transcriptome. At the core of the circadian system is the oscillator, made up of interconnected feedback loops, involving transcriptional regulation of clock genes and post-translational modification of clock proteins. Recently, it has become clear that post-transcriptional events are also critical for shaping rhythmic mRNA and protein profiles. This review covers regulation at the RNA level of both the core clock and output genes in Arabidopsis (Arabidopsis thaliana), with comparisons with other model organisms. We discuss the role of splicing, mRNA decay and translational regulation as well as recent insights into rhythms of noncoding regulatory RNAs.
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Affiliation(s)
- Dorothee Staiger
- Molecular Cell Physiology, Bielefeld University, D-33501 Bielefeld, Germany.
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50
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Downstream of the plant circadian clock: output pathways for the control of physiology and development. Essays Biochem 2011; 49:53-69. [DOI: 10.1042/bse0490053] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The plant circadian clock controls many aspects of growth and development, allowing an individual to adapt its physiology and metabolism in anticipation of diurnal and seasonal environmental changes. Circadian regulation of hormone levels and hormonal signalling modulates many features of development, including daily growth patterns and the breaking of seed dormancy. The clock also plays a role in seasonal day-length perception, allowing plants to optimally time key development transitions, such as reproduction. Moreover, the clock restricts (gates) the sensitivity of a plant's response to environmental cues, such as light and stress, to specific times of the day, ensuring that the plant can distinguish between normal fluctuations and longer-term changes. The central oscillator controls many of these output pathways via rhythmic gene expression, with several of the core clock components encoding transcription factors. Post-transcriptional processes are also likely to make an important contribution to the circadian regulation of output pathways. The plant circadian clock plays a role in regulating fitness, hybrid vigour and numerous stress responses. Thus elucidating the complexities of the circadian output mechanisms and their regulation may provide new avenues for crop enhancement.
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