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Wu S, Gao Y, Zhang Q, Liu F, Hu W. Application of Multi-Omics Technologies to the Study of Phytochromes in Plants. Antioxidants (Basel) 2024; 13:99. [PMID: 38247523 PMCID: PMC10812741 DOI: 10.3390/antiox13010099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Phytochromes (phy) are distributed in various plant organs, and their physiological effects influence plant germination, flowering, fruiting, and senescence, as well as regulate morphogenesis throughout the plant life cycle. Reactive oxygen species (ROS) are a key regulatory factor in plant systemic responses to environmental stimuli, with an attractive regulatory relationship with phytochromes. With the development of high-throughput sequencing technology, omics techniques have become powerful tools, and researchers have used omics techniques to facilitate the big data revolution. For an in-depth analysis of phytochrome-mediated signaling pathways, integrated multi-omics (transcriptomics, proteomics, and metabolomics) approaches may provide the answer from a global perspective. This article comprehensively elaborates on applying multi-omics techniques in studying phytochromes. We describe the current research status and future directions on transcriptome-, proteome-, and metabolome-related network components mediated by phytochromes when cells are subjected to various stimulation. We emphasize the importance of multi-omics technologies in exploring the effects of phytochromes on cells and their molecular mechanisms. Additionally, we provide methods and ideas for future crop improvement.
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Affiliation(s)
- Shumei Wu
- Basic Medical Experiment Center, School of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang 330004, China; (S.W.); (Y.G.); (Q.Z.)
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332000, China
| | - Yue Gao
- Basic Medical Experiment Center, School of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang 330004, China; (S.W.); (Y.G.); (Q.Z.)
| | - Qi Zhang
- Basic Medical Experiment Center, School of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang 330004, China; (S.W.); (Y.G.); (Q.Z.)
| | - Fen Liu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332000, China
| | - Weiming Hu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332000, China
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2
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Lin X, Huang Y, Rao Y, Ouyang L, Zhou D, Zhu C, Fu J, Chen C, Yin J, Bian J, He H, Zou G, Xu J. A base substitution in OsphyC disturbs its Interaction with OsphyB and affects flowering time and chlorophyll synthesis in rice. BMC PLANT BIOLOGY 2022; 22:612. [PMID: 36572865 PMCID: PMC9793604 DOI: 10.1186/s12870-022-04011-y] [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: 08/24/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Phytochromes are important photoreceptors in plants, and play essential roles in photomorphogenesis. The functions of PhyA and PhyB in plants have been fully analyzed, while those of PhyC in plant are not well understood. RESULTS A rice mutant, late heading date 3 (lhd3), was characterized, and the gene LHD3 was identified with a map-based cloning strategy. LHD3 encodes phytochrome C in rice. Animo acid substitution in OsphyC disrupted its interaction with OsphyB or itself, restraining functional forms of homodimer or heterodimer formation. Compared with wild-type plants, the lhd3 mutant exhibited delayed flowering under both LD (long-day) and SD (short-day) conditions, and delayed flowering time was positively associated with the day length via the Ehd1 pathway. In addition, lhd3 showed a pale-green-leaf phenotype and a slower chlorophyll synthesis rate during the greening process. The transcription patterns of many key genes involved in photoperiod-mediated flowering and chlorophyll synthesis were altered in lhd3. CONCLUSION The dimerization of OsPhyC is important for its functions in the regulation of chlorophyll synthesis and heading. Our findings will facilitate efforts to further elucidate the function and mechanism of OsphyC and during light signal transduction in rice.
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Affiliation(s)
- Xiaoli Lin
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Yongping Huang
- National Engineering Laboratory of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
| | - Yuchun Rao
- College of Chemistry and Life Sciences, Zhejiang Normal University, 321004, Jinhua, China
| | - Linjuan Ouyang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Dahu Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Changlan Zhu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Junru Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Chunlian Chen
- National Engineering Laboratory of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
| | - Jianhua Yin
- National Engineering Laboratory of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
| | - Jianmin Bian
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 330045, Nanchang, China.
| | - Guoxing Zou
- National Engineering Laboratory of Rice (Nanchang), Rice Research Institute, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China.
| | - Jie Xu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 330045, Nanchang, China.
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Wang H, Jia G, Zhang N, Zhi H, Xing L, Zhang H, Sui Y, Tang S, Li M, Zhang H, Feng B, Wu C, Diao X. Domestication-associated PHYTOCHROME C is a flowering time repressor and a key factor determining Setaria as a short-day plant. THE NEW PHYTOLOGIST 2022; 236:1809-1823. [PMID: 36178253 DOI: 10.1111/nph.18493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Phytochromes play vital roles in the regulation of flowering time, but little is known in Panicoideae species, especially the C4 model Setaria. Here, genomic variations of PHYTOCHROME C (PHYC) between wild and cultivated Setaria gene pools were analysed and three SiphyC mutants were identified. The function of SiPHYC was verified by CRISPR-Cas9 approach and transcriptome sequencing. Furthermore, efficiency of indoor cultivation of SiphyC mutants were systematically evaluated. An extreme purified selection of PHYC was detected in wild to cultivated domestication process of Setaria. SiphyC mutants and knockout transgenic plants showed an early heading date and a loss of response to short-day photoperiod. Furthermore, variable expression of SiFTa, SiMADS14 and SiMADS15 might be responsible for promoting flowering of SiphyC mutants. Moreover, SiphyC mutant was four times that of the indoor plot ratio of wild-type and produced over 200 seeds within 45 d per individual. Our results suggest that domestication-associated SiPHYC repressed flowering and determined Setaria as a short-day plant, and SiphyC mutants possess the potential for creating efficient indoor cultivation system suitable for research on Setaria as a model, and either for maize or sorghum as well.
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Affiliation(s)
- Hailong Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712000, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ning Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lihe Xing
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haoshan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yi Sui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mingzhe Li
- Institute of Dry-land Agriculture, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, Hebei, 053000, China
| | - Haijin Zhang
- Institute of Dry Land Agroforestry, Liaoning Academy of Agricultural Sciences, Chaoyang, Liaoning, 122000, China
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712000, China
| | - Chuanyin Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Li B, Du X, Fei Y, Wang F, Xu Y, LI X, Li W, Chen Z, Fan F, Wang J, Tao Y, Jiang Y, Zhu QH, Yang J. Efficient Breeding of Early-Maturing Rice Cultivar by Editing PHYC via CRISPR/Cas9. RICE (NEW YORK, N.Y.) 2021; 14:86. [PMID: 34643821 PMCID: PMC8514591 DOI: 10.1186/s12284-021-00527-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/03/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Bin Li
- Institute of Life Science, Jiangsu University, Zhenjiang, 212013 Jiangsu China
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
| | - Xi Du
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yunyan Fei
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Fangquan Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yang Xu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Xia LI
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Wenqi Li
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Zhihui Chen
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Fangjun Fan
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Jun Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yajun Tao
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yanjie Jiang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT Australia
| | - Jie Yang
- Institute of Life Science, Jiangsu University, Zhenjiang, 212013 Jiangsu China
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Nanjing Branch of Chinese National Center for Rice Improvement, Nanjing, 210014 Jiangsu China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 Jiangsu China
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Arefian M, Bhagya N, Prasad TSK. Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops. Biol Rev Camb Philos Soc 2021; 96:2164-2191. [PMID: 34047006 DOI: 10.1111/brv.12748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.
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Affiliation(s)
- Mohammad Arefian
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - N Bhagya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
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6
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De Luca G, Fochesato S, Lavergne J, Forest KT, Barakat M, Ortet P, Achouak W, Heulin T, Verméglio A. Light on the cell cycle of the non-photosynthetic bacterium Ramlibacter tataouinensis. Sci Rep 2019; 9:16505. [PMID: 31712689 PMCID: PMC6848086 DOI: 10.1038/s41598-019-52927-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/22/2019] [Indexed: 12/27/2022] Open
Abstract
Ramlibacter tataouinensis TTB310, a non-photosynthetic betaproteobacterium isolated from a semi-arid region of southern Tunisia, forms both rods and cysts. Cysts are resistant to desiccation and divide when water and nutrients are available. Rods are motile and capable of dissemination. Due to the strong correlation between sunlight and desiccation, light is probably an important external signal for anticipating desiccating conditions. Six genes encoding potential light sensors were identified in strain TTB310. Two genes encode for bacteriophytochromes, while the four remaining genes encode for putative blue light receptors. We determined the spectral and photochemical properties of the two recombinant bacteriophytochromes RtBphP1 and RtBphP2. In both cases, they act as sensitive red light detectors. Cyst divisions and a complete cyst-rod-cyst cycle are the main processes in darkness, whereas rod divisions predominate in red or far-red light. Mutant phenotypes caused by the inactivation of genes encoding bacteriophytochromes or heme oxygenase clearly show that both bacteriophytochromes are involved in regulating the rod-rod division. This process could favor rapid rod divisions at sunrise, after dew formation but before the progressive onset of desiccation. Our study provides the first evidence of a light-based strategy evolved in a non-photosynthetic bacterium to exploit scarse water in a desert environment.
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Affiliation(s)
- Gilles De Luca
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Sylvain Fochesato
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Jérôme Lavergne
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Katrina T Forest
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mohamed Barakat
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Philippe Ortet
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
| | - Thierry Heulin
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France.
| | - André Verméglio
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMiRE, Saint Paul-Lez-Durance, F-13108, France
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7
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Lin C, Sauter M. Control of Adventitious Root Architecture in Rice by Darkness, Light, and Gravity. PLANT PHYSIOLOGY 2018; 176:1352-1364. [PMID: 29242375 PMCID: PMC5813538 DOI: 10.1104/pp.17.01540] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/10/2017] [Indexed: 05/17/2023]
Abstract
Rice (Oryza sativa) is a semiaquatic plant that is well adapted to partial flooding. Rice stems develop adventitious root (AR) primordia at each node that slowly mature but emerge only when the plant gets flooded, leading to the formation of a whole new secondary root system upon flooding. AR growth is induced by ethylene that accumulates in submerged plant tissues due to its lowered diffusion rate in water. Here, we report that the architecture of the secondary root system in flooded rice plants is controlled not only by altered gas diffusion but also by gravity and light. While ethylene promotes the emergence and growth of ARs, gravity and light determine their gravitropic setpoint angle (i.e. the deviation of growth direction relative to vertical). ARs grow upward at about 120° in the dark and downward at 54° in the light. The upward growth direction is conserved in indica and japonica rice varieties, suggestive of a conserved trait in rice. Experiments with a klinostat and with inverted stem orientation revealed that gravity promotes upward growth by about 10°. Red, far-red, and blue light lead to negative phototropism in a dose-dependent manner, with blue light being most effective, indicating that phytochrome and blue light signaling control AR system architecture. The cpt1 (coleoptile phototropism1) mutant, which lacks one of the phototropin-interacting CPT proteins, shows reduced sensitivity to blue light. Hence, the gravitropic setpoint angle of rice ARs is controlled by genetic and environmental factors that likely balance the need for oxygen supply (upward growth) with avoidance of root desiccation (downward growth).
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Affiliation(s)
- Chen Lin
- Plant Developmental Biology and Plant Physiology, University of Kiel, 24118 Kiel, Germany
| | - Margret Sauter
- Plant Developmental Biology and Plant Physiology, University of Kiel, 24118 Kiel, Germany
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8
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Inoue K, Nishihama R, Kohchi T. Evolutionary origin of phytochrome responses and signaling in land plants. PLANT, CELL & ENVIRONMENT 2017; 40:2502-2508. [PMID: 28098347 DOI: 10.1111/pce.12908] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 06/06/2023]
Abstract
Phytochromes comprise one of the major photoreceptor families in plants, and they regulate many aspects of plant growth and development throughout the plant life cycle. A canonical land plant phytochrome originated in the common ancestor of streptophytes. Phytochromes have diversified in seed plants and some basal land plants because of lineage-specific gene duplications that occurred during the course of land plant evolution. Molecular genetic analyses using Arabidopsis thaliana suggested that there are two types of phytochromes in angiosperms, light-labile type I and light-stable type II, which have different signaling mechanisms and which regulate distinct responses. In basal land plants, little is known about molecular mechanisms of phytochrome signaling, although red light/far-red photoreversible physiological responses and the distribution of phytochrome genes are relatively well documented. Recent advances in molecular genetics using the moss Physcomitrella patens and the liverwort Marchantia polymorpha revealed that basal land plants show far-red-induced responses and that the establishment of phytochrome-mediated transcriptional regulation dates back to at least the common ancestor of land plants. In this review, we summarize our knowledge concerning functions of land plant phytochromes, especially in basal land plants, and discuss subfunctionalization/neofunctionalization of phytochrome signaling during the course of land plant evolution.
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Affiliation(s)
- Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
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9
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Kim JY, Song JT, Seo HS. COP1 regulates plant growth and development in response to light at the post-translational level. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4737-4748. [PMID: 28992300 DOI: 10.1093/jxb/erx312] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Photoreceptors perceive different wavelengths of light and transduce light signals downstream via a range of proteins. COP1, an E3 ubiquitin ligase, regulates light signaling by mediating the ubiquitination and subsequent proteasomal degradation of photoreceptors such as phytochromes and cryptochromes, as well as various development-related proteins including other light-responsive proteins. COP1 is itself regulated by direct interactions with several signaling molecules that modulate its activity. The control of photomorphogenesis by COP1 is also regulated by its localization to the cytoplasm in response to light. COP1 thus acts as a tightly regulated switch that determines whether development is skotomorphogenic or photomorphogenic. In this review, we discuss the effects of COP1 on the abundance and activity of various development-related proteins, including photoreceptors, and summarize the regulatory mechanisms that influence COP1 activity and stability in plants.
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Affiliation(s)
- Joo Yong Kim
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Jong Tae Song
- School of Applied Biosciences, Kyungpook National University, Daegu 702-701, Korea
| | - Hak Soo Seo
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
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10
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Sánchez-Lamas M, Lorenzo CD, Cerdán PD. Bottom-up Assembly of the Phytochrome Network. PLoS Genet 2016; 12:e1006413. [PMID: 27820825 PMCID: PMC5098793 DOI: 10.1371/journal.pgen.1006413] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 10/10/2016] [Indexed: 11/19/2022] Open
Abstract
Plants have developed sophisticated systems to monitor and rapidly acclimate to environmental fluctuations. Light is an essential source of environmental information throughout the plant's life cycle. The model plant Arabidopsis thaliana possesses five phytochromes (phyA-phyE) with important roles in germination, seedling establishment, shade avoidance, and flowering. However, our understanding of the phytochrome signaling network is incomplete, and little is known about the individual roles of phytochromes and how they function cooperatively to mediate light responses. Here, we used a bottom-up approach to study the phytochrome network. We added each of the five phytochromes to a phytochrome-less background to study their individual roles and then added the phytochromes by pairs to study their interactions. By analyzing the 16 resulting genotypes, we revealed unique roles for each phytochrome and identified novel phytochrome interactions that regulate germination and the onset of flowering. Furthermore, we found that ambient temperature has both phytochrome-dependent and -independent effects, suggesting that multiple pathways integrate temperature and light signaling. Surprisingly, none of the phytochromes alone conferred a photoperiodic response. Although phyE and phyB were the strongest repressors of flowering, both phyB and phyC were needed to confer a flowering response to photoperiod. Thus, a specific combination of phytochromes is required to detect changes in photoperiod, whereas single phytochromes are sufficient to respond to light quality, indicating how phytochromes signal different light cues.
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Affiliation(s)
| | | | - Pablo D. Cerdán
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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11
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Lee YS, Yi J, An G. OsPhyA modulates rice flowering time mainly through OsGI under short days and Ghd7 under long days in the absence of phytochrome B. PLANT MOLECULAR BIOLOGY 2016; 91:413-427. [PMID: 27039184 DOI: 10.1007/s11103-016-0474-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 03/27/2016] [Indexed: 06/05/2023]
Abstract
Phytochromes recognize light signals and control diverse developmental processes. In rice, all three phytochrome genes-OsphyA, OsphyB, and OsphyC-are involved in regulating flowering time. We investigated the role of OsPhyA by comparing the osphyA osphyB double mutant to an osphyB single mutant. Plants of the double mutant flowered later than the single under short days (SD) but bolted earlier under long days (LD). Under SD, this delayed-flowering phenotype was primarily due to the decreased expression of Oryza sativa GIGANTEA (OsGI), which controls three flowering activators: Heading date 1 (Hd1), OsMADS51, and Oryza sativa Indeterminate 1 (OsId1). Under LD, although the expression of several repressors, e.g., Hd1, Oryza sativa CONSTANS-like 4 (OsCOL4), and AP2 genes, was affected in the double mutant, that of Grain number, plant height and heading date 7 (Ghd7) was the most significantly reduced. These results indicated that OsPhyA influences flowering time mainly by affecting the expression of OsGI under SD and Ghd7 under LD when phytochrome B is absent. We also demonstrated that far-red light delays flowering time via both OsPhyA and OsPhyB.
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Affiliation(s)
- Yang-Seok Lee
- Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea
- Department of Genetic Engineering, Kyung Hee University, Yongin, 446-701, Korea
| | - Jakyung Yi
- Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea
- Department of Genetic Engineering, Kyung Hee University, Yongin, 446-701, Korea
| | - Gynheung An
- Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea.
- Department of Genetic Engineering, Kyung Hee University, Yongin, 446-701, Korea.
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Inoue K, Nishihama R, Kataoka H, Hosaka M, Manabe R, Nomoto M, Tada Y, Ishizaki K, Kohchi T. Phytochrome Signaling Is Mediated by PHYTOCHROME INTERACTING FACTOR in the Liverwort Marchantia polymorpha. THE PLANT CELL 2016; 28:1406-21. [PMID: 27252292 PMCID: PMC4944405 DOI: 10.1105/tpc.15.01063] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 05/18/2016] [Accepted: 05/30/2016] [Indexed: 05/18/2023]
Abstract
Phytochromes are red light (R) and far-red light (FR) receptors that play important roles in many aspects of plant growth and development. Phytochromes mainly function in the nucleus and regulate sets of genes by inhibiting negatively acting basic helix-loop-helix transcription factors named PHYTOCHROME INTERACTING FACTORs (PIFs) in Arabidopsis thaliana Although R/FR photoreversible responses and phytochrome genes are well documented in diverse lineages of plants, the extent to which phytochrome signaling is mediated by gene regulation beyond angiosperms remains largely unclear. Here, we show that the liverwort Marchantia polymorpha, an emerging model basal land plant, has only one phytochrome gene, Mp-PHY, and only one PIF gene, Mp-PIF These genes mediate typical low fluence responses, which are reversibly elicited by R and FR, and regulate gene expression. Mp-phy is light-stable and translocates into the nucleus upon irradiation with either R or FR, demonstrating that the single phytochrome Mp-phy exhibits combined biochemical and cell-biological characteristics of type I and type II phytochromes. Mp-phy photoreversibly regulates gemma germination and downstream gene expression by interacting with Mp-PIF and targeting it for degradation in an R-dependent manner. Our findings suggest that the molecular mechanisms for light-dependent transcriptional regulation mediated by PIF transcription factors were established early in land plant evolution.
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Affiliation(s)
- Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Hideo Kataoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Masashi Hosaka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ryo Manabe
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Mika Nomoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Kimitsune Ishizaki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
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Jones MA, Hu W, Litthauer S, Lagarias JC, Harmer SL. A Constitutively Active Allele of Phytochrome B Maintains Circadian Robustness in the Absence of Light. PLANT PHYSIOLOGY 2015; 169:814-25. [PMID: 26157113 PMCID: PMC4577416 DOI: 10.1104/pp.15.00782] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/06/2015] [Indexed: 05/18/2023]
Abstract
The sensitivity of the circadian system to light allows entrainment of the clock, permitting coordination of plant metabolic function and flowering time across seasons. Light affects the circadian system via both photoreceptors, such as phytochromes and cryptochromes, and sugar production by photosynthesis. In the present study, we introduce a constitutively active version of phytochrome B-Y276H (YHB) into both wild-type and phytochrome null backgrounds of Arabidopsis (Arabidopsis thaliana) to distinguish the effects of photoreceptor signaling on clock function from those of photosynthesis. We find that the YHB mutation is sufficient to phenocopy red light input into the circadian mechanism and to sustain robust rhythms in steady-state mRNA levels even in plants grown without light or exogenous sugars. The pace of the clock is insensitive to light intensity in YHB plants, indicating that light input to the clock is constitutively activated by this allele. Mutation of YHB so that it is retained in the cytoplasm abrogates its effects on clock function, indicating that nuclear localization of phytochrome is necessary for its clock regulatory activity. We also demonstrate a role for phytochrome C as part of the red light sensing network that modulates phytochrome B signaling input into the circadian system. Our findings indicate that phytochrome signaling in the nucleus plays a critical role in sustaining robust clock function under red light, even in the absence of photosynthesis or exogenous sources of energy.
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Affiliation(s)
- Matthew Alan Jones
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, United Kingdom (M.A.J., S.L.); andDepartment of Plant Biology, College of Biological Sciences (M.A.J., S.L.H.) and Department of Molecular and Cellular Biology (W.H., J.C.L.), University of California, Davis, California 95616
| | - Wei Hu
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, United Kingdom (M.A.J., S.L.); andDepartment of Plant Biology, College of Biological Sciences (M.A.J., S.L.H.) and Department of Molecular and Cellular Biology (W.H., J.C.L.), University of California, Davis, California 95616
| | - Suzanne Litthauer
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, United Kingdom (M.A.J., S.L.); andDepartment of Plant Biology, College of Biological Sciences (M.A.J., S.L.H.) and Department of Molecular and Cellular Biology (W.H., J.C.L.), University of California, Davis, California 95616
| | - J Clark Lagarias
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, United Kingdom (M.A.J., S.L.); andDepartment of Plant Biology, College of Biological Sciences (M.A.J., S.L.H.) and Department of Molecular and Cellular Biology (W.H., J.C.L.), University of California, Davis, California 95616
| | - Stacey Lynn Harmer
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, United Kingdom (M.A.J., S.L.); andDepartment of Plant Biology, College of Biological Sciences (M.A.J., S.L.H.) and Department of Molecular and Cellular Biology (W.H., J.C.L.), University of California, Davis, California 95616
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Sun W, Xu XH, Wu X, Wang Y, Lu X, Sun H, Xie X. Genome-wide identification of microRNAs and their targets in wild type and phyB mutant provides a key link between microRNAs and the phyB-mediated light signaling pathway in rice. FRONTIERS IN PLANT SCIENCE 2015; 6:372. [PMID: 26074936 PMCID: PMC4448008 DOI: 10.3389/fpls.2015.00372] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/11/2015] [Indexed: 05/20/2023]
Abstract
Phytochrome B (phyB), a member of the phytochrome family in rice, plays important roles in regulating a range of developmental processes and stress responses. However, little information about the mechanisms involved in the phyB-mediated light signaling pathway has been reported in rice. MicroRNAs (miRNAs) also perform important roles in plant development and stress responses. Thus, it is intriguing to explore the role of miRNAs in the phyB-mediated light signaling pathway in rice. In this study, comparative high-throughput sequencing and degradome analysis were used to identify candidate miRNAs and their targets that participate in the phyB-mediated light signaling pathway. A total of 720 known miRNAs, 704 novel miRNAs and 1957 target genes were identified from the fourth leaves of wild-type (WT) and phyB mutant rice at the five-leaf stage. Among them, 135 miRNAs showed differential expression, suggesting that the expression of these miRNAs is directly or indirectly under the control of phyB. In addition, 32 out of the 135 differentially expressed miRNAs were found to slice 70 genes in the rice genome. Analysis of these target genes showed that members of various transcription factor families constituted the largest proportion, indicating miRNAs are probably involved in the phyB-mediated light signaling pathway mainly by regulating the expression of transcription factors. Our results provide new clues for functional characterization of miRNAs in the phyB-mediated light signaling pathway, which should be helpful in comprehensively uncovering the molecular mechanisms of phytochrome-mediated photomorphogenesis and stress responses in plants.
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Affiliation(s)
- Wei Sun
- Shandong Rice Research Institute, Shandong Academy of Agricultural SciencesJinan, China
| | - Xiao Hui Xu
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural SciencesJinan, China
| | - Xiu Wu
- Shandong Rice Research Institute, Shandong Academy of Agricultural SciencesJinan, China
| | - Yong Wang
- Shandong Academy of Agricultural SciencesJinan, China
| | - Xingbo Lu
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural SciencesJinan, China
| | - Hongwei Sun
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural SciencesJinan, China
| | - Xianzhi Xie
- Shandong Rice Research Institute, Shandong Academy of Agricultural SciencesJinan, China
- *Correspondence: Xianzhi Xie, Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, No.2 Sangyuan Road, Jinan, 250100, China
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