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de Los Reyes P, Serrano-Bueno G, Romero-Campero FJ, Gao H, Romero JM, Valverde F. CONSTANS alters the circadian clock in Arabidopsis thaliana. MOLECULAR PLANT 2024; 17:1204-1220. [PMID: 38894538 DOI: 10.1016/j.molp.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 04/23/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
Plants are sessile organisms that have acquired highly plastic developmental strategies to adapt to the environment. Among these processes, the floral transition is essential to ensure reproductive success and is finely regulated by several internal and external genetic networks. The photoperiodic pathway, which controls plant response to day length, is one of the most important pathways controlling flowering. In Arabidopsis photoperiodic flowering, CONSTANS (CO) is the central gene activating the expression of the florigen FLOWERING LOCUS T (FT) in the leaves at the end of a long day. The circadian clock strongly regulates CO expression. However, to date, no evidence has been reported regarding a feedback loop from the photoperiod pathway back to the circadian clock. Using transcriptional networks, we have identified relevant network motifs regulating the interplay between the circadian clock and the photoperiod pathway. Gene expression, chromatin immunoprecipitation experiments, and phenotypic analysis allowed us to elucidate the role of CO over the circadian clock. Plants with altered CO expression showed a different internal clock period, measured by daily leaf rhythmic movements. We showed that CO upregulates the expression of key genes related to the circadian clock, such as CCA1, LHY, PRR5, and GI, at the end of a long day by binding to specific sites on their promoters. Moreover, a high number of PRR5-repressed target genes are upregulated by CO, and this could explain the phase transition promoted by CO. The CO-PRR5 complex interacts with the bZIP transcription factor HY5 and helps to localize the complex in the promoters of clock genes. Taken together, our results indicate that there may be a feedback loop in which CO communicates back to the circadian clock, providing seasonal information to the circadian system.
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Affiliation(s)
- Pedro de Los Reyes
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain
| | - Gloria Serrano-Bueno
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain; Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, Seville, Spain
| | - Francisco J Romero-Campero
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain; Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Seville, Spain
| | - He Gao
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jose M Romero
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain; Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, Seville, Spain
| | - Federico Valverde
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain.
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2
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Bao G, Sun G, Wang J, Shi T, Xu X, Zhai L, Bian S, Li X. Soybean RVE8a confers salt and drought tolerance in Arabidopsis. Biochem Biophys Res Commun 2024; 704:149660. [PMID: 38428303 DOI: 10.1016/j.bbrc.2024.149660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/26/2024] [Accepted: 02/07/2024] [Indexed: 03/03/2024]
Abstract
Soybean is an economically important crop, which often suffers various abiotic stresses. REVEILLE (RVE) genes have been generally considered as circadian oscillators to mediate diverse developmental processes and plant response to environmental stresses. Addressing their roles is of significance for utilizing them to enhance agronomic traits in crops. However, our understanding of soybean RVEs is extremely limited. In the study, we investigated the expression patterns of soybean CCA1-like genes under salt stress using our RNA-Seq data. Subsequently, a salt stress-inducible gene, GmRVE8a, was chosen for further study. Phylogenetic analysis indicated that GmRVE8a is most closely related to Arabidopsis RVE4 and RVE8. Also, GmRVE8a showed circadian expression pattern with 24 h rhythmic period, suggesting that it might be a clock-regulated gene. Moreover, transgenic Arabidopsis lines over-expressing GmRVE8a were generated. It was observed that ectopic over-expression of GmRVE8a caused a significant delay in flowering. Further observation indicated that under salt and drought stress, transgenic seedlings were stronger than wild type. Consistently, three-week-old transgenic plants grew better than wild type under salt and drought conditions, and the MDA content in transgenic lines was significantly lower than wild type, suggesting that GmRVE8a might be a positive regulator in response to salt and drought stress. Intriguingly, Y2H assay indicated that GmRVE8a physically interacted with a drought-tolerant protein, GmNAC17. Overall, our findings provided preliminary information regarding the functional roles of GmRVE8a in response to salt and drought stress.
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Affiliation(s)
- Guohua Bao
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Guoqing Sun
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Jingying Wang
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Tianran Shi
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Xiao Xu
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Lulu Zhai
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Shaomin Bian
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China.
| | - Xuyan Li
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China.
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3
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Wang X, Zhang J, Liu X, Kong Y, Han L. The Roles of the PSEUDO-RESPONSE REGULATORs in Circadian Clock and Flowering Time in Medicago truncatula. Int J Mol Sci 2023; 24:16834. [PMID: 38069157 PMCID: PMC10706769 DOI: 10.3390/ijms242316834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
PSEUDO-RESPONSE REGULATORs (PRRs) play key roles in the circadian rhythms and flowering in plants. Here, we identified the four members of the PRR family in Medicago truncatula, including MtPRR9a, MtPRR9b, MtPRR7 and MtPRR5, and isolated their Tnt1 retrotransposon-tagged mutants. They were expressed in different organs and were nuclear-localized. The four MtPRRs genes played important roles in normal clock rhythmicity maintenance by negatively regulating the expression of MtGI and MtLHY. Surprisingly, the four MtPRRs functioned redundantly in regulating flowering time under long-day conditions, and the quadruple mutant flowered earlier. Moreover, MtPRR can recruit the MtTPL/MtTPR corepressors and the other MtPRRs to form heterodimers to constitute the core mechanism of the circadian oscillator.
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Affiliation(s)
- Xiao Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
| | - Juanjuan Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
| | - Xiu Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
| | - Yiming Kong
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Lu Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (X.W.); (J.Z.); (X.L.); (Y.K.)
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4
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Li J, Qiu JX, Zeng QH, Zhang N, Xu SX, Jin J, Dong ZC, Chen L, Huang W. OsTOC1 plays dual roles in the regulation of plant circadian clock by functioning as a direct transcription activator or repressor. Cell Rep 2023; 42:112765. [PMID: 37421622 DOI: 10.1016/j.celrep.2023.112765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/28/2023] [Accepted: 06/22/2023] [Indexed: 07/10/2023] Open
Abstract
Plant clock function relies on precise timing of gene expression through complex regulatory networks consisting of activators and repressors at the core of oscillators. Although TIMING OF CAB EXPRESSION 1 (TOC1) has been recognized as a repressor involved in shaping oscillations and regulating clock-driven processes, its potential to directly activate gene expression remains unclear. In this study, we find that OsTOC1 primarily acts as a transcriptional repressor for core clock components, including OsLHY and OsGI. Here, we show that OsTOC1 possesses the ability to directly activate the expression of circadian target genes. Through binding to the promoters of OsTGAL3a/b, transient activation of OsTOC1 induces the expression of OsTGAL3a/b, indicating its role as an activator contributing to pathogen resistance. Moreover, TOC1 participates in regulating multiple yield-related traits in rice. These findings suggest that TOC1's function as a transcriptional repressor is not inherent, providing flexibility to circadian regulations, particularly in outputs.
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Affiliation(s)
- Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Jia-Xin Qiu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Qing-Hua Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Ning Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Shu-Xuan Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Jian Jin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Zhi-Cheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
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Gombos M, Hapek N, Kozma-Bognár L, Grezal G, Zombori Z, Kiss E, Györgyey J. Limited water stress modulates expression of circadian clock genes in Brachypodium distachyon roots. Sci Rep 2023; 13:1241. [PMID: 36690685 PMCID: PMC9870971 DOI: 10.1038/s41598-022-27287-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 12/29/2022] [Indexed: 01/24/2023] Open
Abstract
Organisms have evolved a circadian clock for the precise timing of their biological processes. Studies primarily on model dicots have shown the complexity of the inner timekeeper responsible for maintaining circadian oscillation in plants and have highlighted that circadian regulation is more than relevant to a wide range of biological processes, especially organ development and timing of flowering. Contribution of the circadian clock to overall plant fitness and yield has also long been known. Nevertheless, the organ- and species-specific functions of the circadian clock and its relation to stress adaptation have only recently been identified. Here we report transcriptional changes of core clock genes of the model monocot Brachypodium distachyon under three different light regimes (18:6 light:dark, 24:0 light and 0:24 dark) in response to mild drought stress in roots and green plant parts. Comparative monitoring of core clock gene expression in roots and green plant parts has shown that both phase and amplitude of expression in the roots of Brachypodium plants differ markedly from those in the green plant parts, even under well-watered conditions. Moreover, circadian clock genes responded to water depletion differently in root and shoot. These results suggest an organ-specific form and functions of the circadian clock in Brachypodium roots.
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Affiliation(s)
- Magdolna Gombos
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary
| | - Nóra Hapek
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary
- Institute of Biochemistry, BRC-Biological Research Centre, Szeged, Hungary
| | - László Kozma-Bognár
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary
- Department of Genetics, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gábor Grezal
- Institute of Biochemistry, BRC-Biological Research Centre, Szeged, Hungary
| | - Zoltán Zombori
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary
| | - Edina Kiss
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary
| | - János Györgyey
- Institute of Plant Biology, BRC-Biological Research Centre, Szeged, Hungary.
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Red Light Resets the Expression Pattern, Phase, and Period of the Circadian Clock in Plants: A Computational Approach. BIOLOGY 2022; 11:biology11101479. [PMID: 36290383 PMCID: PMC9598827 DOI: 10.3390/biology11101479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/02/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Simple Summary Progress in computational biology has provided a comprehensive understanding of the dynamics of the plant circadian clock. Previously proposed models of the plant circadian clock have intended to model its entrainment using white-light/dark cycles. However, these models have failed to take into account the effect of light quality on circadian rhythms, which has been experimentally observed. In this work, we developed a computational approach to characterizing the effects of light quality on plant circadian rhythms. The results demonstrated that red light can reset the expression patterns, phases, and periods of clock component genes. The circadian period, amplitude, and phase can be co-optimized for high-quality and efficient breeding. Abstract Recent research in the fields of biochemistry and molecular biology has shown that different light qualities have extremely different effects on plant development, and optimizing light quality conditions can speed up plant growth. Clock-regulated red-light signaling, can enhance hypocotyl elongation, and increase seedling height and flower and fruit productivity. In order to investigate the effect of red light on circadian clocks in plants, a novel computational model was established. The expression profiles of the circadian element CCA1 from previous related studies were used to fit the model. The simulation results were validated by the expression patterns of CCA1 in Arabidopsis, including wild types and mutants, and by the phase shifts of CCA1 after red-light pulse. The model was used to further explore the complex responses to various photoperiods, such as the natural white-light/dark cycles, red/white/dark cycles, and extreme 24 h photoperiods. These results demonstrated that red light can reset the expression pattern, period, and phase of the circadian clock. Finally, we identified the dependence of phase shifts on the length of red-light pulse and the minimum red-light pulse length required for producing an observable phase shift. This work provides a promising computational approach to investigating the response of the circadian clock to other light qualities.
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7
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Fan T, Aslam MM, Zhou JL, Chen MX, Zhang J, Du S, Zhang KL, Chen YS. A crosstalk of circadian clock and alternative splicing under abiotic stresses in the plants. FRONTIERS IN PLANT SCIENCE 2022; 13:976807. [PMID: 36275558 PMCID: PMC9583901 DOI: 10.3389/fpls.2022.976807] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
The circadian clock is an internal time-keeping mechanism that synchronizes the physiological adaptation of an organism to its surroundings based on day and night transition in a period of 24 h, suggesting the circadian clock provides fitness by adjusting environmental constrains. The circadian clock is driven by positive and negative elements that regulate transcriptionally and post-transcriptionally. Alternative splicing (AS) is a crucial transcriptional regulator capable of generating large numbers of mRNA transcripts from limited numbers of genes, leading to proteome diversity, which is involved in circadian to deal with abiotic stresses. Over the past decade, AS and circadian control have been suggested to coordinately regulate plant performance under fluctuating environmental conditions. However, only a few reports have reported the regulatory mechanism of this complex crosstalk. Based on the emerging evidence, this review elaborates on the existing links between circadian and AS in response to abiotic stresses, suggesting an uncovered regulatory network among circadian, AS, and abiotic stresses. Therefore, the rhythmically expressed splicing factors and core clock oscillators fill the role of temporal regulators participating in improving plant growth, development, and increasing plant tolerance against abiotic stresses.
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Affiliation(s)
- Tao Fan
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, China
- Co-Innovation Center for Sustainable Forestry in Southern China & Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Mehtab Muhammad Aslam
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Jian-Li Zhou
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, China
| | - Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China & Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Shenxiu Du
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kai-Lu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China & Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yun-Sheng Chen
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, China
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Genome-Wide Identification and Characterization of PRR Gene Family and their Diurnal Rhythmic Expression Profile in Maize. Int J Genomics 2022; 2022:6941607. [PMID: 35615408 PMCID: PMC9126661 DOI: 10.1155/2022/6941607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
As essential components of the circadian clock, the pseudo-response regulator (PRR) gene family plays critical roles in plant photoperiod pathway. In this study, we performed a genome-wide identification and a systematic analysis of the PRR gene family in maize. Nine ZmPRRs were identified, and the gene structure, conserved motif, evolution relationship, and expression pattern of ZmPRRs were analyzed comprehensively. Phylogenetic analysis indicated that the nine ZmPRR genes were divided into three groups, except for ZmPRR73, two of which were highly homologous to each of the AtPRR or OsPRR quintet members. Promoter cis-element analysis of ZmPRRs demonstrated that they might be involved in multiple signaling transduction pathways, such as light response, biological or abiotic stress response, and hormone response. qRT-PCR analysis revealed that the levels of ZmPRRs transcripts varied considerably and exhibited a diurnal rhythmic oscillation expression pattern in the given 24-h period under both SD and LD conditions, which indicated that the level of transcription of ZmPRRs expression is subjected to a circadian rhythm and modulated by light and the circadian clock. The present study will provide an insight into further exploring the biological function and regulatory mechanism of ZmPRR genes in circadian rhythm and response to photoperiod in maize.
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9
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Li X, Liang T, Liu H. How plants coordinate their development in response to light and temperature signals. THE PLANT CELL 2022; 34:955-966. [PMID: 34904672 PMCID: PMC8894937 DOI: 10.1093/plcell/koab302] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/06/2021] [Indexed: 05/12/2023]
Abstract
Light and temperature change constantly under natural conditions and profoundly affect plant growth and development. Light and warmer temperatures promote flowering, higher light intensity inhibits hypocotyl and petiole elongation, and warmer temperatures promote hypocotyl and petiole elongation. Moreover, exogenous light and temperature signals must be integrated with endogenous signals to fine-tune phytohormone metabolism and plant morphology. Plants perceive and respond to light and ambient temperature using common sets of factors, such as photoreceptors and multiple light signal transduction components. These highly structured signaling networks are critical for plant survival and adaptation. This review discusses how plants respond to variable light and temperature conditions using common elements to coordinate their development. Future directions for research on light and temperature signaling pathways are also discussed.
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Affiliation(s)
- Xu Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Tong Liang
- Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Hongtao Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Author for correspondence:
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Li C, Liu XJ, Yan Y, Alam MS, Liu Z, Yang ZK, Tao RF, Yue EK, Duan MH, Xu JH. OsLHY is involved in regulating flowering through the Hd1- and Ehd1- mediated pathways in rice (Oryza sativa L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 315:111145. [PMID: 35067308 DOI: 10.1016/j.plantsci.2021.111145] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Flowering time (or heading date in crops) is a critical agronomic trait for rice reproduction and adaptation. The circadian clock is an endogenous oscillator that is involved in controlling photoperiodic flowering. The rice LATE ELONGATED HYPOCOTYL (OsLHY), the core oscillator component of circadian clock, is a homolog of the LHY/CCA1 in Arabidopsis. Here we showed that CRISPR/Cas9-engineered mutations in OsLHY caused late flowering in rice only under natural long-day (nLD) and short-day (nSD) conditions, but not artificial SD (10 h light/14 h dark) conditions. In the oslhy mutant, the diurnal expression of circadian clock-related genes was seriously affected under both LD and SD conditions. Furthermore, the expression of the flowering activators Ehd1, Hd3a and RFT1 was down-regulated and flowering repressors Hd1 and Ghd7 was up-regulated in the oslhy mutant under LD conditions. While the transcripts of flowering-related genes were not dramatically influenced under SD conditions. Dual-luciferase assays showed that OsLHY repressed the transcription of OsGI, Hd1, Ghd7, Hd3a, RFT1 and OsELF3, and activated the transcription of Ehd1. Moreover, the yeast one hybrid assay and electrophoretic mobility shift assay confirmed that OsLHY directly repressed OsGI, RFT1 and OsELF3 by binding to their promoters, which is consistent with that in Arabidopsis. These results suggested that the OsLHY can promote rice flowering mainly through regulating Hd1 and Ehd1.
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Affiliation(s)
- Chao Li
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China; Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Shandong, 276034, China
| | - Xue-Jiao Liu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Yan Yan
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Mohammad Shah Alam
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Zhen Liu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Zhen-Kun Yang
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Ruo-Fu Tao
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Er-Kui Yue
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Ming-Hua Duan
- Zhejiang Zhengjingyuan Pharmacy Chain Co., Ltd. & Hangzhou Zhengcaiyuan Pharmaceutical Co., Ltd., Hangzhou, 310021, China
| | - Jian-Hong Xu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China; Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Shandong, 276034, China.
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11
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Ma K, Luo X, Han L, Zhao Y, Mamat A, Li N, Mei C, Yan P, Zhang R, Hu J, Wang J. Transcriptome profiling based on Illumina- and SMRT-based RNA-seq reveals circadian regulation of key pathways in flower bud development in walnut. PLoS One 2021; 16:e0260017. [PMID: 34793486 PMCID: PMC8601540 DOI: 10.1371/journal.pone.0260017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 11/01/2021] [Indexed: 11/19/2022] Open
Abstract
Flower bud development is a defining feature of walnut, which contributes to the kernel yield, yield stability, fruit quality and commodity value. However, little is known about the mechanism of the flower bud development in walnut. Here, the stages of walnut female flower bud development were divided into five period (P01-05) by using histological observation. They were further studied through PacBio Iso-Seq and RNA-seq analysis. Accordingly, we obtained 52,875 full-length transcripts, where 4,579 were new transcripts, 3,065 were novel genes, 1,437 were consensus lncRNAs and 20,813 were alternatively spliced isoforms. These transcripts greatly improved the current genome annotation and enhanced our understanding of the walnut transcriptome. Next, RNA sequencing of female flower buds at five periods revealed that circadian rhythm-plant was commonly enriched along with the flower bud developmental gradient. A total of 14 differentially expressed genes (DEGs) were identified, and six of them were confirmed by real-time quantitative analysis. Additionally, six and two differentially expressed clock genes were detected to be regulated by AS events and lncRNAs, respectively. All these detected plant circadian genes form a complex interconnected network to regulate the flower bud development. Thus, investigation of key genes associated with the circadian clock could clarify the process of flower bud development in walnut.
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Affiliation(s)
- Kai Ma
- College of Horticulture, China Agricultural University, Beijing, China
- Institute of Horticultural and Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xiang Luo
- State Key Laboratory of Crop Stress Adaption and Improvement, Henan University, Kaifeng, China
| | - Liqun Han
- Institute of Horticultural and Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Yu Zhao
- Institute of Horticultural and Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Aisajan Mamat
- Institute of Horticultural and Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ning Li
- Institute of Horticultural and Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Chuang Mei
- Institute of Horticultural and Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Peng Yan
- Institute of Horticultural and Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Rui Zhang
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alaer, China
| | - Jianfang Hu
- College of Horticulture, China Agricultural University, Beijing, China
- * E-mail: (JH); (JW)
| | - Jixun Wang
- Institute of Horticultural and Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- * E-mail: (JH); (JW)
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12
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Sun C, Zhang K, Zhou Y, Xiang L, He C, Zhong C, Li K, Wang Q, Yang C, Wang Q, Chen C, Chen D, Wang Y, Liu C, Yang B, Wu H, Chen X, Li W, Wang J, Xu P, Wang P, Fang J, Chu C, Deng X. Dual function of clock component OsLHY sets critical day length for photoperiodic flowering in rice. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1644-1657. [PMID: 33740293 PMCID: PMC8384598 DOI: 10.1111/pbi.13580] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/18/2021] [Accepted: 03/08/2021] [Indexed: 05/11/2023]
Abstract
Circadian clock, an endogenous time-setting mechanism, allows plants to adapt to unstable photoperiod conditions and induces flowering with proper timing. In Arabidopsis, the central clock oscillator was formed by a series of interlocked transcriptional feedback loops, but little is known in rice so far. By MutMap technique, we identified the candidate gene OsLHY from a later flowering mutant lem1 and further confirmed it through genetic complementation, RNA interference knockdown, and CRISPR/Cas9-knockout. Global transcriptome profiling and expression analyses revealed that OsLHY might be a vital circadian rhythm component. Interestingly, oslhy flowered later under ≥12 h day length but headed earlier under ≤11 h day length. qRT-PCR results exhibited that OsLHY might function through OsGI-Hd1 pathway. Subsequent one-hybrid assays in yeast, DNA affinity purification qPCR, and electrophoretic mobility shift assays confirmed OsLHY could directly bind to the CBS element in OsGI promoter. Moreover, the critical day length (CDL) for function reversal of OsLHY in oslhy (11-12 h) was prolonged in the double mutant oslhy osgi (about 13.5 h), indicating that the CDL set by OsLHY was OsGI dependent. Additionally, the dual function of OsLHY entirely relied on Hd1, as the double mutant oslhy hd1 showed the same heading date with hd1 under about 11.5, 13.5, and 14 h day lengths. Together, OsLHY could fine-tune the CDL by directly regulating OsGI, and Hd1 acts as the final effector of CDL downstream of OsLHY. Our study illustrates a new regulatory mechanism between the circadian clock and photoperiodic flowering.
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Affiliation(s)
- Changhui Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Kuan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yi Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Lin Xiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Changcai He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Chao Zhong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Ke Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Qiuxia Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Chuanpeng Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Qian Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Congping Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Dan Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Chuanqiang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Bin Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Hualin Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Xiaoqiong Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Weitao Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Jing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Peizhou Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Pingrong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
| | - Jun Fang
- Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
| | - Chengcai Chu
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyThe Innovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Xiaojian Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaRice Research InstituteSichuan Agricultural UniversityChengduChina
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13
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Romanowski A, Schlaen RG, Perez-Santangelo S, Mancini E, Yanovsky MJ. Global transcriptome analysis reveals circadian control of splicing events in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:889-902. [PMID: 32314836 DOI: 10.1111/tpj.14776] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/26/2020] [Accepted: 04/01/2020] [Indexed: 05/21/2023]
Abstract
The circadian clock of Arabidopsis thaliana controls many physiological and molecular processes, allowing plants to anticipate daily changes in their environment. However, developing a detailed understanding of how oscillations in mRNA levels are connected to oscillations in co/post-transcriptional processes, such as splicing, has remained a challenge. Here we applied a combined approach using deep transcriptome sequencing and bioinformatics tools to identify novel circadian-regulated genes and splicing events. Using a stringent approach, we identified 300 intron retention, eight exon skipping, 79 alternative 3' splice site usage, 48 alternative 5' splice site usage, and 350 multiple (more than one event type) annotated events under circadian regulation. We also found seven and 721 novel alternative exonic and intronic events. Depletion of the circadian-regulated splicing factor AtSPF30 homologue resulted in the disruption of a subset of clock-controlled splicing events. Altogether, our global circadian RNA-seq coupled with an in silico, event-centred, splicing analysis tool offers a new approach for studying the interplay between the circadian clock and the splicing machinery at a global scale. The identification of many circadian-regulated splicing events broadens our current understanding of the level of control that the circadian clock has over this co/post-transcriptional regulatory layer.
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Affiliation(s)
- Andrés Romanowski
- Comparative Genomics of Plant Development, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE, Buenos Aires, Argentina
| | - Rubén G Schlaen
- Comparative Genomics of Plant Development, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE, Buenos Aires, Argentina
| | - Soledad Perez-Santangelo
- Comparative Genomics of Plant Development, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE, Buenos Aires, Argentina
| | - Estefanía Mancini
- Comparative Genomics of Plant Development, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE, Buenos Aires, Argentina
| | - Marcelo J Yanovsky
- Comparative Genomics of Plant Development, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE, Buenos Aires, Argentina
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14
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Wang Y, Yuan L, Su T, Wang Q, Gao Y, Zhang S, Jia Q, Yu G, Fu Y, Cheng Q, Liu B, Kong F, Zhang X, Song CP, Xu X, Xie Q. Light- and temperature-entrainable circadian clock in soybean development. PLANT, CELL & ENVIRONMENT 2020; 43:637-648. [PMID: 31724182 DOI: 10.1111/pce.13678] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 10/13/2019] [Accepted: 11/08/2019] [Indexed: 05/07/2023]
Abstract
In plants, the spatiotemporal expression of circadian oscillators provides adaptive advantages in diverse species. However, the molecular basis of circadian clock in soybean is not known. In this study, we used soybean hairy roots expression system to monitor endogenous circadian rhythms and the sensitivity of circadian clock to environmental stimuli. We discovered in experiments with constant light and temperature conditions that the promoters of clock genes GmLCLb2 and GmPRR9b1 drive a self-sustained, robust oscillation of about 24-h in soybean hairy roots. Moreover, we demonstrate that circadian clock is entrainable by ambient light/dark or temperature cycles. Specifically, we show that light and cold temperature pulses can induce phase shifts of circadian rhythm, and we found that the magnitude and direction of phase responses depends on the specific time of these two zeitgeber stimuli. We obtained a quadruple mutant lacking the soybean gene GmLCLa1, LCLa2, LCLb1, and LCLb2 using CRISPR, and found that loss-of-function of these four GmLCL orthologs leads to an extreme short-period circadian rhythm and late-flowering phenotype in transgenic soybean. Our study establishes that the morning-phased GmLCLs genes act constitutively to maintain circadian rhythmicity and demonstrates that their absence delays the transition from vegetative growth to reproductive development.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Li Yuan
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Tong Su
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiao Wang
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ya Gao
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Siyuan Zhang
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Qian Jia
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Guolong Yu
- MOA Key Lab of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongfu Fu
- MOA Key Lab of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qun Cheng
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Baohui Liu
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Fanjiang Kong
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xiao Zhang
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Chun-Peng Song
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Xiaodong Xu
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Qiguang Xie
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
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15
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Hearn TJ, Webb AAR. Recent advances in understanding regulation of the Arabidopsis circadian clock by local cellular environment. F1000Res 2020; 9. [PMID: 32047621 PMCID: PMC6993837 DOI: 10.12688/f1000research.21307.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/20/2020] [Indexed: 11/20/2022] Open
Abstract
Circadian clocks have evolved to synchronise an organism’s physiology with the environmental rhythms driven by the Earth’s rotation on its axis. Over the past two decades, many of the genetic components of the
Arabidopsis thaliana circadian oscillator have been identified. The interactions between these components have been formulized into mathematical models that describe the transcriptional translational feedback loops of the oscillator. More recently, focus has turned to the regulation and functions of the circadian clock. These studies have shown that the system dynamically responds to environmental signals and small molecules. We describe advances that have been made in discovering the cellular mechanisms by which signals regulate the circadian oscillator of Arabidopsis in the context of tissue-specific regulation.
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Affiliation(s)
- Timothy J Hearn
- Department of Plant Sciences, University of Cambridge, Downing Site, Cambridge, CB2 3EA, UK.,Research Department of Cell and Developmental Biology, Rockefeller Building, University College London, London, WC1E 6DE, UK.,Academic Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Alex A R Webb
- Department of Plant Sciences, University of Cambridge, Downing Site, Cambridge, CB2 3EA, UK
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16
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Airoldi CA, Hearn TJ, Brockington SF, Webb AAR, Glover BJ. TTG1 proteins regulate circadian activity as well as epidermal cell fate and pigmentation. NATURE PLANTS 2019; 5:1145-1153. [PMID: 31712761 DOI: 10.1038/s41477-019-0544-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/08/2019] [Indexed: 05/26/2023]
Abstract
The Arabidopsis genome contains three genes encoding proteins of the TRANSPARENT TESTA GLABRA 1 (TTG1) WD-repeat (WDR) subfamily. TTG1 is a known regulator of epidermal cell differentiation and pigment production, while LIGHT-REGULATED WD1 and LIGHT-REGULATED WD2 are known regulators of the circadian clock. Here, we discovered a new central role for TTG1 WDR proteins as regulators of the circadian system, as evidenced by the lack of detectable circadian rhythms in a triple lwd1 lwd2 ttg1 mutant. This shows that there has been subfunctionalization via protein changes within the angiosperms, with some TTG1 WDR proteins developing a stronger role in circadian clock regulation while losing the protein characteristics essential for pigment production and epidermal cell specification, and others weakening their ability to drive circadian clock regulation. Our work shows that even where proteins are very conserved, small changes can drive big functional differences.
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Affiliation(s)
- Chiara A Airoldi
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Timothy J Hearn
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | | | - Alex A R Webb
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
| | - Beverley J Glover
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
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17
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Adeola HA, Papagerakis S, Papagerakis P. Systems Biology Approaches and Precision Oral Health: A Circadian Clock Perspective. Front Physiol 2019; 10:399. [PMID: 31040792 PMCID: PMC6476986 DOI: 10.3389/fphys.2019.00399] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/22/2019] [Indexed: 12/20/2022] Open
Abstract
A vast majority of the pathophysiological and metabolic processes in humans are temporally controlled by a master circadian clock located centrally in the hypothalamic suprachiasmatic nucleus of the brain, as well as by specialized peripheral oscillators located in other body tissues. This circadian clock system generates a rhythmical diurnal transcriptional-translational cycle in clock genes and protein expression and activities regulating numerous downstream target genes. Clock genes as key regulators of physiological function and dysfunction of the circadian clock have been linked to various diseases and multiple morbidities. Emerging omics technologies permits largescale multi-dimensional investigations of the molecular landscape of a given disease and the comprehensive characterization of its underlying cellular components (e.g., proteins, genes, lipids, metabolites), their mechanism of actions, functional networks and regulatory systems. Ultimately, they can be used to better understand disease and interpatient heterogeneity, individual profile, identify personalized targetable key molecules and pathways, discover novel biomarkers and genetic alterations, which collectively can allow for a better patient stratification into clinically relevant subgroups to improve disease prediction and prevention, early diagnostic, clinical outcomes, therapeutic benefits, patient's quality of life and survival. The use of “omics” technologies has allowed for recent breakthroughs in several scientific domains, including in the field of circadian clock biology. Although studies have explored the role of clock genes using circadiOmics (which integrates circadian omics, such as genomics, transcriptomics, proteomics and metabolomics) in human disease, no such studies have investigated the implications of circadian disruption in oral, head and neck pathologies using multi-omics approaches and linking the omics data to patient-specific circadian profiles. There is a burgeoning body of evidence that circadian clock controls the development and homeostasis of oral and maxillofacial structures, such as salivary glands, teeth and oral epithelium. Hence, in the current era of precision medicine and dentistry and patient-centered health care, it is becoming evident that a multi-omics approach is needed to improve our understanding of the role of circadian clock-controlled key players in the regulation of head and neck pathologies. This review discusses current knowledge on the role of the circadian clock and the contribution of omics-based approaches toward a novel precision health era for diagnosing and treating head and neck pathologies, with an emphasis on oral, head and neck cancer and Sjögren's syndrome.
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Affiliation(s)
- Henry A Adeola
- Hair and Skin Research Laboratory, Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, University of the Western Cape and Tygerberg Hospital, Cape Town, South Africa
| | - Silvana Papagerakis
- Laboratory of Oral, Head & Neck Cancer-Personalized Diagnostics and Therapeutics, Division of Head and Neck Surgery, Department of Surgery, University of Saskatchewan, Saskatoon, SK, Canada
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18
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Feke A, Liu W, Hong J, Li MW, Lee CM, Zhou EK, Gendron JM. Decoys provide a scalable platform for the identification of plant E3 ubiquitin ligases that regulate circadian function. eLife 2019; 8:44558. [PMID: 30950791 PMCID: PMC6483598 DOI: 10.7554/elife.44558] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/04/2019] [Indexed: 12/30/2022] Open
Abstract
The circadian clock relies on regulated degradation of clock proteins to maintain rhythmicity. Despite this, we know few components that mediate protein degradation. This is due to high levels of functional redundancy within plant E3 ubiquitin ligase families. In order to overcome this issue and discover E3 ubiquitin ligases that control circadian function, we generated a library of transgenic Arabidopsis plants expressing dominant-negative ‘decoy’ E3 ubiquitin ligases. We determined their effects on the circadian clock and identified dozens of new potential regulators of circadian function. To demonstrate the potency of the decoy screening methodology to overcome redundancy and identify bona fide clock regulators, we performed follow-up studies on MAC3A (PUB59) and MAC3B (PUB60). We show that they redundantly control circadian period by regulating splicing. This work demonstrates the viability of ubiquitin ligase decoys as a screening platform to overcome genetic challenges and discover E3 ubiquitin ligases that regulate plant development. Plants have an internal time keeper known as the circadian clock that operates in 24-hour cycles to coordinate the plants behaviors with the environment. The clock is made of many different proteins and plants carefully control when they make and destroy these proteins to regulate the cycle. Inside plant cells, enzymes known as E3 ubiquitin ligases determine which proteins are destroyed by labelling target proteins with a small tag. Plants have hundreds of different E3 ubiquitin ligases, leading to overlaps in the roles the different enzymes play. These overlaps make it difficult to identify the specific E3 ubiquitin ligases that are involved in a particular process. As a result, only few E3 ubiquitin ligases implicated in the circadian clock have been identified so far. A small weed known as Arabidopsis is often used in research studies because it grows quickly and the genes can be easily manipulated. Here, Feke et al. set out to develop a new tool to identify the specific E3 ubiquitin ligases involved in regulating the circadian clock in Arabidopsis. The team created a library of hundreds of Arabidopsis plants producing different decoy E3 ubiquitin ligases that retained their ability to bind to target proteins but were unable to degrade them. Nearly a quarter of the E3 ligases found in Arabidopsis were represented in this library. The decoy enzymes protected the target proteins from being degraded by the normal E3 ubiquitin ligases, resulting in the library plants having presumably higher levels of these target proteins compared to normal Arabidopsis plants. By tracking circadian rhythms in these plants, the team was able to identify the individual E3 ligases that control the circadian clock. The experiments revealed several E3 ligases that may regulate the circadian clock, including two enzymes called MAC3A and MAC3B. Further experiments demonstrated that MAC3A and MAC3B have similar roles in regulating the circadian clock and can compensate for the absence of the other. The library of Arabidopsis plants generated by Feke et al. is now available for other researchers to use in their studies. In the future this approach could be adapted to make similar libraries for crops and other plants that have even more E3 ligase enzymes than Arabidopsis.
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Affiliation(s)
- Ann Feke
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Wei Liu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Jing Hong
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States.,School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Man-Wah Li
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Chin-Mei Lee
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Elton K Zhou
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Joshua M Gendron
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
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19
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Loros JJ. Principles of the animal molecular clock learned from Neurospora. Eur J Neurosci 2019; 51:19-33. [PMID: 30687965 DOI: 10.1111/ejn.14354] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 12/10/2018] [Accepted: 12/13/2018] [Indexed: 12/28/2022]
Abstract
Study of Neurospora, a model system evolutionarily related to animals and sharing a circadian system having nearly identical regulatory architecture to that of animals, has advanced our understanding of all circadian rhythms. Work on the molecular bases of the Oscillator began in Neurospora before any clock genes were cloned and provided the second example of a clock gene, frq, as well as the first direct experimental proof that the core of the Oscillator was built around a transcriptional translational negative feedback loop (TTFL). Proof that FRQ was a clock component provided the basis for understanding how light resets the clock, and this in turn provided the generally accepted understanding for how light resets all animal and fungal clocks. Experiments probing the mechanism of light resetting led to the first identification of a heterodimeric transcriptional activator as the positive element in a circadian feedback loop, and to the general description of the fungal/animal clock as a single step TTFL. The common means through which DNA damage impacts the Oscillator in fungi and animals was first described in Neurospora. Lastly, the systematic study of Output was pioneered in Neurospora, providing the vocabulary and conceptual framework for understanding how Output works in all cells. This model system has contributed to the current appreciation of the role of Intrinsic Disorder in clock proteins and to the documentation of the essential roles of protein post-translational modification, as distinct from turnover, in building a circadian clock.
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Affiliation(s)
- Jennifer J Loros
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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20
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Joanito I, Chu JW, Wu SH, Hsu CP. An incoherent feed-forward loop switches the Arabidopsis clock rapidly between two hysteretic states. Sci Rep 2018; 8:13944. [PMID: 30224713 PMCID: PMC6141573 DOI: 10.1038/s41598-018-32030-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/24/2018] [Indexed: 12/02/2022] Open
Abstract
In higher plants (e.g., Arabidopsis thaliana), the core structure of the circadian clock is mostly governed by a repression process with very few direct activators. With a series of simplified models, we studied the underlying mechanism and found that the Arabidopsis clock consists of type-2 incoherent feed-forward loops (IFFLs), one of them creating a pulse-like expression in PRR9/7. The double-negative feedback loop between CCA1/LHY and PRR5/TOC1 generates a bistable, hysteretic behavior in the Arabidopsis circadian clock. We found that the IFFL involving PRR9/7 breaks the bistability and moves the system forward with a rapid pulse in the daytime, and the evening complex (EC) breaks it in the evening. With this illustration, we can intuitively explain the behavior of the clock under mutant conditions. Thus, our results provide new insights into the underlying network structures of the Arabidopsis core oscillator.
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Affiliation(s)
- Ignasius Joanito
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Bioinformatics and System Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Jhih-Wei Chu
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Bioinformatics and System Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan
| | - Chao-Ping Hsu
- Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan.
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan.
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21
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Cochetel N, Escudié F, Cookson SJ, Dai Z, Vivin P, Bert PF, Muñoz MS, Delrot S, Klopp C, Ollat N, Lauvergeat V. Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4339-4355. [PMID: 28922755 PMCID: PMC5854021 DOI: 10.1093/jxb/erx224] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 06/06/2017] [Indexed: 05/11/2023]
Abstract
In many fruit species, including grapevine, grafting is used to improve scion productivity and quality and to adapt the plant to environmental conditions. However, the mechanisms underlying the rootstock control of scion development are still poorly understood. The ability of rootstocks to regulate nitrogen uptake and assimilation may contribute to this control. A split-root system was used to grow heterografted grapevines and to investigate the molecular responses to changes in nitrate availability of two rootstocks known to affect scion growth differently. Transcriptome profiling by RNA sequencing was performed on root samples collected 3 and 24 h after nitrogen supply. The results demonstrated a common response involving nitrogen-related genes, as well as a more pronounced transcriptomic reprogramming in the genotype conferring the lower scion growth. A weighted gene co-expression network analysis allowed the identification of co-regulated gene modules, suggesting a role for nitrate transporter 2 family genes and some transcription factors as main actors controlling this genotype-dependent response to heterogeneous nitrogen supply. The relationship between nitrate, ethylene, and strigolactone hormonal pathways was found to differ between the two genotypes. These findings indicated that the genotypes responded differently to heterogeneous nitrogen availability, and this may contribute to their contrasting effect on scion growth.
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Affiliation(s)
- Noé Cochetel
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Frédéric Escudié
- Genotoul Bioinformatics Platform, UR875 Mathematics and Applied Informatics of Toulouse, INRA, Castanet-Tolosan, France
| | - Sarah Jane Cookson
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Zhanwu Dai
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Philippe Vivin
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Pierre-François Bert
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Mindy Stephania Muñoz
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Alameda, Santiago, Chile
| | - Serge Delrot
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Christophe Klopp
- Genotoul Bioinformatics Platform, UR875 Mathematics and Applied Informatics of Toulouse, INRA, Castanet-Tolosan, France
| | - Nathalie Ollat
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Virginie Lauvergeat
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d’Ornon, France
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22
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Serrano-Bueno G, Romero-Campero FJ, Lucas-Reina E, Romero JM, Valverde F. Evolution of photoperiod sensing in plants and algae. CURRENT OPINION IN PLANT BIOLOGY 2017; 37:10-17. [PMID: 28391047 DOI: 10.1016/j.pbi.2017.03.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 05/21/2023]
Abstract
Measuring day length confers a strong fitness improvement to photosynthetic organisms as it allows them to anticipate light phases and take the best decisions preceding diurnal transitions. In close association with signals from the circadian clock and the photoreceptors, photoperiodic sensing constitutes also a precise way to determine the passing of the seasons and to take annual decisions such as the best time to flower or the beginning of dormancy. Photoperiodic sensing in photosynthetic organisms is ancient and two major stages in its evolution could be identified, the cyanobacterial time sensing and the evolutionary tool kit that arose in green algae and developed into the photoperiodic system of modern plants. The most recent discoveries about the evolution of the perception of light, measurement of day length and relationship with the circadian clock along the evolution of the eukaryotic green lineage will be discussed in this review.
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Affiliation(s)
- Gloria Serrano-Bueno
- Plant Development Unit, Institute for Plan Biochemistry and Photosynthesis, CSIC-Universidad de Sevilla, 49th, Americo Vespucio Av., 41092 Sevilla, Spain
| | - Francisco J Romero-Campero
- Plant Development Unit, Institute for Plan Biochemistry and Photosynthesis, CSIC-Universidad de Sevilla, 49th, Americo Vespucio Av., 41092 Sevilla, Spain
| | - Eva Lucas-Reina
- Plant Development Unit, Institute for Plan Biochemistry and Photosynthesis, CSIC-Universidad de Sevilla, 49th, Americo Vespucio Av., 41092 Sevilla, Spain
| | - Jose M Romero
- Plant Development Unit, Institute for Plan Biochemistry and Photosynthesis, CSIC-Universidad de Sevilla, 49th, Americo Vespucio Av., 41092 Sevilla, Spain
| | - Federico Valverde
- Plant Development Unit, Institute for Plan Biochemistry and Photosynthesis, CSIC-Universidad de Sevilla, 49th, Americo Vespucio Av., 41092 Sevilla, Spain.
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23
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You Y, Sawikowska A, Neumann M, Posé D, Capovilla G, Langenecker T, Neher RA, Krajewski P, Schmid M. Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering. Nat Commun 2017; 8:15120. [PMID: 28513600 PMCID: PMC5442315 DOI: 10.1038/ncomms15120] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 03/01/2017] [Indexed: 02/04/2023] Open
Abstract
Plants can produce organs throughout their entire life from pluripotent stem cells located at their growing tip, the shoot apical meristem (SAM). At the time of flowering, the SAM of Arabidopsis thaliana switches fate and starts producing flowers instead of leaves. Correct timing of flowering in part determines reproductive success, and is therefore under environmental and endogenous control. How epigenetic regulation contributes to the floral transition has eluded analysis so far, mostly because of the poor accessibility of the SAM. Here we report the temporal dynamics of the chromatin modifications H3K4me3 and H3K27me3 and their correlation with transcriptional changes at the SAM in response to photoperiod-induced flowering. Emphasizing the importance of tissue-specific epigenomic analyses we detect enrichments of chromatin states in the SAM that were not apparent in whole seedlings. Furthermore, our results suggest that regulation of translation might be involved in adjusting meristem function during the induction of flowering. When plants flower, the shoot apical meristem switches fate to produce floral organs instead of leaves. Here You et al. perform tissue-specific epigenome profiling and show that during this transition changes in histone methylation are correlated with transcriptional responses in the meristem.
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Affiliation(s)
- Yuan You
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Aneta Sawikowska
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | - Manuela Neumann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - David Posé
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Giovanna Capovilla
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Tobias Langenecker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Richard A Neher
- Evolutionary Dynamics and Biophysics Group, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | - Markus Schmid
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.,Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
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24
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Rubenach AJS, Hecht V, Vander Schoor JK, Liew LC, Aubert G, Burstin J, Weller JL. EARLY FLOWERING3 Redundancy Fine-Tunes Photoperiod Sensitivity. PLANT PHYSIOLOGY 2017; 173:2253-2264. [PMID: 28202598 PMCID: PMC5373058 DOI: 10.1104/pp.16.01738] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/13/2017] [Indexed: 05/07/2023]
Abstract
Three pea (Pisum sativum) loci controlling photoperiod sensitivity, HIGH RESPONSE (HR), DIE NEUTRALIS (DNE), and STERILE NODES (SN), have recently been shown to correspond to orthologs of Arabidopsis (Arabidopsis thaliana) circadian clock genes EARLY FLOWERING3 (ELF3), ELF4, and LUX ARRHYTHMO, respectively. A fourth pea locus, PHOTOPERIOD (PPD), also contributes to the photoperiod response in a similar manner to SN and DNE, and recessive ppd mutants on a spring-flowering hr mutant background show early, photoperiod-insensitive flowering. However, the molecular identity of PPD has so far remained elusive. Here, we show that the PPD locus also has a role in maintenance of diurnal and circadian gene expression rhythms and identify PPD as an ELF3 co-ortholog, termed ELF3b Genetic interactions between pea ELF3 genes suggest that loss of PPD function does not affect flowering time in the presence of functional HR, whereas PPD can compensate only partially for the lack of HR These results provide an illustration of how gene duplication and divergence can generate potential for the emergence of more subtle variations in phenotype that may be adaptively significant.
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Affiliation(s)
- Andrew J S Rubenach
- School of Plant Science, University of Tasmania, Hobart, Tasmania 7001, Australia (A.J.S.R., V.H., J.K.V., L.C.L., J.L.W.); and
- INRA, UMR1347 Agroécologie, F-21065, Dijon, France (G.A., J.B.)
| | - Valérie Hecht
- School of Plant Science, University of Tasmania, Hobart, Tasmania 7001, Australia (A.J.S.R., V.H., J.K.V., L.C.L., J.L.W.); and
- INRA, UMR1347 Agroécologie, F-21065, Dijon, France (G.A., J.B.)
| | - Jacqueline K Vander Schoor
- School of Plant Science, University of Tasmania, Hobart, Tasmania 7001, Australia (A.J.S.R., V.H., J.K.V., L.C.L., J.L.W.); and
- INRA, UMR1347 Agroécologie, F-21065, Dijon, France (G.A., J.B.)
| | - Lim Chee Liew
- School of Plant Science, University of Tasmania, Hobart, Tasmania 7001, Australia (A.J.S.R., V.H., J.K.V., L.C.L., J.L.W.); and
- INRA, UMR1347 Agroécologie, F-21065, Dijon, France (G.A., J.B.)
| | - Gregoire Aubert
- School of Plant Science, University of Tasmania, Hobart, Tasmania 7001, Australia (A.J.S.R., V.H., J.K.V., L.C.L., J.L.W.); and
- INRA, UMR1347 Agroécologie, F-21065, Dijon, France (G.A., J.B.)
| | - Judith Burstin
- School of Plant Science, University of Tasmania, Hobart, Tasmania 7001, Australia (A.J.S.R., V.H., J.K.V., L.C.L., J.L.W.); and
- INRA, UMR1347 Agroécologie, F-21065, Dijon, France (G.A., J.B.)
| | - James L Weller
- School of Plant Science, University of Tasmania, Hobart, Tasmania 7001, Australia (A.J.S.R., V.H., J.K.V., L.C.L., J.L.W.); and
- INRA, UMR1347 Agroécologie, F-21065, Dijon, France (G.A., J.B.)
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25
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Gray JA, Shalit-Kaneh A, Chu DN, Hsu PY, Harmer SL. The REVEILLE Clock Genes Inhibit Growth of Juvenile and Adult Plants by Control of Cell Size. PLANT PHYSIOLOGY 2017; 173:2308-2322. [PMID: 28254761 PMCID: PMC5373068 DOI: 10.1104/pp.17.00109] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 02/28/2017] [Indexed: 05/25/2023]
Abstract
The circadian clock is a complex regulatory network that enhances plant growth and fitness in a constantly changing environment. In Arabidopsis (Arabidopsis thaliana), the clock is composed of numerous regulatory feedback loops in which REVEILLE8 (RVE8) and its homologs RVE4 and RVE6 act in a partially redundant manner to promote clock pace. Here, we report that the remaining members of the RVE8 clade, RVE3 and RVE5, play only minor roles in the regulation of clock function. However, we find that RVE8 clade proteins have unexpected functions in the modulation of light input to the clock and the control of plant growth at multiple stages of development. In seedlings, these proteins repress hypocotyl elongation in a daylength- and sucrose-dependent manner. Strikingly, adult rve4 6 8 and rve3 4 5 6 8 mutants are much larger than wild-type plants, with both increased leaf area and biomass. This size phenotype is associated with a faster growth rate and larger cell size and is not simply due to a delay in the transition to flowering. Gene expression and epistasis analysis reveal that the growth phenotypes of rve mutants are due to the misregulation of PHYTOCHROME INTERACTING FACTOR4 (PIF4) and PIF5 expression. Our results show that even small changes in PIF gene expression caused by the perturbation of clock gene function can have large effects on the growth of adult plants.
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Affiliation(s)
- Jennifer A Gray
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California 95616
| | - Akiva Shalit-Kaneh
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California 95616
| | - Dalena Nhu Chu
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California 95616
| | - Polly Yingshan Hsu
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California 95616
| | - Stacey L Harmer
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California 95616
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26
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Jeong YY, Seo PJ. Bidirectional regulation between circadian clock and ABA signaling. Commun Integr Biol 2017. [PMCID: PMC5398209 DOI: 10.1080/19420889.2017.1296999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Circadian clock ensures coordination of rhythmic biological processes with environmental cycles. Correct matching of internal and external rhythmic cycles maximizes plant fitness and environmental adaptation capability and also ensures efficient energy consumption through circadian gating of a variety of physiological processes. Accumulating evidences support that circadian oscillator components extensively participate in circadian gating of output processes. Here, we provide remarkable examples illustrating molecular mechanisms underlying circadian gating of environmental sensitivity. In addition, bidirectional interactions between circadian oscillator and output pathways have been observed in abscisic acid (ABA)-related physiological processes, emphasizing the biological relevance of extensive crosstalk surrounding circadian clock in acute time-of-day responses.
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Affiliation(s)
- Young Yeop Jeong
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
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27
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Yi H, Li X, Lee SH, Nou IS, Lim YP, Hur Y. Natural variation in CIRCADIAN CLOCK ASSOCIATED 1 is associated with flowering time in Brassica rapa. Genome 2016; 60:402-413. [PMID: 28177832 DOI: 10.1139/gen-2016-0052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Flowering time is a very important agronomic trait and the development of molecular markers associated with this trait can facilitate crop breeding. CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), a core oscillator component of circadian rhythms that affect metabolic pathways in plants, has been implicated in flowering time control in species of Brassica. CCA1 gene sequences from three Brassica rapa inbred lines, showing either early flowering or late flowering phenotypes, were analyzed and a high level of sequence variation was identified, especially within the fourth intron. Using this information, three PCR primer sets were designed and tested using various inbred lines of B. rapa. The usage of InDel markers was further validated by evaluation of flowering time and high resolution melting (HRM) analysis. Both methods, PCR and HRM, validated the use of newly developed markers. Additional sequence analyses of Brassica plants with diploid (AA, BB, or CC) and allotetraploid genomes further confirmed a large number of sequence polymorphisms in the CCA1 gene, including insertions/deletions in the fourth intron. Our results demonstrated that sequence variations in CCA1 can be used to develop valuable trait-related molecular markers for Brassica crop breeding.
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Affiliation(s)
- Hankuil Yi
- a Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Xiaonan Li
- b Department of Horticulture, Chungnam National University, Gung-Dong, Yuseong-Gu, Daejeon 305-764, Republic of Korea.,d Department of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Seong Ho Lee
- b Department of Horticulture, Chungnam National University, Gung-Dong, Yuseong-Gu, Daejeon 305-764, Republic of Korea
| | - Ill-Sup Nou
- c Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
| | - Yong Pyo Lim
- b Department of Horticulture, Chungnam National University, Gung-Dong, Yuseong-Gu, Daejeon 305-764, Republic of Korea
| | - Yoonkang Hur
- a Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 305-764, Republic of Korea
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28
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Alternative Splicing of Barley Clock Genes in Response to Low Temperature. PLoS One 2016; 11:e0168028. [PMID: 27959947 PMCID: PMC5154542 DOI: 10.1371/journal.pone.0168028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/23/2016] [Indexed: 12/12/2022] Open
Abstract
Alternative splicing (AS) is a regulated mechanism that generates multiple transcripts from individual genes. It is widespread in eukaryotic genomes and provides an effective way to control gene expression. At low temperatures, AS regulates Arabidopsis clock genes through dynamic changes in the levels of productive mRNAs. We examined AS in barley clock genes to assess whether temperature-dependent AS responses also occur in a monocotyledonous crop species. We identify changes in AS of various barley core clock genes including the barley orthologues of Arabidopsis AtLHY and AtPRR7 which showed the most pronounced AS changes in response to low temperature. The AS events modulate the levels of functional and translatable mRNAs, and potentially protein levels, upon transition to cold. There is some conservation of AS events and/or splicing behaviour of clock genes between Arabidopsis and barley. In addition, novel temperature-dependent AS of the core clock gene HvPPD-H1 (a major determinant of photoperiod response and AtPRR7 orthologue) is conserved in monocots. HvPPD-H1 showed a rapid, temperature-sensitive isoform switch which resulted in changes in abundance of AS variants encoding different protein isoforms. This novel layer of low temperature control of clock gene expression, observed in two very different species, will help our understanding of plant adaptation to different environments and ultimately offer a new range of targets for plant improvement.
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29
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Li X, Ma D, Lu SX, Hu X, Huang R, Liang T, Xu T, Tobin EM, Liu H. Blue Light- and Low Temperature-Regulated COR27 and COR28 Play Roles in the Arabidopsis Circadian Clock. THE PLANT CELL 2016; 28:2755-2769. [PMID: 27837007 PMCID: PMC5155342 DOI: 10.1105/tpc.16.00354] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/18/2016] [Accepted: 11/11/2016] [Indexed: 05/18/2023]
Abstract
Light and temperature are two key environmental signals that profoundly affect plant growth and development, but underlying molecular mechanisms of how light and temperature signals affect the circadian clock are largely unknown. Here, we report that COR27 and COR28 are regulated not only by low temperatures but also by light signals. COR27 and COR28 are negative regulators of freezing tolerance but positive regulators of flowering, possibly representing a trade-off between freezing tolerance and flowering. Furthermore, loss-of-function mutations in COR27 and COR28 result in period lengthening of various circadian output rhythms and affect central clock gene expression. Also, the cor27 cor28 double mutation affects the pace of the circadian clock. Additionally, COR27 and COR28 are direct targets of CCA1, which represses their transcription via chromatin binding. Finally, we report that COR27 and COR28 bind to the chromatin of TOC1 and PRR5 to repress their transcription, suggesting that their effects on rhythms are in part due to their regulation of TOC1 and PRR5 These data demonstrate that blue light and low temperature-regulated COR27 and COR28 regulate the circadian clock as well as freezing tolerance and flowering time.
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Affiliation(s)
- Xu Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, P.R. China
| | - Dingbang Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, P.R. China
- University of Chinese Academy of Sciences, Shanghai 200032, P.R. China
| | - Sheen X Lu
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095
| | - Xinyi Hu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, P.R. China
- University of Chinese Academy of Sciences, Shanghai 200032, P.R. China
| | - Rongfeng Huang
- University of Chinese Academy of Sciences, Shanghai 200032, P.R. China
- Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 201602 Shanghai, P.R. China
| | - Tong Liang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, P.R. China
- University of Chinese Academy of Sciences, Shanghai 200032, P.R. China
| | - Tongda Xu
- Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 201602 Shanghai, P.R. China
| | - Elaine M Tobin
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095
| | - Hongtao Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032 Shanghai, P.R. China
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30
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Wu JF, Tsai HL, Joanito I, Wu YC, Chang CW, Li YH, Wang Y, Hong JC, Chu JW, Hsu CP, Wu SH. LWD-TCP complex activates the morning gene CCA1 in Arabidopsis. Nat Commun 2016; 7:13181. [PMID: 27734958 PMCID: PMC5065627 DOI: 10.1038/ncomms13181] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/09/2016] [Indexed: 12/31/2022] Open
Abstract
A double-negative feedback loop formed by the morning genes CIRCADIAN CLOCK ASSOCIATED1 (CCA1)/LATE ELONGATED HYPOCOTYL (LHY) and the evening gene TIMING OF CAB EXPRESSION1 (TOC1) contributes to regulation of the circadian clock in Arabidopsis. A 24-h circadian cycle starts with the peak expression of CCA1 at dawn. Although CCA1 is targeted by multiple transcriptional repressors, including PSEUDO-RESPONSE REGULATOR9 (PRR9), PRR7, PRR5 and CCA1 HIKING EXPEDITION (CHE), activators of CCA1 remain elusive. Here we use mathematical modelling to infer a co-activator role for LIGHT-REGULATED WD1 (LWD1) in CCA1 expression. We show that the TEOSINTE BRANCHED 1-CYCLOIDEA-PCF20 (TCP20) and TCP22 proteins act as LWD-interacting transcriptional activators. The concomitant binding of LWD1 and TCP20/TCP22 to the TCP-binding site in the CCA1 promoter activates CCA1. Our study reveals activators of the morning gene CCA1 and provides an action mechanism that ensures elevated expression of CCA1 at dawn to sustain a robust clock.
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Affiliation(s)
- Jing-Fen Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Huang-Lung Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ignasius Joanito
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Institute of Bioinformatics and System Biology, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Yi-Chen Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chin-Wen Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Hang Li
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ying Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Jong Chan Hong
- Division of Life Science, Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
- Division of Plant Sciences, University of Missouri, Columbia, South Carolina MO 65211-7310, USA
| | - Jhih-Wei Chu
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Institute of Bioinformatics and System Biology, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Chao-Ping Hsu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei 106, Taiwan
| | - Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei 106, Taiwan
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Marshall CM, Tartaglio V, Duarte M, Harmon FG. The Arabidopsis sickle Mutant Exhibits Altered Circadian Clock Responses to Cool Temperatures and Temperature-Dependent Alternative Splicing. THE PLANT CELL 2016; 28:2560-2575. [PMID: 27624757 PMCID: PMC5134976 DOI: 10.1105/tpc.16.00223] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 08/29/2016] [Accepted: 09/08/2016] [Indexed: 05/20/2023]
Abstract
The circadian clock allows plants to anticipate and respond to daily changes in ambient temperature. Mechanisms establishing the timing of circadian rhythms in Arabidopsis thaliana through temperature entrainment remain unclear. Also incompletely understood is the temperature compensation mechanism that maintains consistent period length within a range of ambient temperatures. A genetic screen for Arabidopsis mutants affecting temperature regulation of the PSEUDO-RESPONSE REGULATOR7 promoter yielded a novel allele of the SICKLE (SIC) gene. This mutant, sic-3, and the existing sic-1 mutant both exhibit low-amplitude or arrhythmic expression of core circadian clock genes under cool ambient temperature cycles, but not under light-dark entrainment. sic mutants also lengthen free running period in a manner consistent with impaired temperature compensation. sic mutant alleles accumulate LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED1 (CCA1) splice variants, among other alternatively spliced transcripts, which is exacerbated by cool temperatures. The cca1-1 lhy-20 double mutant is epistatic to sic-3, indicating the LHY and CCA1 splice variants are needed for sic-3 circadian clock phenotypes. It is not expected that SIC is directly involved in the circadian clock mechanism; instead, SIC likely contributes to pre-mRNA metabolism, and the splice variants that accumulate in sic mutants likely affect the circadian clock response to cool ambient temperature.
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Affiliation(s)
- Carine M Marshall
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, California 94710
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Virginia Tartaglio
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, California 94710
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Maritza Duarte
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, California 94710
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Frank G Harmon
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service, Albany, California 94710
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
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32
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Atamian HS, Harmer SL. Circadian regulation of hormone signaling and plant physiology. PLANT MOLECULAR BIOLOGY 2016; 91:691-702. [PMID: 27061301 DOI: 10.1007/s11103-016-0477-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 03/31/2016] [Indexed: 05/20/2023]
Abstract
The survival and reproduction of plants depend on their ability to cope with a wide range of daily and seasonal environmental fluctuations during their life cycle. Phytohormones are plant growth regulators that are involved in almost every aspect of growth and development as well as plant adaptation to myriad abiotic and biotic conditions. The circadian clock, an endogenous and cell-autonomous biological timekeeper that produces rhythmic outputs with close to 24-h rhythms, provides an adaptive advantage by synchronizing plant physiological and metabolic processes to the external environment. The circadian clock regulates phytohormone biosynthesis and signaling pathways to generate daily rhythms in hormone activity that fine-tune a range of plant processes, enhancing adaptation to local conditions. This review explores our current understanding of the interplay between the circadian clock and hormone signaling pathways.
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Affiliation(s)
- Hagop S Atamian
- Department of Plant Biology, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Stacey L Harmer
- Department of Plant Biology, University of California, One Shields Avenue, Davis, CA, 95616, USA.
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Kamioka M, Takao S, Suzuki T, Taki K, Higashiyama T, Kinoshita T, Nakamichi N. Direct Repression of Evening Genes by CIRCADIAN CLOCK-ASSOCIATED1 in the Arabidopsis Circadian Clock. THE PLANT CELL 2016; 28:696-711. [PMID: 26941090 PMCID: PMC4826007 DOI: 10.1105/tpc.15.00737] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 02/11/2016] [Accepted: 02/26/2016] [Indexed: 05/18/2023]
Abstract
The circadian clock is a biological timekeeping system that provides organisms with the ability to adapt to day-night cycles. Timing of the expression of four members of the Arabidopsis thaliana PSEUDO-RESPONSE REGULATOR(PRR) family is crucial for proper clock function, and transcriptional control of PRRs remains incompletely defined. Here, we demonstrate that direct regulation of PRR5 by CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) determines the repression state of PRR5 in the morning. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) analyses indicated that CCA1 associates with three separate regions upstream of PRR5 CCA1 and its homolog LATE ELONGATED HYPOCOTYL (LHY) suppressed PRR5 promoter activity in a transient assay. The regions bound by CCA1 in the PRR5 promoter gave rhythmic patterns with troughs in the morning, when CCA1 and LHY are at high levels. Furthermore,ChIP-seq revealed that CCA1 associates with at least 449 loci with 863 adjacent genes. Importantly, this gene set contains genes that are repressed but upregulated incca1 lhy double mutants in the morning. This study shows that direct binding by CCA1 in the morning provides strong repression of PRR5, and repression by CCA1 also temporally regulates an evening-expressed gene set that includes PRR5.
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Affiliation(s)
- Mari Kamioka
- School of Agriculture, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Saori Takao
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Takamasa Suzuki
- Exploratory Research for Advanced Technology (ERATO) Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan College of Bioscience and Biotechnology, Chub University, Kasugai 487-8501, Japan Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan
| | - Kyomi Taki
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan Exploratory Research for Advanced Technology (ERATO) Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan
| | - Toshinori Kinoshita
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan
| | - Norihito Nakamichi
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8602, Japan
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Comparative transcriptome and proteome analysis to reveal the biosynthesis of gold nanoparticles in Arabidopsis. Sci Rep 2016; 6:21733. [PMID: 26902325 PMCID: PMC4763195 DOI: 10.1038/srep21733] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 01/29/2016] [Indexed: 01/18/2023] Open
Abstract
A large number of plants have been tested and exploited in search of a green chemistry approach for the fabrication of gold or other precious metal nanomaterials. Despite the potential of plant based methods, very little is known about the underlying biochemical reactions and genes involved in the biotransformation mechanism of AuCl4 into gold nanoparticles (AuNPs). In this research, we thus focused on studying the effect of Au on growth and nanoparticles formation by analyses of transcriptome, proteome and ionome shift in Arabidopsis. Au exposure favored the growth of Arabidopsis seedling and induced formation of nanoparticles in root and shoot, as indicated by optical and hyperspectral imaging. Root transcriptome analysis demonstrated the differential expression of the members of WRKY, MYB and BHLH gene families, which are involved in the Fe and other essential metals homeostasis. The proteome analysis revealed that Glutathione S-transferases were induced in the shoot and suggested its potential role in the biosynthesis AuNPs. This study also demonstrated the role of plant hormone auxin in determining the Au induced root system architecture. This is the first study using an integrated approach to understand the in planta biotransformation of KAuCl4 into AuNPs.
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Ryo M, Matsuo T, Yamashino T, Ichinose M, Sugita M, Aoki S. Diversity of plant circadian clocks: Insights from studies of Chlamydomonas reinhardtii and Physcomitrella patens. PLANT SIGNALING & BEHAVIOR 2016; 11:e1116661. [PMID: 26645746 PMCID: PMC4871632 DOI: 10.1080/15592324.2015.1116661] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Arabidopsis thaliana has long been the model plant of choice for elucidating the mechanisms of the circadian clock. Recently, relevant results have accumulated in other species of green plant lineages, including green algae. This mini-review describes a comparison of the mechanism of the A. thaliana clock to those of the green alga Chlamydomonas reinhardtii and the moss Physcomitrella patens, focusing on commonalities and divergences of subsystems of the clock. The potential of such an approach from an evolutionary viewpoint is discussed.
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Affiliation(s)
- Masashi Ryo
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Takuya Matsuo
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Takafumi Yamashino
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Mizuho Ichinose
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Mamoru Sugita
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Setsuyuki Aoki
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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36
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Domestication selected for deceleration of the circadian clock in cultivated tomato. Nat Genet 2015; 48:89-93. [PMID: 26569124 DOI: 10.1038/ng.3447] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/21/2015] [Indexed: 12/15/2022]
Abstract
The circadian clock is a critical regulator of plant physiology and development, controlling key agricultural traits in crop plants. In addition, natural variation in circadian rhythms is important for local adaptation. However, quantitative modulation of circadian rhythms due to artificial selection has not yet been reported. Here we show that the circadian clock of cultivated tomato (Solanum lycopersicum) has slowed during domestication. Allelic variation of the tomato homolog of the Arabidopsis gene EID1 is responsible for a phase delay. Notably, the genomic region harboring EID1 shows signatures of a selective sweep. We find that the EID1 allele in cultivated tomatoes enhances plant performance specifically under long day photoperiods, suggesting that humans selected slower circadian rhythms to adapt the cultivated species to the long summer days it encountered as it was moved away from the equator.
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37
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38
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Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis. Proc Natl Acad Sci U S A 2015; 112:E4802-10. [PMID: 26261339 DOI: 10.1073/pnas.1513609112] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The circadian clock in Arabidopsis exerts a critical role in timing multiple biological processes and stress responses through the regulation of up to 80% of the transcriptome. As a key component of the clock, the Myb-like transcription factor CIRCADIAN CLOCK ASSOCIATED1 (CCA1) is able to initiate and set the phase of clock-controlled rhythms and has been shown to regulate gene expression by binding directly to the evening element (EE) motif found in target gene promoters. However, the precise molecular mechanisms underlying clock regulation of the rhythmic transcriptome, specifically how clock components connect to clock output pathways, is poorly understood. In this study, using ChIP followed by deep sequencing of CCA1 in constant light (LL) and diel (LD) conditions, more than 1,000 genomic regions occupied by CCA1 were identified. CCA1 targets are enriched for a myriad of biological processes and stress responses, providing direct links to clock-controlled pathways and suggesting that CCA1 plays an important role in regulating a large subset of the rhythmic transcriptome. Although many of these target genes are evening expressed and contain the EE motif, a significant subset is morning phased and enriched for previously unrecognized motifs associated with CCA1 function. Furthermore, this work revealed several CCA1 targets that do not cycle in either LL or LD conditions. Together, our results emphasize an expanded role for the clock in regulating a diverse category of genes and key pathways in Arabidopsis and provide a comprehensive resource for future functional studies.
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39
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Bendix C, Marshall CM, Harmon FG. Circadian Clock Genes Universally Control Key Agricultural Traits. MOLECULAR PLANT 2015; 8:1135-52. [PMID: 25772379 DOI: 10.1016/j.molp.2015.03.003] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 02/26/2015] [Accepted: 03/04/2015] [Indexed: 05/17/2023]
Abstract
Circadian clocks are endogenous timers that enable plants to synchronize biological processes with daily and seasonal environmental conditions in order to allocate resources during the most beneficial times of day and year. The circadian clock regulates a number of central plant activities, including growth, development, and reproduction, primarily through controlling a substantial proportion of transcriptional activity and protein function. This review examines the roles that alleles of circadian clock genes have played in domestication and improvement of crop plants. The focus here is on three groups of circadian clock genes essential to clock function in Arabidopsis thaliana: PSEUDO-RESPONSE REGULATORs, GIGANTEA, and the evening complex genes early flowering 3, early flowering 4, and lux arrhythmo. homologous genes from each group underlie quantitative trait loci that have beneficial influences on key agricultural traits, especially flowering time but also yield, biomass, and biennial growth habit. Emerging insights into circadian clock regulation of other fundamental plant processes, including responses to abiotic and biotic stresses, are discussed to highlight promising avenues for further crop improvement.
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Affiliation(s)
- Claire Bendix
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, USA; Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Carine M Marshall
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, USA; Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Frank G Harmon
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, USA; Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA.
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40
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Nakamichi N. Adaptation to the local environment by modifications of the photoperiod response in crops. PLANT & CELL PHYSIOLOGY 2015; 56:594-604. [PMID: 25432974 PMCID: PMC4387313 DOI: 10.1093/pcp/pcu181] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 11/12/2014] [Indexed: 05/02/2023]
Abstract
Flowering plants produce a meristem at the shoot tip where specialized tissue generates shoot apical meristems at the appropriate time to differentiate into reproductive structures, pollinate and efficiently generate seeds. The complex set of molecular and phenological events culminating in development of a flowering meristem is referred to as 'flowering time'. Flowering time affects plant productivity because plants dedicate energy to produce flowers and seeds rather than vegetative tissue once the molecular decision to initiate flowering has been taken. Thus, initiation of flowering time is an important decision in plants, especially in annual plants including crops. Humans have introduced crops into latitudes and climate areas far from their origin or natural ecosystem, requiring in many cases modification of native flowering times. Recent molecular-genetic studies shed light on the genetic basis related to such introductions. In this review, recent progress regarding crop introductions and their genetic bases are summarized, as well as the potential of other agricultural plants to be introduced into different climatic zones.
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Affiliation(s)
- Norihito Nakamichi
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602 Japan Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602 Japan Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0022 Japan
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41
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Allelic polymorphism of GIGANTEA is responsible for naturally occurring variation in circadian period in Brassica rapa. Proc Natl Acad Sci U S A 2015; 112:3829-34. [PMID: 25775524 DOI: 10.1073/pnas.1421803112] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
GIGANTEA (GI) was originally identified by a late-flowering mutant in Arabidopsis, but subsequently has been shown to act in circadian period determination, light inhibition of hypocotyl elongation, and responses to multiple abiotic stresses, including tolerance to high salt and cold (freezing) temperature. Genetic mapping and analysis of families of heterogeneous inbred lines showed that natural variation in GI is responsible for a major quantitative trait locus in circadian period in Brassica rapa. We confirmed this conclusion by transgenic rescue of an Arabidopsis gi-201 loss of function mutant. The two B. rapa GI alleles each fully rescued the delayed flowering of Arabidopsis gi-201 but showed differential rescue of perturbations in red light inhibition of hypocotyl elongation and altered cold and salt tolerance. The B. rapa R500 GI allele, which failed to rescue the hypocotyl and abiotic stress phenotypes, disrupted circadian period determination in Arabidopsis. Analysis of chimeric B. rapa GI alleles identified the causal nucleotide polymorphism, which results in an amino acid substitution (S264A) between the two GI proteins. This polymorphism underlies variation in circadian period, cold and salt tolerance, and red light inhibition of hypocotyl elongation. Loss-of-function mutations of B. rapa GI confer delayed flowering, perturbed circadian rhythms in leaf movement, and increased freezing and increased salt tolerance, consistent with effects of similar mutations in Arabidopsis. Collectively, these data suggest that allelic variation of GI-and possibly of clock genes in general-offers an attractive target for molecular breeding for enhanced stress tolerance and potentially for improved crop yield.
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42
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Sharma M, Bhatt D. The circadian clock and defence signalling in plants. MOLECULAR PLANT PATHOLOGY 2015; 16:210-8. [PMID: 25081907 PMCID: PMC6638510 DOI: 10.1111/mpp.12178] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The circadian clock is the internal time-keeping machinery in higher organisms. Cross-talk between the circadian clock and a diverse range of physiological processes in plants, including stress acclimatization, hormone signalling, photomorphogenesis and defence signalling, is currently being explored. Recent studies on circadian clock genes and genes involved in defence signalling have indicated a possible reciprocal interaction between the two. It has been proposed that the circadian clock shapes the outcome of plant-pathogen interactions. In this review, we highlight the studies carried out so far on two model plant pathogens, namely Pseudomonas syringae and Hyaloperonospora arabidopsidis, and the involvement of the circadian clock in gating effector-triggered immunity and pathogen-associated molecular pattern-triggered immunity. We focus on how the circadian clock gates the expression of various stress-related transcripts in a prolific manner to enhance plant fitness. An understanding of this dynamic relationship between clock and stress will open up new avenues in the understanding of endogenous mechanisms of defence signalling in plants.
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Affiliation(s)
- Mayank Sharma
- Mahyco Life Science Research Center, PO Box 76, Jalna (MS), 431203, India
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43
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Evolutionary relationships among barley and Arabidopsis core circadian clock and clock-associated genes. J Mol Evol 2015; 80:108-19. [PMID: 25608480 PMCID: PMC4320304 DOI: 10.1007/s00239-015-9665-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/06/2015] [Indexed: 12/13/2022]
Abstract
The circadian clock regulates a multitude of plant developmental and metabolic processes. In crop species, it contributes significantly to plant performance and productivity and to the adaptation and geographical range over which crops can be grown. To understand the clock in barley and how it relates to the components in the Arabidopsis thaliana clock, we have performed a systematic analysis of core circadian clock and clock-associated genes in barley, Arabidopsis and another eight species including tomato, potato, a range of monocotyledonous species and the moss, Physcomitrella patens. We have identified orthologues and paralogues of Arabidopsis genes which are conserved in all species, monocot/dicot differences, species-specific differences and variation in gene copy number (e.g. gene duplications among the various species). We propose that the common ancestor of barley and Arabidopsis had two-thirds of the key clock components identified in Arabidopsis prior to the separation of the monocot/dicot groups. After this separation, multiple independent gene duplication events took place in both monocot and dicot ancestors.
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44
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Romanowski A, Yanovsky MJ. Circadian rhythms and post-transcriptional regulation in higher plants. FRONTIERS IN PLANT SCIENCE 2015; 6:437. [PMID: 26124767 PMCID: PMC4464108 DOI: 10.3389/fpls.2015.00437] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 05/28/2015] [Indexed: 05/06/2023]
Abstract
The circadian clock of plants allows them to cope with daily changes in their environment. This is accomplished by the rhythmic regulation of gene expression, in a process that involves many regulatory steps. One of the key steps involved at the RNA level is post-transcriptional regulation, which ensures a correct control on the different amounts and types of mRNA that will ultimately define the current physiological state of the plant cell. Recent advances in the study of the processes of regulation of pre-mRNA processing, RNA turn-over and surveillance, regulation of translation, function of lncRNAs, biogenesis and function of small RNAs, and the development of bioinformatics tools have helped to vastly expand our understanding of how this regulatory step performs its role. In this work we review the current progress in circadian regulation at the post-transcriptional level research in plants. It is the continuous interaction of all the information flow control post-transcriptional processes that allow a plant to precisely time and predict daily environmental changes.
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Affiliation(s)
| | - Marcelo J. Yanovsky
- *Correspondence: Marcelo J. Yanovsky, Laboratorio de Genómica Comparativa del Desarrollo Vegetal, Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina,
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45
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Xing H, Wang P, Cui X, Zhang C, Wang L, Liu X, Yuan L, Li Y, Xie Q, Xu X. LNK1 and LNK2 recruitment to the evening element require morning expressed circadian related MYB-like transcription factors. PLANT SIGNALING & BEHAVIOR 2015; 10:e1010888. [PMID: 25848708 PMCID: PMC4622603 DOI: 10.1080/15592324.2015.1010888] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/10/2015] [Accepted: 01/15/2015] [Indexed: 05/25/2023]
Abstract
Transcriptional feedback loops in Arabidopsis circadian clock is composed of more repressive components, while the knowledge of activation mechanism remains limited. We recently reported 2 members from a family of NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED genes, LNK1 and LNK2, dynamically interact with morning-phased transcriptional factors, like CIRCADIAN CLOCK ASSOCIATED1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), REVEILLE8 (RVE8) and RVE4, and function as coactivators for the expression of TIMING OF CAB EXPRESSION1 (TOC1) and PSEUDO-RESPONSE REGULATOR5 (PRR5) via transcriptional factors RVE8 and RVE4. Here we provide evidence that both LNK1 and LNK2 play critical role in the transcriptional activation of PRR5, LNK1 may contribute more than LNK2 did under experimental conditions. We also identified that both LNK1 and LNK2 recruitment to the evening element of PRR5 promoter via LNK1-RVE8 or LNK2-RVE8 proteins complex through electrophoretic mobility shift assay. Therefore LNK1 and LNK2 function as coactivator of dawn-phased MYB-like transcription factors, such as RVE8 in morning complex to regulate the target genes expression.
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Affiliation(s)
- Hongya Xing
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Peng Wang
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Xuan Cui
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Chenguang Zhang
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Lingbao Wang
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Xian Liu
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Li Yuan
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Yue Li
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Qiguang Xie
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
| | - Xiaodong Xu
- Hebei Key Laboratory of Molecular and Cellular Biology; Key Laboratory of Molecular and Cellular Biology of Ministry of Education; College of Life Sciences; Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling; Shijiazhuang, China
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Filo J, Wu A, Eliason E, Richardson T, Thines BC, Harmon FG. Gibberellin driven growth in elf3 mutants requires PIF4 and PIF5. PLANT SIGNALING & BEHAVIOR 2015; 10:e992707. [PMID: 25738547 PMCID: PMC4622946 DOI: 10.4161/15592324.2014.992707] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/22/2014] [Accepted: 11/24/2014] [Indexed: 05/18/2023]
Abstract
The regulatory connections between the circadian clock and hormone signaling are essential to understand, as these two regulatory processes work together to time growth processes relative to predictable environmental events. Gibberellins (GAs) are phytohormones that control many growth processes throughout all stages of the plant life cycle, including germination and flowering. An increasing number of examples demonstrate that the circadian clock directly influences GA biosynthesis and signaling. EARLY FLOWERING 3 (ELF3) participates in a tripartite transcriptional complex known as the Evening Complex (EC). In this capacity, ELF3 is fundamental to core circadian clock activity, as well as time-of-day specific regulation of genes directly responsible for growth control, namely the PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF5 genes. Here we show that the GA biosynthesis inhibitor paclobutrazol substantially reduces the long hypocotyl and petiole phenotypes of Arabidopsis elf3 mutants. In addition, loss of ELF3 activity causes upregulation of the key GA biosynthesis genes GA20ox1 and GA20ox2. Moreover, GA20ox1 and GA20ox2 expression depends strongly on the redundant activities of PIF4 and PIF5. These findings indicate that the defining growth phenotypes of elf3 mutants arise from altered GA biosynthesis due to misregulation of PIF4 and PIF5. These observations agree with recent work linking increased GA production with the elongated growth phenotypes of the barley elf3 mutant. Thus, the role of the EC in regulation of GA biosynthesis and signaling in eudicots is shared with monocots and, therefore, is a highly conserved mechanism for growth control.
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Key Words
- CO, CONSTANS
- Col-0, Columbia
- EC, Evening Complex
- ELF3, EARLY FLOWERING 3
- ELF4, EARLY FLOWERING 4
- EMS, ethyl methanesulfonate
- FT, FLOWERING LOCUS T
- GA, gibberellin
- GA20ox, gibberellin 20-oxidase
- GA3ox, gibberellin 3-oxidase
- LD, long day
- LUX, LUX ARRHYTHMO
- PAC, paclobutrazol
- PIF - PHYTOCHROME INTERACTING FACTOR
- PIF4
- SD, short day
- WT, wild type
- ZT, Zeitgeiber Time.
- circadian clock
- early flowering 3
- gibberellin
- phytochrome interacting factor
- phytohormone
- plant growth
- qPCR, quantitative RT-PCR
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Affiliation(s)
- Julie Filo
- Keck Science Department; Pitzer College; Claremont, CA USA
| | - Austin Wu
- Keck Science Department; Claremont McKenna College; Claremont, CA USA
| | - Erica Eliason
- Keck Science Department; Pitzer College; Claremont, CA USA
| | - Timothy Richardson
- Plant Gene Expression Center; USDA-ARS; Albany, CA USA
- Department of Plant and Microbial Biology; University of California; Berkeley, CA USA
| | - Bryan C Thines
- Plant Gene Expression Center; USDA-ARS; Albany, CA USA
- Department of Plant and Microbial Biology; University of California; Berkeley, CA USA
- Claremont McKenna; Pitzer; and Scripps Colleges; Claremont, CA USA
| | - Frank G Harmon
- Plant Gene Expression Center; USDA-ARS; Albany, CA USA
- Department of Plant and Microbial Biology; University of California; Berkeley, CA USA
- Correspondence to: Frank G Harmon;
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Xie Q, Wang P, Liu X, Yuan L, Wang L, Zhang C, Li Y, Xing H, Zhi L, Yue Z, Zhao C, McClung CR, Xu X. LNK1 and LNK2 are transcriptional coactivators in the Arabidopsis circadian oscillator. THE PLANT CELL 2014; 26:2843-57. [PMID: 25012192 PMCID: PMC4145118 DOI: 10.1105/tpc.114.126573] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/08/2014] [Accepted: 06/20/2014] [Indexed: 05/18/2023]
Abstract
Transcriptional feedback loops are central to the architecture of eukaryotic circadian clocks. Models of the Arabidopsis thaliana circadian clock have emphasized transcriptional repressors, but recently, Myb-like REVEILLE (RVE) transcription factors have been established as transcriptional activators of central clock components, including PSEUDO-RESPONSE REGULATOR5 (PRR5) and TIMING OF CAB EXPRESSION1 (TOC1). We show here that NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED1 (LNK1) and LNK2, members of a small family of four LNK proteins, dynamically interact with morning-expressed oscillator components, including RVE4 and RVE8. Mutational disruption of LNK1 and LNK2 function prevents transcriptional activation of PRR5 by RVE8. The LNKs lack known DNA binding domains, yet LNK1 acts as a transcriptional activator in yeast and in planta. Chromatin immunoprecipitation shows that LNK1 is recruited to the PRR5 and TOC1 promoters in planta. We conclude that LNK1 is a transcriptional coactivator necessary for expression of the clock genes PRR5 and TOC1 through recruitment to their promoters via interaction with bona fide DNA binding proteins such as RVE4 and RVE8.
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Affiliation(s)
- Qiguang Xie
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Peng Wang
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Xian Liu
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Li Yuan
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Lingbao Wang
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Chenguang Zhang
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Yue Li
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Hongya Xing
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Liya Zhi
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Zhiliang Yue
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - Chunsheng Zhao
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
| | - C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755-3563
| | - Xiaodong Xu
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of the Ministry of Education, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, Hebei 050024, China
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Tissot N, Przybyla-Toscano J, Reyt G, Castel B, Duc C, Boucherez J, Gaymard F, Briat JF, Dubos C. Iron around the clock. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 224:112-9. [PMID: 24908512 DOI: 10.1016/j.plantsci.2014.03.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/14/2014] [Accepted: 03/15/2014] [Indexed: 05/26/2023]
Abstract
Carbon assimilation, a key determinant of plant biomass production, is under circadian regulation. Light and temperature are major inputs of the plant clock that control various daily rhythms. Such rhythms confer adaptive advantages to the organisms by adjusting their metabolism in anticipation of environmental fluctuations. The relationship between the circadian clock and nutrition extends far beyond the regulation of carbon assimilation as mineral nutrition, and specially iron homeostasis, is regulated through this mechanism. Conversely, iron status was identified as a new and important input regulating the central oscillator, raising the question of the nature of the Fe-dependent signal that modulates the period of the circadian clock. Several lines of evidence strongly suggest that fully developed and functional chloroplasts as well as early light signalling events, involving phytochromes, are essential to couple the clock to Fe responses. Nevertheless, the exact nature of the signal, which most probably involves unknown or not yet fully characterized elements of the chloroplast-to-nucleus retrograde signalling pathway, remains to be identified. Finally, this regulation may also involves epigenetic components.
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Affiliation(s)
- Nicolas Tissot
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes (INRA, CNRS, Montpellier SupAgro, Université Montpellier 2), 34060 Montpellier Cedex 2, France
| | - Jonathan Przybyla-Toscano
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes (INRA, CNRS, Montpellier SupAgro, Université Montpellier 2), 34060 Montpellier Cedex 2, France
| | - Guilhem Reyt
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes (INRA, CNRS, Montpellier SupAgro, Université Montpellier 2), 34060 Montpellier Cedex 2, France
| | - Baptiste Castel
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes (INRA, CNRS, Montpellier SupAgro, Université Montpellier 2), 34060 Montpellier Cedex 2, France
| | - Céline Duc
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes (INRA, CNRS, Montpellier SupAgro, Université Montpellier 2), 34060 Montpellier Cedex 2, France
| | - Jossia Boucherez
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes (INRA, CNRS, Montpellier SupAgro, Université Montpellier 2), 34060 Montpellier Cedex 2, France
| | - Frédéric Gaymard
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes (INRA, CNRS, Montpellier SupAgro, Université Montpellier 2), 34060 Montpellier Cedex 2, France
| | - Jean-François Briat
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes (INRA, CNRS, Montpellier SupAgro, Université Montpellier 2), 34060 Montpellier Cedex 2, France.
| | - Christian Dubos
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes (INRA, CNRS, Montpellier SupAgro, Université Montpellier 2), 34060 Montpellier Cedex 2, France.
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