151
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Liu Y, Li X, Ma D, Chen Z, Wang JW, Liu H. CIB1 and CO interact to mediate CRY2-dependent regulation of flowering. EMBO Rep 2018; 19:embr.201845762. [PMID: 30126927 DOI: 10.15252/embr.201845762] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 07/30/2018] [Accepted: 08/02/2018] [Indexed: 11/09/2022] Open
Abstract
Cryptochromes are photolyase-like photoreceptors. Arabidopsis CRY2 (cryptochrome 2) primarily mediates the photoperiodic regulation of floral initiation. CRY2 has been shown to promote FT (FLOWERING LOCUS T) mRNA expression in response to blue light by suppressing the degradation of the CO (CONSTANS) protein and activating CIB1 (CRY2-interacting bHLH1). Although CIB1 and CO are both transcriptional activators of FT, their relationship is unknown. Here, we show that CIB1 physically interacts with CO and promotes FT transcription in a CO-dependent manner. CRY2, CIB1, and CO form a protein complex in response to blue light to activate FT transcription, and the complex is regulated by the photoperiod and peaks at dusk along with higher FT expression. We also determined that CRY2 was recruited to the FT chromatin by CIB1 and CO and that all three proteins are bound to the same region within the FT promoter. Therefore, there is crosstalk between the CRY2-CO and CRY2-CIBs pathways, and CIB1 and CO act together to regulate FT transcription and flowering.
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Affiliation(s)
- Yawen 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, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - 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, China
| | - Dingbang Ma
- 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, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Ziru Chen
- 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, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Jia-Wei Wang
- 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, China
| | - 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, China
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152
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Severing E, Faino L, Jamge S, Busscher M, Kuijer-Zhang Y, Bellinazzo F, Busscher-Lange J, Fernández V, Angenent GC, Immink RGH, Pajoro A. Arabidopsis thaliana ambient temperature responsive lncRNAs. BMC PLANT BIOLOGY 2018; 18:145. [PMID: 30005624 PMCID: PMC6045843 DOI: 10.1186/s12870-018-1362-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 07/04/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have emerged as new class of regulatory molecules in animals where they regulate gene expression at transcriptional and post-transcriptional level. Recent studies also identified lncRNAs in plant genomes, revealing a new level of transcriptional complexity in plants. Thousands of lncRNAs have been predicted in the Arabidopsis thaliana genome, but only a few have been studied in depth. RESULTS Here we report the identification of Arabidopsis lncRNAs that are expressed during the vegetative stage of development in either the shoot apical meristem or in leaves. We found that hundreds of lncRNAs are expressed in these tissues, of which 50 show differential expression upon an increase in ambient temperature. One of these lncRNAs, FLINC, is down-regulated at higher ambient temperature and affects ambient temperature-mediated flowering in Arabidopsis. CONCLUSION A number of ambient temperature responsive lncRNAs were identified with potential roles in the regulation of temperature-dependent developmental changes, such as the transition from the vegetative to the reproductive (flowering) phase. The challenge for the future is to characterize the biological function and molecular mode of action of the large number of ambient temperature-regulated lncRNAs that have been identified in this study.
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Affiliation(s)
- Edouard Severing
- Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Suraj Jamge
- Laboratory of Molecular Biology, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Marco Busscher
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Yang Kuijer-Zhang
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Francesca Bellinazzo
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | | | | | - Gerco C. Angenent
- Laboratory of Molecular Biology, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Richard G. H. Immink
- Laboratory of Molecular Biology, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
| | - Alice Pajoro
- Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Laboratory of Molecular Biology, Wageningen University and Research, 6708PB, Wageningen, The Netherlands
- Bioscience, Wageningen University and Research, 6708PB Wageningen, The Netherlands
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153
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Lee CM, Feke A, Li MW, Adamchek C, Webb K, Pruneda-Paz J, Bennett EJ, Kay SA, Gendron JM. Decoys Untangle Complicated Redundancy and Reveal Targets of Circadian Clock F-Box Proteins. PLANT PHYSIOLOGY 2018; 177:1170-1186. [PMID: 29794020 PMCID: PMC6052990 DOI: 10.1104/pp.18.00331] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/07/2018] [Indexed: 05/11/2023]
Abstract
Eukaryotic circadian clocks utilize the ubiquitin proteasome system to precisely degrade clock proteins. In plants, the F-box-type E3 ubiquitin ligases ZEITLUPE (ZTL), FLAVIN-BINDING, KELCH REPEAT, F-BOX1 (FKF1), and LOV KELCH PROTEIN2 (LKP2) regulate clock period and couple the clock to photoperiodic flowering in response to end-of-day light conditions. To better understand their functions, we expressed decoy ZTL, FKF1, and LKP2 proteins that associate with target proteins but are unable to ubiquitylate their targets in Arabidopsis (Arabidopsis thaliana). These dominant-negative forms of the proteins inhibit the ubiquitylation of target proteins and allow for the study of ubiquitylation-independent and -dependent functions of ZTL, FKF1, and LKP2. We demonstrate the effects of expressing ZTL, FKF1, and LKP2 decoys on the circadian clock and flowering time. Furthermore, the decoy E3 ligases trap substrate interactions, and using immunoprecipitation-mass spectrometry, we identify interacting partners. We focus studies on the clock transcription factor CCA1 HIKING EXPEDITION (CHE) and show that ZTL interacts directly with CHE and can mediate CHE ubiquitylation. We also demonstrate that CHE protein is degraded in the dark and that degradation is reduced in a ztl mutant plant, showing that CHE is a bona fide ZTL target protein. This work increases our understanding of the genetic and biochemical roles for ZTL, FKF1, and LKP2 and also demonstrates an effective methodology for studying complicated genetic redundancy among E3 ubiquitin ligases.
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Affiliation(s)
- Chin-Mei Lee
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511
| | - Ann Feke
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511
| | - Man-Wah Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511
| | - Christopher Adamchek
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511
| | - Kristofor Webb
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - José Pruneda-Paz
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - Eric J Bennett
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - Steve A Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, California 90089
| | - Joshua M Gendron
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511
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154
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Ding J, Böhlenius H, Rühl MG, Chen P, Sane S, Zambrano JA, Zheng B, Eriksson ME, Nilsson O. GIGANTEA-like genes control seasonal growth cessation in Populus. THE NEW PHYTOLOGIST 2018. [PMID: 29532940 DOI: 10.1111/nph.15087] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Survival of trees growing in temperate zones requires cycling between active growth and dormancy. This involves growth cessation in the autumn triggered by a photoperiod shorter than the critical day length. Variations in GIGANTEA (GI)-like genes have been associated with phenology in a range of different tree species, but characterization of the functions of these genes in the process is still lacking. We describe the identification of the Populus orthologs of GI and their critical role in short-day-induced growth cessation. Using ectopic expression and silencing, gene expression analysis, protein interaction and chromatin immunoprecipitation experiments, we show that PttGIs are likely to act in a complex with PttFKF1s (FLAVIN-BINDING, KELCH REPEAT, F-BOX 1) and PttCDFs (CYCLING DOF FACTOR) to control the expression of PttFT2, the key gene regulating short-day-induced growth cessation in Populus. In contrast to Arabidopsis, in which the GI-CONSTANS (CO)-FLOWERING LOCUS T (FT) regulon is a crucial day-length sensor for flowering time, our study suggests that, in Populus, PttCO-independent regulation of PttFT2 by PttGI is more important in the photoperiodic control of growth cessation and bud set.
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Affiliation(s)
- Jihua Ding
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Henrik Böhlenius
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, 230 53, Alnarp, Sweden
| | - Mark Georg Rühl
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Peng Chen
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Shashank Sane
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Jose A Zambrano
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry, Huazhong Agricultural University, 430070, Wuhan, China
| | - Maria E Eriksson
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden
| | - Ove Nilsson
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
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155
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Gnesutta N, Mantovani R, Fornara F. Plant Flowering: Imposing DNA Specificity on Histone-Fold Subunits. TRENDS IN PLANT SCIENCE 2018; 23:293-301. [PMID: 29331540 DOI: 10.1016/j.tplants.2017.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 12/11/2017] [Accepted: 12/14/2017] [Indexed: 05/27/2023]
Abstract
CONSTANS (CO) is a master regulator of flowering time, although the mechanisms underlying its role as a transcriptional regulator are not well understood. The DNA-binding domain of CO shares homology with that of NUCLEAR FACTOR YA (NF-YA), a subunit of the CCAAT-binding trimer NF-Y. Recent publications indicate that CO and its rice homolog HEADING DATE 1 (Hd1) form heterotrimers with the histone-fold subunits of NF-Y to efficiently bind promoter elements in the florigen genes. Differences in the DNA-binding specificities of NF-Y and NF-CO can be conceptualized based on our knowledge of the 3D structure of the NF-Y/CCAAT complex. Here we discuss the modes of assembly of NF-Y-like heterotrimers and possible models for their activity as flexible sequence-specific transcriptional regulators.
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Affiliation(s)
- Nerina Gnesutta
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
| | - Roberto Mantovani
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Fabio Fornara
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
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156
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Mariz-Ponte N, Mendes RJ, Sario S, Ferreira de Oliveira JMP, Melo P, Santos C. Tomato plants use non-enzymatic antioxidant pathways to cope with moderate UV-A/B irradiation: A contribution to the use of UV-A/B in horticulture. JOURNAL OF PLANT PHYSIOLOGY 2018; 221:32-42. [PMID: 29223880 DOI: 10.1016/j.jplph.2017.11.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 05/21/2023]
Abstract
Plants developed receptors for solar UV-A/B radiation, which regulate a complex network of functions through the plant's life cycle. However, greenhouse grown crops, like tomato, are exposed to strongly reduced UV radiation, contrarily to their open-field counterparts. A new paradigm of modern horticulture is to supplement adequate levels of UV to greenhouse cultures, inducing a positive mild stress necessary to stimulate oxidative stress pathways and antioxidant mechanisms. Protected cultures of Solanum (cv MicroTom) were supplemented with moderate UV-A (1h and 4h) and UV-B (1min and 5min) doses during the flowering/fruiting period. After 30days, flowering/fruit ripening synchronization were enhanced, paralleled by the upregulation of blue/UV-A and UV-B receptors' genes cry1a and uvr8. UV-B caused moreover an increase in the expression of hy5, of HY5 repressor cop1 and of a repressor of COP1, uvr8. While all UV-A/B conditions increased SOD activity, increases of the generated H2O2, as well as lipid peroxidation and cell mebrane disruption, were minimal. However, the activity of antioxidant enzymes downstream from SOD (CAT, APX, GPX) was not significant. These results suggest that the major antioxidant pathways involve phenylpropanoid compounds, which also have an important role in UV screening. This hypothesis was confirmed by the increase of phenolic compounds and by the upregulation of chs and fls, coding for CHS and FLS enzymes involved in the phenylpropanoid synthesis. Overall, all doses of UV-A or UV-B were beneficial to flowering/fruiting but lower UV-A/B doses induced lower redox disorders and were more effective in the fruiting process/synchronization. Considering the benefits observed on flowering/fruiting, with minimal impacts in the vegetative part, we demonstrate that both UV-A/B could be used in protected tomato horticulture systems.
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Affiliation(s)
- N Mariz-Ponte
- Department of Biology & LAQV/REQUIMTE, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - R J Mendes
- Department of Biology & LAQV/REQUIMTE, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - S Sario
- Department of Biology & LAQV/REQUIMTE, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - J M P Ferreira de Oliveira
- Department of Biology & LAQV/REQUIMTE, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal; UCIBIO, REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313, Porto, Portugal
| | - P Melo
- Department of Biology & BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Porto, Rua Campo Alegre, 4169-007, Porto, Portugal
| | - C Santos
- Department of Biology & LAQV/REQUIMTE, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
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157
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Triozzi PM, Ramos-Sánchez JM, Hernández-Verdeja T, Moreno-Cortés A, Allona I, Perales M. Photoperiodic Regulation of Shoot Apical Growth in Poplar. FRONTIERS IN PLANT SCIENCE 2018; 9:1030. [PMID: 30057588 PMCID: PMC6053638 DOI: 10.3389/fpls.2018.01030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/25/2018] [Indexed: 05/19/2023]
Abstract
Woody perennials adapt their genetic traits to local climate conditions. Day length plays an essential role in the seasonal growth of poplar trees. When photoperiod falls below a given critical day length, poplars undergo growth cessation and bud set. A leaf-localized mechanism of photoperiod measurement triggers the transcriptional modulation of a long distance signaling molecule, FLOWERING LOCUS T (FT). This molecule targets meristem function giving rise to these seasonal responses. Studies over the past decade have identified conserved orthologous genes involved in photoperiodic flowering in Arabidopsis that regulate poplar vegetative growth. However, phenological and molecular examination of key photoperiod signaling molecules reveals functional differences between these two plant model systems suggesting alternative components and/or regulatory mechanisms operating during poplar vegetative growth. Here, we review current knowledge and provide new data regarding the molecular components of the photoperiod measuring mechanism that regulates annual growth in poplar focusing on main achievements and new perspectives.
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Affiliation(s)
- Paolo M. Triozzi
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
| | - José M. Ramos-Sánchez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
| | - Tamara Hernández-Verdeja
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
| | - Alicia Moreno-Cortés
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
| | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de MadridMadrid, Spain
- *Correspondence: Isabel Allona
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
- Mariano Perales
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158
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Hayama R, Mizoguchi T, Coupland G. Differential effects of light-to-dark transitions on phase setting in circadian expression among clock-controlled genes in Pharbitis nil. PLANT SIGNALING & BEHAVIOR 2018; 13:e1473686. [PMID: 29944436 PMCID: PMC6110364 DOI: 10.1080/15592324.2018.1473686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 04/27/2018] [Indexed: 05/18/2023]
Abstract
The circadian clock is synchronized by the day-night cycle to allow plants to anticipate daily environmental changes and to recognize annual changes in day length enabling seasonal flowering. This clock system has been extensively studied in Arabidopsis thaliana and was found to be reset by the dark to light transition at dawn. By contrast, studies on photoperiodic flowering of Pharbitis nil revealed the presence of a clock system reset by the transition from light to dark at dusk to measure the duration of the night. However, a Pharbitis photosynthetic gene was also shown to be insensitive to this dusk transition and to be set by dawn. Thus Pharbitis appeared to have two clock systems, one set by dusk that controls photoperiodic flowering and a second controlling photosynthetic gene expression similar to that of Arabidopsis. Here, we show that circadian mRNA expression of Pharbitis homologs of a series of Arabidopsis clock or clock-controlled genes are insensitive to the dusk transition. These data further define the presence in Pharbitis of a clock system that is analogous to the Arabidopsis system, which co-exists and functions with the dusk-set system dedicated to the control of photoperiodic flowering.
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Affiliation(s)
- R. Hayama
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- CONTACT Ryosuke Hayama Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, D-50829 Cologne, Germany
| | - T. Mizoguchi
- Department of Natural Sciences, International Christian University, Tokyo, Japan
| | - G. Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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159
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Inoue K, Araki T, Endo M. Circadian clock during plant development. JOURNAL OF PLANT RESEARCH 2018; 131:59-66. [PMID: 29134443 PMCID: PMC5897470 DOI: 10.1007/s10265-017-0991-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/06/2017] [Indexed: 05/14/2023]
Abstract
Plants have endogenous biological clocks that allow organisms to anticipate and prepare for daily and seasonal environmental changes and increase their fitness in changing environments. The circadian clock in plants, as in animals and insects, mainly consists of multiple interlocking transcriptional/translational feedback loops. The circadian clock can be entrained by environmental cues such as light, temperature and nutrient status to synchronize internal biological rhythms with surrounding environments. Output pathways link the circadian oscillator to various physiological, developmental, and reproductive processes for adjusting the timing of these biological processes to an appropriate time of day or a suitable season. Recent genomic studies have demonstrated that polymorphism in circadian clock genes may contribute to local adaptations over a wide range of latitudes in many plant species. In the present review, we summarize the circadian regulation of biological processes throughout the life cycle of plants, and describe the contribution of the circadian clock to local adaptation.
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Affiliation(s)
- Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Motomu Endo
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
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160
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Lee BD, Kim MR, Kang MY, Cha JY, Han SH, Nawkar GM, Sakuraba Y, Lee SY, Imaizumi T, McClung CR, Kim WY, Paek NC. The F-box protein FKF1 inhibits dimerization of COP1 in the control of photoperiodic flowering. Nat Commun 2017; 8:2259. [PMID: 29273730 PMCID: PMC5741637 DOI: 10.1038/s41467-017-02476-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 12/04/2017] [Indexed: 01/12/2023] Open
Abstract
In Arabidopsis thaliana, CONSTANS (CO) plays an essential role in the regulation of photoperiodic flowering under long-day conditions. CO protein is stable only in the afternoon of long days, when it induces the expression of FLOWERING LOCUS T (FT), which promotes flowering. The blue-light photoreceptor FLAVIN-BINDING, KELCH REPEAT, F-BOX1 (FKF1) interacts with CO and stabilizes it by an unknown mechanism. Here, we provide genetic and biochemical evidence that FKF1 inhibits CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1)-dependent CO degradation. Light-activated FKF1 has no apparent effect on COP1 stability but can interact with and negatively regulate COP1. We show that FKF1 can inhibit COP1 homo-dimerization. Mutation of the coiled-coil domain in COP1, which prevents dimer formation, impairs COP1 function in coordinating flowering time. Based on these results, we propose a model whereby the light- and day length-dependent interaction between FKF1 and COP1 controls CO stability to regulate flowering time. CONSTANS promotes flowering under long-day conditions in Arabidopsis but is rapidly degraded in short-day conditions. Here the authors show that the blue-light photoreceptor FKF1 can interact with the E3 ligase COP1 in a light-dependent manner and prevent degradation of CO in long-day conditions.
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Affiliation(s)
- Byoung-Doo Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Mi Ri Kim
- Division of Applied Life Science (BK21Plus), PMBBRC & IALS, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Min-Young Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Joon-Yung Cha
- Division of Applied Life Science (BK21Plus), PMBBRC & IALS, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Su-Hyun Han
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ganesh M Nawkar
- Division of Applied Life Science (BK21Plus), PMBBRC & IALS, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Yasuhito Sakuraba
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21Plus), PMBBRC & IALS, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
| | - C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755-3563, USA
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), PMBBRC & IALS, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Nam-Chon Paek
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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161
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Liu L, Wu Y, Liao Z, Xiong J, Wu F, Xu J, Lan H, Tang Q, Zhou S, Liu Y, Lu Y. Evolutionary conservation and functional divergence of the LFK gene family play important roles in the photoperiodic flowering pathway of land plants. Heredity (Edinb) 2017; 120:310-328. [PMID: 29225355 DOI: 10.1038/s41437-017-0006-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 08/15/2017] [Accepted: 08/22/2017] [Indexed: 12/22/2022] Open
Abstract
ZEITLUPE (ZTL), LOV KELCH PROTEIN 2 (LKP2), and FLAVIN-BINDING KELCH REPEAT F-BOX 1 (FKF1)-blue-light photoreceptors-play important roles in regulating the circadian clock and photoperiodic flowering pathway in plants. In this study, phylogenetic analysis revealed that the LOV (Light, Oxygen, or Voltage) and Kelch repeat-containing F-box (LFK) gene family can be classified into two clades, ZTL/LKP2 and FKF1, with clear differentiation between monocots and dicots within each clade. The LFK family genes underwent strong purifying selection; however, signatures of positive selection to adapt to local conditions still existed in 18 specific codons. In 87 diverse maize inbred lines, significant differences were identified (P ≤ 0.01) for days to female flowering between the haplotypes consisting of eight positive selection sites at ZmFKF1b corresponding to tropical and temperate maize groups of the phylogenetic tree, indicating a key role of ZmFKF1b in maize adaptive evolution. In addition, positive coevolution was detected in the domains of the LFK family for long-term cooperation to targets. The Type-I and Type-II functional divergence analysis revealed subfunctionalization or neofunctionalization of the LFKs, and the ZTL subfamily is most likely to maintain the ancestral function of LFKs. Over 50% of critical amino acid sites involved in the functional divergence were identified in the Kelch repeat domain, resulting in the distinction of substrates for ubiquitination and degradation. These results suggest that evolutionary conservation contributes to the maintenance of critical physiological functions, whereas functional divergence after duplication helps to generate diverse molecular regulation mechanisms.
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Affiliation(s)
- Ling Liu
- Maize Research Institute, Sichuan Agricultural University, 611130, Wenjiang, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, China
| | - Yuanqi Wu
- Maize Research Institute, Sichuan Agricultural University, 611130, Wenjiang, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, China
| | - Zhengqiao Liao
- Maize Research Institute, Sichuan Agricultural University, 611130, Wenjiang, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, China
| | - Jing Xiong
- Maize Research Institute, Sichuan Agricultural University, 611130, Wenjiang, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, 611130, Wenjiang, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, China
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural University, 611130, Wenjiang, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, China
| | - Hai Lan
- Maize Research Institute, Sichuan Agricultural University, 611130, Wenjiang, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, China
| | - Qiling Tang
- Maize Research Institute, Sichuan Agricultural University, 611130, Wenjiang, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, China
| | - Shufeng Zhou
- Maize Research Institute, Sichuan Agricultural University, 611130, Wenjiang, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Wenjiang, Sichuan, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, 611130, Wenjiang, Sichuan, China. .,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, China.
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162
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Bloomer RH, Dean C. Fine-tuning timing: natural variation informs the mechanistic basis of the switch to flowering in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5439-5452. [PMID: 28992087 DOI: 10.1093/jxb/erx270] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The evolution of diverse life history strategies has allowed Arabidopsis thaliana to adapt to worldwide locations, spanning a range of latitudinal and environmental conditions. Arabidopsis thaliana accessions are either vernalization-requiring winter annuals or rapid cyclers, with extensive natural variation in vernalization requirement and response. Genetic and molecular analysis of this variation has enhanced our understanding of the mechanisms involved in life history determination, with translation to both natural and crop systems in the Brassicaceae and beyond.
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Affiliation(s)
- R H Bloomer
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - C Dean
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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163
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Oakenfull RJ, Davis SJ. Shining a light on the Arabidopsis circadian clock. PLANT, CELL & ENVIRONMENT 2017; 40:2571-2585. [PMID: 28732105 DOI: 10.1111/pce.13033] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 07/10/2017] [Accepted: 07/11/2017] [Indexed: 05/23/2023]
Abstract
The circadian clock provides essential timing information to ensure optimal growth to prevailing external environmental conditions. A major time-setting mechanism (zeitgeber) in clock synchronization is light. Differing light wavelengths, intensities, and photoperiodic duration are processed for the clock-setting mechanism. Many studies on light-input pathways to the clock have focused on Arabidopsis thaliana. Photoreceptors are specific chromic proteins that detect light signals and transmit this information to the central circadian oscillator through a number of different signalling mechanisms. The most well-characterized clock-mediating photoreceptors are cryptochromes and phytochromes, detecting blue, red, and far-red wavelengths of light. Ultraviolet and shaded light are also processed signals to the oscillator. Notably, the clock reciprocally generates rhythms of photoreceptor action leading to so-called gating of light responses. Intermediate proteins, such as Phytochrome interacting factors (PIFs), constitutive photomorphogenic 1 (COP1) and EARLY FLOWERING 3 (ELF3), have been established in signalling pathways downstream of photoreceptor activation. However, the precise details for these signalling mechanisms are not fully established. This review highlights both historical and recent efforts made to understand overall light input to the oscillator, first looking at how each wavelength of light is detected, this is then related to known input mechanisms and their interactions.
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Affiliation(s)
| | - Seth J Davis
- Department of Biology, University of York, York, YO10 5DD, UK
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164
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Henriques R, Wang H, Liu J, Boix M, Huang LF, Chua NH. The antiphasic regulatory module comprising CDF5 and its antisense RNA FLORE links the circadian clock to photoperiodic flowering. THE NEW PHYTOLOGIST 2017; 216:854-867. [PMID: 28758689 DOI: 10.1111/nph.14703] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/12/2017] [Indexed: 05/19/2023]
Abstract
Circadian rhythms of gene expression are generated by the combinatorial action of transcriptional and translational feedback loops as well as chromatin remodelling events. Recently, long noncoding RNAs (lncRNAs) that are natural antisense transcripts (NATs) to transcripts encoding central oscillator components were proposed as modulators of core clock function in mammals (Per) and fungi (frq/qrf). Although oscillating lncRNAs exist in plants, their functional characterization is at an initial stage. By screening an Arabidopsis thaliana lncRNA custom-made array we identified CDF5 LONG NONCODING RNA (FLORE), a circadian-regulated lncRNA that is a NAT of CDF5. Quantitative real-time RT-PCR confirmed the circadian regulation of FLORE, whereas GUS-staining and flowering time evaluation were used to determine its biological function. FLORE and CDF5 antiphasic expression reflects mutual inhibition in a similar way to frq/qrf. Moreover, whereas the CDF5 protein delays flowering by directly repressing FT transcription, FLORE promotes it by repressing several CDFs (CDF1, CDF3, CDF5) and increasing FT transcript levels, indicating both cis and trans function. We propose that the CDF5/FLORE NAT pair constitutes an additional circadian regulatory module with conserved (mutual inhibition) and unique (function in trans) features, able to fine-tune its own circadian oscillation, and consequently, adjust the onset of flowering to favourable environmental conditions.
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Affiliation(s)
- Rossana Henriques
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065-6399, USA
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Huan Wang
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065-6399, USA
| | - Jun Liu
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065-6399, USA
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Marc Boix
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Li-Fang Huang
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065-6399, USA
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065-6399, USA
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165
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Shibuta M, Abe M. FE Controls the Transcription of Downstream Flowering Regulators Through Two Distinct Mechanisms in Leaf Phloem Companion Cells. PLANT & CELL PHYSIOLOGY 2017; 58:2017-2025. [PMID: 29036620 DOI: 10.1093/pcp/pcx133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 08/30/2017] [Indexed: 05/21/2023]
Abstract
In the facultative long-day plant Arabidopsis thaliana, FLOWERING LOCUS T (FT), encoding the mobile hormone florigen, plays an essential role in modulating the optimal timing of flowering to ensure reproductive success. Under inductive long-day conditions, the transcription of FT is activated by the CONSTANS (CO)/NUCLEAR FACTOR-Y (NF-Y) protein complex in leaf phloem companion cells. FT is transported to the shoot apical meristem through interaction with florigen transporters, such as SODIUM POTASSIUM ROOT DEFECTIVE 1 (NaKR1). Some regulators involved in photoperiod-dependent FT function have been reported previously; however, the molecular mechanism that coordinates FT protein synthesis and transport efficiently needs to be investigated. The present study examined the role of an Myb-related transcription factor, FE, in the activation of FT gene transcription and FT protein transport. Expression analysis using FE-inducible systems and chromatin immunoprecipitation assays showed that FE directly bound to the FT and NaKR1 promoters and activated the transcription of downstream target genes. FE failed to activate FT expression without CO function, whereas FE-mediated NaKR1 induction was not affected by CO function. Taken together, our data indicate that FE regulates the transcription of FT and florigen transporter genes via different mechanisms.
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Affiliation(s)
- Mio Shibuta
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033 Japan
| | - Mitsutomo Abe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033 Japan
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166
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Wu Q, Liu X, Yin D, Yuan H, Xie Q, Zhao X, Li X, Zhu L, Li S, Li D. Constitutive expression of OsDof4, encoding a C 2-C 2 zinc finger transcription factor, confesses its distinct flowering effects under long- and short-day photoperiods in rice (Oryza sativa L.). BMC PLANT BIOLOGY 2017; 17:166. [PMID: 29052517 PMCID: PMC5649077 DOI: 10.1186/s12870-017-1109-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 10/04/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Dof (DNA binding with one finger) proteins, a class of plant-specific transcription factors which contain a conserved C2-C2-type zinc finger domain, are involved in many fundamental processes. In the Arabidopsis photoperiod response pathway, CDF (CYCLING DOF FACTOR) proteins have a primary role as acting via transcriptional repression of the direct FLOWERING LOCUS T (FT) activator CONSTANS (CO). Our previous study indicated that one of CDF homologs, OsDOf12, was involved in photoperiodic flowering. However, the functional characterization of other rice CDF like genes is still in progress. Here, we characterized the function of OsDof4 in rice. RESULTS Phylogenic analysis indicated that OsDof4 is closely clustered into the same subgroup with CDFs and OsDof12. The subcellular localization experiment and transcriptional activity assay suggested that OsDof4 may function as a transcription factor. The diurnal expression pattern indicated that OsDof4 was regulated by endogenous circadian clock. Overexpression of OsDof4 led to earlier flowering under natural long-day field conditions (NLDs) and late flowering under natural short-day field conditions (NSDs), respectively. We compared the expression level of key floral genes in vector line and OsDof4-ox lines grown under long-day conditions (LDs) and short-day conditions (SDs). Real-time q-PCR results demonstrated that under LDs, Hd3a, RFT1 and Ehd1 were up-regulated whereas under SDs they were down-regulated. Hd1 was down-regulated at dusk period independent of photoperiods. CONCLUSIONS Taken these results together, we may speculate that the abnormal flowering responses in OsDof4-ox plants under LDs and SDs might be mediated by Ehd1 and Hd1.
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Affiliation(s)
- Qi Wu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 100101, China
- Rice Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, 611130, China
- National Research and Development Center for Coarse Cereal Processing, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Xue Liu
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dedong Yin
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Hua Yuan
- Rice Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, 611130, China
| | - Qi Xie
- Institute of Turfgrass Science, College of Forestry, Beijing Forestry University, Beijing, 100083, China
| | - Xianfeng Zhao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Xiaobing Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Lihuang Zhu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Shigui Li
- Rice Research Institute, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, 611130, China.
| | - Dayong Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing, 100101, China.
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167
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Kurokura T, Samad S, Koskela E, Mouhu K, Hytönen T. Fragaria vesca CONSTANS controls photoperiodic flowering and vegetative development. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4839-4850. [PMID: 29048562 PMCID: PMC5853477 DOI: 10.1093/jxb/erx301] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 08/02/2017] [Indexed: 05/18/2023]
Abstract
According to the external coincidence model, photoperiodic flowering occurs when CONSTANS (CO) mRNA expression coincides with light in the afternoon of long days (LDs), leading to the activation of FLOWERING LOCUS T (FT). CO has evolved in Brassicaceae from other Group Ia CO-like (COL) proteins which do not control photoperiodic flowering in Arabidopsis. COLs in other species have evolved different functions as floral activators or even as repressors. To understand photoperiodic development in the perennial rosaceous model species woodland strawberry, we functionally characterized FvCO, the only Group Ia COL in its genome. We demonstrate that FvCO has a major role in the photoperiodic control of flowering and vegetative reproduction through runners. FvCO is needed to generate a bimodal rhythm of FvFT1 which encodes a floral activator in the LD accession Hawaii-4: a sharp FvCO expression peak at dawn is followed by the FvFT1 morning peak in LDs indicating possible direct regulation, but additional factors that may include FvGI and FvFKF1 are probably needed to schedule the second FvFT1 peak around dusk. These results demonstrate that although FvCO and FvFT1 play major roles in photoperiodic development, the CO-based external coincidence around dusk is not fully applicable to the woodland strawberry.
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Affiliation(s)
- Takeshi Kurokura
- School of Biological Sciences, University of Reading, Reading, Berkshire RG6 6AS, UK
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, PO Box 27, FIN-00014 Helsinki, Finland
- Faculty of Agriculture, Utsunomiya University, Tochigi, 321-8505, Japan
| | - Samia Samad
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, PO Box 27, FIN-00014 Helsinki, Finland
| | - Elli Koskela
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, PO Box 27, FIN-00014 Helsinki, Finland
| | - Katriina Mouhu
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, PO Box 27, FIN-00014 Helsinki, Finland
| | - Timo Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, PO Box 27, FIN-00014 Helsinki, Finland
- Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, PO Box 56, FIN-00014 Helsinki, Finland
- Correspondence:
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168
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Goralogia GS, Liu T, Zhao L, Panipinto PM, Groover ED, Bains YS, Imaizumi T. CYCLING DOF FACTOR 1 represses transcription through the TOPLESS co-repressor to control photoperiodic flowering in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:244-262. [PMID: 28752516 PMCID: PMC5634919 DOI: 10.1111/tpj.13649] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/15/2017] [Accepted: 07/21/2017] [Indexed: 05/18/2023]
Abstract
CYCLING DOF FACTOR 1 (CDF1) and its homologs play an important role in the floral transition by repressing the expression of floral activator genes such as CONSTANS (CO) and FLOWERING LOCUS T (FT) in Arabidopsis. The day-length-specific removal of CDF1-dependent repression is a critical mechanism in photoperiodic flowering. However, the mechanism by which CDF1 represses CO and FT transcription remained elusive. Here we demonstrate that Arabidopsis CDF proteins contain non-EAR motif-like conserved domains required for interaction with the TOPLESS (TPL) co-repressor protein. This TPL interaction confers a repressive function on CDF1, as mutations of the N-terminal TPL binding domain largely impair the ability of CDF1 protein to repress its targets. TPL proteins are present on specific regions of the CO and FT promoters where CDF1 binds during the morning. In addition, TPL binding increases when CDF1 expression is elevated, suggesting that TPL is recruited to these promoters in a time-dependent fashion by CDFs. Moreover, reduction of TPL activity induced by expressing a dominant negative version of TPL (tpl-1) in phloem companion cells results in early flowering and a decreased sensitivity to photoperiod in a manner similar to a cdf loss-of-function mutant. Our results indicate that the mechanism of CDF1 repression is through the formation of a CDF-TPL transcriptional complex, which reduces the expression levels of CO and FT during the morning for seasonal flowering.
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Affiliation(s)
- Greg S. Goralogia
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
| | - Tongkun Liu
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lin Zhao
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China
| | - Paul M. Panipinto
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
| | - Evan D. Groover
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
| | - Yashkarn S. Bains
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA
- For correspondence:
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169
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He R, Li X, Zhong M, Yan J, Ji R, Li X, Wang Q, Wu D, Sun M, Tang D, Lin J, Li H, Liu B, Liu H, Liu X, Zhao X, Lin C. A photo-responsive F-box protein FOF2 regulates floral initiation by promoting FLC expression in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:788-801. [PMID: 28608936 DOI: 10.1111/tpj.13607] [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: 02/10/2017] [Revised: 04/08/2017] [Accepted: 05/13/2017] [Indexed: 05/09/2023]
Abstract
Floral initiation is regulated by various genetic pathways in response to light, temperature, hormones and developmental status; however, the molecular mechanisms underlying the interactions between different genetic pathways are not fully understood. Here, we show that the photoresponsive gene FOF2 (F-box of flowering 2) negatively regulates flowering. FOF2 encodes a putative F-box protein that interacts specifically with ASK14, and its overexpression results in later flowering under both long-day and short-day photoperiods. Conversely, transgenic plants expressing the F-box domain deletion mutant of FOF2 (FOF2ΔF), or double loss of function mutant of FOF2 and FOL1 (FOF2-LIKE 1) present early flowering phenotypes. The late flowering phenotype of the FOF2 overexpression lines is suppressed by the flc-3 loss-of-function mutation. Furthermore, FOF2 mRNA expression is regulated by autonomous pathway gene FCA, and the repressive effect of FOF2 in flowering can be overcome by vernalization. Interestingly, FOF2 expression is regulated by light. The protein level of FOF2 accumulates in response to light, whereas it is degraded under dark conditions via the 26S proteasome pathway. Our findings suggest a possible mechanistic link between light conditions and the autonomous floral promotion pathway in Arabidopsis.
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Affiliation(s)
- Reqing He
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Xinmei Li
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Ming Zhong
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Jindong Yan
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Ronghuan Ji
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xu Li
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qin Wang
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Dan Wu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Mengsi Sun
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Dongying Tang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Jianzhong Lin
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Hongyu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Bin Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongtao Liu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xuanming Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Xiaoying Zhao
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China
| | - Chentao Lin
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA, 90095, USA
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170
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Yan J, Mao D, Liu X, Wang L, Xu F, Wang G, Zhang W, Liao Y. Isolation and functional characterization of a circadian-regulated CONSTANS homolog (GbCO) from Ginkgo biloba. PLANT CELL REPORTS 2017; 36:1387-1399. [PMID: 28616659 DOI: 10.1007/s00299-017-2162-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/01/2017] [Indexed: 06/07/2023]
Abstract
This is the first report to clone and functionally characterize a flowering time gene GbCO in perennial gymnosperm Ginkgo biloba. GbCO complements the co mutant of Arabidopsis, restoring normal early flowering. CONSTANS (CO) is a central regulator of photoperiod pathway, which channels inputs from light, day length, and circadian clock to promote the floral transition. In order to understand the role of CO in gymnosperm Ginkgo biloba, which has a long juvenile phase (15-20 years), a CO homolog (GbCO) was isolated and characterized from G. biloba. GbCO encodes a 1741-bp gene with a predicted protein of 400 amino acids with two zinc finger domains (B-box I and B-box II) and a CCT domain. Phylogenic analysis classified GbCO into the group 1a clade of CO families in accordance with the grouping scheme for Arabidopsis CO (AtCO). Southern blot analysis indicated that GbCO belongs to a multigene family in G. biloba. Real-time PCR analysis showed that GbCO was expressed in aerial parts of Ginkgo, with the highest transcript level of GbCO being observed in shoot apexes. GbCO transcript level exhibited a strong diurnal rhythm under flowering-inductive long days and peaked during early morning, suggesting that GbCO is tightly coupled to the floral inductive long-day signal. In addition, an increasing trend of GbCO transcript level was observed both in shoot tips and leaves as the shoot growth under long-day condition, whereas GbCO transcript level decreased in both tissues under short-day condition prior to growth cessation of shoot in G. biloba. GbCO complemented the Arabidopsis co-2 mutant, restoring normal early flowering. All the evidence being taken together, our findings suggested that GbCO served as a potential inducer of flowering in G. biloba.
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Affiliation(s)
- Jiaping Yan
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Dun Mao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Xiaomeng Liu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Lanlan Wang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Guiyuan Wang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
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171
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Lee HJ, Park YJ, Ha JH, Baldwin IT, Park CM. Multiple Routes of Light Signaling during Root Photomorphogenesis. TRENDS IN PLANT SCIENCE 2017; 22:803-812. [PMID: 28705537 DOI: 10.1016/j.tplants.2017.06.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 06/08/2017] [Accepted: 06/12/2017] [Indexed: 05/06/2023]
Abstract
Plants dynamically adjust their architecture to optimize growth and performance under fluctuating light environments, a process termed photomorphogenesis. A variety of photomorphogenic responses have been studied extensively in the shoots, where diverse photoreceptors and signaling molecules have been functionally characterized. Notably, accumulating evidence demonstrates that the underground roots also undergo photomorphogenesis, raising the question of how roots perceive and respond to aboveground light. Recent findings indicate that root photomorphogenesis is mediated by multiple signaling routes, including shoot-to-root transmission of mobile signaling molecules, direct sensing of light by the roots, and light channeling through the plant body. In this review we discuss recent advances in how light signals are transmitted to the roots to trigger photomorphogenic responses.
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Affiliation(s)
- Hyo-Jun Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; These authors contributed equally to this work
| | - Young-Joon Park
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; These authors contributed equally to this work
| | - Jun-Ho Ha
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.
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172
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ePlant for quantitative and predictive plant science research in the big data era—Lay the foundation for the future model guided crop breeding, engineering and agronomy. QUANTITATIVE BIOLOGY 2017. [DOI: 10.1007/s40484-017-0110-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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173
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Du A, Tian W, Wei M, Yan W, He H, Zhou D, Huang X, Li S, Ouyang X. The DTH8-Hd1 Module Mediates Day-Length-Dependent Regulation of Rice Flowering. MOLECULAR PLANT 2017; 10:948-961. [PMID: 28549969 DOI: 10.1016/j.molp.2017.05.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/02/2017] [Accepted: 05/14/2017] [Indexed: 05/04/2023]
Abstract
Photoperiodic flowering is one of the most important pathways to govern flowering in rice (Oryza sativa), in which Heading date 1 (Hd1), an ortholog of the Arabidopsis CONSTANS gene, encodes a pivotal regulator. Hd1 promotes flowering under short-day conditions (SD) but represses flowering under long-day conditions (LD) by regulating the expression of Heading date 3a (Hd3a), the FLOWERING LOCUS T (FT) ortholog in rice. However, the molecular mechanism of how Hd1 changes its regulatory activity in response to day length remains largely unknown. In this study, we demonstrated that the repression of flowering in LD by Hd1 is dependent on the transcription factor DAYS TO HEADING 8 (DTH8). Loss of DTH8 function results in the activation of Hd3a by Hd1, leading to early flowering. We found that Hd1 directly interacts with DTH8 and that the formation of the DTH8-Hd1 complex is necessary for the transcriptional repression of Hd3a by Hd1 in LD, implicating that the switch of Hd1 function is mediated by DTH8 in LD rather than in SD. Furthermore, we revealed that DTH8 associates with the Hd3a promoter to modulate the level of H3K27 trimethylation (H3K27me3) at the Hd3a locus. In the presence of the DTH8-Hd1 complex, the H3K27me3 level was increased at Hd3a, whereas loss of DTH8 function resulted in decreased H3K27me3 level at Hd3a. Taken together, our findings indicate that, in response to day length, DTH8 plays a critical role in mediating the transcriptional regulation of Hd3a by Hd1 through the DTH8-Hd1 module to shape epigenetic modifications in photoperiodic flowering.
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Affiliation(s)
- Anping Du
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Wei Tian
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Menghao Wei
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Wei Yan
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Hang He
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Da Zhou
- School of Mathematical Sciences, Xiamen University, Xiamen 361005, China
| | - Xi Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Shigui Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
| | - Xinhao Ouyang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China.
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174
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Kubota A, Ito S, Shim JS, Johnson RS, Song YH, Breton G, Goralogia GS, Kwon MS, Laboy Cintrón D, Koyama T, Ohme-Takagi M, Pruneda-Paz JL, Kay SA, MacCoss MJ, Imaizumi T. TCP4-dependent induction of CONSTANS transcription requires GIGANTEA in photoperiodic flowering in Arabidopsis. PLoS Genet 2017. [PMID: 28628608 PMCID: PMC5495492 DOI: 10.1371/journal.pgen.1006856] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Photoperiod is one of the most reliable environmental cues for plants to regulate flowering timing. In Arabidopsis thaliana, CONSTANS (CO) transcription factor plays a central role in regulating photoperiodic flowering. In contrast to posttranslational regulation of CO protein, still little was known about CO transcriptional regulation. Here we show that the CINCINNATA (CIN) clade of class II TEOSINTE BRANCHED 1/ CYCLOIDEA/ PROLIFERATING CELL NUCLEAR ANTIGEN FACTOR (TCP) proteins act as CO activators. Our yeast one-hybrid analysis revealed that class II CIN-TCPs, including TCP4, bind to the CO promoter. TCP4 induces CO expression around dusk by directly associating with the CO promoter in vivo. In addition, TCP4 binds to another flowering regulator, GIGANTEA (GI), in the nucleus, and induces CO expression in a GI-dependent manner. The physical association of TCP4 with the CO promoter was reduced in the gi mutant, suggesting that GI may enhance the DNA-binding ability of TCP4. Our tandem affinity purification coupled with mass spectrometry (TAP-MS) analysis identified all class II CIN-TCPs as the components of the in vivo TCP4 complex, and the gi mutant did not alter the composition of the TCP4 complex. Taken together, our results demonstrate a novel function of CIN-TCPs as photoperiodic flowering regulators, which may contribute to coordinating plant development with flowering regulation. For plant adaptation to seasonal environments, a crucial developmental event is flowering, as proper timing of flowering affects reproductive success. Although plants monitor various environmental parameters to optimize this timing, photoperiod information is important for plants to regulate seasonal flowering time, because changes in photoperiod occur in a predictable manner throughout the year. The model plant Arabidopsis thaliana responds to photoperiodic changes and flowers under long-day conditions. Based on genetic analyses using mutants defective in the photoperiodic flowering response, we learned that the transcription factor referred to as CONSTANS (CO) plays a central role in regulating the timing of flowering by directly controlling the expression of florigen (flowering-inducing substrate) gene. Long-day afternoon expression of CO is critical for this regulation; however, we had limited knowledge of CO transcriptional regulation. Here we identified that a group of plant-specific transcription factors belonging to the TCP gene family function as novel CO transcriptional activators. We demonstrated that TCP transcription factors regulate CO transcription together with known regulators of CO. Our results imply that plants utilize multiple transcription factors to precisely coordinate the expression of the key regulator gene, CO, which will directly affect flowering time.
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Affiliation(s)
- Akane Kubota
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Shogo Ito
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Jae Sung Shim
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Richard S. Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Yong Hun Song
- Department of Life Sciences, Ajou University, Suwon, Korea
| | - Ghislain Breton
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, United States of America
| | - Greg S. Goralogia
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Michael S. Kwon
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Dianne Laboy Cintrón
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Tomotsugu Koyama
- Bioorganic Research Center, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Masaru Ohme-Takagi
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Jose L. Pruneda-Paz
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, United States of America
| | - Steve A. Kay
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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175
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Hannapel DJ, Sharma P, Lin T, Banerjee AK. The Multiple Signals That Control Tuber Formation. PLANT PHYSIOLOGY 2017; 174:845-856. [PMID: 28520554 PMCID: PMC5462066 DOI: 10.1104/pp.17.00272] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 04/11/2017] [Indexed: 05/04/2023]
Abstract
The three critical switches that regulate the onset of tuber formation in potato interact in a dynamic signaling pathway.
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Affiliation(s)
- David J Hannapel
- Plant Biology Department, Iowa State University, Ames, Iowa 50011-1100 (D.J.H., P.S., T.L.); and
- Biology Division, Indian Institute of Science Education and Research, Pashan, Pune 411008, India (A.K.B.)
| | - Pooja Sharma
- Plant Biology Department, Iowa State University, Ames, Iowa 50011-1100 (D.J.H., P.S., T.L.); and
- Biology Division, Indian Institute of Science Education and Research, Pashan, Pune 411008, India (A.K.B.)
| | - Tian Lin
- Plant Biology Department, Iowa State University, Ames, Iowa 50011-1100 (D.J.H., P.S., T.L.); and
- Biology Division, Indian Institute of Science Education and Research, Pashan, Pune 411008, India (A.K.B.)
| | - Anjan K Banerjee
- Plant Biology Department, Iowa State University, Ames, Iowa 50011-1100 (D.J.H., P.S., T.L.); and
- Biology Division, Indian Institute of Science Education and Research, Pashan, Pune 411008, India (A.K.B.)
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176
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Gnesutta N, Kumimoto RW, Swain S, Chiara M, Siriwardana C, Horner DS, Holt BF, Mantovani R. CONSTANS Imparts DNA Sequence Specificity to the Histone Fold NF-YB/NF-YC Dimer. THE PLANT CELL 2017; 29:1516-1532. [PMID: 28526714 PMCID: PMC5502446 DOI: 10.1105/tpc.16.00864] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 04/07/2017] [Accepted: 05/18/2017] [Indexed: 05/19/2023]
Abstract
Nuclear Factor Y (NF-Y) is a heterotrimeric transcription factor that binds CCAAT elements. The NF-Y trimer is composed of a Histone Fold Domain (HFD) dimer (NF-YB/NF-YC) and NF-YA, which confers DNA sequence specificity. NF-YA shares a conserved domain with the CONSTANS, CONSTANS-LIKE, TOC1 (CCT) proteins. We show that CONSTANS (CO/B-BOX PROTEIN1 BBX1), a master flowering regulator, forms a trimer with Arabidopsis thaliana NF-YB2/NF-YC3 to efficiently bind the CORE element of the FLOWERING LOCUS T promoter. We term this complex NF-CO. Using saturation mutagenesis, electrophoretic mobility shift assays, and RNA-sequencing profiling of co, nf-yb, and nf-yc mutants, we identify CCACA elements as the core NF-CO binding site. CO physically interacts with the same HFD surface required for NF-YA association, as determined by mutations in NF-YB2 and NF-YC9, and tested in vitro and in vivo. The co-7 mutation in the CCT domain, corresponding to an NF-YA arginine directly involved in CCAAT recognition, abolishes NF-CO binding to DNA. In summary, a unifying molecular mechanism of CO function relates it to the NF-YA paradigm, as part of a trimeric complex imparting sequence specificity to HFD/DNA interactions. It is likely that members of the large CCT family participate in similar complexes with At-NF-YB and At-NF-YC, broadening HFD combinatorial possibilities in terms of trimerization, DNA binding specificities, and transcriptional regulation.
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Affiliation(s)
- Nerina Gnesutta
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
| | - Roderick W Kumimoto
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019
| | - Swadhin Swain
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019
| | - Matteo Chiara
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
| | - Chamindika Siriwardana
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019
| | - David S Horner
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
| | - Ben F Holt
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
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177
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Liu J, Cheng X, Liu P, Li D, Chen T, Gu X, Sun J. MicroRNA319-regulated TCPs interact with FBHs and PFT1 to activate CO transcription and control flowering time in Arabidopsis. PLoS Genet 2017; 13:e1006833. [PMID: 28558040 PMCID: PMC5469495 DOI: 10.1371/journal.pgen.1006833] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 06/13/2017] [Accepted: 05/22/2017] [Indexed: 01/06/2023] Open
Abstract
The transcription factor CONSTANS (CO) is a central component that promotes Arabidopsis flowering under long-day conditions (LDs). Here, we show that the microRNA319-regulated TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) transcription factors promote photoperiodic flowering through binding to the CO promoter and activating its transcription. Meanwhile, these TCPs directly interact with the flowering activators FLOWERING BHLH (FBHs), but not the flowering repressors CYCLING DOF FACTORs (CDFs), to additively activate CO expression. Furthermore, both the TCPs and FBHs physically interact with the flowering time regulator PHYTOCHROME AND FLOWERING TIME 1 (PFT1) to facilitate CO transcription. Our findings provide evidence that a set of transcriptional activators act directly and additively at the CO promoter to promote CO transcription, and establish a molecular mechanism underlying the regulation of photoperiodic flowering time in Arabidopsis. Plants monitor day-length changes (photoperiod) throughout the year to precisely align their flowering time, which is crucial for successful reproduction. In Arabidopsis, some components, such as CONSTANS (CO), have been proved to play central roles in promoting the photoperiodic flowering under long-day conditions (LDs). In this study, we demonstrate that the microRNA319-regulated TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) transcription factors directly bind to the CO promoter. Meanwhile, these TCPs physically interact with the flowering activators FLOWERING BHLH (FBHs) and the flowering regulator PHYTOCHROME AND FLOWERING TIME 1 (PFT1) to form a complex to activate CO transcription and promote photoperiodic flowering under LDs. Our results emphasize the importance of miR319-regulated TCPs in regulating plant flowering time.
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Affiliation(s)
- Jie Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiliu Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pan Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dayong Li
- State Key Laboratory of Plant Genome, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Tao Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaqiang Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail:
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178
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Mao T, Li J, Wen Z, Wu T, Wu C, Sun S, Jiang B, Hou W, Li W, Song Q, Wang D, Han T. Association mapping of loci controlling genetic and environmental interaction of soybean flowering time under various photo-thermal conditions. BMC Genomics 2017; 18:415. [PMID: 28549456 PMCID: PMC5446728 DOI: 10.1186/s12864-017-3778-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 05/10/2017] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Soybean (Glycine max (L.) Merr.) is a short day plant. Its flowering and maturity time are controlled by genetic and environmental factors, as well the interaction between the two factors. Previous studies have shown that both genetic and environmental factors, mainly photoperiod and temperature, control flowering time of soybean. Additionally, these studies have reported gene × gene and gene × environment interactions on flowering time. However, the effects of quantitative trait loci (QTL) in response to photoperiod and temperature have not been well evaluated. The objectives of the current study were to identify the effects of loci associated with flowering time under different photo-thermal conditions and to understand the effects of interaction between loci and environment on soybean flowering. METHODS Different photoperiod and temperature combinations were obtained by adjusting sowing dates (spring sowing and summer sowing) or day-length (12 h, 16 h). Association mapping was performed on 91 soybean cultivars from different maturity groups (MG000-VIII) using 172 SSR markers and 5107 SNPs from the Illumina SoySNP6K iSelectBeadChip. The effects of the interaction between QTL and environments on flowering time were also analysed using the QTXNetwork. RESULTS Large-effect loci were detected on Gm 11, Gm 16 and Gm 20 as in previous reports. Most loci associated with flowering time are sensitive to photo-thermal conditions. Number of loci associated with flowering time was more under the long day (LD) than under the short day (SD) condition. The variation of flowering time among the soybean cultivars mostly resulted from the epistasis × environment and additive × environment interactions. Among the three candidate loci, i.e. Gm04_4497001 (near GmCOL3a), Gm16_30766209 (near GmFT2a and GmFT2b) and Gm19_47514601 (E3 or GmPhyA3), the Gm04_4497001 may be the key locus interacting with other loci for controlling soybean flowering time. CONCLUSION The effects of loci associated with the flowering time of soybean were dependent upon the photo-thermal conditions. This study facilitates the understanding of the genetic mechanism of soybean flowering and molecular breeding for the improvement of soybean adaptability to specific and/or broad regions.
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Affiliation(s)
- Tingting Mao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 Heilongjiang China
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, the Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Jinyu Li
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, the Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Zixiang Wen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI 48824-1325 USA
| | - Tingting Wu
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, the Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Cunxiang Wu
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, the Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Shi Sun
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, the Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Bingjun Jiang
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, the Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Wensheng Hou
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, the Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Wenbin Li
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 Heilongjiang China
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, US Department of Agriculture, Agricultural Research Service (USDA-ARS), 10300 Baltimore Ave, Beltsville, MD 20705 USA
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI 48824-1325 USA
| | - Tianfu Han
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 Heilongjiang China
- MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, the Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
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179
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Marshall-Colon A, Long SP, Allen DK, Allen G, Beard DA, Benes B, von Caemmerer S, Christensen AJ, Cox DJ, Hart JC, Hirst PM, Kannan K, Katz DS, Lynch JP, Millar AJ, Panneerselvam B, Price ND, Prusinkiewicz P, Raila D, Shekar RG, Shrivastava S, Shukla D, Srinivasan V, Stitt M, Turk MJ, Voit EO, Wang Y, Yin X, Zhu XG. Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform. FRONTIERS IN PLANT SCIENCE 2017; 8:786. [PMID: 28555150 PMCID: PMC5430029 DOI: 10.3389/fpls.2017.00786] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/26/2017] [Indexed: 05/18/2023]
Abstract
Multi-scale models can facilitate whole plant simulations by linking gene networks, protein synthesis, metabolic pathways, physiology, and growth. Whole plant models can be further integrated with ecosystem, weather, and climate models to predict how various interactions respond to environmental perturbations. These models have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts. Outcomes will potentially accelerate improvement of crop yield, sustainability, and increase future food security. It is time for a paradigm shift in plant modeling, from largely isolated efforts to a connected community that takes advantage of advances in high performance computing and mechanistic understanding of plant processes. Tools for guiding future crop breeding and engineering, understanding the implications of discoveries at the molecular level for whole plant behavior, and improved prediction of plant and ecosystem responses to the environment are urgently needed. The purpose of this perspective is to introduce Crops in silico (cropsinsilico.org), an integrative and multi-scale modeling platform, as one solution that combines isolated modeling efforts toward the generation of virtual crops, which is open and accessible to the entire plant biology community. The major challenges involved both in the development and deployment of a shared, multi-scale modeling platform, which are summarized in this prospectus, were recently identified during the first Crops in silico Symposium and Workshop.
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Affiliation(s)
- Amy Marshall-Colon
- Department of Plant Biology, University of Illinois at Urbana–Champaign, UrbanaIL, USA
| | - Stephen P. Long
- Department of Plant Biology, University of Illinois at Urbana–Champaign, UrbanaIL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana–Champaign, UrbanaIL, USA
- Department of Crop Sciences, University of Illinois, UrbanaIL, USA
| | - Douglas K. Allen
- United States Department of Agriculture – Agricultural Research Service–Donald Danforth Plant Science Center, St. LouisMO, USA
| | - Gabrielle Allen
- Department of Astronomy–College of Education, University of Illinois at Urbana–Champaign, UrbanaIL, USA
| | - Daniel A. Beard
- Department of Molecular & Integrative Physiology, University of Michigan, Ann ArborMI, USA
| | - Bedrich Benes
- Department of Computer Graphics Technology, Purdue University, West LafayetteIN, USA
| | - Susanne von Caemmerer
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biological Sciences, Australian National University, ActonACT, Australia
| | - A. J. Christensen
- National Center for Supercomputing Applications, University of Illinois at Urbana–Champaign, UrbanaIL, USA
| | - Donna J. Cox
- National Center for Supercomputing Applications, University of Illinois at Urbana–Champaign, UrbanaIL, USA
| | - John C. Hart
- Department of Computer Science, University of Illinois at Urbana–Champaign, UrbanaIL, USA
| | - Peter M. Hirst
- Department of Horticulture and Landscape Architecture, Purdue University, West LafayetteIN, USA
| | - Kavya Kannan
- Department of Plant Biology, University of Illinois at Urbana–Champaign, UrbanaIL, USA
| | - Daniel S. Katz
- National Center for Supercomputing Applications, University of Illinois at Urbana–Champaign, UrbanaIL, USA
| | - Jonathan P. Lynch
- Department of Plant Science, Pennsylvania State University, University ParkPA, USA
- Centre for Plant Integrative Biology, University of NottinghamNottingham, UK
| | - Andrew J. Millar
- SynthSys and School of Biological Sciences, Edinburgh UniversityEdinburgh, UK
| | - Balaji Panneerselvam
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana–Champaign, UrbanaIL, USA
| | | | | | - David Raila
- National Center for Supercomputing Applications, University of Illinois at Urbana–Champaign, UrbanaIL, USA
| | - Rachel G. Shekar
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana–Champaign, UrbanaIL, USA
| | - Stuti Shrivastava
- Department of Plant Biology, University of Illinois at Urbana–Champaign, UrbanaIL, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana–Champaign, UrbanaIL, USA
| | - Venkatraman Srinivasan
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana–Champaign, UrbanaIL, USA
| | - Mark Stitt
- Max Planck Institute of Molecular Plant PhysiologyGolm, Germany
| | - Matthew J. Turk
- School of Information Science, University of Illinois, Urbana–Champaign, UrbanaIL, USA
| | - Eberhard O. Voit
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech and Emory University, AtlantaGA, USA
| | - Yu Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana–Champaign, UrbanaIL, USA
| | - Xinyou Yin
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & ResearchWageningen, Netherlands
| | - Xin-Guang Zhu
- CAS Key Laboratory for Computational Biology–State Key Laboratory for Hybrid Rice, Partner Institute for Computational Biology, Chinese Academy of SciencesShanghai, China
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180
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Cao D, Takeshima R, Zhao C, Liu B, Jun A, Kong F. Molecular mechanisms of flowering under long days and stem growth habit in soybean. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1873-1884. [PMID: 28338712 DOI: 10.1093/jxb/erw394] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Precise timing of flowering is critical to crop adaptation and productivity in a given environment. A number of classical E genes controlling flowering time and maturity have been identified in soybean [Glycine max (L.) Merr.]. The public availability of the soybean genome sequence has accelerated the identification of orthologues of Arabidopsis flowering genes and their functional analysis, and has allowed notable progress towards understanding the molecular mechanisms of flowering in soybean. Great progress has been made particularly in identifying genes and modules that inhibit flowering in long-day conditions, because a reduced or absent inhibition of flowering by long daylengths is an essential trait for soybean, a short-day (SD) plant, to expand its adaptability toward higher latitude environments. In contrast, the molecular mechanism of floral induction by SDs remains elusive in soybean. Here we present an update on recent work on molecular mechanisms of flowering under long days and of stem growth habit, outlining the progress in the identification of genes responsible, the interplay between photoperiod and age-dependent miRNA-mediated modules, and the conservation and divergence in photoperiodic flowering and stem growth habit in soybean relative to other legumes, Arabidopsis, and rice (Oryza sativa L.).
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Affiliation(s)
- Dong Cao
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Ryoma Takeshima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Chen Zhao
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Baohui Liu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Abe Jun
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Fanjiang Kong
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
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181
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Conti L. Hormonal control of the floral transition: Can one catch them all? Dev Biol 2017; 430:288-301. [PMID: 28351648 DOI: 10.1016/j.ydbio.2017.03.024] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 01/05/2023]
Abstract
The transition to flowering marks a key adaptive developmental switch in plants which impacts on their survival and fitness. Different signaling pathways control the floral transition, conveying both endogenous and environmental cues. These cues are often relayed and/or modulated by different hormones, which might confer additional developmental flexibility to the floral process in the face of varying conditions. Among the different hormonal pathways, the phytohormone gibberellic acid (GA) plays a dominant role. GA is connected with the other floral pathways through the GA-regulated DELLA proteins, acting as versatile interacting modules for different signaling proteins. In this review, I will highlight the role of DELLAs as spatial and temporal modulators of different consolidated floral pathways. Next, building on recent data, I will provide an update on some emerging themes connecting other hormone signaling cascades to flowering time control. I will finally provide examples for some established as well as potential cross-regulatory mechanisms between hormonal pathways mediated by the DELLA proteins.
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Affiliation(s)
- Lucio Conti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
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182
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Hayama R, Sarid-Krebs L, Richter R, Fernández V, Jang S, Coupland G. PSEUDO RESPONSE REGULATORs stabilize CONSTANS protein to promote flowering in response to day length. EMBO J 2017; 36:904-918. [PMID: 28270524 PMCID: PMC5376961 DOI: 10.15252/embj.201693907] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 11/09/2022] Open
Abstract
Seasonal reproduction in many organisms requires detection of day length. This is achieved by integrating information on the light environment with an internal photoperiodic time-keeping mechanism. Arabidopsis thaliana promotes flowering in response to long days (LDs), and CONSTANS (CO) transcription factor represents a photoperiodic timer whose stability is higher when plants are exposed to light under LDs. Here, we show that PSEUDO RESPONSE REGULATOR (PRR) proteins directly mediate this stabilization. PRRs interact with and stabilize CO at specific times during the day, thereby mediating its accumulation under LDs. PRR-mediated stabilization increases binding of CO to the promoter of FLOWERING LOCUS T (FT), leading to enhanced FT transcription and early flowering under these conditions. PRRs were previously reported to contribute to timekeeping by regulating CO transcription through their roles in the circadian clock. We propose an additional role for PRRs in which they act upon CO protein to promote flowering, directly coupling information on light exposure to the timekeeper and allowing recognition of LDs.
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Affiliation(s)
- Ryosuke Hayama
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Liron Sarid-Krebs
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - René Richter
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Virginia Fernández
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Seonghoe Jang
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - George Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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183
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Kerr SC, Gaiti F, Beveridge CA, Tanurdzic M. De novo transcriptome assembly reveals high transcriptional complexity in Pisum sativum axillary buds and shows rapid changes in expression of diurnally regulated genes. BMC Genomics 2017; 18:221. [PMID: 28253862 PMCID: PMC5335751 DOI: 10.1186/s12864-017-3577-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 02/09/2017] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The decision for a bud to grow into a branch is a key regulatory process affecting plant architecture. In order to study molecular processes regulating axillary bud outgrowth in the model plant garden pea (Pisum sativum), we sequenced the axillary bud transcriptome and performed de novo transcriptome assembly. RESULTS We assembled a pea axillary bud transcriptome into 81,774 transcripts comprised of 194,067 isoforms. This new pea transcriptome resource is both comprehensive and representative, as shown by comparison to other available pea sequence resources. Over half of the transcriptome could be annotated based on sequence homology to Arabidopsis thaliana proteins, while almost one quarter of the isoforms were identified as putative long non-coding RNAs (lncRNAs). This transcriptome will be useful in studies of pea buds because it includes genes expressed specifically in buds which are not represented in other transcriptome studies. We also investigated the impact of a short time collection series on gene expression. Differential gene expression analysis identified 142 transcripts changing within the short 170 min time frame that the buds were harvested within. Thirty-three of these transcripts are implicated in diurnal fluctuations in other flowering plants, while the remaining transcripts include 31 putative lncRNA. Further investigation of the differentially expressed transcripts found an enrichment of genes involved in post-transcriptional regulation, including RNA processing and modification, as well as genes involved in fatty acid biosynthesis and oxidative phosphorylation. CONCLUSIONS We have sequenced and assembled a high quality pea bud transcriptome containing both coding and non-coding RNA transcripts that will be useful for further studies into axillary bud outgrowth. Over the short sample collection time frame of just 170 min, we identified differentially expressed coding and non-coding RNA, some of which are implicated in diurnal regulation, highlighting the utility of our transcriptome resource in identifying gene expression changes and informing future experimental designs.
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Affiliation(s)
- Stephanie C. Kerr
- The University of Queensland, School of Biological Sciences, St Lucia, QLD 4072 Australia
| | - Federico Gaiti
- The University of Queensland, School of Biological Sciences, St Lucia, QLD 4072 Australia
| | - Christine A. Beveridge
- The University of Queensland, School of Biological Sciences, St Lucia, QLD 4072 Australia
| | - Milos Tanurdzic
- The University of Queensland, School of Biological Sciences, St Lucia, QLD 4072 Australia
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184
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Wendell M, Ripel L, Lee Y, Rognli OA, Torre S, Olsen JE. Thermoperiodic Control of Floral Induction Involves Modulation of the Diurnal FLOWERING LOCUS T Expression Pattern. PLANT & CELL PHYSIOLOGY 2017; 58:466-477. [PMID: 28028164 DOI: 10.1093/pcp/pcw221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/05/2016] [Indexed: 06/06/2023]
Abstract
Thermoperiodism is defined as the ability to discriminate between day temperature (DT) and night temperature (NT). Our aim was to shed light on the mechanistic basis of thermoperiodic floral induction with acceleration under lower DT than NT compared with other DT-NT combinations at the same average daily temperature (ADT), a response exploited in temperate area greenhouses. Arabidopsis thaliana floral pathway mutants and a lhy circadian clock mutant as well as the expression of floral integrators and LHY (LATE ELONGATED HYPOCOTYL) were studied under different DT-NT combinations, all at the same ADT. We show that acceleration of floral induction under lower DT than NT is linked to increased FT expression early during the day and generally increased LFY expression preceding visible flower buds, compared with higher DT than NT or equal DT and NT. Consistent with FLOWERING LOCUS T (FT) action through LEAFY (LFY), time to floral transition in ft-1 and lfy-1 was similar under all treatments, in contrast to the situation for soc1-1, which behaved like the wild type (WT). The lhy-21 mutants did not discriminate between opposite DT-NT combinations, whereas LHY expression in the WT differed in these temperature regimes. This might suggest that LHY plays a role in thermoperiodic control of floral induction. We conclude that thermoperiodic control of floral transition is associated with modulation of the diurnal expression patterns of FT, with timing of temperature alteration being important rather than ADT.
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Affiliation(s)
- Micael Wendell
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Norway
| | - Linda Ripel
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Norway
| | - YeonKyeong Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Odd Arne Rognli
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Sissel Torre
- Norwegian University of Life Sciences, Department of Mathematical Sciences and Technology, Aas, Norway
| | - Jorunn E Olsen
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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185
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Pudasaini A, Shim JS, Song YH, Shi H, Kiba T, Somers DE, Imaizumi T, Zoltowski BD. Kinetics of the LOV domain of ZEITLUPE determine its circadian function in Arabidopsis. eLife 2017; 6. [PMID: 28244872 PMCID: PMC5370183 DOI: 10.7554/elife.21646] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 02/26/2017] [Indexed: 11/13/2022] Open
Abstract
A LOV (Light, Oxygen, or Voltage) domain containing blue-light photoreceptor ZEITLUPE (ZTL) directs circadian timing by degrading clock proteins in plants. Functions hinge upon allosteric differences coupled to the ZTL photocycle; however, structural and kinetic information was unavailable. Herein, we tune the ZTL photocycle over two orders of magnitude. These variants reveal that ZTL complexes with targets independent of light, but dictates enhanced protein degradation in the dark. In vivo experiments definitively show photocycle kinetics dictate the rate of clock component degradation, thereby impacting circadian period. Structural studies demonstrate that photocycle dependent activation of ZTL depends on an unusual dark-state conformation of ZTL. Crystal structures of ZTL LOV domain confirm delineation of structural and kinetic mechanisms and identify an evolutionarily selected allosteric hinge differentiating modes of PAS/LOV signal transduction. The combined biochemical, genetic and structural studies provide new mechanisms indicating how PAS/LOV proteins integrate environmental variables in complex networks.
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Affiliation(s)
- Ashutosh Pudasaini
- Department of Chemistry, Southern Methodist University, Dallas, United States.,Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, United States
| | - Jae Sung Shim
- Department of Biology, University of Washington, Seattle, United States
| | - Young Hun Song
- Department of Biology, University of Washington, Seattle, United States.,Department of Life Sciences, Ajou University, Suwon, Korea
| | - Hua Shi
- Department of Molecular Genetics, Ohio State University, Columbus, United States
| | - Takatoshi Kiba
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - David E Somers
- Department of Molecular Genetics, Ohio State University, Columbus, United States
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, United States
| | - Brian D Zoltowski
- Department of Chemistry, Southern Methodist University, Dallas, United States.,Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, United States
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186
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Goretti D, Martignago D, Landini M, Brambilla V, Gómez-Ariza J, Gnesutta N, Galbiati F, Collani S, Takagi H, Terauchi R, Mantovani R, Fornara F. Transcriptional and Post-transcriptional Mechanisms Limit Heading Date 1 (Hd1) Function to Adapt Rice to High Latitudes. PLoS Genet 2017; 13:e1006530. [PMID: 28068345 PMCID: PMC5221825 DOI: 10.1371/journal.pgen.1006530] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 12/08/2016] [Indexed: 11/24/2022] Open
Abstract
Rice flowering is controlled by changes in the photoperiod that promote the transition to the reproductive phase as days become shorter. Natural genetic variation for flowering time has been largely documented and has been instrumental to define the genetics of the photoperiodic pathway, as well as providing valuable material for artificial selection of varieties better adapted to local environments. We mined genetic variation in a collection of rice varieties highly adapted to European regions and isolated distinct variants of the long day repressor HEADING DATE 1 (Hd1) that perturb its expression or protein function. Specific variants allowed us to define novel features of the photoperiodic flowering pathway. We demonstrate that a histone fold domain scaffold formed by GRAIN YIELD, PLANT HEIGHT AND HEADING DATE 8 (Ghd8) and several NF-YC subunits can accommodate distinct proteins, including Hd1 and PSEUDO RESPONSE REGULATOR 37 (PRR37), and that the resulting OsNF-Y complex containing Hd1 can bind a specific sequence in the promoter of HEADING DATE 3A (Hd3a). Artificial selection has locally favored an Hd1 variant unable to assemble in such heterotrimeric complex. The causal polymorphism was defined as a single conserved lysine in the CCT domain of the Hd1 protein. Our results indicate how genetic variation can be stratified and explored at multiple levels, and how its description can contribute to the molecular understanding of basic developmental processes. Many plant species flower in response to changes in day length and can be categorized depending on their requirements for long or short days. Rice has tropical origins and normally flowers in response to shortening days. However, artificial selection operated by ancient farmers or modern breeders adapted rice cultivation to several environments, including those typical of temperate regions characterized by long days during the cropping season. Modifications of the genetic network controlling flowering that are causal to such expansion have been the subject of extensive studies, but the full complement of genes that regulate it and the molecular bases of their activity remains unknown. We took advantage of germplasm cultivated in Europe—and highly adapted to flower under long days–to isolate widespread variants of the HEADING DATE 1 (Hd1) gene that limits flowering in temperate areas, and showed that such variants are non-functional and unable to prevent long day flowering. We identified the DNA changes causing the gene to be non-functional and used such mutant alleles as tools to demonstrate that Hd1 can bind a specific DNA sequence in the promoter of a florigenic rice gene. Mining genetic diversity becomes thus instrumental to define the molecular properties of regulatory pathways.
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Affiliation(s)
- Daniela Goretti
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Damiano Martignago
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, United Kingdom
| | - Martina Landini
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
| | - Vittoria Brambilla
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
- Department of Agricultural and Environmental Sciences–Production, Territory, Agroenergy, University of Milan, Via Celoria 2, Milan, Italy
| | - Jorge Gómez-Ariza
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
| | - Nerina Gnesutta
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
| | - Francesca Galbiati
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
| | - Silvio Collani
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Hiroki Takagi
- Iwate Biotechnology Research Center and Laboratory of Crop Evolution, Graduate School of Agricultural Sciences, Kyoto University, Mozume, Muko, Kyoto, Japan
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center and Laboratory of Crop Evolution, Graduate School of Agricultural Sciences, Kyoto University, Mozume, Muko, Kyoto, Japan
| | - Roberto Mantovani
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
| | - Fabio Fornara
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
- * E-mail:
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187
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Pavicic M, Mouhu K, Wang F, Bilicka M, Chovanček E, Himanen K. Genomic and Phenomic Screens for Flower Related RING Type Ubiquitin E3 Ligases in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2017; 8:416. [PMID: 28400782 PMCID: PMC5368169 DOI: 10.3389/fpls.2017.00416] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 03/10/2017] [Indexed: 05/10/2023]
Abstract
Flowering time control integrates endogenous as well as environmental signals to promote flower development. The pathways and molecular networks involved are complex and integrate many modes of signal transduction. In plants ubiquitin mediated protein degradation pathway has been proposed to be as important mode of signaling as phosphorylation and transcription. To systematically study the role of ubiquitin signaling in the molecular regulation of flowering we have taken a genomic approach to identify flower related Ubiquitin Proteasome System components. As a large and versatile gene family the RING type ubiquitin E3 ligases were chosen as targets of the genomic screen. The complete list of Arabidopsis RING E3 ligases were retrieved and verified in the Arabidopsis genome v11 and their differential expression was used for their categorization into flower organs or developmental stages. Known regulators of flowering time or floral organ development were identified in these categories through literature search and representative mutants for each category were purchased for functional characterization by growth and morphological phenotyping. To this end, a workflow was developed for high throughput phenotypic screening of growth, morphology and flowering of nearly a thousand Arabidopsis plants in one experimental round.
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Affiliation(s)
- Mirko Pavicic
- Department of Agricultural Sciences, University of HelsinkiHelsinki, Finland
- Viikki Plant Science Centre, University of HelsinkiHelsinki, Finland
| | - Katriina Mouhu
- Department of Agricultural Sciences, University of HelsinkiHelsinki, Finland
- Viikki Plant Science Centre, University of HelsinkiHelsinki, Finland
| | - Feng Wang
- Department of Agricultural Sciences, University of HelsinkiHelsinki, Finland
- Viikki Plant Science Centre, University of HelsinkiHelsinki, Finland
| | - Marcelina Bilicka
- Department of Agricultural Sciences, University of HelsinkiHelsinki, Finland
- Viikki Plant Science Centre, University of HelsinkiHelsinki, Finland
| | - Erik Chovanček
- Department of Agricultural Sciences, University of HelsinkiHelsinki, Finland
| | - Kristiina Himanen
- Department of Agricultural Sciences, University of HelsinkiHelsinki, Finland
- Viikki Plant Science Centre, University of HelsinkiHelsinki, Finland
- *Correspondence: Kristiina Himanen
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188
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Samad S, Kurokura T, Koskela E, Toivainen T, Patel V, Mouhu K, Sargent DJ, Hytönen T. Additive QTLs on three chromosomes control flowering time in woodland strawberry ( Fragaria vesca L.). HORTICULTURE RESEARCH 2017; 4:17020. [PMID: 28580150 PMCID: PMC5442962 DOI: 10.1038/hortres.2017.20] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 04/21/2017] [Accepted: 04/21/2017] [Indexed: 05/18/2023]
Abstract
Flowering time is an important trait that affects survival, reproduction and yield in both wild and cultivated plants. Therefore, many studies have focused on the identification of flowering time quantitative trait locus (QTLs) in different crops, and molecular control of this trait has been extensively investigated in model species. Here we report the mapping of QTLs for flowering time and vegetative traits in a large woodland strawberry mapping population that was phenotyped both under field conditions and in a greenhouse after flower induction in the field. The greenhouse experiment revealed additive QTLs in three linkage groups (LG), two on both LG4 and LG7, and one on LG6 that explain about half of the flowering time variance in the population. Three of the QTLs were newly identified in this study, and one co-localized with the previously characterized FvTFL1 gene. An additional strong QTL corresponding to previously mapped PFRU was detected in both field and greenhouse experiments indicating that gene(s) in this locus can control the timing of flowering in different environments in addition to the duration of flowering and axillary bud differentiation to runners and branch crowns. Several putative flowering time genes were identified in these QTL regions that await functional validation. Our results indicate that a few major QTLs may control flowering time and axillary bud differentiation in strawberries. We suggest that the identification of causal genes in the diploid strawberry may enable fine tuning of flowering time and vegetative growth in the closely related octoploid cultivated strawberry.
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Affiliation(s)
- Samia Samad
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele All'adige, 38010 TN, Italy
| | - Takeshi Kurokura
- Faculty of Agriculture, Utsunomiya University, Tochigi, 321-8505, Japan
| | - Elli Koskela
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Tuomas Toivainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Vipul Patel
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Katriina Mouhu
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Daniel James Sargent
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele All'adige, 38010 TN, Italy
- Driscoll’s Genetics Limited, East Malling Enterprise Centre, East Malling, Kent ME19 6BJ, UK
| | - Timo Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
- Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
- ()
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189
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Gil KE, Park MJ, Lee HJ, Park YJ, Han SH, Kwon YJ, Seo PJ, Jung JH, Park CM. Alternative splicing provides a proactive mechanism for the diurnal CONSTANS dynamics in Arabidopsis photoperiodic flowering. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:128-140. [PMID: 27607358 DOI: 10.1111/tpj.13351] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 05/19/2023]
Abstract
The circadian clock control of CONSTANS (CO) transcription and the light-mediated stabilization of its encoded protein coordinately adjust photoperiodic flowering by triggering rhythmic expression of the floral integrator flowering locus T (FT). Diurnal accumulation of CO is modulated sequentially by distinct E3 ubiquitin ligases, allowing peak CO to occur in the late afternoon under long days. Here we show that CO abundance is not simply targeted by E3 enzymes but is also actively self-adjusted through dynamic interactions between two CO isoforms. Alternative splicing of CO produces two protein variants, the full-size COα and the truncated COβ lacking DNA-binding affinity. Notably, COβ, which is resistant to E3 enzymes, induces the interaction of COα with CO-destabilizing E3 enzymes but inhibits the association of COα with CO-stabilizing E3 ligase. These observations demonstrate that CO plays an active role in sustaining its diurnal accumulation dynamics during Arabidopsis photoperiodic flowering.
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Affiliation(s)
- Kyung-Eun Gil
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Mi-Jeong Park
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Hyo-Jun Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Young-Joon Park
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Shin-Hee Han
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Young-Ju Kwon
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Jae-Hoon Jung
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
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190
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Shim JS, Kubota A, Imaizumi T. Circadian Clock and Photoperiodic Flowering in Arabidopsis: CONSTANS Is a Hub for Signal Integration. PLANT PHYSIOLOGY 2017; 173:5-15. [PMID: 27688622 PMCID: PMC5210731 DOI: 10.1104/pp.16.01327] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 09/27/2016] [Indexed: 05/19/2023]
Abstract
The circadian clock and light signaling regulate CONSTANS function through intricate mechanisms that reside in phloem companion cells of leaves for controlling photoperiodic flowering in Arabidopsis.
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Affiliation(s)
- Jae Sung Shim
- Department of Biology, University of Washington, Seattle, Washington 98195-1800 (J.S.S., A.K., T.I.)
| | - Akane Kubota
- Department of Biology, University of Washington, Seattle, Washington 98195-1800 (J.S.S., A.K., T.I.)
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, Washington 98195-1800 (J.S.S., A.K., T.I.)
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191
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Brambilla V, Gomez-Ariza J, Cerise M, Fornara F. The Importance of Being on Time: Regulatory Networks Controlling Photoperiodic Flowering in Cereals. FRONTIERS IN PLANT SCIENCE 2017; 8:665. [PMID: 28491078 PMCID: PMC5405123 DOI: 10.3389/fpls.2017.00665] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/11/2017] [Indexed: 05/04/2023]
Abstract
Flowering is the result of the coordination between genetic information and environmental cues. Gene regulatory networks have evolved in plants in order to measure diurnal and seasonal variation of day length (or photoperiod), thus aligning the reproductive phase with the most favorable season of the year. The capacity of plants to discriminate distinct photoperiods classifies them into long and short day species, depending on the conditions that induce flowering. Plants of tropical origin and adapted to short day lengths include rice, maize, and sorghum, whereas wheat and barley were originally domesticated in the Fertile Crescent and are considered long day species. In these and other crops, day length measurement mechanisms have been artificially modified during domestication and breeding to adapt plants to novel areas, to the extent that a wide diversity of responses exists within any given species. Notwithstanding the ample natural and artificial variation of day length responses, some of the basic molecular elements governing photoperiodic flowering are widely conserved. However, as our understanding of the underlying mechanisms improves, it becomes evident that specific regulators exist in many lineages that are not shared by others, while apparently conserved components can be recruited to novel functions during evolution.
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192
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Ionescu IA, Møller BL, Sánchez-Pérez R. Chemical control of flowering time. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:369-382. [PMID: 28204655 DOI: 10.1093/jxb/erw427] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Flowering at the right time is of great importance; it secures seed production and therefore species survival and crop yield. In addition to the genetic network controlling flowering time, there are a number of much less studied metabolites and exogenously applied chemicals that may influence the transition to flowering as well as flower opening. Increased emphasis on research within this area has the potential to counteract the negative effects of global warming on flowering time, especially in perennial crop plants. Perennial crops have a requirement for winter chill, but winters become increasingly warm in temperate regions. This has dramatic effects on crop yield. Different strategies are therefore being developed to engineer flowering time to match local growing conditions. The majority of these efforts are within plant breeding, which benefits from a substantial amount of knowledge on the genetic aspects of flowering time regulation in annuals, but less so in perennials. An alternative to plant breeding approaches is to engineer flowering time chemically via the external application of flower-inducing compounds. This review discusses a variety of exogenously applied compounds used in fruit farming to date, as well as endogenous growth substances and metabolites that can influence flowering time of annuals and perennials.
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Affiliation(s)
- Irina Alexandra Ionescu
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Villum Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Villum Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Raquel Sánchez-Pérez
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
- Villum Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen, Denmark
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193
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NUCLEAR FACTOR Y, Subunit A (NF-YA) Proteins Positively Regulate Flowering and Act Through FLOWERING LOCUS T. PLoS Genet 2016; 12:e1006496. [PMID: 27977687 PMCID: PMC5157953 DOI: 10.1371/journal.pgen.1006496] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/18/2016] [Indexed: 12/12/2022] Open
Abstract
Photoperiod dependent flowering is one of several mechanisms used by plants to initiate the developmental transition from vegetative growth to reproductive growth. The NUCLEAR FACTOR Y (NF-Y) transcription factors are heterotrimeric complexes composed of NF-YA and histone-fold domain (HFD) containing NF-YB/NF-YC, that initiate photoperiod-dependent flowering by cooperatively interacting with CONSTANS (CO) to drive the expression of FLOWERING LOCUS T (FT). This involves NF-Y and CO binding at distal CCAAT and proximal “CORE” elements, respectively, in the FT promoter. While this is well established for the HFD subunits, there remains some question over the potential role of NF-YA as either positive or negative regulators of this process. Here we provide strong support, in the form of genetic and biochemical analyses, that NF-YA, in complex with NF-YB/NF-YC proteins, can directly bind the distal CCAAT box in the FT promoter and are positive regulators of flowering in an FT-dependent manner. For plants to have reproductive success, they must time their flowering with the most beneficial biotic and abiotic environmental conditions—after all, reproductive success would likely be low if flowers developed when pollinators were not present or freezing temperatures were on the horizon. Proper timing mechanisms for flowering vary significantly between different species, but can be connected to a variety of environmental cues, including water availability, temperature, and day length. Numerous labs have studied the molecular aspects of these timing mechanisms and discovered that many of these pathways converge on the gene FLOWERING LOCUS T (FT). This means that understanding precisely how this gene is regulated can teach us a lot about many plant species in both natural and agricultural settings. In the current study, we focus on day length as an essential cue for flowering in the plant species Arabidopsis thaliana. We further unravel the complexity of FT regulation by clarifying the roles of NUCLEAR FACTOR Y genes in day length perception.
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194
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Susila H, Jin S, Ahn JH. Light Intensity and Floral Transition: Chloroplast Says "Time to Flower!". MOLECULAR PLANT 2016; 9:1551-1553. [PMID: 27793786 DOI: 10.1016/j.molp.2016.10.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 10/06/2016] [Accepted: 10/21/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Hendry Susila
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, South Korea
| | - Suhyun Jin
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, South Korea
| | - Ji Hoon Ahn
- Creative Research Initiatives, Department of Life Sciences, Korea University, Seoul 02841, South Korea.
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195
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Weng L, Bai X, Zhao F, Li R, Xiao H. Manipulation of flowering time and branching by overexpression of the tomato transcription factor SlZFP2. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:2310-2321. [PMID: 27214796 PMCID: PMC5103233 DOI: 10.1111/pbi.12584] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/12/2016] [Accepted: 05/19/2016] [Indexed: 05/02/2023]
Abstract
Flowering of higher plants is orchestrated by complex regulatory networks through integration of various environmental signals such as photoperiod, temperature, light quality and developmental cues. In Arabidopsis, transcription of the flowering integrator gene FLOWERING LOCUS T (FT) that several flowering pathways converge to is directly regulated by more than ten transcription factors. However, very little is known about the transcriptional regulation of the FT homolog SINGLE FLOWER TRUESS (SFT) in the day-neutral plant tomato (Solanum lycopersicum). Previously, we showed that the zinc finger transcription factor SlZFP2 plays important roles in regulation of seed germination and fruit ripening in tomato and also found that overexpression of SlZFP2 impacted flowering and branching. Here, we characterized in detail the early flowering and high branching phenotypes by overexpression of this transcription factor. Our data showed that overexpression of SlZFP2 accelerated flowering in an SFT-dependent manner as demonstrated by elevated SFT expression in the leaves and the transcription factor's binding ability to SFT promoter in vitro and in vivo. Furthermore, overexpression of the SlZFP2 gene in the sft plants failed to rescue the mutant's late flowering. Through analysis of grafting phenotype, growth response of branches to auxin application and transcriptome profiling by RNA sequencing, we also showed that overexpression of SlZFP2 affected shoot apical dominance through multiple regulatory pathways. Our results suggest that the transcription factor SlZFP2 has potential applications in genetic modification of plant architecture and flowering time for tomato production and other crops as well.
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Affiliation(s)
- Lin Weng
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Xiaodong Bai
- Center for RNA Molecular BiologyCase Western Reserve UniversitySchool of MedicineClevelandOHUSA
| | - Fangfang Zhao
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Rong Li
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Han Xiao
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
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196
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Riboni M, Robustelli Test A, Galbiati M, Tonelli C, Conti L. ABA-dependent control of GIGANTEA signalling enables drought escape via up-regulation of FLOWERING LOCUS T in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6309-6322. [PMID: 27733440 PMCID: PMC5181575 DOI: 10.1093/jxb/erw384] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
One strategy deployed by plants to endure water scarcity is to accelerate the transition to flowering adaptively via the drought escape (DE) response. In Arabidopsis thaliana, activation of the DE response requires the photoperiodic response gene GIGANTEA (GI) and the florigen genes FLOWERING LOCUS T (FT) and TWIN SISTER OF FT (TSF). The phytohormone abscisic acid (ABA) is also required for the DE response, by promoting the transcriptional up-regulation of the florigen genes. The mode of interaction between ABA and the photoperiodic genes remains obscure. In this work we use a genetic approach to demonstrate that ABA modulates GI signalling and consequently its ability to activate the florigen genes. We also reveal that the ABA-dependent activation of FT, but not TSF, requires CONSTANS (CO) and that impairing ABA signalling dramatically reduces the expression of florigen genes with little effect on the CO transcript profile. ABA signalling thus has an impact on the core genes of photoperiodic signalling GI and CO by modulating their downstream function and/or activities rather than their transcript accumulation. In addition, we show that as well as promoting flowering, ABA simultaneously represses flowering, independent of the florigen genes. Genetic analysis indicates that the target of the repressive function of ABA is the flowering-promoting gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), a transcription factor integrating floral cues in the shoot meristem. Our study suggests that variations in ABA signalling provide different developmental information that allows plants to co-ordinate the onset of the reproductive phase according to the available water resources.
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Affiliation(s)
- Matteo Riboni
- Department of BioSciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Alice Robustelli Test
- Department of BioSciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Massimo Galbiati
- Department of BioSciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Chiara Tonelli
- Department of BioSciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Lucio Conti
- Department of BioSciences, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
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197
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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: 42] [Impact Index Per Article: 5.3] [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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198
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Song YH. The Effect of Fluctuations in Photoperiod and Ambient Temperature on the Timing of Flowering: Time to Move on Natural Environmental Conditions. Mol Cells 2016; 39:715-721. [PMID: 27788575 PMCID: PMC5104878 DOI: 10.14348/molcells.2016.0237] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 10/17/2016] [Indexed: 11/27/2022] Open
Abstract
Plants have become physiologically adapted to a seasonally shifting environment by evolving many sensory mechanisms. Seasonal flowering is a good example of adaptation to local environmental demands and is crucial for maximizing reproductive fitness. Photoperiod and temperature are major environmental stimuli that control flowering through expression of a floral inducer, FLOWERING LOCUS T (FT) protein. Recent discoveries made using the model plant Arabidopsis thaliana have shown that the functions of photoreceptors are essential for the timing of FT gene induction, via modulation of the transcriptional activator CONSTANS (CO) at transcriptional and posttranslational levels in response to seasonal variations. The activation of FT transcription by the fine-tuned CO protein enables plants to switch from vegetative growth to flowering under inductive environmental conditions. The present review briefly summarizes our current understanding of the molecular mechanisms by which the information of environmental stimuli is sensed and transduced to trigger FT induction in leaves.
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Affiliation(s)
- Young Hun Song
- Department of Life Sciences, Ajou University, Suwon 16499,
Korea
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199
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Ridge S, Sussmilch FC, Hecht V, Vander Schoor JK, Lee R, Aubert G, Burstin J, Macknight RC, Weller JL. Identification of LATE BLOOMER2 as a CYCLING DOF FACTOR Homolog Reveals Conserved and Divergent Features of the Flowering Response to Photoperiod in Pea. THE PLANT CELL 2016; 28:2545-2559. [PMID: 27670672 PMCID: PMC5134971 DOI: 10.1105/tpc.15.01011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 08/25/2016] [Accepted: 09/23/2016] [Indexed: 05/21/2023]
Abstract
The molecular pathways responsible for the flowering response to photoperiod have been extensively studied in Arabidopsis thaliana and cereals but remain poorly understood in other major plant groups. Here, we describe a dominant mutant at the LATE BLOOMER2 (LATE2) locus in pea (Pisum sativum) that is late-flowering with a reduced response to photoperiod. LATE2 acts downstream of light signaling and the circadian clock to control expression of the main photoperiod-regulated FT gene, FTb2, implying that it plays a primary role in photoperiod measurement. Mapping identified the CYCLING DOF FACTOR gene CDFc1 as a strong candidate for LATE2, and the late2-1D mutant was found to carry a missense mutation in CDFc1 that impairs its capacity to bind to the blue-light photoreceptor FKF1 in yeast two-hybrid assays and delays flowering in Arabidopsis when overexpressed. Arabidopsis CDF genes are important negative regulators of CONSTANS (CO) transcription, but we found no effect of LATE2 on the transcription of pea CO-LIKE genes, nor on genes in any other families previously implicated in the activation of FT in Arabidopsis. Our results reveal an important component of the pea photoperiod response pathway and support the view that regulation of FTb2 expression by photoperiod occurs via a CO-independent mechanism.
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Affiliation(s)
- Stephen Ridge
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Frances C Sussmilch
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Valérie Hecht
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | | | - Robyn Lee
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | | | | | | | - James L Weller
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
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200
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Abstract
Light is a major environmental factor regulating flowering time, thus ensuring reproductive success of higher plants. In contrast to our detailed understanding of light quality and photoperiod mechanisms involved, the molecular basis underlying high light-promoted flowering remains elusive. Here we show that, in Arabidopsis, a chloroplast-derived signal is critical for high light-regulated flowering mediated by the FLOWERING LOCUS C (FLC). We also demonstrate that PTM, a PHD transcription factor involved in chloroplast retrograde signaling, perceives such a signal and mediates transcriptional repression of FLC through recruitment of FVE, a component of the histone deacetylase complex. Thus, our data suggest that chloroplasts function as essential sensors of high light to regulate flowering and adaptive responses by triggering nuclear transcriptional changes at the chromatin level.
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