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Hajdu A, Nyári D, Terecskei K, Gyula P, Ádám É, Dobos O, Mérai Z, Kozma-Bognár L. LIP1 Regulates the Plant Circadian Oscillator by Modulating the Function of the Clock Component GIGANTEA. Cells 2024; 13:1503. [PMID: 39273073 PMCID: PMC11394198 DOI: 10.3390/cells13171503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 09/04/2024] [Accepted: 09/06/2024] [Indexed: 09/15/2024] Open
Abstract
Circadian clocks are biochemical timers regulating many physiological and molecular processes according to the day/night cycles. The function of the oscillator relies on negative transcriptional/translational feedback loops operated by the so-called clock genes and the encoded clock proteins. Previously, we identified the small GTPase LIGHT INSENSITIVE PERIOD 1 (LIP1) as a circadian-clock-associated protein that regulates light input to the clock in the model plant Arabidopsis thaliana. We showed that LIP1 is also required for suppressing red and blue light-mediated photomorphogenesis, pavement cell shape determination and tolerance to salt stress. Here, we demonstrate that LIP1 is present in a complex of clock proteins GIGANTEA (GI), ZEITLUPE (ZTL) and TIMING OF CAB 1 (TOC1). LIP1 participates in this complex via GUANINE EX-CHANGE FACTOR 7. Analysis of genetic interactions proved that LIP1 affects the oscillator via modulating the function of GI. We show that LIP1 and GI independently and additively regulate photomorphogenesis and salt stress responses, whereas controlling cell shape and photoperiodic flowering are not shared functions of LIP1 and GI. Collectively, our results suggest that LIP1 affects a specific function of GI, possibly by altering binding of GI to downstream signalling components.
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Affiliation(s)
- Anita Hajdu
- Department of Genetics, Faculty of Sciences and Informatics, University of Szeged, H-6726 Szeged, Hungary
- Institute of Plant Biology, HUN-REN Biological Research Centre, H-6726 Szeged, Hungary
- Department of Medical Genetics, Faculty of Medicine, University of Szeged, H-6720 Szeged, Hungary
| | - Dóra Nyári
- Department of Genetics, Faculty of Sciences and Informatics, University of Szeged, H-6726 Szeged, Hungary
- Institute of Plant Biology, HUN-REN Biological Research Centre, H-6726 Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Kata Terecskei
- Institute of Plant Biology, HUN-REN Biological Research Centre, H-6726 Szeged, Hungary
| | - Péter Gyula
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary
| | - Éva Ádám
- Institute of Plant Biology, HUN-REN Biological Research Centre, H-6726 Szeged, Hungary
- Department of Medical Genetics, Faculty of Medicine, University of Szeged, H-6720 Szeged, Hungary
| | - Orsolya Dobos
- Institute of Plant Biology, HUN-REN Biological Research Centre, H-6726 Szeged, Hungary
| | - Zsuzsanna Mérai
- Gregor Mendel Institute of Molecular Plant Biology GmbH, 1030 Vienna, Austria
| | - László Kozma-Bognár
- Department of Genetics, Faculty of Sciences and Informatics, University of Szeged, H-6726 Szeged, Hungary
- Institute of Plant Biology, HUN-REN Biological Research Centre, H-6726 Szeged, Hungary
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Mallano AI, Li W, Tabys D, Chao C, Yang Y, Anwar S, Almas HI, Nisa ZU, Li Y. The soybean GmNFY-B1 transcription factor positively regulates flowering in transgenic Arabidopsis. Mol Biol Rep 2021; 48:1589-1599. [PMID: 33512627 DOI: 10.1007/s11033-021-06164-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 01/15/2021] [Indexed: 01/18/2023]
Abstract
Nuclear Factor Y (NF-Y) gene family regulates numbers of flowering processes. Two independent transgenic Arabidopsis lines overexpressing (OX) GmNFY-B1 and GmNFYB1-GR (GmNFYB1 fused with the glucocorticoid receptor) were used to investigate the function of NFY-B1 in flowering. Furthermore, GmNFYB1-GR lines were chemically treated with dexamethasone (Dex, synthetic steroid hormone), cycloheximide (Cyc, an inhibitor of protein biosynthesis), and ethanol to examine their effects on different flowering related marker genes. Our results indicated that the transgenic lines produced longer hypocotyl lengths and had fewer numbers of rosette leaves compared to the wild-type and nf-yb1 mutant plants under both long and short-day (LD and SD) conditions. The qRT-PCR assays revealed that transcript levels of all flowering time regulating genes, i.e. SOC, FLC, FT, TSF, LFY, GI2, AGL, and FCA showed higher transcript abundance in lines OX GmNFYB1-GR. However, FT and GI genes showed higher transcript levels under Dex and Dex/Cyc treatments compared to Cyc and ethanol. Additionally, 24 differentially expressed genes were identified and verified through RNA-seq and RT-qPCR in GmNF-YB1-GR lines under Cyc and Dex/Cyc treatments from which 14 genes were up-regulated and 10 were down-regulated. These genes are involved in regulatory functions of circadian rhythm, regulation of flower development in photoperiodic, and GA pathways. The overexpression of GmNF-YB1 and GmNF-YB1-GR promote flowering through the higher expression of flowering-related genes. Further GmNF-YB1 and its attachment with the GR receptor can regulate its target genes under Dex/Cyc treatment and might act as flowering inducer under LD and SD conditions.
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Affiliation(s)
- Ali Inayat Mallano
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, 150030, People's Republic of China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, People's Republic of China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Dina Tabys
- Department of Biomedical Sciences, Nazarbayev University School of Medicine, Nur-Sultan, 010000, Kazakhstan
| | - Chen Chao
- School of Life Science and Technology, Harbin Normal University, Harbin, People's Republic of China
| | - Yu Yang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, People's Republic of China
| | - Sumera Anwar
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Hafiza Iqra Almas
- Department of Botany, University of Agriculture, Faisalabad, Pakistan
| | - Zaib Un Nisa
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan.
| | - Yongguang Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, 150030, People's Republic of China.
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Sun X, Wang X, Zheng C, Xing S, Shu H. Cloning, sequence, and expression analyses of the Chrysanthemum morifolium flowering-related gene CmCOL (CONSTANS-like). GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Aggarwal P, Challa KR, Rath M, Sunkara P, Nath U. Generation of Inducible Transgenic Lines of Arabidopsis Transcription Factors Regulated by MicroRNAs. Methods Mol Biol 2018; 1830:61-79. [PMID: 30043364 DOI: 10.1007/978-1-4939-8657-6_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Transcription factors play key regulatory roles in all the life processes across kingdoms. In plants, the genome of a typical model species such as Arabidopsis thaliana encodes over 1500 transcription factors that regulate the expression dynamics of all the genes in time and space. Therefore, studying their function by analyzing the loss and gain-of-function lines is of prime importance in basic plant biology and its agricultural application. However, the current approach of knocking out genes often causes embryonic lethal phenotype, while inactivating one or two members of a redundant gene family yields little phenotypic changes, thereby making the functional analysis a technically challenging task. In such cases, inducible knock-down or overexpression of transcription factors appears to be a more effective approach. Restricting the transcription factors in the cytoplasm by fusing them with animal glucocorticoid/estrogen receptors (GR/ER) and then re-localizing them to the nucleus by external application of animal hormone analogues has been a useful method of gene function analysis in the model plants. In this chapter, we describe the recent advancements in the GR and ER expression systems and their use in analyzing the function of transcription factors in Arabidopsis.
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Affiliation(s)
- Pooja Aggarwal
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Krishna Reddy Challa
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Monalisha Rath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Preethi Sunkara
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Utpal Nath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.
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5
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van Dijk ADJ, Molenaar J. Floral pathway integrator gene expression mediates gradual transmission of environmental and endogenous cues to flowering time. PeerJ 2017; 5:e3197. [PMID: 28439467 PMCID: PMC5399868 DOI: 10.7717/peerj.3197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/17/2017] [Indexed: 11/20/2022] Open
Abstract
The appropriate timing of flowering is crucial for the reproductive success of plants. Hence, intricate genetic networks integrate various environmental and endogenous cues such as temperature or hormonal statues. These signals integrate into a network of floral pathway integrator genes. At a quantitative level, it is currently unclear how the impact of genetic variation in signaling pathways on flowering time is mediated by floral pathway integrator genes. Here, using datasets available from literature, we connect Arabidopsis thaliana flowering time in genetic backgrounds varying in upstream signalling components with the expression levels of floral pathway integrator genes in these genetic backgrounds. Our modelling results indicate that flowering time depends in a quite linear way on expression levels of floral pathway integrator genes. This gradual, proportional response of flowering time to upstream changes enables a gradual adaptation to changing environmental factors such as temperature and light.
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Affiliation(s)
- Aalt D J van Dijk
- Biometris, Department for Mathematical and Statistical Methods, Wageningen University, Wageningen, The Netherlands.,Laboratory of Bioinformatics, Wageningen University, Wageningen, The Netherlands.,Bioscience, Wageningen University and Research, Wageningen, The Netherlands
| | - Jaap Molenaar
- Biometris, Department for Mathematical and Statistical Methods, Wageningen University, Wageningen, The Netherlands
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Okada R, Nemoto Y, Endo-Higashi N, Izawa T. Synthetic control of flowering in rice independent of the cultivation environment. NATURE PLANTS 2017; 3:17039. [PMID: 28346447 DOI: 10.1038/nplants.2017.39] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 02/26/2017] [Indexed: 05/03/2023]
Abstract
For genetically homogeneous crops, the timing of flowering is determined largely by the cultivation environment and is strongly associated with the yield and quality of the harvest1. Flowering time and other agronomical traits are often tightly correlated, which can lead to difficulty excluding the effects of flowering time when evaluating the characteristics of different genetic varieties2. Here, we describe the development of transgenic rice plants whose flowering time can be controlled by specific agrochemicals. We first developed non-flowering rice plants by overexpressing a floral repressor gene, Grain number, plant height and heading date 7 (Ghd7)3,4, to inhibit any environmentally induced spontaneous flowering. We then co-transformed plants with a rice florigen gene, Heading date 3a (Hd3a)5, which is induced by the application of specific agrochemicals. This permitted the flowering time to be experimentally controlled regardless of the cultivation environment: some transgenic plants flowered only after agrochemical treatment. Furthermore, plant size and yield-related traits could, in some cases, be increased owing to both a longer duration of vegetative growth and an increased panicle size. This ability to control flowering time experimentally, independently of environmental variables, may lead to production of crops suitable for growth in different climates and facilitate breeding for various agronomical traits.
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Affiliation(s)
- Ryo Okada
- Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Yasue Nemoto
- Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Naokuni Endo-Higashi
- Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Takeshi Izawa
- Functional Plant Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
- Laoratory of Plant Breeding &Genetics, Department of Agriculture, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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Amanda D, Doblin MS, Galletti R, Bacic A, Ingram GC, Johnson KL. DEFECTIVE KERNEL1 (DEK1) Regulates Cell Walls in the Leaf Epidermis. PLANT PHYSIOLOGY 2016; 172:2204-2218. [PMID: 27756823 PMCID: PMC5129726 DOI: 10.1104/pp.16.01401] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/14/2016] [Indexed: 05/25/2023]
Abstract
The plant epidermis is crucial to survival, regulating interactions with the environment and controlling plant growth. The phytocalpain DEFECTIVE KERNEL1 (DEK1) is a master regulator of epidermal differentiation and maintenance, acting upstream of epidermis-specific transcription factors, and is required for correct cell adhesion. It is currently unclear how changes in DEK1 lead to cellular defects in the epidermis and the pathways through which DEK1 acts. We have combined growth kinematic studies, cell wall analysis, and transcriptional analysis of genes downstream of DEK1 to determine the cause of phenotypic changes observed in DEK1-modulated lines of Arabidopsis (Arabidopsis thaliana). We reveal a novel role for DEK1 in the regulation of leaf epidermal cell wall structure. Lines with altered DEK1 activity have epidermis-specific changes in the thickness and polysaccharide composition of cell walls that likely underlie the loss of adhesion between epidermal cells in plants with reduced levels of DEK1 and changes in leaf shape and size in plants constitutively overexpressing the active CALPAIN domain of DEK1. Calpain-overexpressing plants also have increased levels of cellulose and pectins in epidermal cell walls, and this is correlated with the expression of several cell wall-related genes, linking transcriptional regulation downstream of DEK1 with cellular effects. These findings significantly advance our understanding of the role of the epidermal cell walls in growth regulation and establish a new role for DEK1 in pathways regulating epidermal cell wall deposition and remodeling.
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Affiliation(s)
- Dhika Amanda
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (D.A., M.S.D., A.B., K.L.J.); and
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5667, Institut National de la Recherche Agronomique Unité Mixte de Recherche 0879, Ecole Normale Supérieure de Lyon, Lyon F-69342, France (R.G., G.C.I.)
| | - Monika S Doblin
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (D.A., M.S.D., A.B., K.L.J.); and
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5667, Institut National de la Recherche Agronomique Unité Mixte de Recherche 0879, Ecole Normale Supérieure de Lyon, Lyon F-69342, France (R.G., G.C.I.)
| | - Roberta Galletti
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (D.A., M.S.D., A.B., K.L.J.); and
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5667, Institut National de la Recherche Agronomique Unité Mixte de Recherche 0879, Ecole Normale Supérieure de Lyon, Lyon F-69342, France (R.G., G.C.I.)
| | - Antony Bacic
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (D.A., M.S.D., A.B., K.L.J.); and
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5667, Institut National de la Recherche Agronomique Unité Mixte de Recherche 0879, Ecole Normale Supérieure de Lyon, Lyon F-69342, France (R.G., G.C.I.)
| | - Gwyneth C Ingram
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (D.A., M.S.D., A.B., K.L.J.); and
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5667, Institut National de la Recherche Agronomique Unité Mixte de Recherche 0879, Ecole Normale Supérieure de Lyon, Lyon F-69342, France (R.G., G.C.I.)
| | - Kim L Johnson
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (D.A., M.S.D., A.B., K.L.J.); and
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5667, Institut National de la Recherche Agronomique Unité Mixte de Recherche 0879, Ecole Normale Supérieure de Lyon, Lyon F-69342, France (R.G., G.C.I.)
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Mishra P, Panigrahi KC. GIGANTEA - an emerging story. FRONTIERS IN PLANT SCIENCE 2015; 6:8. [PMID: 25674098 PMCID: PMC4306306 DOI: 10.3389/fpls.2015.00008] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 01/06/2015] [Indexed: 05/02/2023]
Abstract
GIGANTEA (GI) is a plant specific nuclear protein and functions in diverse physiological processes such as flowering time regulation, light signaling, hypocotyl elongation, control of circadian rhythm, sucrose signaling, starch accumulation, chlorophyll accumulation, transpiration, herbicide tolerance, cold tolerance, drought tolerance, and miRNA processing. It has been five decades since its discovery but the biochemical function of GI and its different domains are still unclear. Although it is known that both GI transcript and GI protein are clock controlled, the regulation of its abundance and functions at the molecular level are still some of the unexplored areas of intensive research. Since GI has many important pleotropic functions as described above scattered through literature, it is worthwhile and about time to encapsulate the available information in a concise review. Therefore, in this review, we are making an attempt to summarize (i) the various interconnected roles that GI possibly plays in the fine-tuning of plant development, and (ii) the known mutations of GI that have been instrumental in understanding its role in distinct physiological processes.
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Affiliation(s)
| | - Kishore C. Panigrahi
- *Correspondence: Kishore C. Panigrahi, Plant Science Lab, School of Biological Sciences, National Institute of Science Education and Research, IOP campus, Sachivalaya Marg, P.O. Sainik School, Bhubaneshwar 751005, Orissa, India e-mail:
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9
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Saijo T, Nagasawa A. Development of a tightly regulated and highly responsive copper-inducible gene expression system and its application to control of flowering time. PLANT CELL REPORTS 2014; 33:47-59. [PMID: 24097281 DOI: 10.1007/s00299-013-1511-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 09/09/2013] [Accepted: 09/20/2013] [Indexed: 06/02/2023]
Abstract
KEY MESSAGE A newly developed copper-inducible gene expression system overcame the mixed results reported earlier, worked well both in cultured cells and a whole plant, and enabled to control flowering timing. Copper is one of the essential microelements and is readily taken up by plants. However, to date, it has rarely been used to control the expression of genes of interest, probably due to the inefficiency of the gene expression systems. In this study, we successfully developed a copper-inducible gene expression system that is based on the regulation of the yeast metallothionein gene. This system can be applied in the field and regulated at approximately one-hundredth of the rate used for registered copper-based fungicides. In the presence of copper, a translational fusion of the ACE1 transcription factor with the VP16 activation domain (VP16AD) of herpes simplex virus strongly activated transcription of the GFP gene in transgenic Arabidopsis. Interestingly, insertion of the To71 sequence, a 5'-untranslated region of the 130k/180k gene of tomato mosaic virus, upstream of the GFP gene reduced the basal expression of GFP in the absence of copper to almost negligible levels, even in soil-grown plants that were supplemented with ordinary liquid nutrients. Exposure of plants to 100 μM copper resulted in an over 1,000-fold induction ratio at the transcriptional level of GFP. This induction was copper-specific and dose-dependent with rapid and reversible responses. Using this expression system, we also succeeded in regulating floral transition by copper treatment. These results indicate that our newly developed copper-inducible system can accelerate gene functional analysis in model plants and can be used to generate novel agronomic traits in crop species.
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Affiliation(s)
- Takanori Saijo
- Biology Group, Discovery, Health & Crop Sciences Research Laboratory, Sumitomo Chemical Co., Ltd., 4-2-1, Takatsukasa, Takarazuka, Hyogo, 665-8555, Japan,
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10
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Balanced nucleocytosolic partitioning defines a spatial network to coordinate circadian physiology in plants. Dev Cell 2013; 26:73-85. [PMID: 23830866 DOI: 10.1016/j.devcel.2013.06.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 03/14/2013] [Accepted: 06/06/2013] [Indexed: 01/13/2023]
Abstract
Biological networks consist of a defined set of regulatory motifs. Subcellular compartmentalization of regulatory molecules can provide a further dimension in implementing regulatory motifs. However, spatial regulatory motifs and their roles in biological networks have rarely been explored. Here we show, using experimentation and mathematical modeling, that spatial segregation of GIGANTEA (GI), a critical component of plant circadian systems, into nuclear and cytosolic compartments leads to differential functions as positive and negative regulators of the circadian core gene, LHY, forming an incoherent feedforward loop to regulate LHY. This regulatory motif formed by nucleocytoplasmic partitioning of GI confers, through the balanced operation of the nuclear and cytosolic GI, strong rhythmicity and robustness to external and internal noises to the circadian system. Our results show that spatial and functional segregation of a single molecule species into different cellular compartments provides a means for extending the regulatory capabilities of biological networks.
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11
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Kim Y, Lim J, Yeom M, Kim H, Kim J, Wang L, Kim WY, Somers DE, Nam HG. ELF4 regulates GIGANTEA chromatin access through subnuclear sequestration. Cell Rep 2013; 3:671-7. [PMID: 23523352 DOI: 10.1016/j.celrep.2013.02.021] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 01/16/2013] [Accepted: 02/19/2013] [Indexed: 11/18/2022] Open
Abstract
Many organisms, including plants, use the circadian clock to measure the duration of day and night. Daily rhythms in the plant circadian system are generated by multiple interlocked transcriptional/translational loops and also by spatial regulations such as nuclear translocation. GIGANTEA (GI), one of the key clock components in Arabidopsis, makes distinctive nuclear bodies like other nuclear-localized circadian regulators. However, little is known about the dynamics or roles of GI subnuclear localization. Here, we characterize GI subnuclear compartmentalization and identify unexpected dynamic changes under diurnal conditions. We further identify EARLY FLOWERING 4 (ELF4) as a regulator of GI nuclear distribution through a physical interaction. ELF4 sequesters GI from the nucleoplasm, where GI binds the promoter of CONSTANS (CO), to discrete nuclear bodies. We suggest that the subnuclear compartmentalization of GI by ELF4 contributes to the regulation of photoperiodic flowering.
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Affiliation(s)
- Yumi Kim
- Department of New Biology, DGIST, Daegu 711-873, Republic of Korea
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12
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Devoghalaere F, Doucen T, Guitton B, Keeling J, Payne W, Ling TJ, Ross JJ, Hallett IC, Gunaseelan K, Dayatilake GA, Diak R, Breen KC, Tustin DS, Costes E, Chagné D, Schaffer RJ, David KM. A genomics approach to understanding the role of auxin in apple (Malus x domestica) fruit size control. BMC PLANT BIOLOGY 2012; 12:7. [PMID: 22243694 PMCID: PMC3398290 DOI: 10.1186/1471-2229-12-7] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 01/13/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Auxin is an important phytohormone for fleshy fruit development, having been shown to be involved in the initial signal for fertilisation, fruit size through the control of cell division and cell expansion, and ripening related events. There is considerable knowledge of auxin-related genes, mostly from work in model species. With the apple genome now available, it is possible to carry out genomics studies on auxin-related genes to identify genes that may play roles in specific stages of apple fruit development. RESULTS High amounts of auxin in the seed compared with the fruit cortex were observed in 'Royal Gala' apples, with amounts increasing through fruit development. Injection of exogenous auxin into developing apples at the start of cell expansion caused an increase in cell size. An expression analysis screen of auxin-related genes involved in auxin reception, homeostasis, and transcriptional regulation showed complex patterns of expression in each class of gene. Two mapping populations were phenotyped for fruit size over multiple seasons, and multiple quantitative trait loci (QTLs) were observed. One QTL mapped to a region containing an Auxin Response Factor (ARF106). This gene is expressed during cell division and cell expansion stages, consistent with a potential role in the control of fruit size. CONCLUSIONS The application of exogenous auxin to apples increased cell expansion, suggesting that endogenous auxin concentrations are at least one of the limiting factors controlling fruit size. The expression analysis of ARF106 linked to a strong QTL for fruit weight suggests that the auxin signal regulating fruit size could partially be modulated through the function of this gene. One class of gene (GH3) removes free auxin by conjugation to amino acids. The lower expression of these GH3 genes during rapid fruit expansion is consistent with the apple maximising auxin concentrations at this point.
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Affiliation(s)
- Fanny Devoghalaere
- The New Zealand Institute for Plant & Food Research Limited (PFR), Private Bag 92169, Auckland 1142, New Zealand
| | - Thomas Doucen
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Baptiste Guitton
- PFR, Private Bag 11600, Palmerston North 4442, New Zealand
- INRA, UMR AGAP, Equipe Architecture et Fonctionnement des Espèces Fruitières, Avenue Agropolis - TA-A-108/03, 34398 Montpellier Cedex 01, France
| | - Jeannette Keeling
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Wendy Payne
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Toby John Ling
- School of Plant Science, University of Tasmania, GPO Box 252-55, Hobart, Tasmania 7001, Australia
| | - John James Ross
- School of Plant Science, University of Tasmania, GPO Box 252-55, Hobart, Tasmania 7001, Australia
| | - Ian Charles Hallett
- The New Zealand Institute for Plant & Food Research Limited (PFR), Private Bag 92169, Auckland 1142, New Zealand
| | - Kularajathevan Gunaseelan
- The New Zealand Institute for Plant & Food Research Limited (PFR), Private Bag 92169, Auckland 1142, New Zealand
| | - GA Dayatilake
- PFR, Private Bag 1401, Havelock North 4157, New Zealand
| | - Robert Diak
- PFR, Old Mill Road, RD3, Motueka 7198, New Zealand
| | - Ken C Breen
- PFR, Private Bag 1401, Havelock North 4157, New Zealand
| | | | - Evelyne Costes
- INRA, UMR AGAP, Equipe Architecture et Fonctionnement des Espèces Fruitières, Avenue Agropolis - TA-A-108/03, 34398 Montpellier Cedex 01, France
| | - David Chagné
- PFR, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Robert James Schaffer
- The New Zealand Institute for Plant & Food Research Limited (PFR), Private Bag 92169, Auckland 1142, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Karine Myriam David
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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Abstract
Synthetic biology methods are routinely applied in the plant field as in other eukaryotic model systems. Several synthetic components have been developed in plants and an increasing number of studies report on the assembly into functional synthetic genetic circuits. This chapter gives an overview of the existing plant genetic networks and describes in detail the application of two systems for inducible gene expression. The ethanol-inducible system relies on the ethanol-responsive interaction of the AlcA transcriptional activator and the AlcR receptor resulting in the transcription of the gene of interest (GOI). In comparison, the translational fusion of GOI and the glucocorticoid receptor (GR) domain leads to the dexamethasone-dependent nuclear translocation of the GOI::GR protein. This chapter contains detailed protocols for the application of both systems in the model plants potato and Arabidopsis, respectively.
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Affiliation(s)
- Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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14
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Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IAP, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z. The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 2011; 43:1035-9. [PMID: 21873998 DOI: 10.1038/ng.919] [Citation(s) in RCA: 1281] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 08/03/2011] [Indexed: 11/09/2022]
Abstract
We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.
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Affiliation(s)
- Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences (IVF, CAAS), Beijing, China
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