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Park J, Lee S, Park G, Cho H, Choi D, Umeda M, Choi Y, Hwang D, Hwang I. CYTOKININ-RESPONSIVE GROWTH REGULATOR regulates cell expansion and cytokinin-mediated cell cycle progression. PLANT PHYSIOLOGY 2021; 186:1734-1746. [PMID: 33909905 PMCID: PMC8260111 DOI: 10.1093/plphys/kiab180] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/31/2021] [Indexed: 05/23/2023]
Abstract
The cytokinin (CK) phytohormones have long been known to activate cell proliferation in plants. However, how CKs regulate cell division and cell expansion remains unclear. Here, we reveal that a basic helix-loop-helix transcription factor, CYTOKININ-RESPONSIVE GROWTH REGULATOR (CKG), mediates CK-dependent regulation of cell expansion and cell cycle progression in Arabidopsis thaliana. The overexpression of CKG increased cell size in a ploidy-independent manner and promoted entry into the S phase of the cell cycle, especially at the seedling stage. Furthermore, CKG enhanced organ growth in a pleiotropic fashion, from embryogenesis to reproductive stages, particularly of cotyledons. In contrast, ckg loss-of-function mutants exhibited smaller cotyledons. CKG mainly regulates the expression of genes involved in the regulation of the cell cycle including WEE1. We propose that CKG provides a regulatory module that connects cell cycle progression and organ growth to CK responses.
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Affiliation(s)
- Joonghyuk Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Seungchul Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Geuntae Park
- School of Biological Sciences, Seoul National University, Seoul 151-747, Korea
| | - Hyunwoo Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Daeseok Choi
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0192, Japan
| | - Yeonhee Choi
- School of Biological Sciences, Seoul National University, Seoul 151-747, Korea
| | - Daehee Hwang
- School of Biological Sciences, Seoul National University, Seoul 151-747, Korea
| | - Ildoo Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
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2
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Wang X, Liu Y, Huai D, Chen Y, Jiang Y, Ding Y, Kang Y, Wang Z, Yan L, Jiang H, Lei Y, Liao B. Genome-wide identification of peanut PIF family genes and their potential roles in early pod development. Gene 2021; 781:145539. [PMID: 33631242 DOI: 10.1016/j.gene.2021.145539] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/09/2021] [Accepted: 02/16/2021] [Indexed: 10/22/2022]
Abstract
Peanut is typically a geocarpic plant. The developing gynophore ('peg') in air could not swell normally until it buries into soil, indicating light-to-dark conversion is necessary for early pod development in peanut. As the subfamily of basic helix-loop-helix (bHLH) transcription factors, phytochrome interacting factors (PIFs) are key regulators involved in light signaling pathways, and play crucial roles in plant growth and development. In the current study, a total of 14 AhPIFs were identified in cultivated peanut genome (Arachis hypogaea L., AABB), while seven AdPIFs and six AiPIFs were discovered in the two wild diploids (A. duranensis (AA), A. ipaensis (BB)) respectively. Phylogenetic analysis revealed that peanut PIFs were clustered into four distinct clades, and members within the same subgroup had conserved motifs and displayed similar exon-intron distribution patterns. Gene synteny analysis indicated most of the PIFs exhibit one-to-one homology relationship between AA and BB subgenome in A. hypogaea, as well as among the three peanut species. Gene duplication detection showed that segmental duplication and purifying selection contributed to the expansion and evolution of peanut PIF gene family. Transcript profiles combined with subcellular localization analysis suggested AhPIF3A4 and AhPIF3B4 may possibly be involved in regulation of peanut early pod development. This study could further facilitate functional characterization of PIFs in peanut and other legumes.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Yue Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Yifei Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Yingbin Ding
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Yanping Kang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Zhihui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China.
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3
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Wang M, Tian Y, Han C, Zhou C, Bai MY, Fan M. Phospho-Mutant Activity Assays Provide Evidence for the Negative Regulation of Transcriptional Regulator PRE1 by Phosphorylation. Int J Mol Sci 2020; 21:ijms21239183. [PMID: 33276448 PMCID: PMC7729563 DOI: 10.3390/ijms21239183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 11/29/2020] [Accepted: 11/29/2020] [Indexed: 11/17/2022] Open
Abstract
The PACLOBUTRAZOL-RESISTANCE (PRE) gene family encodes a group of atypical helix-loop-helix (HLH) proteins that act as the major hub integrating a wide range of environmental and hormonal signals to regulate plant growth and development. PRE1, as a positive regulator of cell elongation, activates HBI1 DNA binding by sequestering its inhibitor IBH1. Furthermore, PRE1 can be phosphorylated at Ser-46 and Ser-67, but how this phosphorylation regulates the functions of PRE1 remains unclear. Here, we used a phospho-mutant activity assay to reveal that the phosphorylation at Ser-67 negatively regulates the functions of PRE1 on cell elongation. Both of mutations of serine 46, either to phospho-dead alanine or phospho-mimicking glutamic acid, had no significant effects on the functions of PRE1. However, the mutation of serine 67 to glutamic acid (PRE1S67E-Ox), but not alanine (PRE1S67A-Ox), significantly reduced the promoting effects of PRE1 on cell elongation. The mutation of Ser-67 to Glu-67 impaired the interaction of PRE1 with IBH1 and resulted in PRE1 failing to inhibit the interaction between IBH1 and HBI1, losing the ability to induce the expression of the subsequent cell elongation-related genes. Furthermore, we showed that PRE1-Ox and PRE1S67A-Ox both suppressed but PRE1S67E-Ox had no strong effects on the dwarf phenotypes of IBH1-Ox. Our study demonstrated that the PRE1 activity is negatively regulated by the phosphorylation at Ser-67.
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4
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Zheng K, Wang Y, Wang S. The non-DNA binding bHLH transcription factor Paclobutrazol Resistances are involved in the regulation of ABA and salt responses in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:239-245. [PMID: 30921735 DOI: 10.1016/j.plaphy.2019.03.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/28/2019] [Accepted: 03/15/2019] [Indexed: 05/15/2023]
Abstract
Abscisic acid (ABA) is the key hormone that regulating plant responses to abiotic stresses. Several basic helix-loop-helix (bHLH) transcription factors have been reported to regulate ABA signaling in Arabidopsis. Paclobutrazol Resistances (PREs) are non-DNA binding bHLH transcription factors involved in the regulation of plant response to several different plant hormones including gibberellin, brassinosteroid and auxin. Here, we show that PREs are involved in the regulation of ABA and salt responses in Arabidopsis. Quantitative RT-PCR results showed that the expression levels of PRE6 as well as several other PRE genes were reduced in response to ABA treatment, but increased to salt treatment. Seed germination assays indicated that ABA sensitivity is reduced in the pre6 mutants, but increased in transgenic plants overexpressing PRE6. On the other hand, the 35S:PRE6 transgenic plants showed enhanced tolerance to salt, whereas little, if any changes were observed in the pre6 mutants. Similar responses to ABA and salt treatments were observed in the pre2 mutants and the transgenic plants overexpressing PRE2, and a slight increased resistance to ABA in seed germination was observed in the pre2 pre6 double mutants. Taken together, our results suggest that at least some of the PRE genes are ABA responsive genes, and PREs may function redundantly to regulate ABA and salt responses in Arabidopsis.
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Affiliation(s)
- Kaijie Zheng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China; Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Yating Wang
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Shucai Wang
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China; College of Life Science, Linyi University, Linyi, China.
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5
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Wang CC, Meng LH, Gao Y, Grierson D, Fu DQ. Manipulation of Light Signal Transduction Factors as a Means of Modifying Steroidal Glycoalkaloids Accumulation in Tomato Leaves. FRONTIERS IN PLANT SCIENCE 2018; 9:437. [PMID: 29706975 PMCID: PMC5906708 DOI: 10.3389/fpls.2018.00437] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/21/2018] [Indexed: 05/19/2023]
Abstract
Steroidal glycoalkaloids (SGAs) are cholesterol-derived specialized metabolites produced by Solanaceous plant species. They contribute to pathogen defense but are considered as anti-nutritional compounds and toxic to humans. Although the genes involved in the SGA biosynthetic pathway have been successfully cloned and identified, transcription factors regulating this pathway are still poorly understood. We report that silencing tomato light signal transduction transcription factors ELONGATED HYPOCOTYL 5 (SlHY5) and PHYTOCHROME INTERACTING FACTOR3 (SlPIF3), by virus-induced gene silencing (VIGS), altered glycoalkaloids levels in tomato leaves compared to control plant. Electrophoretic mobility shift assay (EMSA) and Chromatin immunoprecipitation (ChIP) analysis confirmed that SlHY5 and SlPIF3 bind to the promoter of target genes of GLYCOALKALOID METABOLISM (GAME1, GAME4, GAME17), affecting the steady-state concentrations of transcripts coding for SGA pathway enzymes. The results indicate that light-signaling transcription factors HY5 and PIF3 regulate the abundance of SGAs by modulating the transcript levels of these GAME genes. This insight into the regulation of SGA biosynthesis can be used for manipulating the level of these metabolites in crops.
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Affiliation(s)
- Cui-cui Wang
- Fruit Biology Laboratory, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Lan-huan Meng
- Fruit Biology Laboratory, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Ying Gao
- Fruit Biology Laboratory, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Da-qi Fu
- Fruit Biology Laboratory, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- *Correspondence: Da-qi Fu
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6
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Ni W, Xu SL, González-Grandío E, Chalkley RJ, Huhmer AFR, Burlingame AL, Wang ZY, Quail PH. PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3. Nat Commun 2017; 8:15236. [PMID: 28492231 PMCID: PMC5437280 DOI: 10.1038/ncomms15236] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 03/10/2017] [Indexed: 12/21/2022] Open
Abstract
Upon light-induced nuclear translocation, phytochrome (phy) sensory photoreceptors interact with, and induce rapid phosphorylation and consequent ubiquitin-mediated degradation of, transcription factors, called PIFs, thereby regulating target gene expression and plant development. Nevertheless, the biochemical mechanism of phy-induced PIF phosphorylation has remained ill-defined. Here we identify a family of nuclear protein kinases, designated Photoregulatory Protein Kinases (PPK1-4; formerly called MUT9-Like Kinases (MLKs)), that interact with PIF3 and phyB in a light-induced manner in vivo. Genetic analyses demonstrate that the PPKs are collectively necessary for the normal light-induced phosphorylation and degradation of PIF3. PPK1 directly phosphorylates PIF3 in vitro, with a phosphosite pattern that strongly mimics the light-induced pattern in vivo. These data establish that the PPKs are directly involved in catalysing the photoactivated-phy-induced phosphorylation of PIF3 in vivo, and thereby are critical components of a transcriptionally centred signalling hub that pleiotropically regulates plant growth and development in response to multiple signalling pathways.
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Affiliation(s)
- Weimin Ni
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- U.S. Department of Agriculture/Agriculture Research Service, Plant Gene Expression Center, Albany, California 94710, USA
| | - Shou-Ling Xu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
- Thermo Fisher Scientific, San Jose, California 95134, USA
| | - Eduardo González-Grandío
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- U.S. Department of Agriculture/Agriculture Research Service, Plant Gene Expression Center, Albany, California 94710, USA
| | - Robert J. Chalkley
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | | | - Alma L. Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Peter H. Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- U.S. Department of Agriculture/Agriculture Research Service, Plant Gene Expression Center, Albany, California 94710, USA
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7
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Tian H, Guo H, Dai X, Cheng Y, Zheng K, Wang X, Wang S. An ABA down-regulated bHLH transcription repressor gene, bHLH129 regulates root elongation and ABA response when overexpressed in Arabidopsis. Sci Rep 2015; 5:17587. [PMID: 26625868 PMCID: PMC4667245 DOI: 10.1038/srep17587] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/02/2015] [Indexed: 11/15/2022] Open
Abstract
Plant hormone abscisic acid (ABA) plays a crucial role in modulating plant responses to environmental stresses. Basic helix-loop-helix (bHLH) transcription factors are one of the largest transcription factor families that regulate multiple aspects of plant growth and development, as well as of plant metabolism in Arabidopsis. Several bHLH transcription factors have been shown to be involved in the regulation of ABA signaling. We report here the characterization of bHLH129, a bHLH transcription factor in Arabidopsis. We found that the expression level of bHLH129 was reduced in response to exogenously applied ABA, and elevated in the ABA biosynthesis mutant aba1-5. Florescence observation of transgenic plants expressing bHLH129-GFP showed that bHLH129 was localized in the nucleus, and transient expression of bHLH129 in protoplasts inhibited reporter gene expression. When expressed in Arabidopsis under the control of the 35S promoter, bHLH129 promoted root elongation, and the transgenic plants were less sensitivity to ABA in root elongation assays. Quantitative RT-PCR results showed that ABA response of several genes involved in ABA signaling, including ABI1, SnRK2.2, SnRK2.3 and SnRK2.6 were altered in the transgenic plants overexpressing bHLH129. Taken together, our study suggests that bHLH129 is a transcription repressor that negatively regulates ABA response in Arabidopsis.
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Affiliation(s)
- Hainan Tian
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, Jilin 130024, China
| | - Hongyan Guo
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, Jilin 130024, China
| | - Xuemei Dai
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, Jilin 130024, China
| | - Yuxin Cheng
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, Jilin 130024, China
| | - Kaijie Zheng
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, Jilin 130024, China
| | - Xiaoping Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, Jilin 130024, China
| | - Shucai Wang
- Key Laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, Jilin 130024, China
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8
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Pedroza-García JA, Nájera-Martínez M, de la Paz Sanchez M, Plasencia J. Arabidopsis thaliana thymidine kinase 1a is ubiquitously expressed during development and contributes to confer tolerance to genotoxic stress. PLANT MOLECULAR BIOLOGY 2015; 87:303-15. [PMID: 25537647 DOI: 10.1007/s11103-014-0277-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/12/2014] [Indexed: 05/23/2023]
Abstract
Thymidine kinase catalyzes the first step in the nucleotide salvage pathway by transferring a phosphate group to a thymidine molecule. In mammals thymidine kinase supplies deoxyribonucleotides for DNA replication and DNA repair, and the expression of the gene is tightly regulated during the cell cycle. Although this gene is phylogenetically conserved in many taxa, its physiological function in plants remains unknown. The genome of the model plant Arabidopsis thaliana has two thymidine kinase genes (AtTK1a and AtTK1b) and microarray data suggest they might have redundant roles. In this study we analyzed the TK1a function by evaluating its expression pattern during development and in response to genotoxic stress. We also studied its role in DNA repair by the characterization of a mutant that contained the T-DNA insertion in the promoter region of the TK1a gene. We found that TK1a is expressed in most tissues during plant development and it was differentially induced by ultraviolet-C radiation because TK1b expression was unaffected. In the mutant, the T-DNA insertion caused a 40 % rise in transcript levels and enzyme activity in Arabidopsis seedlings compared to wild-type plants. This elevation was enough to confer tolerance to ultraviolet-C irradiation in dark conditions, as determined by root growth, and meristem length and structure. TK1a overexpression also provided tolerance to genotoxins that induce double-strand break. Our results suggest that thymidine kinase contributes to several DNA repair pathways by providing deoxythymidine triphosphate that serve as precursors for DNA repair and to balance deoxyribonucleotides pools.
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MESH Headings
- Arabidopsis/enzymology
- Arabidopsis/genetics
- Arabidopsis/radiation effects
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Base Sequence
- DNA Damage
- DNA, Bacterial/genetics
- DNA, Plant/genetics
- Gene Expression Regulation, Developmental/radiation effects
- Gene Expression Regulation, Enzymologic/radiation effects
- Gene Expression Regulation, Plant/radiation effects
- Genes, Plant/radiation effects
- Molecular Sequence Data
- Mutagenesis, Insertional
- Plants, Genetically Modified/enzymology
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/radiation effects
- Promoter Regions, Genetic
- Seedlings/enzymology
- Seedlings/genetics
- Seedlings/radiation effects
- Thymidine Kinase/genetics
- Thymidine Kinase/metabolism
- Ultraviolet Rays/adverse effects
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Affiliation(s)
- José Antonio Pedroza-García
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, 04510, México, D.F., México
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9
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Zhao H, Li X, Ma L. Basic helix-loop-helix transcription factors and epidermal cell fate determination in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2012; 7:1556-60. [PMID: 23073001 PMCID: PMC3578892 DOI: 10.4161/psb.22404] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Cell fate determination is an important process in multicellular organisms. Plant epidermis is a readily-accessible, well-used model for the study of cell fate determination. Our knowledge of cell fate determination is growing steadily due to genetic and molecular analyses of root hairs, trichomes, and stomata, which are derived from the epidermal cells of roots and aerial tissues. Studies have shown that a large number of factors are involved in the establishment of these cell types, especially members of the basic helix-loop-helix (bHLH) superfamily, which is an important family of transcription factors. In this mini-review, we focus on the role of bHLH transcription factors in cell fate determination in Arabidopsis.
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Affiliation(s)
- Hongtao Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering; Center of Agricultural Resources; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Shijiazhuang, P.R. China
| | - Xia Li
- State Key Laboratory of Plant Cell and Chromosome Engineering; Center of Agricultural Resources; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Shijiazhuang, P.R. China
| | - Ligeng Ma
- College of Life Sciences; Capital Normal University; Beijing, P.R. China
- Correspondence to: Ligeng Ma,
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10
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Carretero-Paulet L, Galstyan A, Roig-Villanova I, Martínez-García JF, Bilbao-Castro JR, Robertson DL. Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae. PLANT PHYSIOLOGY 2010; 153:1398-412. [PMID: 20472752 PMCID: PMC2899937 DOI: 10.1104/pp.110.153593] [Citation(s) in RCA: 375] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 05/13/2010] [Indexed: 05/18/2023]
Abstract
Basic helix-loop-helix proteins (bHLHs) are found throughout the three eukaryotic kingdoms and constitute one of the largest families of transcription factors. A growing number of bHLH proteins have been functionally characterized in plants. However, some of these have not been previously classified. We present here an updated and comprehensive classification of the bHLHs encoded by the whole sequenced genomes of Arabidopsis (Arabidopsis thaliana), Populus trichocarpa, Oryza sativa, Physcomitrella patens, and five algae species. We define a plant bHLH consensus motif, which allowed the identification of novel highly diverged atypical bHLHs. Using yeast two-hybrid assays, we confirm that (1) a highly diverged bHLH has retained protein interaction activity and (2) the two most conserved positions in the consensus play an essential role in dimerization. Phylogenetic analysis permitted classification of the 638 bHLH genes identified into 32 subfamilies. Evolutionary and functional relationships within subfamilies are supported by intron patterns, predicted DNA-binding motifs, and the architecture of conserved protein motifs. Our analyses reveal the origin and evolutionary diversification of plant bHLHs through differential expansions, domain shuffling, and extensive sequence divergence. At the functional level, this would translate into different subfamilies evolving specific DNA-binding and protein interaction activities as well as differential transcriptional regulatory roles. Our results suggest a role for bHLH proteins in generating plant phenotypic diversity and provide a solid framework for further investigations into the role carried out in the transcriptional regulation of key growth and developmental processes.
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11
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Abstract
The phytochrome-interacting factor PIF3 has been proposed to act as a positive regulator of chloroplast development. Here, we show that the pif3 mutant has a phenotype that is similar to the pif1 mutant, lacking the repressor of chloroplast development PIF1, and that a pif1pif3 double mutant has an additive phenotype in all respects. The pif mutants showed elevated protochlorophyllide levels in the dark, and etioplasts of pif mutants contained smaller prolamellar bodies and more prothylakoid membranes than corresponding wild-type seedlings, similar to previous reports of constitutive photomorphogenic mutants. Consistent with this observation, pif1, pif3, and pif1pif3 showed reduced hypocotyl elongation and increased cotyledon opening in the dark. Transfer of 4-d-old dark-grown seedlings to white light resulted in more chlorophyll synthesis in pif mutants over the first 2 h, and analysis of gene expression in dark-grown pif mutants indicated that key tetrapyrrole regulatory genes such as HEMA1 encoding the rate-limiting step in tetrapyrrole synthesis were already elevated 2 d after germination. Circadian regulation of HEMA1 in the dark also showed reduced amplitude and a shorter, variable period in the pif mutants, whereas expression of the core clock components TOC1, CCA1, and LHY was largely unaffected. Expression of both PIF1 and PIF3 was circadian regulated in dark-grown seedlings. PIF1 and PIF3 are proposed to be negative regulators that function to integrate light and circadian control in the regulation of chloroplast development.
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12
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Paul LK, Khurana JP. Phytochrome-mediated light signaling in plants: emerging trends. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2008; 14:9-22. [PMID: 23572870 PMCID: PMC3550659 DOI: 10.1007/s12298-008-0002-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Phytochromes maximally absorb in the red and far-red region of the solar spectrum and play a key role in regulating plant growth and development. Our understanding of the phytochrome-mediated light perception and signal transduction has improved dramatically during the past decade. However, some recent findings challenge a few of the well-accepted earlier models regarding phytochrome structure and function. Identification of a serine/threonine specific protein phosphatase 2A (FyPP) and a type 5 protein phosphatases (PAPP5), and the phytochrome-mediated phosphorylation of phytochrome interacting factor 3 (PIF3), auxin inducible genes (Aux/IAA) and cryptochromes have opened new vistas in phytochrome biology. Importantly, the significance of proteolysis and chromatin-remodeling pathways in phytochrome signaling is becoming more apparent. The emerging concept of phytochrome as a master regulator in orchestrating downstream signaling components has become more convincing with the advent of global expression profiling of genes. Upcoming data also provide fresh insights into the nuclear localization, speckle formation, nucleo-cytoplasmic partitioning and organ-specificity aspects of phytochromes. This article highlights recent advances in phytochrome biology with emphasis on the elucidation of novel components of light signal transduction.
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Affiliation(s)
- Laju K. Paul
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021 India
| | - Jitendra P. Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021 India
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13
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Abstract
The threat to plant survival presented by light limitation has driven the evolution of highly plastic adaptive strategies to either tolerate or avoid shading by neighbouring vegetation. When subject to vegetational shading, plants are exposed to a variety of informational signals, which include altered light quality and a reduction in light quantity. The former includes a decrease in the ratio of red to far-red wavelengths (low R : FR) and is detected by the phytochrome family of plant photoreceptors. Monitoring of R : FR ratio can provide an early and unambiguous warning of the presence of competing vegetation, thereby evoking escape responses before plants are actually shaded. The molecular mechanisms underlying physiological responses to alterations in light quality have now started to emerge, with major roles suggested for the PIF (PHYTOCHROME INTERACTING FACTOR) and DELLA families of transcriptional regulators. Such studies suggest a complex interplay between endogenous and exogenous signals, mediated by multiple photoreceptors. The phenotypic similarities between physiological responses habitually referred to as 'the shade avoidance syndrome' and other abiotic stress responses suggest plants may integrate common signalling mechanisms to respond to multiple perturbations in their natural environment.
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Affiliation(s)
- Keara A Franklin
- Department of Biology, University of Leicester, Leicester LE2 7RH, UK
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14
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15
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Phee BK, Shin DH, Cho JH, Kim SH, Kim JI, Lee YH, Jeon JS, Bhoo SH, Hahn TR. Identification of phytochrome-interacting protein candidates in Arabidopsis thaliana by co-immunoprecipitation coupled with MALDI-TOF MS. Proteomics 2006; 6:3671-80. [PMID: 16705748 DOI: 10.1002/pmic.200500222] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Phytochrome-interacting proteins have been extensively studied to elucidate light-signaling pathway in plants. However, most of these proteins have been identified by yeast two-hybrid screening using the C-terminal domain of phytochromes. We used co-immunoprecipitation followed by proteomic analysis in plant cell extracts in an attempt to screen for proteins interacting either directly or indirectly with native holophytochromes including the N-terminal domain as well as C-terminal domain. A total of 16 protein candidates were identified, and were selected from 2-DE experiments. Using MALDI-TOF MS analysis, 7 of these candidates were predicted to be putative phytochrome A-interacting proteins and the remaining ones to be phytochrome B-interacting proteins. Among these putative interacting proteins, protein phosphatase type 2C (PP2C) and a 66-kDa protein were strong candidates as novel phytochrome-interacting proteins, as knockout mutants for the genes encoding these two proteins had impaired light-signaling functions. A transgenic knockout Arabidopsis study showed that a 66-kDa protein candidate regulates hypocotyl elongation in a light-specific manner, and altered cotyledon development under white light during early developmental stages. The PP2C knockout plants also displayed light-specific changes in hypocotyl elongation. These results suggest that co-immunoprecipitation, followed by proteomic analysis, is a useful method for identifying novel interacting proteins and determining real protein-protein interactions in the cell.
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Affiliation(s)
- Bong-Kwan Phee
- Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Suwon, Korea
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16
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Molas ML, Kiss JZ, Correll MJ. Gene profiling of the red light signalling pathways in roots. JOURNAL OF EXPERIMENTAL BOTANY 2006; 57:3217-29. [PMID: 16908503 DOI: 10.1093/jxb/erl086] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Red light, acting through the phytochromes, controls numerous aspects of plant development. Many of the signal transduction elements downstream of the phytochromes have been identified in the aerial portions of the plant; however, very few elements in red-light signalling have been identified specifically for roots. Gene profiling studies using microarrays and quantitative Real-Time PCR were performed to characterize gene expression changes in roots of Arabidopsis seedlings exposed to 1 h of red light. Several factors acting downstream of phytochromes in red-light signalling in roots were identified. Some of the genes found to be differentially expressed in this study have already been characterized in the red-light-signalling pathway for whole plants. For example, PHYTOCHROME KINASE 1 (PKS1), LONG HYPOCOTYL 5 (HY5), EARLY FLOWERING 4 (ELF4), and GIGANTEA (GI) were all significantly up-regulated in roots of seedlings exposed to 1 h of red light. The up-regulation of SUPPRESSOR OF PHYTOCHROME A RESPONSES 1 (SPA1) and CONSTITUTIVE PHOTOMORPHOGENIC 1-like (COP1-like) genes suggests that the PHYA-mediated pathway was attenuated by red light. In addition, genes involved in lateral root and root hair formation, root plastid development, phenylpropanoid metabolism, and hormone signalling were also regulated by exposure to red light. Interestingly, members of the RPT2/NPH3 (ROOT PHOTOTROPIC 2/NON PHOTOTROPIC HYPOCOTYL 3) family, which have been shown to mediate blue-light-induced phototropism, were also differentially regulated in roots in red light. Therefore, these results suggest that red and blue light pathways interact in roots of seedlings and that many elements involved in red-light-signalling found in the aerial portions of the plant are differentially expressed in roots within 1 h of red light exposure.
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Affiliation(s)
- Maria Lia Molas
- Department of Botany, Miami University, Oxford, OH 45056, USA
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17
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Viczián A, Kircher S, Fejes E, Millar AJ, Schäfer E, Kozma-Bognár L, Nagy F. Functional characterization of phytochrome interacting factor 3 for the Arabidopsis thaliana circadian clockwork. PLANT & CELL PHYSIOLOGY 2005; 46:1591-602. [PMID: 16055924 DOI: 10.1093/pcp/pci175] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Light, in a quality- and quantity-dependent fashion, induces nuclear import of the plant photoreceptors phytochromes and promotes interaction of these receptors with transcription factors including PHYTOCHROME INTERACTING FACTOR 3 (PIF3). PIF3 was shown to form in vitro a ternary complex with the G-box element of the promoters of LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and the Pfr conformer of phytochromes. CCA1 and LHY together with TIMING OF CAB EXPRESSION 1 (TOC1) constitute a transcriptional feed-back loop that is essential for a functional circadian clock in Arabidopsis. These findings led to the hypothesis that the PIF3-containing ternary complex regulates transcription of light-responsive genes and is involved in phototransduction to the central circadian clockwork. Here we report that (i) overexpression or lack of biologically functional PIF3 does not affect period length of rhythmic gene expression or red-light-induced resetting of the circadian clock and (ii) the transcription of PIF3 displays a low-amplitude circadian rhythm. We demonstrated previously that irradiation of etiolated seedlings induces rapid, phytochrome-controlled degradation of PIF3. Here we show that nuclear-localized PIF3 accumulates to relatively high levels by the end of the light phase in seedlings grown under diurnal conditions. Taken together, we show that (i) PIF3 does not play a significant role in controlling light input to and function of the circadian clockwork and (ii) a yet unknown mechanism limits phytochrome-induced degradation of PIF3 at the end of the day under diurnal conditions.
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Affiliation(s)
- András Viczián
- Plant Biology Institute, Biological Research Center, Szeged, Hungary
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18
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Kang X, Chong J, Ni M. HYPERSENSITIVE TO RED AND BLUE 1, a ZZ-type zinc finger protein, regulates phytochrome B-mediated red and cryptochrome-mediated blue light responses. THE PLANT CELL 2005; 17:822-35. [PMID: 15705950 PMCID: PMC1069701 DOI: 10.1105/tpc.104.029165] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2004] [Accepted: 12/15/2004] [Indexed: 05/19/2023]
Abstract
Plant photoreceptors that regulate photomorphogenic development include red/far-red-light-absorbing phytochromes and blue/UV-A-light-absorbing cryptochromes. We have undertaken a genetic screen to identify additional components downstream of the photoreceptors in Arabidopsis thaliana. We identified a short hypocotyl mutant under red and blue light, hypersensitive to red and blue 1 (hrb1). Mutation in HRB1 also enhances the end-of-day far-red light response, inhibits leaf expansion and petiole elongation, and attenuates the expression of CAB3 and CHS. Double mutant analysis indicates that phyB is epistatic to hrb1 under red light, and cry1 cry2 is epistatic to hrb1 under blue light for both hypocotyl growth and light-regulated gene expression responses. HRB1 localizes to the nucleus and belongs to a protein family of Drought induced 19 (Di19). HRB1 and all other family members contain a ZZ-type zinc finger domain, which in other organisms is implicated in protein-protein interactions between dystrophin and calmodulin and between transcriptional adaptors and activators. HRB1 activity is also required for red and blue light-induced expression of PHYTOCHROME INTERACTING FACTOR 4 (PIF4). pif4 shows a very similar hypersensitive response as hrb1 to both red light and blue light and is epistatic to hrb1 in control of light-regulated gene expression responses. Thus, the roles of HRB1 and PIF4 together in regulating both red and blue light responses may represent points where red light signaling and blue light signaling intersect.
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Affiliation(s)
- Xiaojun Kang
- Department of Plant Biology, University of Minesota, St. Paul, Minesota 55108, USA
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19
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Bertrand C, Benhamed M, Li YF, Ayadi M, Lemonnier G, Renou JP, Delarue M, Zhou DX. Arabidopsis HAF2 Gene Encoding TATA-binding Protein (TBP)-associated Factor TAF1, Is Required to Integrate Light Signals to Regulate Gene Expression and Growth. J Biol Chem 2005; 280:1465-73. [PMID: 15525647 DOI: 10.1074/jbc.m409000200] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Plant growth and development are sensitive to light. Light-responsive DNA-binding transcription factors have been functionally identified. However, how transcription initiation complex integrates light signals from enhancer-bound transcription factors remains unknown. In this work, we characterized mutations within the Arabidopsis HAF2 gene encoding TATA-binding protein-associated factor TAF1 (or TAF(II)250). The mutation of HAF2 induced decreases on chlorophyll accumulation, light-induced mRNA levels, and promoter activity. Genetic analysis indicated that HAF2 is involved in the pathways of both red/far-red and blue light signals. Double mutants between haf2-1 and hy5-1, a mutation of a light signaling positive DNA-binding transcription factor gene, had a synergistic effect on photomorphogenic traits and light-activated gene expression under different light wavelengths, suggesting that HAF2 is required for interaction with additional light-responsive DNA-binding transcription factors to fully respond to light induction. Chromatin immunoprecipitation assays showed that the mutation of HAF2 reduced acetylation of histone H3 in light-responsive promoters. In addition, transcriptome analysis showed that the mutation altered the expression of about 9% of genes in young leaves. These data indicate that TAF1 encoded by the Arabidopsis HAF2 gene functions as a coactivator capable of integrating light signals and acetylating histones to activate light-induced gene transcription.
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Affiliation(s)
- Claire Bertrand
- Institut de Biotechnologie des Plantes, UMR8618, Université Paris-sud XI, 91405 Orsay, France
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20
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Tsygankova VA, Galkina LA, Musatenko LI, Sytnik KM. Genetical and epigenetical control of plant growth and development. Genes of photomorphogenesis and regulation of their expression by light. ACTA ACUST UNITED AC 2004. [DOI: 10.7124/bc.0006cb] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- V. A. Tsygankova
- V. Ye. Lashkaryov Institute of Semiconductor Physics, National Academy of Sciences of Ukraine
| | - L. A. Galkina
- V. Ye. Lashkaryov Institute of Semiconductor Physics, National Academy of Sciences of Ukraine
| | - L. I. Musatenko
- V. Ye. Lashkaryov Institute of Semiconductor Physics, National Academy of Sciences of Ukraine
| | - K. M. Sytnik
- M. G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine
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21
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Monte E, Tepperman JM, Al-Sady B, Kaczorowski KA, Alonso JM, Ecker JR, Li X, Zhang Y, Quail PH. The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development. Proc Natl Acad Sci U S A 2004; 101:16091-8. [PMID: 15505214 PMCID: PMC528976 DOI: 10.1073/pnas.0407107101] [Citation(s) in RCA: 224] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The phytochrome (phy) family of sensory photoreceptors transduce informational light signals to selected nuclear genes, inducing plant growth and developmental responses appropriate to the environment. Existing data suggest that one signaling pathway by which this occurs involves direct, intranuclear interaction of the photoactivated phy molecule with PIF3, a basic helix-loop-helix transcription factor. Here, we provide evidence from recently identified pif3 mutant alleles that PIF3 is necessary for early chloroplast greening and rapid phy-induced expression of nuclear genes encoding chloroplast components upon first exposure of seedlings to light. Therefore, these data indicate that PIF3 functions to transduce phy signals to genes involved in a critical facet of the early seedling deetiolation process, the generation of a functional photosynthetic apparatus. When transgenically expressed GUS:PIF3 fusion protein constructs were used, we found that PIF3 protein levels are rapidly and reversibly modulated by the photoreceptor over diurnal cycles in Arabidopsis seedlings. The PIF3 protein declines rapidly to a basal steady-state level upon initial light exposure, but reaccumulates to preirradiation levels in darkness during the subsequent night period. These data suggest that PIF3 may function in early phy signaling at the dark-to-light transition, not only during initial seedling deetiolation, but daily at dawn under diurnal light-dark cycles.
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Affiliation(s)
- Elena Monte
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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22
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Huq E, Al-Sady B, Hudson M, Kim C, Apel K, Quail PH. Phytochrome-interacting factor 1 is a critical bHLH regulator of chlorophyll biosynthesis. Science 2004; 305:1937-41. [PMID: 15448264 DOI: 10.1126/science.1099728] [Citation(s) in RCA: 303] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Photosynthetic organisms must achieve a delicate balance between the light energy absorbed by chlorophyll and their capacity to channel that energy into productive photochemical reactions. Release of excess absorbed energy in the cell can cause lethal photooxidative damage. We identified a basic helix-loop-helix (bHLH) transcription factor, designated PHYTOCHROME-INTERACTING FACTOR 1 (PIF1), that negatively regulates chlorophyll biosynthesis. pif1 mutant seedlings accumulate excess free protochlorophyllide when grown in the dark, with consequent lethal bleaching upon exposure to light. PIF1 interacts specifically with the photoactivated conformer of phytochromes A and B, suggesting a signaling pathway by which chlorophyll biosynthetic rates are tightly controlled during the critical initial emergence of seedlings from subterranean darkness into sunlight.
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Affiliation(s)
- Enamul Huq
- Section of Molecular Cell and Developmental Biology and Institute of Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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23
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Affiliation(s)
- Haiyang Wang
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
| | - Xing Wang Deng
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8104, USA
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24
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Bauer D, Viczián A, Kircher S, Nobis T, Nitschke R, Kunkel T, Panigrahi KCS, Adám E, Fejes E, Schäfer E, Nagy F. Constitutive photomorphogenesis 1 and multiple photoreceptors control degradation of phytochrome interacting factor 3, a transcription factor required for light signaling in Arabidopsis. THE PLANT CELL 2004; 16:1433-45. [PMID: 15155879 PMCID: PMC490037 DOI: 10.1105/tpc.021568] [Citation(s) in RCA: 336] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2004] [Accepted: 03/09/2004] [Indexed: 05/18/2023]
Abstract
Light, in a quality- and quantity-dependent fashion, induces nuclear import of the plant photoreceptors phytochrome, promotes interaction of phytochrome A (phyA) and phyB with transcription factors including phytochrome interacting factor 3 (PIF3), and is thought to trigger a transcriptional cascade to regulate the expression of approximately 2500 genes in Arabidopsis thaliana. Here, we show that controlled degradation of the transcription factor PIF3 is a major regulatory step in light signaling. We demonstrate that accumulation of PIF3 in the nucleus in dark requires constitutive photomorphogenesis 1 (COP1), a negative regulator of photomorphogenesis, and show that red (R) and far-red light (FR) induce rapid degradation of the PIF3 protein. This process is controlled by the concerted action of the R/FR absorbing phyA, phyB, and phyD photoreceptors, and it is not affected by COP1. Rapid light-induced degradation of PIF3 indicates that interaction of PIF3 with these phytochrome species is transient. In addition, we provide evidence that the poc1 mutant, a postulated PIF3 overexpressor that displays hypersensitivity to R but not to FR, lacks detectable amounts of the PIF3 protein. Thus, we propose that PIF3 acts transiently, and its major function is to mediate phytochrome-induced signaling during the developmental switch from skotomorphogenesis to photomorphogenesis and/or dark to light transitions.
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Affiliation(s)
- Diana Bauer
- Biologie II/Institut für Botanik, University of Freiburg, Freiburg, Germany D-79104
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25
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Hall A, Bastow RM, Davis SJ, Hanano S, McWatters HG, Hibberd V, Doyle MR, Sung S, Halliday KJ, Amasino RM, Millar AJ. The TIME FOR COFFEE gene maintains the amplitude and timing of Arabidopsis circadian clocks. THE PLANT CELL 2003; 15:2719-29. [PMID: 14555691 PMCID: PMC280574 DOI: 10.1105/tpc.013730] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2003] [Accepted: 09/03/2003] [Indexed: 05/18/2023]
Abstract
Plants synchronize developmental and metabolic processes with the earth's 24-h rotation through the integration of circadian rhythms and responses to light. We characterize the time for coffee (tic) mutant that disrupts circadian gating, photoperiodism, and multiple circadian rhythms, with differential effects among rhythms. TIC is distinct in physiological functions and genetic map position from other rhythm mutants and their homologous loci. Detailed rhythm analysis shows that the chlorophyll a/b-binding protein gene expression rhythm requires TIC function in the mid to late subjective night, when human activity may require coffee, in contrast to the function of EARLY-FLOWERING3 (ELF3) in the late day to early night. tic mutants misexpress genes that are thought to be critical for circadian timing, consistent with our functional analysis. Thus, we identify TIC as a regulator of the clock gene circuit. In contrast to tic and elf3 single mutants, tic elf3 double mutants are completely arrhythmic. Even the robust circadian clock of plants cannot function with defects at two different phases.
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Affiliation(s)
- Anthony Hall
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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26
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Albrecht V, Weinl S, Blazevic D, D'Angelo C, Batistic O, Kolukisaoglu U, Bock R, Schulz B, Harter K, Kudla J. The calcium sensor CBL1 integrates plant responses to abiotic stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 36:457-70. [PMID: 14617077 DOI: 10.1046/j.1365-313x.2003.01892.x] [Citation(s) in RCA: 163] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Calcium ions represent both an integrative signal and an important convergence point of many disparate signaling pathways. Calcium-binding proteins, like calcineurin B-like (CBL) proteins, have been implicated as important relays in calcium signaling. Here, we report the in vivo study of CBL1 function in Arabidopsis. Analyses of loss-of-function as well as CBL1-overexpressing lines indicate a crucial function of this calcium sensor protein in abiotic stress responses. Mutation of CBL1 impairs plant responses to drought and salt stresses and affects gene expression of cold-regulated genes, but does not affect abscisic acid (ABA) responsiveness. Conversely, overexpression of CBL1 reduces transpirational water loss and induces the expression of early stress-responsive transcription factors and stress adaptation genes in non-stressed plants. Together, our data indicate that the calcium sensor protein CBL1 may constitute an integrative node in plant responses to abiotic stimuli and contributes to the regulation of early stress-related transcription factors of the C-Repeat-Binding Factor/dehydration-responsive element (CBF/DREB) type.
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Affiliation(s)
- Verónica Albrecht
- Molekulare Botanik, Universität Ulm, Albert-Einstein-Allee 11, 89069 Ulm, Germany
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27
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Kim J, Yi H, Choi G, Shin B, Song PS, Choi G. Functional characterization of phytochrome interacting factor 3 in phytochrome-mediated light signal transduction. THE PLANT CELL 2003; 15:2399-407. [PMID: 14508006 PMCID: PMC197304 DOI: 10.1105/tpc.014498] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2003] [Accepted: 08/15/2003] [Indexed: 05/17/2023]
Abstract
Phytochromes regulate various light responses through their interactions with different signaling proteins, such as phytochrome interacting factor 3 (PIF3). However, the physiological functions of PIF3 in light signaling are not yet fully understood. To increase our understanding of these roles, we characterized a T-DNA insertional pif3 mutant and transgenic plants overexpressing the full-length PIF3. Transgenic overexpressing lines displayed longer hypocotyls and smaller cotyledons under red light and reduced cotyledon opening under both red and far-red light, whereas the pif3 mutant showed the opposite phenotypes. The accumulation of anthocyanin and chlorophyll further indicated complicated features of PIF3 function. The accumulation of anthocyanin was increased and the content of chlorophyll was decreased in the overexpression lines. Our data indicate that PIF3 plays complex roles depending on the type of light response and the light conditions.
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Affiliation(s)
- Jonghyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
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28
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Duek PD, Fankhauser C. HFR1, a putative bHLH transcription factor, mediates both phytochrome A and cryptochrome signalling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 34:827-36. [PMID: 12795702 DOI: 10.1046/j.1365-313x.2003.01770.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plants are very sensitive to their light environment. They use cryptochromes and phytochromes to scan the light spectrum. Those two families of photoreceptors mediate a number of similar physiological responses. The putative bHLH (basic Helix Loop Helix) transcription factor long hypocotyl in far-red (HFR1) is important for a subset of phytochrome A (phyA)-mediated light responses. Interestingly, hfr1 alleles also have reduced de-etiolation responses, including hypocotyl growth, cotyledon opening and anthocyanin accumulation, when grown in blue light. This phenotype is particularly apparent under high fluence rates. The analysis of double mutants between hfr1 and different blue light photoreceptor mutants demonstrates that, in addition to its role in phyA signalling, HFR1 is a component of cryptochrome 1 (cry1)-mediated light signalling. Moreover, HFR1 mRNA levels are high both in blue and in far-red light but low in red light. These results identify HFR1 as a positively acting component of cry1 signalling and indicate that HFR1 integrates light signals from both phyA and cry1.
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Affiliation(s)
- Paula D Duek
- Department of Molecular Biology, 30 quai E Ansermet, 1211 Genève 4, Switzerland
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29
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Casal JJ, Luccioni LG, Oliverio KA, Boccalandro HE. Light, phytochrome signalling and photomorphogenesis in Arabidopsis. Photochem Photobiol Sci 2003; 2:625-36. [PMID: 12859146 DOI: 10.1039/b300094j] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The phytochromes is a family of plant photoreceptors that control growth and development in response to environmental cues. Red and far-red light are the most efficient wavebands to induce conformational changes of phytochromes and consequently modify their kinetics, nuclear/cytoplasmic partitioning, ability to phosphorylate substrates, and physical interaction with proteins that bind DNA. Many players in phytochrome signalling have been identified and a complex, highly regulated network is envisaged. Here we describe the connection between different features of the phytochrome signalling network and the versatile relationship between light signals and physiological outputs shown by phytochromes.
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Affiliation(s)
- Jorge J Casal
- IFEVA, Faculty of Agronomy, University of Buenos Aires and National Research Council, Av. San Martín 4453, 1417 Buenos Aires, Argentina.
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30
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Park DH, Lim PO, Kim JS, Cho DS, Hong SH, Nam HG. The Arabidopsis COG1 gene encodes a Dof domain transcription factor and negatively regulates phytochrome signaling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 34:161-71. [PMID: 12694592 DOI: 10.1046/j.1365-313x.2003.01710.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Light is a critical environmental factor that influences almost all developmental aspects of plants, including seed germination, seedling morphogenesis, and transition to reproductive growth. Plants have therefore developed an intricate network of mechanisms to perceive and process environmental light information. To further characterize the molecular basis of light-signaling processes in plants, we screened an activation tagging pool of Arabidopsis for altered photoresponses. A dominant mutation, cog1-D, attenuated various red (R) and far-red (FR) light-dependent photoresponses. The mutation was caused by overexpression of a gene encoding a member of the Dof family of transcription factors. The photoresponses in Arabidopsis were inversely correlated with the expression levels of COG1 mRNA. When the COG1 gene was overexpressed in transgenic plants, the plants exhibited hyposensitive responses to R and FR light in a manner inversely dependent on COG1 mRNA levels. On the other hand, transgenic lines expressing antisense COG1 were hypersensitive to R and FR light. Expression of the COG1 gene is light inducible and requires phytochrome A (phyA) for FR light-induced expression and phytochrome B (phyB) for R light-induced expression. Thus, the COG1 gene functions as a negative regulator in both the phyA- and phyB-signaling pathways. We suggest that these phytochromes positively regulate the expression of COG1, a negative regulator, as a mechanism for fine tuning the light-signaling pathway.
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Affiliation(s)
- Don Ha Park
- Division of Molecular Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea
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31
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Kim JI, Kozhukh GV, Song PS. Phytochrome-mediated signal transduction pathways in plants. Biochem Biophys Res Commun 2002; 298:457-63. [PMID: 12408973 DOI: 10.1016/s0006-291x(02)02494-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Phytochromes are photoreceptors that regulate plant growth and development in response to the solar radiation environment. Recent studies reveal how phytochrome-mediated light signals can be transduced to the cells for their responses. The possible signal transduction pathways of phytochromes include: (a) direct regulation of gene transcription and (b) typical kinase-involved signaling pathways and its regulation by phosphorylation, dephosphorylation, and proteolytic degradation. This review highlights some of the recent findings.
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Affiliation(s)
- Jeong-Il Kim
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
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32
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Sato E, Nakamichi N, Yamashino T, Mizuno T. Aberrant expression of the Arabidopsis circadian-regulated APRR5 gene belonging to the APRR1/TOC1 quintet results in early flowering and hypersensitiveness to light in early photomorphogenesis. PLANT & CELL PHYSIOLOGY 2002; 43:1374-85. [PMID: 12461138 DOI: 10.1093/pcp/pcf166] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In Arabidopsis thaliana, the transcripts of the APRR1/TOC1 family genes each start accumulating after dawn rhythmically and one after another at intervals in the order of APRR9-->APRR7-->APRR5-->APRR3-->APRR1/TOC1 under continuous light. Except for the well-characterized APRR1/TOC1, however, no evidence has been provided that other APRR1/TOC1 family genes are indeed implicated in the mechanisms underlying circadian rhythms. We here attempted to provide such evidence by characterizing transgenic plants that constitutively express the APRR5 gene. The resulting APRR5-overexpressing (APRR5-ox) plants showed intriguing properties with regard to not only circadian rhythms, but also control of flowering time and light response. First, the aberrant expression of APRR5 in such transgenic plants resulted in a characteristic phenotype with regard to transcriptional events, in which free-running rhythms were considerably altered for certain circadian-regulated genes, including CCA1, LHY, APRR1/TOC1, other APRR1/TOC1 members, GI and CAB2, although each rhythm was clearly sustained even after plants were transferred to continuous light. With regard to biological events, APRR5-ox plants flowered much earlier than wild-type plants, more or less, in a manner independent of photoperiodicity (or under short-day conditions). Furthermore, APRR5-ox plants showed an SRL (short-hypocotyls under red light) phenotype that is indicative of hypersensitiveness to red light in early photomorphogenesis. Both APRR1-ox and APRR9-ox plants also showed the same phenotype. Therefore, APRR5 (together with APRR1/TOC1 and APRR9) must be taken into consideration for a better understanding of the molecular links between circadian rhythms, control of flowering time through the photoperiodic long-day pathway, and also light signaling-controlled plant development.
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Affiliation(s)
- Eriko Sato
- Laboratory of Molecular Microbiology, School of Agriculture, Nagoya University, Chikusa-ku, Nagoya, 464-8601 Japan
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33
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McCormac AC, Terry MJ. Light-signalling pathways leading to the co-ordinated expression of HEMA1 and Lhcb during chloroplast development in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 32:549-59. [PMID: 12445126 DOI: 10.1046/j.1365-313x.2002.01443.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
During de-etiolation, the co-ordinated synthesis of chlorophyll and the chlorophyll a/b-binding proteins is critical to the development of functional light-harvesting complexes. To understand how this co-ordination is achieved, we have made a detailed study of the light-regulated signalling pathways mediating the expression of the HEMA1 and Lhcb genes encoding glutamyl-tRNA reductase, the first committed enzyme of 5-aminolaevulinic acid formation, and chlorophyll a/b-binding proteins, respectively. To do this, we have screened 7 photoreceptor and 12 light-signalling mutants of Arabidopsis thaliana L. for induction of HEMA1 and Lhcb expression in continuous red, far-red and blue light and following a red pulse. We have categorised these mutants into two groups. The phyA, phyB, phyAphyB, cry1, cry2, cop1, det1, poc1, eid1, and far1 mutations lead to diverse effects on the light regulation of HEMA1, but affect Lhcb expression to a similar degree. The hy1, hy2, hy5, fin219, fhy1, fhy3, spa1, ndpk2, and pat1 mutants also affect light regulation of both HEMA1 and Lhcb expression, but with differences in the relative magnitude of the two responses. The fhy1 and fhy3 mutants show the most significant differences in light regulation between the two genes, with both showing a strong inhibition of HEMA1 expression under continuous red light. These results demonstrate that co-ordinated regulation of HEMA1 and Lhcb is largely achieved through parallel light regulation mediated by shared phytochrome- and cryptochrome-signalling pathways. However, glutamyl-tRNA reductase is also required for the synthesis of other tetrapyrroles and this dual role may account for the observed differences in these light-signalling pathways.
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Affiliation(s)
- Alex C McCormac
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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34
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Raina S, Mahalingam R, Chen F, Fedoroff N. A collection of sequenced and mapped Ds transposon insertion sites in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2002; 50:93-110. [PMID: 12139012 DOI: 10.1023/a:1016099215667] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Insertional mutagenesis is a powerful tool for generating knockout mutations that facilitate associating biological functions with as yet uncharacterized open reading frames (ORFs) identified by genomic sequencing or represented in EST databases. We have generated a collection of Dissociation (Ds) transposon lines with insertions on all 5 Arabidopsis chromosomes. Here we report the insertion sites in 260 independent single-transposon lines, derived from four different Ds donor sites. We amplified and determined the genomic sequence flanking each transposon, then mapped its insertion site by identity of the flanking sequences to the corresponding sequence in the Arabidopsis genome database. This constitutes the largest collection of sequence-mapped Ds insertion sites unbiased by selection against the donor site. Insertion site clusters have been identified around three of the four donor sites on chromosomes 1 and 5, as well as near the nucleolus organizers on chromosomes 2 and 4. The distribution of insertions between ORFs and intergenic sequences is roughly proportional to the ratio of genic to intergenic sequence. Within ORFs, insertions cluster near the translational start codon, although we have not detected insertion site selectivity at the nucleotide sequence level. A searchable database of insertion site sequences for the 260 transposon insertion sites is available at http://sgio2.biotec.psu.edu/sr. This and other collections of Arabidopsis lines with sequence-identified transposon insertion sites are a valuable genetic resource for functional genomics studies because the transposon location is precisely known, the transposon can be remobilized to generate revertants, and the Ds insertion can be used to initiate further local mutagenesis.
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Affiliation(s)
- Surabhi Raina
- Life Sciences Consortium and Biotechnology Institute, Pennsylvania State University, University Park 16802, USA
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35
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Møller SG, Ingles PJ, Whitelam GC. The cell biology of phytochrome signalling. THE NEW PHYTOLOGIST 2002; 154:553-590. [PMID: 33873456 DOI: 10.1046/j.1469-8137.2002.00419.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Phytochrome signal transduction has in the past often been viewed as being a nonspatially separated linear chain of events. However, through a combination of molecular, genetic and cell biological approaches, it is becoming increasingly evident that phytochrome signalling constitutes a highly ordered multidimensional network of events. The discovery that some phytochromes and signalling intermediates show light-dependent nucleo-cytoplasmic partitioning has not only led to the suggestion that early signalling events take place in the nucleus, but also that subcellular localization patterns most probably represent an important signalling control point. Moreover, detailed characterization of signalling intermediates has demonstrated that various branches of the signalling network are spatially separated and take place in different cellular compartments including the nucleus, cytosol, and chloroplasts. In addition, proteasome-mediated degradation of signalling intermediates most probably act in concert with subcellular partitioning events as an integrated checkpoint. An emerging view from this is that phytochrome signalling is separated into several subcellular organelles and that these are interconnected in order to execute accurate responses to changes in the light environment. By integrating the available data, both at the cellular and subcellular level, we should be able to construct a solid foundation for further dissection of phytochrome signal transduction in plants. Contents Summary 553 I. Introduction 554 II. Nucleus vs cytoplasm 556 III. The nucleus 562 IV. The cytoplasm 571 V. Interactions with other signalling pathways 577 VI. Conclusions and the future 582 Acknowledgements 583 References 583.
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Affiliation(s)
- Simon G Møller
- Department of Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Patricia J Ingles
- Department of Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Garry C Whitelam
- Department of Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
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36
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Holm M, Ma LG, Qu LJ, Deng XW. Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis. Genes Dev 2002; 16:1247-59. [PMID: 12023303 PMCID: PMC186273 DOI: 10.1101/gad.969702] [Citation(s) in RCA: 447] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Arabidopsis COP1 acts to repress photomorphogenesis in the absence of light. It was shown that in the dark, COP1 directly interacts with the bZIP transcription factor HY5, a positive regulator of photomorphogenesis, and promotes its proteasome-mediated degradation. Here we identify a novel bZIP protein HYH, as a new target of COP1. We identify a physical and genetic interaction between HYH and COP1 and show that this interaction results in dark-specific degradation of HYH. Genetic analysis indicates that HYH is predominantly involved in blue-light regulation of development and gene expression, and that the function of HYH in part overlaps with that of HY5. The accumulation of HYH protein, not the mRNA, is dependent on the presence of HY5. Our data suggest that HYH and HY5 can, respectively, act as heterodimers and homodimers, thus mediating light-regulated expression of overlapping as well as distinct target genes. We propose that COP1 mediates light control of gene expression through targeted degradation of multiple photomorphogenesis-promoting transcription factors in the nucleus.
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Affiliation(s)
- Magnus Holm
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104, USA
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37
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Huq E, Quail PH. PIF4, a phytochrome-interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis. EMBO J 2002; 21:2441-50. [PMID: 12006496 PMCID: PMC126004 DOI: 10.1093/emboj/21.10.2441] [Citation(s) in RCA: 401] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Plants sense and respond to red and far-red light using the phytochrome (phy) family of photoreceptors. However, the mechanism of light signal transduction is not well defined. Here, we report the identification of a new mutant Arabidopsis locus, srl2 (short under red-light 2), which confers selective hypersensitivity to continuous red, but not far-red, light. This hypersensitivity is eliminated in srl2phyB, but not srl2phyA, double mutants, indicating that this locus functions selectively and negatively in phyB signaling. The SRL2 gene encodes a bHLH factor, designated PIF4 (phytochrome-interacting factor 4), which binds selectively to the biologically active Pfr form of phyB, but has little affinity for phyA. Despite its hypersensitive morphological phenotype, the srl2 mutant displays no perturbation of light-induced expression of marker genes for chloroplast development. These data suggest that PIF4 may function specifically in a branch of the phyB signaling network that regulates a subset of genes involved in cell expansion. Consistent with this proposal, PIF4 localizes to the nucleus and can bind to a G-box DNA sequence motif found in various light-regulated promoters.
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Affiliation(s)
| | - Peter H. Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 and US Department of Agriculture/Agricultural Research Service, Plant Gene Expression Center, 800 Buchanan Street, Albany, CA 94710, USA
Corresponding author e-mail:
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38
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Holm M, Ma LG, Qu LJ, Deng XW. Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis. Genes Dev 2002. [PMID: 12023303 DOI: 10.1101/gad.969702.ing] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Arabidopsis COP1 acts to repress photomorphogenesis in the absence of light. It was shown that in the dark, COP1 directly interacts with the bZIP transcription factor HY5, a positive regulator of photomorphogenesis, and promotes its proteasome-mediated degradation. Here we identify a novel bZIP protein HYH, as a new target of COP1. We identify a physical and genetic interaction between HYH and COP1 and show that this interaction results in dark-specific degradation of HYH. Genetic analysis indicates that HYH is predominantly involved in blue-light regulation of development and gene expression, and that the function of HYH in part overlaps with that of HY5. The accumulation of HYH protein, not the mRNA, is dependent on the presence of HY5. Our data suggest that HYH and HY5 can, respectively, act as heterodimers and homodimers, thus mediating light-regulated expression of overlapping as well as distinct target genes. We propose that COP1 mediates light control of gene expression through targeted degradation of multiple photomorphogenesis-promoting transcription factors in the nucleus.
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Affiliation(s)
- Magnus Holm
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104, USA
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39
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Riechmann JL. Transcriptional regulation: a genomic overview. THE ARABIDOPSIS BOOK 2002; 1:e0085. [PMID: 22303220 PMCID: PMC3243377 DOI: 10.1199/tab.0085] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The availability of the Arabidopsis thaliana genome sequence allows a comprehensive analysis of transcriptional regulation in plants using novel genomic approaches and methodologies. Such a genomic view of transcription first necessitates the compilation of lists of elements. Transcription factors are the most numerous of the different types of proteins involved in transcription in eukaryotes, and the Arabidopsis genome codes for more than 1,500 of them, or approximately 6% of its total number of genes. A genome-wide comparison of transcription factors across the three eukaryotic kingdoms reveals the evolutionary generation of diversity in the components of the regulatory machinery of transcription. However, as illustrated by Arabidopsis, transcription in plants follows similar basic principles and logic to those in animals and fungi. A global view and understanding of transcription at a cellular and organismal level requires the characterization of the Arabidopsis transcriptome and promoterome, as well as of the interactome, the localizome, and the phenome of the proteins involved in transcription.
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Affiliation(s)
- José Luis Riechmann
- Mendel Biotechnology, 21375 Cabot Blvd., Hayward, CA 94545, USA
- California Institute of Technology, Division of Biology 156-29, Pasadena, CA 91125
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40
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Abstract
Light is life for plants. To continuously assess and adapt to fluctuations in the quality and quantity of this essential commodity, plants deploy sensory photoreceptors, including the phytochromes. Having captured an incoming photon, the activated phytochrome molecule must relay this information to nuclear genes that are poised to respond by directing appropriate adjustments in growth and development. Defining the intricate intracellular signalling networks through which this sensory information is transduced is an area of intense research activity.
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Affiliation(s)
- Peter H Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.
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41
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Abstract
Phytochromes are plant photoreceptors that regulate plant growth and development with respect to the light environment. Following the initial light-perception event, the phytochromes initiate a signal-transduction process that eventually results in alterations in cellular behavior, including gene expression. Here we describe the molecular cloning and functional characterization of Arabidopsis FHY1. FHY1 encodes a product (FHY1) that specifically transduces signals downstream of the far-red (FR) light-responsive phytochrome A (PHYA) photoreceptor. We show that FHY1 is a novel light-regulated protein that accumulates in dark (D)-grown but not in FR-grown hypocotyl cells. In addition, FHY1 transcript levels are regulated by light, and by the product of FHY3, another gene implicated in FR signaling. These observations indicate that FHY1 function is both FR-signal transducing and FR-signal regulated, suggesting a negative feedback regulation of FHY1 function. Seedlings homozygous for loss-of-function fhy1 alleles are partially blind to FR, whereas seedlings overexpressing FHY1 exhibit increased responses to FR, but not to white (WL) or red (R) light. The increased FR-responses conferred by overexpression of FHY1 are abolished in a PHYA-deficient mutant background, showing that FHY1 requires a signal from PHYA for function, and cannot modulate growth independently of PHYA.
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Affiliation(s)
- T Desnos
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
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42
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Ballesteros ML, Bolle C, Lois LM, Moore JM, Vielle-Calzada JP, Grossniklaus U, Chua NH. LAF1, a MYB transcription activator for phytochrome A signaling. Genes Dev 2001; 15:2613-25. [PMID: 11581165 PMCID: PMC312796 DOI: 10.1101/gad.915001] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The photoreceptor phytochrome (phy) A has a well-defined role in regulating gene expression in response to specific light signals. Here, we describe a new Arabidopsis mutant, laf1 (long after far-red light 1) that has an elongated hypocotyl specifically under far-red light. Gene expression studies showed that laf1 has reduced responsiveness to continuous far-red light but retains wild-type responses to other light wavelengths. As far-red light is only perceived by phyA, our results suggest that LAF1 is specifically involved in phyA signal transduction. Further analyses revealed that laf1 is affected in a subset of phyA-dependent responses and the phenotype is more severe at low far-red fluence rates. LAF1 encodes a nuclear protein with strong homology with the R2R3-MYB family of DNA-binding proteins. Experiments using yeast cells identified a transactivation domain in the C-terminal portion of the protein. LAF1 is constitutively targeted to the nucleus by signals in its N-terminal portion, and the full-length protein accumulates in distinct nuclear speckles. This accumulation in speckles is abolished by a point mutation in a lysine residue (K258R), which might serve as a modification site by a small ubiquitin-like protein (SUMO).
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Affiliation(s)
- M L Ballesteros
- Laboratory of Plant Molecular Biology, The Rockefeller University, New York, NY 10021-6399, USA
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43
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Liu XL, Covington MF, Fankhauser C, Chory J, Wagner DR. ELF3 encodes a circadian clock-regulated nuclear protein that functions in an Arabidopsis PHYB signal transduction pathway. THE PLANT CELL 2001. [PMID: 11402161 DOI: 10.2307/3871296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Many aspects of plant development are regulated by photoreceptor function and the circadian clock. Loss-of-function mutations in the Arabidopsis EARLY FLOWERING 3 (ELF3) and PHYTOCHROME B (PHYB) genes cause early flowering and influence the activity of circadian clock-regulated processes. We demonstrate here that the relative abundance of the ELF3 protein, which is a novel nucleus-localized protein, displays circadian regulation that follows the pattern of circadian accumulation of ELF3 transcript. Furthermore, the ELF3 protein interacts with PHYB in the yeast two-hybrid assay and in vitro. Genetic analyses show that ELF3 requires PHYB function in early morphogenesis but not for the regulation of flowering time. This suggests that ELF3 is a component of a PHYB signaling complex that controls early events in plant development but that ELF3 and PHYB control flowering via independent signal transduction pathways.
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Affiliation(s)
- X L Liu
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
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44
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Liu XL, Covington MF, Fankhauser C, Chory J, Wagner DR. ELF3 encodes a circadian clock-regulated nuclear protein that functions in an Arabidopsis PHYB signal transduction pathway. THE PLANT CELL 2001; 13:1293-304. [PMID: 11402161 PMCID: PMC135570 DOI: 10.1105/tpc.13.6.1293] [Citation(s) in RCA: 139] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2000] [Accepted: 03/05/2001] [Indexed: 05/18/2023]
Abstract
Many aspects of plant development are regulated by photoreceptor function and the circadian clock. Loss-of-function mutations in the Arabidopsis EARLY FLOWERING 3 (ELF3) and PHYTOCHROME B (PHYB) genes cause early flowering and influence the activity of circadian clock-regulated processes. We demonstrate here that the relative abundance of the ELF3 protein, which is a novel nucleus-localized protein, displays circadian regulation that follows the pattern of circadian accumulation of ELF3 transcript. Furthermore, the ELF3 protein interacts with PHYB in the yeast two-hybrid assay and in vitro. Genetic analyses show that ELF3 requires PHYB function in early morphogenesis but not for the regulation of flowering time. This suggests that ELF3 is a component of a PHYB signaling complex that controls early events in plant development but that ELF3 and PHYB control flowering via independent signal transduction pathways.
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Affiliation(s)
- X L Liu
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
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45
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Abstract
The phytochrome family of sensory photoreceptors transduces environmental light signals to responsive nuclear genes by poorly defined pathways. The recent application of yeast two-hybrid library screens to the identification of components that physically interact with members of the phytochrome family has dramatically altered previous views of the likely intracellular signaling pathways. The evidence indicates that one pathway involves light-triggered translocation of the photoreceptor molecule from cytoplasm to nucleus where it binds specifically in its biologically active form to a promoter-bound basic helix-loop-helix protein. The phytochrome molecules are proposed to function as integral, light-switchable components of transcriptional regulator complexes targeting environmental light signals directly and instantly to specific gene promoters.
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Affiliation(s)
- P H Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
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46
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Abstract
The application of Arabidopsis genetics to research into the responses of plants to light has enabled rapid recent advances in this field. The plant photoreceptor phytochrome mediates well-defined responses that can be exploited to provide elegant and specific genetic screens. By this means, not only have mutants affecting the phytochromes themselves been isolated, but also mutants affecting the transduction of phytochrome signals. The genes involved in these processes have now begun to be characterized by using this genetic approach to isolate signal transduction components. Most of the components characterized so far are capable of being translocated to the cell nucleus, and they may help to define a new system of regulation of gene expression. This review summarises the ongoing contribution made by genetics to our understanding of light perception and signal transduction by the phytochrome system.
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Affiliation(s)
- M E Hudson
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
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47
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Abstract
Many phytochrome responses in plants are induced by red light and inhibited by far-red light. To explain the biochemical basis of these observations, it was speculated that plant phytochromes are light-regulated enzymes more than 40 years ago. The search for such an enzymatic activity has a long and rather tumultuous history. Biochemical data in the late 1980s had suggested that oat phytochrome might be a light-regulated protein kinase. The topic was the subject of intense debate, but solid experimental data backing the kinase model has been published recently. Two lines of research played a key role in this finding: the production of biologically active highly purified recombinant phytochrome and the discovery of phytochromes in prokaryotes. This review discusses the key steps of this discovery, and suggests some hypotheses for the role of protein kinase activity in photomorphogenesis.
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Affiliation(s)
- C Fankhauser
- Department of Molecular Biology, University of Geneva, 30 quai E. Ansermet, Geneva 4, 1211, Switzerland.
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48
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Spiegelman JI, Mindrinos MN, Fankhauser C, Richards D, Lutes J, Chory J, Oefner PJ. Cloning of the Arabidopsis RSF1 gene by using a mapping strategy based on high-density DNA arrays and denaturing high-performance liquid chromatography. THE PLANT CELL 2000; 12:2485-2498. [PMID: 11148292 PMCID: PMC102232 DOI: 10.1105/tpc.12.12.2485] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2000] [Accepted: 11/07/2000] [Indexed: 05/18/2023]
Abstract
Mapping genes by chromosome walking is a widely used technique applicable to cloning virtually any gene that is identifiable by mutagenesis. We isolated the gene responsible for the recessive mutation rsf1 (for reduced sensitivity to far-red light) in the Arabidopsis Columbia accession by using classical genetic analysis and two recently developed technologies: genotyping high-density oligonucleotide DNA array and denaturing high-performance liquid chromatography (DHPLC). The Arabidopsis AT412 genotyping array and 32 F(2) plants were used to map the rsf1 mutation close to the top of chromosome 1 to an interval of approximately 500 kb. Using DHPLC, we found and genotyped additional markers for fine mapping, shortening the interval to approximately 50 kb. The mutant gene was directly identified by DHPLC by comparing amplicons generated separately from the rsf1 mutant and the parent strain Columbia. DHPLC analysis yielded polymorphic profiles in two overlapping polymorphic amplicons attributable to a 13-bp deletion in the third of five exons of a gene encoding a 292-amino acid protein with a basic helix-loop-helix (bHLH) domain. The mutation in rsf1 results in a truncated protein consisting of the first 129 amino acids but lacking the bHLH domain. Cloning the RSF1 gene strongly suggests that numerous phytochrome A-mediated responses require a bHLH class transcription factor.
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Affiliation(s)
- J I Spiegelman
- Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
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49
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Abstract
For plants, the sensing of light in the environment is as important as vision is for animals. Fluctuations in light can be crucial to competition and survival. One way plants sense light is through the phytochromes, a small family of diverse photochromic protein photoreceptors whose origins have been traced to the photosynthetic prokaryotes. During their evolution, the phytochromes have acquired sophisticated mechanisms to monitor light. Recent advances in understanding the molecular mechanisms of phytochromes and their significance to evolutionary biology make possible an interim synthesis of this rapidly advancing branch of photobiology.
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Affiliation(s)
- H Smith
- Department of Biology, University of Leicester, UK.
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50
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Riechmann JL, Ratcliffe OJ. A genomic perspective on plant transcription factors. CURRENT OPINION IN PLANT BIOLOGY 2000; 3:423-34. [PMID: 11019812 DOI: 10.1016/s1369-5266(00)00107-2] [Citation(s) in RCA: 194] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Data from the Arabidopsis genome project suggest that more than 5% of the genes of this plant encode transcription factors. The necessity for the use of genomic analytical approaches becomes clear when it is considered that less than 10% of these factors have been genetically characterized. A variety of tools for functional genomic analyses in plants have been developed over the past few years. The availability of the full complement of Arabidopsis transcription factors, together with the results of recent studies that illustrate some of the challenges to their functional characterization, now provides the basic framework for future analyses of transcriptional regulation in plants.
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Affiliation(s)
- J L Riechmann
- Mendel Biotechnology, Hayward, California 94545, USA.
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