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Sng BJR, Van Vu K, Choi IKY, Chin HJ, Jang IC. LONG HYPOCOTYL IN FAR-RED 1 mediates a trade-off between growth and defense under shade in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad088. [PMID: 36882154 DOI: 10.1093/jxb/erad088] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Indexed: 06/18/2023]
Abstract
Plants respond to vegetative shade with developmental and physiological changes that is collectively known as shade avoidance syndrome (SAS). Although LONG HYPOCOTYL IN FAR-RED 1 (HFR1) is known to be a negative regulator of SAS by forming heterodimers with other basic helix-loop-helix (bHLH) transcription factors to inhibit them, its function in genome-wide transcriptional regulation is not fully elucidated. Here, we performed RNA-sequencing analyses of hfr1-5 and HFR1 overexpression line (HFR1(ΔN)-OE) to comprehensively identify HFR1-regulated genes at different time points of shade treatment. We found that HFR1 mediates the trade-off between shade-induced growth and shade-repressed defense, by regulating the expression of relevant genes in shade. Genes involved in promoting growth, such as for auxin biosynthesis, transport, signaling and response were induced by shade but suppressed by HFR1 at both short and long durations of shade. Likewise, most ethylene-related genes were shade-induced and HFR1-repressed. On the other hand, shade suppressed defense-related genes while HFR1 induced their expression, especially under long duration of shade treatment. We demonstrated that HFR1 confers increased resistance to bacterial infection under shade.
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Affiliation(s)
- Benny Jian Rong Sng
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Kien Van Vu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Ian Kin Yuen Choi
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Hui Jun Chin
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - In-Cheol Jang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
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2
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Miao W, Wang J. Genetic Transformation of Cotton with the Harpin-Encoding Gene hpa Xoo of Xanthomonas oryzae pv. oryzae and Evaluation of Resistance Against Verticillium Wilt. Methods Mol Biol 2019; 1902:257-280. [PMID: 30543078 DOI: 10.1007/978-1-4939-8952-2_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The soilborne fungal pathogen Verticillium dahliae Kleb causes Verticillium wilt in a wide range of crops including cotton (Gossypium hirsutum). To date, most upland cotton varieties are susceptible to V. dahliae, and the breeding for cotton varieties with the resistance to Verticillium wilt has not been successful. Hpa1Xoo is a harpin protein from Xanthomonas oryzae pv. oryzae which induces the hypersensitive cell death in plants. When hpa1Xoo was transformed into the susceptible cotton line Z35 through Agrobacterium-mediated transformation, the transgenic cotton line (T-34) with an improved resistance to Verticillium dahliae was obtained. Here, we describe the related research approach, such as Western blot, Southern blot, immuno-gold labeling, evaluation of resistance to Verticillium dahliae, and how to detect the micro-hypersensitive response and oxidative burst elicited by harpinXoo in plant tissue.
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Affiliation(s)
- Weiguo Miao
- College of Plant Protection, Hainan University, Haikou, People's Republic of China.
| | - Jingsheng Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, People's Republic of China
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3
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Lee I, Kim K, Lee S, Lee S, Hwang E, Shin K, Kim D, Choi J, Choi H, Cha JS, Kim H, Lee RA, Jeong S, Kim J, Kim Y, Nam HG, Park SK, Cho HS, Soh MS. A missense allele of KARRIKIN-INSENSITIVE2 impairs ligand-binding and downstream signaling in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3609-3623. [PMID: 29722815 PMCID: PMC6022639 DOI: 10.1093/jxb/ery164] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/24/2018] [Indexed: 05/26/2023]
Abstract
A smoke-derived compound, karrikin (KAR), and an endogenous but as yet unidentified KARRIKIN INSENSITIVE2 (KAI2) ligand (KL) have been identified as chemical cues in higher plants that impact on multiple aspects of growth and development. Genetic screening of light-signaling mutants in Arabidopsis thaliana has identified a mutant designated as ply2 (pleiotropic long hypocotyl2) that has pleiotropic light-response defects. In this study, we used positional cloning to identify the molecular lesion of ply2 as a missense mutation of KAI2/HYPOSENSITIVE TO LIGHT, which causes a single amino acid substitution, Ala219Val. Physiological analysis and genetic epistasis analysis with the KL-signaling components MORE AXILLARY GROWTH2 (MAX2) and SUPPRESSOR OF MAX2 1 suggested that the pleiotropic phenotypes of the ply2 mutant can be ascribed to a defect in KL-signaling. Molecular and biochemical analyses revealed that the mutant KAI2ply2 protein is impaired in its ligand-binding activity. In support of this conclusion, X-ray crystallography studies suggested that the KAI2ply2 mutation not only results in a narrowed entrance gate for the ligand but also alters the structural flexibility of the helical lid domains. We discuss the structural implications of the Ala219 residue with regard to ligand-specific binding and signaling of KAI2, together with potential functions of KL-signaling in the context of the light-regulatory network in Arabidopsis thaliana.
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Affiliation(s)
- Inhye Lee
- Division of Integrative Bioscience and Biotechnology, School of Life Science, Sejong University, Seoul, Republic of Korea
| | - Kuglae Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Sumin Lee
- Division of Integrative Bioscience and Biotechnology, School of Life Science, Sejong University, Seoul, Republic of Korea
| | - Seungjun Lee
- Division of Integrative Bioscience and Biotechnology, School of Life Science, Sejong University, Seoul, Republic of Korea
| | - Eunjin Hwang
- Division of Integrative Bioscience and Biotechnology, School of Life Science, Sejong University, Seoul, Republic of Korea
| | - Kihye Shin
- Division of Integrative Bioscience and Biotechnology, School of Life Science, Sejong University, Seoul, Republic of Korea
| | - Dayoung Kim
- Division of Integrative Bioscience and Biotechnology, School of Life Science, Sejong University, Seoul, Republic of Korea
| | - Jungki Choi
- Division of Integrative Bioscience and Biotechnology, School of Life Science, Sejong University, Seoul, Republic of Korea
| | - Hyunmo Choi
- Division of Integrative Bioscience and Biotechnology, School of Life Science, Sejong University, Seoul, Republic of Korea
| | - Jeong Seok Cha
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Hoyoung Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Rin-A Lee
- Division of Integrative Bioscience and Biotechnology, School of Life Science, Sejong University, Seoul, Republic of Korea
| | - Suyeong Jeong
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
| | - Jeongsik Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
| | - Yumi Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
- Department of New Biology, DGIST, Daegu, Republic of Korea
| | - Soon-Ki Park
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Hyun-Soo Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Moon-Soo Soh
- Division of Integrative Bioscience and Biotechnology, School of Life Science, Sejong University, Seoul, Republic of Korea
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4
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Xin X, Chen W, Wang B, Zhu F, Li Y, Yang H, Li J, Ren D. Arabidopsis MKK10-MPK6 mediates red-light-regulated opening of seedling cotyledons through phosphorylation of PIF3. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:423-439. [PMID: 29244171 PMCID: PMC5853512 DOI: 10.1093/jxb/erx418] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/31/2017] [Indexed: 05/21/2023]
Abstract
Photomorphogenesis is an important process in which seedlings emerge from soil and begin autotrophic growth. Mechanisms of photomorphogenesis include light signal perception, signal transduction, and the modulation of expression of light-responsive genes, ultimately leading to cellular and developmental changes. Phytochrome-interacting factors (PIFs) play negative regulatory roles in photomorphogenesis. Light-induced activation of phytochromes triggers rapid phosphorylation and degradation of PIFs, but the kinases responsible for the phosphorylation of PIFs are largely unknown. Here, we show that Arabidopsis MPK6 is a kinase involved in phosphorylating PIF3 and regulating red light-induced cotyledon opening, a crucial process during seedling photomorphogenesis. MPK6 was activated by red light, and the cotyledon opening angle in red light was reduced in mpk6 seedlings. MKK10, a MAPKK whose function is currently unclear, appears to act as a kinase upstream of MPK6 in regulating cotyledon opening. Activation of MPK6 by MKK10 led to the phosphorylation of PIF3 and accelerated its turnover in transgenic seedlings. Accordingly, the overexpression of PIF3 suppressed MKK10-induced cotyledon opening. MKK10 and MPK6 function downstream of phyB in regulating seedling cotyledon opening in red light. Therefore, the MKK10-MPK6 cascade appears to mediate the regulation of red-light-controlled seedling photomorphogenesis via a mechanism that might involve the phosphorylation of PIF3.
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Affiliation(s)
- Xiaoyun Xin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, China
| | - Wenhao Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, China
| | - Bo Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, China
| | - Fan Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, China
| | - Yuan Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, China
| | - Hailian Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, China
| | - Dongtao Ren
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, China
- Collaborative Innovation Center of Crop Stress Biology, China
- Correspondence:
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5
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Carriedo LG, Maloof JN, Brady SM. Molecular control of crop shade avoidance. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:151-8. [PMID: 27016665 DOI: 10.1016/j.pbi.2016.03.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 05/20/2023]
Abstract
The shade avoidance response (SAR) in crops can be detrimental to yield, as precious carbon resources are redirected to stem or petiole elongation at the expense of biomass production. While breeding efforts have inadvertently attenuated this response in staple crops through correlated selection for yield at high density, it has not been eliminated. The extensive work done in Arabidopsis has provided a detailed understanding of the SAR and can be used as a framework for understanding the SAR in crop species. Recent crop SAR works point to auxin as a key factor in regulating the SAR in several crop species. These works also clearly demonstrate that one model for crop SAR will not fit all, and thus we need to move forward with studying the genetic players of the SAR in several model crop species. In this review, we provide the current knowledge of the SAR as reported at the physiological and molecular levels.
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Affiliation(s)
- Leonela G Carriedo
- Section of Plant Biology, Division of Biological Sciences, One Shields Avenue, University of California, Davis, CA 95616, USA
| | - Julin N Maloof
- Section of Plant Biology, Division of Biological Sciences, One Shields Avenue, University of California, Davis, CA 95616, USA.
| | - Siobhan M Brady
- Section of Plant Biology, Division of Biological Sciences, One Shields Avenue, University of California, Davis, CA 95616, USA.
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6
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Shi H, Zhong S, Mo X, Liu N, Nezames CD, Deng XW. HFR1 sequesters PIF1 to govern the transcriptional network underlying light-initiated seed germination in Arabidopsis. THE PLANT CELL 2013; 25:3770-84. [PMID: 24179122 PMCID: PMC3877798 DOI: 10.1105/tpc.113.117424] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 09/30/2013] [Accepted: 10/14/2013] [Indexed: 05/19/2023]
Abstract
Seed germination is the first step for seed plants to initiate a new life cycle. Light plays a predominant role in promoting seed germination, where the initial phase is mediated by photoreceptor phytochrome B (phyB). Previous studies showed that phytochrome-interacting factor1 (PIF1) represses seed germination downstream of phyB. Here, we identify a positive regulator of phyB-dependent seed germination, long hypocotyl in far-red1 (HFR1). HFR1 blocks PIF1 transcriptional activity by forming a heterodimer with PIF1 that prevents PIF1 from binding to DNA. Our whole-genomic analysis shows that HFR1 and PIF1 oppositely mediate the light-regulated transcriptome in imbibed seeds. Through the HFR1-PIF1 module, light regulates expression of numerous genes involved in cell wall loosening, cell division, and hormone pathways to initiate seed germination. The functionally antagonistic HFR1-PIF1 pair constructs a fail-safe mechanism for fine-tuning seed germination during low-level illumination, ensuring a rapid response to favorable environmental changes. This study identifies the HFR1-PIF1 pair as a central module directing the whole genomic transcriptional network to rapidly initiate light-induced seed germination.
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Affiliation(s)
- Hui Shi
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Shangwei Zhong
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Xiaorong Mo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Na Liu
- Yale Stem Cell Center and Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06519
| | - Cynthia D. Nezames
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Xing Wang Deng
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
- Address correspondence to
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7
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Hong SY, Seo PJ, Ryu JY, Cho SH, Woo JC, Park CM. A competitive peptide inhibitor KIDARI negatively regulates HFR1 by forming nonfunctional heterodimers in Arabidopsis photomorphogenesis. Mol Cells 2013; 35:25-31. [PMID: 23224238 PMCID: PMC3887847 DOI: 10.1007/s10059-013-2159-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 08/06/2012] [Accepted: 11/14/2012] [Indexed: 01/09/2023] Open
Abstract
Dynamic dimer formation is an elaborate means of modulating transcription factor activities in diverse cellular processes. The basic helix-loop-helix (bHLH) transcription factor LONG HYPOCOTYL IN FAR-RED 1 (HFR1), for example, plays a role in plant photomorphogenesis by forming non-DNA binding heterodimers with PHYTOCHROMEINTERACTING FACTORS (PIFs). Recent studies have shown that a small HLH protein KIDARI (KDR) negatively regulates the HFR1 activity in the process. However, molecular mechanisms underlying the KDR control of the HFR1 activity are unknown. Here, we demonstrate that KDR attenuates the HFR1 activity by competitively forming nonfunctional heterodimers, causing liberation of PIF4 from the transcriptionally inactive HFR1-PIF4 complex. Accordingly, the photomorphogenic hypocotyl growth of the HFR1-overexpressing plants can be suppressed by KDR coexpression, as observed in the HFR1-deficient hfr1-201 mutant. These results indicate that the PIF4 activity is modulated through a double layer of competitive inhibition by HFR1 and KDR, which could in turn ensure fine-tuning of the PIF4 activity under fluctuating light conditions.
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Affiliation(s)
- Shin-Young Hong
- Department of Chemistry, Seoul National University, Seoul 151-742,
Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 151-742,
Korea
- Department of Chemistry, Chonbuk National University, Jeonju 561-756,
Korea
| | - Jae Yong Ryu
- Department of Chemistry, Seoul National University, Seoul 151-742,
Korea
| | - Shin-Hae Cho
- Department of Chemistry, Seoul National University, Seoul 151-742,
Korea
| | - Je-Chang Woo
- Department of Biological Science, Mokpo National University, Muan 534-729,
Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 151-742,
Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-742,
Korea
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8
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Miao W, Wang J. Genetic transformation of cotton with a harpin-encoding gene hpaXoo confers an enhanced defense response against Verticillium dahliae Kleb. Methods Mol Biol 2013; 958:223-46. [PMID: 23143497 DOI: 10.1007/978-1-62703-212-4_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The soil-borne fungal pathogen Verticillium dahliae Kleb causes Verticillium wilt in a wide range of crops including cotton (Gossypium hirsutum). To date, most upland cotton varieties are susceptible to V. dahliae and the breeding for cotton varieties with the resistance to Verticillium wilt has not been successful. Hpa1Xoo is a harpin protein from Xanthomonas oryzae pv. oryzae which induces the hypersensitive cell death in plants. When hpa1Xoo was transformed into the susceptible cotton line Z35 through Agrobacterium-mediated transformation, the transgenic cotton line (T-34) with an improved resistance to Verticillium dahliae was obtained. Here, we describe the related research approach, such as Western blot, Southern blot, immuno-gold labeling, evaluation of resistance to Verticillium dahliae, and how to detect the micro-hypersensitive response and oxidative burst elicited by harpin(Xoo) in plant tissue.
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Affiliation(s)
- Weiguo Miao
- College of Environment and Plant Protection, Hainan University, Haikou, People's Republic of China.
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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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Ruckle ME, Burgoon LD, Lawrence LA, Sinkler CA, Larkin RM. Plastids are major regulators of light signaling in Arabidopsis. PLANT PHYSIOLOGY 2012; 159:366-90. [PMID: 22383539 PMCID: PMC3375971 DOI: 10.1104/pp.112.193599] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 02/29/2012] [Indexed: 05/20/2023]
Abstract
We previously provided evidence that plastid signaling regulates the downstream components of a light signaling network and that this signal integration coordinates chloroplast biogenesis with both the light environment and development by regulating gene expression. We tested these ideas by analyzing light- and plastid-regulated transcriptomes in Arabidopsis (Arabidopsis thaliana). We found that the enrichment of Gene Ontology terms in these transcriptomes is consistent with the integration of light and plastid signaling (1) down-regulating photosynthesis and inducing both repair and stress tolerance in dysfunctional chloroplasts and (2) helping coordinate processes such as growth, the circadian rhythm, and stress responses with the degree of chloroplast function. We then tested whether factors that contribute to this signal integration are also regulated by light and plastid signals by characterizing T-DNA insertion alleles of genes that are regulated by light and plastid signaling and that encode proteins that are annotated as contributing to signaling, transcription, or no known function. We found that a high proportion of these mutant alleles induce chloroplast biogenesis during deetiolation. We quantified the expression of four photosynthesis-related genes in seven of these enhanced deetiolation (end) mutants and found that photosynthesis-related gene expression is attenuated. This attenuation is particularly striking for Photosystem II subunit S expression. We conclude that the integration of light and plastid signaling regulates a number of END genes that help optimize chloroplast function and that at least some END genes affect photosynthesis-related gene expression.
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Affiliation(s)
| | | | | | | | - Robert M. Larkin
- Michigan State University-Department of Energy Plant Research Laboratory (M.E.R., L.A.L., C.A.S., R.M.L.), Department of Biochemistry and Molecular Biology (M.E.R., L.D.B., R.M.L.), and Gene Expression in Development and Disease Initiative (L.D.B.), Michigan State University, East Lansing, Michigan 48824
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11
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Prasad BRV, Kumar SV, Nandi A, Chattopadhyay S. Functional interconnections of HY1 with MYC2 and HY5 in Arabidopsis seedling development. BMC PLANT BIOLOGY 2012; 12:37. [PMID: 22424472 PMCID: PMC3353174 DOI: 10.1186/1471-2229-12-37] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 03/17/2012] [Indexed: 05/19/2023]
Abstract
Arabidopsis seedling development is controlled by many regulatory genes involved in multiple signaling pathways. The functional relationships of these genes working in multiple signaling cascades have started to be unraveled. Arabidopsis HY1/HO1 is a rate-limiting enzyme involved in biosynthesis of phytochrome chromophore. HY5 (a bZIP protein) promotes photomorphogenesis, however ZBF1/MYC2 (a bHLH protein) works as a negative regulator of photomorphogenic growth and light regulated gene expression. Further, MYC2 and HY1 have been shown to play important roles in jasmonic acid (JA) signaling pathways. Here, we show the genetic interactions of HY1 with two key transcription factor genes of light signaling, HY5 and MYC2, in Arabidopsis seedling development. Our studies reveal that although HY1 acts in an additive manner with HY5, it is epistatic to MYC2 in light-mediated seedling growth and gene expression. This study further demonstrates that HY1 additively or synergistically functions with HY5, however it works upstream to MYC2 in JA signaling pathways. Taken together, this study demonstrates the functional interrelations of HY1, MYC2 and HY5 in light and JA signaling pathways.
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Affiliation(s)
| | - Selva V Kumar
- National Institute of Plant Genome Research, New Delhi, India
| | - Ashis Nandi
- School of Life Sciences, Jawharlal Neheru University, New Delhi, India
| | - Sudip Chattopadhyay
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur 713209, West Bengal, India
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12
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Li J, Li G, Wang H, Wang Deng X. Phytochrome signaling mechanisms. THE ARABIDOPSIS BOOK 2011; 9:e0148. [PMID: 22303272 PMCID: PMC3268501 DOI: 10.1199/tab.0148] [Citation(s) in RCA: 241] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Phytochromes are red (R)/far-red (FR) light photoreceptors that play fundamental roles in photoperception of the light environment and the subsequent adaptation of plant growth and development. There are five distinct phytochromes in Arabidopsis thaliana, designated phytochrome A (phyA) to phyE. phyA is light-labile and is the primary photoreceptor responsible for mediating photomorphogenic responses in FR light, whereas phyB-phyE are light stable, and phyB is the predominant phytochrome regulating de-etiolation responses in R light. Phytochromes are synthesized in the cytosol in their inactive Pr form. Upon light irradiation, phytochromes are converted to the biologically active Pfr form, and translocate into the nucleus. phyB can enter the nucleus by itself in response to R light, whereas phyA nuclear import depends on two small plant-specific proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). Phytochromes may function as light-regulated serine/threonine kinases, and can phosphorylate several substrates, including themselves in vitro. Phytochromes are phosphoproteins, and can be dephosphorylated by a few protein phosphatases. Photoactivated phytochromes rapidly change the expression of light-responsive genes by repressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase targeting several photomorphogenesis-promoting transcription factors for degradation, and by inducing rapid phosphorylation and degradation of Phytochrome-Interacting Factors (PIFs), a group of bHLH transcription factors repressing photomorphogenesis. Phytochromes are targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway.
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Affiliation(s)
- Jigang Li
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Gang Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Haiyang Wang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Xing Wang Deng
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
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Ruberti I, Sessa G, Ciolfi A, Possenti M, Carabelli M, Morelli G. Plant adaptation to dynamically changing environment: the shade avoidance response. Biotechnol Adv 2011; 30:1047-58. [PMID: 21888962 DOI: 10.1016/j.biotechadv.2011.08.014] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 07/23/2011] [Accepted: 08/16/2011] [Indexed: 11/30/2022]
Abstract
The success of competitive interactions between plants determines the chance of survival of individuals and eventually of whole plant species. Shade-tolerant plants have adapted their photosynthesis to function optimally under low-light conditions. These plants are therefore capable of long-term survival under a canopy shade. In contrast, shade-avoiding plants adapt their growth to perceive maximum sunlight and therefore rapidly dominate gaps in a canopy. Daylight contains roughly equal proportions of red and far-red light, but within vegetation that ratio is lowered as a result of red absorption by photosynthetic pigments. This light quality change is perceived through the phytochrome system as an unambiguous signal of the proximity of neighbors resulting in a suite of developmental responses (termed the shade avoidance response) that, when successful, result in the overgrowth of those neighbors. Shoot elongation induced by low red/far-red light may confer high relative fitness in natural dense communities. However, since elongation is often achieved at the expense of leaf and root growth, shade avoidance may lead to reduction in crop plant productivity. Over the past decade, major progresses have been achieved in the understanding of the molecular basis of shade avoidance. However, uncovering the mechanisms underpinning plant response and adaptation to changes in the ratio of red to far-red light is key to design new strategies to precise modulate shade avoidance in time and space without impairing the overall crop ability to compete for light.
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Affiliation(s)
- I Ruberti
- Institute of Molecular Biology and Pathology, National Research Council, Piazzalle Aldo Moro 5, Rome, Italy.
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14
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Chen M, Chory J. Phytochrome signaling mechanisms and the control of plant development. Trends Cell Biol 2011; 21:664-71. [PMID: 21852137 DOI: 10.1016/j.tcb.2011.07.002] [Citation(s) in RCA: 268] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 07/01/2011] [Accepted: 07/05/2011] [Indexed: 11/18/2022]
Abstract
As they emerge from the ground, seedlings adopt a photosynthetic lifestyle, which is accompanied by dramatic changes in morphology and global alterations in gene expression that optimizes the plant body plan for light capture. Phytochromes are red and far-red photoreceptors that play a major role during photomorphogenesis, a complex developmental program that seedlings initiate when they first encounter light. The earliest phytochrome signaling events after excitation by red light include their rapid translocation from the cytoplasm to subnuclear bodies (photobodies) that contain other proteins involved in photomorphogenesis, including a number of transcription factors and E3 ligases. In the light, phytochromes and negatively acting transcriptional regulators that interact directly with phytochromes are destabilized, whereas positively acting transcriptional regulators are stabilized. Here, we discuss recent advances in our knowledge of the mechanisms linking phytochrome photoactivation in the cytoplasm and transcriptional regulation in the nucleus.
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Affiliation(s)
- Meng Chen
- Department of Biology, Duke University, Durham, NC 27708, USA.
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15
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Galstyan A, Cifuentes-Esquivel N, Bou-Torrent J, Martinez-Garcia JF. The shade avoidance syndrome in Arabidopsis: a fundamental role for atypical basic helix-loop-helix proteins as transcriptional cofactors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 66:258-67. [PMID: 21205034 DOI: 10.1111/j.1365-313x.2011.04485.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The shade avoidance syndrome (SAS) refers to a set of plant responses aimed at anticipating eventual shading by potential competitors. The SAS is initiated after perception of nearby vegetation as a reduction in the red to far-red ratio (R:FR) of the incoming light. Low R:FR light is perceived by the phytochromes, triggering dramatic changes in gene expression that, in seedlings, eventually result in an increased hypocotyl elongation to overgrow competitors. This response is inhibited by genes such as PHYTOCHROME RAPIDLY REGULATED 1 (PAR1), PAR2 and LONG HYPOCOTYL IN FR 1 (HFR1), which are transcriptionally induced by low R:FR. Although PAR1/PAR2 and HFR1 proteins belong to different groups of basic helix-loop-helix (bHLH) transcriptional regulators, they all lack a typical basic domain required for binding to E-box and G-box motifs in the promoter of target genes. By overexpressing derivatives of PAR1 and HFR1 we show that these proteins are actually transcriptional cofactors that do not need to bind DNA to directly regulate transcription. We conclude that protein-protein interactions involving the HLH domain of PAR1 and HFR1 are a fundamental aspect of the mechanism by which these proteins regulate gene expression, most likely through interaction with true transcription factors that do bind to the target genes and eventually unleash the observed SAS responses.
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Affiliation(s)
- Anahit Galstyan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB, 08034-Barcelona, Spain
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16
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Leivar P, Quail PH. PIFs: pivotal components in a cellular signaling hub. TRENDS IN PLANT SCIENCE 2011; 16:19-28. [PMID: 20833098 PMCID: PMC3019249 DOI: 10.1016/j.tplants.2010.08.003] [Citation(s) in RCA: 685] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Revised: 08/09/2010] [Accepted: 08/11/2010] [Indexed: 05/18/2023]
Abstract
A small subset of basic helix-loop-helix transcription factors called PIFs (phytochrome-interacting factors) act to repress seed germination, promote seedling skotomorphogenesis and promote shade-avoidance through regulated expression of over a thousand genes. Light-activated phytochrome molecules directly reverse these activities by inducing rapid degradation of the PIF proteins. Here, we review recent advances in dissecting this signaling pathway and examine emerging evidence that indicates that other pathways also converge to regulate PIF activity, including the gibberellin pathway, the circadian clock and high temperature. Thus PIFs have broader roles than previously appreciated, functioning as a cellular signaling hub that integrates multiple signals to orchestrate regulation of the transcriptional network that drives multiple facets of downstream morphogenesis. The relative contributions of the individual PIFs to this spectrum of regulatory functions ranges from quantitatively redundant to qualitatively distinct.
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Affiliation(s)
- Pablo Leivar
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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17
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Li J, Li G, Wang H, Wang Deng X. Phytochrome signaling mechanisms. THE ARABIDOPSIS BOOK 2011. [PMID: 22303272 DOI: 10.1199/2ftab.0148e0148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Phytochromes are red (R)/far-red (FR) light photoreceptors that play fundamental roles in photoperception of the light environment and the subsequent adaptation of plant growth and development. There are five distinct phytochromes in Arabidopsis thaliana, designated phytochrome A (phyA) to phyE. phyA is light-labile and is the primary photoreceptor responsible for mediating photomorphogenic responses in FR light, whereas phyB-phyE are light stable, and phyB is the predominant phytochrome regulating de-etiolation responses in R light. Phytochromes are synthesized in the cytosol in their inactive Pr form. Upon light irradiation, phytochromes are converted to the biologically active Pfr form, and translocate into the nucleus. phyB can enter the nucleus by itself in response to R light, whereas phyA nuclear import depends on two small plant-specific proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). Phytochromes may function as light-regulated serine/threonine kinases, and can phosphorylate several substrates, including themselves in vitro. Phytochromes are phosphoproteins, and can be dephosphorylated by a few protein phosphatases. Photoactivated phytochromes rapidly change the expression of light-responsive genes by repressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase targeting several photomorphogenesis-promoting transcription factors for degradation, and by inducing rapid phosphorylation and degradation of Phytochrome-Interacting Factors (PIFs), a group of bHLH transcription factors repressing photomorphogenesis. Phytochromes are targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway.
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18
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Salinas-Mondragon RE, Kajla JD, Perera IY, Brown CS, Sederoff HW. Role of inositol 1,4,5-triphosphate signalling in gravitropic and phototropic gene expression. PLANT, CELL & ENVIRONMENT 2010; 33:2041-55. [PMID: 20584147 DOI: 10.1111/j.1365-3040.2010.02204.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants sense light and gravity to orient their direction of growth. One common component in the early events of both phototropic and gravitropic signal transduction is activation of phospholipase C (PLC), which leads to an increase in inositol 1,4,5-triphosphate (InsP(3)) levels. The InsP(3) signal is terminated by hydrolysis of InsP(3) through inositolpolyphosphate-5-phosphatases (InsP 5-ptases). Arabidopsis plants expressing a heterologous InsP 5-ptase have low basal InsP(3) levels and exhibit reduced gravitropic and phototropic bending. Downstream effects of InsP(3)-mediated signalling are not understood. We used comparative transcript profiling to characterize gene expression changes in gravity- or light-stimulated Arabidopsis root apices that were manipulated in their InsP(3) metabolism either through inhibition of PLC activity or expression of InsP 5-ptase. We identified InsP(3)-dependent and InsP(3)-independent co-regulated gene sets in response to gravity or light stimulation. Inhibition of PLC activity in wild-type plants caused similar changes in transcript abundance in response to gravitropic and phototropic stimulation as in the transgenic lines. Therefore, we conclude that changes in gene expression in response to gravitropic and phototropic stimulation are mediated by two signal transduction pathways that vary in their dependence on changes in InsP(3).
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19
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Penfield S, Josse EM, Halliday KJ. A role for an alternative splice variant of PIF6 in the control of Arabidopsis primary seed dormancy. PLANT MOLECULAR BIOLOGY 2010; 73:89-95. [PMID: 19911288 DOI: 10.1007/s11103-009-9571-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Accepted: 11/02/2009] [Indexed: 05/22/2023]
Abstract
Phytochrome interacting factor (PIF) transcription factors have been shown to be important in the regulation of seed dormancy and germination by environmental cues. Many PIF-family transcription factors are expressed in seeds but only PIF1 and SPATULA (SPT) have been tested for a role in germination control. Here we show that PIF6 is expressed strongly during seed development, and that two splice variants exist, one full length (the alpha form), and a second, the beta form, in which a cryptic intron containing the potential DNA binding domain is spliced out, predicted to lead to the generation of a premature stop codon. Loss of PIF6 increases primary seed dormancy, whereas overexpression of the beta form, but not the alpha form, reduce dormancy. Our data show the potential for natural splice variants of PIF transcription factors to be important in the evolution of the control of environmental signalling in plants.
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Affiliation(s)
- Steven Penfield
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, Yo105YW, UK.
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20
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Miao W, Wang X, Li M, Song C, Wang Y, Hu D, Wang J. Genetic transformation of cotton with a harpin-encoding gene hpaXoo confers an enhanced defense response against different pathogens through a priming mechanism. BMC PLANT BIOLOGY 2010; 10:67. [PMID: 20398293 PMCID: PMC3095341 DOI: 10.1186/1471-2229-10-67] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 04/15/2010] [Indexed: 05/19/2023]
Abstract
BACKGROUND The soil-borne fungal pathogen Verticillium dahliae Kleb causes Verticillium wilt in a wide range of crops including cotton (Gossypium hirsutum). To date, most upland cotton varieties are susceptible to V. dahliae and the breeding for cotton varieties with the resistance to Verticillium wilt has not been successful. RESULTS Hpa1Xoo is a harpin protein from Xanthomonas oryzae pv. oryzae which induces the hypersensitive cell death in plants. When hpa1Xoo was transformed into the susceptible cotton line Z35 through Agrobacterium-mediated transformation, the transgenic cotton line (T-34) with an improved resistance to Verticillium dahliae was obtained. Cells of the transgenic T-34, when mixed with the conidia suspension of V. dahliae, had a higher tolerance to V. dahliae compared to cells of untransformed Z35. Cells of T-34 were more viable 12 h after mixing with V. dahliae conidia suspension. Immunocytological analysis showed that Hpa1Xoo, expressed in T-34, accumulated as clustered particles along the cell walls of T-34. In response to the infection caused by V. dahliae, the microscopic cell death and the generation of reactive oxygen intermediates were observed in leaves of T-34 and these responses were absent in leaves of Z35 inoculated with V. dahliae. Quantitative RT-PCR analysis indicated that five defense-related genes, ghAOX1, hin1, npr1, ghdhg-OMT, and hsr203J, were up-regulated in T-34 inoculated with V. dahliae. The up-regulations of these defense-relate genes were not observed or in a less extent in leaves of Z-35 after the inoculation. CONCLUSIONS Hpa1Xoo accumulates along the cell walls of the transgenic T-34, where it triggers the generation of H2O2 as an endogenous elicitor. T-34 is thus in a primed state, ready to protect the host from the pathogen. The results of this study suggest that the transformation of cotton with hpa1Xoo could be an effective approach for the development of cotton varieties with the improved resistance against soil-borne pathogens.
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Affiliation(s)
- Weiguo Miao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- College of Environment and Plant Protection, Hainan University, Haikou 570228, China
| | - Xiben Wang
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Manitoba, R3T 2N9, Canada
| | - Ming Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Congfeng Song
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Dongwei Hu
- Biotechnology Institute of Zhejiang University, Hangzhou 310029, China
| | - Jinsheng Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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21
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Mara CD, Huang T, Irish VF. The Arabidopsis floral homeotic proteins APETALA3 and PISTILLATA negatively regulate the BANQUO genes implicated in light signaling. THE PLANT CELL 2010; 22:690-702. [PMID: 20305124 PMCID: PMC2861465 DOI: 10.1105/tpc.109.065946] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2009] [Revised: 02/17/2010] [Accepted: 03/07/2010] [Indexed: 05/20/2023]
Abstract
The Arabidopsis thaliana MADS box transcription factors APETALA3 (AP3) and PISTILLATA (PI) heterodimerize and are required to specify petal identity, yet many details of how this regulatory process is effected are unclear. We have identified three related genes, BHLH136/BANQUO1 (BNQ1), BHLH134/BANQUO2 (BNQ2), and BHLH161/BANQUO3 (BNQ3), as being directly and negatively regulated by AP3 and PI in petals. BNQ1, BNQ2, and BNQ3 encode products belonging to a family of atypical non-DNA binding basic helix-loop-helix (bHLH) proteins that heterodimerize with and negatively regulate bHLH transcription factors. We show that bnq3 mutants have pale-green sepals and carpels and decreased chlorophyll levels, suggesting that BNQ3 has a role in regulating light responses. The ap3 bnq3 double mutant displays pale second-whorl organs, supporting the hypothesis that BNQ3 is downstream of AP3. Consistent with a role in light response, we show that the BNQ gene products regulate the function of HFR1 (for LONG HYPOCOTYL IN FAR-RED1), which encodes a bHLH protein that regulates photomorphogenesis through modulating phytochrome and cryptochrome signaling. The BNQ genes also are required for appropriate regulation of flowering time. Our results suggest that petal identity is specified in part through downregulation of BNQ-dependent photomorphogenic and developmental signaling pathways.
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22
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Inhibition of the shade avoidance response by formation of non-DNA binding bHLH heterodimers. EMBO J 2010; 28:3893-902. [PMID: 19851283 DOI: 10.1038/emboj.2009.306] [Citation(s) in RCA: 298] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Accepted: 09/23/2009] [Indexed: 11/08/2022] Open
Abstract
In shade-intolerant plants such as Arabidopsis, a reduction in the red/far-red (R/FR) ratio, indicative of competition from other plants, triggers a suite of responses known as the shade avoidance syndrome (SAS). The phytochrome photoreceptors measure the R/FR ratio and control the SAS. The phytochrome-interacting factors 4 and 5 (PIF4 and PIF5) are stabilized in the shade and are required for a full SAS, whereas the related bHLH factor HFR1 (long hypocotyl in FR light) is transcriptionally induced by shade and inhibits this response. Here we show that HFR1 interacts with PIF4 and PIF5 and limits their capacity to induce the expression of shade marker genes and to promote elongation growth. HFR1 directly inhibits these PIFs by forming non-DNA-binding heterodimers with PIF4 and PIF5. Our data indicate that PIF4 and PIF5 promote SAS by directly binding to G-boxes present in the promoter of shade marker genes, but their action is limited later in the shade when HFR1 accumulates and forms non-DNA-binding heterodimers. This negative feedback loop is important to limit the response of plants to shade.
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23
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Lorrain S, Trevisan M, Pradervand S, Fankhauser C. Phytochrome interacting factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 60:449-61. [PMID: 19619162 DOI: 10.1111/j.1365-313x.2009.03971.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Phytochromes are red/far-red photosensors that regulate numerous developmental programs in plants. Among them, phytochrome A (phyA) is essential to enable seedling de-etiolation under continuous far-red (FR) light, a condition that mimics the environment under a dense canopy. The ecological relevance of this response is demonstrated by the high mortality rate of phyA mutant plants that germinate in deep vegetational shade. phyA signaling involves direct interaction of the photoreceptor with phytochrome-interacting factors PIF1 and PIF3, members of the bHLH transcription factor family. Here we investigated the involvement of PIF4 and PIF5 in phyA signaling, and found that they redundantly control de-etiolation in FR light. The pif4 pif5 double mutant is hypersensitive to low fluence rates of FR light. This phenotype is dependent on FR light perception by phyA, but does not rely on alterations in the phyA level. Our microarray analysis shows that PIF4 and PIF5 are part of an inhibitory mechanism that represses the expression of some light-responsive genes in the dark, and that they are also needed for full expression of several growth-related genes in the light. Unlike PIF1 and PIF3, PIF4 and PIF5 are not degraded in response to FR light, indicating that they are light-regulated by a different mechanism. Our genetic analysis suggests that this is achieved through sequestration of these PIFs by the closely related bHLH transcription factor HFR1 (long hypocotyl in FR light).
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Affiliation(s)
- Séverine Lorrain
- Center for Integrative Genomics, University of Lausanne, Genopode Building, CH-1015 Lausanne, Switzerland
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24
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Phytochromes promote seedling light responses by inhibiting four negatively-acting phytochrome-interacting factors. Proc Natl Acad Sci U S A 2009; 106:7660-5. [PMID: 19380720 DOI: 10.1073/pnas.0812219106] [Citation(s) in RCA: 340] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
PIF3 is a phytochrome-interacting basic helix-loop-helix transcription factor that negatively regulates light responses, including hypocotyl elongation, cotyledon opening, and hypocotyl negative gravitropism. However, the role of PIF3 in chlorophyll biosynthesis has not been clearly defined. Here, we show that PIF3 also negatively regulates chlorophyll biosynthesis by repressing biosynthetic genes in the dark. Consistent with the gene expression patterns, the etiolated pif3 mutant accumulated a higher amount of protochlorophyllide and was bleached severely when transferred into light. The photobleaching phenotype of pif3 could be suppressed by the gun5 mutation and mimicked by overexpression of GUN5. When 4 negative phytochrome-interacting protein genes (PIF1, PIF3, PIF4, and PIF5) were mutated, the resulting quadruple mutant seedlings displayed constitutive photomorphogenic phenotypes, including short hypocotyls, open cotyledons, and disrupted hypocotyl gravitropism in the dark. Microarray analysis further confirmed that the dark-grown quadruple mutant has a gene expression pattern similar to that of red light-grown WT. Together, our data indicate that 4 phytochrome-interacting proteins are required for skotomorphogenesis and phytochromes activate photomorphogenesis by inhibiting these factors.
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25
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HFR1 is crucial for transcriptome regulation in the cryptochrome 1-mediated early response to blue light in Arabidopsis thaliana. PLoS One 2008; 3:e3563. [PMID: 18974779 PMCID: PMC2570330 DOI: 10.1371/journal.pone.0003563] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Accepted: 10/10/2008] [Indexed: 12/24/2022] Open
Abstract
Cryptochromes are blue light photoreceptors involved in development and circadian clock regulation. They are found in both eukaryotes and prokaryotes as light sensors. Long Hypocotyl in Far-Red 1 (HFR1) has been identified as a positive regulator and a possible transcription factor in both blue and far-red light signaling in plants. However, the gene targets that are regulated by HFR1 in cryptochrome 1 (cry1)-mediated blue light signaling have not been globally addressed. We examined the transcriptome profiles in a cry1- and HFR1-dependent manner in response to 1 hour of blue light. Strikingly, more than 70% of the genes induced by blue light in an HFR1-dependent manner were dependent on cry1, and vice versa. High overrepresentation of W-boxes and OCS elements were found in these genes, indicating that this strong cry1 and HFR1 co-regulation on gene expression is possibly through these two cis-elements. We also found that cry1 was required for maintaining the HFR1 protein level in blue light, and that the HFR1 protein level is strongly correlated with the global gene expression pattern. In summary, HFR1, which is fine-tuned by cry1, is crucial for regulating global gene expression in cry1-mediated early blue light signaling, especially for the function of genes containing W-boxes and OCS elements.
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26
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Roig-Villanova I, Bou-Torrent J, Galstyan A, Carretero-Paulet L, Portolés S, Rodríguez-Concepción M, Martínez-García JF. Interaction of shade avoidance and auxin responses: a role for two novel atypical bHLH proteins. EMBO J 2007; 26:4756-67. [PMID: 17948056 PMCID: PMC2080812 DOI: 10.1038/sj.emboj.7601890] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 09/24/2007] [Indexed: 11/08/2022] Open
Abstract
Plants sense the presence of potentially competing nearby individuals as a reduction in the red to far-red ratio of the incoming light. In anticipation of eventual shading, a set of plant responses known as the shade avoidance syndrome (SAS) is initiated soon after detection of this signal by the phytochrome photoreceptors. Here we analyze the function of PHYTOCHROME RAPIDLY REGULATED1 (PAR1) and PAR2, two Arabidopsis thaliana genes rapidly upregulated after simulated shade perception. These genes encode two closely related atypical basic helix-loop-helix proteins with no previously assigned function in plant development. Using reverse genetic approaches, we show that PAR1 and PAR2 act in the nucleus to broadly control plant development, acting as negative regulators of a variety of SAS responses, including seedling elongation and photosynthetic pigment accumulation. Molecularly, PAR1 and PAR2 act as direct transcriptional repressors of two auxin-responsive genes, SMALL AUXIN UPREGULATED15 (SAUR15) and SAUR68. Additional results support that PAR1 and PAR2 function in integrating shade and hormone transcriptional networks, rapidly connecting phytochrome-sensed light changes with auxin responsiveness.
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Affiliation(s)
- Irma Roig-Villanova
- Laboratori de Genètica Molecular Vegetal Consorci CSIC-IRTA, Departament de Genètica Molecular, Barcelona, Spain
| | - Jordi Bou-Torrent
- Laboratori de Genètica Molecular Vegetal Consorci CSIC-IRTA, Departament de Genètica Molecular, Barcelona, Spain
| | - Anahit Galstyan
- Laboratori de Genètica Molecular Vegetal Consorci CSIC-IRTA, Departament de Genètica Molecular, Barcelona, Spain
| | - Lorenzo Carretero-Paulet
- Laboratori de Genètica Molecular Vegetal Consorci CSIC-IRTA, Departament de Genètica Molecular, Barcelona, Spain
| | - Sergi Portolés
- Laboratori de Genètica Molecular Vegetal Consorci CSIC-IRTA, Departament de Genètica Molecular, Barcelona, Spain
| | - Manuel Rodríguez-Concepción
- Laboratori de Genètica Molecular Vegetal Consorci CSIC-IRTA, Departament de Genètica Molecular, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain
| | - Jaime F Martínez-García
- Laboratori de Genètica Molecular Vegetal Consorci CSIC-IRTA, Departament de Genètica Molecular, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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27
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Zhang X, Chen Y, Wang ZY, Chen Z, Gu H, Qu LJ. Constitutive expression of CIR1 (RVE2) affects several circadian-regulated processes and seed germination in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 51:512-25. [PMID: 17587236 DOI: 10.1111/j.1365-313x.2007.03156.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Circadian clocks are endogenous auto-regulatory mechanisms that allow organisms, from bacteria to humans, to advantageously time a wide range of activities within 24 h environmental cycles. Here we report the identification and characterization of an MYB-related gene, designated Circadian 1 (CIR1), that is involved in circadian regulation in Arabidopsis. Expression of CIR1 is transiently induced by light and oscillates with a circadian rhythm. The rhythmic expression of CIR1 is controlled by the central oscillator. Constitutive expression of CIR1 resulted in a shorter period length for the rhythms of four central oscillator components, and much lower amplitude for the rhythms of central oscillator components CCA1 and LHY. Furthermore, CIR1 over-expression severely affected the circadian rhythms of its own RNA and those of the slave oscillator EPR1 and effector genes Lhcb and CAT3. Plants that constitutively expressed CIR1 displayed delayed flowering, longer hypocotyls and reduced seed germination in the dark. These results suggest that CIR1 is possibly part of a regulatory feedback loop that controls a subset of the circadian outputs and modulates the central oscillator.
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Affiliation(s)
- Xiangbo Zhang
- National Laboratory for Protein Engineering and Plant Genetic Engineering, Peking-Yale Joint Research Center for Plant Molecular Genetics and AgroBiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
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28
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Abstract
Plants have evolved complex and sophisticated transcriptional networks that mediate developmental changes in response to light. These light-regulated processes include seedling photomorphogenesis, seed germination and the shade-avoidance and photoperiod responses. Understanding the components and hierarchical structure of the transcriptional networks that are activated during these processes has long been of great interest to plant scientists. Traditional genetic and molecular approaches have proved powerful in identifying key regulatory factors and their positions within these networks. Recent genomic studies have further revealed that light induces massive reprogramming of the plant transcriptome, and that the early light-responsive genes are enriched in transcription factors. These combined approaches provide new insights into light-regulated transcriptional networks.
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Affiliation(s)
- Yuling Jiao
- Department of Molecular, Cellular and Developmental Biology, 165 Prospect Street, Yale University, New Haven, Connecticut 06520-8104, USA
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Duek PD, Elmer MV, van Oosten VR, Fankhauser C. The degradation of HFR1, a putative bHLH class transcription factor involved in light signaling, is regulated by phosphorylation and requires COP1. Curr Biol 2005; 14:2296-301. [PMID: 15620659 DOI: 10.1016/j.cub.2004.12.026] [Citation(s) in RCA: 157] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Revised: 10/06/2004] [Accepted: 10/19/2004] [Indexed: 10/26/2022]
Abstract
All developmental transitions throughout the life cycle of a plant are influenced by light. In Arabidopsis, multiple photoreceptors including the UV-A/blue-sensing cryptochromes (cry1-2) and the red/far-red responsive phytochromes (phyA-E) monitor the ambient light conditions. Light-regulated protein stability is a major control point of photomorphogenesis. The ubiquitin E3 ligase COP1 (constitutively photomorphogenic 1) regulates the stability of several light-signaling components. HFR1 (long hypocotyl in far-red light) is a putative transcription factor with a bHLH domain acting downstream of both phyA and the cryptochromes. HFR1 is closely related to PIF1, PIF3, and PIF4 (phytochrome interacting factor 1, 3 and 4), but in contrast to the latter three, there is no evidence for a direct interaction between HFR1 and the phytochromes. Here, we show that the protein abundance of HFR1 is tightly controlled by light. HFR1 is an unstable phosphoprotein, particularly in the dark. The proteasome and COP1 are required in vivo to degrade phosphorylated HFR1. In addition, HFR1 can interact with COP1, consistent with the idea of COP1 directly mediating HFR1 degradation. We identify a domain, conserved among several bHLH class proteins involved in light signaling , as a determinant of HFR1 stability. Our physiological experiments indicate that the control of HFR1 protein abundance is important for a normal de-etiolation response.
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Affiliation(s)
- Paula D Duek
- Department of Molecular Biology, University of Geneva, 30 quai Ernest Ansermet, 1211 Genève 4, Switzerland
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Yang J, Lin R, Sullivan J, Hoecker U, Liu B, Xu L, Deng XW, Wang H. Light regulates COP1-mediated degradation of HFR1, a transcription factor essential for light signaling in Arabidopsis. THE PLANT CELL 2005; 17:804-21. [PMID: 15705947 PMCID: PMC1069700 DOI: 10.1105/tpc.104.030205] [Citation(s) in RCA: 239] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Arabidopsis thaliana seedlings undergo photomorphogenesis in the light and etiolation in the dark. Long Hypocotyl in Far-Red 1 (HFR1), a basic helix-loop-helix transcription factor, is required for both phytochrome A-mediated far-red and cryptochrome 1-mediated blue light signaling. Here, we report that HFR1 is a short-lived protein in darkness and is degraded through a 26S proteasome-dependent pathway. Light, irrespective of its quality, enhances HFR1 protein accumulation via promoting its stabilization. We demonstrate that HFR1 physically interacts with Constitutive Photomorphogenesis 1 (COP1) and that COP1 exhibits ubiquitin ligase activity toward HFR1 in vitro. In addition, we show that COP1 is required for degradation of HFR1 in vivo. Furthermore, plants overexpressing a C-terminal 161-amino acid fragment of HFR1 (CT161) display enhanced photomorphogenesis, suggesting an autonomous function of CT161 in promoting light signaling. This truncated HFR1 gene product is more stable than the full-length HFR1 protein in darkness, indicating that the COP1-interacting N-terminal portion of HFR1 is essential for COP1-mediated destabilization of HFR1. These results suggest that light enhances HFR1 protein accumulation by abrogating COP1-mediated degradation of HFR1, which is necessary and sufficient for promoting light signaling. Additionally, our results substantiate the E3 ligase activity of COP1 and its critical role in desensitizing light signaling.
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Affiliation(s)
- Jianping Yang
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA
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31
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Jang IC, Yang JY, Seo HS, Chua NH. HFR1 is targeted by COP1 E3 ligase for post-translational proteolysis during phytochrome A signaling. Genes Dev 2005; 19:593-602. [PMID: 15741320 PMCID: PMC551579 DOI: 10.1101/gad.1247205] [Citation(s) in RCA: 224] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2004] [Accepted: 01/14/2005] [Indexed: 11/25/2022]
Abstract
Upon activation by far-red light, phytochrome A signals are transduced through several pathways to promote photomorphogenesis. The COP1 E3 ligase represses photomorphogenesis in part by targeting transcription activators such as LAF1 and HY5 for destruction. Another positive regulator of photomorphogenesis is HFR1, a basic helix-loop-helix (bHLH) transcription factor. Here, we show that HFR1 colocalizes with COP1 in nuclear bodies, and that the HFR1 N-terminal region (amino acids 1-131) interacts with the COP1 WD40 domain. HFR1(DeltaN), an HFR1 mutant lacking the two N-terminal, COP1-interacting motifs, still localizes in nuclear bodies and retains weak affinity for COP1. Both HFR1 and HFR1(DeltaN) can be ubiquitinated by COP1, although with different efficiencies. Expression of 35S-HFR1(DeltaN) in wild-type plants confers greater hypersensitivity to FR than 35S-HFR1 expression, and only seedlings expressing 35S-HFR1(DeltaN) display constitutive photomorphogenesis. These phenotypic differences can be attributed to the instability of HFR1 compared with HFR1(DeltaN). In transgenic plants, HFR1 levels are significantly elevated upon induced expression of a dominant-negative COP1 mutant that interferes with endogenous COP1 E3 activity. Moreover, induced expression of wild-type COP1 in transgenic plants accelerates post-translational degradation of HFR1 under FR light. Taken together, our results show that HFR1 is ubiquitinated by COP1 E3 ligase and marked for post-translational degradation during photomorphogenesis.
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Affiliation(s)
- In-Cheol Jang
- Laboratory of Plant Molecular Biology, Rockefeller University, New York, New York 10021, USA
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Oh E, Kim J, Park E, Kim JI, Kang C, Choi G. PIL5, a phytochrome-interacting basic helix-loop-helix protein, is a key negative regulator of seed germination in Arabidopsis thaliana. THE PLANT CELL 2004; 16:3045-58. [PMID: 15486102 PMCID: PMC527197 DOI: 10.1105/tpc.104.025163] [Citation(s) in RCA: 324] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2004] [Accepted: 09/02/2004] [Indexed: 05/18/2023]
Abstract
The first decision made by an angiosperm seed, whether to germinate or not, is based on integration of various environmental signals such as water and light. The phytochromes (Phys) act as red and far-red light (Pfr) photoreceptors to mediate light signaling through yet uncharacterized pathways. We report here that the PIF3-like 5 (PIL5) protein, a basic helix-loop-helix transcription factor, is a key negative regulator of phytochrome-mediated seed germination. PIL5 preferentially interacts with the Pfr forms of Phytochrome A (PhyA) and Phytochrome B (PhyB). Analyses of a pil5 mutant in conjunction with phyA and phyB mutants, a pif3 pil5 double mutant, and PIL5 overexpression lines indicate that PIL5 is a negative factor in Phy-mediated promotion of seed germination, inhibition of hypocotyl negative gravitropism, and inhibition of hypocotyl elongation. Our data identify PIL5 as the first Phy-interacting protein that regulates seed germination.
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Affiliation(s)
- Eunkyoo Oh
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
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33
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Kimbrough JM, Salinas-Mondragon R, Boss WF, Brown CS, Sederoff HW. The fast and transient transcriptional network of gravity and mechanical stimulation in the Arabidopsis root apex. PLANT PHYSIOLOGY 2004; 136:2790-805. [PMID: 15347791 PMCID: PMC523342 DOI: 10.1104/pp.104.044594] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2004] [Revised: 05/28/2004] [Accepted: 05/30/2004] [Indexed: 05/18/2023]
Abstract
Plant root growth is affected by both gravity and mechanical stimulation (Massa GD, Gilroy S [2003] Plant J 33: 435-445). A coordinated response to both stimuli requires specific and common elements. To delineate the transcriptional response mechanisms, we carried out whole-genome microarray analysis of Arabidopsis root apices after gravity stimulation (reorientation) and mechanical stimulation and monitored transcript levels of 22,744 genes in a time course during the first hour after either stimulus. Rapid, transient changes in the relative abundance of specific transcripts occurred in response to gravity or mechanical stimulation, and these transcript level changes reveal clusters of coordinated events. Transcriptional regulation occurs in the root apices within less than 2 min after either stimulus. We identified genes responding specifically to each stimulus as well as transcripts regulated in both signal transduction pathways. Several unknown genes were specifically induced only during gravitropic stimulation (gravity induced genes). We also analyzed the network of transcriptional regulation during the early stages of gravitropism and mechanical stimulation.
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Affiliation(s)
- Jeffery M Kimbrough
- Department of Botany, North Carolina State University, Raleigh, NC 27695-7612, USA
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