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Mou SJ, Angon PB. Genome-wide characterization and expression profiling of FARL (FHY3/FAR1) family genes in Zea mays. J Genet Eng Biotechnol 2024; 22:100401. [PMID: 39179323 PMCID: PMC11342881 DOI: 10.1016/j.jgeb.2024.100401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 08/26/2024]
Abstract
A significant role of the plant is played by the transcription factor FARL, which is light signal transduction as well as plant growth and development. Despite being transposases, FARL has developed a variety of dominant biological actions in evolution and speciation. On the other hand, little is known about the Zea mays FARL protein family. This study identifies and characterizes fifteen ZmFARL genes genome-wide, and RNA sequencing data was used to profile their expression. 105 FARL proteins from five plant species were classified into five groups based on sequence alignment and phylogeny. The ZmFARL genes' exon-intron and motif distribution were conserved based on their evolutionary group. The fifteen ZmFARL genes were distributed over seven of the ten Z. mays chromosomes, although no duplication was discovered. Cis-element analysis reveals that ZmFARL genes play a variety of activities, including tissue-specific, stress- and hormone-responsive expressions. Furthermore, the results of the RNA sequencing used to profile expression showed that the genes ZmFARL2 and ZmFARL5 were much more expressed than other genes in various tissues, particularly in leaf characteristics. The identification of likely genes involved in cellular activity in Z. mays and related species will be aided by the characterization of the FARL genes.
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Affiliation(s)
- Sharah Jabeen Mou
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Prodipto Bishnu Angon
- Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
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2
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Zhao D, Guan P, Wei L, Gao J, Guo L, Tian D, Li Q, Guo Z, Cui H, Li Y, Guo J. Comprehensive identification and expression analysis of FAR1/FHY3 genes under drought stress in maize ( Zea mays L.). PeerJ 2024; 12:e17684. [PMID: 38952979 PMCID: PMC11216215 DOI: 10.7717/peerj.17684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024] Open
Abstract
Background FAR1/FHY3 transcription factors are derived from transposase, which play important roles in light signal transduction, growth and development, and response to stress by regulating downstream gene expression. Although many FAR1/FHY3 members have been identified in various species, the FAR1/FHY3 genes in maize are not well characterized and their function in drought are unknown. Method The FAR1/FHY3 family in the maize genome was identified using PlantTFDB, Pfam, Smart, and NCBI-CDD websites. In order to investigate the evolution and functions of FAR1 genes in maize, the information of protein sequences, chromosome localization, subcellular localization, conserved motifs, evolutionary relationships and tissue expression patterns were analyzed by bioinformatics, and the expression patterns under drought stress were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Results A total of 24 ZmFAR members in maize genome, which can be divided into five subfamilies, with large differences in protein and gene structures among subfamilies. The promoter regions of ZmFARs contain abundant abiotic stress-responsive and hormone-respovensive cis-elements. Among them, drought-responsive cis-elements are quite abundant. ZmFARs were expressed in all tissues detected, but the expression level varies widely. The expression of ZmFARs were mostly down-regulated in primary roots, seminal roots, lateral roots, and mesocotyls under water deficit. Most ZmFARs were down-regulated in root after PEG-simulated drought stress. Conclusions We performed a genome-wide and systematic identification of FAR1/FHY3 genes in maize. And most ZmFARs were down-regulated in root after drought stress. These results indicate that FAR1/FHY3 transcription factors have important roles in drought stress response, which can lay a foundation for further analysis of the functions of ZmFARs in response to drought stress.
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Affiliation(s)
- Dongbo Zhao
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Peiyan Guan
- College of Life Science, Dezhou University, Dezhou, Shandong, China
| | - Longxue Wei
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Jiansheng Gao
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Lianghai Guo
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Dianbin Tian
- Pingyuan County Rural Revitalization Service Center, Pingyuan, Shandong, China
| | - Qingfang Li
- Linyi County Agricultural and Rural Bureau, Linyi, Shandong, China
| | - Zhihui Guo
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Huini Cui
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Yongjun Li
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Jianjun Guo
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
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Jiang Y, Zeng Z, He G, Liu M, Liu C, Liu M, Lv T, Wang A, Wang Y, Zhao M, Wang K, Zhang M. Genome-wide identification and integrated analysis of the FAR1/FHY3 gene family and genes expression analysis under methyl jasmonate treatment in Panax ginseng C. A. Mey. BMC PLANT BIOLOGY 2024; 24:549. [PMID: 38872078 DOI: 10.1186/s12870-024-05239-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 06/03/2024] [Indexed: 06/15/2024]
Abstract
Ginseng (Panax ginseng C. A. Mey.) is an important and valuable medicinal plant species used in traditional Chinese medicine, and its metabolite ginsenoside is the primary active ingredient. The FAR1/FHY3 gene family members play critical roles in plant growth and development as well as participate in a variety of physiological processes, including plant development and signaling of hormones. Studies have indicated that methyl jasmonate treatment of ginseng adventitious roots resulted in a significant increase in the content of protopanaxadiol ginsenosides. Therefore, it is highly significant to screen the FAR1/FHY3 gene family members in ginseng and preliminarily investigate their expression patterns in response to methyl jasmonic acid signaling. In this study, we screened and identified the FAR1/FHY3 family genes in the ginseng transcriptome databases. And then, we analyzed their gene structure and phylogeny, chromosomal localization and expression patterns, and promoter cis-acting elements, and made GO functional annotations on the members of this family. After that, we treated the ginseng adventitious roots with 200 mM methyl jasmonate and investigated the trend of the expression of four genes containing the largest number of methyl jasmonate cis-acting elements at different treatment times. All four genes were able to respond to methyl jasmonate, the most significant change was in the PgFAR40 gene. This study provides data support for subsequent studies of this family member in ginseng and provides experimental reference for subsequent validation of the function of this family member under methyl jasmonic acid signaling.
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Affiliation(s)
- Yang Jiang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Zixia Zeng
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Gaohui He
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Mengna Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Chang Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Mingming Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Tingting Lv
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Aimin Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China.
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China.
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China.
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Chen S, Chen Y, Liang M, Qu S, Shen L, Zeng Y, Hou N. Genome-wide identification and molecular expression profile analysis of FHY3/FAR1 gene family in walnut (Juglans sigillata L.) development. BMC Genomics 2023; 24:673. [PMID: 37940838 PMCID: PMC10634098 DOI: 10.1186/s12864-023-09629-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/26/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Juglans sigillata L. (walnut) has a high economic value for nuts and wood and has been widely grown and eaten around the world. Light plays an important role in regulating the development of the walnut embryo and promoting nucleolus enlargement, which is one of the factors affecting the yield and quality of walnut. However, little is known about the effect of light on the growth and quality of walnuts. Studies have shown that far red prolonged hypocotyl 3 (FHY3) and far red damaged response (FAR1) play important roles in plant growth, light response, and resistance. Therefore, FHY3/FAR1 genes were identified in walnuts on a genome-wide basis during their growth and development to reveal the potential regulation mechanisms involved in walnut kernel growth and development. RESULTS In the present study, a total of 61 FHY3/FAR1 gene family members in walnuts have been identified, ranging in length from 117 aa to 895 aa. These gene family members have FHY3 or FAR1 conserved domains, which are unevenly distributed on the 15 chromosomes (Chr) of the walnut (except for the Chr16). All 61 FHY3/FAR1 genes were divided into five subclasses (I, II, III, IV, and V) by phylogenetic tree analysis. The results indicated that FHY3/FAR1 genes in the same subclasses with similar structures might be involved in regulating the growth and development of walnut. The gene expression profiles were analyzed in different walnut kernel varieties (Q, T, and F). The result showed that some FHY3/FAR1 genes might be involved in the regulation of walnut kernel ripening and seed coat color formation. Seven genes (OF07056-RA, OF09665-RA, OF24282-RA, OF26012-RA, OF28029-RA, OF28030-RA, and OF08124-RA) were predicted to be associated with flavonoid biosynthetic gene regulation cis-acting elements in promoter sequences. RT-PCR was used to verify the expression levels of candidate genes during the development and color change of walnut kernels. In addition, light responsiveness and MeJA responsiveness are important promoter regulatory elements in the FHY3/FAR1 gene family, which are potentially involved in the light response, growth, and development of walnut plants. CONCLUSION The results of this study provide a valuable reference for supplementing the genomic sequencing results of walnut, and pave the way for further research on the FHY3/FAR1 gene function of walnut.
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Affiliation(s)
- Shengqun Chen
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
| | - Yingfu Chen
- Guizhou Province Forestry Science and Technology Extension Station, Guiyang, 550000, China
| | - Mei Liang
- Guizhou Province Forestry Science and Technology Extension Station, Guiyang, 550000, China
| | - Shuang Qu
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
| | - Lianwen Shen
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
- Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
| | - Yajun Zeng
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China.
| | - Na Hou
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China.
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Lin S, Medina CA, Wang G, Combs D, Shewmaker G, Fransen S, Llewellyn D, Norberg S, Yu LX. Identification of genetic loci associated with five agronomic traits in alfalfa using multi-environment trials. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:121. [PMID: 37119337 DOI: 10.1007/s00122-023-04364-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/13/2023] [Indexed: 06/19/2023]
Abstract
The use of multi-environment trials to test yield-related traits in a diverse alfalfa panel allowed to find multiple molecular markers associated with complex agronomic traits. Yield is one of the most important target traits in alfalfa breeding; however, yield is a complex trait affected by genetic and environmental factors. In this study, we used multi-environment trials to test yield-related traits in a diverse panel composed of 200 alfalfa accessions and varieties. Phenotypic data of maturity stage measured as mean stage by count (MSC), dry matter content, plant height (PH), biomass yield (Yi), and fall dormancy (FD) were collected in three locations in Idaho, Oregon, and Washington from 2018 to 2020. Single-trial and stagewise analyses were used to obtain estimated trait means of entries by environment. The plants were genotyped using a genotyping by sequencing approach and obtained a genotypic matrix with 97,345 single nucleotide polymorphisms. Genome-wide association studies identified a total of 84 markers associated with the traits analyzed. Of those, 29 markers were in noncoding regions and 55 markers were in coding regions. Ten significant SNPs at the same locus were associated with FD and they were linked to a gene annotated as a nuclear fusion defective 4-like (NFD4). Additional SNPs associated with MSC, PH, and Yi were annotated as transcription factors such as Cysteine3Histidine (C3H), Hap3/NF-YB family, and serine/threonine-protein phosphatase 7 proteins, respectively. Our results provide insight into the genetic factors that influence alfalfa maturity, yield, and dormancy, which is helpful to speed up the genetic gain toward alfalfa yield improvement.
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Affiliation(s)
- Sen Lin
- USA Department of Agriculture - Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA, USA
| | - Cesar A Medina
- USA Department of Agriculture - Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA, USA
| | - Guojie Wang
- Department of Crop and Soil Science, Oregon State University, LaGrande, OR, USA
| | - David Combs
- Department of Dairy Science, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Steve Fransen
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Don Llewellyn
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Steven Norberg
- Franklin County Extension Office, Washington State University, Pasco, WA, USA.
| | - Long-Xi Yu
- USA Department of Agriculture - Agricultural Research Service, Plant Germplasm Introduction and Testing Research, Prosser, WA, USA.
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Dai J, Sun J, Peng W, Liao W, Zhou Y, Zhou XR, Qin Y, Cheng Y, Cao S. FAR1/FHY3 Transcription Factors Positively Regulate the Salt and Temperature Stress Responses in Eucalyptus grandis. FRONTIERS IN PLANT SCIENCE 2022; 13:883654. [PMID: 35599891 PMCID: PMC9115564 DOI: 10.3389/fpls.2022.883654] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
Abstract
FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1), which play pivotal roles in plant growth and development, are essential for the photo-induced phyA nuclear accumulation and subsequent photoreaction. The FAR1/FHY3 family has been systematically characterized in some plants, but not in Eucalyptus grandis. In this study, genome-wide identification of FAR1/FHY3 genes in E. grandis was performed using bioinformatic methods. The gene structures, chromosomal locations, the encoded protein characteristics, 3D models, phylogenetic relationships, and promoter cis-elements were analyzed with this gene family. A total of 33 FAR1/FHY3 genes were identified in E. grandis, which were divided into three groups based on their phylogenetic relationships. A total of 21 pairs of duplicated repeats were identified by homology analysis. Gene expression analysis showed that most FAR1/FHY3 genes were differentially expressed in a spatial-specific manner. Gene expression analysis also showed that FAR1/FHY3 genes responded to salt and temperature stresses. These results and observation will enhance our understanding of the evolution and function of the FAR1/FHY3 genes in E. grandis and facilitate further studies on the molecular mechanism of the FAR1/FHY3 gene family in growth and development regulations, especially in response to salt and temperature.
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Affiliation(s)
- Jiahao Dai
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- University Key Laboratory of Forest Stress Physiology, Ecology and Molecular Biology of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jin Sun
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenjing Peng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenhai Liao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- University Key Laboratory of Forest Stress Physiology, Ecology and Molecular Biology of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhan Zhou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xue-Rong Zhou
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT, Australia
| | - Yuan Qin
- Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, College of Life Science, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yan Cheng
- Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, College of Life Science, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- University Key Laboratory of Forest Stress Physiology, Ecology and Molecular Biology of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
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Wang F, Wang X, Zhang Y, Yan J, Ahammed GJ, Bu X, Sun X, Liu Y, Xu T, Qi H, Qi M, Li T. SlFHY3 and SlHY5 act compliantly to enhance cold tolerance through the integration of myo-inositol and light signaling in tomato. THE NEW PHYTOLOGIST 2022; 233:2127-2143. [PMID: 34936108 DOI: 10.1111/nph.17934] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Plants have evolved sophisticated regulatory networks to cope with dynamically changing light and temperature environments during day-night and seasonal cycles. However, the integration mechanisms of light and low temperature remain largely unclear. Here, we show that low red : far-red ratio (LR : FR) induces FAR-RED ELONGATED HYPOCOTYL3 (SlFHY3) transcription under cold stress in tomato (Solanum lycopersicum). Reverse genetic approaches revealed that knocking out SlFHY3 decreases myo-inositol accumulation and increases cold susceptibility, whereas overexpressing SlFHY3 induces myo-inositol accumulation and enhances cold tolerance in tomato plants. SlFHY3 physically interacts with ELONGATED HYPOCOTYL5 (SlHY5) to promote the transcriptional activity of SlHY5 on MYO-INOSITOL-1-PHOSPHATE SYNTHASE 3 (SlMIPS3) and induce myo-inositol accumulation in tomato plants under cold stress. Disruption of SlHY5 and SlMIPS3 largely suppresses the cold tolerance of SlFHY3-overexpressing plants and myo-inositol accumulation in tomato. Furthermore, silencing of SlMIPS3 drastically reduces myo-inositol accumulation and compromises LR : FR-induced cold tolerance in tomato. Together, our results reveal a crucial role of SlFHY3 in LR : FR-induced cold tolerance in tomato and unravel a novel regulatory mechanism whereby plants integrate dynamic environmental light signals and internal cues (inositol biosynthesis) to induce and control cold tolerance in tomato plants.
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Affiliation(s)
- Feng Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, 110866, China
| | - Xiujie Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Ying Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jiarong Yan
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Golam Jalal Ahammed
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471000, China
| | - Xin Bu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xin Sun
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yufeng Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, 110866, China
| | - Tao Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, 110866, China
| | - Hongyan Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, 110866, China
| | - Mingfang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, 110866, China
| | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, 110866, China
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8
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Li C, Qi L, Zhang S, Dong X, Jing Y, Cheng J, Feng Z, Peng J, Li H, Zhou Y, Wang X, Han R, Duan J, Terzaghi W, Lin R, Li J. Mutual upregulation of HY5 and TZP in mediating phytochrome A signaling. THE PLANT CELL 2022; 34:633-654. [PMID: 34741605 PMCID: PMC8774092 DOI: 10.1093/plcell/koab254] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/08/2021] [Indexed: 05/25/2023]
Abstract
Phytochrome A (phyA) is the far-red (FR) light photoreceptor in plants that is essential for seedling de-etiolation under FR-rich environments, such as canopy shade. TANDEM ZINC-FINGER/PLUS3 (TZP) was recently identified as a key component of phyA signal transduction in Arabidopsis thaliana; however, how TZP is integrated into the phyA signaling networks remains largely obscure. Here, we demonstrate that ELONGATED HYPOCOTYL5 (HY5), a well-characterized transcription factor promoting photomorphogenesis, mediates FR light induction of TZP expression by directly binding to a G-box motif in the TZP promoter. Furthermore, TZP physically interacts with CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), an E3 ubiquitin ligase targeting HY5 for 26S proteasome-mediated degradation, and this interaction inhibits COP1 interaction with HY5. Consistent with those results, TZP post-translationally promotes HY5 protein stability in FR light, and in turn, TZP protein itself is destabilized by COP1 in both dark and FR light conditions. Moreover, tzp hy5 double mutants display an additive phenotype relative to their respective single mutants under high FR light intensities, indicating that TZP and HY5 also function in largely independent pathways. Together, our data demonstrate that HY5 and TZP mutually upregulate each other in transmitting the FR light signal, thus providing insights into the complicated but delicate control of phyA signaling networks.
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Affiliation(s)
- Cong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lijuan Qi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shaoman Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaojing Dong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jinkui Cheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ziyi Feng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jing Peng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yangyang Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaoji Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Run Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jie Duan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania 18766, USA
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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9
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Li Z, Zhou W, Wang P, Chen Y, Huo S, Wang J, Tian D, Niu J, Zhao Y, Song X. Transcriptome Analysis Reveals the Senescence Process Controlling the Flower Opening and Closure Rhythm in the Waterlilies ( Nymphaea L.). FRONTIERS IN PLANT SCIENCE 2021; 12:701633. [PMID: 34671367 PMCID: PMC8521120 DOI: 10.3389/fpls.2021.701633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Most waterlily flowers open at dawn and close after noon usually for three to four days, and thereafter wilt. The short lifespan of flowers restricts the development of the flower postharvest industry. The termination of flower movements is a key event during flower aging process. However, it is still unclear when the senescence process initiates and how it terminates the movement rhythm. In this study, we observed that the opening diameter of flowers was the smallest on the fourth (last) flowering day. Subsequent transcriptome profiles generated from petals at different flowering stages showed that the multiple signaling pathways were activated at the last closure stage (Time 3, T3) of the flowers, including Ca2+, reactive oxygen species and far red light signaling pathways, as well as auxin, ethylene and jasmonic acid signaling pathways. Moreover, In terms of cell metabolism regulation, the genes related to hydrolase (protease, phospholipase, nuclease) were upregulated at T3 stage, indicating that petals entered the senescence stage at that time; and the genes related to water transport and cell wall modification were also differentially regulated at T3 stage, which would affect the ability of cell expand and contract, and eventually lead to petal not open after the fourth day. Collectively, our data provided a new insight into the termination of flower opening in the waterlilies, and a global understanding of the senescence process of those opening-closure rhythm flowers.
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Affiliation(s)
- Zhaoji Li
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Weijuan Zhou
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Peng Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yanfu Chen
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Shaojie Huo
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Jian Wang
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Daike Tian
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Centre, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jun Niu
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Ying Zhao
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Xiqiang Song
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
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10
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Liu S, Yang L, Li J, Tang W, Li J, Lin R. FHY3 interacts with phytochrome B and regulates seed dormancy and germination. PLANT PHYSIOLOGY 2021; 187:289-302. [PMID: 33764465 PMCID: PMC8418400 DOI: 10.1093/plphys/kiab147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/12/2021] [Indexed: 05/11/2023]
Abstract
Seed dormancy and germination are fundamental processes for plant propagation, both of which are tightly regulated by internal and external cues. Phytochrome B (phyB) is a major red/far-red-absorbing photoreceptor that senses light signals that modulate seed dormancy and germination. However, the components that directly transduce that signal downstream of phyB are mostly unknown. Here, we show that the transposase-derived transcription factor FAR-RED ELONGATED HYPOCOTYL3 (FHY3) inhibits seed dormancy and promotes phyB-mediated seed germination in Arabidopsis thaliana. FHY3 physically interacts with phyB in vitro and in vivo. RNA-sequencing and reverse transcription-quantitative polymerase chain reaction analyses showed that FHY3 regulates multiple downstream genes, including REVEILLE2 (RVE2), RVE7, and SPATULA (SPT). Yeast one-hybrid, electrophoresis mobility shift, and chromatin immunoprecipitation assays demonstrated that FHY3 directly binds these genes via a conserved FBS cis-element in their promoters. Furthermore, RVE2, RVE7, and GIBBERELLIN 3-OXIDASE 2 (GA3ox2) genetically act downstream of FHY3. Strikingly, light and phyB promote FHY3 protein accumulation. Our study reveals a transcriptional cascade consisting of phyB-FHY3-RVE2/RVE7/SPT-GA3ox2 that relays environmental light signals and thereby controls seed dormancy and germination.
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Affiliation(s)
- Shuangrong Liu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liwen Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jialong Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weijiang Tang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Author for communication:
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11
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Liu Z, An C, Zhao Y, Xiao Y, Bao L, Gong C, Gao Y. Genome-Wide Identification and Characterization of the CsFHY3/FAR1 Gene Family and Expression Analysis under Biotic and Abiotic Stresses in Tea Plants ( Camellia sinensis). PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10030570. [PMID: 33802900 PMCID: PMC8002597 DOI: 10.3390/plants10030570] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 05/17/2023]
Abstract
The FHY3/FAR1 transcription factor family, derived from transposases, plays important roles in light signal transduction, and in the growth and development of plants. However, the homologous genes in tea plants have not been studied. In this study, 25 CsFHY3/FAR1 genes were identified in the tea plant genome through a genome-wide study, and were classified into five subgroups based on their phylogenic relationships. Their potential regulatory roles in light signal transduction and photomorphogenesis, plant growth and development, and hormone responses were verified by the existence of the corresponding cis-acting elements. The transcriptome data showed that these genes could respond to salt stress and shading treatment. An expression analysis revealed that, in different tissues, especially in leaves, CsFHY3/FAR1s were strongly expressed, and most of these genes were positively expressed under salt stress (NaCl), and negatively expressed under low temperature (4 °C) stress. In addition, a potential interaction network demonstrated that PHYA, PHYC, PHYE, LHY, FHL, HY5, and other FRSs were directly or indirectly associated with CsFHY3/FAR1 members. These results will provide the foundation for functional studies of the CsFHY3/FAR1 family, and will contribute to the breeding of tea varieties with high light efficiency and strong stress resistance.
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Affiliation(s)
- Zhengjun Liu
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (Z.L.); (Y.Z.); (L.B.); (C.G.)
| | - Chuanjing An
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China;
| | - Yiqing Zhao
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (Z.L.); (Y.Z.); (L.B.); (C.G.)
| | - Yao Xiao
- Department of Foreign Languages, Northwest A&F University, Xianyang 712100, China;
| | - Lu Bao
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (Z.L.); (Y.Z.); (L.B.); (C.G.)
| | - Chunmei Gong
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (Z.L.); (Y.Z.); (L.B.); (C.G.)
| | - Yuefang Gao
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (Z.L.); (Y.Z.); (L.B.); (C.G.)
- Correspondence: ; Tel.: +86-029-8708-2613
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12
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Fernández-Calvo P, Iñigo S, Glauser G, Vanden Bossche R, Tang M, Li B, De Clercq R, Nagels Durand A, Eeckhout D, Gevaert K, De Jaeger G, Brady SM, Kliebenstein DJ, Pauwels L, Goossens A, Ritter A. FRS7 and FRS12 recruit NINJA to regulate expression of glucosinolate biosynthesis genes. THE NEW PHYTOLOGIST 2020; 227:1124-1137. [PMID: 32266972 DOI: 10.1111/nph.16586] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/25/2020] [Indexed: 05/24/2023]
Abstract
The sessile lifestyle of plants requires accurate physiology adjustments to be able to thrive in a changing environment. Plants integrate environmental timing signals to control developmental and stress responses. Here, we identified Far1 Related Sequence (FRS) 7 and FRS12, two transcriptional repressors that accumulate in short-day conditions, as regulators of Arabidopsis glucosinolate (GSL) biosynthesis. Loss of function of FRS7 and FRS12 results in plants with increased amplitudes of diurnal expression of GSL pathway genes. Protein interaction analyses revealed that FRS7 and FRS12 recruit the NOVEL INTERACTOR OF JAZ (NINJA) to assemble a transcriptional repressor complex. Genetic and molecular evidence demonstrated that FRS7, FRS12 and NINJA jointly regulate the expression of GSL biosynthetic genes, and thus constitute a molecular mechanism that modulates specialized metabolite accumulation.
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Affiliation(s)
- Patricia Fernández-Calvo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Sabrina Iñigo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Gaétan Glauser
- Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, Avenue de Bellevaux 51, 2000, Neuchâtel, Switzerland
| | - Robin Vanden Bossche
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Michelle Tang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Graduate Group in Plant Biology, University of California, Davis, CA, 95616, USA
| | - Baohua Li
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Rebecca De Clercq
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Astrid Nagels Durand
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, B-9000, Ghent, Belgium
- VIB Center for Medical Biotechnology, Albert Baertsoenkaai 3, B-9000, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- DynaMo Center of Excellence, University of Copenhagen, DK-1871, Frederiksberg C, Denmark
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Andrés Ritter
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
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13
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Liu Y, Ma M, Li G, Yuan L, Xie Y, Wei H, Ma X, Li Q, Devlin PF, Xu X, Wang H. Transcription Factors FHY3 and FAR1 Regulate Light-Induced CIRCADIAN CLOCK ASSOCIATED1 Gene Expression in Arabidopsis. THE PLANT CELL 2020; 32:1464-1478. [PMID: 32152179 PMCID: PMC7203938 DOI: 10.1105/tpc.19.00981] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/27/2020] [Accepted: 03/08/2020] [Indexed: 05/22/2023]
Abstract
The circadian clock provides a time-keeping mechanism that synchronizes various biological activities with the surrounding environment. Arabidopsis (Arabidopsis thaliana) CIRCADIAN CLOCK ASSOCIATED1 (CCA1), encoding a MYB-related transcription factor, is a key component of the core oscillator of the circadian clock, with peak expression in the morning. The molecular mechanisms regulating the light induction and rhythmic expression of CCA1 remain elusive. In this study, we show that two phytochrome signaling proteins, FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and its paralog FAR-RED IMPAIRED RESPONSE1 (FAR1), are essential for the light-induced expression of CCA1 FHY3 and FAR1 directly bind to the CCA1 promoter and activate its expression, whereas PHYTOCHROME INTERACTING FACTOR5 (PIF5) directly binds to its promoter and represses its expression. Furthermore, PIF5 and TIMING OF CAB EXPRESSION1 physically interact with FHY3 and FAR1 to repress their transcriptional activation activity on CCA1 expression. These findings demonstrate that the photosensory-signaling pathway integrates with circadian oscillators to orchestrate clock gene expression. This mechanism might form the molecular basis of the regulation of the clock system by light in response to daily changes in the light environment, thus increasing plant fitness.
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Affiliation(s)
- Yang Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mengdi Ma
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Li Yuan
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yurong Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongbin Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Xiaojing Ma
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Quanquan Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Paul F Devlin
- School of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, United Kingdom
| | - Xiaodong Xu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
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14
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Arabidopsis FHY3 and FAR1 integrate light and strigolactone signaling to regulate branching. Nat Commun 2020; 11:1955. [PMID: 32327664 PMCID: PMC7181604 DOI: 10.1038/s41467-020-15893-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 04/01/2020] [Indexed: 11/10/2022] Open
Abstract
Branching/tillering is an important parameter of plant architecture and is tightly regulated by both internal factors (such as plant hormones) and external factors (such as light conditions). How the various signaling pathways converge to coordinately regulate branching is not well understood. Here, we report that in Arabidopsis, FHY3 and FAR1, two homologous transcription factors essential for phytochrome A-mediated light signaling, and SMXL6/SMXL7/SMXL8, three key repressors of the strigolactone (SL) signaling pathway, directly interact with SPL9 and SPL15 and suppress their transcriptional activation of BRC1, a key repressor of branching, thus promoting branching. In addition, FHY3 and FAR1 also directly up-regulate the expression of SMXL6 and SMXL7 to promote branching. Simulated shade treatment reduces the accumulation of FHY3 protein, leading to increased expression of BRC1 and reduced branching. Our results establish an integrated model of light and SL coordinately regulating BRC1 expression and branching through converging at the BRC1 promoter. In plants, branching is regulated by both hormones and external cues such as light. Here the authors show that in Arabidopsis, the phytochrome A-signaling components FHY3 and FAR1, and SMXL proteins that repress strigolactone signaling, both interact with SPL proteins to control expression of the branching regulator BRC1.
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15
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Xie Y, Zhou Q, Zhao Y, Li Q, Liu Y, Ma M, Wang B, Shen R, Zheng Z, Wang H. FHY3 and FAR1 Integrate Light Signals with the miR156-SPL Module-Mediated Aging Pathway to Regulate Arabidopsis Flowering. MOLECULAR PLANT 2020; 13:483-498. [PMID: 32017999 DOI: 10.1016/j.molp.2020.01.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/13/2020] [Accepted: 01/28/2020] [Indexed: 05/15/2023]
Abstract
In response to competition for light from their neighbors, shade-intolerant plants flower precociously to ensure reproductive success and survival. However, the molecular mechanisms underlying this key developmental switch are not well understood. Here, we show that a pair of Arabidopsis transcription factors essential for phytochrome A signaling, FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED IMPAIRED RESPONSE1 (FAR1), regulate flowering time by integrating environmental light signals with the miR156-SPL module-mediated aging pathway. We found that FHY3 and FAR1 directly interact with three flowering-promoting SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors, SPL3, SPL4, and SPL5, and inhibit their binding to the promoters of several key flowering regulatory genes, including FRUITFUL (FUL), LEAFY (LFY), APETALA1 (AP1), and MIR172C, thus downregulating their transcript levels and delaying flowering. Under simulated shade conditions, levels of SPL3/4/5 proteins increase, whereas levels of FHY3 and FAR1 proteins decline, thus releasing SPL3/4/5 from FHY3/FAR1 inhibition to allow activation of FUL, LFY, AP1, and MIR172C and, consequently, early flowering. Taken together, these results unravel a novel mechanism whereby plants regulate flowering time by integrating environmental cues (such as light conditions) and an internal developmental program (the miR156-SPL module-mediated aging pathway).
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Affiliation(s)
- Yurong Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qin Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yongping Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Quanquan Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China
| | - Yang Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mengdi Ma
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rongxin Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Zhigang Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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16
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Zhang S, Li C, Zhou Y, Wang X, Li H, Feng Z, Chen H, Qin G, Jin D, Terzaghi W, Gu H, Qu LJ, Kang D, Deng XW, Li J. TANDEM ZINC-FINGER/PLUS3 Is a Key Component of Phytochrome A Signaling. THE PLANT CELL 2018; 30:835-852. [PMID: 29588390 PMCID: PMC5973844 DOI: 10.1105/tpc.17.00677] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 01/19/2018] [Accepted: 03/24/2018] [Indexed: 05/17/2023]
Abstract
Phytochrome A (phyA) is the primary plant photoreceptor responsible for perceiving and mediating various responses to far-red (FR) light and is essential for survival in canopy shade. In this study, we identified two Arabidopsis thaliana mutants that grew longer hypocotyls in FR light. Genetic analyses showed that they were allelic and their FR phenotypes were caused by mutations in the gene named TANDEM ZINC-FINGER/PLUS3 (TZP), previously shown to encode a nuclear protein involved in blue light signaling and phyB-dependent regulation of photoperiodic flowering. We show that the expression of TZP is dramatically induced by light and that TZP proteins are differentially modified in different light conditions. Furthermore, we show that TZP interacts with both phyA and FAR-RED ELONGATED HYPOCOTYL1 (FHY1) and regulates the abundance of phyA, FHY1, and ELONGATED HYPOCOTYL5 proteins in FR light. Moreover, our data indicate that TZP is required for the formation of a phosphorylated form of phyA in the nucleus in FR light. Together, our results identify TZP as a positive regulator of phyA signaling required for phosphorylation of the phyA photoreceptor, thus suggesting an important role of phosphorylated phyA in inducing the FR light response.
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Affiliation(s)
- Shaoman Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- MOE Key Laboratory of Crop Heterosis and Utilization, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Cong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yangyang Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaoji Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ziyi Feng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Haodong Chen
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Genji Qin
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dan Jin
- Key Laboratory of Biotechnology and Crop Quality Improvement of Ministry of Agriculture, Biotechnology Research Center, Southwest University, Chongqing 400716, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania 18766
| | - Hongya Gu
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Li-Jia Qu
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dingming Kang
- MOE Key Laboratory of Crop Heterosis and Utilization, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, The Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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17
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Ma L, Xue N, Fu X, Zhang H, Li G. Arabidopsis thaliana FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1) modulate starch synthesis in response to light and sugar. THE NEW PHYTOLOGIST 2017; 213:1682-1696. [PMID: 27859295 DOI: 10.1111/nph.14300] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/22/2016] [Indexed: 05/25/2023]
Abstract
In living organisms, daily light/dark cycles profoundly affect cellular processes. In plants, optimal growth and development, and adaptation to daily light-dark cycles, require starch synthesis and turnover. However, the underlying molecular mechanisms coordinating daily starch metabolism remain poorly understood. To explore the roles of Arabidopsis thaliana light signal transduction proteins FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1) in starch metabolism, the contents of starch and water-soluble polysaccharides, and the structure of starch granules were investigated in fhy3, far1 and fhy3 far1 mutant plants. Disruption of FHY3 or FAR1 reduced starch accumulation and altered starch granule structure in the fhy3-4, far1-2, and fhy3-4 far1-2 mutant plants. Furthermore, molecular and genetic evidence revealed that the gene encoding the starch-debranching enzyme ISOAMYLASE2 (ISA2) is a direct target of FHY3 and FAR1, and functions in light-induced starch synthesis. Our data establish the first molecular link between light signal transduction and starch synthesis, suggesting that the light-signaling proteins FHY3 and FAR1 influence starch synthesis and starch granule formation through transcriptional activation of ISA2.
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Affiliation(s)
- Lin Ma
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Na Xue
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiaoyu Fu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Haisen Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
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18
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Gupta P, Nutan KK, Singla-Pareek SL, Pareek A. Abiotic Stresses Cause Differential Regulation of Alternative Splice Forms of GATA Transcription Factor in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1944. [PMID: 29181013 PMCID: PMC5693882 DOI: 10.3389/fpls.2017.01944] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 10/30/2017] [Indexed: 05/05/2023]
Abstract
The GATA gene family is one of the most conserved families of transcription factors, playing a significant role in different aspects of cellular processes, in organisms ranging from fungi to angiosperms. GATA transcription factors are DNA-binding proteins, having a class IV zinc-finger motif CX2CX17-20CX2C followed by a highly basic region and are known to bind a consensus sequence WGATAR. In plants, GATAs are known to be involved in light-dependent gene regulation and nitrate assimilation. However, a comprehensive analysis of these GATA gene members has not yet been highlighted in rice when subjected to environmental stresses. In this study, we present an overview of the GATA gene family in rice (OsGATA) in terms of, their chromosomal distribution, domain architecture, and phylogeny. Our study has revealed the presence of 28 genes, encoding 35 putative GATA transcription factors belonging to seven subfamilies in the rice genome. Transcript abundance analysis in contrasting genotypes of rice-IR64 (salt sensitive) and Pokkali (salt tolerant), for individual GATA members indicated their differential expression in response to various abiotic stresses such as salinity, drought, and exogenous ABA. One of the members of subfamily VII-OsGATA23a, emerged as a multi-stress responsive transcription factor giving elevated expression levels in response to salinity and drought. ABA also induces expression of OsGATA23a by 35 and 55-folds in IR64 and Pokkali respectively. However, OsGATA23b, an alternative splice variant of OsGATA23 did not respond to above-mentioned stresses. Developmental regulation of the OsGATA genes based on a publicly available microarray database showed distinct expression patterns for most of the GATA members throughout different stages of rice development. Altogether, our results suggest inherent roles of diverse OsGATA factors in abiotic stress signaling and also throw some light on the tight regulation of the spliced variants of OsGATA genes in response to different environmental conditions.
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Affiliation(s)
- Priyanka Gupta
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Kamlesh K. Nutan
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh L. Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- *Correspondence: Ashwani Pareek
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19
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Liu L, Li B, Liu X. FAR-RED ELONGATED HYPOCOTYL3 promotes floral meristem determinacy in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2016; 11:e1238545. [PMID: 27660915 PMCID: PMC5155416 DOI: 10.1080/15592324.2016.1238545] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 05/20/2023]
Abstract
The transposase-derived transcription factor genes FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED IMPAIRED RESPONSE1 (FAR1) have redundant and multifaceted roles in plant growth and development during the vegetative stage, including phytochrome A-mediated far-red light (FR) signaling and circadian clock entrainment. Little is known about their functions in the reproductive stage. We recently demonstrated that FHY3 plays important roles in shoot apical meristem (SAM) maintenance and floral meristem (FM) determinacy through its target genes CLAVATA3 (CLV3), SEPALLATA1 (SEP1) and SEP2. Here we present data that FHY3 but not its homolog, FAR1, has a distinct role in FM determinacy in a manner independent of its light signaling and circadian pathway functions. Moreover, genome-wide gene expression profiling showed that the homeostasis of the FM is critical for the regulation of FM activity.
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Affiliation(s)
- Luping Liu
- State Key Laboratory of Plant Cell and
Chromosome Engineering, Center for Agricultural Resources Research, Institute of
Genetics and Developmental Biology, Chinese Academy of Sciences,
Shijiazhuang, China
- College of Life Sciences, University of
Chinese Academy of Sciences, Beijing, China
| | - Bo Li
- State Key Laboratory of Plant Cell and
Chromosome Engineering, Center for Agricultural Resources Research, Institute of
Genetics and Developmental Biology, Chinese Academy of Sciences,
Shijiazhuang, China
- College of Life Sciences, University of
Chinese Academy of Sciences, Beijing, China
| | - Xigang Liu
- State Key Laboratory of Plant Cell and
Chromosome Engineering, Center for Agricultural Resources Research, Institute of
Genetics and Developmental Biology, Chinese Academy of Sciences,
Shijiazhuang, China
- CONTACT Xigang Liu , Center for Agricultural Resources
Research, 286 Huaizhong Rd, Shijiazhuang 050021,
China
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20
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Joly-Lopez Z, Hoen DR, Blanchette M, Bureau TE. Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements. Mol Biol Evol 2016; 33:1937-56. [PMID: 27189548 PMCID: PMC4948706 DOI: 10.1093/molbev/msw067] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Once perceived as merely selfish, transposable elements (TEs) are now recognized as potent agents of adaptation. One way TEs contribute to evolution is through TE exaptation, a process whereby TEs, which persist by replicating in the genome, transform into novel host genes, which persist by conferring phenotypic benefits. Known exapted TEs (ETEs) contribute diverse and vital functions, and may facilitate punctuated equilibrium, yet little is known about this process. To better understand TE exaptation, we designed an approach to resolve the phylogenetic context and timing of exaptation events and subsequent patterns of ETE diversification. Starting with known ETEs, we search in diverse genomes for basal ETEs and closely related TEs, carefully curate the numerous candidate sequences, and infer detailed phylogenies. To distinguish TEs from ETEs, we also weigh several key genomic characteristics including repetitiveness, terminal repeats, pseudogenic features, and conserved domains. Applying this approach to the well-characterized plant ETEs MUG and FHY3, we show that each group is paraphyletic and we argue that this pattern demonstrates that each originated in not one but multiple exaptation events. These exaptations and subsequent ETE diversification occurred throughout angiosperm evolution including the crown group expansion, the angiosperm radiation, and the primitive evolution of angiosperms. In addition, we detect evidence of several putative novel ETE families. Our findings support the hypothesis that TE exaptation generates novel genes more frequently than is currently thought, often coinciding with key periods of evolution.
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Affiliation(s)
- Zoé Joly-Lopez
- Department of Biology, McGill University, Montréal, QC, Canada
| | - Douglas R Hoen
- Department of Biology, McGill University, Montréal, QC, Canada
| | | | - Thomas E Bureau
- Department of Biology, McGill University, Montréal, QC, Canada
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21
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Ma L, Tian T, Lin R, Deng XW, Wang H, Li G. Arabidopsis FHY3 and FAR1 Regulate Light-Induced myo-Inositol Biosynthesis and Oxidative Stress Responses by Transcriptional Activation of MIPS1. MOLECULAR PLANT 2016; 9:541-57. [PMID: 26714049 DOI: 10.1016/j.molp.2015.12.013] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 11/07/2015] [Accepted: 12/14/2015] [Indexed: 05/25/2023]
Abstract
myo-Inositol-1-phosphate synthase (MIPS) catalyzes the limiting step of inositol biosynthesis and has crucial roles in plant growth and development. In response to stress, the transcription of MIPS1 is induced and the biosynthesis of inositol or inositol derivatives is promoted by unknown mechanisms. Here, we found that the light signaling protein FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1) regulate light-induced inositol biosynthesis and oxidative stress responses by activating the transcription of MIPS1. Disruption of FHY3 and FAR1 caused light-induced cell death after dark-light transition, precocious leaf senescence, and increased sensitivity to oxidative stress. Reduction of salicylic acid (SA) accumulation by overexpression of SALICYLIC ACID 3-HYDROXYLASE largely suppressed the cell death phenotype of fhy3 far1 mutant plants, suggesting that FHY3- and FAR1-mediated cell death is dependent on SA. Furthermore, comparative analysis of chromatin immunoprecipitation sequencing and microarray results revealed that FHY3 and FAR1 directly target both MIPS1 and MIPS2. The fhy3 far1 mutant plants showed severely decreased MIPS1/2 transcript levels and reduced inositol levels. Conversely, constitutive expression of MIPS1 partially rescued the inositol contents, caused reduced transcript levels of SA-biosynthesis genes, and prevented oxidative stress in fhy3 far1. Taken together, our results indicate that the light signaling proteins FHY3 and FAR1 directly bind the promoter of MIPS1 to activate its expression and thereby promote inositol biosynthesis to prevent light-induced oxidative stress and SA-dependent cell death.
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Affiliation(s)
- Lin Ma
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Tian Tian
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Xing-Wang Deng
- National Laboratory of Protein and Plant Gene Research, Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Haiyang Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China.
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22
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Wang H, Wang H. Multifaceted roles of FHY3 and FAR1 in light signaling and beyond. TRENDS IN PLANT SCIENCE 2015; 20:453-61. [PMID: 25956482 DOI: 10.1016/j.tplants.2015.04.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 03/23/2015] [Accepted: 04/01/2015] [Indexed: 05/03/2023]
Abstract
FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), initially identified as crucial components of phytochrome A (phyA)-mediated far-red (FR) light signaling in Arabidopsis thaliana, are the founding members of the FAR1-related sequence (FRS) family of transcription factors present in most angiosperms. These proteins share extensive similarity with the Mutator-like transposases, indicative of their evolutionary history of 'molecular domestication'. Here we review emerging multifaceted roles of FHY3/FAR1 in diverse developmental and physiological processes, including UV-B signaling, circadian clock entrainment, flowering, chloroplast biogenesis, chlorophyll biosynthesis, programmed cell death, reactive oxygen species (ROS) homeostasis, abscisic acid (ABA) signaling, and branching. The domestication of FHY3/FAR1 may enable angiosperms to better integrate various endogenous and exogenous signals for coordinated regulation of growth and development, thus enhancing their fitness and adaptation.
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Affiliation(s)
- Hai Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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23
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Joly-Lopez Z, Bureau TE. Diversity and evolution of transposable elements in Arabidopsis. Chromosome Res 2015; 22:203-16. [PMID: 24801342 DOI: 10.1007/s10577-014-9418-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Transposable elements are mobile genetic elements that have successfully populated eukaryotic genomes and show diversity in their structure and transposition mechanisms. Although first viewed solely as selfish, transposable elements are now known as important vectors to drive the adaptation and evolution of their host genome. Transposable elements can affect host gene structures, gene copy number, gene expression, and even as a source for novel genes. For example, a number of transposable element sequences have been co-opted to contribute to evolutionary innovation, such as the mammalian placenta and the vertebrate immune system. In plants, the need to adapt rapidly to changing environmental conditions is essential and is reflected, as will be discussed, by genome plasticity and an abundance of diverse, active transposon families. This review focuses on transposable elements in plants, particularly those that have beneficial effects on the host. We also emphasize the importance of having proper tools to annotate and classify transposons to better understand their biology.
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Affiliation(s)
- Zoé Joly-Lopez
- Department of Biology, McGill University, Montreal, QC, Canada
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24
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Aguilar-Martínez JA, Uchida N, Townsley B, West DA, Yanez A, Lynn N, Kimura S, Sinha N. Transcriptional, posttranscriptional, and posttranslational regulation of SHOOT MERISTEMLESS gene expression in Arabidopsis determines gene function in the shoot apex. PLANT PHYSIOLOGY 2015; 167:424-42. [PMID: 25524441 PMCID: PMC4326739 DOI: 10.1104/pp.114.248625] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/12/2014] [Indexed: 05/21/2023]
Abstract
The activity of SHOOT MERISTEMLESS (STM) is required for the functioning of the shoot apical meristem (SAM). STM is expressed in the SAM but is down-regulated at the site of leaf initiation. STM is also required for the formation of compound leaves. However, how the activity of STM is regulated at the transcriptional, posttranscriptional, and posttranslational levels is poorly understood. We previously found two conserved noncoding sequences in the promoters of STM-like genes across angiosperms, the K-box and the RB-box. Here, we characterize the function of the RB-box in Arabidopsis (Arabidopsis thaliana). The RB-box, along with the K-box, regulates the expression of STM in leaf sinuses, which are areas on the leaf blade with meristematic potential. The RB-box also contributes to restrict STM expression to the SAM. We identified FAR1-RELATED SEQUENCES-RELATED FACTOR1 (FRF1) as a binding factor to the RB-box region. FRF1 is an uncharacterized member of a subfamily of four truncated proteins related to the FAR1-RELATED SEQUENCES factors. Internal deletion analysis of the STM promoter identified a region required to repress the expression of STM in hypocotyls. Expression of STM in leaf primordia under the control of the JAGGED promoter produced plants with partially undifferentiated leaves. We further found that the ELK domain has a role in the posttranslational regulation of STM by affecting the nuclear localization of STM.
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Affiliation(s)
- José Antonio Aguilar-Martínez
- Department of Plant Biology, University of California, Davis, California 95616 (J.A.A.-M., N.U., B.T., D.A.W., A.Y., N.L., S.K., N.S.);World Premier International Research Center Initiative-Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan (N.U.); andDepartment of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan (S.K.)
| | - Naoyuki Uchida
- Department of Plant Biology, University of California, Davis, California 95616 (J.A.A.-M., N.U., B.T., D.A.W., A.Y., N.L., S.K., N.S.);World Premier International Research Center Initiative-Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan (N.U.); andDepartment of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan (S.K.)
| | - Brad Townsley
- Department of Plant Biology, University of California, Davis, California 95616 (J.A.A.-M., N.U., B.T., D.A.W., A.Y., N.L., S.K., N.S.);World Premier International Research Center Initiative-Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan (N.U.); andDepartment of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan (S.K.)
| | - Donnelly Ann West
- Department of Plant Biology, University of California, Davis, California 95616 (J.A.A.-M., N.U., B.T., D.A.W., A.Y., N.L., S.K., N.S.);World Premier International Research Center Initiative-Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan (N.U.); andDepartment of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan (S.K.)
| | - Andrea Yanez
- Department of Plant Biology, University of California, Davis, California 95616 (J.A.A.-M., N.U., B.T., D.A.W., A.Y., N.L., S.K., N.S.);World Premier International Research Center Initiative-Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan (N.U.); andDepartment of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan (S.K.)
| | - Nafeesa Lynn
- Department of Plant Biology, University of California, Davis, California 95616 (J.A.A.-M., N.U., B.T., D.A.W., A.Y., N.L., S.K., N.S.);World Premier International Research Center Initiative-Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan (N.U.); andDepartment of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan (S.K.)
| | - Seisuke Kimura
- Department of Plant Biology, University of California, Davis, California 95616 (J.A.A.-M., N.U., B.T., D.A.W., A.Y., N.L., S.K., N.S.);World Premier International Research Center Initiative-Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan (N.U.); andDepartment of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan (S.K.)
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, California 95616 (J.A.A.-M., N.U., B.T., D.A.W., A.Y., N.L., S.K., N.S.);World Premier International Research Center Initiative-Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan (N.U.); andDepartment of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan (S.K.)
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25
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Tang W, Ji Q, Huang Y, Jiang Z, Bao M, Wang H, Lin R. FAR-RED ELONGATED HYPOCOTYL3 and FAR-RED IMPAIRED RESPONSE1 transcription factors integrate light and abscisic acid signaling in Arabidopsis. PLANT PHYSIOLOGY 2013; 163:857-66. [PMID: 23946351 PMCID: PMC3793063 DOI: 10.1104/pp.113.224386] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Light and the phytohormone abscisic acid (ABA) regulate overlapping processes in plants, such as seed germination and seedling development. However, the molecular mechanism underlying the interaction between light and ABA signaling is largely unknown. Here, we show that FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED IMPAIRED RESPONSE1 (FAR1), two key positive transcription factors in the phytochrome A pathway, directly bind to the promoter of ABA-Insensitive5 and activate its expression in Arabidopsis (Arabidopsis thaliana). Disruption of FHY3 and/or FAR1 reduces the sensitivity to ABA-mediated inhibition of seed germination, seedling development, and primary root growth. The seed germination of the fhy3 mutant is also less sensitive to salt and osmotic stress than that of the wild type. Constitutive expression of ABA-Insensitive5 restores the seed germination response of fhy3. Furthermore, the expression of several ABA-responsive genes is decreased in the fhy3 and/or far1 mutants during seed imbibition. Consistently, FHY3 and FAR1 transcripts are up-regulated by ABA and abiotic stresses. Moreover, the fhy3 and far1 mutants have wider stomata, lose water faster, and are more sensitive to drought than the wild type. These findings demonstrate that FHY3 and FAR1 are positive regulators of ABA signaling and provide insight into the integration of light and ABA signaling, a process that may allow plants to better adapt to environmental stresses.
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26
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Gao Y, Liu H, An C, Shi Y, Liu X, Yuan W, Zhang B, Yang J, Yu C, Gao H. Arabidopsis FRS4/CPD25 and FHY3/CPD45 work cooperatively to promote the expression of the chloroplast division gene ARC5 and chloroplast division. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:795-807. [PMID: 23662592 DOI: 10.1111/tpj.12240] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/01/2013] [Accepted: 05/08/2013] [Indexed: 05/21/2023]
Abstract
ARC5 is a dynamin-related GTPase essential for the division of chloroplasts in plants. The arc5 mutant frequently exhibits enlarged, dumbbell-shaped chloroplasts, indicating a role for ARC5 in the constriction of the chloroplast division site. In a screen for chloroplast division mutants with a phenotype similar to arc5, two mutants, cpd25 and cpd45, were obtained. CPD45 was identified as being the same gene as FHY3, a key regulator of far-red light signaling recently shown to be involved in the regulation of ARC5. CPD25 was previously named FRS4 and is homologous to FHY3. We found that CPD25 is also required for the expression of ARC5, suggesting that its function is not redundant to that of FHY3. Moreover, cpd25 does not have the far-red light-sensing defect present in fhy3 and far1. Both FRS4/CPD25 and FHY3/CPD45 could bind to the FBS-like 'ACGCGC' motifs in the promoter region of ARC5, and the binding efficiency of FRS4/CPD25 was much higher than that of FHY3/CPD45. Unlike FHY3/CPD45, FRS4/CPD25 has no ARC5 activation activity. Our data suggest that FRS4/CPD25 and FHY3/CPD45 function as a heterodimer that cooperatively activates ARC5, that FRS4/CPD25 plays the major role in promoter binding, and that FHY3/CPD45 is largely responsible for the gene activation. This study not only provides insight into the mechanisms underlying the regulation of chloroplast division in higher plants, but also suggests a model that shows how members of a transcription factor family can evolve to have different DNA-binding and gene activation features.
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Affiliation(s)
- Yuefang Gao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
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27
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Huang X, Ouyang X, Yang P, Lau OS, Li G, Li J, Chen H, Deng XW. Arabidopsis FHY3 and HY5 positively mediate induction of COP1 transcription in response to photomorphogenic UV-B light. THE PLANT CELL 2012; 24:4590-606. [PMID: 23150635 PMCID: PMC3531854 DOI: 10.1105/tpc.112.103994] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 10/19/2012] [Accepted: 10/28/2012] [Indexed: 05/19/2023]
Abstract
As sessile organisms, higher plants have evolved the capacity to sense and interpret diverse light signals to modulate their development. In Arabidopsis thaliana, low-intensity and long-wavelength UV-B light is perceived as an informational signal to mediate UV-B-induced photomorphogenesis. Here, we report that the multifunctional E3 ubiquitin ligase, CONSTITUTIVE PHOTOMORPHOGENESIS1 (COP1), a known key player in UV-B photomorphogenic responses, is also a UV-B-inducible gene. Two transcription factors, FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and ELONGATED HYPOCOTYL5 (HY5), directly bind to distinct regulatory elements within the COP1 promoter, which are essential for the induction of the COP1 gene mediated by photomorphogenic UV-B signaling. Absence of FHY3 results in impaired UV-B-induced hypocotyl growth and reduced tolerance against damaging UV-B. Thus, FHY3 positively regulates UV-B-induced photomorphogenesis by directly activating COP1 transcription, while HY5 promotes COP1 expression via a positive feedback loop. Furthermore, FHY3 and HY5 physically interact with each other, and this interaction is diminished by UV-B. Together, our findings reveal that COP1 gene expression in response to photomorphogenic UV-B is controlled by a combinatorial regulation of FHY3 and HY5, and this UV-B-specific working mode of FHY3 and HY5 is distinct from that in far-red light and circadian conditions.
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Affiliation(s)
- Xi Huang
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Xinhao Ouyang
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
- Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Panyu Yang
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Botany, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - On Sun Lau
- 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
| | - Jigang Li
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Haodong Chen
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
- Shenzhen Institute of Crop Molecular Design, Shenzhen 518107, China
- Address correspondence to
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Joly-Lopez Z, Forczek E, Hoen DR, Juretic N, Bureau TE. A gene family derived from transposable elements during early angiosperm evolution has reproductive fitness benefits in Arabidopsis thaliana. PLoS Genet 2012; 8:e1002931. [PMID: 22969437 PMCID: PMC3435246 DOI: 10.1371/journal.pgen.1002931] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 07/16/2012] [Indexed: 01/08/2023] Open
Abstract
The benefits of ever-growing numbers of sequenced eukaryotic genomes will not be fully realized until we learn to decipher vast stretches of noncoding DNA, largely composed of transposable elements. Transposable elements persist through self-replication, but some genes once encoded by transposable elements have, through a process called molecular domestication, evolved new functions that increase fitness. Although they have conferred numerous adaptations, the number of such domesticated transposable element genes remains unknown, so their evolutionary and functional impact cannot be fully assessed. Systematic searches that exploit genomic signatures of natural selection have been employed to identify potential domesticated genes, but their predictions have yet to be experimentally verified. To this end, we investigated a family of domesticated genes called MUSTANG (MUG), identified in a previous bioinformatic search of plant genomes. We show that MUG genes are functional. Mutants of Arabidopsis thaliana MUG genes yield phenotypes with severely reduced plant fitness through decreased plant size, delayed flowering, abnormal development of floral organs, and markedly reduced fertility. MUG genes are present in all flowering plants, but not in any non-flowering plant lineages, such as gymnosperms, suggesting that the molecular domestication of MUG may have been an integral part of early angiosperm evolution. This study shows that systematic searches can be successful at identifying functional genetic elements in noncoding regions and demonstrates how to combine systematic searches with reverse genetics in a fruitful way to decipher eukaryotic genomes. The genomes of complex organisms are mostly made up not of ordinary genes but of transposable elements. Transposable elements have been called “selfish DNA” because they normally persist by copying themselves, not by helping the organism to survive or reproduce. Yet transposable elements can help organisms to evolve; for instance, transposable element genes sometimes acquire new functions that do benefit the organism. Because they are difficult to distinguish from transposable elements, little is known about these “domesticated genes.” Although studies have attempted to identify them computationally, the predictions have not been verified experimentally. Here, we examine some of the first domesticated genes to be predicted computationally, the MUSTANG family of plant genes. We show that the predictions were correct: MUSTANGs are, like ordinary genes, functional. MUSTANG mutations result in serious defects in how plants grow, flower, and reproduce. Since they are present only in flowering plants, MUSTANG probably originated when flowers first evolved, perhaps taking on a key role. This study is important both because it shows that MUSTANG is critical to plant fitness and because, in the future, a similar approach can be used to find additional domesticated genes and to better understand how transposable elements contribute to evolution.
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Affiliation(s)
| | | | | | | | - Thomas E. Bureau
- Department of Biology, McGill University, Montreal, Quebec, Canada
- * E-mail:
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29
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Manetti ME, Rossi M, Cruz GMQ, Saccaro NL, Nakabashi M, Altebarmakian V, Rodier-Goud M, Domingues D, D’Hont A, Van Sluys MA. Mutator System Derivatives Isolated from Sugarcane Genome Sequence. TROPICAL PLANT BIOLOGY 2012; 5:233-243. [PMID: 22905278 PMCID: PMC3418495 DOI: 10.1007/s12042-012-9104-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 05/03/2012] [Indexed: 06/01/2023]
Abstract
Mutator-like transposase is the most represented transposon transcript in the sugarcane transcriptome. Phylogenetic reconstructions derived from sequenced transcripts provided evidence that at least four distinct classes exist (I-IV) and that diversification among these classes occurred early in Angiosperms, prior to the divergence of Monocots/Eudicots. The four previously described classes served as probes to select and further sequence six BAC clones from a genomic library of cultivar R570. A total of 579,352 sugarcane base pairs were produced from these "Mutator system" BAC containing regions for further characterization. The analyzed genomic regions confirmed that the predicted structure and organization of the Mutator system in sugarcane is composed of two true transposon lineages, each containing a specific terminal inverted repeat and two transposase lineages considered to be domesticated. Each Mutator transposase class displayed a particular molecular structure supporting lineage specific evolution. MUSTANG, previously described domesticated genes, are located in syntenic regions across Sacharineae and, as expected for a host functional gene, posses the same gene structure as in other Poaceae. Two sequenced BACs correspond to hom(eo)logous locus with specific retrotransposon insertions that discriminate sugarcane haplotypes. The comparative studies presented, add information to the Mutator systems previously identified in the maize and rice genomes by describing lineage specific molecular structure and genomic distribution pattern in the sugarcane genome. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12042-012-9104-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M. E. Manetti
- Departamento de Botânica-IB-USP, GaTE Lab, Brasil, Rua do Matão, 277, 05508-900 São Paulo, SP Brazil
| | - M. Rossi
- Departamento de Botânica-IB-USP, GaTE Lab, Brasil, Rua do Matão, 277, 05508-900 São Paulo, SP Brazil
| | - G. M. Q. Cruz
- Departamento de Botânica-IB-USP, GaTE Lab, Brasil, Rua do Matão, 277, 05508-900 São Paulo, SP Brazil
| | - N. L. Saccaro
- Departamento de Botânica-IB-USP, GaTE Lab, Brasil, Rua do Matão, 277, 05508-900 São Paulo, SP Brazil
| | - M. Nakabashi
- Departamento de Botânica-IB-USP, GaTE Lab, Brasil, Rua do Matão, 277, 05508-900 São Paulo, SP Brazil
| | - V. Altebarmakian
- Departamento de Botânica-IB-USP, GaTE Lab, Brasil, Rua do Matão, 277, 05508-900 São Paulo, SP Brazil
| | - M. Rodier-Goud
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - D. Domingues
- Departamento de Botânica-IB-USP, GaTE Lab, Brasil, Rua do Matão, 277, 05508-900 São Paulo, SP Brazil
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - A. D’Hont
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - M. A. Van Sluys
- Departamento de Botânica-IB-USP, GaTE Lab, Brasil, Rua do Matão, 277, 05508-900 São Paulo, SP Brazil
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30
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Stirnberg P, Zhao S, Williamson L, Ward S, Leyser O. FHY3 promotes shoot branching and stress tolerance in Arabidopsis in an AXR1-dependent manner. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:907-20. [PMID: 22540368 DOI: 10.1111/j.1365-313x.2012.05038.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The transposase-related transcription factor FAR-RED ELONGATED HYPOCOTYL3 (FHY3) promotes seedling de-etiolation in far-red light, which is perceived by phytochrome A (phyA). In this role, FHY3 indirectly mediates the nuclear import of light-activated phyA, which triggers downstream transcriptional responses. Here, we present genetic evidence for additional roles of FHY3 in plant development and growth. New fhy3 alleles were isolated as suppressors of max2-1 (more axillary branching2-1), a strigolactone-insensitive mutant characterised by highly branched shoots. Branching suppression by fhy3, in both wild-type and max2-1 backgrounds, resulted from inhibition of axillary bud outgrowth. Additional roles in axillary meristem initiation were revealed in the revoluta (rev) fhy3 double mutant, with fhy3 enhancing rev mutant defects in axillary shoot meristem formation, as well as in floral meristem maintenance. fhy3 also affected embryonic and floral patterning with low penetrance, and displayed oxidative stress-related phenotypes of retarded leaf growth and of cell death. The fhy3 phenotypes of axillary bud outgrowth suppression and of stress-induced leaf growth retardation both required the AUXIN-RESISTANT1 gene, and are independent of phyA. Consistent with the recent discovery that FHY3 regulates many Arabidopsis promoters, our results suggest much wider roles for FHY3 in growth and development, either in concert with, or beyond, light signalling.
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Affiliation(s)
- Petra Stirnberg
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
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31
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Tang W, Wang W, Chen D, Ji Q, Jing Y, Wang H, Lin R. Transposase-derived proteins FHY3/FAR1 interact with PHYTOCHROME-INTERACTING FACTOR1 to regulate chlorophyll biosynthesis by modulating HEMB1 during deetiolation in Arabidopsis. THE PLANT CELL 2012; 24:1984-2000. [PMID: 22634759 PMCID: PMC3442582 DOI: 10.1105/tpc.112.097022] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 04/30/2012] [Accepted: 05/10/2012] [Indexed: 05/18/2023]
Abstract
Successful chlorophyll biosynthesis during initial light exposure is critical for plant survival and growth, as excess accumulation of chlorophyll precursors in darkness can cause photooxidative damage to cells. Therefore, efficient mechanisms have evolved to precisely regulate chlorophyll biosynthesis in plants. Here, we identify FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED IMPAIRED RESPONSE1 (FAR1), two transposase-derived transcription factors, as positive regulators of chlorophyll biosynthesis in Arabidopsis thaliana. We show that null mutations in FHY3 and FAR1 cause reduced protochlorophyllide (a precursor of chlorophyll) levels in darkness and less photobleaching in the light. We find that FHY3 directly binds to the promoter and activates expression of HEMB1, which encodes 5-aminolevulinic acid dehydratase in the chlorophyll biosynthetic pathway. We reveal that PHYTOCHROME-INTERACTING FACTOR1 physically interacts with the DNA binding domain of FHY3, thereby partly repressing FHY3/FAR1-activated HEMB1 expression. Strikingly, FHY3 expression is upregulated by white light. In addition, our genetic data indicate that overexpression, severe reduction, or lack of HEMB1 impairs plant growth and development. Together, our findings reveal a crucial role of FHY3/FAR1 in regulating chlorophyll biosynthesis, thus uncovering a new layer of regulation by which light promotes plant dark-light transition in early seedling development.
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Affiliation(s)
- Weijiang Tang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wanqing Wang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100049, China
| | - Dongqin Chen
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Qiang Ji
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Haiyang Wang
- College of Life Sciences, Capital Normal University, Beijing 100048, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Address correspondence to
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32
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Li J, Terzaghi W, Deng XW. Genomic basis for light control of plant development. Protein Cell 2012; 3:106-16. [PMID: 22426979 PMCID: PMC4875414 DOI: 10.1007/s13238-012-2016-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 02/05/2012] [Indexed: 10/28/2022] Open
Abstract
Light is one of the key environmental signals regulating plant growth and development. Therefore, understanding the mechanisms by which light controls plant development has long been of great interest to plant biologists. Traditional genetic and molecular approaches have successfully identified key regulatory factors in light signaling, but recent genomic studies have revealed massive reprogramming of plant transcriptomes by light, identified binding sites across the entire genome of several pivotal transcription factors in light signaling, and discovered the involvement of epigenetic regulation in light-regulated gene expression. This review summarizes the key genomic work conducted in the last decade which provides new insights into light control of plant development.
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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, CT 06520-8104 USA
| | - William Terzaghi
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8104 USA
- Department of Biology, Wilkes University, Wilkes-Barre, PA 18766 USA
| | - 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, CT 06520-8104 USA
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34
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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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Bohne A, Zhou Q, Darras A, Schmidt C, Schartl M, Galiana-Arnoux D, Volff JN. Zisupton--A Novel Superfamily of DNA Transposable Elements Recently Active in Fish. Mol Biol Evol 2011; 29:631-45. [DOI: 10.1093/molbev/msr208] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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36
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Smirnova OG, Stepanenko IL, Shumnyi VK. The role of the COP1, SPA, and PIF proteins in plant photomorphogenesis. ACTA ACUST UNITED AC 2011. [DOI: 10.1134/s2079086411040098] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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37
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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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38
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Ouyang X, Li J, Li G, Li B, Chen B, Shen H, Huang X, Mo X, Wan X, Lin R, Li S, Wang H, Deng XW. Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development. THE PLANT CELL 2011; 23:2514-35. [PMID: 21803941 PMCID: PMC3226222 DOI: 10.1105/tpc.111.085126] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 07/10/2011] [Accepted: 07/17/2011] [Indexed: 05/18/2023]
Abstract
FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1), two transposase-derived transcription factors, are key components in phytochrome A signaling and the circadian clock. Here, we use chromatin immunoprecipitation-based sequencing (ChIP-seq) to identify 1559 and 1009 FHY3 direct target genes in darkness (D) and far-red (FR) light conditions, respectively, in the Arabidopsis thaliana genome. FHY3 preferentially binds to promoters through the FHY3/FAR1 binding motif (CACGCGC). Interestingly, FHY3 also binds to two motifs in the 178-bp Arabidopsis centromeric repeats. Comparison between the ChIP-seq and microarray data indicates that FHY3 quickly regulates the expression of 197 and 86 genes in D and FR, respectively. FHY3 also coregulates a number of common target genes with PHYTOCHROME INTERACTING FACTOR 3-LIKE5 and ELONGATED HYPOCOTYL5. Moreover, we uncover a role for FHY3 in controlling chloroplast development by directly activating the expression of ACCUMULATION AND REPLICATION OF CHLOROPLASTS5, whose product is a structural component of the latter stages of chloroplast division in Arabidopsis. Taken together, our data suggest that FHY3 regulates multiple facets of plant development, thus providing insights into its functions beyond light and circadian pathways.
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Affiliation(s)
- Xinhao Ouyang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
- Rice Research Institute of Sichuan Agriculture University, Chengdu, Sichuan 611130, China
| | - Jigang Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
| | - Gang Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Bosheng Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Beibei Chen
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Huaishun Shen
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Xi Huang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Xiaorong Mo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Xiangyuan Wan
- National Engineering Research Center for Crop Molecular Design, Beijing 100085, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shigui Li
- Rice Research Institute of Sichuan Agriculture University, Chengdu, Sichuan 611130, China
| | - Haiyang Wang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
- National Engineering Research Center for Crop Molecular Design, Beijing 100085, China
| | - Xing Wang Deng
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
- National Engineering Research Center for Crop Molecular Design, Beijing 100085, China
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39
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Li G, Siddiqui H, Teng Y, Lin R, Wan XY, Li J, Lau OS, Ouyang X, Dai M, Wan J, Devlin PF, Deng XW, Wang H. Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nat Cell Biol 2011; 13:616-22. [PMID: 21499259 DOI: 10.1038/ncb2219] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 01/28/2011] [Indexed: 12/23/2022]
Abstract
The circadian clock controls many metabolic, developmental and physiological processes in a time-of-day-specific manner in both plants and animals. The photoreceptors involved in the perception of light and entrainment of the circadian clock have been well characterized in plants. However, how light signals are transduced from the photoreceptors to the central circadian oscillator, and how the rhythmic expression pattern of a clock gene is generated and maintained by diurnal light signals remain unclear. Here, we show that in Arabidopsis thaliana, FHY3, FAR1 and HY5, three positive regulators of the phytochrome A signalling pathway, directly bind to the promoter of ELF4, a proposed component of the central oscillator, and activate its expression during the day, whereas the circadian-controlled CCA1 and LHY proteins directly suppress ELF4 expression periodically at dawn through physical interactions with these transcription-promoting factors. Our findings provide evidence that a set of light- and circadian-regulated transcription factors act directly and coordinately at the ELF4 promoter to regulate its cyclic expression, and establish a potential molecular link connecting the environmental light-dark cycle to the central oscillator.
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Affiliation(s)
- Gang Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
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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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41
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Li J, Li G, Gao S, Martinez C, He G, Zhou Z, Huang X, Lee JH, Zhang H, Shen Y, Wang H, Deng XW. Arabidopsis transcription factor ELONGATED HYPOCOTYL5 plays a role in the feedback regulation of phytochrome A signaling. THE PLANT CELL 2010; 22:3634-49. [PMID: 21097709 PMCID: PMC3015127 DOI: 10.1105/tpc.110.075788] [Citation(s) in RCA: 143] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 10/28/2010] [Accepted: 11/05/2010] [Indexed: 05/19/2023]
Abstract
Phytochrome A (phyA) is the primary photoreceptor responsible for perceiving and mediating various responses to far-red light in Arabidopsis thaliana. FAR-RED ELONGATED HYPOCOTYL1 (FHY1) and its homolog FHY1-LIKE (FHL) are two small plant-specific proteins essential for light-regulated phyA nuclear accumulation and subsequent phyA signaling processes. FHY3 and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1) are two transposase-derived transcription factors that directly activate FHY1/FHL transcription and thus mediate subsequent phyA nuclear accumulation and responses. Here, we report that ELONGATED HYPOCOTYL5 (HY5), a well-characterized bZIP transcription factor involved in promoting photomorphogenesis, directly binds ACGT-containing elements a few base pairs away from the FHY3/FAR1 binding sites in the FHY1/FHL promoters. We demonstrate that HY5 physically interacts with FHY3/FAR1 through their respective DNA binding domains and negatively regulates FHY3/FAR1-activated FHY1/FHL expression under far-red light. Together, our data show that HY5 plays a role in negative feedback regulation of phyA signaling by attenuating FHY3/FAR1-activated FHY1/FHL expression, providing a mechanism for fine-tuning phyA signaling homeostasis.
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Affiliation(s)
- Jigang Li
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, 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
| | - Shumin Gao
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Cristina Martinez
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Guangming He
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Zhenzhen Zhou
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Xi Huang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Jae-Hoon Lee
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Huiyong Zhang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Yunping Shen
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
- 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, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
- Address correspondence to
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