1
|
Zhou H, Zeng H, Yan T, Chen S, Fu Y, Qin G, Zhao X, Heng Y, Li J, Lin F, Xu D, Wei N, Deng XW. Light regulates nuclear detainment of intron-retained transcripts through COP1-spliceosome to modulate photomorphogenesis. Nat Commun 2024; 15:5130. [PMID: 38879536 PMCID: PMC11180117 DOI: 10.1038/s41467-024-49571-9] [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: 05/28/2023] [Accepted: 06/10/2024] [Indexed: 06/19/2024] Open
Abstract
Intron retention (IR) is the most common alternative splicing event in Arabidopsis. An increasing number of studies have demonstrated the major role of IR in gene expression regulation. The impacts of IR on plant growth and development and response to environments remain underexplored. Here, we found that IR functions directly in gene expression regulation on a genome-wide scale through the detainment of intron-retained transcripts (IRTs) in the nucleus. Nuclear-retained IRTs can be kept away from translation through this mechanism. COP1-dependent light modulation of the IRTs of light signaling genes, such as PIF4, RVE1, and ABA3, contribute to seedling morphological development in response to changing light conditions. Furthermore, light-induced IR changes are under the control of the spliceosome, and in part through COP1-dependent ubiquitination and degradation of DCS1, a plant-specific spliceosomal component. Our data suggest that light regulates the activity of the spliceosome and the consequent IRT nucleus detainment to modulate photomorphogenesis through COP1.
Collapse
Affiliation(s)
- Hua Zhou
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Haiyue Zeng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, 61000, Shandong, China
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Tingting Yan
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Fu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, 61000, Shandong, China
| | - Guochen Qin
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, 61000, Shandong, China
| | - Xianhai Zhao
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yueqin Heng
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jian Li
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Fang Lin
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, 730000, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ning Wei
- School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xing Wang Deng
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Southern University of Science and Technology, Shenzhen, 518055, China.
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, 61000, Shandong, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.
| |
Collapse
|
2
|
Chen L, Meng Y, Yang W, Lv Q, Zhou L, Liu S, Tang C, Xie Y, Li X. Genome-wide analysis and identification of TaRING-H2 gene family and TaSDIR1 positively regulates salt stress tolerance in wheat. Int J Biol Macromol 2023:125162. [PMID: 37263334 DOI: 10.1016/j.ijbiomac.2023.125162] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/18/2023] [Accepted: 05/29/2023] [Indexed: 06/03/2023]
Abstract
Salt stress is an abiotic stress factor that limits high yields, and thus identifying salt tolerance genes is very important for improving the tolerance of salt in wheat. In this study we identified 274 TaRING-H2 family members and analyzed their gene positions, gene structures, conserved structural domains, promoter cis-acting elements and covariance relationships. And we investigated TaRING-H2-120 (TaSDIR1) in salt stress. Transgenic lines exhibited higher salt tolerance in the germination and seedling stages. Compared with the wild type, overexpression of TaSDIR1 upregulated the expression of genes encoding enzymes related to the control of reactive oxygen species (ROS), thereby reducing the accumulation of ROS, as well as increased the expression of ion transport-related genes to limit the inward flow of Na+ in vivo and maintain a higher K+/Na+ ratio. The expression levels of these genes were opposite in lines where TaSDIR1 was silenced by BSMV-VIGS, and the silenced wheat exhibited higher salt sensitivity. Arabidopsis mutants and heterologous TaSDIR1 overexpressing lines had similar salt stress tolerance phenotypes. We also demonstrated that TaSDIR1 interacted with TaSDIR1P2 in vivo and in vitro. A sequence of 80-100 amino acids in TaSDIR1P2 encoded a coiled coil domain that was important for the activity of E3 ubiquitin ligase, and it was also the core region for the interaction between TaSDIR1 and TaSDIR1P2. Overall, our results suggest that TaSDIR1 positively regulates salt stress tolerance in wheat.
Collapse
Affiliation(s)
- Liuping Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ying Meng
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weibing Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Qian Lv
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ling Zhou
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuqing Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chenghan Tang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanzhou Xie
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xuejun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| |
Collapse
|
3
|
Lan H, Heng Y, Li J, Zhang M, Bian Y, Chu L, Jiang Y, Wang X, Xu D, Deng XW. COP1 SUPPRESSOR 6 represses the PIF4 and PIF5 action to promote light-inhibited hypocotyl growth. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2097-2110. [PMID: 36029156 DOI: 10.1111/jipb.13350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Light signaling precisely controls photomorphogenic development in plants. PHYTOCHROME INTERACTING FACTOR 4 and 5 (PIF4 and PIF5) play critical roles in the regulation of this developmental process. In this study, we report CONSTITUTIVELY PHOTOMORPHOGENIC 1 SUPPRESSOR 6 (CSU6) functions as a key regulator of light signaling. Loss of CSU6 function largely rescues the cop1-6 constitutively photomorphogenic phenotype. CSU6 promotes hypocotyl growth in the dark, but inhibits hypocotyl elongation in the light. CSU6 not only associates with the promoter regions of PIF4 and PIF5 to inhibit their expression in the morning, but also directly interacts with both PIF4 and PIF5 to repress their transcriptional activation activity. CSU6 negatively controls a group of PIF4- and PIF5-regulated gene expressions. Mutations in PIF4 and/or PIF5 are epistatic to the loss of CSU6, suggesting that CSU6 acts upstream of PIF4 and PIF5. Taken together, CSU6 promotes light-inhibited hypocotyl elongation by negatively regulating PIF4 and PIF5 transcription and biochemical activity.
Collapse
Affiliation(s)
- Hongxia Lan
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yueqin Heng
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jian Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Mengdi Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yeting Bian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li Chu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Jiang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuncheng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xing Wang Deng
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
| |
Collapse
|
4
|
Kang H, Zhang TT, Li YY, Lin-Wang K, Espley RV, Du YP, Guan QM, Ma FW, Hao YJ, You CX, Wang XF. The apple BTB protein MdBT2 positively regulates MdCOP1 abundance to repress anthocyanin biosynthesis. PLANT PHYSIOLOGY 2022; 190:305-318. [PMID: 35674376 PMCID: PMC9434159 DOI: 10.1093/plphys/kiac279] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/11/2022] [Indexed: 05/27/2023]
Abstract
The ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) plays a central role in light-induced anthocyanin biosynthesis. However, the upstream regulatory factors of COP1 remain poorly understood, particularly in horticultural plants. Here, we identified an MdCOP1-interacting protein, BROAD-COMPLEX, TRAMTRACK AND BRIC A BRAC2 (MdBT2), in apple (Malus domestica). MdBT2 is a BTB protein that directly interacts with and stabilizes MdCOP1 by inhibiting self-ubiquitination. Fluorescence observation and cell fractionation assays showed that MdBT2 increased the abundance of MdCOP1 in the nucleus. Moreover, a series of phenotypic analyses indicated that MdBT2 promoted MdCOP1-mediated ubiquitination and degradation of the MdMYB1 transcription factor, inhibiting the expression of anthocyanin biosynthesis genes and anthocyanin accumulation. Overall, our findings reveal a molecular mechanism by which MdBT2 positively regulates MdCOP1, providing insight into MdCOP1-mediated anthocyanin biosynthesis.
Collapse
Affiliation(s)
- Hui Kang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yang-Ling, Shaanxi 712100, China
| | - Ting-Ting Zhang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Yuan-Yuan Li
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Kui Lin-Wang
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert, Auckland 92169, New Zealand
| | - Richard V Espley
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert, Auckland 92169, New Zealand
| | - Yuan-Peng Du
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Qing-Mei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yang-Ling, Shaanxi 712100, China
| | - Feng-Wang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yang-Ling, Shaanxi 712100, China
| | | | | | | |
Collapse
|
5
|
Zhou H, Zhu W, Wang X, Bian Y, Jiang Y, Li J, Wang L, Yin P, Deng XW, Xu D. A missense mutation in WRKY32 converts its function from a positive regulator to a repressor of photomorphogenesis. THE NEW PHYTOLOGIST 2022; 235:111-125. [PMID: 34935148 DOI: 10.1111/nph.17932] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) mediates various cellular and physiological processes in plants by targeting a large number of substrates for ubiquitination and degradation. In this study, we reveal that a substitution of Pro for Leu at amino acid position 409 in WRKY32 largely suppresses the short hypocotyls and expanded cotyledon phenotypes of cop1-6. WRKY32P409L promotes hypocotyl growth and inhibits the opening of cotyledons in Arabidopsis. Loss of WRKY32 function mutant seedlings display elongated hypocotyls, whereas overexpression of WRKY32 leads to shortened hypocotyls. WRKY32 directly associates with the promoter regions of HY5 to activate its transcription. COP1 interacts with and targets WRKY32 for ubiquitination and degradation in darkness. WRKY32P409L exhibits enhanced DNA binding ability and affects the expression of more genes compared with WRKY32 in Arabidopsis. Our results not only reveal the basic role for WRKY32 in promoting photomorphogenesis, but also provide insights into manipulating plant growth by engineering key components of light signaling.
Collapse
Affiliation(s)
- Hua Zhou
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wei Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuncheng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yeting Bian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Jiang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jian Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Lixia Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xing Wang Deng
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
6
|
Koranne R, Brown K, Vandenbroek H, Taylor WR. C9ORF78 partially localizes to centromeres and plays a role in chromosome segregation. Exp Cell Res 2022; 413:113063. [PMID: 35167828 DOI: 10.1016/j.yexcr.2022.113063] [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: 09/13/2021] [Revised: 02/04/2022] [Accepted: 02/11/2022] [Indexed: 11/23/2022]
Abstract
C9ORF78 is a poorly characterized protein found in diverse eukaryotes. Previous work indicated overexpression of C9ORF78 in malignant tissues indicating a possible involvement in growth regulatory pathways. Additional studies in fission yeast and humans uncover a potential function in regulating the spliceosome. In studies of GFP-tagged C9ORF78 we observed a dramatic reduction in protein abundance in cells grown to confluence and/or deprived of serum growth factors. Serum stimulation induced synchronous re-expression of the protein in HeLa cells. This effect was also observed with the endogenous protein. Overexpressing either E2F1 or N-Myc resulted in elevated C9ORF78 expression potentially explaining the serum-dependent upregulation of the protein. Immunofluorescence analysis indicates that C9ORF78 localizes to nuclei in interphase but does not appear to concentrate in speckles as would be expected for a splicing protein. Surprisingly, a subpopulation of C9ORF78 co-localizes with ACA, Mad1 and Ndc80 in mitotic cells suggesting that this protein associates with kinetochores or centromeres. Levels of C9ORF78 at the centromere/kinetochore also increased upon activation of the mitotic checkpoint. Furthermore, knocking-down C9ORF78 caused mitotic defects. These studies uncover novel mitotic function and subcellular localization of C9ORF78.
Collapse
Affiliation(s)
- Radhika Koranne
- Department of Biological Sciences, University of Toledo, 2801 W. Bancroft Street, MS 601, Toledo, OH, 43606, USA
| | - Kayla Brown
- Department of Biological Sciences, University of Toledo, 2801 W. Bancroft Street, MS 601, Toledo, OH, 43606, USA
| | - Hannah Vandenbroek
- Department of Biological Sciences, University of Toledo, 2801 W. Bancroft Street, MS 601, Toledo, OH, 43606, USA
| | - William R Taylor
- Department of Biological Sciences, University of Toledo, 2801 W. Bancroft Street, MS 601, Toledo, OH, 43606, USA.
| |
Collapse
|
7
|
Xiao Y, Chu L, Zhang Y, Bian Y, Xiao J, Xu D. HY5: A Pivotal Regulator of Light-Dependent Development in Higher Plants. FRONTIERS IN PLANT SCIENCE 2022; 12:800989. [PMID: 35111179 PMCID: PMC8801436 DOI: 10.3389/fpls.2021.800989] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/17/2021] [Indexed: 05/10/2023]
Abstract
ELONGATED HYPOCOTYL5 (HY5), a bZIP-type transcription factor, acts as a master regulator that regulates various physiological and biological processes in plants such as photomorphogenesis, root growth, flavonoid biosynthesis and accumulation, nutrient acquisition, and response to abiotic stresses. HY5 is evolutionally conserved in function among various plant species. HY5 acts as a master regulator of light-mediated transcriptional regulatory hub that directly or indirectly controls the transcription of approximately one-third of genes at the whole genome level. The transcription, protein abundance, and activity of HY5 are tightly modulated by a variety of factors through distinct regulatory mechanisms. This review primarily summarizes recent advances on HY5-mediated molecular and physiological processes and regulatory mechanisms on HY5 in the model plant Arabidopsis as well as in crops.
Collapse
Affiliation(s)
| | | | | | | | | | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
8
|
Wu T, Ali A, Wang J, Song J, Fang Y, Zhou T, Luo Y, Zhang H, Chen X, Liao Y, Liu Y, Xu P, Wu X. A homologous gene of OsREL2/ASP1, ASP-LSL regulates pleiotropic phenotype including long sterile lemma in rice. BMC PLANT BIOLOGY 2021; 21:390. [PMID: 34418975 PMCID: PMC8379857 DOI: 10.1186/s12870-021-03163-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Panicle is a harvesting organ of rice, and its morphology and development are closely associated with grain yield. The current study was carried on a mutant screened through an EMS (ethyl-methane sulphonate) mutagenized population of a Japonica cultivar Kitaake (WT). RESULTS A mutant, named as asp-lsl (aberrant spikelet-long sterile lemma), showed a significant decrease in plant height, number of tillers, thousand-grains weight, seed setting rate, spikelet length, kernel length and effective number of grains per panicle as compared to WT. Asp-lsl showed a pleiotropic phenotype coupled with the obvious presence of a long sterile lemma. Cross-sections of lemma showed an increase in the cell volume rather than the number of cells. Genetic segregation analysis revealed its phenotypic trait is controlled by a single recessive nuclear gene. Primary and fine mapping indicated that candidate gene controlling the phenotype of asp-lsl was located in an interval of 212 kb on the short arm of chromosome 8 between RM22445 and RM22453. Further sequencing and indels markers analysis revealed LOC_Os08g06480 harbors a single base substitution (G→A), resulting in a change of 521st amino acid(Gly→Glu. The homology comparison and phylogenetic tree analysis revealed mutation was occurred in a highly conserved domain and had a high degree of similarity in Arabidopsis, corn, and sorghum. The CRISPR/Cas9 mutant line of ASP-LSL produced a similar phenotype as that of asp-lsl. Subcellular localization of ASP-LSL revealed that its protein is localized in the nucleus. Relative expression analysis revealed ASP-LSL was preferentially expressed in panicle, stem, and leaves. The endogenous contents of GA, CTK, and IAA were found significantly decreased in asp-lsl as compared to WT. CONCLUSIONS Current study presents the novel phenotype of asp-lsl and also validate the previously reported function of OsREL2 (ROMOSA ENHANCER LOCI2), / ASP1(ABERRANT SPIKELET AND PANICLE 1).
Collapse
Affiliation(s)
- Tingkai Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Asif Ali
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Jinhao Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Jiahe Song
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yongqiong Fang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Tingting Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yi Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Hongyu Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Xiaoqiong Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yongxiang Liao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yutong Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Peizhou Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Xianjun Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China.
| |
Collapse
|
9
|
Kim B, Piao R, Lee G, Koh E, Lee Y, Woo S, Jiang W, Septiningsih EM, Thomson MJ, Koh HJ. OsCOP1 regulates embryo development and flavonoid biosynthesis in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2587-2601. [PMID: 33950284 PMCID: PMC8277627 DOI: 10.1007/s00122-021-03844-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/22/2021] [Indexed: 06/07/2023]
Abstract
Novel mutations of OsCOP1 were identified to be responsible for yellowish pericarp and embryo lethal phenotype, which revealed that OsCOP1 plays a crucial role in flavonoid biosynthesis and embryogenesis in rice seed. Successful production of viable seeds is a major component of plant life cycles, and seed development is a complex, highly regulated process that affects characteristics such as seed viability and color. In this study, three yellowish-pericarp embryo lethal (yel) mutants, yel-hc, yel-sk, and yel-cc, were produced from three different japonica cultivars of rice (Oryza sativa L). Mutant seeds had yellowish pericarps and exhibited embryonic lethality, with significantly reduced grain size and weight. Morphological aberrations were apparent by 5 days after pollination, with abnormal embryo development and increased flavonoid accumulation observed in the yel mutants. Genetic analysis and mapping revealed that the phenotype of the three yel mutants was controlled by a single recessive gene, LOC_Os02g53140, an ortholog of Arabidopsis thaliana CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). The yel-hc, yel-sk, and yel-cc mutants carried mutations in the RING finger, coiled-coil, and WD40 repeat domains, respectively, of OsCOP1. CRISPR/Cas9-targeted mutagenesis was used to knock out OsCOP1 by targeting its functional domains, and transgenic seed displayed the yel mutant phenotype. Overexpression of OsCOP1 in a homozygous yel-hc mutant background restored pericarp color, and the aberrant flavonoid accumulation observed in yel-hc mutant was significantly reduced in the embryo and endosperm. These results demonstrate that OsCOP1 is associated with embryo development and flavonoid biosynthesis in rice grains. This study will facilitate a better understanding of the functional roles of OsCOP1 involved in early embryogenesis and flavonoid biosynthesis in rice seeds.
Collapse
Affiliation(s)
- Backki Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77483 USA
| | - Rihua Piao
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin, 136100 China
| | - Gileung Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
| | - Eunbyeol Koh
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
| | - Yunjoo Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
| | - Sunmin Woo
- College of Pharmacy and Research Institute of Pharmaceutical Science, Seoul National University, Seoul, 08826 Republic of Korea
| | - Wenzhu Jiang
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, 130062 China
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77483 USA
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77483 USA
| | - Hee-Jong Koh
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
| |
Collapse
|
10
|
Kubra G, Khan M, Munir F, Gul A, Shah T, Hussain A, Caparrós-Ruiz D, Amir R. Expression Characterization of Flavonoid Biosynthetic Pathway Genes and Transcription Factors in Peanut Under Water Deficit Conditions. FRONTIERS IN PLANT SCIENCE 2021; 12:680368. [PMID: 34220900 PMCID: PMC8253228 DOI: 10.3389/fpls.2021.680368] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 05/19/2021] [Indexed: 05/30/2023]
Abstract
Drought is one of the hostile environmental stresses that limit the yield production of crop plants by modulating their growth and development. Peanut (Arachis hypogaea) has a wide range of adaptations to arid and semi-arid climates, but its yield is prone to loss due to drought. Other than beneficial fatty acids and micronutrients, peanut harbors various bioactive compounds including flavonoids that hold a prominent position as antioxidants in plants and protect them from oxidative stress. In this study, understanding of the biosynthesis of flavonoids in peanut under water deficit conditions was developed through expression analysis and correlational analysis and determining the accumulation pattern of phenols, flavonols, and anthocyanins. Six peanut varieties (BARD479, BARI2011, BARI2000, GOLDEN, PG1102, and PG1265) having variable responses against drought stress have been selected. Higher water retention and flavonoid accumulation have been observed in BARI2011 but downregulation has been observed in the expression of genes and transcription factors (TFs) which indicated the maintenance of normal homeostasis. ANOVA revealed that the expression of flavonoid genes and TFs is highly dependent upon the genotype of peanut in a spatiotemporal manner. Correlation analysis between expression of flavonoid biosynthetic genes and TFs indicated the role of AhMYB111 and AhMYB7 as an inhibitor for AhF3H and AhFLS, respectively, and AhMYB7, AhTTG1, and AhCSU2 as a positive regulator for the expression of Ah4CL, AhCHS, and AhF3H, respectively. However, AhbHLH and AhGL3 revealed nil-to-little relation with the expression of flavonoid biosynthetic pathway genes. Correlational analysis between the expression of TFs related to the biosynthesis of flavonoids and the accumulation of phenolics, flavonols, and anthocyanins indicated coregulation of flavonoid synthesis by TFs under water deficit conditions in peanut. This study would provide insight into the role of flavonoid biosynthetic pathway in drought response in peanut and would aid to develop drought-tolerant varieties of peanut.
Collapse
Affiliation(s)
- Ghulam Kubra
- Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Maryam Khan
- Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Faiza Munir
- Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Alvina Gul
- Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Tariq Shah
- Department of Agronomy, Faculty of Crop Production Sciences, University of Agriculture Peshawar, Peshawar, Pakistan
- College of Agriculture, Michigan State University, East Lansing, MI, United States
| | - Adil Hussain
- Department of Agriculture, Abdul Wali Khan University, Mardan, Pakistan
| | - David Caparrós-Ruiz
- Centre for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Rabia Amir
- Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| |
Collapse
|
11
|
Kang H, Zhang TT, Fu LL, Yao YX, You CX, Wang XF, Hao YJ. The apple MdCOP1-interacting protein 1 negatively regulates hypocotyl elongation and anthocyanin biosynthesis. BMC PLANT BIOLOGY 2021; 21:15. [PMID: 33407118 PMCID: PMC7789773 DOI: 10.1186/s12870-020-02789-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/08/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND In plants, CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) is a key negative regulator in photoperiod response. However, the biological function of COP1-interacting protein 1 (CIP1) and the regulatory mechanism of the CIP1-COP1 interaction are not fully understood. RESULTS Here, we identified the apple MdCIP1 gene based on the Arabidopsis AtCIP1 gene. Expression pattern analysis showed that MdCIP1 was constitutively expressed in various tissues of apple, and responded to stress and hormone signals at the transcriptional level. Ectopic expression of MdCIP1 complemented the phenotypes of the Arabidopsis cip1 mutant, and MdCIP1 inhibited anthocyanin biosynthesis in apple calli. In addition, the biochemical assay demonstrated that MdCIP1 could interact with MdCOP1 protein by their coiled-coil domain, and MdCIP1-OX/cop1-4 had a similar phenotype in photomorphogenesis with the cop1-4 mutant, suggesting that COP1 is epistatic to CIP1. Furthermore, the transient transformation assay indicated that MdCIP1 repressed anthocyanin biosynthesis in an MdCOP1-mediated pathway. CONCLUSION Take together, this study finds that MdCIP1 acts as a repressor in regulating hypocotyl elongation and anthocyanin biosynthesis through MdCOP1 in apple.
Collapse
Affiliation(s)
- Hui Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yang-Ling, 712100, Shaanxi, China
| | - Ting-Ting Zhang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Lu-Lu Fu
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Yu-Xin Yao
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Chun-Xiang You
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Xiao-Fei Wang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
| | - Yu-Jin Hao
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
| |
Collapse
|
12
|
Ponnu J, Hoecker U. Illuminating the COP1/SPA Ubiquitin Ligase: Fresh Insights Into Its Structure and Functions During Plant Photomorphogenesis. FRONTIERS IN PLANT SCIENCE 2021; 12:662793. [PMID: 33841486 PMCID: PMC8024647 DOI: 10.3389/fpls.2021.662793] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/04/2021] [Indexed: 05/07/2023]
Abstract
CONSTITUTIVE PHOTOMORPHOGENIC 1 functions as an E3 ubiquitin ligase in plants and animals. Discovered originally in Arabidopsis thaliana, COP1 acts in a complex with SPA proteins as a central repressor of light-mediated responses in plants. By ubiquitinating and promoting the degradation of several substrates, COP1/SPA regulates many aspects of plant growth, development and metabolism. In contrast to plants, human COP1 acts as a crucial regulator of tumorigenesis. In this review, we discuss the recent important findings in COP1/SPA research including a brief comparison between COP1 activity in plants and humans.
Collapse
|
13
|
Xu D. COP1 and BBXs-HY5-mediated light signal transduction in plants. THE NEW PHYTOLOGIST 2020; 228:1748-1753. [PMID: 31664720 DOI: 10.1111/nph.16296] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/17/2019] [Indexed: 05/24/2023]
Abstract
Light is one of the most essential environmental factors affecting many aspects of growth and developmental processes in plants. Plants undergo skotomorphogenic or photomorphogenic development dependent on the absence or presence of light. These two developmental programs enable a germinated seed to become a healthy seedling at the early stage of the plant life cycle. CULLIN 4-DNA DAMAGE-BINDING PROTEIN 1 (DDB1)-based CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1)-SUPPRESSOR OF PHYA and COP10-DEETIOLATED 1-DDB1 E3 ubiquitin ligase complexes promote the skotomorphogenesis by ubiquitinating and degrading a number of photomorphogenic-promoting factors in darkness. Photoreceptors sense and transduce light information to downstream signaling, thereby initiating a set of molecular events and subsequent photomorphogenesis. These processes are precisely modulated by a group of components including various photoreceptors, E3 ubiquitin ligase, and transcription factors at the molecular level. This review provides an overview of the current understanding of the COP1, ELONGATED HYPOCOTYL 5, and B-BOX CONTAINING PROTEINs-mediated light signal transduction pathway and highlights still open questions in the field.
Collapse
Affiliation(s)
- Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
14
|
COP1 SUPPRESSOR 4 promotes seedling photomorphogenesis by repressing CCA1 and PIF4 expression in Arabidopsis. Proc Natl Acad Sci U S A 2018; 115:11631-11636. [PMID: 30352855 DOI: 10.1073/pnas.1813171115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and DE-ETIOLATED 1 (DET1) are founding components of two central repressor complexes of photomorphogenesis that trigger the degradation of a larger number of photomorphogenic-promoting factors in darkness. Here, we identify COP1 SUPPRESSOR 4 (CSU4) as a genetic suppressor of the cop1-6 mutation. Mutations in CSU4 largely rescued the constitutively photomorphogenic phenotype of cop1-6 and det1-1 in darkness. Loss of CSU4 function resulted in significantly longer hypocotyl in the light. Further biochemical studies revealed that CSU4 physically interacts with CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) and negatively regulates its transcriptional repression activity toward its targets. CSU4 represses the expression of CCA1 in the early morning and of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) in the early evening. Our study suggests that CSU4 acts as a negative regulator of CCA1 via physically associating with CCA1, which in turn, likely serves to repress expression of CCA1 and PIF4 to promote photomorphogenesis.
Collapse
|
15
|
Xu D, Jiang Y, Li J, Holm M, Deng XW. The B-Box Domain Protein BBX21 Promotes Photomorphogenesis. PLANT PHYSIOLOGY 2018; 176:2365-2375. [PMID: 29259103 PMCID: PMC5841706 DOI: 10.1104/pp.17.01305] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/14/2017] [Indexed: 05/20/2023]
Abstract
B-box-containing (BBX) proteins play critical roles in a variety of cellular and developmental processes in plants. BBX21 (also known as SALT TOLERANCE HOMOLOG2), which contains two B-box domains in tandem at the N terminus, has been previously demonstrated as a key component involved in the COP1-HY5 signaling hub. However, the exact molecular and physiological roles of B-box domains in BBX21 are largely unclear. Here, we found that structurally disruption of the second B-box domain, but not the first one, in BBX21 completely abolishes its biological and physiological activity in conferring hyperphotomorphogenetic phenotype in Arabidopsis (Arabidopsis thaliana). Intact B-box domains in BBX21 are not required for interaction with COP1 and its degradation by COP1 via the 26S proteasome system. However, disruption of the second B-box of BBX21 nearly impairs its ability for binding of T/G-box within the HY5 promoter both in vitro and in vivo, as well as controlling HY5 and HY5-regulated gene expression in Arabidopsis seedlings. Taken together, this study provides a mechanistic framework in which BBX21 directly binds to the T/G-box present in the HY5 promoter possibly through its second B-box domain, which in turn controls HY5 and HY5-regulated gene expression to promote photomorphogenesis.
Collapse
Affiliation(s)
- Dongqing Xu
- Institute of Plant and Food Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas 78712
| | - Yan Jiang
- Institute of Plant and Food Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jian Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Magnus Holm
- Department of Biological and Environmental Sciences, Gothenburg University, SE-405 30 Gothenburg, Sweden
| | - Xing Wang Deng
- Institute of Plant and Food Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
16
|
COP1 mediates dark-specific degradation of microtubule-associated protein WDL3 in regulating Arabidopsis hypocotyl elongation. Proc Natl Acad Sci U S A 2017; 114:12321-12326. [PMID: 29087315 PMCID: PMC5699047 DOI: 10.1073/pnas.1708087114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) is an E3 ubiquitin ligase acting as a central repressor of seedling photomorphogenesis in plants. Many nuclear-localized COP1 substrates have been identified in the last two decades; however, whether COP1 targets cytoplasmic factors for ubiquitination and degradation remains largely unknown. In this study, we show that COP1 interacts with a microtubule-associated protein, WAVE-DAMPENED 2-LIKE 3 (WDL3), in a dark-dependent manner at cortical microtubules. Thus, COP1 targets WDL3 for 26S proteasome-mediated degradation to control hypocotyl elongation in etiolated Arabidopsis seedlings. Collectively, our study uncovers a cytoplasmic substrate of COP1 that functions as a microtubule-associated protein in mediating hypocotyl cell elongation. CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), a well-known E3 ubiquitin ligase, functions as a central regulator of plant growth and photomorphogenic development in plants, including hypocotyl elongation. It has been well-established that, in darkness, COP1 targets many photomorphogenesis-promoting factors for ubiquitination and degradation in the nucleus. However, increasing evidence has shown that a proportion of COP1 is also localized outside the nucleus in dark-grown seedlings, but the physiological function of this localization remains largely unclear. In this study, we demonstrate that COP1 directly targets and mediates the degradation of WAVE-DAMPENED 2-LIKE 3 (WDL3) protein, a member of the microtubule-associated protein (MAP) WVD2/WDL family involved in regulating hypocotyl cell elongation of Arabidopsis seedlings. We show that COP1 interacts with WDL3 in vivo in a dark-dependent manner at cortical microtubules. Moreover, our data indicate that COP1 directly ubiquitinates WDL3 in vitro and that WDL3 protein is degraded in WT seedlings but is abundant in the cop1 mutant in the dark. Consistently, introduction of the wdl3 mutation weakened, whereas overexpression of WDL3 enhanced, the short-hypocotyl phenotype of cop1 mutant in darkness. Together, this study reveals a function of COP1 in regulating the protein turnover of a cytosol-localized MAP in etiolated hypocotyls, thus providing insights into COP1-mediated degradation of downstream factors to control seedling photomorphogenesis.
Collapse
|
17
|
Kim JY, Song JT, Seo HS. COP1 regulates plant growth and development in response to light at the post-translational level. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4737-4748. [PMID: 28992300 DOI: 10.1093/jxb/erx312] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Photoreceptors perceive different wavelengths of light and transduce light signals downstream via a range of proteins. COP1, an E3 ubiquitin ligase, regulates light signaling by mediating the ubiquitination and subsequent proteasomal degradation of photoreceptors such as phytochromes and cryptochromes, as well as various development-related proteins including other light-responsive proteins. COP1 is itself regulated by direct interactions with several signaling molecules that modulate its activity. The control of photomorphogenesis by COP1 is also regulated by its localization to the cytoplasm in response to light. COP1 thus acts as a tightly regulated switch that determines whether development is skotomorphogenic or photomorphogenic. In this review, we discuss the effects of COP1 on the abundance and activity of various development-related proteins, including photoreceptors, and summarize the regulatory mechanisms that influence COP1 activity and stability in plants.
Collapse
Affiliation(s)
- Joo Yong Kim
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Jong Tae Song
- School of Applied Biosciences, Kyungpook National University, Daegu 702-701, Korea
| | - Hak Soo Seo
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea
| |
Collapse
|
18
|
Shu K, Yang W. E3 Ubiquitin Ligases: Ubiquitous Actors in Plant Development and Abiotic Stress Responses. PLANT & CELL PHYSIOLOGY 2017; 58:1461-1476. [PMID: 28541504 PMCID: PMC5914405 DOI: 10.1093/pcp/pcx071] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 05/05/2017] [Indexed: 05/05/2023]
Abstract
Understanding the precise regulatory mechanisms of plant development and stress responses at the post-translational level is currently a topic of intensive research. Protein ubiquitination, including the sequential performances of ubiquitin-activating (E1), ubiquitin-conjugating (E2) and ubiquitin ligase (E3) enzymes, is a refined post-translational modification ubiquitous in all eukaryotes. Plants are an integral part of our ecosystem and, as sessile organisms, the ability to perceive internal and external signals and to adapt well to various environmental challenges is crucial for their survival. Over recent decades, extensive studies have demonstrated that protein ubiquitination plays key roles in multiple plant developmental stages (e.g. seed dormancy and germination, root growth, flowering time control, self-incompatibility and chloroplast development) and several abiotic stress responses (e.g. drought and high salinity), by regulating the abundance, activities or subcellular localizations of a variety of regulatory polypeptides and enzymes. Importantly, diverse E3 ligases are involved in these regulatory pathways by mediating phytohormone and light signaling or other pathways. In this updated review, we mainly summarize recent advances in our understanding of the regulatory roles of protein ubiquitination in plant development and plant-environment interactions, and primarily focus on different types of E3 ligases because they play critical roles in determining substrate specificity.
Collapse
Affiliation(s)
- Kai Shu
- Department of Plant Physiology and Biochemistry, Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
- Corresponding authors: Kai Shu, E-mail, ; Wenyu Yang, E-mail,
| | - Wenyu Yang
- Department of Plant Physiology and Biochemistry, Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
- Corresponding authors: Kai Shu, E-mail, ; Wenyu Yang, E-mail,
| |
Collapse
|
19
|
Phosphorylation and negative regulation of CONSTITUTIVELY PHOTOMORPHOGENIC 1 by PINOID in Arabidopsis. Proc Natl Acad Sci U S A 2017; 114:6617-6622. [PMID: 28584104 DOI: 10.1073/pnas.1702984114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) plays crucial roles in various cellular processes via its E3 ubiquitin ligase activity in organisms, ranging from fungi to humans. As a key component in regulating various biological events, COP1 itself is precisely controlled at multiple layers. Here, we report a negative regulator of COP1, PINOID (PID), which positively mediates photomorphogenic development. Specifically, PID genetically and physically interacts with COP1 and directly phosphorylates COP1 at Ser20. As a result, this posttranslational modification serves to repress COP1 activity and promote photomorphogenesis. Our findings signify a key regulatory mechanism for precisely maintaining COP1 activity, thereby ensuring appropriate development in plants.
Collapse
|
20
|
Hoecker U. The activities of the E3 ubiquitin ligase COP1/SPA, a key repressor in light signaling. CURRENT OPINION IN PLANT BIOLOGY 2017; 37:63-69. [PMID: 28433946 DOI: 10.1016/j.pbi.2017.03.015] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/17/2017] [Accepted: 03/28/2017] [Indexed: 05/21/2023]
Abstract
Light is a critical signal to integrate plant growth and development with the environment. Downstream of photoreceptors, the E3 ubiquitin ligase COP1/SPA is a key repressor of photomorphogenesis which targets many positive regulators of light signaling, mainly transcription factors, for degradation in darkness. In light-grown plants COP1/SPA activity is repressed, allowing light responses to occur. This review provides an overview on our current knowledge on COP1/SPA repressor function, focusing in particular on the roles of the respective protein domains and the mechanisms of light-induced inactivation of COP1/SPA. Moreover, we summarize how COP1 activity is regulated by other interacting proteins, such as a SUMO E3 ligase and Phytochrome-Interacting Factors (PIFs), as well as by hormones. At last, several novel functions of COP1 that were recently revealed are included.
Collapse
Affiliation(s)
- Ute Hoecker
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, D-50674 Cologne, Germany.
| |
Collapse
|
21
|
BBX21, an Arabidopsis B-box protein, directly activates HY5 and is targeted by COP1 for 26S proteasome-mediated degradation. Proc Natl Acad Sci U S A 2016; 113:7655-60. [PMID: 27325768 DOI: 10.1073/pnas.1607687113] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BBX21 (also known as SALT TOLERANCE HOMOLOG 2), a B-box (BBX)-containing protein, has been previously identified as a positive regulator of light signaling; however, the precise role of BBX21 in regulating seedling photomorphogenesis remains largely unclear. In this study, we report that CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) interacts with BBX21 in vivo and is able to ubiquitinate BBX21 in vitro. Thus, BBX21 is targeted for 26S proteasome-mediated degradation in dark-grown Arabidopsis seedlings in a COP1-dependent manner. Moreover, we show that BBX21 binds to the T/G-box in the ELONGATED HYPOCOTYL 5 (HY5) promoter and directly activates HY5 expression in the light. Transgenic seedlings overexpressing BBX21 exhibit dramatically shortened hypocotyls in the light, and this phenotype is dependent on a functional HY5. Taken together, our data suggest a molecular base underlying BBX21-mediated seedling photomorphogenesis, indicating that BBX21 is a pivotal component involved in the COP1-HY5 regulatory hub.
Collapse
|
22
|
Lin XL, Niu D, Hu ZL, Kim DH, Jin YH, Cai B, Liu P, Miura K, Yun DJ, Kim WY, Lin R, Jin JB. An Arabidopsis SUMO E3 Ligase, SIZ1, Negatively Regulates Photomorphogenesis by Promoting COP1 Activity. PLoS Genet 2016; 12:e1006016. [PMID: 27128446 PMCID: PMC4851335 DOI: 10.1371/journal.pgen.1006016] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 04/07/2016] [Indexed: 12/20/2022] Open
Abstract
COP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1), a ubiquitin E3 ligase, is a central negative regulator of photomorphogenesis. However, how COP1 activity is regulated by post-translational modifications remains largely unknown. Here we show that SUMO (small ubiquitin-like modifier) modification enhances COP1 activity. Loss-of-function siz1 mutant seedlings exhibit a weak constitutive photomorphogenic phenotype. SIZ1 physically interacts with COP1 and mediates the sumoylation of COP1. A K193R substitution in COP1 blocks its SUMO modification and reduces COP1 activity in vitro and in planta. Consistently, COP1 activity is reduced in siz1 and the level of HY5, a COP1 target protein, is increased in siz1. Sumoylated COP1 may exhibits higher transubiquitination activity than does non-sumoylated COP1, but SIZ1-mediated SUMO modification does not affect COP1 dimerization, COP1-HY5 interaction, and nuclear accumulation of COP1. Interestingly, prolonged light exposure reduces the sumoylation level of COP1, and COP1 mediates the ubiquitination and degradation of SIZ1. These regulatory mechanisms may maintain the homeostasis of COP1 activity, ensuing proper photomorphogenic development in changing light environment. Our genetic and biochemical studies identify a function for SIZ1 in photomorphogenesis and reveal a novel SUMO-regulated ubiquitin ligase, COP1, in plants. In darkness, the ubiquitin E3 ligase COP1 accumulates in the nucleus and mediates ubiquitination and degradation of positive regulators of photomorphogenesis, such as HY5. In response to light, COP1 activity is reduced to ensure proper photomorphogenic development. However, post-translational modifications that regulate COP1 activity are largely unknown. We have found that the Arabidopsis SUMO E3 ligase SIZ1 negatively regulates photomorphogenesis. Genetic and biochemical lines of evidence demonstrate that SIZ1-mediated SUMO modification of COP1 enhances its E3 ubiquitin ligase activity, which causes increased ubiquitination and degradation of HY5. In response to the light, sumoylation level of COP1 is decreased, which may also contributes to the reduction of COP1 activity in the light. Moreover, COP1 mediates ubiquitination and 26S proteasome-dependent degradation of SIZ1 and this feedback repression may ensure the moderate levels of COP1 activity. Our study established a post-translational regulatory modular consisting of SIZ1-mediated sumoylation and COP1-mediated ubiquitination that tightly regulate photomorphogenesis.
Collapse
Affiliation(s)
- Xiao-Li Lin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - De Niu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zi-Liang Hu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Dae Heon Kim
- Department of Biology, Sunchon National University, Sunchon, Republic of Korea
| | - Yin Hua Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Bin Cai
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Peng Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Kenji Miura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Dae-Jin Yun
- Division of Applied Life Science (BK21Plus), PMBBRC & IALS, Gyeongsang National University, Jinju, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), PMBBRC & IALS, Gyeongsang National University, Jinju, Republic of Korea
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jing Bo Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- * E-mail:
| |
Collapse
|