1
|
Frangedakis E, Yelina NE, Billakurthi K, Hua L, Schreier T, Dickinson PJ, Tomaselli M, Haseloff J, Hibberd JM. MYB-related transcription factors control chloroplast biogenesis. Cell 2024; 187:4859-4876.e22. [PMID: 39047726 DOI: 10.1016/j.cell.2024.06.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/21/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024]
Abstract
Chloroplast biogenesis is dependent on master regulators from the GOLDEN2-LIKE (GLK) family of transcription factors. However, glk mutants contain residual chlorophyll, indicating that other proteins must be involved. Here, we identify MYB-related transcription factors as regulators of chloroplast biogenesis in the liverwort Marchantia polymorpha and angiosperm Arabidopsis thaliana. In both species, double-mutant alleles in MYB-related genes show very limited chloroplast development, and photosynthesis gene expression is perturbed to a greater extent than in GLK mutants. Genes encoding enzymes of chlorophyll biosynthesis are controlled by MYB-related and GLK proteins, whereas those allowing CO2 fixation, photorespiration, and photosystem assembly and repair require MYB-related proteins. Regulation between the MYB-related and GLK transcription factors appears more extensive in A. thaliana than in M. polymorpha. Thus, MYB-related and GLK genes have overlapping as well as distinct targets. We conclude that MYB-related and GLK transcription factors orchestrate chloroplast development in land plants.
Collapse
Affiliation(s)
| | - Nataliya E Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Kumari Billakurthi
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Lei Hua
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Tina Schreier
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Patrick J Dickinson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Marta Tomaselli
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.
| |
Collapse
|
2
|
Yelina NE, Frangedakis E, Wang Z, Schreier TB, Rever J, Tomaselli M, Forestier ECF, Billakurthi K, Ren S, Bai Y, Stewart-Wood J, Haseloff J, Zhong S, Hibberd JM. Streamlined regulation of chloroplast development in the liverwort Marchantia polymorpha. Cell Rep 2024; 43:114696. [PMID: 39235940 DOI: 10.1016/j.celrep.2024.114696] [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: 02/02/2024] [Revised: 07/23/2024] [Accepted: 08/13/2024] [Indexed: 09/07/2024] Open
Abstract
Chloroplasts develop from undifferentiated plastids in response to light. In angiosperms, after the perception of light, the Elongated Hypocotyl 5 (HY5) transcription factor initiates photomorphogenesis, and two families of transcription factors known as GOLDEN2-LIKE (GLK) and GATA are considered master regulators of chloroplast development. In addition, the MIR171-targeted SCARECROW-LIKE GRAS transcription factors also impact chlorophyll biosynthesis. The extent to which these proteins carry out conserved roles in non-seed plants is not known. Using the model liverwort Marchantia polymorpha, we show that GLK controls chloroplast biogenesis, and HY5 shows a small conditional effect on chlorophyll content. Chromatin immunoprecipitation sequencing (ChIP-seq) revealed that MpGLK has a broader set of targets than has been reported in angiosperms. We also identified a functional GLK homolog in green algae. In summary, our data support the hypothesis that GLK carries out a conserved role relating to chloroplast biogenesis in land plants and green algae.
Collapse
Affiliation(s)
- Nataliya E Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | | | - Zhemin Wang
- The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Tina B Schreier
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Jenna Rever
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Marta Tomaselli
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | | | - Kumari Billakurthi
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Sibo Ren
- The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yahui Bai
- The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Julia Stewart-Wood
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK
| | - Silin Zhong
- The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB3 EA, UK.
| |
Collapse
|
3
|
Plackett ARG, Hibberd JM. Rice bundle sheath cell shape is regulated by the timing of light exposure during leaf development. PLANT, CELL & ENVIRONMENT 2024; 47:2597-2613. [PMID: 38549236 DOI: 10.1111/pce.14902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/14/2024] [Accepted: 03/16/2024] [Indexed: 06/06/2024]
Abstract
Plant leaves contain multiple cell types which achieve distinct characteristics whilst still coordinating development within the leaf. The bundle sheath possesses larger individual cells and lower chloroplast content than the adjacent mesophyll, but how this morphology is achieved remains unknown. To identify regulatory mechanisms determining bundle sheath cell morphology we tested the effects of perturbing environmental (light) and endogenous signals (hormones) during leaf development of Oryza sativa (rice). Total chloroplast area in bundle sheath cells was found to increase with cell size as in the mesophyll but did not maintain a 'set-point' relationship, with the longest bundle sheath cells demonstrating the lowest chloroplast content. Application of exogenous cytokinin and gibberellin significantly altered the relationship between cell size and chloroplast biosynthesis in the bundle sheath, increasing chloroplast content of the longest cells. Delayed exposure to light reduced the mean length of bundle sheath cells but increased corresponding leaf length, whereas premature light reduced final leaf length but did not affect bundle sheath cells. This suggests that the plant hormones cytokinin and gibberellin are regulators of the bundle sheath cell-chloroplast relationship and that final bundle sheath length may potentially be affected by light-mediated control of exit from the cell cycle.
Collapse
Affiliation(s)
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| |
Collapse
|
4
|
Zhang T, Zhang R, Zeng XY, Lee S, Ye LH, Tian SL, Zhang YJ, Busch W, Zhou WB, Zhu XG, Wang P. GLK transcription factors accompany ELONGATED HYPOCOTYL5 to orchestrate light-induced seedling development in Arabidopsis. PLANT PHYSIOLOGY 2024; 194:2400-2421. [PMID: 38180123 DOI: 10.1093/plphys/kiae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 01/06/2024]
Abstract
Light-induced de-etiolation is an important aspect of seedling photomorphogenesis. GOLDEN2 LIKE (GLK) transcriptional regulators are involved in chloroplast development, but to what extent they participate in photomorphogenesis is not clear. Here, we show that ELONGATED HYPOCOTYL5 (HY5) binds to GLK promoters to activate their expression, and also interacts with GLK proteins in Arabidopsis (Arabidopsis thaliana). The chlorophyll content in the de-etiolating Arabidopsis seedlings of the hy5 glk2 double mutants was lower than that in the hy5 single mutant. GLKs inhibited hypocotyl elongation, and the phenotype could superimpose on the hy5 phenotype. Correspondingly, GLK2 regulated the expression of photosynthesis and cell elongation genes partially independent of HY5. Before exposure to light, DE-ETIOLATED 1 (DET1) affected accumulation of GLK proteins. The enhanced etioplast development and photosystem gene expression observed in the det1 mutant were attenuated in the det1 glk2 double mutant. Our study reveals that GLKs act downstream of HY5, or additive to HY5, and are likely quantitatively adjusted by DET1, to orchestrate multiple developmental traits during the light-induced skotomorphogenesis-to-photomorphogenesis transition in Arabidopsis.
Collapse
Affiliation(s)
- Ting Zhang
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Rui Zhang
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China
| | - Xi-Yu Zeng
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Sanghwa Lee
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Lu-Huan Ye
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China
| | - Shi-Long Tian
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yi-Jing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Wen-Bin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin-Guang Zhu
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China
| | - Peng Wang
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- Key Laboratory of Plant Carbon Capture, CAS, Shanghai 200032, China
| |
Collapse
|
5
|
Mahapatra K, Mukherjee A, Suyal S, Dar MA, Bhagavatula L, Datta S. Regulation of chloroplast biogenesis, development, and signaling by endogenous and exogenous cues. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:167-183. [PMID: 38623168 PMCID: PMC11016055 DOI: 10.1007/s12298-024-01427-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 02/07/2024] [Accepted: 02/27/2024] [Indexed: 04/17/2024]
Abstract
Chloroplasts are one of the defining features in most plants, primarily known for their unique property to carry out photosynthesis. Besides this, chloroplasts are also associated with hormone and metabolite productions. For this, biogenesis and development of chloroplast are required to be synchronized with the seedling growth to corroborate the maximum rate of photosynthesis following the emergence of seedlings. Chloroplast biogenesis and development are dependent on the signaling to and from the chloroplast, which are in turn regulated by several endogenous and exogenous cues. Light and hormones play a crucial role in chloroplast maturation and development. Chloroplast signaling involves a coordinated two-way connection between the chloroplast and nucleus, termed retrograde and anterograde signaling, respectively. Anterograde and retrograde signaling are involved in regulation at the transcriptional level and downstream modifications and are modulated by several metabolic and external cues. The communication between chloroplast and nucleus is essential for plants to develop strategies to cope with various stresses including high light or high heat. In this review, we have summarized several aspects of chloroplast development and its regulation through the interplay of various external and internal factors. We have also discussed the involvement of chloroplasts as sensors of various external environment stress factors including high light and temperature, and communicate via a series of retrograde signals to the nucleus, thus playing an essential role in plants' abiotic stress response.
Collapse
Affiliation(s)
- Kalyan Mahapatra
- Plant Cell and Developmental Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh 462066 India
| | - Arpan Mukherjee
- Plant Cell and Developmental Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh 462066 India
| | - Shikha Suyal
- Plant Cell and Developmental Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh 462066 India
| | - Mansoor Ali Dar
- Plant Cell and Developmental Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh 462066 India
| | | | - Sourav Datta
- Plant Cell and Developmental Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh 462066 India
| |
Collapse
|
6
|
Wei X, Li Y, Zhu X, Liu X, Ye X, Zhou M, Zhang Z. The GATA transcription factor TaGATA1 recruits demethylase TaELF6-A1 and enhances seed dormancy in wheat by directly regulating TaABI5. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1262-1276. [PMID: 36534453 DOI: 10.1111/jipb.13437] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/13/2022] [Indexed: 05/13/2023]
Abstract
Seed dormancy is an important agronomic trait in crops, and plants with low dormancy are prone to preharvest sprouting (PHS) under high-temperature and humid conditions. In this study, we report that the GATA transcription factor TaGATA1 is a positive regulator of seed dormancy by regulating TaABI5 expression in wheat. Our results demonstrate that TaGATA1 overexpression significantly enhances seed dormancy and increases resistance to PHS in wheat. Gene expression patterns, abscisic acid (ABA) response assay, and transcriptome analysis all indicate that TaGATA1 functions through the ABA signaling pathway. The transcript abundance of TaABI5, an essential regulator in the ABA signaling pathway, is significantly elevated in plants overexpressing TaGATA1. Chromatin immunoprecipitation assay (ChIP) and transient expression analysis showed that TaGATA1 binds to the GATA motifs at the promoter of TaABI5 and induces its expression. We also demonstrate that TaGATA1 physically interacts with the putative demethylase TaELF6-A1, the wheat orthologue of Arabidopsis ELF6. ChIP-qPCR analysis showed that H3K27me3 levels significantly decline at the TaABI5 promoter in the TaGATA1-overexpression wheat line and that transient expression of TaELF6-A1 reduces methylation levels at the TaABI5 promoter, increasing TaABI5 expression. These findings reveal a new transcription module, including TaGATA1-TaELF6-A1-TaABI5, which contributes to seed dormancy through the ABA signaling pathway and epigenetic reprogramming at the target site. TaGATA1 could be a candidate gene for improving PHS resistance.
Collapse
Affiliation(s)
- Xuening Wei
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuyan Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuliang Zhu
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xingguo Ye
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Miaoping Zhou
- Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Zengyan Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| |
Collapse
|
7
|
Luan J, Ju J, Li X, Wang X, Tan Y, Xia G. Functional identification of moss PpGATA1 provides insights into the evolution of LLM-domain B-GATA transcription factors in plants. Gene 2023; 855:147103. [PMID: 36513191 DOI: 10.1016/j.gene.2022.147103] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/28/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
B-GATA transcription factors with the LLM domain (LLM-domain B-GATAs) play important roles in developmental processes and environmental responses in flowering plants. Their characterization can therefore provide insights into the structural and functional evolution of functional gene families. Phylogenetic and sequence analysis suggests that LLM-domain B-GATAs evolved from ancestral GATA transcription factors before the divergence of chlorophyte algae and Streptophyta. We compared the function of PpGATA1, a LLM-domain B-GATA gene in moss Physcomitrium patens, with Arabidopsis thaliana counterparts and showed that, in P. patens, PpGATA1 controls growth and greening in haploid gametophytes, while in transgenic Arabidopsis it affects germination, leaf development, flowering time, greening and light responses in diploid sporophytes. These PpGATA1 functions are similar to those of Arabidopsis counterparts, AtGNC, AtGNL and AtGATA17. PpGATA1 was able to complement the role of GNC and GNL in a gnc gnl double mutant, and the LLM domains of PpGATA1 and GNC behaved similarly. The functions of LLM-domain B-GATAs regulating hypocotyl elongation and cotyledon epinasty in flowering plants pre-exist before the divergence of mosses and the lineage leading to flowering plants. This study sheds light on adaption of PpGATA1 and its homologs to new developmental designs during the evolution.
Collapse
Affiliation(s)
- Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong 266237, China; The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China.
| | - Jianfang Ju
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaochen Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiuling Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong 266237, China
| | - Yufei Tan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong 266237, China
| | - Guangmin Xia
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China.
| |
Collapse
|
8
|
Lv X, Huang S, Wang J, Han D, Li J, Guo D, Zhu H. Genome-wide identification of Mg 2+ transporters and functional characteristics of DlMGT1 in Dimocarpus longan. FRONTIERS IN PLANT SCIENCE 2023; 14:1110005. [PMID: 36818860 PMCID: PMC9932547 DOI: 10.3389/fpls.2023.1110005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Longan (Dimocarpus Longan) is one of the most important fruit crops in Southern China. Lack of available Mg in acidic soil conditions is a limitation to further increasing longan yield. Magnesium transporter (MGT/MRS2) mediates the uptake, transport, and redistribution of Mg2+ in higher plants. To understand the role of MGTs family members in longan Mg deficiency. We identified and analyzed the protein characteristics, phylogeny, expression changes, subcellular localization, and transcriptional regulation of DlMGTs members. The results showed that, twelve DlMGTs are localized in the cell membrane, chloroplast, and nucleus. The evolutionary differences in MGTs between herbaceous and woody species in different plants. The DlMGTs promoters contained many cis-acting elements and transcription factor binding sites related to the hormone, environmental, and stress response. Subcellular localization assays showed that DlMGT1 localizes in the cell membrane of Arabidopsis protoplasts. The candidate transcription factor DlGATA16, which may regulate the expression of DlMGT1, was localized in the nucleus of tobacco leaves. Dual luciferase analysis demonstrated that DlGATA16 is a potential factor regulating the transcriptional activity of DlMGT1. In this study, we identified and analyzed DlMGTs on a genome-wide scale and the subcellular localization and interaction of DlMGT1 and DlGATA16, which has important implications for further functional analysis studies of MGTs and the use of MGT for longan genetic improvement.
Collapse
Affiliation(s)
- Xinmin Lv
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China
| | - Shilian Huang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China
| | - Jing Wang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China
| | - Dongmei Han
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China
| | - Jianguang Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China
| | - Dongliang Guo
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Guangzhou, China
| | - Haifeng Zhu
- Key Laboratory of Crop Harvesting Equipment Technology of Zhejiang Province, Jinhua Polytechnic, Jinhua, China
| |
Collapse
|
9
|
Genome‑wide identification, phylogenetic and expression pattern analysis of GATA family genes in foxtail millet (Setaria italica). BMC Genomics 2022; 23:549. [PMID: 35918632 PMCID: PMC9347092 DOI: 10.1186/s12864-022-08786-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/18/2022] [Indexed: 11/27/2022] Open
Abstract
Background Transcription factors (TFs) play important roles in plants. Among the major TFs, GATA plays a crucial role in plant development, growth, and stress responses. However, there have been few studies on the GATA gene family in foxtail millet (Setaria italica). The release of the foxtail millet reference genome presents an opportunity for the genome-wide characterization of these GATA genes. Results In this study, we identified 28 GATA genes in foxtail millet distributed on seven chromosomes. According to the classification method of GATA members in Arabidopsis, SiGATA was divided into four subfamilies, namely subfamilies I, II, III, and IV. Structural analysis of the SiGATA genes showed that subfamily III had more introns than other subfamilies, and a large number of cis-acting elements were abundant in the promoter region of the SiGATA genes. Three tandem duplications and five segmental duplications were found among SiGATA genes. Tissue-specific results showed that the SiGATA genes were mainly expressed in foxtail millet leaves, followed by peels and seeds. Many genes were significantly induced under the eight abiotic stresses, such as SiGATA10, SiGATA16, SiGATA18, and SiGATA25, which deserve further attention. Conclusions Collectively, these findings will be helpful for further in-depth studies of the biological function of SiGATA, and will provide a reference for the future molecular breeding of foxtail millet. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08786-0.
Collapse
|
10
|
Schwechheimer C, Schröder PM, Blaby-Haas CE. Plant GATA Factors: Their Biology, Phylogeny, and Phylogenomics. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:123-148. [PMID: 35130446 DOI: 10.1146/annurev-arplant-072221-092913] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
GATA factors are evolutionarily conserved transcription factors that are found in animals, fungi, and plants. Compared to that of animals, the size of the plant GATA family is increased. In angiosperms, four main GATA classes and seven structural subfamilies can be defined. In recent years, knowledge about the biological role and regulation of plant GATAs has substantially improved. Individual family members have been implicated in the regulation of photomorphogenic growth, chlorophyll biosynthesis, chloroplast development, photosynthesis, and stomata formation, as well as root, leaf, and flower development. In this review, we summarize the current knowledge of plant GATA factors. Using phylogenomic analysis, we trace the evolutionary origin of the GATA classes in the green lineage and examine their relationship to animal and fungal GATAs. Finally, we speculate about a possible conservation of GATA-regulated functions across the animal, fungal, and plant kingdoms.
Collapse
Affiliation(s)
- Claus Schwechheimer
- School of Life Sciences, Plant Systems Biology, Technical University of Munich, Freising, Germany;
| | - Peter Michael Schröder
- School of Life Sciences, Plant Systems Biology, Technical University of Munich, Freising, Germany;
| | - Crysten E Blaby-Haas
- Biology Department, Brookhaven National Laboratory, Upton, New York, USA;
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| |
Collapse
|
11
|
Genome-Wide Characterization and Expression Analysis of GATA Transcription Factors in Response to Methyl Jasmonate in Salvia miltiorrhiza. Genes (Basel) 2022; 13:genes13050822. [PMID: 35627207 PMCID: PMC9140432 DOI: 10.3390/genes13050822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 02/01/2023] Open
Abstract
Salvia miltiorrhiza is an important medicinal plant, which is mainly used for treatment of cardiovascular and cerebrovascular diseases. GATA transcription factors are evolutionarily conser-ved proteins that play essential roles in biological process of plants. In this study, we systematically characterized the GATA transcription factors in S. miltiorrhiza. A total 28 SmGATA genes were identified and divided into four subfamilies based on phylogenetic analysis and domain. SmGATA genes being clustered into a subfamily have similar conserved motifs and exon-intron patterns, and unevenly distribute on eight chromosomes of S. miltiorrhiza. Tissue-specific expression analysis based on transcriptome datasets showed that the majority of SmGATA genes were preferentially expressed in roots. Under methyl jasmonate (MeJA) treatment, the quantitative real-time PCR (qRT-PCR) analysis indicated that several SmGATA genes in roots showed distinct upregulation post-MeJA treatment, especially SmGATA08, which was highly responsive to MeJA, and might be involved in the jasmonate signal, thereby affecting root growth, development, tolerance to various stresses, or secondary metabolites biosynthesis. The study found that several SmGATAs, like SmGATA08, are highly responsive to MeJA, indicating that these SmGATAs might be vital in the biosynthesis of tanshinones and phenolic acids by regulating the response to MeJA in S. miltiorrhiza. Our results laid the foundation for understanding their biological roles and quality improvement in S. miltiorrhiza.
Collapse
|
12
|
Cackett L, Luginbuehl LH, Schreier TB, Lopez-Juez E, Hibberd JM. Chloroplast development in green plant tissues: the interplay between light, hormone, and transcriptional regulation. THE NEW PHYTOLOGIST 2022; 233:2000-2016. [PMID: 34729790 DOI: 10.1111/nph.17839] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/09/2021] [Indexed: 05/20/2023]
Abstract
Chloroplasts are best known for their role in photosynthesis, but they also allow nitrogen and sulphur assimilation, amino acid, fatty acid, nucleotide and hormone synthesis. How chloroplasts develop is therefore relevant to these diverse and fundamental biological processes, but also to attempts at their rational redesign. Light is strictly required for chloroplast formation in all angiosperms and directly regulates the expression of hundreds of chloroplast-related genes. Light also modulates the levels of several hormones including brassinosteriods, cytokinins, auxins and gibberellins, which themselves control chloroplast development particularly during early stages of plant development. Transcription factors such as GOLDENLIKE1&2 (GLK1&2), GATA NITRATE-INDUCIBLE CARBON METABOLISM-INVOLVED (GNC) and CYTOKININ-RESPONSIVE GATA FACTOR 1 (CGA1) act downstream of both light and phytohormone signalling to regulate chloroplast development. Thus, in green tissues transcription factors, light signalling and hormone signalling form a complex network regulating the transcription of chloroplast- and photosynthesis-related genes to control the development and number of chloroplasts per cell. We use this conceptual framework to identify points of regulation that could be harnessed to modulate chloroplast abundance and increase photosynthetic efficiency of crops, and to highlight future avenues to overcome gaps in current knowledge.
Collapse
Affiliation(s)
- Lee Cackett
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Leonie H Luginbuehl
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Tina B Schreier
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Enrique Lopez-Juez
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| |
Collapse
|
13
|
Yang J, Xu Y, Wang J, Gao S, Huang Y, Hung FY, Li T, Li Q, Yue L, Wu K, Yang S. The chromatin remodelling ATPase BRAHMA interacts with GATA-family transcription factor GNC to regulate flowering time in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:835-847. [PMID: 34545936 DOI: 10.1093/jxb/erab430] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/20/2021] [Indexed: 05/13/2023]
Abstract
BRAHMA (BRM) is the ATPase of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodelling complex, which is indispensable for transcriptional inhibition and activation, associated with vegetative and reproductive development in Arabidopsis thaliana. Here, we show that BRM directly binds to the chromatin of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), which integrates multiple flowering signals to regulate floral transition, leading to flowering. In addition, genetic and molecular analysis showed that BRM interacts with GNC (GATA, NITRATE-INDUCIBLE, CARBON METABOLISM INVOLVED), a GATA transcription factor that represses flowering by directly repressing SOC1 expression. Furthermore, BRM is recruited by GNC to directly bind to the chromatin of SOC1. The transcript level of SOC1 is elevated in brm-3, gnc, and brm-3/gnc mutants, which is associated with increased histone H3 lysine 4 tri-methylation (H3K4Me3) but decreased DNA methylation. Taken together, our results indicate that BRM associates with GNC to regulate SOC1 expression and flowering time.
Collapse
Affiliation(s)
- Jie Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yingchao Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhao Wang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Sujuan Gao
- College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Academy of Contemporary Agricultural Engineering Innovations, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yisui Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Fu-Yu Hung
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Tao Li
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qing Li
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agrobiological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Lin Yue
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| |
Collapse
|
14
|
Lee D, Hua L, Khoshravesh R, Giuliani R, Kumar I, Cousins A, Sage TL, Hibberd JM, Brutnell TP. Engineering chloroplast development in rice through cell-specific control of endogenous genetic circuits. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2291-2303. [PMID: 34328250 PMCID: PMC8541780 DOI: 10.1111/pbi.13660] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/21/2021] [Accepted: 06/25/2021] [Indexed: 05/03/2023]
Abstract
The engineering of C4 photosynthetic activity into the C3 plant rice has the potential to nearly double rice yields. To engineer a two-cell photosynthetic system in rice, the rice bundle sheath (BS) must be rewired to enhance photosynthetic capacity. Here, we show that BS chloroplast biogenesis is enhanced when the transcriptional activator, Oryza sativa Cytokinin GATA transcription factor 1 (OsCGA1), is driven by a vascular specific promoter. Ectopic expression of OsCGA1 resulted in increased BS chloroplast planar area and increased expression of photosynthesis-associated nuclear genes (PhANG), required for the biogenesis of photosynthetically active chloroplasts in BS cells of rice. A further refinement using a DNAse dead Cas9 (dCas9) activation module driven by the same cell-type specific promoter, directed enhanced chloroplast development of the BS cells when gRNA sequences were delivered by the dCas9 module to the promoter of the endogenous OsCGA1 gene. Single gRNA expression was sufficient to mediate the transactivation of both the endogenous gene and a transgenic GUS reporter fused with OsCGA1 promoter. Our results illustrate the potential for tissue-specific dCas9-activation and the co-regulation of genes needed for multistep engineering of C4 rice.
Collapse
Affiliation(s)
| | - Lei Hua
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Roxana Khoshravesh
- Department of Ecology and Evolutionary Biologythe University of TorontoTorontoONCanada
- Department of Biologythe University of New MexicoAlbuquerqueNMUSA
| | - Rita Giuliani
- School of Biological SciencesWashington State UniversityPullmanWAUSA
| | | | - Asaph Cousins
- School of Biological SciencesWashington State UniversityPullmanWAUSA
| | - Tammy L. Sage
- Department of Ecology and Evolutionary Biologythe University of TorontoTorontoONCanada
| | | | - Thomas P. Brutnell
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice DevelopmentBiotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| |
Collapse
|
15
|
Kim M, Xi H, Park J. Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors. PLoS One 2021; 16:e0252181. [PMID: 34038437 PMCID: PMC8153473 DOI: 10.1371/journal.pone.0252181] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 05/11/2021] [Indexed: 12/30/2022] Open
Abstract
GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.
Collapse
Affiliation(s)
- Mangi Kim
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| |
Collapse
|
16
|
Zhu W, Guo Y, Chen Y, Wu D, Jiang L. Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus. BMC PLANT BIOLOGY 2020; 20:543. [PMID: 33276730 PMCID: PMC7716463 DOI: 10.1186/s12870-020-02752-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/24/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Transcription factors GATAs are involved in plant developmental processes and respond to environmental stresses through binding DNA regulatory regions to regulate their downstream genes. However, little information on the GATA genes in Brassica napus is available. The release of the reference genome of B. napus provides a good opportunity to perform a genome-wide characterization of GATA family genes in rapeseed. RESULTS In this study, 96 GATA genes randomly distributing on 19 chromosomes were identified in B. napus, which were classified into four subfamilies based on phylogenetic analysis and their domain structures. The amino acids of BnGATAs were obvious divergence among four subfamilies in terms of their GATA domains, structures and motif compositions. Gene duplication and synteny between the genomes of B. napus and A. thaliana were also analyzed to provide insights into evolutionary characteristics. Moreover, BnGATAs showed different expression patterns in various tissues and under diverse abiotic stresses. Single nucleotide polymorphisms (SNPs) distributions of BnGATAs in a core collection germplasm are probably associated with functional disparity under environmental stress condition in different genotypes of B. napus. CONCLUSION The present study was investigated genomic structures, evolution features, expression patterns and SNP distributions of 96 BnGATAs. The results enrich our understanding of the GATA genes in rapeseed.
Collapse
Affiliation(s)
- Weizhuo Zhu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Yiyi Guo
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Yeke Chen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| | - Dezhi Wu
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China.
| | - Lixi Jiang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China
| |
Collapse
|
17
|
Zhang C, Huang Y, Xiao Z, Yang H, Hao Q, Yuan S, Chen H, Chen L, Chen S, Zhou X, Huang W. A GATA Transcription Factor from Soybean ( Glycine max) Regulates Chlorophyll Biosynthesis and Suppresses Growth in the Transgenic Arabidopsis thaliana. PLANTS 2020; 9:plants9081036. [PMID: 32824119 PMCID: PMC7464611 DOI: 10.3390/plants9081036] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/09/2020] [Accepted: 08/11/2020] [Indexed: 11/16/2022]
Abstract
Chlorophyll plays an essential role in photosynthetic light harvesting and energy transduction in green tissues of higher plants and is closely related to photosynthesis and crop yield. Identification of transcription factors (TFs) involved in regulating chlorophyll biosynthesis is still limited in soybean (Glycine max), and the previously identified GmGATA58 is suggested to potentially modulate chlorophyll and nitrogen metabolisms, but its complete function is still unknown. In this study, subcellular localization assay showed that GmGATA58 was localized in the nucleus. Histochemical GUS assay and qPCR assay indicated that GmGATA58 was mainly expressed in leaves and responded to nitrogen, light and phytohormone treatments. Overexpression of GmGATA58 in the Arabidopsis thaliana ortholog AtGATA21 (gnc) mutant complemented the greening defect, while overexpression in Arabidopsis wild-type led to increasing chlorophyll content in leaves through up-regulating the expression levels of the large of chlorophyll biosynthetic pathway genes, but suppressing plant growth and yield, although the net photosynthetic rate was slightly improved. Dual-luciferase reporter assay also supported that GmGATA58 activated the transcription activities of three promoters of key chlorophyll biosynthetic genes of soybean in transformed protoplast of Arabidopsis. It is concluded that GmGATA58 played an important role in regulating chlorophyll biosynthesis, but suppressed plant growth and yield in transgenic Arabidopsis.
Collapse
Affiliation(s)
- Chanjuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (C.Z.); (Y.H.); (Z.X.); (H.Y.); (Q.H.); (S.Y.); (H.C.); (L.C.); (S.C.)
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (C.Z.); (Y.H.); (Z.X.); (H.Y.); (Q.H.); (S.Y.); (H.C.); (L.C.); (S.C.)
| | - Zhiyuan Xiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (C.Z.); (Y.H.); (Z.X.); (H.Y.); (Q.H.); (S.Y.); (H.C.); (L.C.); (S.C.)
| | - Hongli Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (C.Z.); (Y.H.); (Z.X.); (H.Y.); (Q.H.); (S.Y.); (H.C.); (L.C.); (S.C.)
| | - Qingnan Hao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (C.Z.); (Y.H.); (Z.X.); (H.Y.); (Q.H.); (S.Y.); (H.C.); (L.C.); (S.C.)
| | - Songli Yuan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (C.Z.); (Y.H.); (Z.X.); (H.Y.); (Q.H.); (S.Y.); (H.C.); (L.C.); (S.C.)
| | - Haifeng Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (C.Z.); (Y.H.); (Z.X.); (H.Y.); (Q.H.); (S.Y.); (H.C.); (L.C.); (S.C.)
| | - Limiao Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (C.Z.); (Y.H.); (Z.X.); (H.Y.); (Q.H.); (S.Y.); (H.C.); (L.C.); (S.C.)
| | - Shuilian Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (C.Z.); (Y.H.); (Z.X.); (H.Y.); (Q.H.); (S.Y.); (H.C.); (L.C.); (S.C.)
| | - Xinan Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (C.Z.); (Y.H.); (Z.X.); (H.Y.); (Q.H.); (S.Y.); (H.C.); (L.C.); (S.C.)
- Correspondence: (X.Z.); (W.H.); Tel.:+86-27-8671-1563 (X.Z.)
| | - Wenjun Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (X.Z.); (W.H.); Tel.:+86-27-8671-1563 (X.Z.)
| |
Collapse
|
18
|
Gururani K, Kumar A, Tiwari A, Agarwal A, Gupta S, Pandey D. Transcriptome wide identification and characterization of regulatory genes involved in EAA metabolism and validation through expression analysis in different developmental stages of finger millet spikes. 3 Biotech 2020; 10:347. [PMID: 32728514 DOI: 10.1007/s13205-020-02337-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 07/12/2020] [Indexed: 12/27/2022] Open
Abstract
Finger millet is a rich source of seed storage proteins (SSPs). Various regulatory genes play an important role to maintain the quality and accumulation of SSPs in crop seeds. In the present study, nine regulatory genes of EAAs metabolic pathway, i.e., aspartate kinase, homoserine dehydrogenase, threonine synthase, threonine dehydratase, dihydrodipicolinate synthase, cystathionine γ synthase, anthranilate synthase, acetolactate synthase and lysine 2-oxoglutarato reductase/saccharopine dehydrogenase (LOR/SD) were identified from the transcriptomic data of developing spikes of two finger millet genotypes, i.e., GP-45 and GP-1. Results of sequence alignment search and motif/domain analysis showed high similarity of nucleotide sequences of identified regulatory genes with their respective homologs in rice. Results of promoter analysis revealed the presence of various cis-regulatory elements, like nitrogen responsive cis-elements (O2-site and GCN4), light responsive cis-elements, and stress responsive cis-elements. The presence of nine regulatory genes identified from the transcriptomic data of GP-45 and GP-1 was further confirmed by real time expression analysis in high and low protein containing genotypes, i.e., GE-3885 and GE-1437. Results of real time expression analysis showed significantly higher expression (p ≤ 0.01) of regulatory genes in GE-3885 rather than GE-1437 under control and treatment condition. Crude protein content of GE-3885 was found to be significantly higher (p ≤ 0.01) in comparison to GE-1437 under control condition, while under treatment condition GE-1437 was found to be more responsive to KNO3 treatment rather than GE-3885.
Collapse
Affiliation(s)
- Kavita Gururani
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, U.S. Nagar, Pantnagar, 263145 Uttarakhand India
| | - Anil Kumar
- Rani Laxmi Bai Central Agriculture University, Jhansi, Uttar Pradesh 284003 India
| | - Apoorv Tiwari
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, U.S. Nagar, Pantnagar, 263145 Uttarakhand India
- Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, 211007 Uttar Pradesh India
| | - Aparna Agarwal
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, U.S. Nagar, Pantnagar, 263145 Uttarakhand India
| | - Supriya Gupta
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, U.S. Nagar, Pantnagar, 263145 Uttarakhand India
| | - Dinesh Pandey
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, U.S. Nagar, Pantnagar, 263145 Uttarakhand India
| |
Collapse
|
19
|
Liu Q, Bischof S, Harris CJ, Zhong Z, Zhan L, Nguyen C, Rashoff A, Barshop WD, Sun F, Feng S, Potok M, Gallego-Bartolome J, Zhai J, Wohlschlegel JA, Carey MF, Long JA, Jacobsen SE. The characterization of Mediator 12 and 13 as conditional positive gene regulators in Arabidopsis. Nat Commun 2020; 11:2798. [PMID: 32493925 PMCID: PMC7271234 DOI: 10.1038/s41467-020-16651-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/14/2020] [Indexed: 12/18/2022] Open
Abstract
Mediator 12 (MED12) and MED13 are components of the Mediator multi-protein complex, that facilitates the initial steps of gene transcription. Here, in an Arabidopsis mutant screen, we identify MED12 and MED13 as positive gene regulators, both of which contribute broadly to morc1 de-repressed gene expression. Both MED12 and MED13 are preferentially required for the expression of genes depleted in active chromatin marks, a chromatin signature shared with morc1 re-activated loci. We further discover that MED12 tends to interact with genes that are responsive to environmental stimuli, including light and radiation. We demonstrate that light-induced transient gene expression depends on MED12, and is accompanied by a concomitant increase in MED12 enrichment during induction. In contrast, the steady-state expression level of these genes show little dependence on MED12, suggesting that MED12 is primarily required to aid the expression of genes in transition from less-active to more active states. Mediator is a multiprotein complex required to activate gene transcription by RNAPII. Here, the authors report that MED12 and MED13 are conditional positive regulators that facilitate the expression of genes depleted in active chromatin marks and the induction of gene expression in response to environmental stimuli in Arabidopsis.
Collapse
Affiliation(s)
- Qikun Liu
- School of Advanced Agricultural Sciences, Peking University, 100871, Beijing, China. .,Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
| | - Sylvain Bischof
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA.,Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - C Jake Harris
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Zhenhui Zhong
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA.,Basic Forestry and Proteomics Center, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Lingyu Zhan
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Calvin Nguyen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Andrew Rashoff
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - William D Barshop
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Fei Sun
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Magdalena Potok
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Javier Gallego-Bartolome
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Jixian Zhai
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Jeffrey A Long
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA. .,Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
| |
Collapse
|
20
|
Kinoshita A, Richter R. Genetic and molecular basis of floral induction in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2490-2504. [PMID: 32067033 PMCID: PMC7210760 DOI: 10.1093/jxb/eraa057] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 02/03/2020] [Indexed: 05/18/2023]
Abstract
Many plants synchronize their life cycles in response to changing seasons and initiate flowering under favourable environmental conditions to ensure reproductive success. To confer a robust seasonal response, plants use diverse genetic programmes that integrate environmental and endogenous cues and converge on central floral regulatory hubs. Technological advances have allowed us to understand these complex processes more completely. Here, we review recent progress in our understanding of genetic and molecular mechanisms that control flowering in Arabidopsis thaliana.
Collapse
Affiliation(s)
- Atsuko Kinoshita
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
- Correspondence: or
| | - René Richter
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Australia
- Correspondence: or
| |
Collapse
|
21
|
Genome-Wide Characterization and Gene Expression Analyses of GATA Transcription Factors in Moso Bamboo ( Phyllostachys edulis). Int J Mol Sci 2019; 21:ijms21010014. [PMID: 31861396 PMCID: PMC6982067 DOI: 10.3390/ijms21010014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/16/2019] [Accepted: 12/16/2019] [Indexed: 01/13/2023] Open
Abstract
Moso bamboo is well-known for its rapid-growth shoots and widespread rhizomes. However, the regulatory genes of these two processes are largely unexplored. GATA transcription factors regulate many developmental processes, but their roles in moso bamboo height control and rhizome development remains unexplored. Here, thirty-one bamboo GATA factors (PeGATAs) were identified, which are evolutionarily closer to rice than Arabidopsis, and their gene expression patterns were analyzed in bamboo development and phytohormone response with bioinformatics and molecular methods. Interestingly, PeGATAs could only be classified into three groups. Phytohormone responsive cis-elements were found in PeGATA promoters and the expression profiles showed that PeGATA genes might respond to gibberellin acid and abscisic acid but not to auxin at the transcriptional level. Furthermore, PeGATA genes have a tissue-specific expression pattern in bamboo rhizomes. Interestingly, most PeGATA genes were down-regulated during the rapid-growth of bamboo shoots. In addition, over-expressing one of the PeGATA genes, PeGATA26, significantly repressed the primary root length and plant height of transgenic Arabidopsis plants, which may be achieved by promoting the gibberellin acid turnover. Overall, our results provide insight into the function of GATA transcription factors in bamboo, and into genetic resources for engineering plant height.
Collapse
|
22
|
Jin Y, Guo W, Hu X, Liu M, Xu X, Hu F, Lan Y, Lv C, Fang Y, Liu M, Shi T, Ma S, Fang Z, Huang J. Static magnetic field regulates Arabidopsis root growth via auxin signaling. Sci Rep 2019; 9:14384. [PMID: 31591431 PMCID: PMC6779896 DOI: 10.1038/s41598-019-50970-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/23/2019] [Indexed: 12/15/2022] Open
Abstract
Static magnetic field (SMF) plays important roles in biological processes of many living organisms. In plants, however, biological significance of SMF and molecular mechanisms underlying SMF action remain largely unknown. To address these questions, we treated Arabidopsis young seedlings with different SMF intensities and directions. Magnetic direction from the north to south pole was adjusted in parallel (N0) with, opposite (N180) and perpendicular to the gravity vector. We discovered that root growth is significantly inhanced by 600 mT treatments except for N180, but not by any 300 mT treatments. N0 treatments lead to more active cell division of the meristem, and higher auxin content that is regulated by coordinated expression of PIN3 and AUX1 in root tips. Consistently, N0-promoted root growth disappears in pin3 and aux1 mutants. Transcriptomic and gene ontology analyses revealed that in roots 85% of the total genes significantly down-regulated by N0 compared to untreatment are enriched in plastid biological processes, such as metabolism and chloroplast development. Lastly, no difference in root length is observed between N0-treated and untreated roots of the double cryptochrome mutant cry1 cry2. Taken together, our data suggest that SMF-regulated root growth is mediated by CRY and auxin signaling pathways in Arabidopsis.
Collapse
Affiliation(s)
- Yue Jin
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Wei Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xupeng Hu
- Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Mengmeng Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xiang Xu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Fenhong Hu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yiheng Lan
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Chenkai Lv
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yanwen Fang
- Heye Health Industrial Research Institute of Zhejiang Heye Health Technology, Anji, Zhejiang, 313300, China
| | - Mengyu Liu
- Heye Health Industrial Research Institute of Zhejiang Heye Health Technology, Anji, Zhejiang, 313300, China
| | - Tieliu Shi
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Shisong Ma
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Zhicai Fang
- Heye Health Industrial Research Institute of Zhejiang Heye Health Technology, Anji, Zhejiang, 313300, China
| | - Jirong Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
| |
Collapse
|
23
|
Kim J, Chun JP, Tucker ML. Transcriptional Regulation of Abscission Zones. PLANTS 2019; 8:plants8060154. [PMID: 31174352 PMCID: PMC6631628 DOI: 10.3390/plants8060154] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/29/2019] [Accepted: 06/04/2019] [Indexed: 12/17/2022]
Abstract
Precise and timely regulation of organ separation from the parent plant (abscission) is consequential to improvement of crop productivity as it influences both the timing of harvest and fruit quality. Abscission is tightly associated with plant fitness as unwanted organs (petals, sepals, filaments) are shed after fertilization while seeds, fruits, and leaves are cast off as means of reproductive success or in response to abiotic/biotic stresses. Floral organ abscission in Arabidopsis has been a useful model to elucidate the molecular mechanisms that underlie the separation processes, and multiple abscission signals associated with the activation and downstream pathways have been uncovered. Concomitantly, large-scale analyses of omics studies in diverse abscission systems of various plants have added valuable insights into the abscission process. The results suggest that there are common molecular events linked to the biosynthesis of a new extracellular matrix as well as cell wall disassembly. Comparative analysis between Arabidopsis and soybean abscission systems has revealed shared and yet disparate regulatory modules that affect the separation processes. In this review, we discuss our current understanding of the transcriptional regulation of abscission in several different plants that has improved on the previously proposed four-phased model of organ separation.
Collapse
Affiliation(s)
- Joonyup Kim
- Department of Horticultural Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea.
| | - Jong-Pil Chun
- Department of Horticultural Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea.
| | - Mark L Tucker
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, USDA Bldg. 006, 10300 Baltimore Ave., Beltsville, MD 20705, USA.
| |
Collapse
|
24
|
Wang P, Hendron RW, Kelly S. Transcriptional control of photosynthetic capacity: conservation and divergence from Arabidopsis to rice. THE NEW PHYTOLOGIST 2017; 216:32-45. [PMID: 28727145 DOI: 10.1111/nph.14682] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 05/16/2017] [Indexed: 05/12/2023]
Abstract
Contents 32 I. 32 II. 33 III. 36 IV. 41 43 References 43 SUMMARY: Photosynthesis is one of the most important biological processes on Earth. It provides the consumable energy upon which almost all organisms are dependent, and modulates the composition of the planet's atmosphere. To carry out photosynthesis, plants require a large cohort of genes. These genes encode proteins that capture light energy, store energy in sugars and build the subcellular structures required to facilitate this energy capture. Although the function of many of these genes is known, little is understood about the transcriptional networks that coordinate their expression. This review places our understanding of the transcriptional regulation of photosynthesis in Arabidopsis thaliana in an evolutionary context, to provide new insight into transcriptional regulatory networks that control photosynthesis gene expression in grasses. The similarities and differences between the rice and Arabidopsis networks are highlighted, revealing substantial disparity between the two systems. In addition, avenues are identified that may be exploited for photosynthesis engineering projects in the future.
Collapse
Affiliation(s)
- Peng Wang
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Ross-William Hendron
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| |
Collapse
|
25
|
Xu Z, Casaretto JA, Bi Y, Rothstein SJ. Genome-wide binding analysis of AtGNC and AtCGA1 demonstrates their cross-regulation and common and specific functions. PLANT DIRECT 2017; 1:e00016. [PMID: 31245665 PMCID: PMC6508505 DOI: 10.1002/pld3.16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/04/2017] [Accepted: 08/21/2017] [Indexed: 05/26/2023]
Abstract
GATA transcription factors are involved in multiple processes in plant growth and development. Two GATA factors, NITRATE-INDUCIBLE,CARBON METABOLISM-INVOLVED (GNC) and CYTOKININ-RESPONSIVE GATA FACTOR 1 (CGA1, also named GNL), are important regulators in greening, flowering, senescence, and hormone signaling. However, their direct target genes related to these biological processes are poorly characterized. Here, GNC and CGA1 are shown to be transcription activators and by using chromatin immunoprecipitation sequencing (ChIP-seq), 1475 and 638 genes are identified to be associated with GNC and CGA1 binding, respectively. Enrichment of diverse motifs in the peak binding regions for GNC and CGA1 suggests the possibility that these two transcription factors also interact with other transcription factors and in addition genes coding for DNA-binding proteins are highly enriched among GNC- and CGA1-associated genes. Despite the fact that these two GATA factors are known to share a large portion of co-expressed genes, our analysis revealed a low percentage of overlapping binding-associated genes for these two homologues. This suggests a possible cross-regulation between these, which is verified using ChIP-qPCR. The common and specific biological processes regulated by GNC and CGA1 also support this notion. Functional analysis of the binding-associated genes revealed that those encoding transcription factors, E3 ligase, as well as genes with roles in plant development are highly enriched, indicating that GNC and CGA1 mediate complex genetic networks in regulating different aspects of plant growth and development.
Collapse
Affiliation(s)
- Zhenhua Xu
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphONCanada
| | - José A. Casaretto
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphONCanada
| | - Yong‐Mei Bi
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphONCanada
| | - Steven J. Rothstein
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphONCanada
| |
Collapse
|
26
|
Kim J, Yang J, Yang R, Sicher RC, Chang C, Tucker ML. Transcriptome Analysis of Soybean Leaf Abscission Identifies Transcriptional Regulators of Organ Polarity and Cell Fate. FRONTIERS IN PLANT SCIENCE 2016; 7:125. [PMID: 26925069 PMCID: PMC4756167 DOI: 10.3389/fpls.2016.00125] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/22/2016] [Indexed: 05/19/2023]
Abstract
Abscission, organ separation, is a developmental process that is modulated by endogenous and environmental factors. To better understand the molecular events underlying the progression of abscission in soybean, an agriculturally important legume, we performed RNA sequencing (RNA-seq) of RNA isolated from the leaf abscission zones (LAZ) and petioles (Non-AZ, NAZ) after treating stem/petiole explants with ethylene for 0, 12, 24, 48, and 72 h. As expected, expression of several families of cell wall modifying enzymes and many pathogenesis-related (PR) genes specifically increased in the LAZ as abscission progressed. Here, we focus on the 5,206 soybean genes we identified as encoding transcription factors (TFs). Of the 5,206 TFs, 1,088 were differentially up- or down-regulated more than eight-fold in the LAZ over time, and, within this group, 188 of the TFs were differentially regulated more than eight-fold in the LAZ relative to the NAZ. These 188 abscission-specific TFs include several TFs containing domains for homeobox, MYB, Zinc finger, bHLH, AP2, NAC, WRKY, YABBY, and auxin-related motifs. To discover the connectivity among the TFs and highlight developmental processes that support organ separation, the 188 abscission-specific TFs were then clustered based on a >four-fold up- or down-regulation in two consecutive time points (i.e., 0 and 12 h, 12 and 24 h, 24 and 48 h, or 48 and 72 h). By requiring a sustained change in expression over two consecutive time intervals and not just one or several time intervals, we could better tie changes in TFs to a particular process or phase of abscission. The greatest number of TFs clustered into the 0 and 12 h group. Transcriptional network analysis for these abscission-specific TFs indicated that most of these TFs are known as key determinants in the maintenance of organ polarity, lateral organ growth, and cell fate. The abscission-specific expression of these TFs prior to the onset of abscission and their functional properties as defined by studies in Arabidopsis indicate that these TFs are involved in defining the separation cells and initiation of separation within the AZ by balancing organ polarity, roles of plant hormones, and cell differentiation.
Collapse
Affiliation(s)
- Joonyup Kim
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of AgricultureBeltsville, MD, USA
- Department of Cell Biology and Molecular Genetics, University of MarylandCollege Park, MD, USA
- *Correspondence: Joonyup Kim
| | - Jinyoung Yang
- Crop Systems and Global Change Laboratory, Agricultural Research Service, United States Department of AgricultureBeltsville, MD, USA
| | - Ronghui Yang
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of AgricultureBeltsville, MD, USA
| | - Richard C. Sicher
- Crop Systems and Global Change Laboratory, Agricultural Research Service, United States Department of AgricultureBeltsville, MD, USA
| | - Caren Chang
- Department of Cell Biology and Molecular Genetics, University of MarylandCollege Park, MD, USA
| | - Mark L. Tucker
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of AgricultureBeltsville, MD, USA
- Mark L. Tucker
| |
Collapse
|
27
|
Barah P, B N MN, Jayavelu ND, Sowdhamini R, Shameer K, Bones AM. Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses. Nucleic Acids Res 2015; 44:3147-64. [PMID: 26681689 PMCID: PMC4838348 DOI: 10.1093/nar/gkv1463] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 11/28/2015] [Indexed: 11/25/2022] Open
Abstract
Differentially evolved responses to various stress conditions in plants are controlled by complex regulatory circuits of transcriptional activators, and repressors, such as transcription factors (TFs). To understand the general and condition-specific activities of the TFs and their regulatory relationships with the target genes (TGs), we have used a homogeneous stress gene expression dataset generated on ten natural ecotypes of the model plant Arabidopsis thaliana, during five single and six combined stress conditions. Knowledge-based profiles of binding sites for 25 stress-responsive TF families (187 TFs) were generated and tested for their enrichment in the regulatory regions of the associated TGs. Condition-dependent regulatory sub-networks have shed light on the differential utilization of the underlying network topology, by stress-specific regulators and multifunctional regulators. The multifunctional regulators maintain the core stress response processes while the transient regulators confer the specificity to certain conditions. Clustering patterns of transcription factor binding sites (TFBS) have reflected the combinatorial nature of transcriptional regulation, and suggested the putative role of the homotypic clusters of TFBS towards maintaining transcriptional robustness against cis-regulatory mutations to facilitate the preservation of stress response processes. The Gene Ontology enrichment analysis of the TGs reflected sequential regulation of stress response mechanisms in plants.
Collapse
Affiliation(s)
- Pankaj Barah
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim N-7491, Norway
| | - Mahantesha Naika B N
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK campus, Bangalore 560 065, India
| | - Naresh Doni Jayavelu
- Department of Chemical Engineering, Norwegian University of Science and Technology, Trondheim N-7491, Norway
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK campus, Bangalore 560 065, India
| | - Khader Shameer
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK campus, Bangalore 560 065, India
| | - Atle M Bones
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, Trondheim N-7491, Norway
| |
Collapse
|
28
|
Cortleven A, Schmülling T. Regulation of chloroplast development and function by cytokinin. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4999-5013. [PMID: 25873684 DOI: 10.1093/jxb/erv132] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A role of the plant hormone cytokinin in regulating the development and activity of chloroplasts was described soon after its discovery as a plant growth regulator more than 50 years ago. Its promoting action on chloroplast ultrastructure and chlorophyll synthesis has been reported repeatedly, especially during etioplast-to-chloroplast transition. Recently, a protective role of the hormone for the photosynthetic apparatus during high light stress was shown. Details about the molecular mechanisms of cytokinin action on plastids are accumulating from genetic and transcriptomic studies. The cytokinin receptors AHK2 and AHK3 are mainly responsible for the transduction of the cytokinin signal to B-type response regulators, in particular ARR1, ARR10, and ARR12, which are transcription factors of the two-component system mediating cytokinin functions. Additional transcription factors linking cytokinin and chloroplast development include CGA1, GNC, HY5, GLK2, and CRF2. In this review, we summarize early and more recent findings of the long-known relationship between the hormone and the organelle and describe crosstalk between cytokinin, light, and other hormones during chloroplast development.
Collapse
Affiliation(s)
- Anne Cortleven
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg 6, D-14195 Berlin, Germany
| | - Thomas Schmülling
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences (DCPS), Freie Universität Berlin, Albrecht-Thaer-Weg 6, D-14195 Berlin, Germany
| |
Collapse
|
29
|
Vercruyssen L, Tognetti VB, Gonzalez N, Van Dingenen J, De Milde L, Bielach A, De Rycke R, Van Breusegem F, Inzé D. GROWTH REGULATING FACTOR5 stimulates Arabidopsis chloroplast division, photosynthesis, and leaf longevity. PLANT PHYSIOLOGY 2015; 167:817-32. [PMID: 25604530 PMCID: PMC4348790 DOI: 10.1104/pp.114.256180] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 01/16/2015] [Indexed: 05/18/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) leaf development relies on subsequent phases of cell proliferation and cell expansion. During the proliferation phase, chloroplasts need to divide extensively, and during the transition from cell proliferation to expansion, they differentiate into photosynthetically active chloroplasts, providing the plant with energy. The transcription factor GROWTH REGULATING FACTOR5 (GRF5) promotes the duration of the cell proliferation period during leaf development. Here, it is shown that GRF5 also stimulates chloroplast division, resulting in a higher chloroplast number per cell with a concomitant increase in chlorophyll levels in 35S:GRF5 leaves, which can sustain higher rates of photosynthesis. Moreover, 35S:GRF5 plants show delayed leaf senescence and are more tolerant for growth on nitrogen-depleted medium. Cytokinins also stimulate leaf growth in part by extending the cell proliferation phase, simultaneously delaying the onset of the cell expansion phase. In addition, cytokinins are known to be involved in chloroplast development, nitrogen signaling, and senescence. Evidence is provided that GRF5 and cytokinins synergistically enhance cell division and chlorophyll retention after dark-induced senescence, which suggests that they also cooperate to stimulate chloroplast division and nitrogen assimilation. Taken together with the increased leaf size, ectopic expression of GRF5 has great potential to improve plant productivity.
Collapse
Affiliation(s)
- Liesbeth Vercruyssen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| | - Vanesa B Tognetti
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| | - Judith Van Dingenen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| | - Liesbeth De Milde
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| | - Agnieszka Bielach
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| | - Riet De Rycke
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (L.V., V.B.T., N.G., J.V.D., L.D.M., A.B., R.D.R., F.V.B., D.I.); and Central European Institute of Technology, 60177 Brno, Czech Republic (V.B.T., A.B.)
| |
Collapse
|
30
|
Behringer C, Schwechheimer C. B-GATA transcription factors - insights into their structure, regulation, and role in plant development. FRONTIERS IN PLANT SCIENCE 2015; 6:90. [PMID: 25755661 PMCID: PMC4337238 DOI: 10.3389/fpls.2015.00090] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 02/03/2015] [Indexed: 05/17/2023]
Abstract
GATA transcription factors are evolutionarily conserved transcriptional regulators that recognize promoter elements with a G-A-T-A core sequence. In comparison to animal genomes, the GATA transcription factor family in plants is comparatively large with approximately 30 members. Here, we review the current knowledge on B-GATAs, one of four GATA factor subfamilies from Arabidopsis thaliana. We show that B-GATAs can be subdivided based on structural features and their biological function into family members with a C-terminal LLM- (leucine-leucine-methionine) domain or an N-terminal HAN- (HANABA TARANU) domain. The paralogous GNC (GATA, NITRATE-INDUCIBLE, CARBON-METABOLISM INVOLVED) and CGA1/GNL (CYTOKININ-INDUCED GATA1/GNC-LIKE) are introduced as LLM-domain containing B-GATAs from Arabidopsis that control germination, greening, senescence, and flowering time downstream from several growth regulatory signals. Arabidopsis HAN and its monocot-specific paralogs from rice (NECK LEAF1), maize (TASSEL SHEATH1), and barley (THIRD OUTER GLUME) are HAN-domain-containing B-GATAs with a predominant role in embryo development and floral development. We also review GATA23, a regulator of lateral root initiation from Arabidopsis that is closely related to GNC and GNL but has a degenerate LLM-domain that is seemingly specific for the Brassicaceae family. The Brassicaceae-specific GATA23 and the monocot-specific HAN-domain GATAs provide evidence that neofunctionalization of B-GATAs was used during plant evolution to expand the functional repertoire of these transcription factors.
Collapse
Affiliation(s)
| | - Claus Schwechheimer
- *Correspondence: Claus Schwechheimer, Department of Plant Systems Biology, Technische Universität München, Emil-Ramann-Straße 4, 85354 Freising, Germany e-mail:
| |
Collapse
|
31
|
Reddy MM, Ulaganathan K. Nitrogen Nutrition, Its Regulation and Biotechnological Approaches to Improve Crop Productivity. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/ajps.2015.618275] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
32
|
Behringer C, Bastakis E, Ranftl QL, Mayer KFX, Schwechheimer C. Functional diversification within the family of B-GATA transcription factors through the leucine-leucine-methionine domain. PLANT PHYSIOLOGY 2014; 166:293-305. [PMID: 25077795 PMCID: PMC4149714 DOI: 10.1104/pp.114.246660] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The transcription of the Arabidopsis (Arabidopsis thaliana) GATA transcription factors GATA, NITRATE-INDUCIBLE, CARBON METABOLISM-INVOLVED (GNC) and GNC-LIKE (GNL)/CYTOKININ-RESPONSIVE GATA FACTOR1 is controlled by several growth regulatory signals including light and the phytohormones auxin, cytokinin, and gibberellin. To date, GNC and GNL have been attributed functions in the control of germination, greening, flowering time, floral development, senescence, and floral organ abscission. GNC and GNL belong to the 11-member family of B-class GATA transcription factors that are characterized to date solely by their high sequence conservation within the GATA DNA-binding domain. The degree of functional conservation among the various B-class GATA family members is not understood. Here, we identify and examine B-class GATAs from Arabidopsis, tomato (Solanum lycopersicon), Brachypodium (Brachypodium distachyon), and barley (Hordeum vulgare). We find that B-class GATAs from these four species can be subdivided based on their short or long N termini and the presence of the 13-amino acid C-terminal leucine-leucine-methionine (LLM) domain with the conserved motif LLM. Through overexpression analyses and by complementation of a gnc gnl double mutant, we provide evidence that the length of the N terminus may not allow distinguishing between the different B-class GATAs at the functional level. In turn, we find that the presence and absence of the LLM domain in the overexpressors has differential effects on hypocotyl elongation, leaf shape, and petiole length, as well as on gene expression. Thus, our analyses identify the LLM domain as an evolutionarily conserved domain that determines B-class GATA factor identity and provides a further subclassification criterion for this transcription factor family.
Collapse
Affiliation(s)
- Carina Behringer
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany (C.B., E.B., Q.L.R., C.S.); andMunich Information Centre for Protein Sequences, Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany (K.F.X.M.)
| | - Emmanouil Bastakis
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany (C.B., E.B., Q.L.R., C.S.); andMunich Information Centre for Protein Sequences, Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany (K.F.X.M.)
| | - Quirin L Ranftl
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany (C.B., E.B., Q.L.R., C.S.); andMunich Information Centre for Protein Sequences, Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany (K.F.X.M.)
| | - Klaus F X Mayer
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany (C.B., E.B., Q.L.R., C.S.); andMunich Information Centre for Protein Sequences, Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany (K.F.X.M.)
| | - Claus Schwechheimer
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany (C.B., E.B., Q.L.R., C.S.); andMunich Information Centre for Protein Sequences, Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany (K.F.X.M.)
| |
Collapse
|
33
|
Li Y, Xu J, Haq NU, Zhang H, Zhu XG. Was low CO2 a driving force of C4 evolution: Arabidopsis responses to long-term low CO2 stress. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3657-67. [PMID: 24855683 PMCID: PMC4085967 DOI: 10.1093/jxb/eru193] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The responses of long-term growth of plants under elevated CO2 have been studied extensively. Comparatively, the responses of plants to subambient CO2 concentrations have not been well studied. This study aims to investigate the responses of the model C3 plant, Arabidopsis thaliana, to low CO2 at the molecular level. Results showed that low CO2 dramatically decreased biomass productivity, together with delayed flowering and increased stomatal density. Furthermore, alteration of thylakoid stacking in both bundle sheath and mesophyll cells, upregulation of PEPC and PEPC-K together with altered expression of a number of regulators known involved in photosynthesis development were observed. These responses to low CO2 are discussed with regard to the fitness of C3 plants under low CO2. This work also briefly discusses the relevance of the data to C4 photosynthesis evolution.
Collapse
Affiliation(s)
- Yuanyuan Li
- State Key Laboratory of Hybrid Rice Research, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiajia Xu
- State Key Laboratory of Hybrid Rice Research, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Noor Ul Haq
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Zhang
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai 200031, China Shandong Normal University, Jinan, Shandong 250014, China
| | - Xin-Guang Zhu
- State Key Laboratory of Hybrid Rice Research, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai 200031, China
| |
Collapse
|
34
|
Abstract
Cytokinins are N (6) substituted adenine derivatives that affect many aspects of plant growth and development, including cell division, shoot initiation and growth, leaf senescence, apical dominance, sink/source relationships, nutrient uptake, phyllotaxis, and vascular, gametophyte, and embryonic development, as well as the response to biotic and abiotic factors. Molecular genetic studies in Arabidopsis have helped elucidate the mechanisms underlying the function of this phytohormone in plants. Here, we review our current understanding of cytokinin biosynthesis and signaling in Arabidopsis, the latter of which is similar to bacterial two-component phosphorelays. We discuss the perception of cytokinin by the ER-localized histidine kinase receptors, the role of the AHPs in mediating the transfer of the phosphoryl group from the receptors to the response regulators (ARRs), and finally the role of the large ARR family in cytokinin function. The identification and genetic manipulation of the genes involved in cytokinin metabolism and signaling have helped illuminate the roles of cytokinins in Arabidopsis. We discuss these diverse roles, and how other signaling pathways influence cytokinin levels and sensitivity though modulation of the expression of cytokinin signaling and metabolic genes.
Collapse
Affiliation(s)
- Joseph J Kieber
- University of North Carolina, Biology Department, Chapel Hill, NC 27599-3280
| | - G Eric Schaller
- Dartmouth College, Department of Biological Sciences, Hanover, NH 03755
| |
Collapse
|
35
|
Richter R, Bastakis E, Schwechheimer C. Cross-repressive interactions between SOC1 and the GATAs GNC and GNL/CGA1 in the control of greening, cold tolerance, and flowering time in Arabidopsis. PLANT PHYSIOLOGY 2013; 162:1992-2004. [PMID: 23739688 PMCID: PMC3729777 DOI: 10.1104/pp.113.219238] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 06/03/2013] [Indexed: 05/20/2023]
Abstract
The paralogous and functionally redundant GATA transcription factors GNC (for GATA, NITRATE-INDUCIBLE, CARBON-METABOLISM INVOLVED) and GNL/CGA1 (for GNC-LIKE/CYTOKININ-RESPONSIVE GATA FACTOR1) from Arabidopsis (Arabidopsis thaliana) promote greening and repress flowering downstream from the phytohormone gibberellin. The target genes of GNC and GNL with regard to flowering time control have not been identified as yet. Here, we show by genetic and molecular analysis that the two GATA factors act upstream from the flowering time regulator SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) to directly repress SOC1 expression and thereby repress flowering. Interestingly, this analysis inversely also reveals that the MADS box transcription factor SOC1 directly represses GNC and GNL expression to control cold tolerance and greening, two further physiological processes that are under the control of SOC1. In summary, these findings support the case of a cross-repressive interaction between the GATA factors GNC and GNL and the MADS box transcription factor SOC1 in flowering time control on the one side and greening and cold tolerance on the other that may be governed by the various signaling inputs that are integrated at the level of SOC1 expression.
Collapse
|
36
|
Convergence of auxin and gibberellin signaling on the regulation of the GATA transcription factors GNC and GNL in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2013; 110:13192-7. [PMID: 23878229 DOI: 10.1073/pnas.1304250110] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Plant growth is regulated by a complex network of signaling events. Points of convergence for the signaling cross-talk between the phytohormones auxin and gibberellin (GA), which partly control overlapping processes during plant development, are largely unknown. At the cellular level, auxin responses are controlled by members of the AUXIN RESPONSE FACTOR (ARF) family of transcription factors as well as AUXIN/INDOLE-3-ACETIC ACID INDUCIBLE (AUX/IAA) proteins that repress the activity of at least a subset of ARFs. Here, we show that the two paralogous GATA transcription factors GATA, NITRATE-INDUCIBLE, CARBON-METABOLISM INVOLVED (GNC) and GNC-LIKE (GNL)/CYTOKININ-RESPONSIVE GATA FACTOR1 (CGA1) are direct and critical transcription targets downstream from ARF2 in the control of greening, flowering time, and senescence. Mutants deficient in the synthesis or signaling of the phytohormone GA are also impaired in greening, flowering, and senescence, and interestingly, GNC and GNL were previously identified as important transcription targets of the GA signaling pathway. In line with a critical regulatory role for GNC and GNL downstream from both auxin and GA signaling, we show here that the constitutive activation of GA signaling is sufficient to suppress arf2 mutant phenotypes through repression of GNC and GNL. In addition, we show that GA promotes ARF2 protein abundance through a translation-dependent mechanism that could serve to override the autoinhibitory negative feedback regulation of ARF2 on its own transcription and thereby further promote GA signaling.
Collapse
|
37
|
Hudson D, Guevara DR, Hand AJ, Xu Z, Hao L, Chen X, Zhu T, Bi YM, Rothstein SJ. Rice cytokinin GATA transcription Factor1 regulates chloroplast development and plant architecture. PLANT PHYSIOLOGY 2013; 162:132-44. [PMID: 23548780 PMCID: PMC3641198 DOI: 10.1104/pp.113.217265] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 03/29/2013] [Indexed: 05/18/2023]
Abstract
Chloroplast biogenesis has been well documented in higher plants, yet the complex methods used to regulate chloroplast activity under fluctuating environmental conditions are not well understood. In rice (Oryza sativa), the CYTOKININ-RESPONSIVE GATA TRANSCRIPTION FACTOR1 (Cga1) shows increased expression following light, nitrogen, and cytokinin treatments, while darkness and gibberellin reduce expression. Strong overexpression of Cga1 produces dark green, semidwarf plants with reduced tillering, whereas RNA interference knockdown results in reduced chlorophyll and increased tillering. Coexpression, microarray, and real-time expression analyses demonstrate a correlation between Cga1 expression and the expression of important nucleus-encoded, chloroplast-localized genes. Constitutive Cga1 overexpression increases both chloroplast biogenesis and starch production but also results in delayed senescence and reduced grain filling. Growing the transgenic lines under different nitrogen regimes indicates potential agricultural applications for Cga1, including manipulation of biomass, chlorophyll/chloroplast content, and harvest index. These results indicate a conserved mechanism by which Cga1 regulates chloroplast development in higher plants.
Collapse
Affiliation(s)
- Darryl Hudson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (D.H., D.R.G., A.J.H., Z.X., L.H., Y.-M.B., S.J.R.); and
- Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (X.C., T.Z.)
| | - David R. Guevara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (D.H., D.R.G., A.J.H., Z.X., L.H., Y.-M.B., S.J.R.); and
- Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (X.C., T.Z.)
| | - Andrew J. Hand
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (D.H., D.R.G., A.J.H., Z.X., L.H., Y.-M.B., S.J.R.); and
- Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (X.C., T.Z.)
| | - Zhenhua Xu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (D.H., D.R.G., A.J.H., Z.X., L.H., Y.-M.B., S.J.R.); and
- Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (X.C., T.Z.)
| | - Lixin Hao
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (D.H., D.R.G., A.J.H., Z.X., L.H., Y.-M.B., S.J.R.); and
- Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (X.C., T.Z.)
| | - Xi Chen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (D.H., D.R.G., A.J.H., Z.X., L.H., Y.-M.B., S.J.R.); and
- Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (X.C., T.Z.)
| | - Tong Zhu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (D.H., D.R.G., A.J.H., Z.X., L.H., Y.-M.B., S.J.R.); and
- Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (X.C., T.Z.)
| | - Yong-Mei Bi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1 (D.H., D.R.G., A.J.H., Z.X., L.H., Y.-M.B., S.J.R.); and
- Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (X.C., T.Z.)
| | | |
Collapse
|
38
|
Zhang X, Zhou Y, Ding L, Wu Z, Liu R, Meyerowitz EM. Transcription repressor HANABA TARANU controls flower development by integrating the actions of multiple hormones, floral organ specification genes, and GATA3 family genes in Arabidopsis. THE PLANT CELL 2013; 25:83-101. [PMID: 23335616 PMCID: PMC3584552 DOI: 10.1105/tpc.112.107854] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 11/29/2012] [Accepted: 12/28/2012] [Indexed: 05/19/2023]
Abstract
Plant inflorescence meristems and floral meristems possess specific boundary domains that result in proper floral organ separation and specification. HANABA TARANU (HAN) encodes a boundary-expressed GATA3-type transcription factor that regulates shoot meristem organization and flower development in Arabidopsis thaliana, but the underlying mechanism remains unclear. Through time-course microarray analyses following transient overexpression of HAN, we found that HAN represses hundreds of genes, especially genes involved in hormone responses and floral organ specification. Transient overexpression of HAN also represses the expression of HAN and three other GATA3 family genes, HANL2 (HAN-LIKE 2), GNC (GATA, NITRATE-INDUCIBLE, CARBON-METABOLISM-INVOLVED), and GNL (GNC-LIKE), forming a negative regulatory feedback loop. Genetic analysis indicates that HAN and the three GATA3 family genes coordinately regulate floral development, and their expression patterns are partially overlapping. HAN can homodimerize and heterodimerize with the three proteins encoded by these genes, and HAN directly binds to its own promoter and the GNC promoter in vivo. These findings, along with the fact that constitutive overexpression of HAN produces an even stronger phenotype than the loss-of-function mutation, support the hypothesis that HAN functions as a key repressor that regulates floral development via regulatory networks involving genes in the GATA3 family, along with genes involved in hormone action and floral organ specification.
Collapse
Affiliation(s)
- Xiaolan Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, People's Republic of China.
| | | | | | | | | | | |
Collapse
|
39
|
|
40
|
Chiang YH, Zubo YO, Tapken W, Kim HJ, Lavanway AM, Howard L, Pilon M, Kieber JJ, Schaller GE. Functional characterization of the GATA transcription factors GNC and CGA1 reveals their key role in chloroplast development, growth, and division in Arabidopsis. PLANT PHYSIOLOGY 2012; 160:332-48. [PMID: 22811435 PMCID: PMC3440210 DOI: 10.1104/pp.112.198705] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 07/16/2012] [Indexed: 05/17/2023]
Abstract
Chloroplasts develop from proplastids in a process that requires the interplay of nuclear and chloroplast genomes, but key steps in this developmental process have yet to be elucidated. Here, we show that the nucleus-localized transcription factors GATA NITRATE-INDUCIBLE CARBON-METABOLISM-INVOLVED (GNC) and CYTOKININ-RESPONSIVE GATA1 (CGA1) regulate chloroplast development, growth, and division in Arabidopsis (Arabidopsis thaliana). GNC and CGA1 are highly expressed in green tissues, and the phytohormone cytokinin regulates their expression. A gnc cga1 mutant exhibits a reduction in overall chlorophyll levels as well as in chloroplast size in the hypocotyl. Ectopic overexpression of either GNC or CGA1 promotes chloroplast biogenesis in hypocotyl cortex and root pericycle cells, based on increases in the number and size of the chloroplasts, and also results in expanded zones of chloroplast production into the epidermis of hypocotyls and cotyledons and into the cortex of roots. Ectopic overexpression also promotes the development of etioplasts from proplastids in dark-grown seedlings, subsequently enhancing the deetiolation process. Inducible expression of GNC demonstrates that GNC-mediated chloroplast biogenesis can be regulated postembryonically, notably so for chloroplast production in cotyledon epidermal cells. Analysis of the gnc cga1 loss-of-function and overexpression lines supports a role for these transcription factors in regulating the effects of cytokinin on chloroplast division. These data support a model in which GNC and CGA1 serve as two of the master transcriptional regulators of chloroplast biogenesis, acting downstream of cytokinin and mediating the development of chloroplasts from proplastids and enhancing chloroplast growth and division in specific tissues.
Collapse
|
41
|
Schwechheimer C. Gibberellin signaling in plants - the extended version. FRONTIERS IN PLANT SCIENCE 2012; 2:107. [PMID: 22645560 PMCID: PMC3355746 DOI: 10.3389/fpls.2011.00107] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 12/13/2011] [Indexed: 05/23/2023]
Abstract
The plant hormone gibberellin (GA) controls major aspects of plant growth such as germination, elongation growth, flower development, and flowering time. In recent years, a number of studies have revealed less apparent roles for GA in a surprisingly broad set of developmental as well as cell biological processes. The identification of GA receptor proteins on the one end of the signaling cascade, DELLA proteins as central repressors of the pathway and transcription regulators such as the phytochrome interacting factors and the GATA-type transcription factors GNC and CGA1/GNL on the current other end of the signaling cascade have extended our knowledge about how GA and DELLAs regulate a diverse set of plant responses.
Collapse
Affiliation(s)
- Claus Schwechheimer
- Plant Systems Biology, Center for Life and Food Sciences Weihenstephan, Technische Universität MünchenFreising, Germany
| |
Collapse
|
42
|
Brenner WG, Ramireddy E, Heyl A, Schmülling T. Gene regulation by cytokinin in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2012; 3:8. [PMID: 22639635 PMCID: PMC3355611 DOI: 10.3389/fpls.2012.00008] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 01/06/2012] [Indexed: 05/18/2023]
Abstract
The plant hormone cytokinin realizes at least part of its signaling output through the regulation of gene expression. A great part of the early transcriptional regulation is mediated by type-B response regulators, which are transcription factors of the MYB family. Other transcription factors, such as the cytokinin response factors of the AP2/ERF family, have also been shown to be involved in this process. Additional transcription factors mediate distinct parts of the cytokinin response through tissue- and cell-specific downstream transcriptional cascades. In Arabidopsis, only a single cytokinin response element, to which type-B response regulators bind, has been clearly proven so far, which has 5'-GAT(T/C)-3' as a core sequence. This motif has served to construct a synthetic cytokinin-sensitive two-component system response element, which is useful for monitoring the cellular cytokinin status. Insight into the extent of transcriptional regulation has been gained by genome-wide gene expression analyses following cytokinin treatment and from plants having an altered cytokinin content or signaling. This review presents a meta analysis of such microarray data resulting in a core list of cytokinin response genes. Genes encoding type-A response regulators displayed the most stable response to cytokinin, but a number of cytokinin metabolism genes (CKX4, CKX5, CYP735A2, UGT76C2) also belong to them, indicating homeostatic mechanisms operating at the transcriptional level. The cytokinin core response genes are also the target of other hormones as well as biotic and abiotic stresses, documenting crosstalk of the cytokinin system with other hormonal and environmental signaling pathways. The multiple links of cytokinin to diverse functions, ranging from control of meristem activity, hormonal crosstalk, nutrient acquisition, and various stress responses, are also corroborated by a compilation of genes that have been repeatedly found by independent gene expression profiling studies. Such functions are, at least in part, supported by genetic studies.
Collapse
Affiliation(s)
- Wolfram G. Brenner
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität BerlinBerlin, Germany
| | - Eswar Ramireddy
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität BerlinBerlin, Germany
| | - Alexander Heyl
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität BerlinBerlin, Germany
- *Correspondence: Alexander Heyl and Thomas Schmülling, Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Albrecht-Thaer-Weg 6, D-14195 Berlin, Germany. e-mail: ;
| | - Thomas Schmülling
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität BerlinBerlin, Germany
- *Correspondence: Alexander Heyl and Thomas Schmülling, Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Albrecht-Thaer-Weg 6, D-14195 Berlin, Germany. e-mail: ;
| |
Collapse
|
43
|
Hudson D, Guevara D, Yaish MW, Hannam C, Long N, Clarke JD, Bi YM, Rothstein SJ. GNC and CGA1 modulate chlorophyll biosynthesis and glutamate synthase (GLU1/Fd-GOGAT) expression in Arabidopsis. PLoS One 2011; 6:e26765. [PMID: 22102866 PMCID: PMC3213100 DOI: 10.1371/journal.pone.0026765] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 10/04/2011] [Indexed: 11/19/2022] Open
Abstract
Chloroplast development is an important determinant of plant productivity and is controlled by environmental factors including amounts of light and nitrogen as well as internal phytohormones including cytokinins and gibberellins (GA). The paralog GATA transcription factors GNC and CGA1/GNL up-regulated by light, nitrogen and cytokinin while also being repressed by GA signaling. Modifying the expression of these genes has previously been shown to influence chlorophyll content in Arabidopsis while also altering aspects of germination, elongation growth and flowering time. In this work, we also use transgenic lines to demonstrate that GNC and CGA1 exhibit a partially redundant control over chlorophyll biosynthesis. We provide novel evidence that GNC and CGA1 influence both chloroplast number and leaf starch in proportion to their transcript level. GNC and CGA1 were found to modify the expression of chloroplast localized GLUTAMATE SYNTHASE (GLU1/Fd-GOGAT), which is the primary factor controlling nitrogen assimilation in green tissue. Altering GNC and CGA1 expression was also found to modulate the expression of important chlorophyll biosynthesis genes (GUN4, HEMA1, PORB, and PORC). As previously demonstrated, the CGA1 transgenic plants demonstrated significantly altered timing to a number of developmental events including germination, leaf production, flowering time and senescence. In contrast, the GNC transgenic lines we analyzed maintain relatively normal growth phenotypes outside of differences in chloroplast development. Despite some evidence for partial divergence, results indicate that regulation of both GNC and CGA1 by light, nitrogen, cytokinin, and GA acts to modulate nitrogen assimilation, chloroplast development and starch production. Understanding the mechanisms controlling these processes is important for agricultural biotechnology.
Collapse
Affiliation(s)
- Darryl Hudson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - David Guevara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Mahmoud W. Yaish
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Carol Hannam
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Nykoll Long
- Syngenta Biotechnology Inc., Research Triangle Park, North Carolina, United States of America
| | - Joseph D. Clarke
- Syngenta Biotechnology Inc., Research Triangle Park, North Carolina, United States of America
| | - Yong-Mei Bi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Steven J. Rothstein
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| |
Collapse
|
44
|
Köllmer I, Werner T, Schmülling T. Ectopic expression of different cytokinin-regulated transcription factor genes of Arabidopsis thaliana alters plant growth and development. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:1320-7. [PMID: 21453984 DOI: 10.1016/j.jplph.2011.02.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 02/18/2011] [Accepted: 02/22/2011] [Indexed: 05/20/2023]
Abstract
The plant hormone cytokinin rapidly alters the steady state transcript levels of a number of transcription factor genes suggesting that these might have a function in mediating cytokinin effects. Here we report the analysis of Arabidopsis thaliana plants with an altered expression level of four different cytokinin-regulated transcription factor genes. These include GATA22 (also known as CGA1/GNL), two genes coding for members of the homeodomain zip (HD zip) class II transcription factor family (HAT4, HAT22), and bHLH64. Ectopic expression of the GATA22 gene induced the development of chloroplasts in root tissue where it is normally suppressed and led to the formation of shorter and less branched roots. Overexpression of HAT22 lowered the seedlings chlorophyll content and caused an earlier onset of leaf senescence. Enhanced expression of the HAT4 gene led to severe defects in inflorescence stem development and to a decrease in root growth and branching, while hat4 insertional mutants developed a larger root system. 35S:bHLH64 transgenic plants showed a pleiotropic phenotype, consisting of larger rosettes, reduced chlorophyll content and an elongated and thickened hypocotyl. Flower development was strongly disturbed leading to sterile plants. The results are consistent with specific functions of these transcription factor genes in regulating part of the cytokinin activities and suggest their action as convergence point with other signalling pathways, particularly those of gibberellin and light.
Collapse
Affiliation(s)
- Ireen Köllmer
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Albrecht-Thaer-Weg 6, Berlin, Germany
| | | | | |
Collapse
|
45
|
Kant S, Bi YM, Rothstein SJ. Understanding plant response to nitrogen limitation for the improvement of crop nitrogen use efficiency. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:1499-509. [PMID: 20926552 DOI: 10.1093/jxb/erq297] [Citation(s) in RCA: 232] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Development of genetic varieties with improved nitrogen use efficiency (NUE) is essential for sustainable agriculture. Generally, NUE can be divided into two parts. First, assimilation efficiency involves nitrogen (N) uptake and assimilation and second utilization efficiency involves N remobilization. Understanding the mechanisms regulating these processes is crucial for the improvement of NUE in crop plants. One important approach is to develop an understanding of the plant response to different N regimes, especially to N limitation, using various methods including transcription profiling, analysing mutants defective in their normal response to N limitation, and studying plants that show better growth under N-limiting conditions. One can then attempt to improve NUE in crop plants using the knowledge gained from these studies. There are several potential genetic and molecular approaches for the improvement of crop NUE discussed in this review. Increased knowledge of how plants respond to different N levels as well as to other environmental conditions is required to achieve this.
Collapse
Affiliation(s)
- Surya Kant
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | | | | |
Collapse
|
46
|
Richter R, Behringer C, Müller IK, Schwechheimer C. The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from DELLA proteins and PHYTOCHROME-INTERACTING FACTORS. Genes Dev 2010; 24:2093-104. [PMID: 20844019 DOI: 10.1101/gad.594910] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The phytohormone gibberellin (GA) regulates various developmental processes in plants such as germination, greening, elongation growth, and flowering time. DELLA proteins, which are degraded in response to GA, repress GA signaling by inhibitory interactions with PHYTOCHROME-INTERACTING FACTOR (PIF) family transcription factors. How GA signaling is controlled downstream from the DELLA and PIF regulators is, at present, unclear. Here, we characterize GNC (GATA, NITRATE-INDUCIBLE, CARBON-METABOLISM INVOLVED) and GNL/CGA1 (GNC-LIKE/CYTOKININ-RESPONSIVE GATA FACTOR1), two homologous GATA-type transcription factors from Arabidopsis thaliana that we initially identified as GA-regulated genes. Our genetic analyses of loss-of-function mutants and overexpression lines establish that GNC and GNL are functionally redundant regulators of germination, greening, elongation growth and flowering time. We further show by chromatin immunoprecipitation that both genes are potentially direct transcription targets of PIF transcription factors, and that their expression is up-regulated in pif mutant backgrounds. In line with a key role of GNC or GNL downstream from DELLA and PIF signaling, we find that their overexpression leads to gene expression changes that largely resemble those observed in a ga1 biosynthesis mutant or a pif quadruple mutant. These findings, together with the fact that gnc and gnl loss-of-function mutations suppress ga1 phenotypes, support the hypothesis that GNC and GNL are important repressors of GA signaling downstream from the DELLA and PIF regulators.
Collapse
Affiliation(s)
- René Richter
- Plant Systems Biology, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany
| | | | | | | |
Collapse
|
47
|
Jiang K, Zhu T, Diao Z, Huang H, Feldman LJ. The maize root stem cell niche: a partnership between two sister cell populations. PLANTA 2010; 231:411-24. [PMID: 20041334 PMCID: PMC2799627 DOI: 10.1007/s00425-009-1059-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 11/05/2009] [Indexed: 05/19/2023]
Abstract
Using transcript profile analysis, we explored the nature of the stem cell niche in roots of maize (Zea mays). Toward assessing a role for specific genes in the establishment and maintenance of the niche, we perturbed the niche and simultaneously monitored the spatial expression patterns of genes hypothesized as essential. Our results allow us to quantify and localize gene activities to specific portions of the niche: to the quiescent center (QC) or the proximal meristem (PM), or to both. The data point to molecular, biochemical and physiological processes associated with the specification and maintenance of the niche, and include reduced expression of metabolism-, redox- and certain cell cycle-associated transcripts in the QC, enrichment of auxin-associated transcripts within the entire niche, controls for the state of differentiation of QC cells, a role for cytokinins specifically in the PM portion of the niche, processes (repair machinery) for maintaining DNA integrity and a role for gene silencing in niche stabilization. To provide additional support for the hypothesized roles of the above-mentioned and other transcripts in niche specification, we overexpressed, in Arabidopsis, homologs of representative genes (eight) identified as highly enriched or reduced in the maize root QC. We conclude that the coordinated changes in expression of auxin-, redox-, cell cycle- and metabolism-associated genes suggest the linkage of gene networks at the level of transcription, thereby providing additional insights into events likely associated with root stem cell niche establishment and maintenance.
Collapse
Affiliation(s)
- Keni Jiang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| | - Tong Zhu
- Syngenta Biotechnology, Inc., 3054 Cornwallis Road, Research Triangle Park, NC 27709 USA
| | - Zhaoyan Diao
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| | - Haiyan Huang
- Department of Statistics, University of California, Berkeley, CA 94720 USA
| | - Lewis J. Feldman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| |
Collapse
|
48
|
To JPC, Kieber JJ. Cytokinin signaling: two-components and more. TRENDS IN PLANT SCIENCE 2008; 13:85-92. [PMID: 18262459 DOI: 10.1016/j.tplants.2007.11.005] [Citation(s) in RCA: 246] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 11/21/2007] [Accepted: 11/23/2007] [Indexed: 05/02/2023]
Abstract
The hormone cytokinin is perceived via a phosphorelay that is similar to the two-component systems with which bacteria sense and respond to environmental stimuli. Characterization of two-component elements in Arabidopsis, maize and rice shows that cytokinin responses are mediated via partially redundant two-component protein families: histidine kinases, histidine phosphotransfer proteins and response regulators, as well as by novel players, such as the cytokinin response factors. Recent studies in the model plant Arabidopsis have revealed that cytokinin regulates these signaling components through a variety of mechanisms, including modulating transcription, controlling phosphorelay and regulating protein localization and stability. Genetic analyses of cytokinin signaling components have clarified the roles of cytokinin signaling in development and revealed novel functions for this 'classic' phytohormone.
Collapse
Affiliation(s)
- Jennifer P C To
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | | |
Collapse
|