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Wang Y, Li X, Mo Y, Jiang C, Zhou Y, Hu J, Zhang Y, Lv J, Zhao K, Lu Z. Identification and expression profiling of SmGATA genes family involved in response to light and phytohormones in eggplant. FRONTIERS IN PLANT SCIENCE 2024; 15:1415921. [PMID: 38863540 PMCID: PMC11165305 DOI: 10.3389/fpls.2024.1415921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/14/2024] [Indexed: 06/13/2024]
Abstract
GATA proteins are transcription factors of zinc finger proteins, which play an important role in plant growth development and abiotic stress. However, there have been no identification or systematic studies of the GATA gene family in eggplant. In this study, 28 SmGATA genes were identified in the genome database of eggplant, which could be divided into four subgroups. Plant development, hormones, and stress-related cis-acting elements were identified in promoter regions of the SmGATA gene family. RT-qPCR indicated that 4 SmGATA genes displayed upregulated expressions during fruit developmental stage, whereas 2 SmGATA genes were down-regulated expression patterns. It was also demonstrated that SmGATA genes may be involved in light signals to regulate fruit anthocyanin biosynthesis. Furthermore, the expression patterns of SmGATA genes under ABA, GA and MeJA treatments showed that the SmGATAs were involved in the process of fruit ripening. Notably, SmGATA4 and SmGATA23 were highly correlated with the expression of anthocyanin biosynthesis genes, light-responsive genes, and genes that function in multiple hormone signaling pathways and the proteins they encoded were localized in the nucleus. All these results showed GATA genes likely play a major role in regulating fruit anthocyanin biosynthesis by integrating the light, ABA, GA and MeJA signaling pathways and provided references for further research on fruit quality in eggplant.
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Affiliation(s)
- Yanyan Wang
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Xinyun Li
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Yunrong Mo
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Caiqian Jiang
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Ying Zhou
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Jingyi Hu
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Youling Zhang
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Junheng Lv
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Kai Zhao
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Zhenya Lu
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
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Shao Y, Zhou Y, Yang L, Mu D, Wilson IW, Zhang Y, Zhu L, Liu X, Luo L, He J, Qiu D, Tang Q. Genome-wide identification of GATA transcription factor family and the effect of different light quality on the accumulation of terpenoid indole alkaloids in Uncaria rhynchophylla. PLANT MOLECULAR BIOLOGY 2024; 114:15. [PMID: 38329633 DOI: 10.1007/s11103-023-01400-1] [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: 06/08/2023] [Accepted: 11/07/2023] [Indexed: 02/09/2024]
Abstract
Uncaria rhynchophylla is an evergreen vine plant, belonging to the Rubiaceae family, that is rich in terpenoid indole alkaloids (TIAs) that have therapeutic effects on hypertension and Alzheimer's disease. GATA transcription factors (TF) are a class of transcription regulators that participate in the light response regulation, chlorophyll synthesis, and metabolism, with the capability to bind to GATA cis-acting elements in the promoter region of target genes. Currently the charactertics of GATA TFs in U. rhynchophylla and how different light qualities affect the expression of GATA and key enzyme genes, thereby affecting the changes in U. rhynchophylla alkaloids have not been investigated. In this study, 25 UrGATA genes belonging to four subgroups were identified based on genome-wide analysis. Intraspecific collinearity analysis revealed that only segmental duplications were identified among the UrGATA gene family. Collinearity analysis of GATA genes between U. rhynchophylla and four representative plant species, Arabidopsis thaliana, Oryza sativa, Coffea Canephora, and Catharanthus roseus was also performed. U. rhynchophylla seedlings grown in either red lights or under reduced light intensity had altered TIAs content after 21 days. Gene expression analysis reveal a complex pattern of expression from the 25 UrGATA genes as well as a number of key TIA enzyme genes. UrGATA7 and UrGATA8 were found to have similar expression profiles to key enzyme TIA genes in response to altered light treatments, implying that they may be involved in the regulation TIA content. In this research, we comprehensively analyzed the UrGATA TFs, and offered insight into the involvement of UrGATA TFs from U. rhynchophylla in TIAs biosynthesis.
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Affiliation(s)
- Yingying Shao
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China
| | - Yu Zhou
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China
| | - Li Yang
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China
| | - Detian Mu
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China.
| | - Iain W Wilson
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Yao Zhang
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China
| | - Lina Zhu
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China
| | - Xinghui Liu
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China
| | - Ling Luo
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China
| | - Jialong He
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China
| | - Deyou Qiu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, 100091, Beijing, China
| | - Qi Tang
- College of Horticulture, National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, 410128, Changsha, China.
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Hu S, Hou Y, Zhao L, Zheng Y, Jin P. Exogenous 24-epibrassinolide alleviates chilling injury in peach fruit through modulating PpGATA12-mediated sucrose and energy metabolisms. Food Chem 2023; 400:133996. [DOI: 10.1016/j.foodchem.2022.133996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/31/2022] [Accepted: 08/20/2022] [Indexed: 11/29/2022]
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Tanvir R, Wang L, Zhang A, Li L. Orphan Genes in Crop Improvement: Enhancing Potato Tuber Protein without Impacting Yield. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223076. [PMID: 36432805 PMCID: PMC9696052 DOI: 10.3390/plants11223076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/31/2022] [Accepted: 11/10/2022] [Indexed: 05/03/2023]
Abstract
Qua-Quine Starch (QQS), an Arabidopsis thaliana orphan gene, and its interactor, Arabidopsis Nuclear Factor Y subunit C4 (AtNF-YC4), can increase the total leaf and seed protein in different plants. Despite their potential in developing protein-rich crop varieties, their influence on the protein content of the stem, modified stem, and tuber was never investigated. Potato (Solanum tuberosum) is one of the most valuable food crops worldwide. This staple food is rich in starch, vitamins (B6, C), phenolics, flavonoids, polyamines, carotenoids, and various minerals but lacks adequate proteins necessary for a healthy human diet. Here we expressed A. thaliana QQS (AtQQS) and overexpressed S. tuberosum NF-YC4 (StNF-YC4) in potatoes to determine their influence on the composition and morphological characteristics of potato tubers. Our data demonstrated higher protein and reduced starch content in potato tubers without significantly compromising the tuber yield, shape, and numbers, when QQS was expressed or StNF-YC4 was overexpressed. Publicly available expression data, promoter region, and protein−protein interaction analyses of StNF-YC4 suggest its potential functionality in potato storage protein, metabolism, stress resistance, and defense against pests and pathogens. The overall outcomes of this study support QQS and NF-YC4’s potential utilization as tools to enhance tuber protein content in plants.
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Affiliation(s)
- Rezwan Tanvir
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39762, USA
| | - Lei Wang
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39762, USA
| | - Amy Zhang
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39762, USA
- Mississippi School for Mathematics and Science, Columbus, MS 39701, USA
| | - Ling Li
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39762, USA
- Correspondence: ; Tel.: +1-662-325-7570
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Liu M, Huang L, Zhang Y, Yan Z, Wang N. Overexpression of PdeGATA3 results in a dwarf phenotype in poplar by promoting the expression of PdeSTM and altering the content of gibberellins. TREE PHYSIOLOGY 2022; 42:tpac086. [PMID: 35980326 DOI: 10.1093/treephys/tpac086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 06/09/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
In previous studies, GA20 oxidase (GA20ox) has been identified to be an important enzyme in the biosynthesis of GA, and SHOOTMERISTEMLESS (STM) can repress the expression of GA20ox. In this study, the GATA transcription factor PdeGATA3 was identified in the poplar line NL895, and its overexpression (OE) transgenic lines showed a dwarf phenotype. RNA sequencing (RNA-Seq) analysis suggested that OE PdeGATA3 could promote the expression of PdeSTM and repress the expression of PdeGA20ox. Therefore, we hypothesized that PdeGATA3 would directly promote the expression of PdeSTM and that PdeSTM would repress the expression of PdeGA20ox. Four experiments, a dual-luciferase reporter assay, GUS transient coexpression assay, yeast one-hybrid assay and electrophoretic mobility shift assay, were conducted and verified that PdeGATA3 could promote the expression of PdeSTM by binding GATA-Boxes in its promoter. OE PdeSTM in poplar resulted in a dwarf phenotype and repressed the expression of PdeGA20ox. GA measurement of the OE PdeSTM and PdeGATA3 lines showed that GA3 and GA4 contents were significantly lower than those in the wild type (WT). Accordingly, we put forward a regulation model involving plant height regulation by PdeGATA3, PdeSTM and PdeGA20ox.
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Affiliation(s)
- Meifeng Liu
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Liyu Huang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Zhang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhaogui Yan
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Nian Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan 430070, China
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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.
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Jin X, Liu Y, Hou Z, Zhang Y, Fang Y, Huang Y, Cai H, Qin Y, Cheng Y. Genome-Wide Investigation of SBT Family Genes in Pineapple and Functional Analysis of AcoSBT1.12 in Floral Transition. Front Genet 2021; 12:730821. [PMID: 34557223 PMCID: PMC8452990 DOI: 10.3389/fgene.2021.730821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
SBT (Subtilisin-like serine protease), a clan of serine proteolytic enzymes, plays a versatile role in plant growth and defense. Although SBT family genes have been obtained from studies of dicots such as Arabidopsis, little is known about the potential functions of SBT in the monocots. In this study, 54 pineapple SBT genes (AcoSBTs) were divided into six subfamilies and then identified to be experienced strong purifying selective pressure and distributed on 25 chromosomes unevenly. Cis-acting element analysis indicated that almost all AcoSBTs promoters contain light-responsive elements. Further, the expression pattern via RNA-seq data showed that different AcoSBTs were preferentially expressed in different above-ground tissues. Transient expression in tobacco showed that AcoSBT1.12 was located in the plasma membrane. Moreover, Transgenic Arabidopsis ectopically overexpressing AcoSBT1.12 exhibited delayed flowering time. In addition, under the guidance of bioinformatic prediction, we found that AcoSBT1.12 could interact with AcoCWF19L, AcoPUF2, AcoCwfJL, Aco012905, and AcoSZF1 by yeast-two hybrid (Y2H). In summary, this study provided valuable information on pineapple SBT genes and illuminated the biological function of AcoSBT1.12 in floral transition.
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Affiliation(s)
- Xingyue Jin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanhui Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhimin Hou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yunfei Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yunying Fang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Youmei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hanyang Cai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Qin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan Cheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
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Saidi A, Hajibarat Z, Hajibarat Z. Phylogeny, gene structure and GATA genes expression in different tissues of solanaceae species. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Zarid M, García-Carpintero V, Esteras C, Esteva J, Bueso MC, Cañizares J, Picó MB, Monforte AJ, Fernández-Trujillo JP. Transcriptomic analysis of a near-isogenic line of melon with high fruit flesh firmness during ripening. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:754-777. [PMID: 32713003 DOI: 10.1002/jsfa.10688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 07/16/2020] [Accepted: 07/26/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND A near-isogenic line (NIL) of melon (SC10-2) with introgression in linkage group X was studied from harvest (at firm-ripe stage of maturity) until day 18 of postharvest storage at 20.5 °C together with its parental control ('Piel de Sapo', PS). RESULTS SC10-2 showed higher flesh firmness and whole fruit hardness but lower juiciness than its parental. SC10-2 showed a decrease in respiration rate accompanied by a decrease in ethylene production during ripening, both of which fell to a greater extent than in PS. The introgression affected 11 volatile organic compounds (VOCs), the levels of which during ripening were generally higher in SC10-2 than in PS. Transcriptomic analysis from RNA-Seq revealed differentially expressed genes (DEGs) associated with the effects studied. For example, 909 DEGs were exclusive to the introgression, and only 23 DEGs were exclusive to postharvest ripening time. Major functions of the DEGs associated with introgression or ripening time were identified by cluster analysis. About 37 genes directly and/or indirectly affected the delay in ripening of SC10-2 compared with PS in general and, more particularly, the physiological and quality traits measured and, probably, the differential non-climacteric response. Of the former genes, we studied in more detail at least five that mapped in the introgression in linkage group (LG) X, and 32 outside it. CONCLUSION There is an apparent control of textural changes, VOCs and fruit ripening by an expression quantitative trait locus located in LG X together with a direct control on them due to genes presented in the introgression (CmTrpD, CmNADH1, CmTCP15, CmGDSL esterase/lipase, and CmHK4-like) and CmNAC18. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Mohamed Zarid
- Department of Agronomical Engineering, Regional Campus of International Excellence 'Campus Mare Nostrum' (CMN), Technical University of Cartagena (UPCT), Cartagena, Spain
| | - Victor García-Carpintero
- Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Ciudad Politécnica de la Innovación, Universitat Politècnica de València (UPV), Valencia, Spain
| | - Cristina Esteras
- Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Ciudad Politécnica de la Innovación, Universitat Politècnica de València (UPV), Valencia, Spain
| | - Juan Esteva
- Department of Agronomical Engineering, Regional Campus of International Excellence 'Campus Mare Nostrum' (CMN), Technical University of Cartagena (UPCT), Cartagena, Spain
| | - María C Bueso
- Department of Applied Mathematics and Statistics, CMN, UPCT, Cartagena, Spain
| | - Joaquín Cañizares
- Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Ciudad Politécnica de la Innovación, Universitat Politècnica de València (UPV), Valencia, Spain
| | - María B Picó
- Centro de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Ciudad Politécnica de la Innovación, Universitat Politècnica de València (UPV), Valencia, Spain
| | - Antonio J Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC/Universidad Politécnica de Valencia (UPV), Ciudad Politécnica de la Innovación, Valencia, Spain
| | - J Pablo Fernández-Trujillo
- Department of Agronomical Engineering, Regional Campus of International Excellence 'Campus Mare Nostrum' (CMN), Technical University of Cartagena (UPCT), Cartagena, Spain
- Institute of Plant Biotechnology, CMN, UPCT, Cartagena, Spain
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Nutan KK, Singla-Pareek SL, Pareek A. The Saltol QTL-localized transcription factor OsGATA8 plays an important role in stress tolerance and seed development in Arabidopsis and rice. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:684-698. [PMID: 31613368 DOI: 10.1093/jxb/erz368] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/06/2019] [Indexed: 05/23/2023]
Abstract
GATA represents a highly conserved family of transcription factors reported in organisms ranging from fungi to angiosperms. A member of this family, OsGATA8, localized within the Saltol QTL in rice, has been reported to be induced by salinity, drought, and ABA. However, its precise role in stress tolerance has not yet been elucidated. Using genetic, molecular, and physiological analyses, in this study we show that OsGATA8 increases seed size and tolerance to abiotic stresses in both Arabidopsis and rice. Transgenic lines of rice were generated with 3-fold overexpression of OsGATA8 compared to the wild-type together with knockdown lines with 2-fold lower expression. The overexpressing lines showed higher biomass accumulation and higher photosynthetic efficiency in seedlings compared to the wild-type and knockdown lines under both normal and salinity-stress conditions. OsGATA8 appeared to be an integrator of diverse cellular processes, including K+/Na+ content, photosynthetic efficiency, relative water content, Fv/Fm ratio, and the stability to sub-cellular organelles. It also contributed to maintaining yield under stress, which was ~46% higher in overexpression plants compared with the wild-type. OsGATA8 produced these effects by regulating the expression of critical genes involved in stress tolerance, scavenging of reactive oxygen species, and chlorophyll biosynthesis.
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Affiliation(s)
- Kamlesh K Nutan
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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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.
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An intron-derived motif strongly increases gene expression from transcribed sequences through a splicing independent mechanism in Arabidopsis thaliana. Sci Rep 2019; 9:13777. [PMID: 31551463 PMCID: PMC6760150 DOI: 10.1038/s41598-019-50389-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/10/2019] [Indexed: 12/29/2022] Open
Abstract
Certain introns significantly increase mRNA accumulation by a poorly understood mechanism. These introns have no effect when located upstream, or more than ~1 Kb downstream, of the start of transcription. We tested the ability of a formerly non-stimulating intron containing 11 copies of the sequence TTNGATYTG, which is over-represented in promoter-proximal introns in Arabidopsis thaliana, to affect expression from various positions. The activity profile of this intron at different locations was similar to that of a natural intron from the UBQ10 gene, suggesting that the motif increases mRNA accumulation by the same mechanism. A series of introns with different numbers of this motif revealed that the effect on expression is linearly dependent on motif copy number up to at least 20, with each copy adding another 1.5-fold increase in mRNA accumulation. Furthermore, 6 copies of the motif stimulated mRNA accumulation to a similar degree from within an intron or when introduced into the 5'-UTR and coding sequences of an intronless construct, demonstrating that splicing is not required for this sequence to boost expression. The ability of this motif to substantially elevate expression from several hundred nucleotides downstream of the transcription start site reveals a novel type of eukaryotic gene regulation.
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13
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Zhang Z, Ren C, Zou L, Wang Y, Li S, Liang Z. Characterization of the GATA gene family in Vitis vinifera: genome-wide analysis, expression profiles, and involvement in light and phytohormone response. Genome 2018; 61:713-723. [PMID: 30092656 DOI: 10.1139/gen-2018-0042] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The plant GATA family is one of the most important transcription factors involved in light-responsive development, nitrogen metabolism, phytohormone signaling, and source/sink balance. However, the function of the GATA gene is less known in grape (Vitis vinifera L.). In this study, we comprehensively analyzed the GATA family in grape, particularly the phylogenetic evolution, duplication patterns, conserved motifs, gene structures, cis-elements, tissue expression patterns, and predicted function of VvGATA genes in response to abiotic stress. The potential roles of VvGATA genes in berry development were also investigated. The GATA transcription factors displayed expression diversity among different grape organs and tissues, and some of them showed preferential expression in a specific tissue. Heterotrophic cultured cells were used as model systems for the functional characterization of the VvGATA gene and study of its response to light and phytohormone. Results indicated that some VvGATA genes displayed differential responses to light and phytohormones, suggesting their role in light and hormone signaling pathways. A thorough analysis of GATA transcription factors in grape (V. vinifera L.) presented the characterization and functional prediction of VvGATA genes. The data presented here lay the foundation for further functional studies of grape GATA transcription factors.
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Affiliation(s)
- Zhan Zhang
- a Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Science, Beijing, 100093, China.,b University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chong Ren
- a Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Science, Beijing, 100093, China.,b University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Luming Zou
- a Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Science, Beijing, 100093, China.,b University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Wang
- a Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Science, Beijing, 100093, China.,b University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shaohua Li
- a Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Science, Beijing, 100093, China
| | - Zhenchang Liang
- a Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Science, Beijing, 100093, China.,c Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
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Watanabe Y, Kadono T, Kira N, Suzuki K, Iwata O, Ohnishi K, Yamaguchi H, Adachi M. Development of endogenous promoters that drive high-level expression of introduced genes in the model diatom Phaeodactylum tricornutum. Mar Genomics 2018; 42:41-48. [PMID: 30509379 DOI: 10.1016/j.margen.2018.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/20/2018] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
Abstract
The marine diatom Phaeodactylum tricornutum is attractive for basic and applied diatom research. We isolated putative endogenous gene promoters derived from genes that are highly expressed in P. tricornutum: the fucoxanthin chlorophyll a/c-binding protein (FCP) C gene, the vacuolar ATP synthase 16-kDa proteolipid subunit (V-ATPase C) gene, the clumping factor A gene and the solute carrier family 34 member 2 gene. Five putative promoter regions were isolated, linked to an antibiotic resistance gene (Sh ble) and transformed into P. tricornutum. Using quantitative RT-PCR, the promoter activities in the transformants were analyzed and compared to that of the diatom endogenous gene promoter, the FCP A gene promoter which has been used for the transformation of P. tricornutum. Among the five isolated potential promoters, the activity of the V-ATPase C gene promoter was approximately 2.73 times higher than that of the FCP A gene promoter. The V-ATPase C gene promoter drove the expression of Sh ble mRNA transcripts under both light and dark conditions at the stationary phase. These results suggest that the V-ATPase C gene promoter is a novel tool for the genetic engineering of P. tricornutum.
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Affiliation(s)
- Yumi Watanabe
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Takashi Kadono
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Nozomu Kira
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Kengo Suzuki
- Euglena Co., Ltd., 22F, Morinaga Plaza Building, Shiba-5-33-1, Minato-ku, Tokyo 108-0019, Japan
| | - Osamu Iwata
- Euglena Co., Ltd., 22F, Morinaga Plaza Building, Shiba-5-33-1, Minato-ku, Tokyo 108-0019, Japan
| | - Kouhei Ohnishi
- Research Institute of Molecular Genetics, Kochi University, Otsu-200, Nankoku, Kochi 783-8502, Japan
| | - Haruo Yamaguchi
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Masao Adachi
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan.
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Roman H, Girault T, Le Gourrierec J, Leduc N. In silico analysis of 3 expansin gene promoters reveals 2 hubs controlling light and cytokinins response during bud outgrowth. PLANT SIGNALING & BEHAVIOR 2017; 12:e1284725. [PMID: 28263675 PMCID: PMC5351728 DOI: 10.1080/15592324.2017.1284725] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Bud outgrowth is under the intricate control of environmental and endogenous factors. In a recent paper, 1 we demonstrated that light perceived by Rosa buds triggers cytokinins (CK) synthesis within 3 hours in the adjacent node followed by their transport to the bud. There, CK control expression of a set of major genes (strigolactones-, auxin-, sugar sink strength-, cells division and elongation-related genes) leading to bud outgrowth in light. Conversely, under dark condition, CK accumulation and transport to the bud are repressed and no bud outgrowth occurs. In this paper, we show that the 3 expansin genes RhEXPA1,2,3 are under the control of both light and CK during bud outgrowth. In silico analysis of promoter sequences highlights 2 regions enriched in light and CK cis-regulatory elements as well as a specific cis-element in pRhEXPA3, potentially responsible for the expression patterns observed in response to CK and light.
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Affiliation(s)
- Hanaé Roman
- IRHS, Université d'Angers, INRA, AGROCAMPUS-Ouest, SFR 4207 QUASAV, Beaucouzé cedex, France
| | - Tiffanie Girault
- IRHS, Université d'Angers, INRA, AGROCAMPUS-Ouest, SFR 4207 QUASAV, Beaucouzé cedex, France
| | - José Le Gourrierec
- IRHS, Université d'Angers, INRA, AGROCAMPUS-Ouest, SFR 4207 QUASAV, Beaucouzé cedex, France
| | - Nathalie Leduc
- IRHS, Université d'Angers, INRA, AGROCAMPUS-Ouest, SFR 4207 QUASAV, Beaucouzé cedex, France
- CONTACT Nathalie Leduc IRHS, Campus du Végétal, 42 rue Georges Morel, 49071 Beaucouzé, France
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Kong SL, Abdullah SNA, Ho CL, Amiruddin MD. Molecular cloning, gene expression profiling and in silico sequence analysis of vitamin E biosynthetic genes from the oil palm. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.plgene.2016.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Zhang C, Hou Y, Hao Q, Chen H, Chen L, Yuan S, Shan Z, Zhang X, Yang Z, Qiu D, Zhou X, Huang W. Genome-wide survey of the soybean GATA transcription factor gene family and expression analysis under low nitrogen stress. PLoS One 2015; 10:e0125174. [PMID: 25886477 PMCID: PMC4401516 DOI: 10.1371/journal.pone.0125174] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 03/21/2015] [Indexed: 01/03/2023] Open
Abstract
GATA transcription factors are transcriptional regulatory proteins that contain a characteristic type-IV zinc finger DNA-binding domain and recognize the conserved GATA motif in the promoter sequence of target genes. Previous studies demonstrated that plant GATA factors possess critical functions in developmental control and responses to the environment. To date, the GATA factors in soybean (Glycine max) have yet to be characterized. Thus, this study identified 64 putative GATA factors from the entire soybean genomic sequence. The chromosomal distributions, gene structures, duplication patterns, phylogenetic tree, tissue expression patterns, and response to low nitrogen stress of the 64 GATA factors in soybean were analyzed to further investigate the functions of these factors. Results indicated that segmental duplication predominantly contributed to the expansion of the GATA factor gene family in soybean. These GATA proteins were phylogenetically clustered into four distinct subfamilies, wherein their gene structure and motif compositions were considerably conserved. A comparative phylogenetic analysis of the GATA factor zinc finger domain sequences in soybean, Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa) revealed four major classes. The GATA factors in soybean exhibited expression diversity among different tissues; some of these factors showed tissue-specific expression patterns. Numerous GATA factors displayed upregulation or downregulation in soybean leaf in response to low nitrogen stress, and two GATA factors GATA44 and GATA58 were likely to be involved in the regulation of nitrogen metabolism in soybean. Overexpression of GmGATA44 complemented the reduced chlorophyll phenotype of the Arabidopsis ortholog AtGATA21 mutant, implying that GmGATA44 played an important role in modulating chlorophyll biosynthesis. Overall, our study provides useful information for the further analysis of the biological functions of GATA factors in soybean and other crops.
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Affiliation(s)
- Chanjuan Zhang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuqing Hou
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Qingnan Hao
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Haifeng Chen
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Limiao Chen
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Songli Yuan
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zhihui Shan
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaojuan Zhang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zhonglu Yang
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dezhen Qiu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xinan Zhou
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Wenjun Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
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Sahoo DK, Sarkar S, Raha S, Maiti IB, Dey N. Comparative analysis of synthetic DNA promoters for high-level gene expression in plants. PLANTA 2014; 240:855-75. [PMID: 25092118 DOI: 10.1007/s00425-014-2135-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/21/2014] [Indexed: 05/25/2023]
Abstract
MAIN CONCLUSION We have designed two near- constitutive and stress-inducible promoters (CmYLCV9.11 and CmYLCV4); those are highly efficient in both dicot and monocot plants and have prospective to substitute the CaMV 35S promoter. We performed structural and functional studies of the full-length transcript promoter from Cestrum yellow leaf curling virus (CmYLCV) employing promoter/leader deletion and activating cis-sequence analysis. We designed a 465-bp long CmYLCV9.11 promoter fragment (-329 to +137 from transcription start site) that showed enhanced promoter activity and was highly responsive to both biotic and abiotic stresses. The CmYLCV9.11 promoter was about 28-fold stronger than the CaMV35S promoter in transient and stable transgenic assays using β-glucuronidase (GUS) reporter gene. The CmYLCV9.11 promoter also demonstrated stronger activity than the previously reported CmYLCV promoter fragments, CmpC (-341 to +5) and CmpS (-349 to +59) in transient systems like maize protoplasts and onion epidermal cells as well as transgenic systems. A good correlation between CmYLCV9.11 promoter-driven GUS-accumulation/enzymatic activities with corresponding uidA-mRNA level in transgenic tobacco plants was shown. Histochemical (X-Gluc) staining of transgenic seedlings, root and floral parts expressing the GUS under the control of CmYLCV9.11, CaMV35S, CmpC and CmpS promoters also support the above findings. The CmYLCV9.11 promoter is a constitutive promoter and the expression level in tissues of transgenic tobacco plants was in the following order: root > leaf > stem. The tobacco transcription factor TGA1a was found to bind strongly to the CmYLCV9.11 promoter region, as shown by Gel-shift assay and South-Western blot analysis. In addition, the CmYLCV9.11 promoter was regulated by a number of abiotic and biotic stresses as studied in transgenic Arabidopsis and tobacco plants. The newly derived CmYLCV9.11 promoter is an efficient tool for biotechnological applications.
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Affiliation(s)
- Dipak Kumar Sahoo
- KTRDC, College of Agriculture, University of Kentucky, Lexington, KY, 40546, USA,
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Li J, Xu RF, Qin RY, Ma H, Li H, Zhang YP, Li L, Wei PC, Yang JB. Isolation and functional characterization of a novel rice constitutive promoter. PLANT CELL REPORTS 2014; 33:1651-60. [PMID: 24980160 DOI: 10.1007/s00299-014-1644-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/15/2014] [Accepted: 06/05/2014] [Indexed: 05/06/2023]
Abstract
A novel rice constitutive promoter (P OsCon1 ) was isolated. The molecular mechanism of the promoter activity was investigated. P OsCon1 could be used as an alternative constitutive promoter for crop transgenic engineering. Monocot constitutive promoter is an important resource for crop transgenic engineering. In this report, we isolated a novel promoter, Oscon1 promoter (P OsCon1 ), from the 5' upstream region of a constitutively expressed rice gene OsDHAR1. In P OsCon1 ::GUS transgenic rice, we showed that P OsCon1 had a broad expression spectrum in all tested tissues. The expression of the promoter was further analyzed in comparison with the previously characterized strong constitutive promoters. P OsCon1 exhibited comparable activity to OsCc1, OsAct1 or ZmUbi promoters in most tissues, and more active than 35S promoter in roots, seeds, and calli. Further quantitative assays indicated that P OsCon1 activity was not affected by developmental stages or by environmental factors. Further, 5'-deletions analysis indicated that the distinct regions might contribute to the strong expression of P OsCon1 in different tissues. Overall, our results suggest that P OsCon1 is a novel constitutive promoter, which could potentially use in transgenic crop development.
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Affiliation(s)
- Juan Li
- Institute of Technical Biology and Agriculture Engineering, Chinese Academy of Sciences, Hefei, 230031, China
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20
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Rabot A, Portemer V, Péron T, Mortreau E, Leduc N, Hamama L, Coutos-Thévenot P, Atanassova R, Sakr S, Le Gourrierec J. Interplay of sugar, light and gibberellins in expression of Rosa hybrida vacuolar invertase 1 regulation. PLANT & CELL PHYSIOLOGY 2014; 55:1734-48. [PMID: 25108242 DOI: 10.1093/pcp/pcu106] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Our previous findings showed that the expression of the Rosa hybrida vacuolar invertase 1 gene (RhVI1) was tightly correlated with the ability of buds to grow out and was under sugar, gibberellin and light control. Here, we aimed to provide an insight into the mechanistic basis of this regulation. In situ hybridization showed that RhVI1 expression was localized in epidermal cells of young leaves of bursting buds. We then isolated a 895 bp fragment of the promoter of RhVI1. In silico analysis identified putative cis-elements involved in the response to sugars, light and gibberellins on its proximal part (595 bp). To carry out functional analysis of the RhVI1 promoter in a homologous system, we developed a direct method for stable transformation of rose cells. 5' deletions of the proximal promoter fused to the uidA reporter gene were inserted into the rose cell genome to study the cell's response to exogenous and endogenous stimuli. Deletion analysis revealed that the 468 bp promoter fragment is sufficient to trigger reporter gene activity in response to light, sugars and gibberellins. This region confers sucrose- and fructose-, but not glucose-, responsive activation in the dark. Inversely, the -595 to -468 bp region that carries the sugar-repressive element (SRE) is required to down-regulate the RhVI1 promoter in response to sucrose and fructose in the dark. We also demonstrate that sugar/light and gibberellin/light act synergistically to up-regulate β-glucuronidase (GUS) activity sharply under the control of the 595 bp pRhVI1 region. These results reveal that the 127 bp promoter fragment located between -595 and -468 bp is critical for light and sugar and light and gibberellins to act synergistically.
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Affiliation(s)
- Amélie Rabot
- Agrocampus-Ouest, Institut de Recherche en Horticulture et Semences (INRA, Agrocampus-Ouest, Université d'Angers), SFR 149 QUASAV, F-49045 Angers, France These authors contributed equally to this work
| | - Virginie Portemer
- Université de Poitiers, UMR 7267 CNRS/Université de Poitiers Écologie et Biologie des Interactions, équipe Physiologie Moléculaire du Transport des Sucres chez les végétaux, 3 rue Jacques Fort, B31, 86 000 Poitiers, France These authors contributed equally to this work. Present address: INRA, Institut Jean Pierre Bourgin, UMR 1318, F-78026 Versailles, France
| | - Thomas Péron
- Agrocampus-Ouest, Institut de Recherche en Horticulture et Semences (INRA, Agrocampus-Ouest, Université d'Angers), SFR 149 QUASAV, F-49045 Angers, France
| | - Eric Mortreau
- Agrocampus-Ouest, Institut de Recherche en Horticulture et Semences (INRA, Agrocampus-Ouest, Université d'Angers), SFR 149 QUASAV, F-49045 Angers, France
| | - Nathalie Leduc
- Université d'Angers, Institut de Recherche en Horticulture et Semences (INRA, Agrocampus-Ouest, Université d'Angers), SFR 149 QUASAV, F-49045 Angers, France
| | - Latifa Hamama
- Agrocampus-Ouest, Institut de Recherche en Horticulture et Semences (INRA, Agrocampus-Ouest, Université d'Angers), SFR 149 QUASAV, F-49045 Angers, France Université d'Angers, Institut de Recherche en Horticulture et Semences (INRA, Agrocampus-Ouest, Université d'Angers), SFR 149 QUASAV, F-49045 Angers, France INRA, Institut de Recherche en Horticulture et Semences (INRA, Agrocampus-Ouest, Université d'Angers), SFR 149 QUASAV, F-49071 Beaucouzé, France
| | - Pierre Coutos-Thévenot
- Université de Poitiers, UMR 7267 CNRS/Université de Poitiers Écologie et Biologie des Interactions, équipe Physiologie Moléculaire du Transport des Sucres chez les végétaux, 3 rue Jacques Fort, B31, 86 000 Poitiers, France
| | - Rossitza Atanassova
- Université de Poitiers, UMR 7267 CNRS/Université de Poitiers Écologie et Biologie des Interactions, équipe Physiologie Moléculaire du Transport des Sucres chez les végétaux, 3 rue Jacques Fort, B31, 86 000 Poitiers, France
| | - Soulaiman Sakr
- Agrocampus-Ouest, Institut de Recherche en Horticulture et Semences (INRA, Agrocampus-Ouest, Université d'Angers), SFR 149 QUASAV, F-49045 Angers, France
| | - José Le Gourrierec
- Université d'Angers, Institut de Recherche en Horticulture et Semences (INRA, Agrocampus-Ouest, Université d'Angers), SFR 149 QUASAV, F-49045 Angers, France
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Vogel MO, Moore M, König K, Pecher P, Alsharafa K, Lee J, Dietz KJ. Fast retrograde signaling in response to high light involves metabolite export, MITOGEN-ACTIVATED PROTEIN KINASE6, and AP2/ERF transcription factors in Arabidopsis. THE PLANT CELL 2014; 26:1151-65. [PMID: 24668746 PMCID: PMC4001375 DOI: 10.1105/tpc.113.121061] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/31/2014] [Accepted: 02/28/2014] [Indexed: 05/18/2023]
Abstract
Regulation of the expression of nuclear genes encoding chloroplast proteins allows for metabolic adjustment in response to changing environmental conditions. This regulation is linked to retrograde signals that transmit information on the metabolic state of the chloroplast to the nucleus. Transcripts of several APETALA2/ETHYLENE RESPONSE FACTOR transcription factors (AP2/ERF-TFs) were found to respond within 10 min after transfer of low-light-acclimated Arabidopsis thaliana plants to high light. Initiation of this transcriptional response was completed within 1 min after transfer to high light. The fast responses of four AP2/ERF genes, ERF6, RRTF1, ERF104, and ERF105, were entirely deregulated in triose phosphate/phosphate translocator (tpt) mutants. Similarly, activation of MITOGEN-ACTIVATED PROTEIN KINASE6 (MPK6) was upregulated after 1 min in the wild type but not in the tpt mutant. Based on this, together with altered transcript regulation in mpk6 and erf6 mutants, a retrograde signal transmission model is proposed starting with metabolite export through the triose phosphate/phosphate translocator with subsequent MPK6 activation leading to initiation of AP2/ERF-TF gene expression and other downstream gene targets. The results show that operational retrograde signaling in response to high light involves a metabolite-linked pathway in addition to previously described redox and hormonal pathways.
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Affiliation(s)
- Marc Oliver Vogel
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany
| | - Marten Moore
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany
| | - Katharina König
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany
| | - Pascal Pecher
- Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Khalid Alsharafa
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany
| | - Justin Lee
- Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Bielefeld University, 33501 Bielefeld, Germany
- Address correspondence to
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Kumar H, Kumar S. A functional (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase exhibits diurnal regulation of expression in Stevia rebaudiana (Bertoni). Gene X 2013; 527:332-8. [PMID: 23800667 DOI: 10.1016/j.gene.2013.06.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 06/06/2013] [Accepted: 06/07/2013] [Indexed: 11/18/2022] Open
Abstract
The leaves of stevia [Stevia rebaudiana (Bertoni)] are a rich source of steviol glycosides that are used as non-calorific sweetener in many countries around the world. Steviol moiety of steviol glycosides is synthesized via plastidial 2C-methyl-D-erythritol 4-phosphate pathway, where (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR) is the key enzyme. HDR catalyzes the simultaneous conversion of (E)-4-hydroxy-3-methylbut-2-enyl diphosphate into five carbon isoprenoid units, isopentenyl diphosphate and dimethylallyl diphosphate. Stevia HDR (SrHDR) successfully rescued HDR lethal mutant strain MG1655 ara<>ispH upon genetic complementation, suggesting SrHDR to encode a functional protein. The gene exhibited diurnal variation in expression. To identify the possible regulatory elements, upstream region of the gene was cloned and putative cis-acting elements were detected by in silico analysis. Electrophoretic mobility shift assay, using a putative light responsive element GATA showed the binding of nuclear proteins (NP) isolated from leaves during light period of the day, but not with the NP from leaves during the dark period. Data suggested the involvement of GATA box in light mediated gene regulation of SrHDR in stevia.
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Affiliation(s)
- Hitesh Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, Himachal Pradesh, India.
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Comparative transcriptome profiling of chilling stress responsiveness in two contrasting rice genotypes. PLoS One 2012; 7:e43274. [PMID: 22912843 PMCID: PMC3422246 DOI: 10.1371/journal.pone.0043274] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 07/18/2012] [Indexed: 02/02/2023] Open
Abstract
Rice is sensitive to chilling stress, especially at the seedling stage. To elucidate the molecular genetic mechanisms of chilling tolerance in rice, comprehensive gene expressions of two rice genotypes (chilling-tolerant LTH and chilling-sensitive IR29) with contrasting responses to chilling stress were comparatively analyzed. Results revealed a differential constitutive gene expression prior to stress and distinct global transcription reprogramming between the two rice genotypes under time-series chilling stress and subsequent recovery conditions. A set of genes with higher basal expression were identified in chilling-tolerant LTH compared with chilling-sensitive IR29, indicating their possible role in intrinsic tolerance to chilling stress. Under chilling stress, the major effect on gene expression was up-regulation in the chilling- tolerant genotype and strong repression in chilling-sensitive genotype. Early responses to chilling stress in both genotypes featured commonly up-regulated genes related to transcription regulation and signal transduction, while functional categories for late phase chilling regulated genes were diverse with a wide range of functional adaptations to continuous stress. Following the cessation of chilling treatments, there was quick and efficient reversion of gene expression in the chilling-tolerant genotype, while the chilling-sensitive genotype displayed considerably slower recovering capacity at the transcriptional level. In addition, the detection of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, were involved in chilling stress tolerance. A number of the chilling-regulated genes identified in this study were co-localized onto previously fine-mapped cold-tolerance-related QTLs, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for chilling tolerance in rice.
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Luo XM, Lin WH, Zhu S, Zhu JY, Sun Y, Fan XY, Cheng M, Hao Y, Oh E, Tian M, Liu L, Zhang M, Xie Q, Chong K, Wang ZY. Integration of light- and brassinosteroid-signaling pathways by a GATA transcription factor in Arabidopsis. Dev Cell 2011; 19:872-83. [PMID: 21145502 DOI: 10.1016/j.devcel.2010.10.023] [Citation(s) in RCA: 175] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 08/26/2010] [Accepted: 10/12/2010] [Indexed: 12/21/2022]
Abstract
Light and brassinosteroid (BR) antagonistically regulate the developmental switch from etiolation in the dark to photomorphogenesis in the light in plants. Here, we identify GATA2 as a key transcriptional regulator that mediates the crosstalk between BR- and light-signaling pathways. Overexpression of GATA2 causes constitutive photomorphogenesis in the dark, whereas suppression of GATA2 reduces photomorphogenesis caused by light, BR deficiency, or the constitutive photomorphogenesis mutant cop1. Genome profiling and chromatin immunoprecipitation experiments show that GATA2 directly regulates genes that respond to both light and BR. BR represses GATA2 transcription through the BR-activated transcription factor BZR1, whereas light causes accumulation of GATA2 protein and feedback inhibition of GATA2 transcription. Dark-induced proteasomal degradation of GATA2 is dependent on the COP1 E3 ubiquitin ligase, and COP1 can ubiquitinate GATA2 in vitro. This study illustrates a molecular framework for antagonistic regulation of gene expression and seedling photomorphogenesis by BR and light.
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Affiliation(s)
- Xiao-Min Luo
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
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25
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Sanz C, Benito EP, Orejas M, Alvarez MI, Eslava AP. Protein-DNA interactions in the promoter region of the Phycomyces carB and carRA genes correlate with the kinetics of their mRNA accumulation in response to light. Fungal Genet Biol 2010; 47:773-81. [PMID: 20580936 DOI: 10.1016/j.fgb.2010.05.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2010] [Revised: 05/17/2010] [Accepted: 05/19/2010] [Indexed: 10/19/2022]
Abstract
Carotene biosynthesis in Phycomyces is photoinducible and carried out by phytoene dehydrogenase (encoded by carB) and a bifunctional enzyme possessing lycopene cyclase and phytoene synthase activities (carRA). A light pulse followed by periods of darkness produced similar biphasic responses in the expression of the carB and carRA genes, indicating their coordinated regulation. Specific binding complexes were formed between the carB-carRA intergenic region and protein extracts from wild type mycelia grown in the dark or 8min after irradiation. These two conditions correspond to the points at which the expression of both genes is minimal, suggesting that these binding complexes are involved in the down-regulation of photocarotenogenesis in Phycomyces. Protein extracts from carotene mutants failed to form the dark retardation complex, suggesting a role of these genes in the regulation of photocarotenogenesis. In contrast, protein extracts from phototropic mutants formed dark retardation complexes identical to that of the wild type.
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Affiliation(s)
- Catalina Sanz
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
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26
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Pathak RR, Das SK, Choudhury D, Raghuram N. Genomewide bioinformatic analysis negates any specific role for Dof, GATA and Ag/cTCA motifs in nitrate responsive gene expression in Arabidopsis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2009; 15:145-50. [PMID: 23572923 PMCID: PMC3550365 DOI: 10.1007/s12298-009-0016-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Nitrate response at the plant level is mediated by the transcriptional regulation of several hundreds of genes, but no common cis-acting nitrate-responsive elements (NREs) have been identified so far. Earlier, we bioinformatically ruled out the possibility that the previously published [(a/t)7Ag/cTCA] motif could act as NRE on its own (Das et al., 2007, Mol. Genet. Genomics, 278: 519-525). In the present study, we examined other motifs such as Dof and GATA binding elements in homologous as well as heterologous pairwise combinations in the Arabidopsis genome in silico. None of the above three motifs revealed any unique association with nitrate responsive genes or their subsets in any combination, either within their ORFs or 1 kb flanking sequences on either side. Additionally, twelve new, top-scoring candidate motifs that were generated using different online motif samplers were analyzed in silico using a subset of 21 'early' nitrate responsive genes, but did not reveal any specificity of occurence. These results underscore the need to continue the search for novel candidate NREs, as possible sites of intervention to understand/improve nitrate-responsive gene expression and nitrate use efficiency.
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Affiliation(s)
- Ravi Ramesh Pathak
- />School of Biotechnology, GGS Indraprastha University, Kashmiri Gate, Delhi, 110403 India
| | - Suman K. Das
- />School of Biotechnology, GGS Indraprastha University, Kashmiri Gate, Delhi, 110403 India
| | - Devapriya Choudhury
- />School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Nandula Raghuram
- />School of Biotechnology, GGS Indraprastha University, Kashmiri Gate, Delhi, 110403 India
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27
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Wang L, Yin H, Qian Q, Yang J, Huang C, Hu X, Luo D. NECK LEAF 1, a GATA type transcription factor, modulates organogenesis by regulating the expression of multiple regulatory genes during reproductive development in rice. Cell Res 2009; 19:598-611. [DOI: 10.1038/cr.2009.36] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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28
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Mara CD, Irish VF. Two GATA transcription factors are downstream effectors of floral homeotic gene action in Arabidopsis. PLANT PHYSIOLOGY 2008; 147:707-18. [PMID: 18417639 PMCID: PMC2409029 DOI: 10.1104/pp.107.115634] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Floral organogenesis is dependent on the combinatorial action of MADS-box transcription factors, which in turn control the expression of suites of genes required for growth, patterning, and differentiation. In Arabidopsis (Arabidopsis thaliana), the specification of petal and stamen identity depends on the action of two MADS-box gene products, APETALA3 (AP3) and PISTILLATA (PI). In a screen for genes whose expression was altered in response to the induction of AP3 activity, we identified GNC (GATA, nitrate-inducible, carbon-metabolism-involved) as being negatively regulated by AP3 and PI. The GNC gene encodes a member of the Arabidopsis GATA transcription factor family and has been implicated in the regulation of chlorophyll biosynthesis as well as carbon and nitrogen metabolism. In addition, we found that the GNC paralog, GNL (GNC-like), is also negatively regulated by AP3 and PI. Using chromatin immunoprecipitation, we showed that promoter sequences of both GNC and GNL are bound by PI protein, suggesting a direct regulatory interaction. Analyses of single and double gnc and gnl mutants indicated that the two genes share redundant roles in promoting chlorophyll biosynthesis, suggesting that in repressing GNC and GNL, AP3/PI have roles in negatively regulating this biosynthetic pathway in flowers. In addition, coexpression analyses of genes regulated by AP3, PI, GNC, and GNL indicate a complex regulatory interplay between these transcription factors in regulating a variety of light and nutrient responsive genes. Together, these results provide new insights into the transcriptional cascades controlling the specification of floral organ identities.
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Affiliation(s)
- Chloe D Mara
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104, USA
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29
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Manfield IW, Devlin PF, Jen CH, Westhead DR, Gilmartin PM. Conservation, convergence, and divergence of light-responsive, circadian-regulated, and tissue-specific expression patterns during evolution of the Arabidopsis GATA gene family. PLANT PHYSIOLOGY 2007; 143:941-58. [PMID: 17208962 PMCID: PMC1803723 DOI: 10.1104/pp.106.090761] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In vitro analyses of plant GATA transcription factors have implicated some proteins in light-mediated and circadian-regulated gene expression, and, more recently, the analysis of mutants has uncovered further diverse roles for plant GATA factors. To facilitate function discovery for the 29 GATA genes in Arabidopsis (Arabidopsis thaliana), we have experimentally verified gene structures and determined expression patterns of all family members across adult tissues and suspension cell cultures, as well as in response to light and signals from the circadian clock. These analyses have identified two genes that are strongly developmentally light regulated, expressed predominantly in photosynthetic tissue, and with transcript abundance peaking before dawn. In contrast, several GATA factor genes are light down-regulated. The products of these light-regulated genes are candidates for those proteins previously implicated in light-regulated transcription. Coexpression of these genes with well-characterized light-responsive transcripts across a large microarray data set supports these predictions. Other genes show additional tissue-specific expression patterns suggesting novel and unpredicted roles. Genome-wide analysis using coexpression scatter plots for paralogous gene pairs reveals unexpected differences in cocorrelated gene expression profiles. Clustering the Arabidopsis GATA factor gene family by similarity of expression patterns reveals that genes of recent descent do not uniformly show conserved current expression profiles, yet some genes showing more distant evolutionary origins have acquired common expression patterns. In addition to defining developmental and environmental dynamics of GATA transcript abundance, these analyses offer new insights into the evolution of gene expression profiles following gene duplication events.
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Affiliation(s)
- Iain W Manfield
- Centre for Plant Sciences, Institute for Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
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30
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Bi YM, Zhang Y, Signorelli T, Zhao R, Zhu T, Rothstein S. Genetic analysis of Arabidopsis GATA transcription factor gene family reveals a nitrate-inducible member important for chlorophyll synthesis and glucose sensitivity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 44:680-92. [PMID: 16262716 DOI: 10.1111/j.1365-313x.2005.02568.x] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The Arabidopsis GATA transcription factor family has 30 members, the biological function of most of which is poorly understood. Homozygous T-DNA insertion lines for 23 of the 30 members were identified and analyzed. Genetic screening of the insertion lines in defined growth conditions revealed one line with an altered phenotype, while the other lines showed no obvious change. This line, SALK_001778, has a T-DNA insertion in the second exon of At5g56860 which prevents the expression of the GATA domain. Genetic analysis of the mutant demonstrated that the phenotypic change is caused by a single gene effect and is recessive to the wild-type allele. In wild-type plants, the expression of At5g56860 is shoot-specific, occurs at an early stage of development and is inducible by nitrate. Loss of expression of At5g56860 in the loss-of-function mutant plants resulted in reduced chlorophyll levels. A transcript profiling experiment revealed that a considerable proportion of genes downregulated in the loss-of-function mutants are involved in carbon metabolism and At5g56860 is thus designated GNC (GATA, nitrate-inducible, carbon metabolism-involved). gnc mutants with no GNC expression are more sensitive to exogenous glucose, and two hexose transporter genes, with a possible connection to glucose signaling, are significantly downregulated, while GNC over-expressing transgenic plants upregulate their expression and are less sensitive to exogenous glucose. These observations suggest a function for GNC in regulating carbon and nitrogen metabolism.
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Affiliation(s)
- Yong-Mei Bi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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31
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Shikata M, Takemura M, Yokota A, Kohchi T. Arabidopsis ZIM, a plant-specific GATA factor, can function as a transcriptional activator. Biosci Biotechnol Biochem 2004; 67:2495-7. [PMID: 14646219 DOI: 10.1271/bbb.67.2495] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Arabidopsis ZIM is a putative transcription factor containing an atypical GATA-type zinc-finger motif. Transcriptional activation by ZIM was tested using a transient GAL4 fusion assay and measuring the expression of a luciferase reporter in tobacco BY-2 cells. ZIM functioned as a transcriptional activator, and the transactivation domain was found to occur in its N-terminal acidic region.
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Affiliation(s)
- Masahito Shikata
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
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32
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Reyes JC, Muro-Pastor MI, Florencio FJ. The GATA family of transcription factors in Arabidopsis and rice. PLANT PHYSIOLOGY 2004; 134:1718-32. [PMID: 15084732 PMCID: PMC419845 DOI: 10.1104/pp.103.037788] [Citation(s) in RCA: 242] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2003] [Revised: 01/29/2004] [Accepted: 01/31/2004] [Indexed: 05/18/2023]
Abstract
GATA transcription factors are a group of DNA binding proteins broadly distributed in eukaryotes. The GATA factors DNA binding domain is a class IV zinc finger motif in the form CX(2)CX(17-20)CX(2)C followed by a basic region. In plants, GATA DNA motifs have been implicated in light-dependent and nitrate-dependent control of transcription. Herein, we show that the Arabidopsis and the rice (Oryza sativa) genomes present 29 and 28 loci, respectively, that encode for putative GATA factors. A phylogenetic analysis of the 57 GATA factors encoding genes, as well as the study of their intron-exon structure, indicates the existence of seven subfamilies of GATA genes. Some of these subfamilies are represented in both species but others are exclusive for one of them. In addition to the GATA zinc finger motif, polypeptides of the different subfamilies are characterized by the presence of additional domains such as an acidic domain, a CCT (CONSTANS, CO-like, and TOC1) domain, or a transposase-like domain also found in FAR1 and FHY3. Subfamily VI comprises genes that encode putative bi-zinc finger polypeptides, also found in metazoan and fungi, and a tri-zinc finger protein which has not been previously reported in eukaryotes. The phylogeny of the GATA zinc finger motif, excluding flanking regions, evidenced the existence of four classes of GATA zinc fingers, three of them containing 18 residues in the zinc finger loop and one containing a 20-residue loop. Our results support multiple models of evolution of the GATA gene family in plants including gene duplication and exon shuffling.
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Affiliation(s)
- José C Reyes
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas, Universidad de Seville, Américo Vespucio s/n, E-41092 Seville, Spain.
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33
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Umemura Y, Ishiduka T, Yamamoto R, Esaka M. The Dof domain, a zinc finger DNA-binding domain conserved only in higher plants, truly functions as a Cys2/Cys2 Zn finger domain. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 37:741-9. [PMID: 14871313 DOI: 10.1111/j.1365-313x.2003.01997.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The Dof (DNA-binding with one finger) proteins are plant transcription factors that have a highly conserved DNA-binding domain, called the Dof domain. The Dof domain, which is composed of 52 amino acid residues, is similar to the Cys2/Cys2 zinc finger DNA-binding domain of GATA1 and steroid hormone receptors, but has a longer putative loop than that in the case of these zinc finger domains. The DNA-binding function of ascorbate oxidase gene binding protein (AOBP), a Dof protein, was investigated by gel retardation analysis. When Cys was replaced by His, the Dof domain could not function as a Cys3/His- or a Cys2/His2-type zinc finger. The characteristic longer loop was essential for DNA-binding activity. Furthermore, heavy metals such as Co(II), Ni(II), Cd(II), Cu(II), Hg(II), Fe(II), and Fe(III) inhibited the DNA-binding activity of the Dof domain. Manganese ion as well as zinc ion was coordinated by the Dof domain in vitro. On the other hand, the analysis using inductively coupled argon plasma mass spectrometry (ICP-MS) showed that the Dof domain contained zinc ion but not manganese ion. Thus, the Dof domain was proved to function as a Cys2/Cys2 zinc finger domain.
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Affiliation(s)
- Yoshimi Umemura
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama 1-4-4, Higashi-Hiroshima 739-8528, Japan
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