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Ali A, Mashwani ZUR, Raja NI, Mohammad S, Luna-Arias JP, Ahmad A, Kaushik P. Phytomediated selenium nanoparticles and light regimes elicited in vitro callus cultures for biomass accumulation and secondary metabolite production in Caralluma tuberculata. FRONTIERS IN PLANT SCIENCE 2023; 14:1253193. [PMID: 37810387 PMCID: PMC10556749 DOI: 10.3389/fpls.2023.1253193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/25/2023] [Indexed: 10/10/2023]
Abstract
Introduction Caralluma tuberculata holds significant importance as a medicinal plant due to its abundance of bioactive metabolites, which offer a wide range of therapeutic potentials. However, the sustainable production of this plant is challenged by overexploitation, changes in natural conditions, slow growth rate, and inadequate biosynthesis of bioactive compounds in wild populations. Therefore, the current study was conducted to establish an in vitro based elicitation strategy (nano elicitors and light regimes) for the enhancement of biomass and production of secondary metabolites. Methods Garlic clove extract was employed as a stabilizing, reducing, or capping agent in the green formulation of Selenium nanoparticles (SeNPs) and various physicochemical characterization analyses such as UV visible spectroscopy, scanning electron microscopy (SEM), energy dispersive X-Ray (EDX) Spectroscopy, fourier transform infrared (FTIR) spectroscopy and X-ray diffraction (XRD) were performed. Furthermore, the effects of phytosynthesized SeNPs at various concentrations (0, 50, 100, 200, and 400 µg/L on callus proliferation and biosynthesis of medicinal metabolites under different light regimes were investigated. Results and discussion Cultures grown on Murashige and Skoog (MS) media containing SeNPs (100 µg/L), in a dark environment for two weeks, and then transferred into normal light, accumulated maximum fresh weight (4,750 mg/L FW), phenolic contents (TPC: 3.91 mg/g DW), flavonoid content (TFC: 2.04 mg/g DW) and 2,2-Diphenyl-1-picrylhydrazyl (DPPH) antioxidant activity (85%). Maximum superoxide dismutase (SOD: 4.36 U/mg) and peroxide dismutase activity (POD: 3.85 U/mg) were determined in those cultures exposed to SeNPs (100 µg/L) under complete dark conditions. While the callus cultures proliferate on media augmented with SeNPs (200 µg/L) and kept under dark conditions for two weeks and then shifted to normal light conditions exhibited the highest catalase (CAT: 3.25 U/mg) and ascorbate peroxidase (APx: 1.93 U/mg) activities. Furthermore, LC-ESI-MS/MS analysis confirmed the effects of SeNPs and light conditions that elicited the antidiabetic metabolites (cumarins, gallic acid, caffeic acid, ferulic acid, catechin, querctin and rutin). This protocol can be scaled up for the industrial production of plant biomass and pharmacologically potent metabolites using in vitro callus cultures of C. tuberculata.
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Affiliation(s)
- Amir Ali
- Department of Botany, Pir Mehr Ali Shah Arid (PMAS) Agriculture University Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - Zia-ur-Rehman Mashwani
- Department of Botany, Pir Mehr Ali Shah Arid (PMAS) Agriculture University Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - Naveed Iqbal Raja
- Department of Botany, Pir Mehr Ali Shah Arid (PMAS) Agriculture University Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - Sher Mohammad
- Biotechnology Laboratory, Agricultural Research Institute (ARI) Tarnab, Peshawar, Pakistan
| | - Juan Pedro Luna-Arias
- Department of Cell Biology, and Nanoscience and Nanotechnology Ph.D. Program, Center for Research and Advanced Studies of the National Polytechnic Institute, Mexico, Mexico
| | - Ajaz Ahmad
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Prashant Kaushik
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
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Luo J, Tang Y, Chu Z, Peng Y, Chen J, Yu H, Shi C, Jafar J, Chen R, Tang Y, Lu Y, Ye Z, Li Y, Ouyang B. SlZF3 regulates tomato plant height by directly repressing SlGA20ox4 in the gibberellic acid biosynthesis pathway. HORTICULTURE RESEARCH 2023; 10:uhad025. [PMID: 37090098 PMCID: PMC10116951 DOI: 10.1093/hr/uhad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/15/2023] [Indexed: 05/03/2023]
Abstract
Plant height is an important target trait for crop genetic improvement. Our previous work has identified a salt-tolerant C2H2 zinc finger, SlZF3, and its overexpression lines also showed a semi-dwarf phenotype, but the molecular mechanism remains to be elucidated. Here, we characterized the dwarf phenotype in detail. The dwarfism is caused by a decrease in stem internode cell elongation and deficiency of bioactive gibberellic acids (GAs), and can be rescued by exogenous GA3 treatment. Gene expression assays detected reduced expression of genes in the GA biosynthesis pathway of the overexpression lines, including SlGA20ox4. Several protein-DNA interaction methods confirmed that SlZF3 can directly bind to the SlGA20ox4 promoter and inhibit its expression, and the interaction can also occur for SlKS and SlKO. Overexpression of SlGA20ox4 in the SlZF3-overexpressing line can recover the dwarf phenotype. Therefore, SlZF3 regulates plant height by directly repressing genes in the tomato GA biosynthesis pathway.
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Affiliation(s)
- Jinying Luo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yunfei Tang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhuannan Chu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuxin Peng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiawei Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Huiyang Yu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunmei Shi
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jahanzeb Jafar
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Rong Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yaping Tang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongen Lu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhibiao Ye
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Li
- Corresponding authors. E-mail: ;
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Roles of Calcium Signaling in Gene Expression and Photosynthetic Acclimatization of Solanum lycopersicum Micro-Tom (MT) after Mechanical Damage. Int J Mol Sci 2022; 23:ijms232113571. [PMID: 36362362 PMCID: PMC9655782 DOI: 10.3390/ijms232113571] [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: 08/19/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/10/2022] Open
Abstract
A momentary increase in cytoplasmic Ca2+ generates an oscillation responsible for the activation of proteins, such as calmodulin and kinases, which interact with reactive oxygen species (ROS) for the transmission of a stress signal. This study investigated the influence of variations in calcium concentrations on plant defense signaling and photosynthetic acclimatization after mechanical damage. Solanum lycopersicum Micro-Tom was grown with 0, 2 and 4 mM Ca2+, with and without mechanical damage. The expression of stress genes was evaluated, along with levels of antioxidant enzymes, hydrogen peroxide, lipid peroxidation, histochemistry, photosynthesis and dry mass of organs. The ROS production generated by mechanical damage was further enhanced by calcium-free conditions due to the inactivation of the oxygen evolution complex, contributing to an increase in reactive species. The results indicated that ROS affected mechanical damage signaling because calcium-free plants exhibited high levels of H2O2 and enhanced expression of kinase and RBOH1 genes, necessary conditions for an efficient response to stress. We conclude that the plants without calcium supply recognized mechanical damage but did not survive. The highest expression of the RBOH1 gene and the accumulation of H2O2 in these plants signaled cell death. Plants grown in the presence of calcium showed higher expression of SlCaM2 and control of H2O2 concentration, thus overcoming the stress caused by mechanical damage, with photosynthetic acclimatization and without damage to dry mass production.
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Kapoor R, Kumar G, Pawar L, Salvi P, Devanna BN, Singh K, Sharma TR. Stress responsive OsHyPRP16 promoter driven early expression of resistance gene Pi54 potentiate the resistance against Magnaporthe oryzae in transgenic rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111413. [PMID: 35963493 DOI: 10.1016/j.plantsci.2022.111413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
The rice Hybrid Proline Rich Protein (HyPRP) encoding gene, OsHyPRP16 expression exhibit early upregulation in response to Magnaporthe oryzae inoculation. Here, we functionally characterized the OsHyPRP16 promoter through deletion analysis in transgenic Arabidopsis using GUS (β-glucuronidase) reporter assay. The promoter fragments, sequentially deleted from the 5' end could induce differential GUS activity in response to stresses induced by different hormones and abiotic stress conditions. In addition, a strong GUS induction was observed in M. oryzae inoculated transgenic Arabidopsis. Based on the insilico and stress-inducibility of D1 promoter fragment against various phytohormones and rice blast fungus, and with no basal activity under control conditions, we rationally selected D1 promoter fragment to drive the expression of a major rice blast resistance gene; Pi54 in the genetic background of blast susceptible TP309 rice line. The D1 promoter fragment was able to induce the expression of Pi54 at immediate-early stages of M. oryzae infection in transgenic rice. The transgenic plants with Pi54 under the control of D1 promoter fragment displayed complete resistance against M. oryzae infection as compared to control plants. The present study suggests that the D1 fragment of OsHyPRP16 promoter is a valuable tool for breeding and development of rice lines with early-inducible and pathogen-responsive enhanced disease resistance.
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Affiliation(s)
- Ritu Kapoor
- National Agri-Food Biotechnology Institute, Mohali 140306, Punjab, India; Department of Biotechnology, Panjab University, Chandigarh, India
| | - Gulshan Kumar
- National Agri-Food Biotechnology Institute, Mohali 140306, Punjab, India
| | - Lata Pawar
- National Agri-Food Biotechnology Institute, Mohali 140306, Punjab, India
| | - Prafull Salvi
- National Agri-Food Biotechnology Institute, Mohali 140306, Punjab, India
| | - Basavantraya N Devanna
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute, Mohali 140306, Punjab, India; Indian council of Agricultural Research, New Delhi, India.
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Mapuranga J, Zhang N, Zhang L, Liu W, Chang J, Yang W. Harnessing genetic resistance to rusts in wheat and integrated rust management methods to develop more durable resistant cultivars. FRONTIERS IN PLANT SCIENCE 2022; 13:951095. [PMID: 36311120 PMCID: PMC9614308 DOI: 10.3389/fpls.2022.951095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Wheat is one of the most important staple foods on earth. Leaf rust, stem rust and stripe rust, caused by Puccini triticina, Puccinia f. sp. graminis and Puccinia f. sp. striiformis, respectively, continue to threaten wheat production worldwide. Utilization of resistant cultivars is the most effective and chemical-free strategy to control rust diseases. Convectional and molecular biology techniques identified more than 200 resistance genes and their associated markers from common wheat and wheat wild relatives, which can be used by breeders in resistance breeding programmes. However, there is continuous emergence of new races of rust pathogens with novel degrees of virulence, thus rendering wheat resistance genes ineffective. An integration of genomic selection, genome editing, molecular breeding and marker-assisted selection, and phenotypic evaluations is required in developing high quality wheat varieties with resistance to multiple pathogens. Although host genotype resistance and application of fungicides are the most generally utilized approaches for controlling wheat rusts, effective agronomic methods are required to reduce disease management costs and increase wheat production sustainability. This review gives a critical overview of the current knowledge of rust resistance, particularly race-specific and non-race specific resistance, the role of pathogenesis-related proteins, non-coding RNAs, and transcription factors in rust resistance, and the molecular basis of interactions between wheat and rust pathogens. It will also discuss the new advances on how integrated rust management methods can assist in developing more durable resistant cultivars in these pathosystems.
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Affiliation(s)
| | | | | | | | | | - Wenxiang Yang
- College of Plant Protection, Technological Innovation Center for Biological Control of Plant Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
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Liao L, Zhang W, Zhang B, Cai Y, Gao L, Ogutu C, Sun J, Zheng B, Wang L, Li L, Han Y. Evaluation of chlorogenic acid accumulation in cultivated and wild apples. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.104156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Takeda J. Molecular Mechanisms of UVR8-Mediated Photomorphogenesis Derived from Revaluation of Action Spectra. Photochem Photobiol 2021; 97:903-910. [PMID: 34097751 DOI: 10.1111/php.13459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 06/03/2021] [Indexed: 11/27/2022]
Abstract
Considering previously reported action spectra and molecular evidence, I propose a hypothetical model for UV RESISTANCE LOCUS8 (UVR8)-mediated photomorphogenesis. Upon UV-B irradiation, a UVR8 dimer dissociates and accumulates in the nucleus and photomorphogenesis begins following two pathways: one in which the UVR8 monomer binds to transcription factor(s) of gene(s) supporting hypocotyl growth to stop gene expression resulting in hypocotyl growth inhibition and the other in which the UVR8 monomer binds both with CONSTITUTIVELY PHOTOMORPHOGENIC1-SUPPRESSOR OF PHYA (COP1-SPA) to release HY5 (referred to as "stabilized") and WRKY DNA-BINDING PROTEIN 36 (WRKY36) on the ELONGATED HYPOCOTYL 5 (HY5) gene to release HY5 transcription, and both HY5 and another UV-B-activated UV-B sensor (denoted the Hyp sensor in this article) through a self-interacting factor (HIF) associates with the HY5 promoter to initiate HY5 transcription, leading to anthocyanin synthesis. These two pathways can be distinguished by action spectra in the UV-B region, with a single peak at 280 nm and two peaks (or a broad peak near 280-300 nm) for the former and the latter, respectively. Expanding the concept to cyanobacteria and other algae, I discuss the evolution of a UV-B sensor in green plants.
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Affiliation(s)
- Junko Takeda
- Laboratory of Applied Microbiology and Biotechnology, Nara Women's University, Nara, Japan
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Transcriptome Analysis Reveals Candidate Genes Related to Anthocyanin Biosynthesis in Different Carrot Genotypes and Tissues. PLANTS 2020; 9:plants9030344. [PMID: 32182858 PMCID: PMC7154819 DOI: 10.3390/plants9030344] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 12/13/2022]
Abstract
Black carrots are characterized by a significant amount of anthocyanins, which are not only a good source of natural food colorant, but can also provide many health benefits to humans. In the present work, taproots of different carrot genotypes were used to identify the candidate genes related to anthocyanin synthesis, with particular a focus on R2R3MYB, bHLH transcription factors, and glutathione S-transferase gene (GST). The RNA-sequencing analysis (RNA-Seq) showed that DcMYB6 and DcMYB7 had a genotypic dependent expression and they are likely involved in the regulation of anthocyanin biosynthesis. They were specifically upregulated in solid black taproots, including both black phloem and xylem. DcbHLH3 (LOC108204485) was upregulated in all black samples compared with the orange ones. We also found that GST1 (LOC108205254) might be an important anthocyanin transporter, and its upregulated expression resulted in the increasing of vacuolar anthocyanin accumulation in black samples. Moreover, high performance liquid chromatographic (HPLC) analysis and liquid chromatography coupled to mass spectrometry (LC-MS) were used to identify the individual anthocyanin in the purple tissues of two carrot cultivars. The results showed that five main anthocyanin compounds and the most abundant anthocyanin were the same in different tissues, while the second-highest anthocyanin between three tissues was different, even in the same cultivar. In conclusion, this study combined anthocyanin profiles and comparative transcriptomic analysis to identify candidate genes involved in anthocyanin biosynthesis in carrots, thus providing a better foundation for improving anthocyanin accumulation in carrots as a source of colorants.
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Identification and Functional Characterization of a Soybean ( Glycine max) Thioesterase that Acts on Intermediates of Fatty Acid Biosynthesis. PLANTS 2019; 8:plants8100397. [PMID: 31597241 PMCID: PMC6843456 DOI: 10.3390/plants8100397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/21/2019] [Accepted: 10/02/2019] [Indexed: 11/16/2022]
Abstract
(1) Background: Plants possess many acyl-acyl carrier protein (acyl-ACP) thioesterases (TEs) with unique specificity. One such TE is methylketone synthase 2 (MKS2), an enzyme with a single-hotdog-fold structure found in several tomato species that hydrolyzes 3-ketoacyl-ACPs to give free 3-ketoacids. (2) Methods: In this study, we identified and characterized a tomato MKS2 homolog gene, namely, GmMKS2, in the genome of soybean (Glycine max). (3) Results: GmMKS2 underwent alternative splicing to produce three alternative transcripts, but only one encodes a protein with thioesterase activity when recombinantly expressed in Escherichia coli. Heterologous expression of the main transcript of GmMKS2, GmMKS2-X2, in E. coli generated various types of fatty acids, including 3-ketoacids-with 3-ketotetradecenoic acid (14:1) being the most abundant-cis-Δ5-dodecanoic acid, and 3-hydroxyacids, suggesting that GmMKS2 acts as an acyl-ACP thioesterase. In plants, the GmMKS2-X2 transcript level was found to be higher in the roots compared to other examined organs. In silico analysis revealed that there is a substantial enrichment of putative cis-regulatory elements related to disease-resistance responses and abiotic stress responses in the promoter of this gene. (4) Conclusions: GmMKS2 showed broad substrate specificities toward a wide range of acyl-ACPs that varied in terms of chain length, oxidation state, and saturation degree. Our results suggest that GmMKS2 might have a stress-related physiological function in G. max.
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A MYB-Related Transcription Factor from Lilium lancifolium L. (LlMYB3) Is Involved in Anthocyanin Biosynthesis Pathway and Enhances Multiple Abiotic Stress Tolerance in Arabidopsis thaliana. Int J Mol Sci 2019; 20:ijms20133195. [PMID: 31261872 PMCID: PMC6651583 DOI: 10.3390/ijms20133195] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/27/2019] [Accepted: 06/27/2019] [Indexed: 12/24/2022] Open
Abstract
Most commercial cultivars of lily are sensitive to abiotic stresses. However, tiger lily (Lilium lancifolium L.), one of the most widely distributed wild lilies in Asia, has strong abiotic stresses resistance. Thus, it is indispensable to identify stress-responsive candidate genes in tiger lily for the stress resistance improvement of plants. In this study, a MYB related homolog (LlMYB3) from tiger lily was functionally characterized as a positive regulator in plant stress tolerance. LlMYB3 is a nuclear protein with transcriptional activation activity at C-terminus. The expression of LlMYB3 gene was induced by multiple stress treatments. Several stress-related cis-acting regulatory elements (MYBRS, MYCRS, LTRE and DRE/CRT) were located within the promoter of LlMYB3; however, the promoter activity was not induced sufficiently by various stresses treatments. Overexpressing LlMYB3 in Arabidopsis thaliana L. transgenic plants showed ABA hypersensitivity and enhanced tolerance to cold, drought, and salt stresses. Furthermore, we found LlMYB3 highly co-expressed with LlCHS2 gene under cold treatment; yeast one-hybrid (Y1H) assays demonstrated LlMYB3 was able to bind to the promoter of LlCHS2. These findings suggest that the stress-responsive LlMYB3 may be involved in anthocyanin biosynthesis pathway to regulate stress tolerance of tiger lily.
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Iorizzo M, Cavagnaro PF, Bostan H, Zhao Y, Zhang J, Simon PW. A Cluster of MYB Transcription Factors Regulates Anthocyanin Biosynthesis in Carrot ( Daucus carota L.) Root and Petiole. FRONTIERS IN PLANT SCIENCE 2019; 9:1927. [PMID: 30693006 PMCID: PMC6339893 DOI: 10.3389/fpls.2018.01927] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/11/2018] [Indexed: 05/24/2023]
Abstract
Purple carrots can accumulate large quantities of anthocyanins in their roots and -in some genetic backgrounds- petioles, and therefore they represent an excellent dietary source of antioxidant phytonutrients. In a previous study, using linkage analysis in a carrot F2 mapping population segregating for root and petiole anthocyanin pigmentation, we identified a region in chromosome 3 with co-localized QTL for all anthocyanin pigments of the carrot root, whereas petiole pigmentation segregated as a single dominant gene and mapped to one of these "root pigmentation" regions conditioning anthocyanin biosynthesis. In the present study, we performed fine mapping combined with gene expression analyses (RNA-Seq and RT-qPCR) to identify candidate genes controlling anthocyanin pigmentation in the carrot root and petiole. Fine mapping was performed in four carrot populations with different genetic backgrounds and patterns of pigmentation. The regions controlling root and petiole pigmentation in chromosome 3 were delimited to 541 and 535 kb, respectively. Genome wide prediction of transcription factor families known to regulate the anthocyanin biosynthetic pathway coupled with orthologous and phylogenetic analyses enabled the identification of a cluster of six MYB transcription factors, denominated DcMYB6 to DcMYB11, associated with the regulation of anthocyanin biosynthesis. No anthocyanin biosynthetic genes were present in this region. Comparative transcriptome analysis indicated that upregulation of DcMYB7 was always associated with anthocyanin pigmentation in both root and petiole tissues, whereas DcMYB11 was only upregulated with pigmentation in petioles. In the petiole, the level of expression of DcMYB11 was higher than DcMYB7. DcMYB6, a gene previously suggested as a key regulator of carrot anthocyanin biosynthesis, was not consistently associated with pigmentation in either tissue. These results strongly suggest that DcMYB7 is a candidate gene for root anthocyanin pigmentation in all the genetic backgrounds included in this study. DcMYB11 is a candidate gene for petiole pigmentation in all the purple carrot sources in this study. Since DcMYB7 is co-expressed with DcMYB11 in purple petioles, the latter gene may act also as a co-regulator of anthocyanin pigmentation in the petioles. This study provides linkage-mapping and functional evidence for the candidacy of these genes for the regulation of carrot anthocyanin biosynthesis.
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Affiliation(s)
- Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Pablo F. Cavagnaro
- National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
- Estación Experimental Agropecuaria La Consulta, Instituto Nacional de Tecnología Agropecuaria (INTA), Mendoza, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Hamed Bostan
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Yunyang Zhao
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Jianhui Zhang
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Philipp W. Simon
- Department of Horticulture, University of Wisconsin–Madison, Madison, WI, United States
- Vegetable Crops Research Unit, United States Department of Agriculture–Agricultural Research Service, Madison, WI, United States
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Shakya P, Marslin G, Siram K, Beerhues L, Franklin G. Elicitation as a tool to improve the profiles of high-value secondary metabolites and pharmacological properties of Hypericum perforatum. ACTA ACUST UNITED AC 2017; 71:70-82. [PMID: 28523644 PMCID: PMC6585710 DOI: 10.1111/jphp.12743] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 04/10/2017] [Indexed: 12/13/2022]
Abstract
OBJECTIVES In this review, we aim at updating the available information on the improvement of the Hypericum perforatum L. (Hypericaceae) phytochemical profile and pharmacological properties via elicitation. KEY FINDINGS Hypericum perforatum seedlings, shoots, roots, calli and cell suspension cultures were treated with diverse elicitors to induce the formation of secondary metabolites. The extracts of the elicitor-treated plant material containing naphthodianthrones, phloroglucinols, xanthones, flavonoids and other new compounds were quantitatively analysed and tested for their bioactivities. While hypericins were mainly produced in H. perforatum cultures containing dark nodules, namely shoots and seedlings, other classes of compounds such as xanthones, phloroglucinols and flavonoids were formed in all types of cultures. The extracts obtained from elicitor-treated samples generally possessed better bioactivities compared to the extract of control biomass. SUMMARY Although elicitation is an excellent tool for the production of valuable secondary metabolites in H. perforatum cell and tissue cultures, its exploitation is still in its infancy mainly due to the lack of reproducibility and difficulties in scaling up biomass production.
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Affiliation(s)
- Preeti Shakya
- Department of Integrative Plant Biology, Institute of Plant Genetics of the Polish Academy of Sciences, Poznań, Wielkopolska, Poland
| | - Gregory Marslin
- Chinese-German Joint Laboratory for Natural Product Research, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C., College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - Karthik Siram
- Department of Pharmaceutics, PSG College of Pharmacy, Coimbatore, Tamil Nadu, India
| | - Ludger Beerhues
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Gregory Franklin
- Department of Integrative Plant Biology, Institute of Plant Genetics of the Polish Academy of Sciences, Poznań, Wielkopolska, Poland
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Chu S, Wang J, Zhu Y, Liu S, Zhou X, Zhang H, Wang CE, Yang W, Tian Z, Cheng H, Yu D. An R2R3-type MYB transcription factor, GmMYB29, regulates isoflavone biosynthesis in soybean. PLoS Genet 2017; 13:e1006770. [PMID: 28489859 PMCID: PMC5443545 DOI: 10.1371/journal.pgen.1006770] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 05/24/2017] [Accepted: 04/21/2017] [Indexed: 11/19/2022] Open
Abstract
Isoflavones comprise a group of secondary metabolites produced almost exclusively by plants in the legume family, including soybean [Glycine max (L.) Merr.]. They play vital roles in plant defense and have many beneficial effects on human health. Isoflavone content is a complex quantitative trait controlled by multiple genes, and the genetic mechanisms underlying isoflavone biosynthesis remain largely unknown. Via a genome-wide association study (GWAS), we identified 28 single nucleotide polymorphisms (SNPs) that are significantly associated with isoflavone concentrations in soybean. One of these 28 SNPs was located in the 5'-untranslated region (5'-UTR) of an R2R3-type MYB transcription factor, GmMYB29, and this gene was thus selected as a candidate gene for further analyses. A subcellular localization study confirmed that GmMYB29 was located in the nucleus. Transient reporter gene assays demonstrated that GmMYB29 activated the IFS2 (isoflavone synthase 2) and CHS8 (chalcone synthase 8) gene promoters. Overexpression and RNAi-mediated silencing of GmMYB29 in soybean hairy roots resulted in increased and decreased isoflavone content, respectively. Moreover, a candidate-gene association analysis revealed that 11 natural GmMYB29 polymorphisms were significantly associated with isoflavone contents, and regulation of GmMYB29 expression could partially contribute to the observed phenotypic variation. Taken together, these results provide important genetic insights into the molecular mechanisms underlying isoflavone biosynthesis in soybean.
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Affiliation(s)
- Shanshan Chu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Department of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jiao Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ying Zhu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoqiong Zhou
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Huairen Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Chun-e Wang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, Jiangxi, China
| | - Wenming Yang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hao Cheng
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Barba-Espín G, Glied S, Crocoll C, Dzhanfezova T, Joernsgaard B, Okkels F, Lütken H, Müller R. Foliar-applied ethephon enhances the content of anthocyanin of black carrot roots (Daucus carota ssp. sativus var. atrorubens Alef.). BMC PLANT BIOLOGY 2017; 17:70. [PMID: 28376712 PMCID: PMC5381149 DOI: 10.1186/s12870-017-1021-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/29/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Black carrots (Daucus carota ssp. sativus var. atrorubens Alef.) constitute a valuable source of anthocyanins, which are used as natural red, blue and purple food colourants. Anthocyanins and phenolic compounds are specialised metabolites, accumulation of which often requires elicitors, which act as molecular signals in plant stress responses. In the present study, ethephon, an ethylene-generating compound was explored as enhancer of anthocyanin and phenolic contents during growth of 'Deep Purple' black carrots. The effects of ethephon on several parameters were investigated, and the expression of biosynthetic anthocyanin genes was studied during growth and anthocyanin accumulation. RESULTS Roots of ethephon-treated carrot plants exhibited an increase in anthocyanin content of approximately 25%, with values ranging from 2.25 to 3.10 mg g-1 fresh weight, compared with values ranging from 1.50 to 1.90 mg g-1 fresh weight in untreated roots. The most rapid accumulation rate for anthocyanins, phenolic compounds, soluble solids and dry matter was observed between 10 and 13 weeks after sowing in both untreated and ethephon-treated carrots. The differences in anthocyanin contents between untreated and treated carrots increased for several weeks after the ethephon treatment was terminated. Five cyanidin-based anthocyanin forms were identified, with variable relative abundance values detected during root growth. Overall, the expression of the anthocyanin biosynthetic genes analysed (PAL1, PAL3, F3H1, DFR1, LDOX2) increased in response to ethephon treatment, as did the expression of the MYB1 transcription factor, which is associated with activation of the phenylpropanoid pathway under stress conditions. In addition, a correlation was proposed between ethylene and sugar contents and the induction of anthocyanin synthesis. CONCLUSIONS This study presents a novel method for enhancing anthocyanin content in black carrots. This finding is of economic importance as increased pigment concentration per unit of biomass implies improved profitability parameters in food colour production. We provide new insight into the accumulation patterns of the different cyanidin-based anthocyanins and phenolic compounds during root growth. Moreover, we show that enhanced anthocyanin content in ethephon-treated carrots is accompanied by increased expression of anthocyanin biosynthetic genes.
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Affiliation(s)
- Gregorio Barba-Espín
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Hoejbakkegaard Alle 9-13, 2630 Taastrup, Denmark
| | - Stephan Glied
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Hoejbakkegaard Alle 9-13, 2630 Taastrup, Denmark
| | - Christoph Crocoll
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Tsaneta Dzhanfezova
- Natural Colors Division, Chr. Hansen A/S, Agern Allé 24, 2970 Hørsholm, Denmark
| | - Bjarne Joernsgaard
- Natural Colors Division, Chr. Hansen A/S, Agern Allé 24, 2970 Hørsholm, Denmark
| | - Finn Okkels
- Natural Colors Division, Chr. Hansen A/S, Agern Allé 24, 2970 Hørsholm, Denmark
| | - Henrik Lütken
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Hoejbakkegaard Alle 9-13, 2630 Taastrup, Denmark
| | - Renate Müller
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Hoejbakkegaard Alle 9-13, 2630 Taastrup, Denmark
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15
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Chezem WR, Clay NK. Regulation of plant secondary metabolism and associated specialized cell development by MYBs and bHLHs. PHYTOCHEMISTRY 2016; 131:26-43. [PMID: 27569707 PMCID: PMC5048601 DOI: 10.1016/j.phytochem.2016.08.006] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 08/10/2016] [Accepted: 08/15/2016] [Indexed: 05/20/2023]
Abstract
Plants are unrivaled in the natural world in both the number and complexity of secondary metabolites they produce, and the ubiquitous phenylpropanoids and the lineage-specific glucosinolates represent two such large and chemically diverse groups. Advances in genome-enabled biochemistry and metabolomic technologies have greatly increased the understanding of their metabolic networks in diverse plant species. There also has been some progress in elucidating the gene regulatory networks that are key to their synthesis, accumulation and function. This review highlights what is currently known about the gene regulatory networks and the stable sub-networks of transcription factors at their cores that regulate the production of these plant secondary metabolites and the differentiation of specialized cell types that are equally important to their defensive function. Remarkably, some of these core components are evolutionarily conserved between secondary metabolism and specialized cell development and across distantly related plant species. These findings suggest that the more ancient gene regulatory networks for the differentiation of fundamental cell types may have been recruited and remodeled for the generation of the vast majority of plant secondary metabolites and their specialized tissues.
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Affiliation(s)
- William R Chezem
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, USA.
| | - Nicole K Clay
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, USA.
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16
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Systematic Analysis of the 4-Coumarate:Coenzyme A Ligase (4CL) Related Genes and Expression Profiling during Fruit Development in the Chinese Pear. Genes (Basel) 2016; 7:genes7100089. [PMID: 27775579 PMCID: PMC5083928 DOI: 10.3390/genes7100089] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 09/24/2016] [Accepted: 10/07/2016] [Indexed: 12/31/2022] Open
Abstract
In plants, 4-coumarate:coenzyme A ligases (4CLs), comprising some of the adenylate-forming enzymes, are key enzymes involved in regulating lignin metabolism and the biosynthesis of flavonoids and other secondary metabolites. Although several 4CL-related proteins were shown to play roles in secondary metabolism, no comprehensive study on 4CL-related genes in the pear and other Rosaceae species has been reported. In this study, we identified 4CL-related genes in the apple, peach, yangmei, and pear genomes using DNATOOLS software and inferred their evolutionary relationships using phylogenetic analysis, collinearity analysis, conserved motif analysis, and structure analysis. A total of 149 4CL-related genes in four Rosaceous species (pear, apple, peach, and yangmei) were identified, with 30 members in the pear. We explored the functions of several 4CL and acyl-coenzyme A synthetase (ACS) genes during the development of pear fruit by quantitative real-time PCR (qRT-PCR). We found that duplication events had occurred in the 30 4CL-related genes in the pear. These duplicated 4CL-related genes are distributed unevenly across all pear chromosomes except chromosomes 4, 8, 11, and 12. The results of this study provide a basis for further investigation of both the functions and evolutionary history of 4CL-related genes.
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Bartley GE, Avena-Bustillos RJ, Du WX, Hidalgo M, Cain B, Breksa AP. Transcriptional regulation of chlorogenic acid biosynthesis in carrot root slices exposed to UV-B light. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.plgene.2016.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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18
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Computational analysis of atpB gene promoter from different Pakistani apple varieties. Comput Biol Chem 2016; 64:1-8. [PMID: 27213556 DOI: 10.1016/j.compbiolchem.2016.05.002] [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: 04/17/2015] [Revised: 04/27/2016] [Accepted: 05/05/2016] [Indexed: 11/20/2022]
Abstract
Apple is the fourth most important fruit crop grown in temperate areas of the world belongs to the family Rosaceae. In the present study, the promoter (∼1000bp) region of atpB gene was used to evaluate the genetic diversity and phylogeny of six local apple varieties. atpB gene is one of the large chloroplastic region which encodes β-subunit of ATP synthase and previously it had been used largely in phylogenetic studies. During the present study, atpB promoter was amplified, sequenced and analyzed using various bioinformatics tools including Place Signal Scan, MEGA6 and BLASTn. During the phylogenetic analysis, obtained phylogram divided the studied varieties into two clusters revealing the monophyletic origin of studied apple varieties. Pairwise distance revealed moderate genetic diversity that ranges from 0.047-0.170 with an average of 0.101. While identifying different cis-acting elements present in the atpB promoter region, results exhibited the occurrence of 56 common and 20 unique cis-regulatory elements among studied varieties. The identified cis-acting regulatory elements were mapped as well. It was observed that Kala Kulu has the highest unique features with reference to the availability of cis-acting elements. Moreover, the possible functions of all regulatory elements present on the promoter sequence of atpB gene were predicted based on already reported information regarding their in vivo role.
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19
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[The roles of MYB transcription factors on plant defense responses and its molecular mechanism.]. YI CHUAN = HEREDITAS 2016; 30:1265-71. [PMID: 18930885 DOI: 10.3724/sp.j.1005.2008.01265] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Transcriptional regulation of defense gene expression is a crucial part of plant defense responses in plant defense environment stresses. As one of the largest plant transcription factor families, MYB (v-myb avian myeloblastosis viral on-cogene homolog) transcription factors play an important role in plant stress tolerance. In this paper, we review the structural features, functional characterization and molecular mechanism of MYB transcription factor family, and discuss the regula-tory roles of transcription factors in plant defense responses.
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20
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Li MY, Xu ZS, Tian C, Huang Y, Wang F, Xiong AS. Genomic identification of WRKY transcription factors in carrot (Daucus carota) and analysis of evolution and homologous groups for plants. Sci Rep 2016; 6:23101. [PMID: 26975939 PMCID: PMC4792144 DOI: 10.1038/srep23101] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 03/01/2016] [Indexed: 11/24/2022] Open
Abstract
WRKY transcription factors belong to one of the largest transcription factor families. These factors possess functions in plant growth and development, signal transduction, and stress response. Here, we identified 95 DcWRKY genes in carrot based on the carrot genomic and transcriptomic data, and divided them into three groups. Phylogenetic analysis of WRKY proteins from carrot and Arabidopsis divided these proteins into seven subgroups. To elucidate the evolution and distribution of WRKY transcription factors in different species, we constructed a schematic of the phylogenetic tree and compared the WRKY family factors among 22 species, which including plants, slime mold and protozoan. An in-depth study was performed to clarify the homologous factor groups of nine divergent taxa in lower and higher plants. Based on the orthologous factors between carrot and Arabidopsis, 38 DcWRKY proteins were calculated to interact with other proteins in the carrot genome. Yeast two-hybrid assay showed that DcWRKY20 can interact with DcMAPK1 and DcMAPK4. The expression patterns of the selected DcWRKY genes based on transcriptome data and qRT-PCR suggested that those selected DcWRKY genes are involved in root development, biotic and abiotic stress response. This comprehensive analysis provides a basis for investigating the evolution and function of WRKY genes.
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Affiliation(s)
- Meng-Yao Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Chang Tian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Ying Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Feng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
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21
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Cao Y, Han Y, Li D, Lin Y, Cai Y. MYB Transcription Factors in Chinese Pear (Pyrus bretschneideri Rehd.): Genome-Wide Identification, Classification, and Expression Profiling during Fruit Development. FRONTIERS IN PLANT SCIENCE 2016; 7:577. [PMID: 27200050 PMCID: PMC4850919 DOI: 10.3389/fpls.2016.00577] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 04/14/2016] [Indexed: 05/18/2023]
Abstract
The MYB family is one of the largest families of transcription factors in plants. Although, some MYBs were reported to play roles in secondary metabolism, no comprehensive study of the MYB family in Chinese pear (Pyrus bretschneideri Rehd.) has been reported. In the present study, we performed genome-wide analysis of MYB genes in Chinese pear, designated as PbMYBs, including analyses of their phylogenic relationships, structures, chromosomal locations, promoter regions, GO annotations, and collinearity. A total of 129 PbMYB genes were identified in the pear genome and were divided into 31 subgroups based on phylogenetic analysis. These PbMYBs were unevenly distributed among 16 chromosomes (total of 17 chromosomes). The occurrence of gene duplication events indicated that whole-genome duplication and segmental duplication likely played key roles in expansion of the PbMYB gene family. Ka/Ks analysis suggested that the duplicated PbMYBs mainly experienced purifying selection with restrictive functional divergence after the duplication events. Interspecies microsynteny analysis revealed maximum orthology between pear and peach, followed by plum and strawberry. Subsequently, the expression patterns of 20 PbMYB genes that may be involved in lignin biosynthesis according to their phylogenetic relationships were examined throughout fruit development. Among the 20 genes examined, PbMYB25 and PbMYB52 exhibited expression patterns consistent with the typical variations in the lignin content previously reported. Moreover, sub-cellular localization analysis revealed that two proteins PbMYB25 and PbMYB52 were localized to the nucleus. All together, PbMYB25 and PbMYB52 were inferred to be candidate genes involved in the regulation of lignin biosynthesis during the development of pear fruit. This study provides useful information for further functional analysis of the MYB gene family in pear.
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Affiliation(s)
- Yunpeng Cao
- These authors have contributed equally to this work.
| | - Yahui Han
- These authors have contributed equally to this work.
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22
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Chakravarthi M, Syamaladevi DP, Harunipriya P, Augustine SM, Subramonian N. A novel PR10 promoter from Erianthus arundinaceus directs high constitutive transgene expression and is enhanced upon wounding in heterologous plant systems. Mol Biol Rep 2016; 43:17-30. [PMID: 26671655 DOI: 10.1007/s11033-015-3934-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 12/08/2015] [Indexed: 10/22/2022]
Abstract
In genetic engineering, inducible promoters play an important role as the expression of genes driven by them can be turned on or off under situations like biotic or abiotic factors. There are few reports on inducible promoters that can be employed in the development of transgenic plants, particularly in sugarcane. In the present study, four wound inducible genes (Chitinase, PR1A, PR10 and HRGP) were selected and were amplified from Erianthus arundinaceus, a distant relative of sugarcane. In order to determine the gene that is highly induced upon wounding, RT-qPCR was performed, which showed that PR10 gene expression was instantaneous and higher upon wounding when compared to the other three genes. Using the random amplification of genomic ends technique, a 592 bp promoter sequence was obtained and in silico analysis of the upstream regulatory region revealed a 469 bp promoter and 123 bp of 5' untranslated region (UTR). Functional analyses of the promoter sequence (with and without 5' UTR) in tobacco, rice and sugarcane using β-glucuronidase (GUS) as the reporter gene revealed the constitutive and inducible nature of the PR10 promoter. Our studies have demonstrated that the PR10 promoter, though highly constitutive, was quickly induced upon wounding as well as on treatment with abscisic acid and methyl jasmonate hormones. This is the first report on the isolation and characterization of a PR10 promoter from a wild grass and is expected to have application for development of transgenic plants.
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Affiliation(s)
- M Chakravarthi
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamilnadu, 641 007, India
| | - Divya P Syamaladevi
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamilnadu, 641 007, India
- Directorate of Rice Research (ICAR), Rajendranagar, Hyderabad, 500 030, India
| | - P Harunipriya
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamilnadu, 641 007, India
| | | | - N Subramonian
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamilnadu, 641 007, India.
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23
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Hedayati V, Mousavi A, Razavi K, Cultrera N, Alagna F, Mariotti R, Hosseini-Mazinani M, Baldoni L. Polymorphisms in the AOX2 gene are associated with the rooting ability of olive cuttings. PLANT CELL REPORTS 2015; 34:1151-64. [PMID: 25749737 DOI: 10.1007/s00299-015-1774-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 02/11/2015] [Accepted: 02/17/2015] [Indexed: 05/05/2023]
Abstract
Different rooting ability candidate genes were tested on an olive cross progeny. Our results demonstrated that only the AOX2 gene was strongly induced. OeAOX2 was fully characterised and correlated to phenotypical traits. The formation of adventitious roots is a key step in the vegetative propagation of trees crop species, and this ability is under strict genetic control. While numerous studies have been carried out to identify genes controlling adventitious root formation, only a few loci have been characterised. In this work, candidate genes that were putatively involved in rooting ability were identified in olive (Olea europaea L.) by similarity with orthologs identified in other plant species. The mRNA levels of these genes were analysed by real-time PCR during root induction in high- (HR) and low-rooting (LR) individuals. Interestingly, alternative oxidase 2 (AOX2), which was previously reported to be a functional marker for rooting in olive cuttings, showed a strong induction in HR individuals. From the OeAOX2 full-length gene, alleles and effective polymorphisms were distinguished and analysed in the cross progeny, which were segregated based on rooting. The results revealed a possible correlation between two single nucleotide polymorphisms of OeAOX2 gene and rooting ability.
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Affiliation(s)
- Vahideh Hedayati
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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24
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Zhang Z, Chen J, Su Y, Liu H, Chen Y, Luo P, Du X, Wang D, Zhang H. TaLHY, a 1R-MYB Transcription Factor, Plays an Important Role in Disease Resistance against Stripe Rust Fungus and Ear Heading in Wheat. PLoS One 2015; 10:e0127723. [PMID: 26010918 PMCID: PMC4444181 DOI: 10.1371/journal.pone.0127723] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/20/2015] [Indexed: 01/10/2023] Open
Abstract
LHY (late elongated hypocotyl) is an important gene that regulates and controls biological rhythms in plants. Additionally, LHY is highly expressed in the SSH (suppression subtractive hybridization) cDNA library-induced stripe rust pathogen (CYR32) in our previous research. To identify the function of the LHY gene in disease resistance against stripe rust, we used RACE-PCR technology to clone TaLHY in the wheat variety Chuannong19. The cDNA of TaLHY is 3085 bp long with an open reading frame of 1947 bp. TaLHY is speculated to encode a 70.3 kDa protein of 648 amino acids , which has one typical plant MYB-DNA binding domain; additionally, phylogenetic tree shows that TaLHY has the highest homology with LHY of Brachypodium distachyon(BdLHY-like). Quantitative fluorescence PCR indicates that TaLHY has higher expression in the leaf, ear and stem of wheat but lower expression in the root. Infestation of CYR32 can result in up-regulated expression of TaLHY, peaking at 72 h. Using VIGS (virus-induced gene silencing) technology to disease-resistant wheat in the fourth leaf stage, plants with silenced TaLHY cannot complete their heading stage. Through the compatible interaction with the stripe rust physiological race CYR32, Chuannong 19 loses its immune capability toward the stripe rust pathogen, indicating that TaLHY may regulate and participate in the heading of wheat, as well as the defense responses against stripe rust infection.
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Affiliation(s)
- Zijin Zhang
- Biophysics and Immune Engineering Lab, Sichuan Agricultural University, Ya’an, Sichuan, People’s Republic of China
| | - Jieming Chen
- Biophysics and Immune Engineering Lab, Sichuan Agricultural University, Ya’an, Sichuan, People’s Republic of China
| | - Yongying Su
- Biophysics and Immune Engineering Lab, Sichuan Agricultural University, Ya’an, Sichuan, People’s Republic of China
| | - Hanmei Liu
- Biophysics and Immune Engineering Lab, Sichuan Agricultural University, Ya’an, Sichuan, People’s Republic of China
| | - Yanger Chen
- Biophysics and Immune Engineering Lab, Sichuan Agricultural University, Ya’an, Sichuan, People’s Republic of China
| | - Peigao Luo
- State Key Laboratory of Plant breeding and Genetics, Sichuan Agricultural University, Chengdu, Sichuan, People’s Republic of China
| | - Xiaogang Du
- Biophysics and Immune Engineering Lab, Sichuan Agricultural University, Ya’an, Sichuan, People’s Republic of China
| | - Dan Wang
- Department of wheat breeding. Puyang Academy of Agricultural Sciences, Puyang, Henan, People’s Republic of China
| | - Huaiyu Zhang
- Biophysics and Immune Engineering Lab, Sichuan Agricultural University, Ya’an, Sichuan, People’s Republic of China
- * E-mail:
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25
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Afrin S, Zhu J, Cao H, Huang J, Xiu H, Luo T, Luo Z. Molecular cloning and expression profile of an abiotic stress and hormone responsive MYB transcription factor gene from Panax ginseng. Acta Biochim Biophys Sin (Shanghai) 2015; 47:267-77. [PMID: 25791525 DOI: 10.1093/abbs/gmv012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The v-myb avian myeloblastosis viral oncogene homolog (MYB) family constitutes one of the most abundant groups of transcription factors and plays vital roles in developmental processes and defense responses in plants. A ginseng (Panax ginseng C.A. Meyer) MYB gene was cloned and designated as PgMYB1. The cDNA of PgMYB1 is 762 base pairs long and encodes the R2R3-type protein consisting 238 amino acids. Subcellular localization showed that PgMYB1-mGFP5 fusion protein was specifically localized in the nucleus. To understand the functional roles of PgMYB1, we investigated the expression patterns of PgMYB1 in different tissues and under various conditions. Quantitative real-time polymerase chain reaction and western blot analysis showed that PgMYB1 was expressed at higher level in roots, leaves, and lateral roots than in stems and seeds. The expression of PgMYB1 was up-regulated by abscisic acid, salicylic acid, NaCl, and cold (chilling), and down-regulated by methyl jasmonate. These results suggest that PgMYB1 might be involved in responding to environmental stresses and hormones.
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Affiliation(s)
- Sadia Afrin
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Jie Zhu
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Hongzhe Cao
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Jingjia Huang
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Hao Xiu
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Tiao Luo
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
| | - Zhiyong Luo
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China
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Fang L, Hou Y, Wang L, Xin H, Wang N, Li S. Myb14, a direct activator of STS, is associated with resveratrol content variation in berry skin in two grape cultivars. PLANT CELL REPORTS 2014; 33:1629-40. [PMID: 24948530 DOI: 10.1007/s00299-014-1642-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 05/21/2014] [Accepted: 06/02/2014] [Indexed: 05/03/2023]
Abstract
High and low resveratrol (Res) contents in two cultivars are correlated with the expression abundance of Myb14 , which could directly activate transcriptional expression of stilbene synthase gene ( STS ). Resveratrol (3,5,4'-trihydroxystilbene) is one of the natural polyphenols produced by secondary metabolism in some plants. Stilbene synthase (STS) is the key enzyme for the final step of precursor formation of resveratrol (Res) in grapevines. In this study, we found that Res contents in ripe berry skin were completely different in two grape cultivars, namely, 'Z168' (Vitis monticola × Vitis riparia) with high-Res and 'Jingzaojing' (Vitis vinifera) with low-Res. Moreover, the level of expression of STS gene was higher in the ripe berry skin of 'Z168' than in that of 'Jingzaojing'. To further investigate the underlying mechanisms, we conducted a co-expression analysis through transcriptomic data. We confirmed that Myb14, an R2R3 Myb transcription factor, is the direct regulator of STS by binding to Box-L5 motif. Moreover, the expression pattern of Myb14 is associated with the variation of Res content. To test this prediction, we conducted a number of experiments in vivo and in vitro. The expression patterns of Myb14 and STS in grapevine leaves were identical under a series of stimulus. Myb14 showed higher expression in the ripe berry skin of 'Z168' than in that of 'Jingzaojing'. Yeast one-hybrid assay indicated that grapevine Myb14 could interact with the promoter of STS in vitro, and the transient overexpression of Myb14 promoted the expression of STS. Furthermore, co-expressing 35S::Myb14 in transgenic Arabidopsis could activate GUS expression promoted by STS promoter. Thus, Myb14 is the direct activator of STS, and its expression pattern is associated with Res content variation in grapes.
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Affiliation(s)
- Linchuan Fang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China,
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Takeda J, Nakata R, Ueno H, Murakami A, Iseki M, Watanabe M. Possible involvement of a tetrahydrobiopterin in photoreception for UV-B-induced anthocyanin synthesis in carrot. Photochem Photobiol 2014; 90:1043-9. [PMID: 24943195 DOI: 10.1111/php.12302] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 06/14/2014] [Indexed: 01/19/2023]
Abstract
Our previous studies of action spectra for UV-B-induced anthocyanin accumulation in cultured carrot cells indicated that a reduced form of pterin, possibly tetrahydrobiopterin, contributes to UV-B photoreception. In this report, we provide additional evidence for the involvement of pterin in UV-B light sensing. UV-B-induced phenylalanine ammonia-lyase (PAL) activity was considerably suppressed by N-acetylserotonin (an inhibitor of tetrahydrobiopterin biosynthesis), and this suppression was partially recovered by adding biopterin or tetrahydrobiobiopterin. In addition, protein(s) specifically bound to biopterin were detected by radiolabeling experiments in N-acetylserotonin-treated cells. Furthermore, diphenyleneiodonium, a potent inhibitor of electron transfer, completely suppressed UV-B-induced PAL activity. These results suggest the occurrence of an unidentified UV-B photoreceptor (other than UVR8, the tryptophan-based UV-B sensor originally identified in Arabidopsis) with reduced pterin in carrot cells. After reexamining published action spectra, we suggest that anthocyanin synthesis is coordinately regulated by these two UV-B sensors.
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Affiliation(s)
- Junko Takeda
- Laboratory of Applied Microbiology and Biochemistry, Nara Women's University, Nara, Japan
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Genome-wide analysis of the R2R3-MYB transcription factor gene family in sweet orange (Citrus sinensis). Mol Biol Rep 2014; 41:6769-85. [DOI: 10.1007/s11033-014-3563-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 06/24/2014] [Indexed: 01/22/2023]
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Yuan Y, Wu C, Liu Y, Yang J, Huang L. The Scutellaria baicalensis R2R3-MYB transcription factors modulates flavonoid biosynthesis by regulating GA metabolism in transgenic tobacco plants. PLoS One 2013; 8:e77275. [PMID: 24143216 PMCID: PMC3797077 DOI: 10.1371/journal.pone.0077275] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 08/30/2013] [Indexed: 01/06/2023] Open
Abstract
R2R3-MYB proteins play role in plant development, response to biotic and abiotic stress, and regulation of primary and secondary metabolism. Little is known about the R2R3-MYB proteins in Scutellaria baicalensis which is an important Chinese medical plant. In this paper, nineteen putative SbMYB genes were identified from a S. baicalensis cDNA library, and eleven R2R3-MYBs were clustered into 5 subgroups according to phylogenetic reconstruction. In the S. baicalensis leaves which were sprayed with GA3, SbMYB2 and SbMYB7 had similar expression pattern with SbPALs, indicating that SbMYB2 and SbMYB7 might be involved in the flavonoid metabolism. Transactivation assay results showed that SbMYB2 and SbMYB7 can function as transcriptional activator. The expression of several flavonoid biosynthesis-related genes were induced or suppressed by overexpression of SbMYB2 or SbMYB7 in transgenic tobacco plants. Consistent with the change of the expression of NtDH29 and NtCHI, the contents of dicaffeoylspermidine and quercetin-3,7-O-diglucoside in SbMYB2-overexpressing or SbMYB7-overexpressing transgenic tobacco plants were decreased. The transcriptional level of NtUFGT in transgenic tobacco overexpressing SbMYB7 and the transcriptional level of NtHCT in SbMYB2-overexpressing tobacco plants were increased; however the application of GA3 inhibited the transcriptional level of these two genes. These results suggest that SbMYB2 and SbMYB7 might regulate the flavonoid biosynthesis through GA metabolism.
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Affiliation(s)
- Yuan Yuan
- National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, China
| | - Chong Wu
- National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, China
| | - Yunjun Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Yang
- National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, China
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Petitot AS, Barsalobres-Cavallari C, Ramiro D, Albuquerque Freire E, Etienne H, Fernandez D. Promoter analysis of the WRKY transcription factors CaWRKY1a and CaWRKY1b homoeologous genes in coffee (Coffea arabica). PLANT CELL REPORTS 2013; 32:1263-76. [PMID: 23568411 DOI: 10.1007/s00299-013-1440-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/22/2013] [Accepted: 03/26/2013] [Indexed: 05/10/2023]
Abstract
KEY MESSAGE The regulation of the CaWRKY1 homoeologous genes were analyzed through the characterization of their promoters. The pW1a promoter is proposed as a new tool for coffee plant biotechnologies. WRKY transcription factors are important elements of the plant immune response. The CaWRKY1 gene from Coffea arabica is induced by several biotic and abiotic stresses, including challenge by the rust fungus Hemileia vastatrix. Two homoeologous CaWRKY1 genes, named CaWRKY1a and CaWRKY1b, were previously identified in the C. arabica allotetraploid genome. To gain insight into the transcriptional regulation of these genes, their promoter sequences, named pW1a and pW1b, respectively, were cloned and characterized in this study. In silico analysis revealed some important defense-associated regulatory elements, including W-boxes and as-1 elements. Promoter activities were analyzed in transient assays conducted by agroinfiltration of tobacco leaves. Exogenous salicylic acid (SA) treatments increased promoter activities corroborating the presence of as-1 regulatory elements. Transactivation assays with the CaWRKY1 protein showed the reduction of both pW1a and pW1b promoter activities, indicating that the CaWRKY1 protein may negatively regulate its own promoters. Stable transgenic C. arabica lines expressing a pW1a::GUS construct were obtained by Agrobacterium-mediated transformation and high GUS activity was observed in leaves subjected to mechanical wounding. Hence, the ability of pW1a to drive transgene expression in coffee plants as well as to enhance expression in response to stresses opens possibilities for using this promoter as a new tool for biotechnological approaches in coffee plants.
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Affiliation(s)
- Anne-Sophie Petitot
- Institut de Recherche pour le Développement, UMR186 IRD-CIRAD-UM2 Résistance des Plantes aux Bioagresseurs, 911 avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France.
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Ambawat S, Sharma P, Yadav NR, Yadav RC. MYB transcription factor genes as regulators for plant responses: an overview. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2013; 19:307-21. [PMID: 24431500 PMCID: PMC3715649 DOI: 10.1007/s12298-013-0179-1] [Citation(s) in RCA: 521] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Regulation of gene expression at the level of transcription controls many crucial biological processes. Transcription factors (TFs) play a great role in controlling cellular processes and MYB TF family is large and involved in controlling various processes like responses to biotic and abiotic stresses, development, differentiation, metabolism, defense etc. Here, we review MYB TFs with particular emphasis on their role in controlling different biological processes. This will provide valuable insights in understanding regulatory networks and associated functions to develop strategies for crop improvement.
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Affiliation(s)
- Supriya Ambawat
- Department of Molecular Biology and Biotechnology, CCS Haryana Agricultural University, Hisar, 125004 India
| | - Poonam Sharma
- Department of Molecular Biology and Biotechnology, CCS Haryana Agricultural University, Hisar, 125004 India
| | - Neelam R. Yadav
- Department of Molecular Biology and Biotechnology, CCS Haryana Agricultural University, Hisar, 125004 India
| | - Ram C. Yadav
- Department of Molecular Biology and Biotechnology, CCS Haryana Agricultural University, Hisar, 125004 India
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Ma S, Bachan S, Porto M, Bohnert HJ, Snyder M, Dinesh-Kumar SP. Discovery of stress responsive DNA regulatory motifs in Arabidopsis. PLoS One 2012; 7:e43198. [PMID: 22912824 PMCID: PMC3418279 DOI: 10.1371/journal.pone.0043198] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 07/17/2012] [Indexed: 11/25/2022] Open
Abstract
The discovery of DNA regulatory motifs in the sequenced genomes using computational methods remains challenging. Here, we present MotifIndexer - a comprehensive strategy for de novo identification of DNA regulatory motifs at a genome level. Using word-counting methods, we indexed the existence of every 8-mer oligo composed of bases A, C, G, T, r, y, s, w, m, k, n or 12-mer oligo composed of A, C, G, T, n, in the promoters of all predicted genes of Arabidopsis thaliana genome and of selected stress-induced co-expressed genes. From this analysis, we identified number of over-represented motifs. Among these, major critical motifs were identified using a position filter. We used a model based on uniform distribution and the z-scores derived from this model to describe position bias. Interestingly, many motifs showed position bias towards the transcription start site. We extended this model to show biased distribution of motifs in the genomes of both A. thaliana and rice. We also used MotifIndexer to identify conserved motifs in co-expressed gene groups from two Arabidopsis species, A. thaliana and A. lyrata. This new comparative genomics method does not depend on alignments of homologous gene promoter sequences.
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Affiliation(s)
- Shisong Ma
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California Davis, Davis, California, United States of America
- * E-mail: (SPD-K); (SM)
| | - Shawn Bachan
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California Davis, Davis, California, United States of America
| | - Matthew Porto
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California Davis, Davis, California, United States of America
| | - Hans J. Bohnert
- Departements of Plant Biology and Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Savithramma P. Dinesh-Kumar
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California Davis, Davis, California, United States of America
- * E-mail: (SPD-K); (SM)
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Shelton D, Stranne M, Mikkelsen L, Pakseresht N, Welham T, Hiraka H, Tabata S, Sato S, Paquette S, Wang TL, Martin C, Bailey P. Transcription factors of Lotus: regulation of isoflavonoid biosynthesis requires coordinated changes in transcription factor activity. PLANT PHYSIOLOGY 2012; 159:531-47. [PMID: 22529285 PMCID: PMC3375922 DOI: 10.1104/pp.112.194753] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 04/23/2012] [Indexed: 05/20/2023]
Abstract
Isoflavonoids are a class of phenylpropanoids made by legumes, and consumption of dietary isoflavonoids confers benefits to human health. Our aim is to understand the regulation of isoflavonoid biosynthesis. Many studies have shown the importance of transcription factors in regulating the transcription of one or more genes encoding enzymes in phenylpropanoid metabolism. In this study, we coupled bioinformatics and coexpression analysis to identify candidate genes encoding transcription factors involved in regulating isoflavonoid biosynthesis in Lotus (Lotus japonicus). Genes encoding proteins belonging to 39 of the main transcription factor families were examined by microarray analysis of RNA from leaf tissue that had been elicited with glutathione. Phylogenetic analyses of each transcription factor family were used to identify subgroups of proteins that were specific to L. japonicus or closely related to known regulators of the phenylpropanoid pathway in other species. R2R3MYB subgroup 2 genes showed increased expression after treatment with glutathione. One member of this subgroup, LjMYB14, was constitutively overexpressed in L. japonicus and induced the expression of at least 12 genes that encoded enzymes in the general phenylpropanoid and isoflavonoid pathways. A distinct set of six R2R3MYB subgroup 2-like genes was identified. We suggest that these subgroup 2 sister group proteins and those belonging to the main subgroup 2 have roles in inducing isoflavonoid biosynthesis. The induction of isoflavonoid production in L. japonicus also involves the coordinated down-regulation of competing biosynthetic pathways by changing the expression of other transcription factors.
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Affiliation(s)
- Dale Shelton
- Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark (D.S., M.S., L.M., C.M.)
- John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom (N.P., T.W., T.L.W., C.M., P.B.)
- Kazusa DNA Research Institute, 292–0818 Chiba, Japan (H.H., S.T., S.S.)
- Department of Genome Science, University of Washington, Seattle, Washington 98195 (S.P.)
| | - Maria Stranne
- Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark (D.S., M.S., L.M., C.M.)
- John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom (N.P., T.W., T.L.W., C.M., P.B.)
- Kazusa DNA Research Institute, 292–0818 Chiba, Japan (H.H., S.T., S.S.)
- Department of Genome Science, University of Washington, Seattle, Washington 98195 (S.P.)
| | - Lisbeth Mikkelsen
- Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark (D.S., M.S., L.M., C.M.)
- John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom (N.P., T.W., T.L.W., C.M., P.B.)
- Kazusa DNA Research Institute, 292–0818 Chiba, Japan (H.H., S.T., S.S.)
- Department of Genome Science, University of Washington, Seattle, Washington 98195 (S.P.)
| | - Nima Pakseresht
- Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark (D.S., M.S., L.M., C.M.)
- John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom (N.P., T.W., T.L.W., C.M., P.B.)
- Kazusa DNA Research Institute, 292–0818 Chiba, Japan (H.H., S.T., S.S.)
- Department of Genome Science, University of Washington, Seattle, Washington 98195 (S.P.)
| | - Tracey Welham
- Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark (D.S., M.S., L.M., C.M.)
- John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom (N.P., T.W., T.L.W., C.M., P.B.)
- Kazusa DNA Research Institute, 292–0818 Chiba, Japan (H.H., S.T., S.S.)
- Department of Genome Science, University of Washington, Seattle, Washington 98195 (S.P.)
| | - Hideki Hiraka
- Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark (D.S., M.S., L.M., C.M.)
- John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom (N.P., T.W., T.L.W., C.M., P.B.)
- Kazusa DNA Research Institute, 292–0818 Chiba, Japan (H.H., S.T., S.S.)
- Department of Genome Science, University of Washington, Seattle, Washington 98195 (S.P.)
| | - Satoshi Tabata
- Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark (D.S., M.S., L.M., C.M.)
- John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom (N.P., T.W., T.L.W., C.M., P.B.)
- Kazusa DNA Research Institute, 292–0818 Chiba, Japan (H.H., S.T., S.S.)
- Department of Genome Science, University of Washington, Seattle, Washington 98195 (S.P.)
| | - Shusei Sato
- Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark (D.S., M.S., L.M., C.M.)
- John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom (N.P., T.W., T.L.W., C.M., P.B.)
- Kazusa DNA Research Institute, 292–0818 Chiba, Japan (H.H., S.T., S.S.)
- Department of Genome Science, University of Washington, Seattle, Washington 98195 (S.P.)
| | - Suzanne Paquette
- Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark (D.S., M.S., L.M., C.M.)
- John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom (N.P., T.W., T.L.W., C.M., P.B.)
- Kazusa DNA Research Institute, 292–0818 Chiba, Japan (H.H., S.T., S.S.)
- Department of Genome Science, University of Washington, Seattle, Washington 98195 (S.P.)
| | - Trevor L. Wang
- Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark (D.S., M.S., L.M., C.M.)
- John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom (N.P., T.W., T.L.W., C.M., P.B.)
- Kazusa DNA Research Institute, 292–0818 Chiba, Japan (H.H., S.T., S.S.)
- Department of Genome Science, University of Washington, Seattle, Washington 98195 (S.P.)
| | | | - Paul Bailey
- Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark (D.S., M.S., L.M., C.M.)
- John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom (N.P., T.W., T.L.W., C.M., P.B.)
- Kazusa DNA Research Institute, 292–0818 Chiba, Japan (H.H., S.T., S.S.)
- Department of Genome Science, University of Washington, Seattle, Washington 98195 (S.P.)
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Amelot N, Dorlhac de Borne F, San Clemente H, Mazars C, Grima-Pettenati J, Brière C. Transcriptome analysis of tobacco BY-2 cells elicited by cryptogein reveals new potential actors of calcium-dependent and calcium-independent plant defense pathways. Cell Calcium 2012; 51:117-30. [PMID: 22177386 DOI: 10.1016/j.ceca.2011.11.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 11/04/2011] [Accepted: 11/24/2011] [Indexed: 11/29/2022]
Abstract
Cryptogein is a proteinaceous elicitor secreted by the oomycete Phytophthora cryptogea, which induces a hypersensitive response in tobacco plants. We have previously reported that in tobacco BY-2 cells treated with cryptogein, most of the genes of the phenylpropanoid pathway were upregulated and cell wall-bound phenolics accumulated. Both events were Ca(2+) dependent. In this study, we designed a microarray covering a large proportion of the tobacco genome and monitored gene expression in cryptogein-elicited BY-2 cells to get a more complete view of the transcriptome changes and to assess their Ca(2+) dependence. The predominant functional gene categories affected by cryptogein included stress- and disease-related proteins, phenylpropanoid pathway, signaling components, transcription factors and cell wall reinforcement. Among the 3819 unigenes whose expression changed more than fourfold, 90% were Ca(2+) dependent, as determined by their sensitivity to lanthanum chloride. The most Ca(2+)-dependent transcripts upregulated by cryptogein were involved in defense responses or the oxylipin pathway. This genome-wide study strongly supports the importance of Ca(2+)-dependent transcriptional regulation of regulatory and defense-related genes contributing to cryptogein responses in tobacco.
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Affiliation(s)
- Nicolas Amelot
- Université de Toulouse, Laboratoire de Recherches en Sciences Végétales, Castanet-Tolosan, France
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Prouse MB, Campbell MM. The interaction between MYB proteins and their target DNA binding sites. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:67-77. [DOI: 10.1016/j.bbagrm.2011.10.010] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 10/17/2011] [Accepted: 10/18/2011] [Indexed: 02/02/2023]
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Tohge T, Kusano M, Fukushima A, Saito K, Fernie AR. Transcriptional and metabolic programs following exposure of plants to UV-B irradiation. PLANT SIGNALING & BEHAVIOR 2011; 6:1987-92. [PMID: 22112450 PMCID: PMC3337192 DOI: 10.4161/psb.6.12.18240] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In order to adapt to environmental changes of light species and intensity, higher plants furnish complicate signaling systems such as the UVR/COP/HY5 cascade which links several diverse classes of photoreceptors. In addition UV-B light provokes accelerated production of UV-B protectants such as flavonoids and vitamins. Following intensive research efforts, genes in the UV-B signaling cascade have been characterized via forward genetics approaches following mutant screens relying on sensitivity to UV-B irradiation. However detailed processes of the linkage between light signaling and the upregulation of metabolite accumulation remain unclear. Here we review both the light signal cascades and metabolite pathways responding to UV-B exposure. Finally we generate co-expression network analysis using published data in order to find novel candidate genes which link light signaling and transcriptional regulation to metabolic biosynthesis in attempt to describe how these processes are interlinked.
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Affiliation(s)
- Takayuki Tohge
- RIKEN Plant Science Center; Yokohama, Japan
- Max-Planck Institute for Molecular Plant Physiology; Potsdam-Golm, Germany
- Correspondence to: Takayuki Tohge, or Alisdair R. Fernie,
| | | | | | - Kazuki Saito
- RIKEN Plant Science Center; Yokohama, Japan
- Graduate School of Pharmaceutical Sciences; Chiba University; Chiba, Japan
| | - Alisdair R. Fernie
- Max-Planck Institute for Molecular Plant Physiology; Potsdam-Golm, Germany
- Correspondence to: Takayuki Tohge, or Alisdair R. Fernie,
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Ruan J, Perez J, Hernandez B, Lei C, Sunter G, Sponsel VM. Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana. BMC Bioinformatics 2011; 12 Suppl 12:S2. [PMID: 22168340 PMCID: PMC3247083 DOI: 10.1186/1471-2105-12-s12-s2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Background Several large-scale gene co-expression networks have been constructed successfully for predicting gene functional modules and cis-regulatory elements in Arabidopsis (Arabidopsis thaliana). However, these networks are usually constructed and analyzed in an ad hoc manner. In this study, we propose a completely parameter-free and systematic method for constructing gene co-expression networks and predicting functional modules as well as cis-regulatory elements. Results Our novel method consists of an automated network construction algorithm, a parameter-free procedure to predict functional modules, and a strategy for finding known cis-regulatory elements that is suitable for consensus scanning without prior knowledge of the allowed extent of degeneracy of the motif. We apply the method to study a large collection of gene expression microarray data in Arabidopsis. We estimate that our co-expression network has ~94% of accuracy, and has topological properties similar to other biological networks, such as being scale-free and having a high clustering coefficient. Remarkably, among the ~300 predicted modules whose sizes are at least 20, 88% have at least one significantly enriched functions, including a few extremely significant ones (ribosome, p < 1E-300, photosynthetic membrane, p < 1.3E-137, proteasome complex, p < 5.9E-126). In addition, we are able to predict cis-regulatory elements for 66.7% of the modules, and the association between the enriched cis-regulatory elements and the enriched functional terms can often be confirmed by the literature. Overall, our results are much more significant than those reported by several previous studies on similar data sets. Finally, we utilize the co-expression network to dissect the promoters of 19 Arabidopsis genes involved in the metabolism and signaling of the important plant hormone gibberellin, and achieved promising results that reveal interesting insight into the biosynthesis and signaling of gibberellin. Conclusions The results show that our method is highly effective in finding functional modules from real microarray data. Our application on Arabidopsis leads to the discovery of the largest number of annotated Arabidopsis functional modules in the literature. Given the high statistical significance of functional enrichment and the agreement between cis-regulatory and functional annotations, we believe our Arabidopsis gene modules can be used to predict the functions of unknown genes in Arabidopsis, and to understand the regulatory mechanisms of many genes.
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Affiliation(s)
- Jianhua Ruan
- Department of Computer Science, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, USA.
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Akagi A, Dandekar AM, Stotz HU. Resistance of Malus domestica fruit to Botrytis cinerea depends on endogenous ethylene biosynthesis. PHYTOPATHOLOGY 2011; 101:1311-21. [PMID: 21809978 DOI: 10.1094/phyto-03-11-0087] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The plant hormone ethylene regulates fruit ripening, other developmental processes, and a subset of defense responses. Here, we show that 1-aminocyclopropane-1-carboxylic acid synthase (ACS)-silenced apple (Malus domestica) fruit that express a sense construct of ACS were more susceptible to Botrytis cinerea than untransformed apple, demonstrating that ethylene strengthens fruit resistance to B. cinerea infection. Because ethylene response factors (ERFs) are known to contribute to resistance against B. cinerea via the ethylene-signaling pathway, we cloned four ERF cDNAs from fruit of M. domestica: MdERF3, -4, -5, and -6. Expression of all four MdERF mRNAs was ethylene dependent and induced by wounding or by B. cinerea infection. B. cinerea infection suppressed rapid induction of wound-related MdERF expression. MdERF3 was the only mRNA induced by wounding and B. cinerea infection in ACS-suppressed apple fruit, although its induction was reduced compared with wild-type apple. Promoter regions of all four MdERF genes were cloned and putative cis-elements were identified in each promoter. Transient expression of MdERF3 in tobacco increased expression of the GCC-box containing gene chitinase 48.
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MESH Headings
- Botrytis/physiology
- Chitinases/genetics
- DNA, Complementary/genetics
- Ethylenes/analysis
- Ethylenes/biosynthesis
- Fruit/enzymology
- Fruit/genetics
- Fruit/immunology
- Fruit/microbiology
- Gene Expression Regulation, Plant
- Lyases/genetics
- Malus/enzymology
- Malus/genetics
- Malus/immunology
- Malus/microbiology
- Mutation
- Phylogeny
- Plant Diseases/genetics
- Plant Diseases/immunology
- Plant Diseases/microbiology
- Plant Growth Regulators/metabolism
- Plant Immunity
- Plant Proteins/genetics
- Plants, Genetically Modified/enzymology
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/immunology
- Plants, Genetically Modified/microbiology
- Promoter Regions, Genetic/genetics
- RNA, Messenger/genetics
- RNA, Plant/genetics
- Signal Transduction
- Stress, Mechanical
- Time Factors
- Nicotiana/genetics
- Nicotiana/metabolism
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Affiliation(s)
- Aya Akagi
- Department of Horticulture, Oregon State University, Corvallis, OR, USA
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Cai H, Tian S, Liu C, Dong H. Identification of a MYB3R gene involved in drought, salt and cold stress in wheat (Triticum aestivum L.). Gene 2011; 485:146-52. [DOI: 10.1016/j.gene.2011.06.026] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 06/12/2011] [Accepted: 06/18/2011] [Indexed: 01/15/2023]
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Lao YM, Xiao L, Ye ZW, Jiang JG, Zhou SS. In silico analysis of phytoene synthase and its promoter reveals hints for regulation mechanisms of carotenogenesis in Duanliella bardawil. Bioinformatics 2011; 27:2201-8. [PMID: 21712245 DOI: 10.1093/bioinformatics/btr371] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Previous researches showed that phytoene synthase (Psy) from Dunaliella bardawil is the first regulatory point in carotenogenesis. We hypothesize certain interactions between the environmental stress factors and the regulatory sequences of Psy in D.bardawil (DbPsy). Consequently, LA PCR-based genomic walking approach was performed for isolation of psy promoter and terminator, respectively. The obtained nucleic acid sequences and the corresponding protein structure of DbPsy were analyzed and predicted using various bioinformatics tools. Finally, we presented some hints for the regulation mechanisms of DbPsy at the molecular level according to the computed results. RESULTS LA PCR-based genomic walking results showed that the isolated sequences are the promoter and terminator of psy, correspondingly. Computational analysis demonstrated several candidate motifs of the promoter exhibiting hypothetic UV-B-, norglurzon- and salt-induced characteristics, as well as some typical domains universally discovered in promoter sequences, such as TATA-box, CCAAT-box and GATA-box, etc. Furthermore, the structure of Psy was also predicted and aligned along with many counterparts at the protein level. Low homology of N-terminus was found in D.bardawil, while a relatively conserved C-terminus was predicted to be involved in the catalytic activity and substrate recognization/binding. Phylogenic analysis classified the DbPsy into a cluster with other algae. These results implied that Psy may share similar regulation mechanisms among algae with respect to their C-termini; while the diversity in N-terminus among Psys, along with the predicted inducible motifs in psy promoter from D.bardawil, may confer the fine tuning differences between D.bardawil and other algae. CONCLUSION By means of computer techniques, we found in D.barawali that two interesting conserved motifs of psy promoter may involve in UV-B, norglurzon and salt regulation correspondingly; and that the diversity of Psy protein mainly lies in the N-termini among algae. These results indicate some hints for regulation mechanisms of carotenogenesis in D.bradawil. CONTACT jgjiang@scut.edu.cn.
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Affiliation(s)
- Yong-Min Lao
- College of Food and Bioengineering, South China University of Technology, Guangzhou, 510640, China
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Liu JJ, Ekramoddoullah AKM. Genomic organization, induced expression and promoter activity of a resistance gene analog (PmTNL1) in western white pine (Pinus monticola). PLANTA 2011; 233:1041-53. [PMID: 21279649 DOI: 10.1007/s00425-011-1353-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 01/05/2011] [Indexed: 05/16/2023]
Abstract
Cronartium ribicola causes white pine blister rust (WPBR) in subgenus Strobus. Various genetic and molecular approaches were used to detect white pine genes contributing to host resistance. The molecular role of the NBS-LRR family is highly related to plant immuno-activity against various pathogens and pests. In the present study, genomic organization of a resistance gene analog (RGA), designated as PmTNL1, and its allelic variants were characterized in Pinus monticola. PmTNL1 showed high identity with TIR-NBS-LRR proteins from other plants. qRT-PCR revealed that the PmTNL1 transcript was expressed at low basal levels in different tissues and exhibited similar patterns during compatible and incompatible interactions of P. monticola with C. ribicola at early stages post inoculation. In comparison, PmTNL1 was up-regulated significantly in diseased P. monticola tissues with WPBR symptoms. Expression of the PmTNL1 promoter::GUS fusion gene in transgenic Arabidopsis demonstrated that GUS signal appeared only inside phloem tissues of young seedlings and at hydathodes and branching and organ-connecting points in mature Arabidopsis plants. Similar to the endogenous expression pattern for this gene in pine, GUS activity was up-regulated significantly around vascular tissues locally at pathogen infection sites, but little or no induction was observed in response to abiotic stresses. A DNA marker was developed based on variation of the LRR-coding region, and PmTNL1 was mapped to one genetic linkage group using a pedigree with major dominant gene (Cr2) conferring HR resistance to C. ribicola. These results suggest that PmTNL1 may play an important role in white pine partial resistance against C. ribicola.
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Affiliation(s)
- Jun-Jun Liu
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5, Canada.
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Gayoso C, Pomar F, Novo-Uzal E, Merino F, Martínez de Ilárduya Ó. The Ve-mediated resistance response of the tomato to Verticillium dahliae involves H2O2, peroxidase and lignins and drives PAL gene expression. BMC PLANT BIOLOGY 2010; 10:232. [PMID: 20977727 PMCID: PMC3095318 DOI: 10.1186/1471-2229-10-232] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 10/26/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND Verticillium dahliae is a fungal pathogen that infects a wide range of hosts. The only known genes for resistance to Verticillium in the Solanaceae are found in the tomato (Solanum lycopersicum) Ve locus, formed by two linked genes, Ve1 and Ve2. To characterize the resistance response mediated by the tomato Ve gene, we inoculated two nearly isogenic tomato lines, LA3030 (ve/ve) and LA3038 (Ve/Ve), with V. dahliae. RESULTS We found induction of H2O2 production in roots of inoculated plants, followed by an increase in peroxidase activity only in roots of inoculated resistant plants. Phenylalanine-ammonia lyase (PAL) activity was also increased in resistant roots 2 hours after inoculation, while induction of PAL activity in susceptible roots was not seen until 48 hours after inoculation. Phenylpropanoid metabolism was also affected, with increases in ferulic acid, p-coumaric acid, vanillin and p-hydroxybenzaldehyde contents in resistant roots after inoculation. Six tomato PAL cDNA sequences (PAL1 - PAL6) were found in the SolGenes tomato EST database. RT-PCR analysis showed that these genes were expressed in all organs of the plant, albeit at different levels. Real-time RT-PCR indicated distinct patterns of expression of the different PAL genes in V. dahliae-inoculated roots. Phylogenetic analysis of 48 partial PAL cDNAs corresponding to 19 plant species grouped angiosperm PAL sequences into four clusters, suggesting functional differences among the six tomato genes, with PAL2 and PAL6 presumably involved in lignification, and the remaining PAL genes implicated in other biological processes. An increase in the synthesis of lignins was found 16 and 28 days after inoculation in both lines; this increase was greater and faster to develop in the resistant line. In both resistant and susceptible inoculated plants, an increase in the ratio of guaiacyl/syringyl units was detected 16 days after inoculation, resulting from the lowered amount of syringyl units in the lignins of inoculated plants. CONCLUSIONS The interaction between the tomato and V. dahliae triggered a number of short- and long-term defensive mechanisms. Differences were found between compatible and incompatible interactions, including onset of H2O2 production and activities of peroxidase and PAL, and phenylpropanoid metabolism and synthesis of lignins.
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Affiliation(s)
- Carmen Gayoso
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de La Coruña, 15071 La Coruña, Spain
- Instituto de Investigaciones Biomédicas de A Coruña (INIBIC), Complejo Hospitalario Universitario de A Coruña, As Xubias s/n, 15006 La Coruña, Spain
| | - Federico Pomar
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de La Coruña, 15071 La Coruña, Spain
| | - Esther Novo-Uzal
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de La Coruña, 15071 La Coruña, Spain
| | - Fuencisla Merino
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de La Coruña, 15071 La Coruña, Spain
| | - Óskar Martínez de Ilárduya
- Instituto de Investigaciones Biomédicas de A Coruña (INIBIC), Complejo Hospitalario Universitario de A Coruña, As Xubias s/n, 15006 La Coruña, Spain
- Networking Center of Biomedical Research in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 15006 La Coruña, Spain
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Du H, Zhang L, Liu L, Tang XF, Yang WJ, Wu YM, Huang YB, Tang YX. Biochemical and molecular characterization of plant MYB transcription factor family. BIOCHEMISTRY (MOSCOW) 2009; 74:1-11. [PMID: 19232042 DOI: 10.1134/s0006297909010015] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
MYB genes are widely distributed in higher plants and comprise one of the largest transcription factors, which are characterized by the presence of a highly conserved MYB domain at their N-termini. Over recent decades, biochemical and molecular characterizations of MYB have been extensively studied and reported to be involved in many physiological and biochemical processes. This review describes current knowledge of their structure characteristic, classification, multi-functionality, mechanism of combinational control, evolution, and function redundancy. It shows that the MYB transcription factors play a key role in plant development, such as secondary metabolism, hormone signal transduction, disease resistance, cell shape, organ development, etc. Furthermore, the expression of some members of the MYB family shows tissue-specificity.
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Affiliation(s)
- Hai Du
- Maize Research Institute, Sichuan Agricultural University, Yaan Sichuan 625014, China
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Kimura S, Chikagawa Y, Kato M, Maeda K, Ozeki Y. Upregulation of the promoter activity of the carrot (Daucus carota) phenylalanine ammonia-lyase gene (DcPAL3) is caused by new members of the transcriptional regulatory proteins, DcERF1 and DcERF2, which bind to the GCC-box homolog and act as an activator to the DcPAL3 promoter. JOURNAL OF PLANT RESEARCH 2008; 121:499-508. [PMID: 18584290 DOI: 10.1007/s10265-008-0170-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Accepted: 10/10/2007] [Indexed: 05/10/2023]
Abstract
The phenylalanine ammonia-lyase (PAL) gene, DcPAL3, was expressed during the synthesis of anthocyanin in suspension-cultured cells of carrot (Daucus carota). There were two putative cis-elements in the DcPAL3 promoter region: the box-L and GCC-box homologs. Both of these are committed to the upregulation of promoter activity. Although box-L is known as the conserved cis-element present in the promoter region of most PAL genes of many plant species targeted by the R2R3-MYB protein, among PAL genes, the GCC-box homolog is unique to the promoter region of the DcPAL3 gene. We have isolated two proteins belonging to the ethylene-responsive element-binding factor (ERF) family, DcERF1 and DcERF2, from two different cDNA libraries prepared from anthocyanin-synthesizing cells of different cultured cell lines of carrot. The methodology employed was yeast one-hybrid screening with the GCC-box homolog as a bait. Both DcERF1 and DcERF2 bound to the GCC-box homolog sequence in vitro. Transient expression analysis showed that, in carrot protoplasts, DcERF1 was able bind to the GCC-box homolog and act as an activator of the DcPAL3 promoter. In contrast, DcERF2 itself had no ability to activate DcPAL3 promoter activity, possibly because transiently expressed DcERF2 may not be exported into the nucleus. These results suggest that DcERF1 and DcERF2 may function in different ways in committing to the upregulation of the DcPAL3 promoter activity in anthocyanin-synthesizing cells of carrot.
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Affiliation(s)
- Soichi Kimura
- Department of Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
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Sakai T, Honing HVD, Nishioka M, Uehara Y, Takahashi M, Fujisawa N, Saji K, Seki M, Shinozaki K, Jones MA, Smirnoff N, Okada K, Wasteneys GO. Armadillo repeat-containing kinesins and a NIMA-related kinase are required for epidermal-cell morphogenesis in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 53:157-71. [PMID: 17971038 DOI: 10.1111/j.1365-313x.2007.03327.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The involvement of kinesin motor proteins in both cell-tip growth and cell-shape determination has been well characterized in various organisms. However, the functions of kinesins during cell morphogenesis in higher plants remain largely unknown. In the current study, we demonstrate that an armadillo repeat-containing kinesin-related protein, ARMADILLO REPEAT KINESIN1 (ARK1), is involved in root-hair morphogenesis. Microtubule polymers are more abundant in ark1 null allele root hairs, but analysis shows that these extra microtubules are concentrated in the endoplasm, and not in the cortical array, suggesting that ARK1 regulates tip growth by limiting the assembly and distribution of endoplasmic microtubules. The ARK1 gene has two homologues in the Arabidopsis genome, ARK2 and ARK3, and our results show that ARK2 is involved in root-cell morphogenesis. We further reveal that a NIMA-related protein kinase, NEK6, binds to the ARK family proteins and has pleiotropic effects on epidermal-cell morphogenesis, suggesting that NEK6 is involved in cell morphogenesis in Arabidopsis via microtubule functions associated with these armadillo repeat-containing kinesins. We discuss the function of NIMA-related protein kinases and armadillo repeat-containing kinesins in the cell morphogenesis of eukaryotes.
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Affiliation(s)
- Tatsuya Sakai
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Gális I, Simek P, Narisawa T, Sasaki M, Horiguchi T, Fukuda H, Matsuoka K. A novel R2R3 MYB transcription factor NtMYBJS1 is a methyl jasmonate-dependent regulator of phenylpropanoid-conjugate biosynthesis in tobacco. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 46:573-92. [PMID: 16640595 DOI: 10.1111/j.1365-313x.2006.02719.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Target metabolic and large-scale transcriptomic analyses of tobacco (Nicotiana tabacum L.) Bright Yellow-2 (BY-2) cells were employed to identify novel gene(s) involved in methyl jasmonate (MJ)-dependent function in plants. At the metabolic level, we describe the specific accumulation of several phenylpropanoid-polyamine conjugates in MJ-treated BY-2 cells. Furthermore, global gene expression analysis of MJ-treated cells using a 16K cDNA microarray containing expressed sequence tags (ESTs) from BY-2 cells revealed 828 genes that were upregulated by MJ treatment within 48 h. Using time-course expression data we identified a novel MJ-inducible R2R3 MYB-type transcription factor (NtMYBJS1) that was co-expressed in a close temporal pattern with the core phenylpropanoid genes phenylalanine ammonia-lyase (PAL) and 4-coumarate:CoA ligase (4CL). Overexpression of NtMYBJS1 in tobacco BY-2 cells caused accumulation of specific phenylpropanoid conjugates in the cells. Subsequent microarray analysis of NtMYBJS1 transgenic lines revealed that a limited number of genes, including PAL and 4CL, were specifically induced in the presence of the NtMYBJS1 transgene. These results, together with results of both antisense expression analysis and of gel mobility shift assays, strongly indicate that the NtMYBJS1 protein functions in tobacco MJ signal transduction, inducing phenylpropanoid biosynthetic genes and the accumulation of phenylpropanoid-polyamine conjugates during stress.
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Affiliation(s)
- Ivan Gális
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku,Yokohama 230-0045, Japan.
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