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Wei W, Li S, Li P, Yu K, Fan G, Wang Y, Zhao F, Zhang X, Feng X, Shi G, Zhang W, Song G, Dan W, Wang F, Zhang Y, Li X, Wang D, Zhang W, Pei J, Wang X, Zhao Z. QTL analysis of important agronomic traits and metabolites in foxtail millet ( Setaria italica) by RIL population and widely targeted metabolome. FRONTIERS IN PLANT SCIENCE 2023; 13:1035906. [PMID: 36704173 PMCID: PMC9872001 DOI: 10.3389/fpls.2022.1035906] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
As a bridge between genome and phenotype, metabolome is closely related to plant growth and development. However, the research on the combination of genome, metabolome and multiple agronomic traits in foxtail millet (Setaria italica) is insufficient. Here, based on the linkage analysis of 3,452 metabolites via with high-quality genetic linkage maps, we detected a total of 1,049 metabolic quantitative trait loci (mQTLs) distributed in 11 hotspots, and 28 metabolite-related candidate genes were mined from 14 mQTLs. In addition, 136 single-environment phenotypic QTL (pQTLs) related to 63 phenotypes were identified by linkage analysis, and there were 12 hotspots on these pQTLs. We futher dissected 39 candidate genes related to agronomic traits through metabolite-phenotype correlation and gene function analysis, including Sd1 semidwarf gene, which can affect plant height by regulating GA synthesis. Combined correlation network and QTL analysis, we found that flavonoid-lignin pathway maybe closely related to plant architecture and yield in foxtail millet. For example, the correlation coefficient between apigenin 7-rutinoside and stem diameter reached 0.98, and they were co-located at 41.33-44.15 Mb of chromosome 5, further gene function analysis revealed that 5 flavonoid pathway genes, as well as Sd1, were located in this interval . Therefore, the correlation and co-localization between flavonoid-lignins and plant architecture may be due to the close linkage of their regulatory genes in millet. Besides, we also found that a combination of genomic and metabolomic for BLUP analysis can better predict plant agronomic traits than genomic or metabolomic data, independently. In conclusion, the combined analysis of mQTL and pQTL in millet have linked genetic, metabolic and agronomic traits, and is of great significance for metabolite-related molecular assisted breeding.
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Affiliation(s)
- Wei Wei
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Shuangdong Li
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Peiyu Li
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Kuohai Yu
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Guangyu Fan
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Yixiang Wang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Fang Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xiaolei Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xiaolei Feng
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Gaolei Shi
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Weiqin Zhang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Guoliang Song
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Wenhan Dan
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Feng Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Yali Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xinru Li
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Dequan Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Wenying Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Jingjing Pei
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xiaoming Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Zhihai Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
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Peniche-Pavía HA, Guzmán TJ, Magaña-Cerino JM, Gurrola-Díaz CM, Tiessen A. Maize Flavonoid Biosynthesis, Regulation, and Human Health Relevance: A Review. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165166. [PMID: 36014406 PMCID: PMC9413827 DOI: 10.3390/molecules27165166] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/01/2022] [Accepted: 08/10/2022] [Indexed: 11/25/2022]
Abstract
Maize is one of the most important crops for human and animal consumption and contains a chemical arsenal essential for survival: flavonoids. Moreover, flavonoids are well known for their beneficial effects on human health. In this review, we decided to organize the information about maize flavonoids into three sections. In the first section, we include updated information about the enzymatic pathway of maize flavonoids. We describe a total of twenty-one genes for the flavonoid pathway of maize. The first three genes participate in the general phenylpropanoid pathway. Four genes are common biosynthetic early genes for flavonoids, and fourteen are specific genes for the flavonoid subgroups, the anthocyanins, and flavone C-glycosides. The second section explains the tissue accumulation and regulation of flavonoids by environmental factors affecting the expression of the MYB-bHLH-WD40 (MBW) transcriptional complex. The study of transcription factors of the MBW complex is fundamental for understanding how the flavonoid profiles generate a palette of colors in the plant tissues. Finally, we also include an update of the biological activities of C3G, the major maize anthocyanin, including anticancer, antidiabetic, and antioxidant effects, among others. This review intends to disclose and integrate the existing knowledge regarding maize flavonoid pigmentation and its relevance in the human health sector.
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Affiliation(s)
- Héctor A. Peniche-Pavía
- Departamento de Bioquímica y Biotecnología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Libramiento Norte Km. 9.6, Irapuato 36824, Guanajuato, Mexico
| | - Tereso J. Guzmán
- Department of Pharmacology, Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Jesús M. Magaña-Cerino
- División Académica de Ciencias de la Salud, Centro de Investigación y Posgrado, Universidad Juárez Autónoma de Tabasco, Av. Gregorio Méndez Magaña 2838-A, Col. Tamulté de las Barrancas, Villahermosa 86150, Tabasco, Mexico
| | - Carmen M. Gurrola-Díaz
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Instituto de Investigación en Enfermedades Crónico Degenerativas, Instituto Transdisciplinar de Investigación e Innovación en Salud, Universidad de Guadalajara, C. Sierra Mojada 950. Col. Independencia, Guadalajara 44340, Jalisco, Mexico
- Correspondence: ; Tel.: +52-33-10585200 (ext. 33930)
| | - Axel Tiessen
- Departamento de Bioquímica y Biotecnología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Libramiento Norte Km. 9.6, Irapuato 36824, Guanajuato, Mexico
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Islam NS, Bett KE, Pauls KP, Marsolais F, Dhaubhadel S. Postharvest seed coat darkening in pinto bean ( Phaseolus vulgaris) is regulated by Psd , an allele of the basic helix-loop-helix transcription factor P. PLANTS, PEOPLE, PLANET 2020; 2:663-677. [PMID: 34268482 PMCID: PMC8262261 DOI: 10.1002/ppp3.10132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 06/13/2023]
Abstract
Pinto bean (Phaseolus vulgaris) is one of the leading market classes of dry beans that is most affected by postharvest seed coat darkening. The process of seed darkening poses a challenge for bean producers and vendors as they encounter significant losses in crop value due to decreased consumer preference for darker beans. Here, we identified a novel allele of the P gene, Psd , responsible for the slow darkening seed coat in pintos, and identified trait-specific sequence polymorphisms which are utilized for the development of new gene-specific molecular markers for breeding. These tools can be deployed to help tackle this economically important issue for bean producers. SUMMARY Postharvest seed coat darkening in pinto bean is an undesirable trait that reduces the market value of the stored crop. Regular darkening (RD) pintos darken faster after harvest and accumulate higher level of proanthocyanidins (PAs) compared to slow darkening (SD) cultivars. Although the markers cosegregating with the SD trait have been known for some time, the SLOW DARKENING (Sd) gene identity had not been proven.Here, we identified Psd as a candidate for controlling the trait. Genetic complementation, transcript abundance, metabolite analysis, and inheritance study confirmed that Psd is the Sd gene. Psd is another allele of the P (Pigment) gene, whose loss-of-function alleles result in a white seed coat. Psd encodes a bHLH transcription factor with two transcript variants but only one is involved in PA biosynthesis. An additional glutamate residue in the activation domain, and/or an arginine to histidine substitution in the bHLH domain of the Psd-1 transcript in the SD cultivar is likely responsible for the reduced activity of this allele compared to the allele in a RD cultivar, leading to reduced PA accumulation.Overall, we demonstrate that a novel allele of P, Psd , is responsible for the SD phenotype, and describe the development of new, gene-specific, markers that could be utilized in breeding to resolve an economically important issue for bean producers.
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Affiliation(s)
- Nishat S. Islam
- London Research and Development CentreAgriculture and Agri‐Food CanadaLondonONCanada
- Department of BiologyUniversity of Western OntarioLondonONCanada
| | - Kirstin E. Bett
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSKCanada
| | - K. Peter Pauls
- Department of Plant AgricultureUniversity of GuelphGuelphONCanada
| | - Frédéric Marsolais
- London Research and Development CentreAgriculture and Agri‐Food CanadaLondonONCanada
- Department of BiologyUniversity of Western OntarioLondonONCanada
| | - Sangeeta Dhaubhadel
- London Research and Development CentreAgriculture and Agri‐Food CanadaLondonONCanada
- Department of BiologyUniversity of Western OntarioLondonONCanada
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Zhao Y, Dong W, Wang K, Zhang B, Allan AC, Lin-Wang K, Chen K, Xu C. Differential Sensitivity of Fruit Pigmentation to Ultraviolet Light between Two Peach Cultivars. FRONTIERS IN PLANT SCIENCE 2017; 8:1552. [PMID: 28943881 PMCID: PMC5596067 DOI: 10.3389/fpls.2017.01552] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/24/2017] [Indexed: 05/23/2023]
Abstract
Anthocyanins provide nutritional benefits and are responsible for red coloration in many fruits. Light affects anthocyanin biosynthesis in peach (Prunus persica). However, some cultivars show differential sensitivity to light. In the present study, 'Hujingmilu (HJ),' a naturally deeply colored cultivar, and 'Yulu (YL),' showing low pigmentation, were used to study the mechanism underlying UV-light-induced anthocyanin biosynthesis. Both UVA and UVB induced fruit pigmentation of 'HJ,' but 'YL' was only sensitive to UVB. Transcriptomic analyses showed over 5000 genes were differentially expressed by pairwise comparisons of RNA libraries isolated from tissue of each cultivar treated with darkness, UVA and UVB. Twenty-three genes related to anthocyanin biosynthesis were identified from the transcriptome data, which were coordinately up-regulated during accumulation of anthocyanins, and down-regulated in the dark. Altered expression of several light receptors, as well as CONSTITUTIVE PHOTOMORPHOGENIC10 (COP10) and ELONGATED HYPOCOTYL 5 homolog (HYH), and a specific anthocyanin transporter glutathione S-transferase (GST), in 'YL' fruit appears to be responsible for the insensitivity to UVA of this cultivar. Expression profiles of several transcription factors of the families MYB, bHLH, bZIP and NAC were highly correlated with those of the anthocyanin biosynthesis genes. The study provides a valuable overview of the underlying molecular mechanisms of UV-light induced anthocyanin response using peach cultivars with differing light sensitivities.
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Affiliation(s)
- Yun Zhao
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang UniversityHangzhou, China
| | - Weiqi Dong
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang UniversityHangzhou, China
| | - Ke Wang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang UniversityHangzhou, China
| | - Bo Zhang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang UniversityHangzhou, China
| | - Andrew C. Allan
- Plant and Food ResearchAuckland, New Zealand
- School of Biological Sciences, University of AucklandAuckland, New Zealand
| | | | - Kunsong Chen
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang UniversityHangzhou, China
| | - Changjie Xu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang UniversityHangzhou, China
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5
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Kim J, Lee HJ, Jung YJ, Kang KK, Tyagi W, Kovach M, Sweeney M, McCouch S, Cho YG. Functional properties of an alternative, tissue-specific promoter for rice NADPH-dependent dihydroflavonol reductase. PLoS One 2017; 12:e0183722. [PMID: 28841686 PMCID: PMC5571921 DOI: 10.1371/journal.pone.0183722] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 08/09/2017] [Indexed: 11/23/2022] Open
Abstract
NADPH-dependent dihydroflavonol reductase (DFR) plays an important role in both anthocyanin biosynthesis and proanthocyanidin synthesis in plants. A specific and quantitative RT-PCR assay for transcription from the DFR promoter detected high expression with limited variability in rice tissues. A 440 bp minimal promoter region was identified by transfection of β-glucuronidase (GUS) reporter constructs into Jeokjinju variety. Alignment of the region with orthologous promoters revealed three conserved segments containing both bHLH (-386 to -381) and Myb (-368 to -362) binding sites. Transfection of β-glucuronidase constructs with targeted point mutations in the minimal promoter defined two sites important for promoter function to the transcription factor binding consensus sequences. The expression study showed that the bHLH binding domain (-386 to -381) is essential for DFR expression, and that a Myb binding domain (-368 to -362) is also required for full expression of the DFR gene, while the two bHLH binding domains (-104 to -99 and -27 to -22) nearest to the transcriptional start site are not necessary for DFR expression.
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Affiliation(s)
- Joonki Kim
- Department of Crop Science, Chungbuk National University, Cheongju, Korea
| | - Hye-Jung Lee
- Department of Crop Science, Chungbuk National University, Cheongju, Korea
| | - Yu-Jin Jung
- Department of Horticultural Life Science, Hankyong National University, Ansung, Korea
| | - Kwon-Kyoo Kang
- Department of Horticultural Life Science, Hankyong National University, Ansung, Korea
| | - Wricha Tyagi
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Michael Kovach
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Megan Sweeney
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Susan McCouch
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail: (SRM); (YGC)
| | - Yong-Gu Cho
- Department of Crop Science, Chungbuk National University, Cheongju, Korea
- * E-mail: (SRM); (YGC)
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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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Cho JS, Nguyen VP, Jeon HW, Kim MH, Eom SH, Lim YJ, Kim WC, Park EJ, Choi YI, Ko JH. Overexpression of PtrMYB119, a R2R3-MYB transcription factor from Populus trichocarpa, promotes anthocyanin production in hybrid poplar. TREE PHYSIOLOGY 2016; 36:1162-76. [PMID: 27259636 DOI: 10.1093/treephys/tpw046] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 04/26/2016] [Indexed: 05/12/2023]
Abstract
Anthocyanins are a group of colorful and bioactive natural pigments with important physiological and ecological functions in plants. We found an MYB transcription factor (PtrMYB119) from Populus trichocarpa that positively regulates anthocyanin production when expressed under the control of the CaMV 35S promoter in transgenic Arabidopsis Amino acid sequence analysis revealed that PtrMYB119 is highly homologous to Arabidopsis PAP1 (PRODUCTION OF ANTHOCYANIN PIGMENT1), a well-known transcriptional activator of anthocyanin biosynthesis. Independently produced transgenic poplars overexpressing PtrMYB119 or PtrMYB120 (a paralogous gene to PtrMYB119) (i.e., 35S::PtrMYB119 and 35S::PtrMYB120, respectively) showed elevated accumulation of anthocyanins in the whole plants, including leaf, stem and even root tissues. Using a reverse-phase high-performance liquid chromatography, we confirmed that the majority of the accumulated anthocyanin in our transgenic poplar is cyanidin-3-O-glucoside. Gene expression analyses revealed that most of the genes involved in the anthocyanin biosynthetic pathway were highly upregulated in 35S::PtrMYB119 poplars compared with the nontransformed control poplar. Among these genes, expression of PtrCHS1 (Chalcone Synthase1) and PtrANS2 (Anthocyanin Synthase2), which catalyze the initial and last steps of anthocyanin biosynthesis, respectively, was upregulated by up to 350-fold. Subsequent transient activation assays confirmed that PtrMYB119 activated the transcription of both PtrCHS1 and PtrANS2 Interestingly, expression of MYB182, a repressor of both anthocyanin and proanthocyanidin (PA) biosynthesis, was largely suppressed in 35S::PtrMYB119 poplars, while expression of MYB134, an activator of PA biosynthesis, was not changed significantly. More interestingly, high-level accumulation of anthocyanins in 35S::PtrMYB119 poplars did not have an adverse effect on plant growth. Taken together, our results demonstrate that PtrMYB119 and PtrMYB120 function as transcriptional activators of anthocyanin accumulation in both Arabidopsis and poplar.
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Affiliation(s)
- Jin-Seong Cho
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 446-701, Yongin 17104, Republic of Korea Division of Forest Biotechnology, Korea Forest Research Institute, Suwon 16631, Republic of Korea
| | - Van Phap Nguyen
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 446-701, Yongin 17104, Republic of Korea
| | - Hyung-Woo Jeon
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 446-701, Yongin 17104, Republic of Korea
| | - Min-Ha Kim
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 446-701, Yongin 17104, Republic of Korea
| | - Seok Hyun Eom
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - You Jin Lim
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Won-Chan Kim
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Eung-Jun Park
- Division of Forest Biotechnology, Korea Forest Research Institute, Suwon 16631, Republic of Korea
| | - Young-Im Choi
- Division of Forest Biotechnology, Korea Forest Research Institute, Suwon 16631, Republic of Korea
| | - Jae-Heung Ko
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 446-701, Yongin 17104, Republic of Korea
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Zhu Z, Wang H, Wang Y, Guan S, Wang F, Tang J, Zhang R, Xie L, Lu Y. Characterization of the cis elements in the proximal promoter regions of the anthocyanin pathway genes reveals a common regulatory logic that governs pathway regulation. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3775-89. [PMID: 25911741 PMCID: PMC4473980 DOI: 10.1093/jxb/erv173] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Cellular activities such as compound synthesis often require the transcriptional activation of an entire pathway; however, the molecular mechanisms underlying pathway activation have rarely been explained. Here, the cis regulatory architecture of the anthocyanin pathway genes targeted by the transcription factor (TF) complex including MYB, bHLH, and WDR was systematically analysed in one species and the findings extended to others. In Ipomoea purpurea, the IpMYB1-IpbHLH2-IpWDR1 (IpMBW) complex was found to be orthologous to the PAP1-GL3-TTG1 (AtPGT) complex of Arabidopsis thaliana, and interacted with a 7-bp MYB-recognizing element (MRE) and a 6-bp bHLH-recognizing element (BRE) at the proximal promoter region of the pathway genes. There was little transcription of the gene in the absence of the MRE or BRE. The cis elements identified experimentally converged on two syntaxes, ANCNNCC for MREs and CACN(A/C/T)(G/T) for BREs, and our bioinformatic analysis showed that these were present within anthocyanin gene promoters in at least 35 species, including both gymnosperms and angiosperms. For the anthocyanin pathway, IpMBW and AtPGT recognized the interspecific promoters of both early and later genes. In A. thaliana, the seed-specific TF complex (TT2, TT8, and TTG1) may regulate all the anthocyanin pathway genes, in addition to the proanthocyanidin-specific BAN. When multiple TF complexes in the anthocyanin pathway were compared, the cis architecture played a role larger than the TF complex in determining the variation in promoter activity. Collectively, a cis logic common to the pathway gene promoters was found, and this logic is essential for the trans factors to regulate the pathway.
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Affiliation(s)
- Zhixin Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailong Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiting Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan Guan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China
| | - Fang Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingyu Tang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruijuan Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lulu Xie
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingqing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
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Lai Y, Li H, Yamagishi M. A review of target gene specificity of flavonoid R2R3-MYB transcription factors and a discussion of factors contributing to the target gene selectivity. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s11515-013-1281-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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10
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Wang H, Guan S, Zhu Z, Wang Y, Lu Y. A valid strategy for precise identifications of transcription factor binding sites in combinatorial regulation using bioinformatic and experimental approaches. PLANT METHODS 2013; 9:34. [PMID: 23971995 PMCID: PMC3847620 DOI: 10.1186/1746-4811-9-34] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 08/13/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Transcription factor (TF) binding sites (cis element) play a central role in gene regulation, and eukaryotic organisms frequently adapt a combinatorial regulation to render sophisticated local gene expression patterns. Knowing the precise cis element on a distal promoter is a prerequisite for studying a typical transcription process; however, identifications of cis elements have lagged behind those of their associated trans acting TFs due to technical difficulties. Consequently, gene regulations via combinatorial TFs, as widely observed across biological processes, have remained vague in many cases. RESULTS We present here a valid strategy for identifying cis elements in combinatorial TF regulations. It consists of bioinformatic searches of available databases to generate candidate cis elements and tests of the candidates using improved experimental assays. Taking the MYB and the bHLH that collaboratively regulate the anthocyanin pathway genes as examples, we demonstrate how candidate cis motifs for the TFs are found on multi-specific promoters of chalcone synthase (CHS) genes, and how to experimentally test the candidate sites by designing DNA fragments hosting the candidate motifs based on a known promoter (us1 allele of Ipomoea purpurea CHS-D in our case) and applying site-mutagenesis at the motifs. It was shown that TF-DNA interactions could be unambiguously analyzed by assays of electrophoretic mobility shift (EMSA) and dual-luciferase transient expressions, and the resulting evidence precisely delineated a cis element. The cis element for R2R3 MYBs including Ipomoea MYB1 and Magnolia MYB1, for instance, was found to be ANCNACC, and that for bHLHs (exemplified by Ipomoea bHLH2 and petunia AN1) was CACNNG. A re-analysis was conducted on previously reported promoter segments recognized by maize C1 and apple MYB10, which indicated that cis elements similar to ANCNACC were indeed present on these segments, and tested positive for their bindings to Ipomoea MYB1. CONCLUSION Identification of cis elements in combinatorial regulation is now feasible with the strategy outlined. The working pipeline integrates the existing databases with experimental techniques, providing an open framework for precisely identifying cis elements. This strategy is widely applicable to various biological systems, and may enhance future analyses on gene regulation.
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Affiliation(s)
- Hailong Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan Guan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China
| | - Zhixin Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China
| | - Yingqing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China
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11
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Xu W, Grain D, Le Gourrierec J, Harscoët E, Berger A, Jauvion V, Scagnelli A, Berger N, Bidzinski P, Kelemen Z, Salsac F, Baudry A, Routaboul JM, Lepiniec L, Dubos C. Regulation of flavonoid biosynthesis involves an unexpected complex transcriptional regulation of TT8 expression, in Arabidopsis. THE NEW PHYTOLOGIST 2013; 198:59-70. [PMID: 23398515 DOI: 10.1111/nph.12142] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/11/2012] [Indexed: 05/20/2023]
Abstract
TT8/bHLH042 is a key regulator of anthocyanins and proanthocyanidins (PAs) biosynthesis in Arabidopsis thaliana. TT8 transcriptional activity has been studied extensively, and relies on its ability to form, with several R2R3-MYB and TTG1 (WD-Repeat protein), different MYB-bHLH-WDR (MBW) protein complexes. By contrast, little is known on how TT8 expression is itself regulated. Transcriptional regulation of TT8 expression was studied using molecular, genetic and biochemical approaches. Functional dissection of the TT8 promoter revealed its modular structure. Two modules were found to specifically drive TT8 promoter activity in PA- and anthocyanin-accumulating cells, by differentially integrating the signals issued from different regulators, in a spatio-temporal manner. Interestingly, this regulation involves at least six different MBW complexes, and an unpredicted positive feedback regulatory loop between TT8 and TTG2. Moreover, the results suggest that some putative new regulators remain to be discovered. Finally, specific cis-regulatory elements through which TT8 expression is regulated were identified and characterized. Together, these results provide a molecular model consistent with the specific and highly regulated expression of TT8. They shed new light into the transcriptional regulation of flavonoid biosynthesis and provide new clues and tools for further investigation in Arabidopsis and other plant species.
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Affiliation(s)
- Wenjia Xu
- INRA, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
| | - Damaris Grain
- INRA, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
| | - José Le Gourrierec
- INRA, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
| | - Erwana Harscoët
- INRA, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
| | - Adeline Berger
- INRA, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
| | - Vincent Jauvion
- INRA, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
| | - Aurélie Scagnelli
- INRA, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
| | - Nathalie Berger
- INRA, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
| | - Przemyslaw Bidzinski
- INRA, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
| | - Zsolt Kelemen
- INRA, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
| | - Fabien Salsac
- INRA, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
| | - Antoine Baudry
- INRA, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
| | - Jean-Marc Routaboul
- INRA, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
| | - Loïc Lepiniec
- INRA, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
| | - Christian Dubos
- INRA, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
- AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, UMR1318, RD10, F-78026, Versailles, France
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12
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Regulatory switch enforced by basic helix-loop-helix and ACT-domain mediated dimerizations of the maize transcription factor R. Proc Natl Acad Sci U S A 2012; 109:E2091-7. [PMID: 22778424 DOI: 10.1073/pnas.1205513109] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The maize R2R3-MYB regulator C1 cooperates with the basic helix-loop-helix (bHLH) factor R to activate the expression of anthocyanin biosynthetic genes coordinately. As is the case for other bHLH factors, R harbors several protein-protein interaction domains. Here we show that not the classical but rather a briefly extended R bHLH region forms homodimers that bind canonical G-box DNA motifs. This bHLH DNA-binding activity is abolished if the C-terminal ACT (aspartokinase, chorismate, and TyrA) domain is licensed to homodimerize. Then the bHLH remains in the monomeric form, allowing it to interact with R-interacting factor 1 (RIF1). In this configuration, the R-RIF1 complex is recruited to the promoters of a subset of anthocyanin biosynthetic genes, such as A1, through the interaction with its MYB partner C1. If, however, the ACT domain remains monomeric, the bHLH region dimerizes and binds to G-boxes present in several anthocyanin genes, such as Bz1. Our results provide a mechanism by which a dimerization domain in a bHLH factor behaves as a switch that permits distinct configurations of a regulatory complex to be tethered to different promoters. Such a combinatorial gene regulatory framework provides one mechanism by which genes lacking obviously conserved cis-regulatory elements are regulated coordinately.
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13
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Morohashi K, Casas MI, Ferreyra LF, Mejía-Guerra MK, Pourcel L, Yilmaz A, Feller A, Carvalho B, Emiliani J, Rodriguez E, Pellegrinet S, McMullen M, Casati P, Grotewold E. A genome-wide regulatory framework identifies maize pericarp color1 controlled genes. THE PLANT CELL 2012; 24:2745-64. [PMID: 22822204 PMCID: PMC3426112 DOI: 10.1105/tpc.112.098004] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Revised: 06/10/2012] [Accepted: 07/02/2012] [Indexed: 05/18/2023]
Abstract
Pericarp Color1 (P1) encodes an R2R3-MYB transcription factor responsible for the accumulation of insecticidal flavones in maize (Zea mays) silks and red phlobaphene pigments in pericarps and other floral tissues, which makes P1 an important visual marker. Using genome-wide expression analyses (RNA sequencing) in pericarps and silks of plants with contrasting P1 alleles combined with chromatin immunoprecipitation coupled with high-throughput sequencing, we show here that the regulatory functions of P1 are much broader than the activation of genes corresponding to enzymes in a branch of flavonoid biosynthesis. P1 modulates the expression of several thousand genes, and ∼1500 of them were identified as putative direct targets of P1. Among them, we identified F2H1, corresponding to a P450 enzyme that converts naringenin into 2-hydroxynaringenin, a key branch point in the P1-controlled pathway and the first step in the formation of insecticidal C-glycosyl flavones. Unexpectedly, the binding of P1 to gene regulatory regions can result in both gene activation and repression. Our results indicate that P1 is the major regulator for a set of genes involved in flavonoid biosynthesis and a minor modulator of the expression of a much larger gene set that includes genes involved in primary metabolism and production of other specialized compounds.
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Affiliation(s)
- Kengo Morohashi
- Department of Molecular Genetics, The Ohio State
University, Columbus, Ohio 43210
- Center for Applied Plant Sciences, The Ohio State
University, Columbus, Ohio 43210
| | - María Isabel Casas
- Center for Applied Plant Sciences, The Ohio State
University, Columbus, Ohio 43210
- Molecular, Cellular, and Developmental Biology
Program, The Ohio State University, Columbus, Ohio 43210
| | - Lorena Falcone Ferreyra
- Centro de Estudios Fotosintéticos y
Bioquímicos, Universidad Nacional de Rosario, Santa Fe S2002LRK,
Argentina
| | - María Katherine Mejía-Guerra
- Center for Applied Plant Sciences, The Ohio State
University, Columbus, Ohio 43210
- Molecular, Cellular, and Developmental Biology
Program, The Ohio State University, Columbus, Ohio 43210
| | - Lucille Pourcel
- Department of Botany and Plant Biology, University of
Geneva, Geneva 1211, Switzerland
| | - Alper Yilmaz
- Center for Applied Plant Sciences, The Ohio State
University, Columbus, Ohio 43210
| | - Antje Feller
- Department of Food Quality and Nutrition, Instituto
Agrario San Michele all’Adige, 38010 San Michele all’Adige,
Italy
| | - Bruna Carvalho
- Center for Applied Plant Sciences, The Ohio State
University, Columbus, Ohio 43210
| | - Julia Emiliani
- Centro de Estudios Fotosintéticos y
Bioquímicos, Universidad Nacional de Rosario, Santa Fe S2002LRK,
Argentina
| | - Eduardo Rodriguez
- Instituto de Biología Molecular y Celular de
Rosario, Rosario, Santa Fe S2002LRK, Argentina
| | | | - Michael McMullen
- Plant Genetics Research Unit, U.S. Department of
Agriculture–Agricultural Research Service, University of Missouri,
Columbia, Missouri 65211
- Division of Plant Sciences, University of Missouri,
Columbia, Missouri 65211
| | - Paula Casati
- Centro de Estudios Fotosintéticos y
Bioquímicos, Universidad Nacional de Rosario, Santa Fe S2002LRK,
Argentina
| | - Erich Grotewold
- Department of Molecular Genetics, The Ohio State
University, Columbus, Ohio 43210
- Center for Applied Plant Sciences, The Ohio State
University, Columbus, Ohio 43210
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14
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Abeynayake SW, Panter S, Chapman R, Webster T, Rochfort S, Mouradov A, Spangenberg G. Biosynthesis of proanthocyanidins in white clover flowers: cross talk within the flavonoid pathway. PLANT PHYSIOLOGY 2012; 158:666-78. [PMID: 22167119 PMCID: PMC3271758 DOI: 10.1104/pp.111.189258] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 12/09/2011] [Indexed: 05/22/2023]
Abstract
Proanthocyanidins and anthocyanins are produced by closely related branches of the flavonoid pathway and utilize the same metabolic intermediates. Previous studies have shown a flexible mechanism of flux diversion at the branch-point between the anthocyanin and proanthocyanidin pathways, but the molecular basis for this mechanism is poorly understood. Floral tissues in white clover plants (Trifolium repens) produce both proanthocyanidins and anthocyanins. This makes white clover amenable to studies of proanthocyanidin and anthocyanin biosynthesis and possible interactions within the flavonoid pathway. Results of this study show that the anthocyanin and proanthocyanidin pathways are spatially colocalized within epidermal cells of petals and temporally overlap in partially open flowers. A correlation between spatiotemporal patterns of anthocyanin and proanthocyanidin biosynthesis with expression profiles of putative flavonoid-related genes indicates that these pathways may recruit different isoforms of flavonoid biosynthetic enzymes. Furthermore, in transgenic white clover plants with down-regulated expression of the anthocyanidin reductase gene, levels of flavan 3-ols, anthocyanins, and flavonol glycosides and the expression levels of a range of genes encoding putative flavonoid biosynthetic enzymes and transcription factors were altered. This is consistent with the hypothesis that flux through the flavonoid pathway may be at least partially regulated by the availability of intermediates.
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15
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Borg M, Brownfield L, Khatab H, Sidorova A, Lingaya M, Twell D. The R2R3 MYB transcription factor DUO1 activates a male germline-specific regulon essential for sperm cell differentiation in Arabidopsis. THE PLANT CELL 2011; 23:534-49. [PMID: 21285328 PMCID: PMC3077786 DOI: 10.1105/tpc.110.081059] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 01/07/2011] [Accepted: 01/12/2011] [Indexed: 05/18/2023]
Abstract
The male germline in flowering plants arises through asymmetric division of a haploid microspore. The resulting germ cell undergoes mitotic division and specialization to produce the two sperm cells required for double fertilization. The male germline-specific R2R3 MYB transcription factor DUO1 POLLEN1 (DUO1) plays an essential role in sperm cell specification by activating a germline-specific differentiation program. Here, we show that ectopic expression of DUO1 upregulates a significant number (~63) of germline-specific or enriched genes, including those required for fertilization. We validated 14 previously unknown DUO1 target genes by demonstrating DUO1-dependent promoter activity in the male germline. DUO1 is shown to directly regulate its target promoters through binding to canonical MYB sites, suggesting that the DUO1 target genes validated thus far are likely to be direct targets. This work advances knowledge of the DUO1 regulon that encompasses genes with a range of cellular functions, including transcription, protein fate, signaling, and transport. Thus, the DUO1 regulon has a major role in shaping the germline transcriptome and functions to commit progenitor germ cells to sperm cell differentiation.
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Affiliation(s)
- Michael Borg
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Lynette Brownfield
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
- Department of Biology and Zurich-Basel Plant Science Centre, Swiss Federal Institute of Technology, CH-8092 Zurich, Switzerland
| | - Hoda Khatab
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Anna Sidorova
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Melanie Lingaya
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - David Twell
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
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16
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Abdeen A, Miki B. The pleiotropic effects of the bar gene and glufosinate on the Arabidopsis transcriptome. PLANT BIOTECHNOLOGY JOURNAL 2009. [PMID: 19222808 DOI: 10.1111/j.1467-7652.2008.00398.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The Arabidopsis transcriptome was studied using the Affymetrix Arabidopsis ATH1 GeneChip in wild-type plants and glufosinate-tolerant transgenic plants expressing the bialaphos resistance (bar) gene. Pleiotropic effects were specifically generated in the transcriptomes of transgenic plants by both the bar gene and glufosinate treatments. In the absence of glufosinate, four genes were differentially expressed in the transgenic lines and another 80 genes were differentially expressed in the presence of glufosinate, 29 of which were specific to transgenic plants. In contrast, the number of differentially expressed genes specific to wild-type plants was 194 during the early response at 6 h of glufosinate treatment, and increased to 3711 during the late response at 48 h. Although the wild-type plants undergo extensive transcriptional reprofiling in response to herbicide-induced stress and, finally, plant death, the transgenic plants appear to activate other detoxification processes to offset the toxic effects of the residual herbicide or its derivatives. This study provides the first description of the pleiotropic effects of the bar gene and glufosinate on the plant transcriptome.
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Affiliation(s)
- Ashraf Abdeen
- Research Branch, Agriculture and Agri-Food Canada, Ottawa, ON, Canada K1A 0C6
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17
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Abdeen A, Miki B. The pleiotropic effects of the bar gene and glufosinate on the Arabidopsis transcriptome. PLANT BIOTECHNOLOGY JOURNAL 2009; 7:266-82. [PMID: 19222808 DOI: 10.1111/j.1467-7652.2009.00398.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The Arabidopsis transcriptome was studied using the Affymetrix Arabidopsis ATH1 GeneChip in wild-type plants and glufosinate-tolerant transgenic plants expressing the bialaphos resistance (bar) gene. Pleiotropic effects were specifically generated in the transcriptomes of transgenic plants by both the bar gene and glufosinate treatments. In the absence of glufosinate, four genes were differentially expressed in the transgenic lines and another 80 genes were differentially expressed in the presence of glufosinate, 29 of which were specific to transgenic plants. In contrast, the number of differentially expressed genes specific to wild-type plants was 194 during the early response at 6 h of glufosinate treatment, and increased to 3711 during the late response at 48 h. Although the wild-type plants undergo extensive transcriptional reprofiling in response to herbicide-induced stress and, finally, plant death, the transgenic plants appear to activate other detoxification processes to offset the toxic effects of the residual herbicide or its derivatives. This study provides the first description of the pleiotropic effects of the bar gene and glufosinate on the plant transcriptome.
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Affiliation(s)
- Ashraf Abdeen
- Research Branch, Agriculture and Agri-Food Canada, Ottawa, ON, Canada K1A 0C6
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18
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Punwani JA, Rabiger DS, Lloyd A, Drews GN. The MYB98 subcircuit of the synergid gene regulatory network includes genes directly and indirectly regulated by MYB98. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 55:406-14. [PMID: 18410484 DOI: 10.1111/j.1365-313x.2008.03514.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The female gametophyte contains two synergid cells that play a role in many steps of the angiosperm reproductive process, including pollen tube guidance. At their micropylar poles, the synergid cells have a thickened and elaborated cell wall: the filiform apparatus that is thought to play a role in the secretion of the pollen tube attractant(s). MYB98 regulates an important subcircuit of the synergid gene regulatory network (GRN) that functions to activate the expression of genes required for pollen tube guidance and filiform apparatus formation. The MYB98 subcircuit comprises at least 83 downstream genes, including 48 genes within four gene families (CRP810, CRP3700, CRP3730 and CRP3740) that encode Cys-rich proteins. We show that the 11 CRP3700 genes, which include DD11 and DD18, are regulated by a common cis-element, GTAACNT, and that a multimer of this sequence confers MYB98-dependent synergid expression. The GTAACNT element contains the MYB98-binding site identified in vitro, suggesting that the 11 CRP3700 genes are direct targets of MYB98. We also show that five of the CRP810 genes, which include DD2, lack a functional GTAACNT element, suggesting that they are not directly regulated by MYB98. In addition, we show that the five CRP810 genes are regulated by the cis-element AACGT, and that a multimer of this sequence confers synergid expression. Together, these results suggest that the MYB98 branch of the synergid GRN is multi-tiered and, therefore, contains at least one additional downstream transcription factor.
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Affiliation(s)
- Jayson A Punwani
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112-0840, USA
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19
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Punwani JA, Rabiger DS, Drews GN. MYB98 positively regulates a battery of synergid-expressed genes encoding filiform apparatus localized proteins. THE PLANT CELL 2007; 19:2557-68. [PMID: 17693534 PMCID: PMC2002610 DOI: 10.1105/tpc.107.052076] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The synergid cells within the female gametophyte are essential for reproduction in angiosperms. MYB98 encodes an R2R3-MYB protein required for pollen tube guidance and filiform apparatus formation by the synergid cells. To test the predicted function of MYB98 as a transcriptional regulator, we determined its subcellular localization and examined its DNA binding properties. We show that MYB98 binds to a specific DNA sequence (TAAC) and that a MYB98-green fluorescent protein fusion protein localizes to the nucleus, consistent with a role in transcriptional regulation. To identify genes regulated by MYB98, we tested previously identified synergid-expressed genes for reduced expression in myb98 female gametophytes and identified 16 such genes. We dissected the promoter of one of the downstream genes, DD11, and show that it contains a MYB98 binding site required for synergid expression, suggesting that DD11 is regulated directly by MYB98. To gain insight into the functions of the downstream genes, we chose five genes and determined the subcellular localization of the encoded proteins. We show that these five proteins are secreted into the filiform apparatus, suggesting that they play a role in either the formation or the function of this unique structure. Together, these data suggest that MYB98 functions as a transcriptional regulator in the synergid cells and activates the expression of genes required for pollen tube guidance and filiform apparatus formation.
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Affiliation(s)
- Jayson A Punwani
- Department of Biology, University of Utah, Salt Lake City, Utah 84112-0840, USA
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20
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Wu XR, Chen Z, Shende A, Dooner HK, Folk WR. Visualizing bz1 missense suppression in Zea mays: an assay for monocot tRNA expression and utilization. PLANT MOLECULAR BIOLOGY 2006; 61:795-8. [PMID: 16897493 DOI: 10.1007/s11103-006-0050-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2006] [Accepted: 03/20/2006] [Indexed: 05/11/2023]
Abstract
Bombardment of a highly expressed dicot tRNA(ala)(GAC) gene into Zea mays bz-E2 or bz-E5 coleoptiles causes suppression of an Ala(458 )-->Val missense mutation, visualized by the development of anthocyanin pigment. Missense suppression is blocked by mutation of tRNA(ala)(GAC) at a site that prevents aminoacylation by the dicot alanyl-tRNA synthetase, indicating that features identified for expression and utilization of dicot tRNAs also function in monocots. This assay of the expression and utilization of tRNA(ala)(GAC) also can be used to study a variety of tRNAs and their genes, most of which can be relatively easily altered to be charged by alanyl tRNA synthetase.
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Affiliation(s)
- Xing Rong Wu
- Department of Biochemistry, University of Missouri-Columbia, 117 Schweitzer Hall, Columbia, MO, 65211, USA
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21
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Boter M, Ruíz-Rivero O, Abdeen A, Prat S. Conserved MYC transcription factors play a key role in jasmonate signaling both in tomato and Arabidopsis. Genes Dev 2004; 18:1577-91. [PMID: 15231736 PMCID: PMC443520 DOI: 10.1101/gad.297704] [Citation(s) in RCA: 416] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Jasmonates (JA) are important regulators of plant defense responses that activate expression of many wound-induced genes including the tomato proteinase inhibitor II (pin2) and leucine aminopeptidase (LAP) genes. Elements required for JA induction of the LAP gene are all present in the -317 to -78 proximal promoter region. Using yeast one-hybrid screening, we have identified the bHLH-leu zipper JAMYC2 and JAMYC10 proteins, specifically recognizing a T/G-box AACGTG motif in this promoter fragment. Mutation of the G-box element decreases JA-responsive LAP promoter expression. Expression of JAMYC2 and JAMYC10 is induced by JA, with a kinetics that precedes that of the LAP or pin2 transcripts. JAMYC overexpression enhanced JA-induced expression of these defense genes in potato, but did not result in constitutive transcript accumulation. Using footprinting assays, an additional protected element was identified, located directly adjacent to the T/G-box motif. Mutation of this element abolishes JA response, showing that recognition of this duplicated element is also required for gene expression. Knockout mutants in the AtMYC2 homolog gene of Arabidopsis are insensitive to JA and exhibit a decreased activation of the JA-responsive genes AtVSP and JR1. Activation of the PDF1.2 and b-CHI, ethylene/JA-responsive genes, is, however, increased in these mutants. These results show that the JAMYC/AtMYC2 transcription factors function as members of a MYC-based regulatory system conserved in dicotyledonous plants with a key role in JA-induced defense gene activation.
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Affiliation(s)
- Marta Boter
- Departament de Genètica Molecular, Institut de Biologia Molecular de Barcelona, CID-CSIC, 08034 Barcelona, Spain
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22
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Jeong S, Goto-Yamamoto N, Kobayashi S, Esaka M. Effects of plant hormones and shading on the accumulation of anthocyanins and the expression of anthocyanin biosynthetic genes in grape berry skins. PLANT SCIENCE 2004; 167:247-252. [PMID: 0 DOI: 10.1016/j.plantsci.2004.03.021] [Citation(s) in RCA: 232] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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23
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Goodman CD, Casati P, Walbot V. A multidrug resistance-associated protein involved in anthocyanin transport in Zea mays. THE PLANT CELL 2004; 16:1812-26. [PMID: 15208386 PMCID: PMC514163 DOI: 10.1105/tpc.022574] [Citation(s) in RCA: 268] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Anthocyanin biosynthesis is one of the most thoroughly studied enzymatic pathways in biology, but little is known about the molecular mechanisms of its final stage: the transport of the anthocyanin pigment into the vacuole. We have identified a multidrug resistance-associated protein (MRP), ZmMrp3, that is required for this transport process in maize (Zea mays). ZmMrp3 expression is controlled by the regulators of anthocyanin biosynthesis and mirrors the expression of other anthocyanin structural genes. Localization of ZmMRP3 in vivo shows its presence in the tonoplast, the site at which anthocyanin transport occurs. Mutants generated using antisense constructs have a distinct pigmentation phenotype in the adult plant that results from a mislocalization of the pigment as well as significant reduction in anthocyanin content, with no alteration in the anthocyanin species produced. Surprisingly, mutant plants did not show a phenotype in the aleurone. This appears to reflect the presence of a second, highly homologous gene, ZmMrp4, that is also coregulated with the anthocyanin pathway but is expressed exclusively in aleurone tissue. This description of a plant MRP with a role in the transport of a known endogenous substrate provides a new model system for examining the biological and biochemical mechanisms involved in the MRP-mediated transport of plant secondary metabolites.
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Debeaujon I, Nesi N, Perez P, Devic M, Grandjean O, Caboche M, Lepiniec L. Proanthocyanidin-accumulating cells in Arabidopsis testa: regulation of differentiation and role in seed development. THE PLANT CELL 2003. [PMID: 14555692 DOI: 10.1105/tpc.014043.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Anthocyanidin reductase encoded by the BANYULS (BAN) gene is the core enzyme in proanthocyanidin (PA) biosynthesis. Here, we analyzed the developmental mechanisms that regulate the spatiotemporal expression of BAN in the developing Arabidopsis seed coat. PA-accumulating cells were localized histochemically in the inner integument (seed body and micropyle) and pigment strand (chalaza). BAN promoter activity was detected specifically in these cells. Gain-of-function experiments showed that an 86-bp promoter fragment functioned as an enhancer specific for PA-accumulating cells. Mutations in regulatory genes of PA biosynthesis abolished BAN promoter activity (transparent testa2 [tt2], tt8, and transparent testa glabra1 [ttg1]), modified its spatial pattern (tt1 and tt16), or had no influence (ttg2), thus revealing complex regulatory interactions at several developmental levels. Genetic ablation of PA-accumulating cells targeted by the BAN promoter fused to BARNASE led to the formation of normal plants that produced viable yellow seeds. Importantly, these seeds had no obvious defects in endosperm and embryo development.
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Affiliation(s)
- Isabelle Debeaujon
- Laboratoire de Biologie des Semences, Unité Mixte de Recherche, 204 Institut National de la Recherche Agronomique, Paris-Grignon, 78026 Versailles, France
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25
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Debeaujon I, Nesi N, Perez P, Devic M, Grandjean O, Caboche M, Lepiniec L. Proanthocyanidin-accumulating cells in Arabidopsis testa: regulation of differentiation and role in seed development. THE PLANT CELL 2003; 15:2514-31. [PMID: 14555692 PMCID: PMC280558 DOI: 10.1105/tpc.014043] [Citation(s) in RCA: 272] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Anthocyanidin reductase encoded by the BANYULS (BAN) gene is the core enzyme in proanthocyanidin (PA) biosynthesis. Here, we analyzed the developmental mechanisms that regulate the spatiotemporal expression of BAN in the developing Arabidopsis seed coat. PA-accumulating cells were localized histochemically in the inner integument (seed body and micropyle) and pigment strand (chalaza). BAN promoter activity was detected specifically in these cells. Gain-of-function experiments showed that an 86-bp promoter fragment functioned as an enhancer specific for PA-accumulating cells. Mutations in regulatory genes of PA biosynthesis abolished BAN promoter activity (transparent testa2 [tt2], tt8, and transparent testa glabra1 [ttg1]), modified its spatial pattern (tt1 and tt16), or had no influence (ttg2), thus revealing complex regulatory interactions at several developmental levels. Genetic ablation of PA-accumulating cells targeted by the BAN promoter fused to BARNASE led to the formation of normal plants that produced viable yellow seeds. Importantly, these seeds had no obvious defects in endosperm and embryo development.
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Affiliation(s)
- Isabelle Debeaujon
- Laboratoire de Biologie des Semences, Unité Mixte de Recherche, 204 Institut National de la Recherche Agronomique, Paris-Grignon, 78026 Versailles, France
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26
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Ramsay NA, Walker AR, Mooney M, Gray JC. Two basic-helix-loop-helix genes (MYC-146 and GL3) from Arabidopsis can activate anthocyanin biosynthesis in a white-flowered Matthiola incana mutant. PLANT MOLECULAR BIOLOGY 2003; 52:679-688. [PMID: 12956536 DOI: 10.1023/a:1024852021124] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Basic helix-loop-helix (bHLH) proteins, similar to mammalian Myc transcription factors, regulate the anthocyanin biosynthetic pathway in both monocots and dicots. Two Arabidopsis bHLH genes, GLABRA3 (GL3) and MYC-146, encode proteins that are similar throughout the predicted amino acid sequence to R and DELILA, which regulate anthocyanin production in maize and snapdragon, respectively. Northern blot analysis indicates that MYC-146 is most highly expressed in flower buds and flowers. Expression of a MYC-146 cDNA from the CaMV 35S promoter was unable to complement the anthocyanin deficiency in a ttg1 mutant of Arabidopsis and resulted in no obvious phenotypic change in Columbia plants. However, transient expression of GL3 and MYC-146 upon microprojectile bombardment of petals of a white-flowered mutant of Matthiola incana was able to complement anthocyanin deficiency. The lack of anthocyanin-deficient Arabidopsis mutants mapping to the locations of GL3 and MYC-146 suggests that the two bHLH proteins may be partially redundant and overlap in function.
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MESH Headings
- Amino Acid Sequence
- Anthocyanins/biosynthesis
- Arabidopsis Proteins/genetics
- Basic Helix-Loop-Helix Leucine Zipper Transcription Factors
- Basic Helix-Loop-Helix Transcription Factors
- Blotting, Northern
- Brassicaceae/genetics
- Brassicaceae/metabolism
- Carrier Proteins/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Plant/isolation & purification
- Gene Expression Regulation, Plant
- Genetic Complementation Test
- Helix-Loop-Helix Motifs/genetics
- Molecular Sequence Data
- Mutation
- Phenotype
- Plants, Genetically Modified
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Trans-Activators/genetics
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Affiliation(s)
- Nicola A Ramsay
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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27
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Irani NG, Hernandez JM, Grotewold E. Chapter three Regulation of anthocyanin pigmentation. RECENT ADVANCES IN PHYTOCHEMISTRY 2003. [DOI: 10.1016/s0079-9920(03)80018-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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28
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Vailleau F, Daniel X, Tronchet M, Montillet JL, Triantaphylidès C, Roby D. A R2R3-MYB gene, AtMYB30, acts as a positive regulator of the hypersensitive cell death program in plants in response to pathogen attack. Proc Natl Acad Sci U S A 2002; 99:10179-84. [PMID: 12119395 PMCID: PMC126644 DOI: 10.1073/pnas.152047199] [Citation(s) in RCA: 190] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2002] [Indexed: 02/06/2023] Open
Abstract
Hypersensitive response (HR) is a programmed cell death that is commonly associated with disease resistance in plants. Among the different HR-related early induced genes, the AtMYB30 gene is specifically, rapidly, and transiently expressed during incompatible interactions between Arabidopsis and bacterial pathogens. Its expression was also shown to be deregulated in Arabidopsis mutants affected in the control of cell death initiation. Here, we demonstrate that overexpression in Arabidopsis and tobacco of AtMYB30 (i) accelerates and intensifies the appearance of the HR in response to different avirulent bacterial pathogens, (ii) causes HR-like responses to virulent strains, and (iii) increases resistance against different bacterial pathogens, and a virulent biotrophic fungal pathogen, Cercospora nicotianae. In antisense AtMYB30 Arabidopsis lines, HR cell death is strongly decreased or suppressed in response to avirulent bacterial strains, resistance against different bacterial pathogens decreased, and the expression of HR- and defense-related genes was altered. Taken together, these results strongly suggest that AtMYB30 is a positive regulator of hypersensitive cell death.
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Affiliation(s)
- Fabienne Vailleau
- Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, Unité Mixte de Recherche Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique 215, BP 27, 31326 Castanet-Tolosan Cedex, France
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29
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Memelink J, Kijne JW, van der Heijden R, Verpoorte R. Genetic modification of plant secondary metabolite pathways using transcriptional regulators. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2002; 72:103-25. [PMID: 11729751 DOI: 10.1007/3-540-45302-4_4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Plant secondary metabolism is the source of many natural products with diverse applications, including pharmaceuticals, food colors, dyes and fragrances. Functions in plants include attraction of pollinating insects and protection against pests and pathogens. An important regulatory step in secondary metabolism is transcription of the biosynthetic genes. The aim of this chapter is to discuss results and opportunities concerning modification of secondary metabolism using transcriptional regulators. The transcriptional regulation of two well-studied secondary pathways, the phenylpropanoid pathway and its flavonoid branch, and the terpenoid indole alkaloid biosynthetic pathway, are reviewed. Some examples of successful engineering of these pathways via transcriptional regulators are discussed.
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Affiliation(s)
- J Memelink
- Institute of Molecular Plant Sciences, Clusius Laboratory, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands.
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30
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Casas AM, Kononowicz AK, Bressan RA, Hasegawa PM. Cereal transformation through particle bombardment. PLANT BREEDING REVIEWS 2001; 13:235-64. [PMID: 11543586 DOI: 10.1002/9780470650059.ch7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- A M Casas
- Laboratorio Asociado de Agronomia y Medio Ambiente (DGA-CSIC), Estacion Experimental de Aula Dei, Zaragoza, Spain
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31
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Sakamoto W, Ohmori T, Kageyama K, Miyazaki C, Saito A, Murata M, Noda K, Maekawa M. The Purple leaf (Pl) locus of rice: the Pl(w) allele has a complex organization and includes two genes encoding basic helix-loop-helix proteins involved in anthocyanin biosynthesis. PLANT & CELL PHYSIOLOGY 2001; 42:982-91. [PMID: 11577193 DOI: 10.1093/pcp/pce128] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The Purple leaf (Pl) locus of rice (Oryza sativa L.) affects regulation of anthocyanin biosynthesis in various plant tissues. The tissue-specific patterns of anthocyanin pigmentation, together with the syntenic relationship, indicate that the rice Pl locus may play a role in the anthocyanin pathway similar to the maize R/B loci. We isolated two cDNAs showing significant identity to the basic helix-loop-helix (bHLH) proteins found in the maize R gene family. OSB1 appeared to be allelic to the previously isolated R homologue, Ra1, but showed a striking difference at the C-terminus because of a 2-bp deletion. Characterization of the corresponding genomic region revealed that the sequence identical to a 5'-portion of OSB2 existed approximately 10-kb downstream of the OSB1 coding region. OSB2 lacks a conserved C-terminal domain. Restriction fragment length polymorphism analyses using an F(2) population indicate that both genes co-segregate with the purple leaf phenotype. A transient complementation assay showed that the anthocyanin pathway is inducible by OSB1 or OSB2. These results suggest that the Pl(w) allele may be complex and composed of at least two genes encoding bHLH proteins.
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Affiliation(s)
- W Sakamoto
- Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, 710-0046 Japan.
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Kobayashi S, Ishimaru M, Ding CK, Yakushiji H, Goto N. Comparison of UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT) gene sequences between white grapes (Vitis vinifera) and their sports with red skin. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2001; 160:543-550. [PMID: 11166442 DOI: 10.1016/s0168-9452(00)00425-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The expression of the UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT) gene has been shown to be critical for anthocyanin biosynthesis in the grape berry. Using white cultivars and bud sports with red skin, we examined the expression of seven anthocyanin biosynthetic genes including the UFGT gene and compared the coding/promoter sequences of the UFGT gene. Northern blot analysis showed that the seven anthocyanin biosynthetic genes were expressed coordinately at higher levels in the red-skin sports than in the white-skin progenitors of the sports. It was especially notable that UFGT gene expression was detected only in the red-skin sports and Kyoho. However, there were no differences in either coding or promoter sequences between Italia (Vitis vinifera) and its red-skin sport Ruby Okuyama, or between Muscat of Alexandria (V. vinifera) and the red-skin sport Flame Muscat. From these findings, the phenotypic change from white to red in the sports is thought to be the result of a mutation in a regulatory gene controlling the expression of UFGT.
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Affiliation(s)
- S Kobayashi
- Persimmon and Grape Research Center, National Institute of Fruit Tree Science, Akitsu, 729-2494, Hiroshima, Japan
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White CN, Rivin CJ. Gibberellins and seed development in maize. II. Gibberellin synthesis inhibition enhances abscisic acid signaling in cultured embryos. PLANT PHYSIOLOGY 2000; 122:1089-97. [PMID: 10759504 PMCID: PMC58943 DOI: 10.1104/pp.122.4.1089] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/1999] [Accepted: 12/23/1999] [Indexed: 05/18/2023]
Abstract
Abscisic acid (ABA) is required for seed maturation in maize (Zea mays L.) and other plants. Gibberellins (GAs) are also present in developing maize embryos, and mutual antagonism of GAs and ABA appears to govern the choice between precocious germination or quiescence and maturation. Exogenous ABA can also induce quiescence and maturation in immature maize embryos in culture. To examine the role of GAs versus ABA in regulating maize embryo maturation, the effects of modulating GA levels were compared with those of ABA in embryos cultured at successive stages of development. The effects of GA synthesis inhibition or exogenous GA application differed markedly in embryos at different stages of development, indicating changes in both endogenous GA levels and in the capacity for GA synthesis as embryogenesis and maturation progress. In immature embryos, the inhibition of GA synthesis mimicked the effects of exogenous ABA, as shown by the suppression of germination, the acquisition of anthocyanin pigments, and the accumulation of a variety of maturation-phase mRNAs. We suggest that GA antagonizes ABA signaling in developing maize embryos, and that the changing hormone balance provides temporal control over the maturation phase.
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Affiliation(s)
- C N White
- Department of Botany and Plant Pathology, Center for Gene Research and Biotechnology, Oregon State University, Corvallis, OR 97331-2902, USA
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Oberholzer V, Durbin ML, Clegg MT. Comparative genomics of chalcone synthase and Myb genes in the grass family. Genes Genet Syst 2000; 75:1-16. [PMID: 10846616 DOI: 10.1266/ggs.75.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Most plant genes occur as members of multigene families where new copies arise through duplication. Duplicate genes that do not confer an adaptive advantage to the plant are expected to rapidly erode into pseudogenes owing to the accumulation of transpositions, insertion/deletion mutations and nucleotide changes. Nonfunctional copies will drift to fixation within a few million years and ultimately erode beyond recognition. Duplicate genes that are retained over longer periods of evolutionary time must be positively selected based on some adaptive advantage conferred on the plant species. We explore the dynamics of the recruitment of new duplicate genes for chalcone synthase, the enzyme that catalyzes the first committed step of flavonoid biosynthesis, and for the myb family of transcriptional activators. Our analyses show that new chs genes are recruited into the genome of grasses at a rate of one new copy every 15 to 25 million years. In contrast, the myb gene family is much older and many duplicate copies appear to predate the separation of the angiosperm lineage from other seed plants. The general pattern suggests a rapid adaptive proliferation of new chs genes but a more ancient elaboration of regulatory gene functions. Our analyses also reveal accelerated rates of protein evolution following gene duplication and evidence is presented for interlocus exchange among duplicate gene loci.
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Affiliation(s)
- V Oberholzer
- Department of Botany & Plant Sciences, University of California, Riverside 92521, USA
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35
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Ganter B, Chao ST, Lipsick JS. Transcriptional activation by the myb proteins requires a specific local promoter structure. FEBS Lett 1999; 460:401-10. [PMID: 10556506 DOI: 10.1016/s0014-5793(99)01373-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The biological effects of the cellular c-Myb and the viral v-Myb proteins are strikingly different. While c-Myb is indispensable for normal hematopoiesis, v-Myb induces acute leukemia. The v-Myb DNA-binding domain (DBD) differs from that of c-Myb mainly by deletion of the first of three repeats which correlates with efficient oncogenic transformation and a decrease in DNA-binding activity. To investigate the difference in DNA-binding and transcriptional activation, oligonucleotide selection and electrophoretic mobility shift assays were employed. The v-Myb DBD (R2R3) shows an intrinsic DNA-binding specificity for an AT-rich downstream extension of the Myb recognition element (MRE) PyAAC(T)/(G)G for efficient binding to this site, whereas R1 within the c-Myb DBD allows for more flexibility for this downstream extension. Therefore, due to the presence of repeat R1, c-Myb can bind to a greater number of target sites. The intrinsic DNA-binding specificity of R2R3 is further supported with the results from in vivo transcriptional activation experiments which demonstrated that both the v-Myb and c-Myb DBDs require an extension of the MRE (motif #1) by a downstream T-stretch (motif #2) for full activity. Surprisingly, the T-stretch improves binding when present on either strand, but is required on a specific strand for transcriptional activation.
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Affiliation(s)
- B Ganter
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA 94305-5324, USA
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Abstract
▪ Abstract Major advances have been made in understanding the role of transcription factors in gene expression in yeast, Drosophila, and man. Transcription factor modification, synergistic events, protein-protein interactions, and chromatin structure have been successfully integrated into transcription factor studies in these organisms. While many putative transcription factors have been isolated from plants, most of them are only poorly characterized. This review summarizes examples where molecular biological techniques have been successfully employed to study plant transcription factors. The functional analysis of transcription factors is described as well as techniques for studying the interactions of transcription factors with other proteins and with DNA.
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Affiliation(s)
- C. Schwechheimer
- Molecular Genetics Department, John Innes Centre, Norwich, Norfolk, NR4 7UH, United Kingdom; e-mail:
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37
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Lesnick ML, Chandler VL. Activation of the maize anthocyanin gene a2 is mediated by an element conserved in many anthocyanin promoters. PLANT PHYSIOLOGY 1998; 117:437-45. [PMID: 9625696 PMCID: PMC34963 DOI: 10.1104/pp.117.2.437] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/1997] [Accepted: 02/19/1998] [Indexed: 05/18/2023]
Abstract
Two transcription factors, C1 (a Myb-domain protein) and B (a basic-helix-loop-helix protein), mediate transcriptional activation of the anthocyanin-biosynthetic genes of maize (Zea mays). To begin to assess the mechanism of activation, the sequences required for C1- and B-mediated induction have been determined for the a2 promoter, which encodes an anthocyanin-biosynthetic enzyme. Analysis of a series of 7- to 13-base-pair substitutions revealed two regions crucial for activation. One region, centered at -99, contained a C1-binding site that abolished C1 binding. The other crucial region was adjacent, centered at -91. C1 binding was not detected at this site, and mutation of this site did not prevent C1 binding at -99. An oligonucleotide dimer containing these two crucial elements was sufficient for C1 and B activation of a heterologous promoter. These data suggest that activation of the anthocyanin genes involves C1 and another factor binding at closely adjacent sites. Mutating a previously postulated anthocyanin consensus sequence within a2 did not significantly reduce activation by C1 and B. However, sequence comparisons of the crucial a2 regions with sequences important for C1- and B-mediated activation in two other anthocyanin promoters led to a revised consensus element shared by these promoters.
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Affiliation(s)
- M L Lesnick
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
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Abe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D, Shinozaki K. Role of arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. THE PLANT CELL 1997; 9:1859-1868. [PMID: 9368419 DOI: 10.1105/tpc.9.10.18591997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In Arabidopsis, the induction of a dehydration-responsive gene, rd22, is mediated by abscisic acid (ABA) and requires protein biosynthesis for ABA-dependent gene expression. Previous experiments established that a 67-bp DNA fragment of the rd22 promoter is sufficient for dehydration- and ABA-induced gene expression and that this DNA fragment contains two closely located putative recognition sites for the basic helix-loop-helix protein MYC and one putative recognition site for MYB. We have carefully analyzed the 67-bp region of the rd22 promoter in transgenic tobacco plants and found that both the first MYC site and the MYB recognition site function as cis-acting elements in the dehydration-induced expression of the rd22 gene. A cDNA encoding a MYC-related DNA binding protein was isolated by DNA-ligand binding screening, using the 67-bp region as a probe, and designated rd22BP1. The rd22BP1 cDNA encodes a 68-kD protein that has a typical DNA binding domain of a basic region helix-loop-helix leucine zipper motif in MYC-related transcription factors. The rd22BP1 protein binds specifically to the first MYC recognition site in the 67-bp fragment. RNA gel blot analysis revealed that transcription of the rd22BP1 gene is induced by dehydration stress and ABA treatment, and its induction precedes that of rd22. We have reported a drought- and ABA-inducible gene that encodes the MYB-related protein ATMYB2. In a transient transactivation experiment using Arabidopsis leaf protoplasts, we demonstrated that both the rd22BP1 and ATMYB2 proteins activate transcription of the rd22 promoter fused to the beta-glucuronidase reporter gene. These results indicate that both the rd22BP1 (MYC) and ATMYB2 (MYB) proteins function as transcriptional activators in the dehydration- and ABA-inducible expression of the rd22 gene.
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Affiliation(s)
- H Abe
- Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Ibaraki, Japan
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39
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Abe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D, Shinozaki K. Role of arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. THE PLANT CELL 1997; 9:1859-68. [PMID: 9368419 PMCID: PMC157027 DOI: 10.1105/tpc.9.10.1859] [Citation(s) in RCA: 479] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In Arabidopsis, the induction of a dehydration-responsive gene, rd22, is mediated by abscisic acid (ABA) and requires protein biosynthesis for ABA-dependent gene expression. Previous experiments established that a 67-bp DNA fragment of the rd22 promoter is sufficient for dehydration- and ABA-induced gene expression and that this DNA fragment contains two closely located putative recognition sites for the basic helix-loop-helix protein MYC and one putative recognition site for MYB. We have carefully analyzed the 67-bp region of the rd22 promoter in transgenic tobacco plants and found that both the first MYC site and the MYB recognition site function as cis-acting elements in the dehydration-induced expression of the rd22 gene. A cDNA encoding a MYC-related DNA binding protein was isolated by DNA-ligand binding screening, using the 67-bp region as a probe, and designated rd22BP1. The rd22BP1 cDNA encodes a 68-kD protein that has a typical DNA binding domain of a basic region helix-loop-helix leucine zipper motif in MYC-related transcription factors. The rd22BP1 protein binds specifically to the first MYC recognition site in the 67-bp fragment. RNA gel blot analysis revealed that transcription of the rd22BP1 gene is induced by dehydration stress and ABA treatment, and its induction precedes that of rd22. We have reported a drought- and ABA-inducible gene that encodes the MYB-related protein ATMYB2. In a transient transactivation experiment using Arabidopsis leaf protoplasts, we demonstrated that both the rd22BP1 and ATMYB2 proteins activate transcription of the rd22 promoter fused to the beta-glucuronidase reporter gene. These results indicate that both the rd22BP1 (MYC) and ATMYB2 (MYB) proteins function as transcriptional activators in the dehydration- and ABA-inducible expression of the rd22 gene.
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Affiliation(s)
- H Abe
- Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Ibaraki, Japan
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40
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Kosugi S, Ohashi Y. PCF1 and PCF2 specifically bind to cis elements in the rice proliferating cell nuclear antigen gene. THE PLANT CELL 1997; 9:1607-19. [PMID: 9338963 PMCID: PMC157037 DOI: 10.1105/tpc.9.9.1607] [Citation(s) in RCA: 211] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We have previously defined the promoter elements, sites IIa and IIb, in the rice proliferating cell nuclear antigen (PCNA) gene that are essential for meristematic tissue-specific expression. In this study, we isolated and characterized cDNAs encoding proteins that specifically bind to sites IIa and IIb. The two DNA binding proteins, designated PCF1 and PCF2, share > 70% homology in common conserved sequences at the N-terminal regions. The conserved regions are responsible for DNA binding and homodimer and heterodimer formation, and they contain a putative basic helix-loop-helix (bHLH) motif. The structure and DNA binding specificity of the bHLH motif are distinguishable from those of other known bHLH proteins that bind to the E-box. The motif is > 70% homologous to several expressed sequence tags from Arabidopsis and rice, suggesting that PCF1 and PCF2 are members of a novel family of proteins that are conserved in monocotyledons and dicotyledons. A supershift assay using an anti-PCF2 antibody showed the involvement of PCF2 in site IIa (site IIb) binding activities in rice nuclear extracts, particularly in meristematic tissues. PCF1 and PCF2 were also more likely to form heterodimers than homodimers. Our results suggest that PCF1 and PCF2 are involved in meristematic tissue-specific expression of the rice PCNA gene through binding to sites IIa and IIb and formation of homodimers or heterodimers.
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Affiliation(s)
- S Kosugi
- National Institute of Agrobiological Resources, Ibaraki, Japan
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Kosugi S, Ohashi Y. PCF1 and PCF2 specifically bind to cis elements in the rice proliferating cell nuclear antigen gene. THE PLANT CELL 1997; 9:1607-1619. [PMID: 9338963 DOI: 10.2307/3870447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We have previously defined the promoter elements, sites IIa and IIb, in the rice proliferating cell nuclear antigen (PCNA) gene that are essential for meristematic tissue-specific expression. In this study, we isolated and characterized cDNAs encoding proteins that specifically bind to sites IIa and IIb. The two DNA binding proteins, designated PCF1 and PCF2, share > 70% homology in common conserved sequences at the N-terminal regions. The conserved regions are responsible for DNA binding and homodimer and heterodimer formation, and they contain a putative basic helix-loop-helix (bHLH) motif. The structure and DNA binding specificity of the bHLH motif are distinguishable from those of other known bHLH proteins that bind to the E-box. The motif is > 70% homologous to several expressed sequence tags from Arabidopsis and rice, suggesting that PCF1 and PCF2 are members of a novel family of proteins that are conserved in monocotyledons and dicotyledons. A supershift assay using an anti-PCF2 antibody showed the involvement of PCF2 in site IIa (site IIb) binding activities in rice nuclear extracts, particularly in meristematic tissues. PCF1 and PCF2 were also more likely to form heterodimers than homodimers. Our results suggest that PCF1 and PCF2 are involved in meristematic tissue-specific expression of the rice PCNA gene through binding to sites IIa and IIb and formation of homodimers or heterodimers.
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Affiliation(s)
- S Kosugi
- National Institute of Agrobiological Resources, Ibaraki, Japan
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Procissi A, Dolfini S, Ronchi A, Tonelli C. Light-Dependent Spatial and Temporal Expression of Pigment Regulatory Genes in Developing Maize Seeds. THE PLANT CELL 1997; 9:1547-1557. [PMID: 12237395 PMCID: PMC157032 DOI: 10.1105/tpc.9.9.1547] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Both light and developmental stimuli are directly involved in the regulation of plant gene expression. In maize, activation of the anthocyanin pathway represents an excellent model system for studying the interactions between an external factor, such as light, and internal factors that regulate plant and seed development. By analyzing in detail the aleurone and pericarp seed layers, different developmental windows for light have been found in the two tissues[mdash]the former in the advanced stages of development and the latter in the early stages of seed development. Transcriptional control of the structural genes involved in anthocyanin deposition within the pericarp is known to be exerted by the Sn and pl genes, whereas the aleurone is controlled by the R and C1 regulatory genes. By using in situ hybridization analysis, we detected tissue-specific expression of Sn and R in the seed layers, revealing a correlation between structural gene activation and anthocyanin accumulation. In addition, RNA gel blot analysis revealed that Sn expression is enhanced by light, whereas the R gene expression is not. However, the light-induced expression of the myb-type genes C1 and pl, detected by reverse transcriptase-polymerase chain reaction, was found to be the limiting factor for conferring the developmental competence of the pericarp and the aleurone layers to light responsiveness.
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Affiliation(s)
- A. Procissi
- Dipartimento di Genetica e di Biologia dei Microrganismi, Via Celoria 26, 20133 Milan, Italy
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Sainz MB, Grotewold E, Chandler VL. Evidence for direct activation of an anthocyanin promoter by the maize C1 protein and comparison of DNA binding by related Myb domain proteins. THE PLANT CELL 1997; 9:611-25. [PMID: 9144964 PMCID: PMC156943 DOI: 10.1105/tpc.9.4.611] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The enzyme-encoding genes of two classes of maize flavonoid pigments, anthocyanins and phlobaphenes, are differentially regulated by distinct transcription factors. Anthocyanin biosynthetic gene activation requires the Myb domain C1 protein and the basic helix-loop-helix B or R proteins. In the phlobaphene pathway, a subset of C1-regulated genes, including a1, are activated by the Myb domain P protein independently of B/R. We show sequence-specific binding to the a1 promoter by C1 in the absence of B. Activation is decreased by mutations in the C1 DNA binding domain or in a1 sequences bound by C1, providing direct evidence for activation of the anthocyanin biosynthetic genes by C1. The two C1 binding sites in the a1 promoter are also bound by P. One site is bound with higher affinity by P relative to C1, whereas the other site is bound with similar lower affinity by both proteins. Interestingly, either site is sufficient for C1 plus B/R or P activation in vivo, demonstrating that differences in DNA binding affinities between P and C1 are insufficient to explain the differential requirement for B. Results of DNA binding site-selection experiments suggest that C1 has a broader DNA binding specificity than does P, which may help C1 to activate a more diverse set of promoters.
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Affiliation(s)
- M B Sainz
- Institute of Molecular Biology, University of Oregon, Eugene 97403, USA
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Sainz MB, Goff SA, Chandler VL. Extensive mutagenesis of a transcriptional activation domain identifies single hydrophobic and acidic amino acids important for activation in vivo. Mol Cell Biol 1997; 17:115-22. [PMID: 8972191 PMCID: PMC231735 DOI: 10.1128/mcb.17.1.115] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
C1 is a transcriptional activator of genes encoding biosynthetic enzymes of the maize anthocyanin pigment pathway. C1 has an amino terminus homologous to Myb DNA-binding domains and an acidic carboxyl terminus that is a transcriptional activation domain in maize and yeast cells. To identify amino acids critical for transcriptional activation, an extensive random mutagenesis of the C1 carboxyl terminus was done. The C1 activation domain is remarkably tolerant of amino acid substitutions, as changes at 34 residues had little or no effect on transcriptional activity. These changes include introduction of helix-incompatible amino acids throughout the C1 activation domain and alteration of most single acidic amino acids, suggesting that a previously postulated amphipathic alpha-helix is not required for activation. Substitutions at two positions revealed amino acids important for transcriptional activation. Replacement of leucine 253 with a proline or glutamine resulted in approximately 10% of wild-type transcriptional activation. Leucine 253 is in a region of C1 in which several hydrophobic residues align with residues important for transcriptional activation by the herpes simplex virus VP16 protein. However, changes at all other hydrophobic residues in C1 indicate that none are critical for C1 transcriptional activation. The other important amino acid in C1 is aspartate 262, as a change to valine resulted in only 24% of wild-type transcriptional activation. Comparison of our C1 results with those from VP16 reveal substantial differences in which amino acids are required for transcriptional activation in vivo by these two acidic activation domains.
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Affiliation(s)
- M B Sainz
- Institute of Molecular Biology, University of Oregon, Eugene 97403-1229, USA
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Bodeau JP, Walbot V. Structure and regulation of the maize Bronze2 promoter. PLANT MOLECULAR BIOLOGY 1996; 32:599-609. [PMID: 8980512 DOI: 10.1007/bf00020201] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The maize Bronze2 (Bz2) gene encodes a glutathione S-transferase that is required for anthocyanin pigment accumulation. Two classes of regulatory proteins, R and C1, are required for transcriptional activation of Bz2 and several additional structural genes. Functional domains of the Bz2 promoter were identified using Bz2 promoter-driven luciferase reporter genes electroporated into maize protoplasts together with R and C1 expression plasmids. Complete regulation was conferred by 224 nt of the Bz2 promoter. Within this region at least two separable regions are independently capable of conferring regulation by R and C1. Predicted regulatory elements corresponding to two classes of sequence motifs, the Myb-box homologous 'C1-motif', TAACTG/CAGTTA, and the G-box and E-box homologous 'R-motif', CACGTG, were shown to be important for full R and C1 activation of the Bz2 promoter. Expression of reconstructed Bz2 genes with mutated promoters was quantified using RNase protection, and this analysis confirmed results obtained using reporter genes.
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Affiliation(s)
- J P Bodeau
- Department of Biological Sciences, Stanford University, CA 94305, USA
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Schläppi M, Raina R, Fedoroff N. A highly sensitive plant hybrid protein assay system based on the Spm promoter and TnpA protein for detection and analysis of transcription activation domains. PLANT MOLECULAR BIOLOGY 1996; 32:717-725. [PMID: 8980523 DOI: 10.1007/bf00020212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
TnpA is a multifunctional DNA binding protein encoded by the maize Suppressor-mutator (Spm) transposable element. TnpA is required for transposition and is a repressor of the unmethylated Spm promoter. While analyzing protein domains using a yeast GAL4-based hybrid system in transiently transformed tobacco cells, we found that TnpA represses the > 10-fold transcriptional activation observed when the GAL4 DNA-binding domain is used alone. By contrast, compared to the backgroundless TnpA DNA-binding domain alone, 33- to 45-fold activation of the Spm promoter was observed when the VP16 activation domain was fused to it. TnpA-binding sites, but no TATA box, were required for transcription activation. Among the TnpA deletion derivatives tested, those retaining the coding sequences for the DNA-binding and protein dimerization domains gave the highest level of transcription activation when fused with the VP16 activation domain. The TnpA gene and TnpA-binding sites in the short Spm promoter therefore provide a novel, highly sensitive single-hybrid system for identifying and studying plant transcription activation domains in plant cells.
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Affiliation(s)
- M Schläppi
- Carnegie Institution of Washington, Department of Embryology, Baltimore, MD 21210, USA
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Abstract
Leaves are produced repeatedly from the shoot apical meristem of plants. Molecular and cellular evidence show that identity of the leaf and its parts is acquired progressively and that the underlying process changes as the leaf matures. The relative importance of cell lineage compared with a position-dependent model for specifying cell fates is discussed.
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Affiliation(s)
- A W Sylvester
- Department of Biological Sciences, University of Idaho, Moscow 83844, USA
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Urao T, Yamaguchi-Shinozaki K, Mitsukawa N, Shibata D, Shinozaki K. Molecular cloning and characterization of a gene that encodes a MYC-related protein in Arabidopsis. PLANT MOLECULAR BIOLOGY 1996; 32:571-6. [PMID: 8980509 DOI: 10.1007/bf00019112] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
In plants, MYC-related proteins function as transcription factors involved in anthocyanin production and trichome development. We cloned a gene, Atmyc1, and its corresponding cDNA, that encodes for a MYC-related protein from Arabidopsis thaliana. The putative protein has a basic/helix-loop-helix motif at the C-terminus and a highly homologous region with that of the maize B/R family at the N-terminus. The promoter region of Atmyc1 contains a Sph box (CATGCATG) that is known as a cis-regulatory element conferring seed-specific expression. In fact, Atmyc1 transcripts were more abundant in developing seeds than in stems and leaves where trichomes are normally expressed. Restriction fragment length polymorphism mapping demonstrated that Atmyc1 is located on the upper region of chromosome 4, which clearly indicates that Atmyc1 is distinct from the ttg (transparent testa glabrous) locus that affects both trichome development and anthocyanin biosynthesis.
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Affiliation(s)
- T Urao
- Biological Resources Division, Japan International Research Center for Agricultural Science (JIRCAS), Ministry of Agriculture, Forestry and Fisheries, Ibaraki, Japan
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Liu Y, Alleman M, Wessler SR. A Ds insertion alters the nuclear localization of the maize transcriptional activator R. Proc Natl Acad Sci U S A 1996; 93:7816-20. [PMID: 8755559 PMCID: PMC38831 DOI: 10.1073/pnas.93.15.7816] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The R-sc gene of maize is a member of the R gene family of transcriptional activators that regulate anthocyanin biosynthesis. A derivative of R-sc, r-m9 conditions a reduced level of aleurone pigmentation due to the presence of a 2.1-kb Ds insertion near the 3' end of the coding region. Excision of Ds from r-m9 leaves a 7-bp insertion in the darker but still mutant v24 derivative. Both the 7-bp insertion in v24 and the 2.1-kb Ds in r-m9 are predicted to truncate their respective R proteins proximal to the carboxyl terminus, which was shown previously to contain one of three nuclear localization sequences. We find that the reduced expression of r-m9 and v24 are not due to mRNA or protein instability, but most likely reflect the inefficient localization of truncated R proteins to the nucleus. To our knowledge this is the first example of a transposable element insertion that alters gene expression by affecting nuclear localization. In addition, our data indicate that the carboxyl terminus of the R protein is far more important than previously suspected and illustrates the utility of natural mutations for defining functional domains in proteins.
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Affiliation(s)
- Y Liu
- Department of Botany, University of Georgia, Athens 30602, USA
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Lin Q, Hamilton WD, Merryweather A. Cloning and initial characterization of 14 myb-related cDNAs from tomato (Lycopersicon esculentum cv. Ailsa Craig). PLANT MOLECULAR BIOLOGY 1996; 30:1009-1020. [PMID: 8639738 DOI: 10.1007/bf00020811] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
myb-related transcription factors contain highly conserved DNA-binding domains. Using a mixture of degenerate oligonucleotides derived from the highly conserved region as probe, 14 myb-related clones were isolated from a cDNA library constructed using tomato hypocoyl mRNA. The expression of these clones was studied by northern blot analysis using poly(A)+ RNA from 7 tissue types (hypocotyl, leaf, root, green and red fruit, immature and mature flower). This study has revealed a wide range of expression patterns which include multiple and single transcripts, some of which show marked tissue specificity. Two clones showing different expression patterns have been fully sequenced. The DNA-binding domains of these two tomato myb clones are compared with myb genes from other plant species and organisms. Of the three clones analysed so far by Southern hybridization, two are single-copy genes and one has multiple genomic copies.
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Affiliation(s)
- Q Lin
- Axis Genetics Ltd., Barbraham, Cambridge, UK
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