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Fattorini R, Khojayori FN, Mellers G, Moyroud E, Herrero E, Kellenberger RT, Walker R, Wang Q, Hill L, Glover BJ. Complex petal spot formation in the Beetle Daisy (Gorteria diffusa) relies on spot-specific accumulation of malonylated anthocyanin regulated by paralogous GdMYBSG6 transcription factors. THE NEW PHYTOLOGIST 2024; 243:240-257. [PMID: 38725421 DOI: 10.1111/nph.19804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 04/18/2024] [Indexed: 06/07/2024]
Abstract
Gorteria diffusa has elaborate petal spots that attract pollinators through sexual deception, but how G. diffusa controls spot development is largely unknown. Here, we investigate how pigmentation is regulated during spot formation. We determined the anthocyanin composition of G. diffusa petals and combined gene expression analysis with protein interaction assays to characterise R2R3-MYBs that likely regulate pigment production in G. diffusa petal spots. We found that cyanidin 3-glucoside pigments G. diffusa ray floret petals. Unlike other petal regions, spots contain a high proportion of malonylated anthocyanin. We identified three subgroup 6 R2R3-MYB transcription factors (GdMYBSG6-1,2,3) that likely activate the production of spot pigmentation. These genes are upregulated in developing spots and induce ectopic anthocyanin production upon heterologous expression in tobacco. Interaction assays suggest that these transcription factors regulate genes encoding three anthocyanin synthesis enzymes. We demonstrate that the elaboration of complex spots in G. diffusa begins with the accumulation of malonylated pigments at the base of ray floret petals, positively regulated by three paralogous R2R3-MYB transcription factors. Our results indicate that the functional diversification of these GdMYBSG6s involved changes in the spatial control of their transcription, and modification of the duration of GdMYBSG6 gene expression contributes towards floral variation within the species.
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Affiliation(s)
- Róisín Fattorini
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, UK
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Farahnoz N Khojayori
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, UK
| | - Gregory Mellers
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, UK
| | - Edwige Moyroud
- Sainsbury Laboratory Cambridge University, Bateman St., Cambridge, CB2 1LR, UK
- Department of Genetics, University of Cambridge, Downing St., Cambridge, CB2 3EH, UK
| | - Eva Herrero
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, UK
| | - Roman T Kellenberger
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, UK
| | - Rachel Walker
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, UK
| | - Qi Wang
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, UK
| | - Lionel Hill
- Biomolecular Analysis Facility, John Innes Centre, Colney, Norwich, NR4 7UH, UK
| | - Beverley J Glover
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, UK
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Li N, Xu Y, Lu Y. A Regulatory Mechanism on Pathways: Modulating Roles of MYC2 and BBX21 in the Flavonoid Network. PLANTS (BASEL, SWITZERLAND) 2024; 13:1156. [PMID: 38674565 PMCID: PMC11054080 DOI: 10.3390/plants13081156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
Genes of metabolic pathways are individually or collectively regulated, often via unclear mechanisms. The anthocyanin pathway, well known for its regulation by the MYB/bHLH/WDR (MBW) complex but less well understood in its connections to MYC2, BBX21, SPL9, PIF3, and HY5, is investigated here for its direct links to the regulators. We show that MYC2 can activate the structural genes of the anthocyanin pathway but also suppress them (except F3'H) in both Arabidopsis and Oryza when a local MBW complex is present. BBX21 or SPL9 can activate all or part of the structural genes, respectively, but the effects can be largely overwritten by the local MBW complex. HY5 primarily influences expressions of the early genes (CHS, CHI, and F3H). TF-TF relationships can be complex here: PIF3, BBX21, or SPL9 can mildly activate MYC2; MYC2 physically interacts with the bHLH (GL3) of the MBW complex and/or competes with strong actions of BBX21 to lessen a stimulus to the anthocyanin pathway. The dual role of MYC2 in regulating the anthocyanin pathway and a similar role of BBX21 in regulating BAN reveal a network-level mechanism, in which pathways are modulated locally and competing interactions between modulators may tone down strong environmental signals before they reach the network.
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Affiliation(s)
- Nan Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunzhang Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Yingqing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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Gao G, Chen M, Mo R, Li N, Xu Y, Lu Y. Linking New Alleles at the Oscillator Loci to Flowering and Expansion of Asian Rice. Genes (Basel) 2023; 14:2027. [PMID: 38002970 PMCID: PMC10671530 DOI: 10.3390/genes14112027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
The central oscillator is believed to be the key mechanism by which plants adapt to new environments. However, impacts from hybridization, the natural environment, and human selection have rarely been assessed on the oscillator of a crop. Here, from clearly identified alleles at oscillator loci (OsCCA1/LHY, OsPRR95, OsPRR37, OsPRR59, and OsPRR1) in ten diverse genomes of Oryza sativa, additional accessions, and functional analysis, we show that rice's oscillator was rebuilt primarily by new alleles from recombining parental sequences and subsequent 5' or/and coding mutations. New alleles may exhibit altered transcript levels from that of a parental allele and are transcribed variably among genetic backgrounds and natural environments in RIL lines. Plants carrying more expressed OsCCA1_a and less transcribed OsPRR1_e flower early in the paddy field. 5' mutations are instrumental in varied transcription, as shown by EMSA tests on one deletion at the 5' region of highly transcribed OsPRR1_a. Compared to relatively balanced mutations at oscillator loci of Arabidopsis thaliana, 5' mutations of OsPRR37 (and OsCCA1 to a less degree) were under negative selection while those of OsPRR1 alleles were under strong positive selection. Together, range expansion of Asian rice can be elucidated by human selection on OsPRR1 alleles via local flowering time-yield relationships.
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Affiliation(s)
- Guangtong Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maoxian Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Mo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunzhang Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, 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; (G.G.); (M.C.); (N.L.); (Y.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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Yan H, Pei X, Zhang H, Li X, Zhang X, Zhao M, Chiang VL, Sederoff RR, Zhao X. MYB-Mediated Regulation of Anthocyanin Biosynthesis. Int J Mol Sci 2021; 22:3103. [PMID: 33803587 PMCID: PMC8002911 DOI: 10.3390/ijms22063103] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 11/16/2022] Open
Abstract
Anthocyanins are natural water-soluble pigments that are important in plants because they endow a variety of colors to vegetative tissues and reproductive plant organs, mainly ranging from red to purple and blue. The colors regulated by anthocyanins give plants different visual effects through different biosynthetic pathways that provide pigmentation for flowers, fruits and seeds to attract pollinators and seed dispersers. The biosynthesis of anthocyanins is genetically determined by structural and regulatory genes. MYB (v-myb avian myeloblastosis viral oncogene homolog) proteins are important transcriptional regulators that play important roles in the regulation of plant secondary metabolism. MYB transcription factors (TFs) occupy a dominant position in the regulatory network of anthocyanin biosynthesis. The TF conserved binding motifs can be combined with other TFs to regulate the enrichment and sedimentation of anthocyanins. In this study, the regulation of anthocyanin biosynthetic mechanisms of MYB-TFs are discussed. The role of the environment in the control of the anthocyanin biosynthesis network is summarized, the complex formation of anthocyanins and the mechanism of environment-induced anthocyanin synthesis are analyzed. Some prospects for MYB-TF to modulate the comprehensive regulation of anthocyanins are put forward, to provide a more relevant basis for further research in this field, and to guide the directed genetic modification of anthocyanins for the improvement of crops for food quality, nutrition and human health.
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Affiliation(s)
- Huiling Yan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (H.Y.); (H.Z.); (X.L.); (X.Z.); (M.Z.); (V.L.C.)
| | - Xiaona Pei
- Harbin Research Institute of Forestry Machinery, State Administration of Forestry and Grassland, Harbin 150086, China;
- Research Center of Cold Temperate Forestry, CAF, Harbin 150086, China
| | - Heng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (H.Y.); (H.Z.); (X.L.); (X.Z.); (M.Z.); (V.L.C.)
| | - Xiang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (H.Y.); (H.Z.); (X.L.); (X.Z.); (M.Z.); (V.L.C.)
| | - Xinxin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (H.Y.); (H.Z.); (X.L.); (X.Z.); (M.Z.); (V.L.C.)
| | - Minghui Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (H.Y.); (H.Z.); (X.L.); (X.Z.); (M.Z.); (V.L.C.)
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (H.Y.); (H.Z.); (X.L.); (X.Z.); (M.Z.); (V.L.C.)
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA;
| | - Ronald Ross Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA;
| | - Xiyang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (H.Y.); (H.Z.); (X.L.); (X.Z.); (M.Z.); (V.L.C.)
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Expression of Pinellia ternata leaf agglutinin under rolC promoter confers resistance against a phytophagous sap sucking aphid, Myzus persicae. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2020.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Deng J, Wu D, Shi J, Balfour K, Wang H, Zhu G, Liu Y, Wang J, Zhu Z. Multiple MYB Activators and Repressors Collaboratively Regulate the Juvenile Red Fading in Leaves of Sweetpotato. FRONTIERS IN PLANT SCIENCE 2020; 11:941. [PMID: 32670334 PMCID: PMC7330089 DOI: 10.3389/fpls.2020.00941] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/10/2020] [Indexed: 05/23/2023]
Abstract
Juvenile red fading describes the phenomenon in plants whereby red young leaves gradually turn green as they mature. While this phenomenon is commonly observed, the underlying molecular mechanism is still obscure as the classic model plants do not exhibit this process. Here, the molecular mechanism for the loss of anthocyanins during juvenile red fading were explored in the sweetpotato (Ipomoea batatas L.) cultivar "Chuanshan Zi". The MYB-bHLH-WDR (MBW) regulatory complexes for anthocyanins were examined with five stages of leaf development from C1 to C5. Alternating accumulation of anthocyanins and chlorophylls caused the leaf color change. Five anthocyanin components were identified by ultra performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS), and their contents were highest at stage C2. Transcriptomic analysis showed massive gene expression alteration during leaf development. The anthocyanin structural genes expressed in sweetpotato leaves were screened and found to be highly comparable with those identified in morning glories. The screened anthocyanin regulatory genes included one bHLH (IbbHLH2), one WDR (IbWDR1), three MYB activators (IbMYB1, IbMYB2, and IbMYB3), and five MYB repressors (IbMYB27, IbMYBx, IbMYB4a, IbMYB4b, and IbMYB4c). The expression trends of MYBs were key to the red fading process: the activators were highly expressed in early red leaves and were all accompanied by simultaneously expressed MYB repressors, which may act to prevent excessive accumulation of anthocyanins. The only antagonistic repressor, IbMYB4b, was highly expressed in green leaves, and may be critical for declined anthocyanin content at later stages. Further functional verification of the above transcription factors were conducted by promoter activation tests. These tests showed that the MBW complexes of IbMYB1/IbMYB2/IbMYB3-IbbHLH2-IbWDR1 not only activated promoters of anthocyanin structural genes IbCHS-D and IbDFR-B, but also promoters for IbbHLH2 and IbMYB27, indicating both hierarchical and feedback regulations. This study outlines the elaborate regulatory network of MBW complexes involving multiple MYBs which allow for the timely accumulation of anthocyanins in sweetpotato leaves. These results may also provide clues for similar studies of juvenile red fading in other plant species.
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Affiliation(s)
- Jiliang Deng
- Key Laboratory of Tropical Biological Resources, Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Danning Wu
- Key Laboratory of Tropical Biological Resources, Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Jie Shi
- Key Laboratory of Tropical Biological Resources, Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Kelly Balfour
- Department of Biology, Algoma University, Sault Sainte Marie, ON, Canada
| | - Huafeng Wang
- Key Laboratory of Tropical Biological Resources, Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Guopeng Zhu
- College of Horticulture, Hainan University, Haikou, China
| | - Yonghua Liu
- College of Horticulture, Hainan University, Haikou, China
| | - Jian Wang
- Key Laboratory of Germplasm Resources Biology of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, Hainan University, Haikou, China
| | - Zhixin Zhu
- Key Laboratory of Tropical Biological Resources, Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
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Amato A, Cavallini E, Walker AR, Pezzotti M, Bliek M, Quattrocchio F, Koes R, Ruperti B, Bertini E, Zenoni S, Tornielli GB. The MYB5-driven MBW complex recruits a WRKY factor to enhance the expression of targets involved in vacuolar hyper-acidification and trafficking in grapevine. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:1220-1241. [PMID: 31125454 DOI: 10.1111/tpj.14419] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/24/2019] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
The accumulation of secondary metabolites and the regulation of tissue acidity contribute to the important traits of grape berry and influence plant performance in response to abiotic and biotic factors. In several plant species a highly conserved MYB-bHLH-WD (MBW) transcriptional regulatory complex controls flavonoid pigment synthesis and transport, and vacuolar acidification in epidermal cells. An additional component, represented by a WRKY-type transcription factor, physically interacts with the complex increasing the expression of some target genes and adding specificity for other targets. Here we investigated the function of MBW(W) complexes involving two MYBs (VvMYB5a and VvMYB5b) and the WRKY factor VvWRKY26 in grapevine (Vitis vinifera L.). Using transgenic grapevine plants we showed that these complexes affected different aspects of morphology, plant development, pH regulation, and pigment accumulation. Transcriptomic analysis identified a core set of putative target genes controlled by VvMYB5a, VvMYB5b, and VvWRKY26 in different tissues. Our data indicated that VvWRKY26 enhances the expression of selected target genes induced by VvMYB5a/b. Among these targets are genes involved in vacuolar hyper-acidification, such as the P-type ATPases VvPH5 and VvPH1, and trafficking, and genes involved in the biosynthesis of flavonoids. In addition, VvWRKY26 is recruited specifically by VvMYB5a, reflecting the functional diversification of VvMYB5a and VvMYB5b. The expression of MBWW complexes in vegetative organs, such as leaves, indicates a possible function of vacuolar hyper-acidification in the repulsion of herbivores and/or in developmental processes, as shown by defects in transgenic grape plants where the complex is inactivated.
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Affiliation(s)
- Alessandra Amato
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Erika Cavallini
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Amanda R Walker
- CSIRO Agriculture & Food, Waite Campus, Urrbrae, South Australia, Australia
| | - Mario Pezzotti
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Mattijs Bliek
- Swammerdam Institute of Life Sciences, University of Amsterdam, 1090GE, Amsterdam, the Netherlands
| | - Francesca Quattrocchio
- Swammerdam Institute of Life Sciences, University of Amsterdam, 1090GE, Amsterdam, the Netherlands
| | - Ronald Koes
- Swammerdam Institute of Life Sciences, University of Amsterdam, 1090GE, Amsterdam, the Netherlands
| | - Benedetto Ruperti
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Edoardo Bertini
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Sara Zenoni
- Department of Biotechnology, University of Verona, Verona, Italy
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Shen Z, Lin Y, Zou Q. Transcription factors–DNA interactions in rice: identification and verification. Brief Bioinform 2019; 21:946-956. [DOI: 10.1093/bib/bbz045] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/25/2019] [Accepted: 03/25/2019] [Indexed: 01/08/2023] Open
Abstract
Abstract
The completion of the rice genome sequence paved the way for rice functional genomics research. Additionally, the functional characterization of transcription factors is currently a popular and crucial objective among researchers. Transcription factors are one of the groups of proteins that bind to either enhancer or promoter regions of genes to regulate expression. On the basis of several typical examples of transcription factor analyses, we herein summarize selected research strategies and methods and introduce their advantages and disadvantages. This review may provide some theoretical and technical guidelines for future investigations of transcription factors, which may be helpful to develop new rice varieties with ideal traits.
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Affiliation(s)
- Zijie Shen
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuan Lin
- Department of System Integration, Sparebanken Vest, Bergen, Norway
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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Xie L, Liu P, Zhu Z, Zhang S, Zhang S, Li F, Zhang H, Li G, Wei Y, Sun R. Phylogeny and Expression Analyses Reveal Important Roles for Plant PKS III Family during the Conquest of Land by Plants and Angiosperm Diversification. FRONTIERS IN PLANT SCIENCE 2016; 7:1312. [PMID: 27625671 PMCID: PMC5004622 DOI: 10.3389/fpls.2016.01312] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/16/2016] [Indexed: 05/06/2023]
Abstract
Polyketide synthases (PKSs) utilize the products of primary metabolism to synthesize a wide array of secondary metabolites in both prokaryotic and eukaryotic organisms. PKSs can be grouped into three distinct classes, types I, II, and III, based on enzyme structure, substrate specificity, and catalytic mechanisms. The type III PKS enzymes function as homodimers, and are the only class of PKS that do not require acyl carrier protein. Plant type III PKS enzymes, also known as chalcone synthase (CHS)-like enzymes, are of particular interest due to their functional diversity. In this study, we mined type III PKS gene sequences from the genomes of six aquatic algae and 25 land plants (1 bryophyte, 1 lycophyte, 2 basal angiosperms, 16 core eudicots, and 5 monocots). PKS III sequences were found relatively conserved in all embryophytes, but not exist in algae. We also examined gene expression patterns by analyzing available transcriptome data, and identified potential cis-regulatory elements in upstream sequences. Phylogenetic trees of dicots angiosperms showed that plant type III PKS proteins fall into three clades. Clade A contains CHS/STS-type enzymes coding genes with diverse transcriptional expression patterns and enzymatic functions, while clade B is further divided into subclades b1 and b2, which consist of anther-specific CHS-like enzymes. Differentiation regions, such as amino acids 196-207 between clades A and B, and predicted positive selected sites within α-helixes in late appeared branches of clade A, account for the major diversification in substrate choice and catalytic reaction. The integrity and location of conserved cis-elements containing MYB and bHLH binding sites can affect transcription levels. Potential binding sites for transcription factors such as WRKY, SPL, or AP2/EREBP may contribute to tissue- or taxon-specific differences in gene expression. Our data shows that gene duplications and functional diversification of plant type III PKS enzymes played a critical role in the ancient conquest of the land by early plants and angiosperm diversification.
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Affiliation(s)
- Lulu Xie
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Pingli Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
| | - Zhixin Zhu
- College of Horticulture and Landscape Architecture, Hainan UniversityHaikou, China
| | - Shifan Zhang
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Shujiang Zhang
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Fei Li
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Hui Zhang
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Guoliang Li
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yunxiao Wei
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Rifei Sun
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
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Hoshino A, Yoneda Y, Kuboyama T. A Stowaway transposon disrupts the InWDR1 gene controlling flower and seed coloration in a medicinal cultivar of the Japanese morning glory. Genes Genet Syst 2016; 91:37-40. [PMID: 27074980 DOI: 10.1266/ggs.15-00062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Floricultural cultivars of the Japanese morning glory (Ipomoea nil) carry transposons of the Tpn1 family as active spontaneous mutagens. Half of the characterized mutations related to floricultural traits were caused by insertion of Tpn1 family elements. In addition, mutations comprising insertions of several bp, presumed to be footprints generated by transposon excisions, were also found. Among these, ca-1 and ca-2 are 7-bp insertions at the same position in the InWDR1 gene, which encodes a multifunctional transcription regulator. InWDR1 enhances anthocyanin pigmentation in blue flowers and red stems, and promotes dark brown seed pigmentation as well as seed-trichome formation. The recessive ca mutants show white flowers and whitish seeds. We characterized here a white flower and whitish seed line that is used as a medicinal herb. The mutant line carries a novel ca allele named ca-3, which is the InWDR1 gene carrying an insertion of a Stowaway-like transposon, InSto1. The ca-3 allele is the first example of a mutation induced by transposons other than those in the Tpn1 family in I. nil. Because InSto1 and the 7-bp putative footprints are inserted at identical positions in InWDR1, ca-3 is likely to be the ancestor of ca-1 and ca-2. According to Japanese historical records on whitish seeds of I. nil, putative ca mutants appeared at the end of the 17th century, at the latest. This is around one hundred years before the appearance of many floricultural mutants. This suggests that ca-3 is one of the oldest mutations, and that its origin is different from that of most floricultural mutations in I. nil.
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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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Barthole G, To A, Marchive C, Brunaud V, Soubigou-Taconnat L, Berger N, Dubreucq B, Lepiniec L, Baud S. MYB118 represses endosperm maturation in seeds of Arabidopsis. THE PLANT CELL 2014; 26:3519-37. [PMID: 25194028 PMCID: PMC4213162 DOI: 10.1105/tpc.114.130021] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/12/2014] [Accepted: 08/21/2014] [Indexed: 05/22/2023]
Abstract
In the exalbuminous species Arabidopsis thaliana, seed maturation is accompanied by the deposition of oil and storage proteins and the reduction of the endosperm to one cell layer. Here, we consider reserve partitioning between embryo and endosperm compartments. The pattern of deposition, final amount, and composition of these reserves differ between the two compartments, with the embryo representing the principal storage tissue in mature seeds. Complex regulatory mechanisms are known to prevent activation of maturation-related programs during embryo morphogenesis and, later, during vegetative growth. Here, we describe a regulator that represses the expression of maturation-related genes during maturation within the endosperm. MYB118 is transcriptionally induced in the maturing endosperm, and seeds of myb118 mutants exhibit an endosperm-specific derepression of maturation-related genes associated with a partial relocation of storage compounds from the embryo to the endosperm. Moreover, MYB118 activates endosperm-induced genes through the recognition of TAACGG elements. These results demonstrate that the differential partitioning of reserves between the embryo and endosperm in exalbuminous Arabidopsis seeds does not only result from developmental programs that establish the embryo as the preponderant tissue within seeds. This differential partitioning is also regulated by MYB118, which regulates the biosynthesis of reserves at the spatial level during maturation.
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Affiliation(s)
- Guillaume Barthole
- INRA, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France
| | - Alexandra To
- INRA, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France
| | - Chloé Marchive
- INRA, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France
| | - Véronique Brunaud
- INRA, Unité de Recherche en Génomique Végétale, Génomique Fonctionnelle d'Arabidopsis, Plateforme Transcriptome, UMR1165, INRA-Université d'Evry Val d'Essonne, ERL8196 CNRS, Saclay Plant Sciences, F-91000 Evry, France
| | - Ludivine Soubigou-Taconnat
- INRA, Unité de Recherche en Génomique Végétale, Génomique Fonctionnelle d'Arabidopsis, Plateforme Transcriptome, UMR1165, INRA-Université d'Evry Val d'Essonne, ERL8196 CNRS, Saclay Plant Sciences, F-91000 Evry, France
| | - Nathalie Berger
- INRA, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France
| | - Bertrand Dubreucq
- INRA, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France
| | - Loïc Lepiniec
- INRA, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France
| | - Sébastien Baud
- INRA, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, F-78000 Versailles, France
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Basu S, Roychoudhury A, Sengupta DN. Deciphering the role of various cis-acting regulatory elements in controlling SamDC gene expression in rice. PLANT SIGNALING & BEHAVIOR 2014; 9:e28391. [PMID: 24603050 PMCID: PMC4091577 DOI: 10.4161/psb.28391] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 02/27/2014] [Accepted: 02/28/2014] [Indexed: 05/09/2023]
Abstract
Lately we have published on the characterization of the upstream of SamDC gene from rice and investigated the involvement of various cis-elements present in the promoter region in its transcriptional regulation. Analysis of SamDC expression showed that it was inducible by abiotic stresses like salinity, drought, and cold as well as by light and ABA treatment. Furthermore, DNA protein interaction studies have identified transacting actors responsible for its expression after abiotic stresses or light inducibility. Here we have further discussed on the possible role of these cis-elements in modulating the transcriptional network and comment on their function in relation to polyamine biosynthesis during periods of abiotic stress in rice.
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Affiliation(s)
- Supratim Basu
- Department of Crop Soil and Environmental Sciences; University of Arkansas; Fayetteville, AR USA
- Division of Plant Biology; Bose Institute; Kolkata, India
| | - Aryadeep Roychoudhury
- Post Graduate Department of Biotechnology; St. Xavier's College (Autonomous); Kolkata, West Bengal, India
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