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Li H, Wang W, Liu R, Tong B, Dai X, Lu Y, Yu Y, Dai S, Ruan L. Long non-coding RNA-mediated competing endogenous RNA regulatory network during flower development and color formation in Melastoma candidum. FRONTIERS IN PLANT SCIENCE 2023; 14:1215044. [PMID: 37575929 PMCID: PMC10415103 DOI: 10.3389/fpls.2023.1215044] [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: 05/01/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023]
Abstract
M. candidum, an evergreen shrubby flower known for its superior adaptation ability in South China, has gained increased attention in garden applications. However, scant attention has been paid to its flower development and color formation process at the non-coding RNA level. To fill this gap, we conducted a comprehensive analysis based on long non-coding RNA sequencing (lncRNA-seq), RNA-seq, small RNA sequencing (sRNA-seq), and widely targeted metabolome detection of three different flower developmental stages of M. candidum. After differentially expressed lncRNAs (DElncRNAs), differentially expressed mRNAs (DEmRNAs), differentially expressed microRNAs (DEmiRNAs), and differentially synthesized metabolites (DSmets) analyses between the different flower developmental stages, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted to identify some key genes and metabolites in flavonoid, flavone, anthocyanin, carotenoid, and alkaloid-related GO terms and biosynthetic pathways. Three direct-acting models, including antisense-acting, cis-acting, and trans-acting between lncRNAs and mRNAs, were detected to illustrate the direct function of lncRNAs on target genes during flower development and color formation. Based on the competitive endogenous RNA (ceRNA) regulatory theory, we constructed a lncRNA-mediated regulatory network composed of DElncRNAs, DEmiRNAs, DEmRNAs, and DSmets to elucidate the indirect role of lncRNAs in the flower development and color formation of M. candidum. By utilizing correlation analyses between DERNAs and DSmets within the ceRNA regulatory network, alongside verification trials of the ceRNA regulatory mechanism, the study successfully illustrated the significance of lncRNAs in flower development and color formation process. This research provides a foundation for improving and regulating flower color at the lncRNA level in M. candidum, and sheds light on the potential applications of non-coding RNA in studies of flower development.
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Affiliation(s)
- Hui Li
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Wei Wang
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
| | - Rui Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Botong Tong
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Yan Lu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Yixun Yu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Seping Dai
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
| | - Lin Ruan
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, China
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Zhang P, Du H, Wang J, Pu Y, Yang C, Yan R, Yang H, Cheng H, Yu D. Multiplex CRISPR/Cas9-mediated metabolic engineering increases soya bean isoflavone content and resistance to soya bean mosaic virus. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1384-1395. [PMID: 31769589 PMCID: PMC7206993 DOI: 10.1111/pbi.13302] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 11/18/2019] [Indexed: 05/18/2023]
Abstract
Isoflavonoids, which include a variety of secondary metabolites, are derived from the phenylpropanoid pathway and are distributed predominantly in leguminous plants. These compounds play a critical role in plant-environment interactions and are beneficial to human health. Isoflavone synthase (IFS) is a key enzyme in isoflavonoid synthesis and shares a common substrate with flavanone-3-hydroxylase (F3H) and flavone synthase II (FNS II). In this study, CRISPR/Cas9-mediated multiplex gene-editing technology was employed to simultaneously target GmF3H1, GmF3H2 and GmFNSII-1 in soya bean hairy roots and plants. Various mutation types and frequencies were observed in hairy roots. Higher mutation efficiencies were found in the T0 transgenic plants, with a triple gene mutation efficiency of 44.44%, and these results of targeted mutagenesis were stably inherited in the progeny. Metabolomic analysis of T0 triple-mutants leaves revealed significant improvement in isoflavone content. Compared with the wild type, the T3 generation homozygous triple mutants had approximately twice the leaf isoflavone content, and the soya bean mosaic virus (SMV) coat protein content was significantly reduced by one-third after infection with strain SC7, suggesting that increased isoflavone content enhanced the leaf resistance to SMV. The isoflavone content in the seeds of T2 triple mutants was also significantly increased. This study provides not only materials for the improvement of soya bean isoflavone content and resistance to SMV but also a simple system to generate multiplex mutations in soya bean, which may be beneficial for further breeding and metabolic engineering.
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Affiliation(s)
- Peipei Zhang
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Hongyang Du
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural ScienceHefeiChina
| | - Jiao Wang
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Yixiang Pu
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Changyun Yang
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Rujuan Yan
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Hui Yang
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
- School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Hao Cheng
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Deyue Yu
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
- School of Life SciencesGuangzhou UniversityGuangzhouChina
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Diretto G, Jin X, Capell T, Zhu C, Gomez-Gomez L. Differential accumulation of pelargonidin glycosides in petals at three different developmental stages of the orange-flowered gentian (Gentiana lutea L. var. aurantiaca). PLoS One 2019; 14:e0212062. [PMID: 30742659 PMCID: PMC6370212 DOI: 10.1371/journal.pone.0212062] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/26/2019] [Indexed: 01/05/2023] Open
Abstract
Corolla color in Gentiana lutea L. exhibits a yellow/orange variation. We previously demonstrated that the orange petal color of G. lutea L. var. aurantiaca is predominantly caused by newly synthesized pelargonidin glycosides that confer a reddish hue to the yellow background color, derived from the carotenoids. However, the anthocyanin molecules of these pelargonidin glycosides are not yet fully identified and characterized. Here, we investigated the regulation, content and type of anthocyanins determining the petal coloration of the orange-flowered G. lutea L. var. aurantiaca. Anthocyanins from the petals of G. lutea L. var. aurantiaca were characterized and quantified by HPLC-ESI-MS/MS (High-performance liquid chromatography-electrospray ionization-tandem mass spectrometry) coupled with a diode array detector in flowers at three different stages of development (S1, S3 and S5). Eleven pelargonidin derivatives were identified in the petals of G. lutea L. var. aurantiaca for the first time, but quantitative and qualitative differences were observed at each developmental stage. The highest levels of these pelargonidin derivatives were reached at the fully open flower stage (S5) where all anthocyanins were detected. In contrast, not all the anthocyanins were detected at the budlet stage (S1) and mature bud stage (S3) and those corresponded to more complex pelargonidin derivatives. The major pelargonidin derivatives found at all the stages were pelargonidin 3-O-glucoside, pelargonidin 3,5-O-diglucoside and pelargonidin 3-O-rutinoside. Furthermore, the expression of DFR (dihydroflavonol 4-reductase), ANS (anthocyanidin synthase), 3GT (UDP-glucose:flavonoid 3-O-glucosyltransferase), 5GT (UDP-glucose:flavonoid 5-O-glucosyltransferase) and 5AT (anthocyanin 5-aromatic acyltransferase) genes was analyzed in the petals of three developmental stages, showing that the expression level of DFR, ANS and 3GT parallels the accumulation of the pelargonidin glucosides. Overall, this study enhances the knowledge of the biochemical basis of flower coloration in Gentiana species, and lays a foundation for breeding of flower color and genetic variation studies on Gentiana varieties.
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Affiliation(s)
- Gianfranco Diretto
- Italian National Agency for New Technologies, Energy and Sustainable Development, Casaccia Research Centre, Rome, Italy
| | - Xin Jin
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-Agrotecnio Center, Lleida, Spain
| | - Teresa Capell
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-Agrotecnio Center, Lleida, Spain
| | - Changfu Zhu
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-Agrotecnio Center, Lleida, Spain
- School of Life Sciences, Changchun Normal University, Changchun, China
| | - Lourdes Gomez-Gomez
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario, Albacete, Spain
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Kovinich N, Saleem A, Rintoul TL, Brown DCW, Arnason JT, Miki B. Coloring genetically modified soybean grains with anthocyanins by suppression of the proanthocyanidin genes ANR1 and ANR2. Transgenic Res 2012; 21:757-71. [PMID: 22083247 DOI: 10.1007/s11248-011-9566-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 09/28/2011] [Indexed: 12/17/2022]
Abstract
Detection and quantification of the levels of adventitious presence of genetically modified (GM) soybeans in non-GM grain shipments currently requires sophisticated tests that can have issues with their reproducibility. We show here that pigment biosynthesis in the soybean seed coat can be manipulated to provide a distinct color that would enable the simple visible detection of the GM soybean grain. We observed that a distinct red-brown grain color could be engineered by the simultaneous suppression of two proanthocyanidin (PA) genes, ANTHOCYANIDIN REDUCTASE1 (ANR1) and ANR2. Multiple reaction monitoring by liquid chromatography tandem mass spectrometry was used to quantify differentially accumulated seed coat metabolites, and revealed the redirection of metabolic flux into the anthocyanin pigment pathway and unexpectedly the flavonol-3-O-glucoside pathway. The upregulations of anthocyanin isogenes (DFR1 and GST26) and the anthocyanin/flavonol-3-O-glycosyltransferase (UGT78K2) were identified by quantitative RT-PCR to be endogenous feedback and feedforward responses to overaccumulation of upstream flavonoid intermediates resulting from ANR1 and ANR2 suppressions. These results suggested the transcription of flavonoid genes to be a key component of the mechanism responsible for the redirection of metabolite flux. This report identifies the suppression of PA genes to be a novel approach for engineering pigmentation in soybean grains.
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Affiliation(s)
- Nik Kovinich
- Bioproducts and Bioprocesses, Research Branch, Agriculture and Agri-Food Canada, Ottawa, ON, Canada.
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Abstract
In maize, mutations in the pr1 locus lead to the accumulation of pelargonidin (red) rather than cyanidin (purple) pigments in aleurone cells where the anthocyanin biosynthetic pathway is active. We characterized pr1 mutation and isolated a putative F3′H encoding gene (Zmf3′h1) and showed by segregation analysis that the red kernel phenotype is linked to this gene. Genetic mapping using SNP markers confirms its position on chromosome 5L. Furthermore, genetic complementation experiments using a CaMV 35S::ZmF3′H1 promoter–gene construct established that the encoded protein product was sufficient to perform a 3′-hydroxylation reaction. The Zmf3′h1-specific transcripts were detected in floral and vegetative tissues of Pr1 plants and were absent in pr1. Four pr1 alleles were characterized: two carry a 24 TA dinucleotide repeat insertion in the 5′-upstream promoter region, a third has a 17-bp deletion near the TATA box, and a fourth contains a Ds insertion in exon1. Genetic and transcription assays demonstrated that the pr1 gene is under the regulatory control of anthocyanin transcription factors red1 and colorless1. The cloning and characterization of pr1 completes the molecular identification of all genes encoding structural enzymes of the anthocyanin pathway of maize.
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Kole C, Michler CH, Abbott AG, Hall TC. Levels and Stability of Expression of Transgenes. TRANSGENIC CROP PLANTS 2010. [PMCID: PMC7122870 DOI: 10.1007/978-3-642-04809-8_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is well known that in a given cell, at a particular time, only a fraction of the entire genome is expressed. Expression of a gene, nuclear, or organellar starts with the onset of transcription and ends in the synthesis of the functional protein. The regulation of gene expression is a complex process that requires the coordinated activity of different proteins and nucleic acids that ultimately determine whether a gene is transcribed, and if transcribed, whether it results in the production of a protein that develops a phenotype. The same also holds true for transgenic crops, which lie at the very core of insert design. There are multiple checkpoints at which the expression of a gene can be regulated and controlled. Much of the emphasis of studies related to gene expression has been on regulation of gene transcription, and a number of methods are used to effect the control of gene expression. Controlling transgene expression for a commercially valuable trait is necessary to capture its value. Many gene functions are either lethal or produce severe deformity (resulting in loss of value) if over-expressed. Thus, expression of a transgene at a particular site or in response to a particular elicitor is always desirable.
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Affiliation(s)
- Chittaranjan Kole
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634 USA
| | - Charles H. Michler
- NSF I/UCRC Center for Tree Genetics, Hardwood Tree Improvement and Regeneration Center at Purdue University, West Lafayette, IN 47907 USA
| | - Albert G. Abbott
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634 USA
| | - Timothy C. Hall
- Institute of Developmental & Molecular Biology Department of Biology, Texas A&M University, College Station, TX 77843 USA
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Zhang W, Curtin C, Franco C. Towards manipulation of post-biosynthetic events in secondary metabolism of plant cell cultures. Enzyme Microb Technol 2002. [DOI: 10.1016/s0141-0229(02)00041-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Chapple C. MOLECULAR-GENETIC ANALYSIS OF PLANT CYTOCHROME P450-DEPENDENT MONOOXYGENASES. ACTA ACUST UNITED AC 1998; 49:311-343. [PMID: 15012237 DOI: 10.1146/annurev.arplant.49.1.311] [Citation(s) in RCA: 232] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cytochrome P450-dependent monooxygenases are a large group of heme-containing enzymes, most of which catalyze NADPH- and O2-dependent hydroxylation reactions. The cloning of plant P450s has been hampered because these membrane-localized proteins are typically present in low abundance and are often unstable to purification. Since the cloning of the first plant P450 gene in 1990, there has been an explosion in the rate at which genes encoding plant P450s have been identified. These successes have largely been the result of advances in purification techniques, as well as the application of alternative methods such as mutant- and PCR-based cloning strategies. The availability of these cloned genes has made possible the analysis of P450 gene regulation and may soon reveal aspects of the evolution of P450s in plants. This new knowledge will significantly improve our understanding of many metabolic pathways and may permit their manipulation in the near future.
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Affiliation(s)
- Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907-1153; e-mail:
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