Identification and Expression Analysis of R2R3-MYB Transcription Factors Associated with Flavonoid Biosynthesis in Panax quinquefolius
Abstract
:1. Introduction
2. Results
2.1. Identification and Physicochemical Properties Analysis
2.2. Phylogenetic Tree, Chromosome Location, and Collinear Analysis
2.3. Motifs and Domains of Protein and cis-Acting Element Analysis
2.4. Expression Pattern Analysis in Different Tissues
2.5. RNA-Seq and qRT-PCR
2.6. Co-Expression Analysis of PqMYBs and Flavonoid Biosynthesis Genes
2.7. Subcellular Localization Analysis
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Growth Conditions
4.2. Identification and Physicochemical Properties Analysis
4.3. Phylogenetic Tree, Chromosome Location, and Collinear Analysis
4.4. Analysis of Motifs and Domains of Proteins and cis-Acting Elements
4.5. Expression Patterns Analysis in Different Tissues
4.6. RNA-Seq Data and qRT-PCR
4.7. Subcellular Localization Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Hsu, B.Y.; Jen, C.T.; Inbaraj, B.S.; Chen, B.H. A Comparative Study on Analysis of Ginsenosides in American Ginseng Root Residue by HPLC-DAD-ESI-MS and UPLC-HRMS-MS/MS. Molecules 2022, 27, 3071. [Google Scholar] [CrossRef] [PubMed]
- Mancuso, C.; Santangelo, R. Panax ginseng and Panax quinquefolius: From pharmacology to toxicology. Food Chem. Toxicol. 2017, 107, 362–372. [Google Scholar] [CrossRef]
- Szczuka, D.; Nowak, A.; Zaklos-Szyda, M.; Kochan, E.; Szymanska, G.; Motyl, I.; Blasiak, J. American Ginseng (Panax quinquefolium L.) as a Source of Bioactive Phytochemicals with Pro-Health Properties. Nutrients 2019, 11, 1041. [Google Scholar] [CrossRef] [PubMed]
- Arring, N.M.; Millstine, D.; Marks, L.A.; Nail, L.M. Ginseng as a Treatment for Fatigue: A Systematic Review. J. Altern. Complement. Med. 2018, 24, 624–633. [Google Scholar] [CrossRef] [PubMed]
- Shen, N.; Wang, T.; Gan, Q.; Liu, S.; Wang, L.; Jin, B. Plant flavonoids: Classification, distribution, biosynthesis, and antioxidant activity. Food Chem. 2022, 383, 132531. [Google Scholar] [CrossRef] [PubMed]
- Yonekura-Sakakibara, K.; Higashi, Y.; Nakabayashi, R. The Origin and Evolution of Plant Flavonoid Metabolism. Front. Plant Sci. 2019, 10, 943. [Google Scholar] [CrossRef] [PubMed]
- Panche, A.N.; Diwan, A.D.; Chandra, S.R. Flavonoids: An overview. J. Nutr. Sci. 2016, 5, e47. [Google Scholar] [CrossRef] [PubMed]
- Ververidis, F.; Trantas, E.; Douglas, C.; Vollmer, G.; Kretzschmar, G.; Panopoulos, N. Biotechnology of flavonoids and other phenylpropanoid-derived natural products. Part II: Reconstruction of multienzyme pathways in plants and microbes. Biotechnol. J. 2007, 2, 1235–1249. [Google Scholar] [CrossRef] [PubMed]
- Zhang, J.; Li, X.G.; Zheng, Y.N.; Xu, C.L. Isolation of Panasenosides from the roots of Panax quinquefolium. Nat. Product. Res. Dev. 2002, 4, 29–30. (In Chinese) [Google Scholar]
- Li, X.G.; Du, X.R.; Yang, S.J. Pharmacological effects of the total flavone of leave of Panax quinquefolium (cultured in China). Chin. Pharmacol. Bull. 2000, 2, 229–230. (In Chinese) [Google Scholar]
- Ganesan, G.; Sankararamasubramanian, H.M.; Harikrishnan, M.; Ashwin, G.; Parida, A. A MYB transcription factor from the grey mangrove is induced by stress and confers NaCl tolerance in tobacco. J. Exp. Bot. 2012, 63, 4549–4561. [Google Scholar] [CrossRef] [PubMed]
- Millard, P.S.; Kragelund, B.B.; Burow, M. R2R3 MYB Transcription Factors—Functions outside the DNA-Binding Domain. Trends Plant Sci. 2019, 24, 934–946. [Google Scholar] [CrossRef] [PubMed]
- Dubos, C.; Stracke, R.; Grotewold, E.; Weisshaar, B.; Martin, C.; Lepiniec, L. MYB transcription factors in Arabidopsis. Trends Plant Sci. 2010, 15, 573–581. [Google Scholar] [CrossRef]
- Katiyar, A.; Smita, S.; Lenka, S.K.; Rajwanshi, R.; Chinnusamy, V.; Bansal, K.C. Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. BMC Genom. 2012, 13, 544. [Google Scholar] [CrossRef]
- Wei, Q.; Liu, Y.; Lan, K.; Wei, X.; Hu, T.; Chen, R.; Zhao, S.; Yin, X.; Xie, T. Identification and Analysis of MYB Gene Family for Discovering Potential Regulators Responding to Abiotic Stresses in Curcuma wenyujin. Front. Genet. 2022, 13, 894928. [Google Scholar] [CrossRef] [PubMed]
- Pratyusha, D.S.; Sarada, D.V.L. MYB transcription factors-master regulators of phenylpropanoid biosynthesis and diverse developmental and stress responses. Plant Cell Rep. 2022, 41, 2245–2260. [Google Scholar] [CrossRef] [PubMed]
- Wen, W.; Alseekh, S.; Fernie, A.R. Conservation and diversification of flavonoid metabolism in the plant kingdom. Curr. Opin. Plant Biol. 2020, 55, 100–108. [Google Scholar] [CrossRef] [PubMed]
- Wang, W.T.; Hu, S.Y.; Zhang, C.J.; Yang, J.; Zhang, T.; Wang, D.H.; Cao, X.Y.; Wang, Z.Z. Systematic Analysis and Functional Characterization of R2R3-MYB Genes in Scutellaria baicalensis Georgi. Int. J. Mol. Sci. 2022, 23, 9342. [Google Scholar] [CrossRef] [PubMed]
- Huang, D.; Ming, R.H.; Xu, S.Q.; Yao, S.C.; Li, L.B.; Huang, R.S.; Tan, Y. Genome-Wide Identification of R2R3-MYB Transcription Factors: Discovery of a “Dual-Function” Regulator of Gypenoside and Flavonol Biosynthesis in Gynostemma pentaphyllum. Front. Plant Sci. 2022, 12, 796248. [Google Scholar] [CrossRef]
- Abubakar, A.S.; Feng, X.K.; Gao, G.; Yu, C.M.; Chen, J.K.; Chen, K.M.; Wang, X.F.; Mou, P.; Shao, D.Y.; Chen, P.; et al. Genome wide characterization of R2R3 MYB transcription factor from Apocynum venetum revealed potential stress tolerance and flavonoid biosynthesis genes. Genomics 2022, 114, 110275. [Google Scholar] [CrossRef]
- Cao, Y.P.; Li, K.; Li, Y.L.; Zhao, X.P.; Wang, L.H. MYB Transcription Factors as Regulators of Secondary Metabolism in Plants. Biology 2020, 9, 61. [Google Scholar] [CrossRef] [PubMed]
- Fang, S.; Qiu, S.; Chen, K.; Lv, Z.; Chen, W. The transcription factors SbMYB45 and SbMYB86.1 regulate flavone biosynthesis in Scutellaria baicalensis. Plant Physiol. Biochem. 2023, 200, 107794. [Google Scholar] [CrossRef] [PubMed]
- Huang, W.; Sun, W.; Lv, H.; Luo, M.; Zeng, S.; Pattanaik, S.; Yuan, L.; Wang, Y. A R2R3-MYB transcription factor from Epimedium sagittatum regulates the flavonoid biosynthetic pathway. PLoS ONE 2013, 8, e70778. [Google Scholar] [CrossRef] [PubMed]
- Yang, F.; Wang, T.; Guo, Q.; Zou, Q.; Yu, S. The CmMYB3 transcription factors isolated from the Chrysanthemum morifolium regulate flavonol biosynthesis in Arabidopsis thaliana. Plant Cell Rep. 2023, 42, 791–803. [Google Scholar] [CrossRef] [PubMed]
- Jiang, L.; Yue, M.; Liu, Y.; Zhang, N.; Lin, Y.; Zhang, Y.; Wang, Y.; Li, M.; Luo, Y.; Zhang, Y.; et al. A novel R2R3-MYB transcription factor FaMYB5 positively regulates anthocyanin and proanthocyanidin biosynthesis in cultivated strawberries (Fragaria x ananassa). Plant Biotechnol. J. 2023, 21, 1140–1158. [Google Scholar] [CrossRef] [PubMed]
- Xu, H.; Dai, X.; Hu, X.; Yu, H.; Wang, Y.; Zheng, B.; Xu, J.; Wu, X. Phylogenetic Analysis of R2R3-MYB Family Genes in Tetrastigma hemsleyanum Diels et Gilg and Roles of ThMYB4 and ThMYB7 in Flavonoid Biosynthesis. Biomolecules 2023, 13, 531. [Google Scholar] [CrossRef] [PubMed]
- Westfall, C.S.; Muehler, A.M.; Jez, J.M. Enzyme action in the regulation of plant hormone responses. J. Biol. Chem. 2013, 288, 19304–19311. [Google Scholar] [CrossRef]
- Wasternack, C. Jasmonates: An update on biosynthesis, signal transduction and action in plant stress response, growth and development. Ann. Bot. 2007, 100, 681–697. [Google Scholar] [CrossRef]
- Liu, T.; Luo, T.; Guo, X.Q.; Zou, X.; Zhou, D.H.; Afrin, S.; Li, G.; Zhang, Y.; Zhang, R.; Luo, Z.Y. PgMYB2, a MeJA-Responsive Transcription Factor, Positively Regulates the Dammarenediol Synthase Gene Expression in Panax ginseng. Int. J. Mol. Sci. 2019, 20, 2219. [Google Scholar] [CrossRef]
- Premathilake, A.T.; Ni, J.B.; Shen, J.Q.; Bai, S.L.; Teng, Y.W. Transcriptome analysis provides new insights into the transcriptional regulation of methyl jasmonate-induced flavonoid biosynthesis in pear calli. BMC Plant Biol. 2020, 20, 388. [Google Scholar] [CrossRef]
- Deng, C.P.; Wang, Y.; Huang, F.F.; Lu, S.J.; Zhao, L.M.; Ma, X.Y.; Kai, G.Y. SmMYB2 promotes salvianolic acid biosynthesis in the medicinal herb Salvia miltiorrhiza. J. Integr. Plant Biol. 2020, 62, 1688–1702. [Google Scholar] [CrossRef] [PubMed]
- Stracke, R.; Ishihara, H.; Huep, G.; Barsch, A.; Mehrtens, F.; Niehaus, K.; Weisshaar, B. Differential regulation of closely related R2R3-MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling. Plant J. 2007, 50, 660–677. [Google Scholar] [CrossRef] [PubMed]
- Song, X.H.; Yang, Q.S.; Liu, Y.; Li, J.J.; Chang, X.C.; Xian, L.H.; Zhang, J. Genome-wide identification of Pistacia R2R3-MYB gene family and function characterization of PcMYB113 during autumn leaf coloration in Pistacia chinensis. Int. J. Biol. Macromol. 2021, 192, 16–27. [Google Scholar] [CrossRef] [PubMed]
- Wang, X.C.; Wu, J.; Guan, M.L.; Zhao, C.H.; Geng, P.; Zhao, Q. Arabidopsis MYB4 plays dual roles in flavonoid biosynthesis. Plant J. 2020, 101, 637–652. [Google Scholar] [CrossRef] [PubMed]
- Fornale, S.; Lopez, E.; Salazar-Henao, J.E.; Fernandez-Nohales, P.; Rigau, J.; Caparros-Ruiz, D. AtMYB7, a new player in the regulation of UV-sunscreens in Arabidopsis thaliana. Plant Cell Physiol. 2014, 55, 507–516. [Google Scholar] [CrossRef] [PubMed]
- Zhang, L.; Duan, Z.; Ma, S.; Sun, S.; Sun, M.; Xiao, Y.; Ni, N.; Irfan, M.; Chen, L.; Sun, Y. SlMYB7, an AtMYB4-Like R2R3-MYB Transcription Factor, Inhibits Anthocyanin Accumulation in Solanum lycopersicum Fruits. J. Agric. Food Chem. 2023, 71, 18758–18768. [Google Scholar] [CrossRef]
- Anwar, M.; Yu, W.; Yao, H.; Zhou, P.; Allan, A.C.; Zeng, L. NtMYB3, an R2R3-MYB from Narcissus, Regulates Flavonoid Biosynthesis. Int. J. Mol. Sci. 2019, 20, 5456. [Google Scholar] [CrossRef] [PubMed]
- Li, J.; Xu, S.; Mei, Y.; Gu, Y.; Sun, M.; Zhang, W.; Wang, J. Genomic-wide identification and expression analysis of R2R3-MYB transcription factors related to flavonol biosynthesis in Morinda officinalis. BMC Plant Biol. 2023, 23, 381. [Google Scholar] [CrossRef] [PubMed]
- Zhang, W.; Xu, F.; Cheng, S.; Liao, Y. Characterization and functional analysis of a MYB gene (GbMYBFL) related to flavonoid accumulation in Ginkgo biloba. Genes Genom. 2018, 40, 49–61. [Google Scholar] [CrossRef]
- Zhang, Y.; Duan, J.; Wang, Q.; Zhang, M.; Zhi, H.; Bai, Z.; Zhang, Y.; Luo, J. The Paeonia qiui R2R3-MYB Transcription Factor PqMYBF1 Positively Regulates Flavonol Accumulation. Plants 2023, 12, 1427. [Google Scholar] [CrossRef]
- Wang, Z.H.; Wang, X.F.; Lu, T.Y.; Li, M.R.; Jiang, P.; Zhao, J.; Liu, S.T.; Fu, X.Q.; Wendel, J.F.; Van de Peer, Y.; et al. Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax. Nat. Commun. 2022, 13, 1902. [Google Scholar] [CrossRef] [PubMed]
- Chen, C.J.; Chen, H.; Zhang, Y.; Thomas, H.R.; Frank, M.H.; He, Y.H.; Xia, R. TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol. Plant 2020, 13, 1194–1202. [Google Scholar] [CrossRef] [PubMed]
- Di, P.; Yan, Y.; Wang, P.; Yan, M.; Wang, Y.-P.; Huang, L.-Q. Integrative SMRT sequencing and ginsenoside profiling analysis provide insights into the biosynthesis of ginsenoside in Panax quinquefolium. Chin. J. Nat. Med. 2022, 20, 614–626. [Google Scholar] [CrossRef] [PubMed]
- Sun, C.; Li, Y.; Wu, Q.; Luo, H.M.; Sun, Y.Z.; Song, J.Y.; Lui, E.M.K.; Chen, S.L. sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis. BMC Genom. 2010, 11, 262. [Google Scholar] [CrossRef] [PubMed]
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Song, G.; Yan, Y.; Guo, C.; Chen, J.; Wang, Y.; Wang, Y.; Zhang, J.; Gao, C.; Lian, J.; Piao, X.; et al. Identification and Expression Analysis of R2R3-MYB Transcription Factors Associated with Flavonoid Biosynthesis in Panax quinquefolius. Int. J. Mol. Sci. 2024, 25, 3709. https://doi.org/10.3390/ijms25073709
Song G, Yan Y, Guo C, Chen J, Wang Y, Wang Y, Zhang J, Gao C, Lian J, Piao X, et al. Identification and Expression Analysis of R2R3-MYB Transcription Factors Associated with Flavonoid Biosynthesis in Panax quinquefolius. International Journal of Molecular Sciences. 2024; 25(7):3709. https://doi.org/10.3390/ijms25073709
Chicago/Turabian StyleSong, Guimei, Yan Yan, Chun Guo, Jiankang Chen, Yumeng Wang, Yingping Wang, Jiaxin Zhang, Chang Gao, Junmei Lian, Xiangmin Piao, and et al. 2024. "Identification and Expression Analysis of R2R3-MYB Transcription Factors Associated with Flavonoid Biosynthesis in Panax quinquefolius" International Journal of Molecular Sciences 25, no. 7: 3709. https://doi.org/10.3390/ijms25073709