The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View
Abstract
:1. Introduction
2. Plant Lignan Biosynthesis and Tissue Compartmentation
3. Genetic Regulation of Plant Lignan Biosynthesis
4. The Involvement of miRNA in Plant Lignan Biosynthesis
5. Current Approaches for Functional Identification of miRNAs in Plant Metabolites Biosynthesis
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Tu, Z.; Xia, H.; Yang, L.; Zhai, X.; Shen, Y.; Li, H. The Roles of microRNA-Long Non-coding RNA-mRNA Networks in the Regulation of Leaf and Flower Development in Liriodendron chinense. Front. Plant Sci. 2022, 13, 816875. [Google Scholar] [CrossRef] [PubMed]
- Chakraborty, S.; Kumar, P.; Sanyal, R.; Mane, D.B.; Prasanth, D.A.; Patil, M.; Dey, A. Unravelling the regulatory role of miRNAs in secondary metabolite production in medicinal crops. Plant Gene 2021, 27, 100303. [Google Scholar] [CrossRef]
- Adjei, M.O.; Zhou, X.; Mao, M.; Rafique, F.; Ma, J. MicroRNAs Roles in Plants Secondary Metabolism. Plant Signal. Behav. 2021, 16, 1915590. [Google Scholar] [CrossRef] [PubMed]
- Anwar, M.; Chen, L.; Xiao, Y.; Wu, J.; Zeng, L.; Li, H.; Wu, Q.; Hu, Z. Recent Advanced Metabolic and Genetic Engineering of Phenylpropanoid Biosynthetic Pathways. Int. J. Mol. Sci. 2021, 22, 9544. [Google Scholar] [CrossRef]
- DellaGreca, M.; Zuppolini, S.; Zarrelli, A. Isolation of lignans as seed germination and plant growth inhibitors from Mediterranean plants and chemical synthesis of some analogues. Phytochem. Rev. 2013, 12, 717–731. [Google Scholar] [CrossRef]
- Zálešák, F.; Bon, D.J.Y.D.; Pospíšil, J. Plant secondary metabolites as a reservoir of biologically active substances. Pharmacol. Res. 2019, 146, 104284. [Google Scholar] [CrossRef]
- Barker, D. Lignans. Molecules 2019, 24, 1424. [Google Scholar] [CrossRef] [Green Version]
- Ramsay, A.; Fliniaux, O.; Quéro, A.; Molinié, R.; Demailly, H.; Hano, C.; Paetz, C.; Roscher, A.; Grand, E.; Kovensky, J.; et al. Kinetics of the incorporation of the main phenolic compounds into the lignan macromolecule during flaxseed development. Food Chem. 2017, 15, 1–8. [Google Scholar] [CrossRef]
- Smeds, A.I.; Eklund, P.C.; Willför, S.M. Content, composition, and stereochemical characterization of lignans in berries and seeds. Food Chem. 2012, 134, 1991–1998. [Google Scholar] [CrossRef]
- Yang, K.; Han, H.; Li, Y.; Ye, J.; Xu, F. Significance of miRNA in enhancement of flavonoid biosynthesis. Plant Biol. J. 2022, 24, 217–226. [Google Scholar] [CrossRef]
- Schmidt, T.J.; Hemmati, S.; Klaes, M.; Konuklugil, B.; Mo-Hagheghzadeh, A.; Ionkova, I.; Fuss, E.; Wilhelm Alfer-mann, A. Lignans in flowering aerial parts of Linum species--chemodiversity in the light of systematics andphylogeny. Phytochemistry 2010, 71, 1714–1728. [Google Scholar] [CrossRef]
- Schmidt, T.J.; Klaes, M.; Sendker, J. Lignans in seeds of Linum species. Phytochemistry 2012, 82, 89–99. [Google Scholar] [CrossRef]
- Dalisay, D.S.; Kim, K.W.; Lee, C.S.; Yang, H.; Rübel, O.; Bowen, B.P.; Davin, L.B.; Lewis, N.G. Dirigent protein-mediated lignan and cyanogenic glucoside formation in flax seed: Integrated omics and MALDI mass spectrometry imaging. J. Nat. Prod. 2015, 78, 1231–1242. [Google Scholar] [CrossRef]
- Kasote, D.M. Flaxseed phenolics as natural antioxidants. Int. Food. Res. J. 2013, 20, 27. [Google Scholar]
- Bjelková, M.; Filip, V.; Kyselka, J.; Ševčík, R.; Větrovcová, M. Výběr a charakteristika lněného semene jako vstupní suroviny (Selection and Characteristics of Flaxseed as an Input Raw Material); Agritec Plant Research Ltd.: Šumperk, Czech Republic, 2017; ISBN 978-80-87360-57-6. [Google Scholar]
- Garros, L.; Drouet, S.; Corbin, C.; Decourtil, C.; Fidel, T.; Lebas de Lacour, J.; Leclerc, E.A.; Renouard, S.; Tungmunnithum, D.; Doussot, J.; et al. Insight into the Influence of Cultivar Type, Cultivation Year, and Site on the Lignans and Related Phenolic Profiles, and the Health-Promoting Antioxidant Potential of Flax (Linum usitatissimum L.) Seeds. Molecules 2018, 23, 2636. [Google Scholar] [CrossRef] [Green Version]
- Yu, Y.; Wu, G.; Yuan, H.; Cheng, L.; Zhao, D.; Huang, W.; Zhang, S.; Zhang, L.; Chen, H.; Zhang, J.; et al. Identification and characterization of miRNAs and targets in flax (Linum usitatissimum) under saline, alkaline, and saline-alkaline stresses. BMC Plant Biol. 2016, 16, 124. [Google Scholar] [CrossRef] [Green Version]
- Zhou, X.; Khare, T.; Kumar, V. Recent trends and advances in identification and functional characterization of plant miRNAs. Acta Physiol. Plant 2020, 42, 25. [Google Scholar] [CrossRef]
- Millar, A.A. The function of miRNAs in plants. Plants 2020, 9, 198. [Google Scholar] [CrossRef] [Green Version]
- Sand, M. The pathway of miRNA maturation. miRNA Maturation 2014, 1095, 3–10. [Google Scholar]
- Sabzehzari, M.; Naghavi, M.R. Phyto-miRNAs-based regulation of metabolites biosynthesis in medicinal plants. Gene 2019, 682, 13–24. [Google Scholar] [CrossRef]
- Samad, A.F.; Sajad, M.; Nazaruddin, N.; Fauzi, I.A.; Murad, A.; Zainal, Z.; Ismail, I. MicroRNA and transcription factor: Key players in plant regulatory network. Front. Plant Sci. 2017, 8, 565. [Google Scholar] [CrossRef] [Green Version]
- Jiang, S.; Cui, J.L.; Li, X.K. MicroRNA-Mediated Gene Regulation of Secondary Metabolism in Plants. Crit Rev. Plant Sci. 2021, 40, 459–478. [Google Scholar] [CrossRef]
- Teponno, R.B.; Kusari, S.; Spiteller, M. Recent advances in research on lignans and neolignans. Nat. Prod. Rep. 2016, 33, 1044–1092. [Google Scholar] [CrossRef] [Green Version]
- Touré, A.; Xueming, X. Flaxseed lignans: Source, biosynthesis, metabolism, antioxidant activity, bio-active components, and health benefits. Compr. Rev. Food. Sci. Food Saf. 2010, 9, 261–269. [Google Scholar] [CrossRef]
- MetaCyc. Available online: https://metacyc.org/ (accessed on 28 March 2022).
- Boerjan, W.; Ralph, J.; Baucher, M. Lignin Biosynthesis. Annu. Rev. Plant Biol. 2003, 54, 519–546. [Google Scholar] [CrossRef]
- Markulin, L.; Corbin, C.; Renouard, S.; Drouet, S.; Durpoix, C.; Mathieu, C.; Lopez, T.; Augin, D.; Hano, C.; Lainé, É. Characterization of LuWRKY36, a flax transcription factor promoting secoisolariciresinol biosynthesis in response to Fusarium oxysporum elicitors in Linum usitatissimum L. hairy roots. Planta 2019, 250, 347–366. [Google Scholar] [CrossRef]
- Le Roy, J.; Blervacq, A.S.; Créach, A.; Huss, B.; Hawkins, S.; Neutelings, G. Spatial regulation of monolignol biosynthesis and laccase genes control developmental and stress-related lignin in flax. BMC Plant Biol. 2017, 17, 124. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Lewis, N.G.; Davin, L.B.; Sarkanen, S. Lignin and Lignan Biosynthesis: Distinctions and Reconciliations. Chapter 1. In ACS Symposium Series; American Chemical Society: Washington, DC, USA, 1998. [Google Scholar]
- Huis, R.; Morreel, K.; Fliniaux, O.; Lucau-Danila, A.; Fénart, S.; Grec, S.; Neutelings, G.; Chabbert, B.; Mesnard, F.; Boerjan, W.; et al. Natural hypolignification is associated with extensive oligolignol accumulation in flax stems. Plant Physiol. 2012, 158, 1893–1915. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Park, H.L.; Bhoo, S.H.; Kwon, M.; Lee, S.W.; Cho, M.H. Biochemical and Expression Analyses of the Rice Cinnamoyl-CoA Reductase Gene Family. Front. Plant Sci. 2017, 8, 2099. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Jardim-Messeder, D.; Felix-Cordeiro, T.; Barzilai, L.; de Souza-Vieira, Y.; Galhego, V.; Bastos, G.A.; Valente-Almeida, G.; Aiube, Y.R.A.; Faria-Reis, A.; Corrêa, R.L.; et al. Genome-wide analysis of general phenylpropanoid and monolignol-specific metabolism genes in sugarcane. Funct. Integr. Genom. 2021, 21, 73–99. [Google Scholar] [CrossRef]
- Moura, J.C.M.S.; Bonine, C.A.V.; De Oliveira Fernandes Viana, J.; Dornelas, M.C.; Mazzafera, P. Abiotic and Biotic Stresses and Changes in the Lignin Content and Composition in Plants. J. Integr. Plant Biol. 2010, 52, 360–376. [Google Scholar] [CrossRef]
- Trumbo, J.L.; Zhang, B.; Stewart, C.N., Jr. Manipulating microRNAs for improved biomass and biofuels from plant feedstocks. Plant Biotechnol. J. 2015, 13, 337–354. [Google Scholar] [CrossRef] [Green Version]
- Lu, S.; Li, Q.; Wei, H.; Chang, M.J.; Tunlaya-Anukit, S.; Kim, H.; Liu, J.; Song, J.; Sun, Y.H.; Yuan, L.; et al. Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa. Proc. Natl. Acad. Sci. USA 2013, 25, 10848–10853. [Google Scholar] [CrossRef] [Green Version]
- Fuss, E. Lignans in plant cell and organ cultures: An overview. Phytochem. Rev. 2003, 2, 307–320. [Google Scholar] [CrossRef]
- Consonni, R.; Ottolina, G. NMR Characterization of Lignans. Molecules 2022, 27, 2340. [Google Scholar] [CrossRef]
- Willför, S.M.; Smeds, A.I.; Holmboma, B.R. Chromatographic analysis of lignans. J. Chromatogr. A 2006, 1112, 64–77. [Google Scholar] [CrossRef]
- Rodríguez-García, C.; Sánchez-Quesada, C.; Toledo, E.; Del-gado-Rodríguez, M.; Gaforio, J.J. Naturallylignan-rich foods: A dietary tool for health promotion? Molecules 2019, 24, 917. [Google Scholar] [CrossRef] [Green Version]
- Suzuki, S.; Umezawa, T.; Shimada, M. Stereo-chemical diversity in lignan biosynthesis of Arctium lappa L. Biosci. Biotechnol. Biochem. 2002, 66, 1262–1269. [Google Scholar] [CrossRef] [Green Version]
- Attoumbré, J.; Bienaimé, C.; Dubois, F.; Fliniaux, M.A.; Chabbert, B.; Baltora-Rosseta, S. Development of antibodies against secoisolariciresinol—Application to the immunolocalization of lignans in Linum usitatissimum seeds. Phytochemistry 2010, 71, 1979–1987. [Google Scholar] [CrossRef]
- Paniagua, C.; Bilkova, A.; Jackson, P.; Dabravolski, S.; Riber, W.; Didi, V.; Houser, J.; Gigli-Bisceglia, N.; Wimmerova, M.; Budínská, E.; et al. Dirigent proteins in plants: Modulating cell wall metabolism during abiotic and biotic stress exposure. J. Exp. Bot. 2017, 68, 3287–3301. [Google Scholar] [CrossRef] [Green Version]
- Corbin, C.; Drouet, S.; Markulin, L.; Auguin, D.; Lainé, É.; Davin, L.B.; Cort, J.R.; Lewis, N.G.; Hano, C. A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: From gene identification and evolution to differential regulation. Plant Mol. Biol. 2018, 97, 73–101. [Google Scholar] [CrossRef]
- Anjum, S.; Komal, A.; Drouet, S.; Kausar, H.; Hano, C.; Abbasi, B.H. Feasible production of lignans and neolignans in root-derived in vitro cultures of flax (Linum usitatissimum L.). Plants 2020, 9, 409. [Google Scholar] [CrossRef] [Green Version]
- Zhao, Q.; Zeng, Y.; Yin, Y.; Pu, Y.; Jackson, L.A.; Engle, N.L.; Martin, M.Z.; Tschaplinski, T.J.; Ding, S.Y.; Ragauskas, A.J.; et al. Pinoresinol reductase 1 impacts lignin distribution during secondary cell wall biosynthesis in Arabidopsis. Phytochemistry 2015, 112, 170–178. [Google Scholar] [CrossRef] [Green Version]
- Hano, C.; Martin, I.; Fliniaux, O.; Legrand, B.; Gutierrez, L.; Arroo, R.R.J.; Mesnard, F.; Lamblin, F.; Lainé, E. Pinoresinol–lariciresinol reductase gene expression and secoisolariciresinol diglucoside accumulation in developing flax (Linum usitatissimum) seeds. Planta 2006, 224, 1291–1301. [Google Scholar] [CrossRef]
- Renouard, S.; Tribalatc, M.A.; Lamblin, F.; Mongelard, G.; Fliniaux, O.; Corbin, C.; Marosevic, D.; Pilard, S.; Demailly, H.; Gutierrez, L.; et al. RNAi-mediated pinoresinol lariciresinol reductase gene silencing in flax (Linum usitatissimum L.) seed coat: Consequences on lignans and neolignans accumulation. J. Plant Physiol. 2014, 171, 1372–1377. [Google Scholar] [CrossRef]
- Fofana, B.; Ghose, K.; McCallum, J.; You, F.M.; Cloutier, S. UGT74S1 is the key player in controlling secoisolariciresinol diglucoside (SDG) formation in flax. BMC Plant Biol. 2017, 17, 35. [Google Scholar] [CrossRef] [Green Version]
- Patra, B.; Schluttenhofer, C.; Wu, Y.; Pattanaik, S.; Yuan, L. Transcriptional regulation of secondary metabolite biosynthesis in plants. Biochim. Biophys. Acta. Gene. Regul. Mech. 2013, 1829, 1236–1247. [Google Scholar] [CrossRef]
- Hemmati, S.; von Heimendahl, C.B.; Klaes, M.; Alfermann, A.W.; Schmidt, T.J.; Fuss, E. Pinoresinol-lariciresinol reductases with opposite enantiospecificity determine the enantiomeric composition of lignans in the different organs of Linum usitatissimum L. Planta Med. 2010, 76, 928–934. [Google Scholar] [CrossRef] [Green Version]
- Ahmad, W.; Zahir, A.; Nadeem, M.; Garros, L.; Drouet, S.; Renouard, S.; Doussot, J.; Giglioli-Guivarc’h, N.; Hano, C.; Abbasi, B.H. Enhanced production of lignans and neolignans in chitosan-treated flax (Linum usitatissimum L.) cell cultures. Process. Biochem. 2019, 79, 155–165. [Google Scholar] [CrossRef]
- Gupta, O.P.; Karkute, S.G.; Banerjee, S.; Meena, N.L.; Dahuja, A. Contemporary understanding of miRNA-based regulation of secondary metabolites biosynthesis in plants. Front. Plant Sci. 2017, 8, 374. [Google Scholar] [CrossRef] [Green Version]
- Arora, S.; Rana, R.; Chhabra, A.; Jaiswal, A.; Rani, V. miRNA–transcription factor interactions: A combinatorial regulation of gene expression. Mol. Genet. Genom. 2013, 288, 77–87. [Google Scholar] [CrossRef] [PubMed]
- Šamec, D.; Karalija, E.; Šola, I.; Vujčić Bok, V.; Salopek-Sondi, B. The Role of Polyphenols in Abiotic Stress Response: The Influence of Molecular Structure. Plants 2021, 10, 118. [Google Scholar] [CrossRef] [PubMed]
- Sharma, A.; Shahzad, B.; Rehman, A.; Bhardwaj, R.; Landi, M.; Zheng, B. Response of phenylpropanoid pathway and the role of polyphenols in plants under abiotic stress. Molecules 2019, 24, 2452. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Umezawa, T. The cinnamate/monolignol pathway. Phytochem. Rev. 2010, 9, 1–17. [Google Scholar] [CrossRef]
- Marcela, V.; Gerardo, V.; Agustín, A.C.; Antonio, G.M.; Oscar, R.; Diego, C.; Cruz-Hernández, A. MicroRNAs Associated with Secondary Metabolites Production. In Plant Physiological Aspects of Phenolic Compounds; Soto-Hernández, M., García-Mateos, R., Palma-Tenango, M., Eds.; IntechOpen: London, UK, 2019. [Google Scholar] [CrossRef] [Green Version]
- Wei, K.; Chen, H. Global identification, structural analysis and expression characterization of cytochrome P450 monooxygenase superfamily in rice. BMC Genom. 2018, 19, 35. [Google Scholar] [CrossRef] [Green Version]
- Zhang, C.; Xu, X.; Xu, X.; Li, Y.; Zhao, P.; Chen, X.; Shen, X.; Zhang, Z.; Chen, Y.; Liu, S.; et al. Genome-wide identification, evolution analysis of cytochrome P450 monooxygenase multigene family and their expression patterns during the early somatic embryogenesis in Dimocarpus longan Lour. Gene 2022, 826, 146453. [Google Scholar] [CrossRef]
- Biswas, S.; Hazra, S.; Chattopadhyay, S. Identification of conserved miRNAs and their putative target genes in Podophyllum hexandrum (Himalayan Mayapple). Plant Gene 2016, 6, 82–89. [Google Scholar] [CrossRef] [Green Version]
- Barvkar, V.T.; Pardeshi, V.C.; Kale, S.M.; Qiu, S.; Rollins, M.; Datla, R.; Gupta, V.S.; Kadoo, N.Y. Genome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum): Characterization of flax miRNA genes. Planta 2013, 237, 1149–1161. [Google Scholar] [CrossRef]
- Yan, F.; Li, H.; Zhao, P. Genome-Wide Identification and Transcriptional Expression of the PAL Gene Family in Common Walnut (Juglans Regia L.). Genes 2019, 10, 46. [Google Scholar] [CrossRef] [Green Version]
- Wang, S.; Liu, S.; Liu, L.; Li, R.; Guo, R.; Xia, X.; Wei, C. miR477 targets the phenylalanine ammonia-lyase gene and enhances the susceptibility of the tea plant (Camellia sinensis) to disease during Pseudopestalotiopsis species infection. Planta 2020, 251, 59. [Google Scholar] [CrossRef]
- Singh, N.; Srivastava, S.; Sharma, A. Identification and analysis of miRNAs and their targets in ginger using bioinformatics approach. Gene 2016, 10, 570–576. [Google Scholar] [CrossRef]
- Liu, M.; Dong, H.; Wang, M.; Liu, Q. Evolutionary divergence of function and expression of laccase genes in plants. J. Genet. 2020, 99, 23. [Google Scholar] [CrossRef]
- Li, C.; Li, D.; Zhou, H.; Li, J.; Lu, S. Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza. PeerJ 2019, 7, e7605. [Google Scholar] [CrossRef] [Green Version]
- Wang, C.Y.; Zhang, S.; Yu, Y.; Luo, Y.C.; Liu, Q.; Ju, C.; Zhang, Y.C.; Qu, L.H.; Lucas, W.J.; Wang, X.; et al. MiR397b regulates both lignin content and seed number in Arabidopsis via modulating a laccase involved in lignin biosynthesis. Plant Biotechnol. J. 2014, 12, 1132–1142. [Google Scholar] [CrossRef] [Green Version]
- Ghose, K.; Selvaraj, K.; McCallum, J.; Kirby, C.W.; Sweeney-Nixon, M.; Cloutier, S.J.; Deyholos, M.; Datla, R.; Fofana, B. Identification and functional characterization of a flax UDP-glycosyltransferase glucosylating secoisolariciresinol (SECO) into secoisolariciresinol monoglucoside (SMG) and diglucoside (SDG). BMC Plant Biol. 2014, 28, 82. [Google Scholar] [CrossRef] [Green Version]
- Tiwari, P.; Sangwan, R.S.; Sangwas, N.S. Plant secondary metabolism linked glycosyltransferases: An update on expanding knowledge and scopes. Biotechnol. Adv. 2016, 34, 714–739. [Google Scholar] [CrossRef]
- Neutelings, G.; Fénart, S.; Lucau-Danila, A.; Hawkins, S. Identification and characterization of miRNAs and their potential targets in flax. J. Plant Physiol. 2012, 169, 1754–1766. [Google Scholar] [CrossRef]
- Abdel-Ghany, S.E.; Pilon, M. MicroRNA-mediated systemic down-regulation of copper protein expression in response to low copper availability in Arabidopsis. J. Biol. Chem. 2008, 23, 15932–15945. [Google Scholar] [CrossRef] [Green Version]
- Arnaud, D.; Déjardin, A.; Leplé, J.C.; Lesage-Descauses, M.C.; Boizot, N.; Villar, M.; Bénédetti, H.; Pilate, G. Expression analysis of LIM gene family in poplar, toward an updated phylogenetic classification. BMC Res. Notes 2012, 17, 102. [Google Scholar] [CrossRef] [Green Version]
- Hong, C.P.; Kim, C.K.; Lee, D.J.; Jeong, H.J.; Lee, Y.; Park, S.G.; Kang, S.H. Long-read transcriptome sequencing provides insight into lignan biosynthesis during fruit development in Schisandra chinensis. BMC Genom. 2022, 23, 17. [Google Scholar] [CrossRef]
- Tamagnone, L.; Merida, A.; Parr, A.; Mackay, S.; Culianez-Macia, F.A.; Roberts, K.; Martin, C. The AmMYB308 and AmMYB330 transcription factors from Antirrhinum regulate phenylpropanoid and lignin biosynthesis in transgenic tobacco. Plant Cell 1998, 10, 135–154. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Mehrtens, F.; Kranz, H.; Bednarek, P.; Weisshaar, B. The Arabidopsis transcription factor MYB12 is a flavonol-specific regulator of phenylpropanoid biosynthesis. Plant Physiol. 2005, 138, 1083–1096. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Sharma, D.; Tiwari, M.; Pandey, A.; Bhatia, C.; Sharma, A.; Trivedi, P.K. MicroRNA858 is a potential regulator of phenylpropanoid pathway and plant development. Plant Physiol. 2016, 171, 944–959. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Debbarma, J.; Sarki, Y.N.; Saikia, B.; Boruah, H.P.D.; Singha, D.L.; Chikkaputtaiah, C.H. Ethylene Response Factor (ERF) Family Proteins in Abiotic Stresses and CRISPR–Cas9 Genome Editing of ERFs for Multiple Abiotic Stress Tolerance in Crop Plants: A Review. Mol. Biotechnol. 2019, 61, 153–172. [Google Scholar] [CrossRef] [PubMed]
- Licausi, F.; Ohme-Takagi, M.; Perata, P. APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors: Mediators of stress responses and developmental programs. New Phytol. 2013, 199, 639–649. [Google Scholar] [CrossRef]
- Ma, R.; Xiao, Y.; Lv, Z.; Tan, H.; Chen, R.; Li, Q.; Chen, J.; Wang, Y.; Yin, J.; Zhang, L.; et al. AP2/ERF transcription factor, Ii049, positively regulates lignan biosynthesis in Isatis indigotica through activating salicylic acid signaling and lignan/lignin pathway genes. Front. Plant Sci. 2017, 8, 1361. [Google Scholar] [CrossRef] [Green Version]
- Xie, d.; Yu, Y.; Dai, Z.; Sun, J.; Su, J. Identification and characterization of miRNAs and target genes in developing flax seeds by multigroup analysis. Biotechnol. Biotechnol. Equip. 2021, 35, 538–550. [Google Scholar] [CrossRef]
- Hossain, R.; Quispe, C.; Saikat, A.S.M.; Jain, D.; Habib, A.; Janmeda, P.; Radha, M.T.I.; Daştan, S.D.; Kumar, M.; Butnariu, M.; et al. Biosynthesis of Secondary Metabolites Based on the Regulation of MicroRNAs. BioMed Res. Int. 2022, 2022, 9349897. [Google Scholar] [CrossRef]
- Bordoloi, K.S.; Baruah, P.M.; Das, M.; Agarwala, N. Unravelling lncRNA mediated gene expression as potential mechanism for regulating secondary metabolism in Citrus limon. Food Biosci. 2022, 46, 101448. [Google Scholar] [CrossRef]
- Bulgakov, V.P.; Avramenko, T.V. New opportunities for the regulation of secondary metabolism in plants: Focus on microRNAs. Biotechnol. Lett. 2015, 37, 1719–1727. [Google Scholar] [CrossRef]
- Xie, W.; Weng, A.; Melzig, M.F. MicroRNAs as new bioactive components in medicinal plants. Planta Med. 2016, 82, 1153–1162. [Google Scholar] [CrossRef] [Green Version]
- Zhang, L.; Ge, X.; Du, J.; Cheng, X.; Peng, X.; Hu, J. Genome-Wide Identification of Long Non-Coding RNAs and Their Potential Functions in Poplar Growth and Phenylalanine Biosynthesis. Front. Genet. 2021, 12, 762678. [Google Scholar] [CrossRef]
- Gutiérrez-García, C.; Ahmed, S.S.; Ramalingam, S.; Selvaraj, D.; Srivastava, A.; Paul, S.; Sharma, A. Identification of microRNAs from Medicinal Plant Murraya koenigii by High-Throughput Sequencing and Their Functional Implications in Secondary Metabolite Biosynthesis. Plants 2021, 11, 46. [Google Scholar] [CrossRef]
- Lin, S.; Singh, R.K.; Moehninsi, M.; Navarre, D.A. R2R3-MYB transcription factors, StmiR858 and sucrose mediate potato flavonol biosynthesis. Hortic. Res. 2021, 8, 25. [Google Scholar] [CrossRef]
- Qiao, Y.; Zhang, J.; Zhang, J.; Wang, Z.; Ran, A.; Guo, H.; Wang, D.; Zhang, J. Integrated RNA-seq and sRNA-seq analysis reveals miRNA effects on secondary metabolism in Solanum tuberosum L. Mol. Genet. Genom. 2017, 292, 37–52. [Google Scholar] [CrossRef]
- Khan, S.; Ali, A.; Saifi, M.; Saxena, P.; Ahlawat, S.; Abdin, M.Z. Identification and the potential involvement of miRNAs in the regulation of artemisinin biosynthesis in A. annua. Sci. Rep. 2020, 10, 13614. [Google Scholar] [CrossRef]
- Sabzehzari, M.; Naghavi, M.R. Phyto-miRNA: A molecule with beneficial abilities for plant biotechnology. Gene 2019, 683, 28–34. [Google Scholar] [CrossRef]
- Ding, C.; Shen, T.; Ran, N.; Zhang, H.; Pan, H.; Su, X.; Xu, M. Integrated Degradome and Srna Sequencing Revealed miRNA-mRNA Regulatory Networks between the Phloem and Developing Xylem of Poplar. Int. J. Mol. Sci. 2022, 23, 4537. [Google Scholar] [CrossRef]
- Li, Y.; Cui, W.; Qi, X.; Lin, M.; Qiao, C.; Zhong, Y.; Hu, C.; Fang, J. MicroRNA858 negatively regulates anthocyanin biosynthesis by repressing AaMYBC1 expression in kiwifruit (Actinidia arguta). Plant Sci. 2020, 296, 110476. [Google Scholar] [CrossRef]
- Ahmed, M.; Ahmed, F.; Ahmed, J.; Akhand, M.R.N.; Azim, K.F.; Imran, M.A.S.; Hoque, S.F.; Hasan, M. In silico identification of conserved miRNAs in the genome of fibre biogenesis crop Corchorus capsularis. Heliyon 2021, 7, e06705. [Google Scholar] [CrossRef]
- Zhang, L.; Xia, H.; Wu, J.; Li, M. MiRNA identification, characterization and integrated network analysis for flavonoid biosynthesis in Brassica raphanus. Hortic. Plant J. 2022, 8, 319–327. [Google Scholar] [CrossRef]
- Hassani, D.; Fu, X.; Shen, Q.; Khalid, M.; Rose, J.K.C.; Tang, K. Parallel Transcriptional Regulation of Artemisinin and Flavonoid Biosynthesis. Trends Plant Sci. 2020, 25, 466–476. [Google Scholar] [CrossRef]
- Geng, D.; Shen, X.; Xie, Y.; Yang, Y.; Bian, R.; Gao, Y.; Li, P.; Sun, L.; Feng, H.; Ma, F.; et al. Regulation of phenylpropanoid biosynthesis by MdMYB88 and MdMYB124 contributes to pathogen and drought resistance in apple. Hortic. Res. 2020, 7, 102. [Google Scholar] [CrossRef]
- Liu, J.; Fan, H.; Wang, Y.; Han, C.; Wang, X.; Yu, J.; Li, D.; Zhang, Y. Genome-wide microRNA profiling using oligonucleotide microarray reveals regulatory networks of microRNAs in Nicotiana benthamiana during Beet necrotic yellow vein virus infection. Viruses 2020, 12, 310. [Google Scholar] [CrossRef] [Green Version]
- Jeena, G.S.; Singh, N.; Shukla, R.K. An insight into microRNA biogenesis and its regulatory role in plant secondary metabolism. Plant Cell Rep. 2022, 1–21. [Google Scholar] [CrossRef]
- Wan, F.; Zhang, L.; Tan, M.; Wang, X.; Wang, G.L.; Qi, M.; Liu, B.; Gao, J.; Pan, Y.; Wang, Y. Genome-wide identification and characterization of laccase family members in eggplant (Solanum melongena L.). PeerJ 2022, 10, e12922. [Google Scholar] [CrossRef]
- Camargo-Ramírez, R.; Val-Torregrosa, B.; San Segundo, B. MiR858-Mediated Regulation of Flavonoid-Specific MYB Transcription Factor Genes Controls Resistance to Pathogen Infection in Arabidopsis. Plant Cell Physiol. 2018, 59, 190–204. [Google Scholar] [CrossRef] [Green Version]
- Chen, R.; Li, Q.; Tan, H.; Chen, J.; Xiao, Y.; Ma, R.; Gao, S.; Zerbe, P.; Chen, W.; Zhang, L. Gene-to-metabolite network for biosynthesis of lignans in MeJA-elicited Isatis indigotica hairy root cultures. Front. Plant Sci. 2015, 3, 952. [Google Scholar] [CrossRef] [Green Version]
- Guillaumie, S.; Mzid, R.; Méchin, V.; Léon, C.; Hichri, I.; Destrac-Irvine, A.; Trossat-Magnin, C.; Delrot, S.; Lauvergeat, V. The grapevine transcription factor WRKY2 influences the lignin pathway and xylem development in tobacco. Plant Mol. Biol. 2010, 72, 215. [Google Scholar] [CrossRef]
- Carbonell, A.; Takeda, A.; Fahlgren, N.; Johnson, S.C.; Cuperus, J.T.; Carrington, J.C. New generation of artificial MicroRNA and synthetic trans-acting small interfering RNA vectors for efficient gene silencing in Arabidopsis. Plant Physiol. 2014, 165, 15–29. [Google Scholar] [CrossRef] [Green Version]
- Mickiewicz, A.; Rybarczyk, A.; Sarzynska, J.; Figlerowicz, M.; Blazewicz, J. AmiRNA Designer-new method of artificial miRNA design. Acta Biochim. Pol. 2016, 63, 71–77. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Karakülah, G.; Kurtoğlu, K.Y.; Unver, T. PeTMbase: A database of plant endogenous target mimics (eTMs). PLoS ONE 2016, 11, e0167698. [Google Scholar] [CrossRef] [PubMed]
- Borah, P.; Das, A.; Milner, M.J.; Ali, A.; Bentley, A.R.; Pandey, R. Long non-coding RNAs as endogenous target mimics and exploration of their role in low nutrient stress tolerance in plants. Genes 2018, 9, 459. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Tang, G.; Yan, J.; Gu, Y.; Qiao, M.; Fan, R.; Mao, Y.; Tang, X. Construction of short tandem target mimic (STTM) to block the functions of plant and animal microRNAs. Methods 2012, 58, 118–125. [Google Scholar] [CrossRef] [Green Version]
- Li, F.; Wang, W.; Zhao, N.; Xiao, B.; Cao, P.; Wu, X.; Ye, C.; Shen, E.; Qiu, J.; Zhu, Q.-H.; et al. Regulation of nicotine biosynthesis by an endogenous target mimicry of microRNA in tobacco. Plant Physiol. 2015, 169, 1062–1071. [Google Scholar] [CrossRef] [Green Version]
- Peng, T.; Qiao, M.; Liu, H.; Teotia, S.; Zhang, Z.; Zhao, Y.; Wang, B.; Zhao, D.; Shi, L.; Zhang, C.; et al. A resource for inactivation of microRNAs using short tandem target mimic technology in model and crop plants. Mol. Plant 2018, 11, 1400–1417. [Google Scholar] [CrossRef] [Green Version]
- Barta, T.; Peskova, L.; Hampl, A. miRNAsong: A web-based tool for generation and testing of miRNA sponge constructs in silico. Sci. Rep. 2016, 6, 36625. [Google Scholar] [CrossRef]
- Eamens, A.L.; McHale, M.; Waterhouse, P.M. The use of artificial microRNA technology to control gene expression in Arabidopsis thaliana. Methods Mol. Biol. 2014, 1062, 211–224. [Google Scholar]
- Kotowska-Zimmer, A.; Pewinska, M.; Olejniczak, M. Artificial miRNAs as therapeutic tools: Challenges and opportunities. Wiley Interdiscip. Rev. RNA 2021, 12, e1640. [Google Scholar] [CrossRef]
- Tiwari, M.; Sharma, D.; Trivedi, P.K. Artificial microRNA mediated gene silencing in plants: Progress and perspectives. Plant Mol. Biol. 2014, 86, 1–18. [Google Scholar] [CrossRef]
- Kluiver, J.; Gibcus, J.H.; Hettinga, C.; Adema, A.; Richter, M.K.; Halsema, N.; Slezak-Prochazka, I.; Ding, Y.; Kroesen, B.J.; van den Berg, A. Rapid generation of microRNA sponges for microRNA inhibition. PLoS ONE 2012, 7, e29275. [Google Scholar] [CrossRef] [Green Version]
- Kluiver, J.; Slezak-Prochazka, I.; Smigielska-Czepiel, K.; Halsema, N.; Kroesen, B.J.; van den Berg, A. Generation of miRNA sponge constructs. Methods 2012, 58, 113–117. [Google Scholar] [CrossRef]
- Qu, J.; Chen, X.; Sun, Y.Z.; Zhao, Y.; Cai, S.B.; Ming, Z.; You, Z.-H.; Li, J.Q. In Silico prediction of small molecule-miRNA associations based on the HeteSim algorithm. Mol. Ther-Nucl. Acids 2019, 14, 274–286. [Google Scholar] [CrossRef] [Green Version]
- Wen, D.; Danquah, M.; Chaudhary, A.K.; Mahato, R.I. Small molecules targeting microRNA for cancer therapy: Promises and obstacles. J. Control. Release 2015, 219, 237–247. [Google Scholar] [CrossRef] [Green Version]
- Haga, C.L.; Velagapudi, S.P.; Strivelli, J.R.; Yang, W.Y.; Disney, M.D.; Phinney, D.G. Small molecule inhibition of miR-544 biogenesis disrupts adaptive responses to hypoxia by modulating ATM-mTOR signaling. ACS Chem. Biol. 2015, 10, 2267–2276. [Google Scholar] [CrossRef] [Green Version]
- Costales, M.G.; Haga, C.L.; Velagapudi, S.P.; Childs-Disney, J.L.; Phinney, D.G.; Disney, M.D. Small molecule inhibition of microRNA-210 reprograms an oncogenic hypoxic circuit. J. Am. Chem. Soc. 2017, 139, 3446–3455. [Google Scholar] [CrossRef] [Green Version]
- Quemener, A.M.; Bachelot, L.; Forestier, A.; Donnou-Fournet, E.; Gilot, D.; Galibert, M.D. The powerful world of antisense oligonucleotides: From bench to bedside. Wires RNA 2020, 11, e1594. [Google Scholar] [CrossRef]
- Quiagen. Available online: https://www.qiagen.com/us/products/discovery-and-translational-research/functional-and-cell-analysis/mirna-functional-analysis/mircury-lna-mirna-power-target-site-blockers/mircury-lna-mirna-power-target-site-blockers/ (accessed on 28 March 2022).
- Louloupi, A.; Ørom, U.A.V. Inhibiting pri-miRNA processing with target site blockers. In miRNA Biogenesis; Springer: New York, NY, USA, 2018; pp. 63–68. [Google Scholar]
- Schmidt, M.F. Drug target miRNAs: Chances and challenges. Trends Biotechnol. 2014, 32, 578–585. [Google Scholar] [CrossRef]
- Othumpangat, S.; Bryan, N.B.; Beezhold, D.H.; Noti, J.D. Upregulation of miRNA-4776 in Influenza Virus Infected Bronchial Epithelial Cells Is Associated with Downregulation of NFKBIB and Increased Viral Survival. Viruses 2017, 9, 94. [Google Scholar] [CrossRef] [Green Version]
- Dalmadi, Á.; Miloro, F.; Bálint, J.; Várallyay, É.; Havelda, Z. Controlled RISC loading efficiency of miR168 defined by miRNA duplex structure adjusts ARGONAUTE1 homeostasis. Nucleic Acids Res. 2021, 49, 12912–12928. [Google Scholar] [CrossRef]
- Kobayashi, H.; Singer, R.H. Single-molecule imaging of microRNA-mediated gene silencing in cells. Nat. Commun. 2022, 13, 1435. [Google Scholar] [CrossRef]
- Peterson, S.M.; Thompson, J.A.; Ufkin, M.L.; Sathyanarayana, P.; Liaw, L.; Congdon, C.B. Common features of microRNA target prediction tools. Front. Genet. 2014, 5, 23. [Google Scholar] [CrossRef] [Green Version]
- Teune, J.H.; Steger, G. NOVOMIR: De novo prediction of microRNA-coding regions in a single plant-genome. J. Nucleic Acids 2010, 2010, 495904. [Google Scholar] [CrossRef] [Green Version]
- Jha, A.; Shankar, R. Employing machine learning for reliable miRNA target identification in plants. BMC Genom. 2011, 12, 636. [Google Scholar] [CrossRef] [Green Version]
- Dai, X.; Zhao, P.X. psRNATarget: A plant small RNA target analysis server. Nucleic Acids Res. 2011, 39, 155–159. [Google Scholar] [CrossRef] [Green Version]
- psRNATarget: A Plant Small RNA Target Analysis Server (2017 Update). Available online: https://www.zhaolab.org/psRNATarget/ (accessed on 28 March 2022).
- Riolo, G.; Cantara, S.; Marzocchi, C.; Ricci, C. miRNA targets: From prediction tools to experimental validation. Methods Protoc. 2021, 4, 1. [Google Scholar] [CrossRef]
- Tools4MIRs. Available online: https://www.tools4mirs.org/ (accessed on 28 March 2022).
- WMD3—Web MicroRNA Designer. Available online: http://wmd3.weigelworld.org/cgi-bin/webapp.cgi/ (accessed on 28 March 2022).
- MiRNAsong. Available online: https://www2.med.muni.cz/histology/miRNAsong/index.php/ (accessed on 28 March 2022).
- PeTMbase. Available online: http://tools.ibg.deu.edu.tr/petmbase/index.php/ (accessed on 28 March 2022).
- P-SAMS. Available online: http://p-sams.carringtonlab.org/ (accessed on 28 March 2022).
- Hanna, J.; Hossain, G.S.; Kocerha, J. The potential for microRNA therapeutics and clinical research. Front. Genet. 2019, 10, 478. [Google Scholar] [CrossRef] [Green Version]
- Neumeier, J.; Meister, G. SiRNA specificity: RNAi mechanisms and strategies to reduce off-target effects. Front. Plant Sci. 2021, 11, 2196. [Google Scholar] [CrossRef]
- Bai, X.; Bian, Z. MicroRNA-21 Is a Versatile Regulator and Potential Treatment Target in Central Nervous System Disorders. Front. Mol. Neurosci. 2022, 15, 842288. [Google Scholar] [CrossRef]
- Hong, D.S.; Kang, Y.K.; Borad, M.; Sachdev, J.; Ejadi, S.; Lim, H.Y.; Brenner, A.J.; Park, K.; Lee, J.-L.; Kim, T.-Y.; et al. Phase 1 study of MRX34, a liposomal miR-34a mimic, in patients with advanced solid tumours. Br. J. Cancer 2020, 122, 1630–1637. [Google Scholar] [CrossRef]
- Dicerna. Available online: https://dicerna.com/ (accessed on 28 March 2022).
Lignans | Lignins |
---|---|
Dimeric | Polymeric |
Stereochemical diversity | Optically inactive |
A variety of structural motifs | Different proportions of three types of monolignols within the lignin fractions |
Species-specific properties of individual types of lignans | Species-specific proportionality of individual monolignols |
Spatially and temporally specific accumulation | Spatially and temporally manner of lignification |
Antioxidant, antibacterial, antiviral, fungicidal, insecticidal, estrogenic, antiestrogenic, anticarcinogenic properties | Mechanical strength of plant tissues, hydrophobicity, defense against pests and pathogens |
miRNAs | Transcription Factors |
---|---|
miR156; miR157; miR159; miR159e; miR160; miR164; miR166; miR166i; miR167; miR167h; miR168b; miR169; miR171; miR172; miR172i; miR172e; miR393a-5p; miR396b; miR396e; miR397; miR397a/b; miR399; miR408; miR408d; miR413; miR440; miR477; miR528a/b; miR530; miR531; miR812; miR829.1; miR830; miR845; miR850; miR857; miR858; miR858a; miR858b; miR894; miR530; miR1536; miR1438; miR1873; miR2275d; miR2891; miR3627; miR4376; miR4391; miR4995; miR5035; miR5298b; miR5384; miR5532; miR5671a; miR6194; miR6223; miR7695; miR7729; miR8154; miR9567; miR9662 | MYB family (MYB1; MYB2; MYB4; MYB5; MYB11; MYB12; MYB021; MYB32; MYB39; MYB44; MYB46; MYB52; MYB58; MYB63; MYB75; MYB88; MYB 111; MYB124; MYB 308; MYB330; MYB340; R2R3-MYB); AP2/ERF; NAC family (NAM; ATAF1/2; CUC2; SND1-A2; VND6-C2); SPL9; bHLH; TCP3; PAP1; WDR; WRKY2; WRKY 36; LIM |
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Ražná, K.; Harenčár, Ľ.; Kučka, M. The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View. Cells 2022, 11, 2151. https://doi.org/10.3390/cells11142151
Ražná K, Harenčár Ľ, Kučka M. The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View. Cells. 2022; 11(14):2151. https://doi.org/10.3390/cells11142151
Chicago/Turabian StyleRažná, Katarína, Ľubomír Harenčár, and Matúš Kučka. 2022. "The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View" Cells 11, no. 14: 2151. https://doi.org/10.3390/cells11142151
APA StyleRažná, K., Harenčár, Ľ., & Kučka, M. (2022). The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View. Cells, 11(14), 2151. https://doi.org/10.3390/cells11142151