Research Progress and Prospect of microRNA in Medicinal Plants

doi:10.13560/j.cnki.biotech.bull.1985.2019-0098

Abstract

Abstract: MicroRNAs（miRNAs）are endogenous ~22 nt non-encoding single-strand RNAs and may play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. The study of plant miRNA has rapidly become a research hotspot in the field of plant molecular biology since the plant miRNA was first reported in 2002. This paper reviews the biogenesis and mechanism of plant miRNAs,focusing on research progress of miRNA in medicinal plants. Moreover,the paper prospects the future research direction in this field,aiming to provide references for future research of miRNA in medicinal plants.

Key words: miRNA, medicinal plants, biosynthetic pathway, identification and verification

YAN Wu-ping, WU You-gen, YU Jing ,YANG Dong-mei, ZHANG Jun-feng. Research Progress and Prospect of microRNA in Medicinal Plants[J]. Biotechnology Bulletin, 2019, 35(8): 178-185.

References

[1] Yu Y, Jia TR, Chen XM.The ‘how’ and ‘where’ of plant microRNAs[J]. New Phytologist, 2017, 216(4):1002-1017.
[2] Lee RC, Feinbaum RL, Ambros V.The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14[J]. Cell, 1993, 75(5):843-854.
[3] Wightman B, Ha I, Ruvkun G.Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans[J]. Cell, 1993, 75(5):855-862.
[4] Reinhart BJ, Slack FJ, Basson M, et al.The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans[J]. Nature, 2000, 403(6772):901-906.
[5] Slack FJ, Basson M, Liu Z, et al. The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor[J]. Molecular Cell, 2000, 5;(4):659-669.
[6] Reinhart BJ, Weinstein EG, Rhoades MW, et al.MicroRNAs in plants[J]. Genes Dev, 2002, 16(13):1616-1626.
[7] Xie M, Zhang SX, Yu B. microRNA biogenesis, degradation and activity in plants[J]. Cellular & Molecular Life Sciences, 2015, 72(1):87-99.
[8] Fukudome A, Fukuhara T.Plant dicer-like proteins:double-stranded RNA-cleaving enzymes for small RNA biogenesis[J]. Journal of Plant Research, 2016, 130(1):1-12.
[9] Kurihara Y, Watanabe Y.Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions[J]. Proc Natl Acad Sci USA, 2004, 101(34):12753-12758.
[10] Liu CG, Axtell MJ, Fedoroff NV.The helicase and RNaseIIIa domains of Arabidopsis Dicer-Like1 modulate catalytic parameters during microRNA biogenesis[J]. Plant Physiology, 2012, 159(2):748-758.
[11] Song L, Axtell MJ, Fedoroff NV.RNA secondary Structural determinants of miRNA precursor processing in Arabidopsis[J]. Current Biology, 2010, 20(1):37-41.
[12] Yu B, Yang ZY, Li JJ, et al.Methylation as a crucial step in plant microRNA biogenesis[J]. Science, 2005, 307(5711):932-935.
[13] Yang ZY, Ebright YW, Yu B, et al.HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2’ OH of the 3' terminal nucleotide[J]. Nucleic Acids Research, 2006, 34(2):667-675.
[14] Papp I, Mette MF, Aufsatz W, et al.Evidence for nuclear processing of plant microRNA and short interfering RNA precursors[J]. Plant Physiology, 2003, 132(3):1382-1390.
[15] Park MY, Wu G, Gonzalez-Sulser A, et al.Nuclear processing and export of microRNAs in Arabidopsis[J]. Proc Natl Acad Sci USA, 2005, 102(10):3691-3696.
[16] Rogersa K, Chen XM.Biogenesis, turnover, and mode of action of plant microRNAs[J]. Plant Cell, 2013, 25(7):2383-2399.
[17] Liu QK, Wang F, Axtella MJ.Analysis of complementarity requirements for plant microRNA targeting using a Nicotiana benthamiana quantitative transient assay[J]. Plant Cell, 2014, 26(2):741.
[18] Li JY, Reichel M, Millar AA.Determinants beyond both complementarity and cleavage govern microR159 efficacy in Arabidopsis[J]. PLoS Genetics, 2014, 10(3):e1004232.
[19] German MA, Pillay M, Jeong DH, et al.Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends[J]. Nature Biotechnology, 2008, 26(8):941-946.
[20] Zhu HL, Hu FQ, Wang RH, et al.Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development[J]. Cell, 2011, 145(2):242-256.
[21] Ji LJ, Liu XG, Yan J, et al.ARGONAUTE10 and ARGONAUTE1 regulate the termination of floral stem cells through two microRNAs in Arabidopsis[J]. PLoS Genetics, 2011, 7(3):e1001358.
[22] Souret FF, Kastenmayer JP, Green PJ.AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets[J]. Molecular Cell, 2004, 15(2):173-183.
[23] Aukerman MJ, Hajime S.Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes[J]. Plant Cell, 2003, 15(11):2730-2741.
[24] Chen XM.A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development[J]. Science, 2004, 303(5666):2022-2025.
[25] Iwakawa HO, Tomari Y.Molecular insights into microRNA-mediated translational repression in plants[J]. Molecular Cell, 2013, 52(4):591-601.
[26] Yang L, Wu G, Poethig RS.Mutations in the GW-repeat protein SUO reveal a developmental function for microRNA-mediated translational repression in Arabidopsis[J]. Proc Natl Acad Sci USA, 2012, 109(1):315-320.
[27] Chen XM.MicroRNA biogenesis and function in plants[J]. FEBS Letters, 2005, 579(26):5923-5931.
[28] Lanet E, Delannoy E, Sormani R, et al.Biochemical evidence for translational repression by Arabidopsis microRNAs[J]. Plant Cell, 2009, 21(6):1762-1768.
[29] Li SB, Liu L, Zhuang XH, et al.MicroRNAs inhibit the translation of target mRNAs on the endoplasmic reticulum in Arabidopsis[J]. Cell, 2013, 153(3):562-574.
[30] Yu X, Willmann MR, Anderson SJ, et al.Genome-wide mapping of uncapped and cleaved transcripts reveals a role for the nuclear mRNA cap-binding complex in co-translational RNA decay in Arabidopsis[J]. Plant Cell, 2016, 28(10):2385.
[31] Zhang BH, Wang QL.MicroRNA-based biotechnology for plant improvement[J]. Journal of Cellular Physiology, 2015, 230(1):1-15.
[32] Ding J, Ruan CJ, Guan Y, et al.Identification of microRNAs involved in lipid biosynthesis and seed size in developing sea buckthorn seeds using high-throughput sequencing[J]. Scientific Reports, 2018, 8(1):4022.
[33] He XF, Shenkute AG, Wang WH, et al.Characterization of conserved and novel microRNAs in Lilium lancifolium Thunb. by high-throughput sequencing[J]. Scientific Reports, 2018, 8(1):2880.
[34] Nadiya F, Anjali N, Jinu T, et al.Deep sequencing identified potential miRNAs involved in defense response, stress and plant growth characteristics of wild genotypes of cardamom[J]. Plant Biology, 2019, 21:3-14.
[35] Xu T, Wang B, Liu X, et al.Microarray-based identification of conserved microRNAs from Pinellia ternata[J]. Gene, 2012, 493(2):267-272.
[36] Dong M, Yang DF, Lang QL, et al.Microarray and degradome sequencing reveal microRNA differential expression profiles and their targets in Pinellia pedatisecta[J]. PLoS One, 2012, 8(9):e75978.
[37] Fan RY, Li YJ, Li CF, et al.Differential microRNA analysis of ;glandular trichomes and young leaves in Xanthium strumarium L. reveals their putative roles in regulating terpenoid biosynthesis;[J]. PLoS One, 2015, 10(9):e0139002.
[38] Hao DC, Yang L, Xiao PG, et al.Identification of Taxus microRNAs and their targets with high-throughput sequencing and degradome analysis[J]. Physiologia Plantarum, 2012, 146(4):388-403.
[39] Gao ZH, Wei JH, Yang Y, et al.Identification of conserved and novel microRNAs in Aquilaria sinensis based on small RNA sequencing and transcriptome sequence data[J]. Gene, 2012, 505(1):167-175.
[40] Wei RC, Qiu DY, Wilson IW, et al.Identification of novel and conserved microRNAs in Panax notoginseng roots by high-throughput sequencing[J]. BMC Genomics, 2015, 16(1):1-10.
[41] Jung I, Kang H, Kim JU, et al.The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature[J]. BMC Systems Biology, 2018, 12(Suppl 2):27.
[42] Boke H, Ozhuner E, Turktas M, et al.Regulation of the alkaloid biosynthesis by miRNA in opium poppy[J]. Plant Biotechnology Journal, 2015, 13(3):409-420.
[43] Yang YH, Chen XJ, Chen JY, et. Identification of novel and conserved microRNAs in Rehmannia glutinosa L. by solexa sequencing[J]. Plant Molecular Biology Reporter, 2011, 29(4):986-996.
[44] Li CF, Zhu YJ, Guo X, et al.Transcriptome analysis reveals ginsenosides biosynthetic genes, microRNAs and simple seqaluence repeats in Panax ginseng C. A. Meyer[J]. BMC Genomics, 2013, 14(1):245-245.
[45] Kumar P, Padhan JK, Kumar A, et al.Transcriptomes of Podophyllum hexandrum unravel candidate miRNAs and their association with the biosynthesis of secondary metabolites[J]. Journal of Plant Biochemistry & Biotechnology, 2017, 27(1):1-9.
[46] Singh N, Srivastava S, Shasany AK, et al.Identification of miRNAs and their targets involved in the secondary metabolic pathways of Mentha spp.[J]. Computational Biology & Chemistry, 2016, 64:154-162.
[47] 易小娅, 杨瑞瑞, 曾幼玲. 植物miRNA的研究方法概述[J]. 植物生理学报, 2015, 51(4):413-423.
[48] Zheng Y, Chen K, Xu ZN, et al.Small RNA profiles from Panax notoginseng roots differing in sizes reveal correlation between miR156 abundances and root biomass levels[J]. Sci Rep, 2017, 7(1):9418.
[49] Singh A, Gautam V, Singh S, et al.Plant small RNAs:advancement in the understanding of biogenesis and role in plant development[J]. Planta, 2018, 248:545-558.
[50] Samad AFA, Nazaruddin N, Murad AMA, et al.Deep sequencing and in silico analysis of small RNA library reveals novel miRNA from leaf Persicaria minor transcriptome[J]. Biotech, 2018, 8(3):136.
[51] Axtell MJ, Bartel DP.Antiquity of microRNAs and their targets in land plants[J]. Plant Cell, 2005, 17(6):1658-1673.
[52] Wang B, Dong M, Chen WD, et al.Microarray identification of conserved microRNAs in Pinellia pedatisecta[J]. Gene, 2012, 498(1):36-40.
[53] 卢鋆, 高伟, 黄璐琦. 药用植物microRNA与次生代谢产物的合成调控[J]. 中国中药杂志, 2018, 43(9):1806-1811.
[54] Li FF, Wang WD, Zhao N, et al.Regulation of nicotine biosynthesis by an endogenous target mimicry of microRNA in tobacco[J]. Plant Physiology, 2015, 169:1062-1071.
[55] Pérez-Quintero ÁL, Sablok G, Conesa A, et al.Mining of miRNAs and potential targets from gene oriented clusters of transcripts sequences of the anti-malarial plant, Artemisia annua[J]. Biotechnology Letters, 2012, 34(4):737-745.
[56] Kumar R.Role of microRNAs in biotic and abiotic stress responses in crop plants[J]. Applied Biochemistry & Biotechnology, 2014, 174(1):93-115.
[57] Sun X, Lin L, Sui N. Regulation mechanism of microRNA in plant response to abiotic stress and breeding[J]. Molecular Biology Reports, 2018, (4).
[58] Wu B, Wang MZ, Ma YM, et al.High-throughput sequencing and characterization of the small RNA transcriptome reveal features of novel and conserved microRNAs in Panax ginseng[J]. PLoS One, 2012, 7(9):e44385.
[59] 苏文华, 张光飞, 李秀华, 等. 植物药材次生代谢产物的积累与环境的关系[J]. 中草药, 2005, 36(9):1415-1418.
[60] Najafabadi AS, Naghavi MR.Mining Ferula gummosa transcriptome to identify miRNAs involved in the regulation and biosynthesis of terpenes[J]. Gene, 2017, 645:41-47.
[61] Gandhi SG, Mahajan V, Bedi YS.Changing trends in biotechnology of secondary metabolism in medicinal and aromatic plants[J]. Planta, 2015, 241(2):303-317.