miRNA related to secondary metabolite production.
Abstract
MicroRNAs (miRNAs) are noncoding RNAs that play an important role in the regulation of the genetic expression in animals and plants by targeting mRNAs for cleavage or translational repression. Several miRNAs regulate the plant development, the metabolism, and the responses to biotic and abiotic stresses. Characterization of an miRNA has helped to show its role in fine tuning the mechanisms of posttranscriptional gene regulation. Although there is a lot of information related to miRNA regulation of some processes, the role of miRNA involved in the regulation of biosynthesis of secondary plant product is still poorly understood. In this chapter, we summarize the identification and characterization of miRNAs that participate in the regulation of the biosynthesis of secondary metabolites in plants and their use in the strategies to manipulate a controlled manipulation.
Keywords
- alkaloids
- flavonoids
- flavonols
- gene expression
- isoprenoids
1. Introduction
1.1. Definition of miRNA
mRNAs are noncoding single-stranded RNA molecules that range from a length of 18 to 28 nucleotides. These molecules play an important role in posttranscriptional regulation by the inhibition of the expression of target genes by binding to mRNA [1]. Eukaryotic organisms, such as plants and animals, and some viruses express this type of molecules [2, 3]. Lin-4 is the first miRNA that was identified in
1.2. Mechanism of action of miRNAs
The biogenesis of miRNAs in plants and animals presents some differences. In both plants and animals, the precursors of miRNAs are polyadenylated caps and RNAs, and transcribed as for any coding RNA by RNA polymerase II (RNAPII) [5, 8]. However, in the plants, the primary transcript (pri-miRNA) that gives rise to the miRNA is produced by the nuclear RNAase dicer-like 1 (DCL1) and its accessory proteins SERRATE (SE) and hyponastic leaves (HYL1) [8]. Also, Drosha gene is absent in plants [5].
In
The expression of miRNAs is regulated by transcription factors. Negative on TATA less 2 (NOT2) promotes the transcription of protein miRNA genes and facilitates efficient DCL1 recruitment in miRNA biogenesis [11]. Cell division cycle 5 (CDC5) acts as a positive transcription factor associating with miRNA genes [12]. Pleiotropic regulatory locus 1 (PRL1) has the ability to bind to DCL1 and pri-miRNAs. The miRNA duplex is transported to the cytoplasm by nuclear export factor
The miRNA target genes can be a single member of a gene family or regulate a multiple family members. Thus, multiple miRNA genes could be targeting a single member, with tissues and stage specificity, and/or a single miRNA gene could be regulating multiple family members. The spatial and temporal expression and abundance of mature miRNAs are tightly regulated; they vary greatly among different miRNAs; and the abundance also varies depending on the tissue types or developmental stages [13].
1.3. Regulatory processes involving miRNAs
In the cytoplasm of cells, the miRNAs regulate the expression of genes at the posttranscriptional level via mRNA degradation and/or translational repression [14]. Unlike animals, in plants, there is a perfect complementarity between miRNA and target mRNA [14]. To carry out the silencing, a ribonucleoprotein RNA-induced silencing complex (RISC) is formed [15]. AGO1, AGO2, AGO4, AGO7, and AGO10 slicer activity has been reported, even though AGO1 is associated with most miRNAs [16]. AGO1-catalyzed RNA cleavage (slicing) represses miRNA targets [17].
2. miRNAs and secondary metabolism in plants
In plants, miRNAs control the expression of genes that encode transcription factors, stress response proteins, and others, which have an impact on biological processes. The miRNAs regulate the biological processes in the plans such as maintenance of genome integrity, primary and secondary metabolism, development, signal transduction, signaling pathways, homeostasis, innate immunity, and adaptive responses to biotic and abiotic stress [18]. Secondary metabolites are a group of phytochemicals that regulate various processes related to the interaction of the plant with its environment [19]. These compounds include terpenoids, alkaloids, phenolics, glycosides, tannins, and saponins, and defend plants from several biotic an abiotic stressors [20]. Even though these types of compounds are synthesized by plants to help in self-defense, they have diverse industrial uses such as insecticides, dyes, flavoring compounds, and nutraceuticals having a positive effect on human health. Commercial importance has resulted in a great interest in studying possibilities of enhancing its production [21]. It is known that miRNAs control several biological processes at the posttranscriptional level. Currently, some studies reveal the role that miRNAs have in the regulation of secondary metabolic pathways [20]. Therefore, the production of compounds derived from secondary metabolism can be managed through the miRNAs. Since they are positively or negatively regulated, the production of desired metabolites can be induced, the production of toxic metabolites can be limited, and new metabolites can be produced [22].
Computational analysis carried out in two transcriptomes of Swertia resulted in the identification of miRNAs associated to secondary metabolites biosynthesis; miR-156a, miR-166a, miR-166b, miR-168, miR-11071, and miR-11320 targeting metabolic enzymes, such as aspartate aminotransferase, ribulose-phosphate 3-epimerase, acetyl-CoA acetyltransferase, phosphoglycerate mutase, and premnaspirodiene oxygenase, also include a gene encoding a homeobox-leucine zipper protein (HD-ZIP) with a possible association in secondary metabolites biosynthesis in
2.1. Flavonoids
Flavonoids are secondary metabolites that possess a polyphenolic structure. Those compounds consist of hydroxylated phenolic substances having a benzo-𝛾-pyrone structure and derived of phenylpropanoid pathway [27]. Within the subgroups of the flavonoids are flavones, flavonols, flavanones, flavanonols, flavanols or catechins, anthocyanins, and chalcones [28]. For plants, this type of compounds is synthesized as a result of the interaction with the environment, other plants, and microorganisms. They have diverse biological functions as anti-oxidative, anti-inflammatory, anti-mutagenic, and anti-carcinogenic properties, which are structure dependent [28]. The above makes flavonoids a compound with nutraceutical, pharmaceutical, medicinal, and cosmetic applications [28]. The production of secondary metabolites is found in cases regulated by the miRNAs (Table 1). Little is known about the miRNAs involved in flavonoid biosynthesis. In
Plant species | miRNA | Target | Function | References |
---|---|---|---|---|
Sunflower | miR2911 | Gamma-tocopherol methyl transferase | Tocopherols biosynthesis | [29] |
miR156 | SPL transcription factor | Accumulation of anthocyanins, whereas reduced miR156 activity results in high levels of flavonols | [51] | |
miR395p-3p and miR858b | bHLH and MYB, respectively | Proanthocyanidin biosynthesis | [30] | |
miRNAs (U436803, U977315, U805963, U3938865 and U4351355) | R2R3-MYB transcription factors | Flavonoid biosynthesis | [2, 3] | |
MicroRNA858a | R2R3-MYB transcription factors | Flavonoid biosynthesis | [31] | |
miR6194 and miR5655 | Flavanone 3-hydroxylase | Flavonols, anthocyanidins proanthocyanidins synthesis | [32] | |
miR1873/miR5532 | Dihydroflavonol 4-reductase C/-hydroxyisoflavanone dehydratase | Flavonoid/isoflavonoid biosynthesis | [33] | |
Opium poppy ( |
pso-miR13, pso-miR2161, and pso-miR408 | 7-O-methyltransferase, |
Benzylisoquinoline alkaloids | [34] |
Tobacco | miRX17, miRX27, miRX20, and miRX19 | QPT1, QPT2, CYP82E4, and PMT2 | Nicotine biosynthesis and catabolism | [35] |
miR164 and miR171 | Taxane 13α hydroxylase and taxane 2α-O-benzoyltransferase | Paclitaxel biosynthetic genes | [36] | |
miR396b | Targets kaempferol 3-O-beta-D-galactosyltransferase | Flavonol glycosides | [37] | |
miR156 | Basic helix-loop-helix (bHLH) | Flavone/flavonol biosynthesis | [38] | |
iRNA-4995 | 3-Deoxy-7-phosphoheptulonate synthase (DAHP synthase) | Terpenoid biosynthesis ultimately affecting the production of picroside-I | [39] | |
Korean ginseng ( |
miR854b and miR854c | 3-Hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR), farnesyl diphosphate synthase (FPS), geranyl-diphosphate synthase, squalene synthase, and squalene epoxidase (SE) | [40] | |
mir-5021 | MYB transcription factor, geranyl diphosphate synthase, GCPE protein, UDP-glucose iridoid glucosyltransferase | Primary and secondary metabolism, Isoprenoid/terpenoid biosynthesis iridoid production in higher plants | [41] | |
miR7539, miR5021, and miR1134 | Nontranscriptional factor proteins, such as DXS, HMGR, IDS, and IDI, essential to produce IPP and DMAPP | Terpenoid biosynthesis | [42] | |
miR7540, miR5183, miR6449, miR5255, miR5491, and miR6435 | R-linalool synthase, gibberellin 3-oxidase, ent-kaurene synthase, squalene epoxidase, beta-amyrin synthase, and germacrene A oxidase | Mono-, sesqui-, di-, and tri-terpenoids biosynthesis | [42] | |
miR2919, miR5251, miR838, miR5021, and miR5658 | SPL7, SPL11, and ATHB13 TFs | Terpene biosynthesis | [43] | |
miRNA156 | Squamosa promoter binding protein-like (SPL) | Sesquiterpene biosynthesis | [44] | |
miR156 | SPL transcription factor | Modulate sesquiterpene synthase gene TPS21 responsible for the biosynthesis of (E)-β-caryophyllene | [44] | |
miR156, miR414, and miR5021 | Basic helix-loop-helix (bHLH) geranyl di-phosphate synthase subunit alpha-like protein (NACA), respectively | Terpenoid backbone biosynthesis, sesquiterpenoid and triterpenoid biosynthesis | [38] | |
miR-168, miR-11320, miR-166a, miR-11071, miR-156a and miR-166b | Acetyl-CoA acetyltransferase (AACT), aspartate aminotransferase (PHAT), premnaspirodiene oxygenase (PSO), ribulose-phosphate 3-epimerase (RPE), phosphoglycerate mutase (PGM), and a gene encoding homeobox-leucine zipper protein (HD-ZIP) | Secondary metabolites biosynthesis | [23] | |
miR163 | Family of small molecules of methyltransferases | Secondary metabolism | [45] | |
miR393 | Auxin receptors (TIR1, AFB2 and AFB3) | Increase of glucosinolate and decrease of camalexin | [46] | |
Potato | mirn79 | AP2/ERF transcription factor | JA-responsive secondary metabolites | [24] |
miRstv_7 | UDP-glycosyltransferase 76G1 (ugt76g1), kaurenoic acid hydroxylase (KAH), and kaurene oxidase (KO) | Steviol glycoside biosynthesis | [47] | |
miR826 and miR5090 | AOP2 | Glucosinolate biosynthesis | [48] | |
miR826 | Alkenyl hydroxyalkyl producing 2 | Glucosinolate synthesis | [49] | |
miR5072 | Acetyl-CoA C-acetyl transferase | Tanshinones biosynthesis | [50] |
2.2. Alkaloids
Alkaloids are naturally compounds that have one or more of their nitrogen atoms. Alkaloids are classified into different groups: indole, piperidine, tropane, purine, pyrrolizidine, imidazole, quinolizidine, isoquinoline, and pyrrolidine alkaloids [52]. Because of their toxicity, alkaloids act as defense compounds against diverse pathogens or herbivores. Understanding the regulation of alkaloid biosynthesis is crucial for its production. Target transcript identification analyses in Opium poppy (
2.3. Terpenoids
Plant terpenoids secondary metabolites are synthesized from C5 precursors isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). They are classified according to the number of carbon atoms as monoterpenes (C10), sesquiterpenes (C15), diterpenes (C20), triterpenes (C30), carotenoids (C40), and polyprenols (>45) [53]. Like the alkaloids and the flavonoids, the biological characteristics and the applications of interest in the industry. Computational identification of miRNAs was done in six transcriptomes of
2.4. Other secondary metabolites
miRNAs were identified from
3. Conclusion
miRNAs are small molecules associated with developmental processes controlling gene expression. The mechanisms involved posttranscriptional and transductional processes. The miRNA secondary metabolism control is a relative new field of study; the knowledge of the regulation of secondary metabolism in plants will help to understand the production of these products in controlled systems. Some of these products have an important economical value because of their use in agricultural, food, and cosmetic industries making these areas (miRNA regulation) very attractive.
Acknowledgments
The authors thank Universidad De la Salle Bajío campus Campestre for financial support. MVH thank to CONACyT for postdoctoral fellowship (288773).
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