Regulation Of Plant Metabolism Research Articles

Emerging mechanistic insights into the regulation of specialized metabolism in plants.

Plants biosynthesize a broad range of natural products through specialized and species-specific metabolic pathways that are fuelled by core metabolism, together forming a metabolic network. Specialized metabolites have important roles in development and adaptation to external cues, and they also have invaluable pharmacological properties. A growing body of evidence has highlighted the impact of translational, transcriptional, epigenetic and chromatin-based regulation and evolution of specialized metabolism genes and metabolic networks. Here we review the forefront of this research field and extrapolate to medicinal plants that synthetize rare molecules. We also discuss how this new knowledge could help in improving strategies to produce useful plant-derived pharmaceuticals.

Strigolactones in Plants and Their Interaction with the Ecological Microbiome in Response to Abiotic Stress.

Phytohormones play an essential role in enhancing plant tolerance by responding to abiotic stresses, such as nutrient deficiency, drought, high temperature, and light stress. Strigolactones (SLs) are carotenoid derivatives that occur naturally in plants and are defined as novel phytohormones that regulate plant metabolism, growth, and development. Strigolactone assists plants in the acquisition of defensive characteristics against drought stress by initiating physiological responses and mediating the interaction with soil microorganisms. Nutrient deficiency is an important abiotic stress factor, hence, plants perform many strategies to survive against nutrient deficiency, such as enhancing the efficiency of nutrient uptake and forming beneficial relationships with microorganisms. Strigolactone attracts various microorganisms and provides the roots with essential elements, including nitrogen and phosphorus. Among these advantageous microorganisms are arbuscular mycorrhiza fungi (AMF), which regulate plant metabolic activities through phosphorus providing in roots. Bacterial nodulations are also nitrogen-fixing microorganisms found in plant roots. This symbiotic relationship is maintained as the plant provides organic molecules, produced in the leaves, that the bacteria could otherwise not independently generate. Related stresses, such as light stress and high-temperature stress, could be affected directly or indirectly by strigolactone. However, the messengers of these processes are unknown. The most prominent connector messengers have been identified upon the discovery of SLs and the understanding of their hormonal effect. In addition to attracting microorganisms, these groups of phytohormones affect photosynthesis, bridge other phytohormones, induce metabolic compounds. In this article, we highlighted the brief information available on SLs as a phytohormone group regarding their common related effects. In addition, we reviewed the status and described the application of SLs and plant response to abiotic stresses. This allowed us to comprehend plants' communication with the ecological microbiome as well as the strategies plants use to survive under various stresses. Furthermore, we identify and classify the SLs that play a role in stress resistance since many ecological microbiomes are unexplained.

Identification and characteristics of SnRK genes and cold stress-induced expression profiles in Liriodendron chinense

BackgroundThe sucrose non-fermenting 1 (SNF1)-related protein kinases (SnRKs) play a vivid role in regulating plant metabolism and stress response, providing a pathway for regulation between metabolism and stress signals. Conducting identification and stress response studies on SnRKs in plants contributes to the development of strategies for tree species that are more tolerant to stress conditions.ResultsIn the present study, a total of 30 LcSnRKs were identified in Liriodendron chinense (L. chinense) genome, which was distributed across 15 chromosomes and 4 scaffolds. It could be divided into three subfamilies: SnRK1, SnRK2, and SnRK3 based on phylogenetic analysis and domain types. The LcSnRK of the three subfamilies shared the same Ser/Thr kinase structure in gene structure and motif composition, while the functional domains, except for the kinase domain, showed significant differences. A total of 13 collinear gene pairs were detected in L. chinense and Arabidopsis thaliana (A. thaliana), and 18 pairs were detected in L. chinense and rice, suggesting that the LcSnRK family genes may be evolutionarily more closely related to rice. Cis-regulation element analysis showed that LcSnRKs were LTR and TC-rich, which could respond to different environmental stresses. Furthermore, the expression patterns of LcSnRKs are different at different times under low-temperature stress. LcSnRK1s expression tended to be down-regulated under low-temperature stress. The expression of LcSnRK2s tended to be up-regulated under low-temperature stress. The expression trend of LcSnRK3s under low-temperature stress was mainly up-or down-regulated.ConclusionThe results of this study will provide valuable information for the functional identification of the LcSnRK gene in the future.

Genome-wide identification, characterization, and expression analysis of UDP-glycosyltransferase genes associated with secondary metabolism in alfalfa (Medicago sativa L.).

Uridine diphosphate glycosyltransferases (UGTs) are enzymes that catalyze glycosylation modifications and play an essential role in regulating plant metabolism. Alfalfa (Medicago sativa L.) is the most important legume in the world due to its high yields and protein content; however, the UGT genes in alfalfa have not yet been studied. Identifying UGT genes with metabolic roles in alfalfa is essential for identifying and modifying genetic traits that are relevant to yield and quality. In this study, 90 of the 239 UGT genes identified from the alfalfa “Zhongmu No. 1” genome database were found to be related to secondary metabolism, and a series of gene family characterization analyses were conducted on each. The results demonstrated that all 90 UGT genes were unevenly distributed on eight chromosomes with few introns and that tandem duplications were the crucial driving force expanding the UGT family in alfalfa. Notably, the 90 UGT genes can be clustered into ten evolutionary groups which contain specific PSPG motifs, and genes in these ten groups have specific tissue expressions. This suggests that the UGT genes in each group could have similar glycosylation roles corresponding to analogous secondary metabolites in alfalfa. Additionally, multiple cis-acting elements found in MsUGT promoter regions, such as phytohormone and flavonoids, indicate that 90 UGT members could be induced by these features, which are also related to secondary metabolism. Therefore, our study identified 90 UGT members inten evolutionary groups that are likely related to glycosylation modifications with secondary metabolites in alfalfa. These findings help uncover pivotal regulatory mechanisms associated with secondary metabolism in plant yield and quality and contribute to genetic modification and breeding in alfalfa and other plant species.

Alternative Splicing and Its Roles in Plant Metabolism.

Plant metabolism, including primary metabolism such as tricarboxylic acid cycle, glycolysis, shikimate and amino acid pathways as well as specialized metabolism such as biosynthesis of phenolics, alkaloids and saponins, contributes to plant survival, growth, development and interactions with the environment. To this end, these metabolic processes are tightly and finely regulated transcriptionally, post-transcriptionally, translationally and post-translationally in response to different growth and developmental stages as well as the constantly changing environment. In this review, we summarize and describe the current knowledge of the regulation of plant metabolism by alternative splicing, a post-transcriptional regulatory mechanism that generates multiple protein isoforms from a single gene by using alternative splice sites during splicing. Numerous genes in plant metabolism have been shown to be alternatively spliced under different developmental stages and stress conditions. In particular, alternative splicing serves as a regulatory mechanism to fine-tune plant metabolism by altering biochemical activities, interaction and subcellular localization of proteins encoded by splice isoforms of various genes.

Light Intensity- and Spectrum-Dependent Redox Regulation of Plant Metabolism.

Both light intensity and spectrum (280–800 nm) affect photosynthesis and, consequently, the formation of reactive oxygen species (ROS) during photosynthetic electron transport. ROS, together with antioxidants, determine the redox environment in tissues and cells, which in turn has a major role in the adjustment of metabolism to changes in environmental conditions. This process is very important since there are great spatial (latitude, altitude) and temporal (daily, seasonal) changes in light conditions which are accompanied by fluctuations in temperature, water supply, and biotic stresses. The blue and red spectral regimens are decisive in the regulation of metabolism because of the absorption maximums of chlorophylls and the sensitivity of photoreceptors. Based on recent publications, photoreceptor-controlled transcription factors such as ELONGATED HYPOCOTYL5 (HY5) and changes in the cellular redox environment may have a major role in the coordinated fine-tuning of metabolic processes during changes in light conditions. This review gives an overview of the current knowledge of the light-associated redox control of basic metabolic pathways (carbon, nitrogen, amino acid, sulphur, lipid, and nucleic acid metabolism), secondary metabolism (terpenoids, flavonoids, and alkaloids), and related molecular mechanisms. Light condition-related reprogramming of metabolism is the basis for proper growth and development of plants; therefore, its better understanding can contribute to more efficient crop production in the future.

Development of approach for flavonoid profiling of biotechnological raw materials Iris sibirica L. by HPLC with high-resolution tandem mass spectrometry.

Iris L. are promising in medicine due to the biological activity of extracts. Iris sibirica L. is spread in Russia but its phytochemical composition has not been studied in detail though it is included in the Red Book. For this reason, I. sibirica L. biotechnology is in high demand. One of the key points in biotechnology is the regulation of plant metabolism using phytohormones. Obtaining of chromatographic metabolite profiles allows to control this process. The aim of this study was to develop an approach for effective control of biotechnological raw materials of I. sibirica L. by flavonoid profiles using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) and to investigate the influence of phytohormones in nutrient media on content of flavonoids. Iris sibirica L. regenerated plants were grown on Murashige-Skoog media with 6-benzylaminopurine (6-BAP) and α-naphtylacetic acid (NAA) additives. To optimise extraction conditions, the design of the experiment was used. Profiles of polyphenols were obtained by HPLC-MS/MS in the positive and negative ionisation modes. The process for efficient extraction from leaves of I. sibirica L. were developed. The factors influencing the extraction efficiency of flavonoids have been determined. A total of 36 compounds were identified by HPLC-MS/MS. Among them isoflavones and their glycosides are the main classes. Addition of an auxin-like hormone increased the non-polar flavonoid levels, but decreased the polar ones. The variation in concentration of cytokinin (6-BAP) affected almost all of the analytes. The methodology for effective control of I. sibirica L. raw plant material biotechnology was developed by analysing obtained chromatographic polyphenol profiles.

Shade and Cd Conditions Strongly Impact the Physiological Responses of Purple Perilla

Plant metabolic regulation is an important strategy for dealing with abiotic stress, which can initiate dramatic changes in metabolite profiles. Metabolomic studies have been extensively used to reveal the responses of plants to abiotic stress, but research concerning how shade growth conditions impact the physiological responses of purple Perilla under Cd stress is still rare. Therefore, the research was designed to observe the important metabolites of purple Perilla under shaded conditions and Cd stress. In this study, we compared the metabolite profiles of purple Perilla exposed to shade and Cd stresses. The results showed that the metabolite profiles of purple Perilla under these stresses could be classified separately. Compared with the normal sunlight treatment, important energy metabolic pathways, including the citrate cycle, and glyoxylate and dicarboxylate metabolism, were inhibited under shade stress. Metabolite analysis revealed that pyruvate was involved in numerous metabolic pathways under Cd stress, and decreased pyruvate was regarded as a metabolite marker for physiological changes. The results show that increased thiamine is an important intermediate that is beneficial for enhancement of Cd stress tolerance.

Metabolic changes in cucumber leaves are enhanced by blue light but differentially affected by UV interactions with light signalling pathways in the visible spectrum.

Ultraviolet radiation (UV, 280–400 nm) as an environmental signal triggers metabolic acclimatory responses. However, how different light qualities affect UV acclimation during growth is poorly understood. Here, cucumber plants (Cucumis sativus) were grown under blue, green, red, or white light in combination with UV. Their effects on leaf metabolites were determined using untargeted metabolomics. Blue and white growth light triggered increased levels of compounds related to primary and secondary metabolism, including amino acids, phenolics, hormones, and compounds related to sugar metabolism and the TCA cycle. In contrast, supplementary UV in a blue or white light background decreased leaf content of amino acids, phenolics, sugars, and TCA-related compounds, without affecting abscisic acid, auxin, zeatin, or jasmonic acid levels. However, in plants grown under green light, UV induced increased levels of phenolics, hormones (auxin, zeatin, dihydrozeatin-7-N-dihydrozeatin, jasmonic acid), amino acids, sugars, and TCA cycle-related compounds. Plants grown under red light with UV mainly showed decreased sugar content. These findings highlight the importance of the blue light component for metabolite accumulation. Also, data on interactions of UV with green light on the one hand, and blue or white light on the other, further contributes to our understanding of light quality regulation of plant metabolism.

Stochastic Variation in DNA Methylation Modulates Nucleosome Occupancy and Alternative Splicing in Arabidopsis thaliana.

Plants use complex gene regulatory mechanisms to overcome diverse environmental challenges. For instance, cold stress induces rapid and massive transcriptome changes via alternative splicing (AS) to confer cold tolerance in plants. In mammals, mounting evidence suggests chromatin structure can regulate co-transcriptional AS. Recent evidence also supports co-transcriptional regulation of AS in plants, but how dynamic changes in DNA methylation and the chromatin structure influence the AS process upon cold stress remains poorly understood. In this study, we used the DNA methylation inhibitor 5-Aza-2′-Deoxycytidine (5-aza-dC) to investigate the role of stochastic variations in DNA methylation and nucleosome occupancy in modulating cold-induced AS, in Arabidopsis thaliana (Arabidopsis). Our results demonstrate that 5-aza-dC derived stochastic hypomethylation modulates nucleosome occupancy and AS profiles of genes implicated in RNA metabolism, plant hormone signal transduction, and of cold-related genes in response to cold stress. We also demonstrate that cold-induced remodelling of DNA methylation regulates genes involved in amino acid metabolism. Collectively, we demonstrate that sudden changes in DNA methylation via drug treatment can influence nucleosome occupancy levels and modulate AS in a temperature-dependent manner to regulate plant metabolism and physiological stress adaptation.

The role of potassium on drought resistance of winter wheat cultivars under cold dryland conditions: Probed by chlorophyll a fluorescence

Potassium (K) is an important cation that regulates plant metabolism. Therefore the effect of different concentrations of potassium (0, 75, 150 kg ha−1 K2SO4) on photosynthesis efficiency of three winter wheat cultivars (Baran, Homa, Hashtrud) was investigated during the growing seasons of 2017–18 and 2018–19 under cold dryland conditions in Maragheh, Iran. Accumulation of potassium ion (K+) was observed to be increased with an increase in the concentration of K2SO4. With an increase in K+ the Hashtrud cultivar was observed to have more relative water content (RWC), normalized differential vegetation index (NDVI), and stomatal conductance (gs) than other cultivars. This resulted in a higher grain yield for the Hashtrud cultivar. RWC (R2 = 0.97), NDVI (R2 = 0.96), and gs (R2 = 0.92) had a positive relationship with KUE (grain yield/unit of K fertilizer used), especially in dryer years. K deficiency induced hydrogen peroxide (H2O2) and malondialdehyde (MDA) concentration in plants. The application of K increased superoxide dismutases and reduced abscisic acid, to maintain the plants' stomatal conductance. Chlorophyll a fluorescence (ChlF) and the calculation of double normalized relative variable fluorescence reveal detailed information's about the response of wheat plants to K application under dryland conditions. The application of a high concentration of K (150 kg ha−1 K2SO4) on Hashtrud plants had a beneficial effect on the ChlF efficiency at different OJIP phases (KJ and JI). We found the efficiency of ChlF at the ΔWK-I phase with the values of FV/FO and PIABS improved with the application of 150 kg ha−1 K2SO4 and can be correlated with total yield improvement. These observations indicated that the application of a high concentration of K in stressed conditions for dryland areas could improve photosynthetic efficiency and wheat plant performance.

Metabolomic analysis of the roots and shoots of tomato seedlings treated with the commercial seaweed-derived biostimulant Afrikelp

Excessive fertilizer use has had severe environmental and economic consequences globally, posing a major challenge to sustainable agriculture. Biostimulants are naturally-occurring biological products that are used to enhance plant productivity by modulating metabolism. One such biostimulant is Afrikelp, which is derived from the brown alga Ecklonia maxima and is purported to enhance plant growth when applied to either the roots or shoots. However, whether a metabolic response is elicited by plants treated with Afrikelp, as well as the manner in which this biostimulant might regulate plant metabolism, has not been scientifically evaluated. In response to this, the present study used gas chromatography-mass spectrometry to explore the changes in primary metabolites between the roots and shoots of tomato (Lycopersicon esculemtum) seedlings treated with Afrikelp and those treated with water alone. Principal components analysis separated the samples treated with Afrikelp and the control, confirming a response to treatment at the metabolite level, particularly in the roots. Fold-change analysis identified many metabolites that were increased in abundance (log2 fold-change > 1.5) in both the shoot and root tissues in comparison with the control. Glycerol-3-phosphate, putrescine, and γ-aminobutyric acid were significantly differentially abundant in the root tissues treated with Afrikelp, possibly suggesting mycorrhizal colonization. In the shoot tissues, the most abundant metabolites included tryptophan, sucrose, and galactinol, and, based on pathway analysis, were largely related to energy metabolism, growth, and hormone synthesis, supporting observations that Afrikelp treatment improves crop growth. Metabolic pathway analysis further suggested the enrichment of carbon and nitrogen metabolism pathways in plants treated with the biostimulant. In summary, Afrikelp appears to increase sugar and nitrogen metabolism in the leaves of tomato plants and might encourage mycorrhizal symbiosis in the roots, thereby promoting growth.

Biosynthesis of Secondary Metabolites Based on the Regulation of MicroRNAs.

MicroRNA (miRNA), a noncoding ribonucleic acid, is considered to be important for the progression of gene expression in plants and animals by rupture or translational repression of targeted mRNAs. Many types of miRNA regulate plant metabolism, growth, and response to biotic and abiotic factors. miRNA characterization helps to expose its function in regulating the process of post-transcriptional genetic regulation. There are a lot of factors associated with miRNA function, but the function of miRNA in the organic synthesis of by-products by natural products is not yet fully elucidated. The current review is aimed at observing and characterizing miRNAs and identifying those involved in the functioning of the biosynthesis of secondary metabolites in plants, with their use in controlled manipulation.

Genetic basis of barley contributions to beer flavor

Barley malt is critical for the malting, brewing, and distilling industries, as it is one of the main ingredients of beer and some types of spirits. There is growing evidence that barley genotype - via malt - can impact the flavors of beers and spirits. However, information on the barley genes involved in these flavors is lacking. Therefore, we used quantitative trait locus (QTL) mapping of malt quality traits, beer sensory descriptors and metabolic compounds on a biparental population of doubled haploids derived from the cross of the cultivars Golden Promise and Full Pint. Putative candidate genes for QTLs were identified by alignment with the reference barley genome sequence. There were thirty-seven QTLs across all chromosomes except 4H, with three QTL clusters located on 3H (1 cluster) and 5H (2 clusters: mid-5H and end-5H). Those “hotspots” contained QTLs for multiple phenotypes. Several candidate genes that regulate plant metabolism were identified within the QTLs and included HvAlaAT, HvDep1, HvMKK3, HvGA20ox1 and HvGA20ox2. These genes are involved in seed dormancy and plant height. Alleles at these loci, and perhaps at physically linked loci, can have key downstream effects on malting quality, beer flavor, and abundance of volatile metabolites.

The transcription factor complex CmAP3-CmPI-CmUIF1 modulates carotenoid metabolism by directly regulating carotenogenic gene CmCCD4a-2 in chrysanthemum.

Carotenoids are one of the most important pigments for the coloring of many plants, fruits, and flowers. Recently, significant progress has been made in carotenoid metabolism. However, our specific understanding of the transcriptional regulation that controls the expression of carotenoid metabolic genes remains extremely limited. Anemone-type chrysanthemums, a special group of chrysanthemum cultivars, contain elongated disc florets in the capitulum that usually differ in color from the ray florets because of their different carotenoid contents. In this study, the carotenoid composition and content of ray and disc florets from the anemone-type chrysanthemum cultivar “Dong Li Fen Gui” were analyzed by high-performance liquid chromatography–tandem mass spectrometry (HPLC–MS/MS), and the key structural gene CmCCD4a-2, whose differential expression resulted in different carotenoid contents in these two types of florets, was identified. The promoter sequence of CmCCD4a-2 was then used as bait to screen a chrysanthemum flower cDNA library, and the transcription factors (TFs) CmAP3 and CmUIF1 were identified. Y2H, BiFC, and Y3H experiments demonstrated that these two TFs were connected by CmPI to form a CmAP3-CmPI-CmUIF1 TF complex. This TF complex regulated carotenoid metabolism by directly activating the expression of CmCCD4a-2. A large number of target genes regulated directly by the CmAP3-CmPI-CmUIF1 TF complex, including carotenoid biosynthetic genes, flavonoid biosynthetic genes, and flower development-related genes, were identified by DNA-affinity purification sequencing (DAP-seq). This result indicated that the CmAP3-CmPI-CmUIF1 TF complex may participate in multiple processes. These findings expand our knowledge of the transcriptional regulation of carotenoid metabolism in plants and will be helpful for manipulating carotenoid accumulation in chrysanthemum.

Root length density (RLD) of oil palm (Elaeis guineensis Jacq) in a haplic Luvisol in Chiapas, Mexico

The tight relationship between root architecture and uptake capacity of soil water and minerals, is well established. Support roots, generally long-lived, perform support functions such as transportation and food storage. Absorbing roots, thin and short-lived, absorb nutrients and regulate plant metabolism. Roots distribution in the soil profile is crucial for plant development. It optimizes resource usage and ensures a prompt response to seasonal changes. This work aimed to study the vertical distribution of the root system of nine-year-old oil palms in a haplic Luvisol, low fertility, moderately acidic, with Nitrogen (N) and Potassium (K) deficiency, average content of Phosphorous (P), and medium to low Cation Exchange Capacity (CEC). Using the cylinder method, soil samples were collected every 10 cm and down to 150 cm of soil depth, from each cardinal side of three soil profiles. The results showed that oil palms had good root development. Most roots (73%) were found in the first 30 cm of soil, with a predominance of fine roots (78%). At 50 cm in depth, fine roots represented 88%, thin roots, 67% and medium roots, 94%. Further study should assess root length density at 15, 20, 25, and 30 years. Highlights - Haplic luvisols are optimal soils for oil palm cultivation due to their depth (> 150cm), over 50% base saturation, and pH of 5.5-6.6. - Root length density (RLD) decreased as soil depth increased. Although most oil palm roots are found in surface horizons, roots can still be found at depths of up to 1.5-5 m. - The highest number of oil palm roots (73%) was found in the first 30 cm, with 78% of fine roots. - Fine roots were distributed throughout the entire soil profile, evidencing high nutrient-absorption and metabolic activities.

Identification of resurrection genes from the transcriptome of dehydrated and rehydrated Selaginella tamariscina

ABSTRACT Selaginella tamariscina is a lycophyta species that survives under extremely dry conditions via the mechanism of resurrection. This phenomenon involves the regulation of numerous genes that play vital roles in desiccation tolerance and subsequent rehydration. To identify resurrection-related genes, we analyzed the transcriptome between dehydration conditions and rehydration conditions of S. tamariscina. The de novo assembly generated 124,417 transcripts with an average size of 1,000 bp and 87,754 unigenes. Among these genes, 1,267 genes and 634 genes were up and down regulated by rehydration compared to dehydration. To understand gene function, we annotated Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The unigenes encoding early light-inducible protein (ELIP) were down-regulated, whereas pentatricopeptide repeat-containing protein (PPR), late embryogenesis abundant proteins (LEA), sucrose nonfermenting protein (SNF), trehalose phosphate phosphatase (TPP), trehalose phosphate synthase (TPS), and ABC transporter G family (ABCG) were significantly up-regulated in response to rehydration conditions by differentially expressed genes (DEGs) analysis. Several studies provide evidence that these genes play a role in stress environment. The ELIP and PPR genes are involved in chloroplast protection during dehydration and rehydration. LEA, SNF, and trehalose genes are known to be oxidant scavengers that protect the cell structure from the deleterious effect of drought. TPP and TPS genes were found in the starch and sucrose metabolism pathways, which are essential sugar-signaling metabolites regulating plant metabolism and other biological processes. ABC-G gene interacts with abscisic acid (ABA) phytohormone in the stomata opening during stress conditions. Our findings provide valuable information and candidate resurrection genes for future functional analysis aimed at improving the drought tolerance of crop plants.

MicroRNA-Mediated Gene Regulation of Secondary Metabolism in Plants

Plant microRNAs (miRNAs), a class of about 21-nucleotide-long small noncoding RNAs (ncRNAs), generally act as key regulators of their target genes by guiding mRNA cleavage or translational repression. Recent researches have reported that miRNAs can interact with pathway-related structural genes, transcription factors (TFs) and noncoding RNAs (ncRNAs) to form regulatory network in secondary metabolite (SM) biosynthetic pathways. The validated interactions can better reflect the real regulatory mechanism of miRNA and convert miRNAs into more efficient tools to control the production of precious SMs. However, there is no systematic review available on this topic especially in plants, particularly model plants and crops. Here, we firstly overviewed the critical secondary metabolic pathways in plants, especially those biosynthetic pathways related structural genes which were well-studied and representative SMs, including phenylpropanoids, terpenoids, alkaloids. Principally, we summarized miRNAs involved in the biosynthesis of SMs, miRNA-target modules and their regulation on the mentioned pathways in the last decade. Significantly, the modules included miRNA-structural gene, miRNA-TF, miRNA-ncRNA interaction pairs carried out by target validation or functional confirmation. This knowledge will promote understanding the sophisticated miRNA-mediated gene regulatory network of SM biosynthesis, and drive the development of synthetic biology.

Regulation of stress-induced inositol metabolism in plants: a phylogenetic search for conserved cis elements

Regulation of stress-induced inositol metabolism in plants: a phylogenetic search for conserved cis elements

Exogenous Application of Non-mature miRNA-Encoded miPEP164c Inhibits Proanthocyanidin Synthesis and Stimulates Anthocyanin Accumulation in Grape Berry Cells.

Secondary metabolic pathways in grape berries are tightly regulated by an array of molecular mechanisms, including microRNA-mediated post-transcriptional regulation. As recently discovered, before being processed into mature microRNAs (miRNAs), the primary transcripts of miRNAs (pri-miRNAs) can encode for small miRNA-encoded peptides (micropeptides – miPEPs) that ultimately lead to an accentuated downregulation of the respective miRNA-targeted genes. Although few studies about miPEPs are available, the discovery of miPEPs reveals a new layer of gene regulation at the post-transcriptional level that opens the possibility to regulate plant metabolism without resorting to gene manipulation. Here, we identified a miPEP encoded in non-mature miR164c putatively targeting grapevine transcription factor VvMYBPA1 (miPEP164c/miPEP-MYBPA1), a positive regulator of key genes in the proanthocyanidin (PA)-biosynthetic pathway, a pathway that competes directly for substrate with the anthocyanin-biosynthetic pathway. Thus, the objective of this work was to test the hypothesis that the exogenous application of miPEP164c (miPEP-MYBPA1) can modulate the secondary metabolism of grape berry cells by inhibiting PA biosynthetic pathway while simultaneously stimulating anthocyanin synthesis. The exogenous application of miPEP164c to suspension-cultured cells from grape berry (cv. Gamay) enhanced the transcription of its corresponding non-mature miR164c, with a maximum effect at 1 μM and after a period of 10 days, thus leading to a more pronounced post-transcriptional silencing of its target VvMYBPA1. This led to a significant inhibition of the PA pathway, mostly via inhibition of leucoanthocyanidin reductase (LAR) and anthocyanidin reductase (ANR) enzymatic activities and VvLAR1 downregulation. In parallel, the anthocyanin-biosynthetic route was stimulated. Anthocyanin content was 31% higher in miPEP164c-treated cells, in agreement with the observed upregulation of VvUFGT1 transcripts and UFGT enzyme activity levels.