BrmiR828 Targets BrPAP1, BrMYB82, and BrTAS4 Involved in the Light Induced Anthocyanin Biosynthetic Pathway in Brassica rapa

Noncoding RNAs in regulation of plant secondary metabolism

Plant secondary metabolites (PSMs) are a large class of structurally diverse molecules, mainly consisting of terpenoids, phenolic compounds, and nitrogen-containing compounds, which play active roles in plant development and stress responses. The biosynthetic processes of PSMs are governed by a sophisticated regulatory network at multiple levels. Noncoding RNAs (ncRNAs) such as microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs) may serve as post-transcriptional regulators for plant secondary metabolism through acting on genes encoding either transcription factors or participating enzymes in relevant metabolic pathways. High-throughput sequencing technologies have facilitated the large-scale identifications of ncRNAs potentially involved in plant secondary metabolism in model plant species as well as certain species with enriched production of specific types of PSMs. Moreover, a series of miRNA-target modules have been functionally characterized to be responsible for regulating PSM biosynthesis and accumulation in plants under abiotic or biotic stresses. In this review, we will provide an overview of current findings on the ncRNA-mediated regulation of plant secondary metabolism with special attention to its participation in plant stress responses, and discuss possible issues to be addressed in future fundamental research and breeding practice.

Role of miRNAs in sucrose stress response, reactive oxygen species, and anthocyanin biosynthesis in Arabidopsis thaliana

In plants, sucrose is the main transported disaccharide that is the primary product of photosynthesis and controls a multitude of aspects of the plant life cycle including structure, growth, development, and stress response. Sucrose is a signaling molecule facilitating various stress adaptations by crosstalk with other hormones, but the molecular mechanisms are not well understood. Accumulation of high sucrose concentrations is a hallmark of many abiotic and biotic stresses, resulting in the accumulation of reactive oxygen species and secondary metabolite anthocyanins that have antioxidant properties. Previous studies have shown that several MYeloBlastosis family/MYB transcription factors are positive and negative regulators of sucrose-induced anthocyanin accumulation and subject to microRNA (miRNA)-mediated post-transcriptional silencing, consistent with the notion that miRNAs may be "nodes" in crosstalk signaling by virtue of their sequence-guided targeting of different homologous family members. In this study, we endeavored to uncover by deep sequencing small RNA and mRNA transcriptomes the effects of exogenous high sucrose stress on miRNA abundances and their validated target transcripts in Arabidopsis. We focused on genotype-by-treatment effects of high sucrose stress in Production of Anthocyanin Pigment 1-Dominant/pap1-D, an activation-tagged dominant allele of MYB75 transcription factor, a positive effector of secondary metabolite anthocyanin pathway. In the process, we discovered links to reactive oxygen species signaling through miR158/161/173-targeted Pentatrico Peptide Repeat genes and two novel non-canonical targets of high sucrose-induced miR408 and miR398b*(star), relevant to carbon metabolic fluxes: Flavonoid 3'-Hydroxlase (F3'H), an important enzyme in determining the B-ring hydroxylation pattern of flavonoids, and ORANGE a post-translational regulator of Phytoene Synthase expression, respectively. Taken together, our results contribute to understanding the molecular mechanisms of carbon flux shifts from primary to secondary metabolites in response to high sugar stress.

miR5298b regulated taxol biosynthesis by acting on TcNPR3, resulting in an alleviation of the strong inhibition of the TcNPR3-TcTGA6 complex in Taxus chinensis

Taxol, a valuable but rare secondary metabolite of the genus Taxus, is an effective anticancer drug. Understanding the regulation of taxol biosynthesis may provide a means to increase taxol content. The microRNA miR5298b was found to promote the accumulation of taxol and upregulate several taxol biosynthesis genes, including DBAT, TASY, and T5H, as demonstrated by experiments using the overexpression and mimicry of transient leaves. Moreover, miR5298b cleaves the mRNA sequence of TcNPR3, a homolog of the salicylic acid receptor AtNPR3/4. Overexpression and knockdown by RNA interference of TcNPR3 confirmed that it repressed taxol biosynthesis. These results indicate that miR5298b enhances taxol biosynthesis via the cleavage of TcNPR3. Yeast two-hybrid bimolecular fluorescence complementation and pull-down assays revealed that TcTGA6, a TGA transcription factor, physically interacted with TcNPR3. Functional experiments showed that TcTGA6 negatively regulates taxol biosynthesis by directly combining with the TGACG motif in the promoters of TASY, T5H, and T10H. TcNPR3 enhances TcTGA6 inhibition Luciferase assays showed that miR5298b alleviated the repression of the TcNPR3-TcTGA6 complex. In summary, miR5298b can cleave TcNPR3, thereby alleviating the inhibition of the TcNPR3-TcTGA6 complex to upregulate taxol biosynthesis genes.

Small RNA and Degradome Sequencing Reveal Roles of miRNAs in the Petal Color Fading of Malus Crabapple

The Malus crabapple is an important woody ornamental plant. The fading of petals during its development significantly affects their ornamental value. Petal color is related to anthocyanin content and miRNAs play an important role in the post-transcriptional regulation of anthocyanin synthesis. However, the mechanisms underlying miRNA regulation of petal fading have rarely been studied. Transcriptome and small RNA sequencing of petals from the blooming phases of Malus. 'Indian Summer' varieties S1 (small bud), S2 (initial-flowering), and S3 (late-flowering) allowed us to identify 230 known miRNAs and 17 novel miRNAs, including 52 differentially expressed miRNAs which targeted 494 genes and formed 823 miRNA-target pairs. Based on the target gene annotation results, miRNA-target pairs were screened that may be involved in the fading process of Malus crabapple petals through three different pathways: anthocyanin synthesis, transport, and degradation, involving mcr-miR858-MYB1\MYB5 and mcr-miR396-McCHI inhibiting anthocyanin synthesis; mcr-miR167, mcr-miR390, mcr-miR535, and mcr-miR858 inhibiting anthocyanin transport from the cytoplasm to the vacuole by targeting ABC transporter genes (ABCB, ABCC, ABCD, and ABCG); and mcr-miR398 targeting the superoxide dismutase genes (CZSOD2 and CCS) to accelerate anthocyanin degradation. These findings offer a novel approach to understanding the mechanism of petal fading and serve as a reference for other plants with floral fading.

Tweaking the Small Non-Coding RNAs to Improve Desirable Traits in Plant

Plant transcriptome contains an enormous amount of non-coding RNAs (ncRNAs) that do not code for proteins but take part in regulating gene expression. Since their discovery in the early 1990s, much research has been conducted to elucidate their function in the gene regulatory network and their involvement in plants' response to biotic/abiotic stresses. Typically, 20-30 nucleotide-long small ncRNAs are a potential target for plant molecular breeders because of their agricultural importance. This review summarizes the current understanding of three major classes of small ncRNAs: short-interfering RNAs (siRNAs), microRNA (miRNA), and transacting siRNAs (tasiRNAs). Furthermore, their biogenesis, mode of action, and how they have been utilized to improve crop productivity and disease resistance are discussed here.

Genome-wide analysis of R2R3-MYB transcription factors in Boehmeria nivea (L.) gaudich revealed potential cadmium tolerance and anthocyanin biosynthesis genes

Gene family, especially MYB as one of the largest transcription factor family in plants, the study of its subfunctional characteristics is a key step in the study of plant gene function. The sequencing of ramie genome provides a good opportunity to study the organization and evolutionary characters of the ramie MYB gene at the whole genome level. In this study, a total of 105 BnGR2R3-MYB genes were identified from ramie genome and subsequently grouped into 35 subfamilies according to phylogeny divergence and sequences similarity. Chromosomal localization, gene structure, synteny analysis, gene duplication, promoter analysis, molecular characteristics and subcellular localization were accomplished using several bioinformatics tools. Collinearity analysis showed that the segmental and tandem duplication events is the dominant form of the gene family expansion, and duplications prominent in distal telomeric regions. Highest syntenic relationship was obtained between BnGR2R3-MYB genes and that of Apocynum venetum (88). Furthermore, transcriptomic data and phylogenetic analysis revealed that BnGMYB60, BnGMYB79/80 and BnGMYB70 might inhibit the biosynthesis of anthocyanins, and UPLC-QTOF-MS data further supported the results. qPCR and phylogenetic analysis revealed that the six genes (BnGMYB9, BnGMYB10, BnGMYB12, BnGMYB28, BnGMYB41, and BnGMYB78) were cadmium stress responsive genes. Especially, the expression of BnGMYB10/12/41 in roots, stems and leaves all increased more than 10-fold after cadmium stress, and in addition they may interact with key genes regulating flavonoid biosynthesis. Thus, a potential link between cadmium stress response and flavonoid synthesis was identified through protein interaction network analysis. The study thus provided significant information into MYB regulatory genes in ramie and may serve as a foundation for genetic enhancement and increased productivity.

Flavonoids in vegetables: improvement of dietary flavonoids by metabolic engineering to promote health

Flavonoids are the most abundant polyphenols in plants, and have antioxidant effects as well as other bioactivities (e.g., anti-inflammatory, anti-cancer, anti-allergic, and neuroprotective effects). Vegetables are rich in flavonoids and are indispensable in our daily diet. Moreover, the vegetables as chassis for producing natural products would emerge as a promising means for cost-effective and sustainable production of flavonoids. Understanding the metabolic engineering of flavonoids in vegetables allows us to improve their nutrient composition. In this review, a comprehensive overview of flavonoids in vegetables, including the characterized types and distribution, health-promoting effects, associated metabolic pathways, and applied metabolic engineering are provided. We also introduce breakthroughs in multi-omics approaches that pertain to the elucidation of flavonoids metabolism in vegetables, as well as prospective and potential genome-editing technologies. Based on the varied composition and content of flavonoids among vegetables, dietary suggestions are further provided for human health.

MicroRNA828 negatively regulates lignin biosynthesis in stem of Populus tomentosa through MYB targets

Lignin biosynthesis in the sclerenchyma cells is strictly controlled by a complex network of genetic and environmental signals. In the last decades, the transcriptional regulation of lignin synthesis in woody species has been established. However, the role of microRNA-mediated post-transcriptional modulation in secondary cell wall biosynthesis remains poorly understood. Here, we identified a microRNA, miR828, involved in the regulation specific to lignin biosynthesis during stem development in Populus tomentosa Carr. miR828 is preferentially expressed in the secondary vascular tissues during stem development. Two MYB genes (MYB171 and MYB011) were validated as direct targets of miR828 by degradome analysis and green fluorescent protein signal detection. Overexpression of miR828 in poplar downregulated genes for lignin biosynthesis, resulting in reduced lignin content in cell walls. Conversely, suppression of miR828 in plants by the short tandem target mimics elevated the expression of lignin biosynthetic genes and increased lignin deposition. We further revealed that poplar MYB171, as the most abundant miR828 target in the stem, is a positive regulator for lignin biosynthesis. Transient expression assays showed that both MYB171 and MYB011 activated PAL1 and CCR2 transcription, whereas the introduction of miR828 significantly suppressed their expression that was induced by MYB171 or MYB011. Collectively, our results demonstrate that the miR828-MYBs module precisely regulates lignin biosynthesis during the stem development in P. tomentosa through transcriptional and post-transcriptional manners.

Identification of microRNAs and their target genes related to the accumulation of anthocyanin in purple potato tubers (Solanum tuberosum)

MicroRNAs (miRNAs) are types of endogenous non-coding small RNAs found in eukaryotes that are 18-25 nucleotides long. miRNAs are considered to be key regulatory factors of the expression of target mRNA. The roles of miRNAs involved in the regulation of anthocyanin accumulation in pigmented potatoes have not been systematically reported. In this study, the differentially expressed miRNAs and their target genes involved in the accumulation of anthocyanin during different developmental stages in purple potato (Solanum tuberosum L.) were identified using small RNA (sRNA) and degradome sequencing. A total of 275 differentially expressed miRNAs were identified in the sRNA libraries. A total of 69,387,200 raw reads were obtained from three degradome libraries. The anthocyanin responsive miRNA-mRNA modules were analyzed, and 37 miRNAs and 23 target genes were obtained. Different miRNAs regulate the key enzymes of anthocyanin synthesis in purple potato. The structural genes included phenylalanine ammonia lyase, chalcone isomerase, flavanone 3-hydroxylase, and anthocyanidin 3-O-glucosyltransferase. The regulatory genes included WD40, MYB, and SPL9. stu-miR172e-5p_L-1R-1, stu-miR828a, stu-miR29b-4-5p, stu-miR8019-5p_L-4R-3, stu-miR396b-5p, stu-miR5303f_L-7R + 2, stu-miR7997a_L-3, stu-miR7997b_L-3, stu-miR7997c_L + 3R-5_2ss2TA3AG, stu-miR156f-5p_L + 1, stu-miR156a, stu-miR156a_R-1, stu-miR156e, stu-miR858, stu-miR5021, stu-miR828 and their target genes were validated by qRT-PCR. They play important roles in the coloration and accumulation of purple potatoes. These results provide new insights into the biosynthesis of anthocyanins in pigmented potatoes.

The Characters of Non-Coding RNAs and Their Biological Roles in Plant Development and Abiotic Stress Response

Plant growth and development are greatly affected by the environment. Many genes have been identified to be involved in regulating plant development and adaption of abiotic stress. Apart from protein-coding genes, more and more evidence indicates that non-coding RNAs (ncRNAs), including small RNAs and long ncRNAs (lncRNAs), can target plant developmental and stress-responsive mRNAs, regulatory genes, DNA regulatory regions, and proteins to regulate the transcription of various genes at the transcriptional, posttranscriptional, and epigenetic level. Currently, the molecular regulatory mechanisms of sRNAs and lncRNAs controlling plant development and abiotic response are being deeply explored. In this review, we summarize the recent research progress of small RNAs and lncRNAs in plants, focusing on the signal factors, expression characters, targets functions, and interplay network of ncRNAs and their targets in plant development and abiotic stress responses. The complex molecular regulatory pathways among small RNAs, lncRNAs, and targets in plants are also discussed. Understanding molecular mechanisms and functional implications of ncRNAs in various abiotic stress responses and development will benefit us in regard to the use of ncRNAs as potential character-determining factors in molecular plant breeding.

The R3-Type MYB Transcription Factor BrMYBL2.1 Negatively Regulates Anthocyanin Biosynthesis in Chinese Cabbage (Brassica rapa L.) by Repressing MYB-bHLH-WD40 Complex Activity

Chinese cabbage (Brassica rapa L.) leaves are purple in color due to anthocyanin accumulation and have nutritional and aesthetic value, as well as antioxidant properties. Here, we identified the R3 MYB transcription factor BrMYBL2.1 as a key negative regulator of anthocyanin biosynthesis. A Chinese cabbage cultivar with green leaves harbored a functional BrMYBL2.1 protein, designated BrMYBL2.1-G, with transcriptional repressor activity of anthocyanin biosynthetic genes. By contrast, BrMYBL2.1 from a Chinese cabbage cultivar with purple leaves carried a poly(A) insertion in the third exon of the gene, resulting in the insertion of multiple lysine residues in the predicted protein, designated BrMYBL2.1-P. Although both BrMYBL2.1 variants localized to the nucleus, only BrMYBL2.1-G interacted with its cognate partner BrTT8. Transient infiltration assays in tobacco leaves revealed that BrMYBL2.1-G, but not BrMYBL2.1-P, actively represses pigment accumulation by inhibiting the transcription of anthocyanin biosynthetic genes. Transient promoter activation assay in Arabidopsis protoplasts verified that BrMYBL2.1-G, but not BrMYBL2.1-P, can repress transcriptional activation of BrCHS and BrDFR, which was activated by co-expression with BrPAP1 and BrTT8. We determined that BrMYBL2.1-P may be more prone to degradation than BrMYBL2.1-G via ubiquitination. Taken together, these results demonstrate that BrMYBL2.1-G blocks the activity of the MBW complex and thus represses anthocyanin biosynthesis, whereas the variant BrMYBL2.1-P from purple Chinese cabbage cannot, thus leading to higher anthocyanin accumulation.

Multilevel regulation of anthocyanin-promoting R2R3-MYB transcription factors in plants

Anthocyanins are common secondary metabolites in plants that confer red, blue, and purple colorations in plants and are highly desired by consumers for their visual appearance and nutritional quality. In the last two decades, the anthocyanin biosynthetic pathway and transcriptional regulation of anthocyanin biosynthetic genes (ABGs) have been well characterized in many plants. From numerous studies on model plants and horticultural crops, many signaling regulators have been found to control anthocyanin accumulation via regulation of anthocyanin-promoting R2R3-MYB transcription factors (so-called R2R3-MYB activators). The regulatory mechanism of R2R3-MYB activators is mediated by multiple environmental factors (e.g., light, temperature) and internal signals (e.g., sugar, ethylene, and JA) in complicated interactions at multiple levels. Here, we summarize the transcriptional control of R2R3-MYB activators as a result of natural variations in the promoter of their encoding genes, upstream transcription factors and epigenetics, and posttranslational modifications of R2R3-MYB that determine color variations of horticultural plants. In addition, we focus on progress in elucidating the integrated regulatory network of anthocyanin biosynthesis mediated by R2R3-MYB activators in response to multiple signals. We also highlight a few gene cascade modules involved in the regulation of anthocyanin-related R2R3-MYB to provide insights into anthocyanin production in horticultural plants.

MicroRNA-mediated bioengineering for climate-resilience in crops

Global projections on the climate change and the dynamic environmental perturbations indicate severe impacts on food security in general, and crop yield, vigor and the quality of produce in particular. Sessile plants respond to environmental challenges such as salt, drought, temperature, heavy metals at transcriptional and/or post-transcriptional levels through the stress-regulated network of pathways including transcription factors, proteins and the small non-coding endogenous RNAs. Amongs these, the miRNAs have gained unprecedented attention in recent years as key regulators for modulating gene expression in plants under stress. Hence, tailoring of miRNAs and their target pathways presents a promising strategy for developing multiple stress-tolerant crops. Plant stress tolerance has been successfully achieved through the over expression of microRNAs such as Os-miR408, Hv-miR82 for drought tolerance; OsmiR535A and artificial DST miRNA for salinity tolerance; and OsmiR535 and miR156 for combined drought and salt stress. Examples of miR408 overexpression also showed improved efficiency of irradiation utilization and carbon dioxide fixation in crop plants. Through this review, we present the current understanding about plant miRNAs, their roles in plant growth and stress-responses, the modern toolbox for identification, characterization and validation of miRNAs and their target genes including in silico tools, machine learning and artificial intelligence. Various approaches for up-regulation or knock-out of miRNAs have been discussed. The main emphasis has been given to the exploration of miRNAs for development of bioengineered climate-smart crops that can withstand changing climates and stressful environments, including combination of stresses, with very less or no yield penalties.

Anthocyanins: From Mechanisms of Regulation in Plants to Health Benefits in Foods

Anthocyanins represent the major red, purple, and blue pigments in many flowers, fruits, vegetables, and cereals. They are also recognized as important health-promoting components in the human diet with protective effects against many chronic diseases, including cardiovascular diseases, obesity, and cancer. Anthocyanin biosynthesis has been studied extensively, and both biosynthetic and key regulatory genes have been isolated in many plant species. Here, we will provide an overview of recent progress in understanding the anthocyanin biosynthetic pathway in plants, focusing on the transcription factors controlling activation or repression of anthocyanin accumulation in cereals and fruits of different plant species, with special emphasis on the differences in molecular mechanisms between monocot and dicot plants. Recently, new insight into the transcriptional regulation of the anthocyanin biosynthesis, including positive and negative feedback control as well as epigenetic and post-translational regulation of MYB-bHLH-WD40 complexes, has been gained. We will consider how knowledge of regulatory mechanisms has helped to produce anthocyanin-enriched foods through conventional breeding and metabolic engineering. Additionally, we will briefly discuss the biological activities of anthocyanins as components of the human diet and recent findings demonstrating the important health benefits of anthocyanin-rich foods against chronic diseases.

Regulatory non-coding RNAs: a new frontier in regulation of plant biology

Beyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant biology has been recognized. ncRNAs act as riboregulators by recognizing specific nucleic acid targets through homologous sequence interactions to regulate plant growth, development, and stress responses. Regulatory ncRNAs, ranging from small to long ncRNAs (lncRNAs), exert their control over a vast array of biological processes. Based on the mode of biogenesis and their function, ncRNAs evolved into different forms that include microRNAs (miRNAs), small interfering RNAs (siRNAs), miRNA variants (isomiRs), lncRNAs, circular RNAs (circRNAs), and derived ncRNAs. This article explains the different classes of ncRNAs and their role in plant development and stress responses. Furthermore, the applications of regulatory ncRNAs in crop improvement, targeting agriculturally important traits, have been discussed.