An insight into microRNA biogenesis and its regulatory role in plant secondary metabolism

The CsMYB44-csi-miR0008-CsCER1 module regulates cuticular wax biosynthesis and drought tolerance in citrus

Cuticular wax covering aboveground organs serves as the first line of defense shielding plants from nonstomatal water loss and diverse environmental stresses. While there have been several wax-related genes identified, the molecular mechanisms responsible for the control of wax biosynthesis remain poorly understood in citrus, particularly at the posttranscriptional level. Here, we demonstrated that the CsMYB44-csi-miR0008-CsCER1 module is responsible for regulating drought tolerance in citrus through its control of cuticular wax biosynthesis. In this study, microRNA (miRNA) sequencing analyses of 'Newhall' navel oranges and the wax-deficient 'Ganqi 3' mutant variety led to the identification of a novel cuticular wax biosynthesis-related miRNA, csi-miR0008. csi-miR0008 suppresses the expression of CsCER1, an aldehyde decarbonylase-encoding gene associated with n-alkane biosynthesis. The leaves of csi-miR0008-silencing and CsCER1-overexpressing plants exhibited increases in total wax levels, with particularly pronounced increases in n-alkane levels, contributing to enhanced drought tolerance. csi-miR0008-overexpressing and CsCER1-silencing plants exhibited the opposite phenotypes. CsMYB44 was confirmed to promote wax accumulation by directly inhibiting the expression of csi-miR0008. Taken together, our study offers new insight into the mechanisms responsible for the posttranscriptional control of citrus cuticular wax biosynthesis, while also providing a foundation for the breeding of novel citrus varieties exhibiting enhanced drought tolerance.

MicroRNA-mediated regulation of ginsenoside biosynthesis in Panax ginseng and its biotechnological implications

Panax ginseng, renowned for its therapeutic properties, derives much of its medicinal value from ginsenosides, a group of bioactive triterpenoid saponins. The biosynthesis of ginsenosides is regulated by various mechanisms, including microRNAs (miRNAs), which play key roles in gene regulation. Recent studies have identified numerous miRNAs in P. ginseng and other plants, highlighting their potential to influence triterpenoid biosynthesis by targeting key genes in the pathway. This mini-review explores the current understanding of miRNA-mediated regulation in P. ginseng and discusses the potential for controlling ginsenoside production through miRNA manipulation. Although miRNA research in P. ginseng is still primitive, ongoing studies suggest its potential for promising applications in agriculture and medicine. Further functional studies on these miRNAs could provide valuable insights into optimizing ginsenoside biosynthesis and enhancing medicinal properties.

Differential miRNA expression and regulatory mechanisms in pigmentation and fiber development of white and brown cotton (Gossypium hirsutum)

Cotton (Gossypium hirsutum) is a major global natural fiber crop used in the textile industry. Although white colored cotton remains the most popular form of cultivated cotton, colored varieties could replace chemically dyed fibers and provide more environmental friendly alternatives. In order to investigate the role of miRNAs in fiber color, we selected white and brown cotton varieties for comparative investigations. Through small RNA sequencing, a number of known miRNA families were discovered (74 in white cotton and 61 in brown cotton, with 44 shared) in which 11 miRNA families were significantly elevated in brown cotton variety. Functional enrichment and network analysis of target genes of these miRNAs revealed their regulatory role in secondary metabolite biosynthesis pathway, particularly the flavonoids pathway, which are known to be associated with fiber coloration. Pigmentation and developmental-related miRNA members such as miR396e-5p, miR167l, and miR1446 were also significantly enriched. Real-time PCR results suggest the regulatory role of miRNAs in these two cotton varieties. Furthermore, 30 and 25 novel miRNAs were also identified in white and brown cotton, respectively. Our findings also show miRNAs associated with fiber coloration and development through the intricate networks of miRNA and targets. Understanding these systems may provide novel insights on improving the fiber color and quality.

The Emerging Applications of Artificial MicroRNA-Mediated Gene Silencing in Plant Biotechnology

Improving crop yield potential is crucial to meet the increasing demands of a rapidly expanding global population in an ever-changing and challenging environment. Therefore, different technological approaches have been proposed over the last decades to accelerate plant breeding. Among them, artificial microRNAs (amiRNAs) represent an innovative tool with remarkable potential to assist plant improvement. MicroRNAs (miRNAs) are a group of endogenous, small (20-24 nucleotides), non-coding RNA molecules that play a crucial role in gene regulation. They are associated with most biological processes of a plant, including reproduction, development, cell differentiation, biotic and abiotic stress responses, metabolism, and plant architecture. In this context, amiRNAs are synthetic molecules engineered to mimic the structure and function of endogenous miRNAs, allowing for the targeted silencing of specific nucleic acids. The current review explores the diverse applications of amiRNAs in plant biology and agriculture, such as the management of infectious agents and pests, the engineering of plant metabolism, and the enhancement of plant resilience to abiotic stress. Moreover, we address future perspectives on plant amiRNA-based gene silencing strategies, highlighting the need for further research to fully comprehend the potential of this technology and to translate its scope toward the widespread adoption of amiRNA-based strategies for plant breeding.

Identification and analysis of miRNA - mRNA regulatory modules associated with resistance to bacterial leaf streak in rice

BACKGROUND B: acterial leaf streak (BLS) is a bacterial disease that severely affects rice leaves, leading to significant yield reductions. microRNAs (miRNAs) are short non-coding RNAs extensively involved in the growth, development, and stress responses of plants and animals. However, miRNAs that regulate the response of rice to bacterial leaf streak are still relatively scarce. RESULTS: The indica rice variety Dular exhibits resistance to BLS, whereas the variety 9311 is highly susceptible to the disease. By conducting miRNA sequencing and transcriptome sequencing on both Dular and 9311 before and after BLS inoculation, we identified 19 miRNAs that were significantly downregulated at both 12 and 24 h post-inoculation in Dular, and 9 miRNAs that were significantly upregulated at the same time points in 9311. Additionally, through degradome sequencing, we identified 23 miRNA- mRNA regulatory modules that likely play crucial roles in rice resistance to BLS, and 4 miRNA- mRNA regulatory modules that may be important in rice susceptibility to the disease. DISCUSSION: Current studies on rice disease resistance miRNAs primarily focus on those involved in resistance to rice blast and bacterial blight, with the miRNA-target mRNA regulatory mechanisms for BLS remaining unclear. This study has identified miRNA-mRNA modules that may play significant roles in rice responses to BLS, contributing to the understanding of the miRNA regulatory network involved in rice defense against BLS infection.

MicroRNAs in Plant Genetic Regulation of Drought Tolerance and Their Function in Enhancing Stress Adaptation

Adverse environmental conditions, including drought stress, pose a significant threat to plant survival and agricultural productivity, necessitating innovative and efficient approaches to enhance their resilience. MicroRNAs (miRNAs) are recognized as key elements in regulating plant adaptation to drought stress, with a notable ability to modulate various physiological and molecular mechanisms. This review provides an in-depth analysis of the role of miRNAs in drought response mechanisms, including abscisic acid (ABA) signaling, reactive oxygen species (ROS) detoxification, and the optimization of root system architecture. Additionally, it examines the effectiveness of bioinformatics tools, such as those employed in in silico analyses, for studying miRNA-mRNA interactions, as well as the potential for their integration with experimental methods. Advanced methods such as microarray analysis, high-throughput sequencing (HTS), and RACE-PCR are discussed for their contributions to miRNA target identification and validation. Moreover, new data and perspectives are presented on the role of miRNAs in plant responses to abiotic stresses, particularly drought adaptation. This review aims to deepen the understanding of genetic regulatory mechanisms in plants and to establish a robust scientific foundation for the development of drought-tolerant crop varieties.

Genomic and cell-specific regulation of benzylisoquinoline alkaloid biosynthesis in opium poppy

Opium poppy is a crop of great commercial value as a source of several opium alkaloids for the pharmaceutical industries including morphine, codeine, thebaine, noscapine, and papaverine. Most enzymes involved in benzylisoquinoline alkaloid (BIA) biosynthesis in opium poppy have been functionally characterized, and opium poppy currently serves as a model system to study BIA metabolism in plants. BIA biosynthesis in opium poppy involves two biosynthetic gene clusters associated respectively with the morphine and noscapine branches. Recent reports have shown that genes in the same cluster are co-expressed, suggesting they might also be co-regulated. However, the transcriptional regulation of opium poppy BIA biosynthesis is not well studied. Opium poppy BIA biosynthesis involves three cell types associated with the phloem system: companion cells, sieve elements, and laticifers. The transcripts and enzymes associated with BIA biosynthesis are distributed across cell types, requiring the translocation of key enzymes and pathway intermediates between cell types. Together, these suggest that the regulation of BIA biosynthesis in opium poppy is multilayered and complex, involving biochemical, genomic, and physiological mechanisms. In this review, we highlight recent advances in genome sequencing and single cell and spatial transcriptomics with a focus on how these efforts can improve our understanding of the genomic and cell-specific regulation of BIA biosynthesis. Such knowledge is vital for opium poppy genetic improvement and metabolic engineering efforts targeting the modulation of alkaloid yield and composition.

Artificial miRNAs and target-mimics as potential tools for crop improvement

MicroRNAs (miRNAs) are endogenous, small molecules that negatively regulate gene expression to control the normal development and stress response in plants. They mediate epigenetic changes and regulate gene expression at both transcriptional and post-transcriptional levels. Synthetic biology approaches have been utilized to design efficient artificial miRNAs (amiRNAs) or target-mimics to regulate specific gene expression for understanding the biological function of genes and crop improvement. The amiRNA based gene silencing is an effective technique to "turn off" gene expression, while miRNA target-mimics or decoys are used for efficiently down regulating miRNAs and "turn on" gene expression. In this context, the development of endogenous target-mimics (eTMs) and short tandem target mimics (STTMs) represent promising biotechnological tools for enhancing crop traits like stress tolerance and disease resistance. Through this review, we present the recent developments in understanding plant miRNA biogenesis, which is utilized for the efficient design and development of amiRNAs. This is important to incorporate the artificially synthesized miRNAs as internal components and utilizing miRNA biogenesis pathways for the programming of synthetic circuits to improve crop tolerance to various abiotic and biotic stress factors. The review also examines the recent developments in the use of miRNA target-mimics or decoys for efficiently down regulating miRNAs for trait improvement. A perspective analysis and challenges on the use of amiRNAs and STTM as potent tools to engineer useful traits in plants have also been presented.

microRNA858 represses the transcription factor gene SbMYB47 and regulates flavonoid biosynthesis in Scutellaria baicalensis

MicroRNAs (miRNAs) are noncoding endogenous single-stranded RNAs that regulate target gene expression by reducing their transcription and translation. Several miRNAs in plants function in secondary metabolism. The dried root of Scutellaria baicalensis Georgi is a traditional Chinese medicine that contains flavonoids (baicalin, wogonoside, and baicalein) as its main active ingredients. Although the S. baicalensis genome sequence has been published, information regarding its miRNAs is lacking. In this study, 12 small RNA libraries of different S. baicalensis tissues were compiled, including roots, stems, leaves, and flowers. A total of 129 miRNAs were identified, including 99 miRNAs from 27 miRNA families and 30 predicted miRNAs. Furthermore, 46 reliable target genes of 15 miRNA families were revealed using psRNATarget and confirmed by degradome sequencing. It was speculated that the microRNA858 (miR858)-SbMYB47 module might be involved in flavonoid biosynthesis. Transient assays in Nicotiana benthamiana leaves indicated that miR858 targets SbMYB47 and suppresses its expression. Artificial miRNA-mediated knockdown of miR858 and overexpression of SbMYB47 significantly increased the flavonoid content in S. baicalensis hairy roots, while SbMYB47 knockdown inhibited flavonoid accumulation. Yeast one-hybrid and dual-luciferase assays indicated that SbMYB47 directly binds to and activates the S. baicalensis phenylalanine ammonia-lyase 3 (SbPAL-3) and flavone synthase II (SbFNSⅡ-2) promoters. Our findings reveal the link between the miR858-SbMYB47 module and flavonoid biosynthesis, providing a potential strategy for the production of flavonoids with important pharmacological activities through metabolic engineering.

Identification of Black Cumin (Nigella sativa) MicroRNAs by Next-Generation Sequencing and Their Implications in Secondary Metabolite Biosynthesis

Secondary metabolites are bioactive compounds believed to contribute to the pharmacological properties of plants. MicroRNAs (miRNAs) are small non-coding RNA molecules involved in post-transcriptional regulation and are thought to play an important role in regulating secondary metabolism biosynthesis. Nevertheless, the extent of miRNA involvement in secondary metabolism remains minimal. Nigella sativa (black cumin/black seed) is a popular medicinal and culinary plant known for its pharmaceutical properties; however, its genomic information is scarce. In this study, next-generation sequencing (NGS) technology was employed to obtain the miRNA profile of N. sativa, and their involvement in secondary metabolite biosynthesis was explored. A total of 25,139,003 unique reads ranging from 16 to 40 nucleotides were attained, out of which 240 conserved and 34 novel miRNAs were identified. Moreover, 6083 potential target genes were recognized in this study. Several conserved and novel black cumin miRNAs were found to target enzymes involved in the terpenoid, diterpenoid, phenylpropanoid, carotenoid, flavonoid, steroid, and ubiquinone biosynthetic pathways, among others, for example, beta-carotene 3-hydroxylase, gibberellin 3 beta-dioxygenase, trimethyltridecatetraene synthase, carboxylic ester hydrolases, acetyl-CoA C-acetyltransferase, isoprene synthase, peroxidase, shikimate O-hydroxycinnamoyltransferase, etc. Furthermore, sequencing data were validated through qPCR by checking the relative expression of eleven randomly selected conserved and novel miRNAs (nsa-miR164d, nsa-miR166a, nsa-miR167b, nsa-miR171a, nsa-miR390b, nsa-miR396, nsa-miR159a, nsa-miRN1, nsa-miRN29, nsa-miRN32, and nsa-miRN34) and their expression patterns were found to be corroborated with the sequencing data. We anticipate that this work will assist in clarifying the implications of miRNAs in plant secondary metabolism and aid in the generation of artificial miRNA-based strategies to overproduce highly valuable secondary metabolites from N. sativa.

Research advances of coloring mechanism regulated by MicroRNAs in plants

In plants, microRNAs (miRNAs) are a class of important small RNAs involved in their growth and development, and play a very significant role in regulating their tissue coloring. In this paper, the mechanisms on miRNA regulation of plant coloring are mainly reviewed from three aspects: macroscopic physiological and molecular foundations related to tissue coloring, miRNA biosynthesis and function, and specific analysis of miRNA regulation studies on leaf color, flower color, fruit color, and other tissue color formation in plants. Furthermore, we also systematically summarize the miRNA regulatory mechanisms identified on pigments biosynthesis and color formation in plants, and the regulatory mechanisms of these miRNAs mentioned on the existing researches can be divided into four main categories: directly targeting the related transcription factors, directly targeting the related structural genes, directly targeting the related long noncoding RNAs (LncRNAs) and miRNA-mediated production of trans-acting small interfering RNAs (ta-siRNAs). Together, these research results aim to provide a theoretical reference for the in-depth study of plant coloring mechanism and molecular breeding study of related plants in the future.

Biosynthesis and signal transduction of plant growth regulators and their effects on bioactive compound production in Salvia miltiorrhiza (Danshen)

Plant growth regulators (PGRs) are involved in multiple aspects of plant life, including plant growth, development, and response to environmental stimuli. They are also vital for the formation of secondary metabolites in various plants. Salvia miltiorrhiza is a famous herbal medicine and has been used commonly for > 2000 years in China, as well as widely used in many other countries. S. miltiorrhiza is extensively used to treat cardiovascular and cerebrovascular diseases in clinical practices and has specific merit against various diseases. Owing to its outstanding medicinal and commercial potential, S. miltiorrhiza has been extensively investigated as an ideal model system for medicinal plant biology. Tanshinones and phenolic acids are primary pharmacological constituents of S. miltiorrhiza. As the growing market for S. miltiorrhiza, the enhancement of its bioactive compounds has become a research hotspot. S. miltiorrhiza exhibits a significant response to various PGRs in the production of phenolic acids and tanshinones. Here, we briefly review the biosynthesis and signal transduction of PGRs in plants. The effects and mechanisms of PGRs on bioactive compound production in S. miltiorrhiza are systematically summarized and future research is discussed. This article provides a scientific basis for further research, cultivation, and metabolic engineering in S. miltiorrhiza.

Plant secondary metabolism in a fluctuating world: climate change perspectives

Climate changes have unpredictable effects on ecosystems and agriculture. Plants adapt metabolically to overcome these challenges, with plant secondary metabolites (PSMs) being crucial for plant-environment interactions. Thus, understanding how PSMs respond to climate change is vital for future cultivation and breeding strategies. Here, we review PSM responses to climate changes such as elevated carbon dioxide, ozone, nitrogen deposition, heat and drought, as well as a combinations of different factors. These responses are complex, depending on stress dosage and duration, and metabolite classes. We finally identify mechanisms by which climate change affects PSM production ecologically and molecularly. While these observations provide insights into PSM responses to climate changes and the underlying regulatory mechanisms, considerable further research is required for a comprehensive understanding.

Understanding the multifaceted role of miRNAs in Alzheimer's disease pathology

Small non-coding RNAs (miRNAs) regulate gene expression by binding to mRNA and mediating its degradation or inhibiting translation. Since miRNAs can regulate the expression of several genes, they have multiple roles to play in biological processes and human diseases. The majority of miRNAs are known to be expressed in the brain and are involved in synaptic functions, thus marking their presence and role in major neurodegenerative disorders, including Alzheimer's disease (AD). In AD, amyloid beta (Aβ) plaques and neurofibrillary tangles (NFTs) are known to be the major hallmarks. The clearance of Aβ and tau is known to be associated with miRNA dysregulation. In addition, the β-site APP cleaving enzyme (BACE 1), which cleaves APP to form Aβ, is also found to be regulated by miRNAs, thus directly affecting Aβ accumulation. Growing evidences suggest that neuroinflammation can be an initial event in AD pathology, and miRNAs have been linked with the regulation of neuroinflammation. Inflammatory disorders have also been associated with AD pathology, and exosomes associated with miRNAs are known to regulate brain inflammation, suggesting for the role of systemic miRNAs in AD pathology. Several miRNAs have been related in AD, years before the clinical symptoms appear, most of which are associated with regulating the cell cycle, immune system, stress responses, cellular senescence, nerve growth factor (NGF) signaling, and synaptic regulation. Phytochemicals, especially polyphenols, alter the expression of various miRNAs by binding to miRNAs or binding to the transcriptional activators of miRNAs, thus control/alter various metabolic pathways. Awing to the sundry biological processes being regulated by miRNAs in the brain and regulation of expression of miRNAs via phytochemicals, miRNAs and the regulatory bioactive phytochemicals can serve as therapeutic agents in the treatment and management of AD.

The applications of CRISPR/Cas-mediated microRNA and lncRNA editing in plant biology: shaping the future of plant non-coding RNA research

MAIN CONCLUSION

CRISPR/Cas technology has greatly facilitated plant non-coding RNA (ncRNA) biology research, establishing itself as a promising tool for ncRNA functional characterization and ncRNA-mediated plant improvement. Throughout the last decade, the promising genome editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated proteins (Cas; CRISPR/Cas) has allowed unprecedented advances in the field of plant functional genomics and crop improvement. Even though CRISPR/Cas-mediated genome editing system has been widely used to elucidate the biological significance of a number of plant protein-coding genes, this technology has been barely applied in the functional analysis of those non-coding RNAs (ncRNAs) that modulate gene expression, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Nevertheless, compelling findings indicate that CRISPR/Cas-based ncRNA editing has remarkable potential for deciphering the biological roles of ncRNAs in plants, as well as for plant breeding. For instance, it has been demonstrated that CRISPR/Cas tool could overcome the challenges associated with other approaches employed in functional genomic studies (e.g., incomplete knockdown and off-target activity). Thus, in this review article, we discuss the current status and progress of CRISPR/Cas-mediated ncRNA editing in plant science in order to provide novel prospects for further assessment and validation of the biological activities of plant ncRNAs and to enhance the development of ncRNA-centered protocols for crop improvement.

Unveiling the biosynthesis, mechanisms, and impacts of miRNAs in drought stress resilience in plants

Drought stress is one of the most serious threats to sustainable agriculture and is predicted to be further intensified in the coming decades. Therefore, understanding the mechanism of drought stress tolerance and the development of drought-resilient crops are the major goals at present. In recent years, noncoding microRNAs (miRNAs) have emerged as key regulators of gene expressions under drought stress conditions and are turning out to be the potential candidates that can be targeted to develop drought-resilient crops in the future. miRNAs are known to target and decrease the expression of various genes to govern the drought stress response in plants. In addition, emerging evidence also suggests a regulatory role of long non-coding RNAs (lncRNAs) in the regulation of miRNAs and the expression of their target genes by a process referred as miRNA sponging. In this review, we present the regulatory roles of miRNAs in the modulation of drought-responsive genes along with discussing their biosynthesis and action mechanisms. Additionally, the interactive roles of miRNAs with phytohormone signaling components have also been highlighted to present the global view of miRNA functioning under drought-stress conditions.

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.

Differences in the intraspecies copy number variation of Arabidopsis thaliana conserved and nonconserved miRNA genes

MicroRNAs (miRNAs) regulate gene expression by RNA interference mechanism. In plants, miRNA genes (MIRs) which are grouped into conserved families, i.e. they are present among the different plant taxa, are involved in the regulation of many developmental and physiological processes. The roles of the nonconserved MIRs-which are MIRs restricted to one plant family, genus, or even species-are less recognized; however, many of them participate in the responses to biotic and abiotic stresses. Both over- and underproduction of miRNAs may influence various biological processes. Consequently, maintaining intracellular miRNA homeostasis seems to be crucial for the organism. Deletions and duplications in the genomic sequence may alter gene dosage and/or activity. We evaluated the extent of copy number variations (CNVs) among Arabidopsis thaliana (Arabidopsis) MIRs in over 1000 natural accessions, using population-based analysis of the short-read sequencing data. We showed that the conserved MIRs were unlikely to display CNVs and their deletions were extremely rare, whereas nonconserved MIRs presented moderate variation. Transposon-derived MIRs displayed exceptionally high diversity. Conversely, MIRs involved in the epigenetic control of transposons reactivated during development were mostly invariable. MIR overlap with the protein-coding genes also limited their variability. At the expression level, a higher rate of nonvariable, nonconserved miRNAs was detectable in Col-0 leaves, inflorescence, and siliques compared to nonconserved variable miRNAs, although the expression of both groups was much lower than that of the conserved MIRs. Our data indicate that CNV rate of Arabidopsis MIRs is related with their age, function, and genomic localization.

MicroRNA-like RNA Functions Are Required for the Biosynthesis of Active Compounds in the Medicinal Fungus Sanghuangporus vaninii

miRNA-like RNAs (milRNAs) have been recognized as sequence-specific regulators of posttranscriptional regulation of gene expression in eukaryotes. However, the functions of hundreds of fungal milRNAs in the biosynthesis of metabolic components are obscure. Sanghuangporus produces diverse bioactive compounds and is widely used in Asian countries. Here, genes encoding two Dicers, four Argonautes, and four RdRPs were identified and characterized in Sanghuangporus vanini. Due to the lack of an efficient gene manipulation system, the efficacy of spray-induced gene silencing (SIGS) was determined in S. vanini, which showed efficient double-stranded RNA (dsRNA) uptake and gene silencing efficiency. SIGS-mediated gene knockdown showed that SVRDRP-3, SVRDRP-4, SVDICER-1, and SVDICER-2 were critical for mycelial biomass, flavonoid, triterpenoid, and polysaccharide production. Illumina deep sequencing was performed to characterize the milRNAs from S. vanini mycelium and fruiting body. A total of 31 milRNAs were identified, out of which, SvmilR10, SvmilR17, and SvmilR33 were Svrdrp-4- and Svdicer-1-dependent milRNAs. Importantly, SIGS-mediated overexpression of SvmilR10 and SvmilR33 resulted in significant changes in the yields of flavonoids, triterpenoids, and polysaccharides. Further analysis showed that these milRNA target genes encoding the retrotransposon-derived protein PEG1 and histone-lysine N-methyltransferase were potentially downregulated in the milRNA overexpressing strain. Our results revealed that S. vanini has high external dsRNA and small RNA uptake efficiency and that milRNAs may play crucial regulatory roles in the biosynthesis of bioactive compounds. IMPORTANCE Fungi can take up environmental RNA that can silence fungal genes with RNA interference, which prompts the development of SIGS. Efficient dsRNA and milRNA uptake in S. vanini, successful dsRNA-targeted gene block, and the increase in intracellular miRNA abundance showed that SIGS technology is an effective and powerful tool for the functional dissection of fungal genes and millRNAs. We found that the RdRP, Dicer, and Argonaute genes are critical for mycelial biomass and bioactive compound production. Our study also demonstrated that overexpressed SVRDRP-4- and SVDICER-1-dependent milRNAs (SvmilR10 and SvmilR33) led to significant changes in the yields of the three active compounds. This study not only provides the first report on SIGS-based gene and milRNA function exploration, but also provides a theoretical platform for exploration of the functions of milRNAs involved in biosynthesis of metabolic compounds in fungi.

The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View

Lignans, as secondary metabolites synthesized within a phenylpropanoid pathway, play various roles in plants, including their involvement in growth and plant defense processes. The health and nutritional benefits of lignans are unquestionable, and many studies have been devoted to these attributes. Although the regulatory role of miRNAs in the biosynthesis of secondary metabolites has been widely reported, there is no systematic review available on the miRNA-based regulatory mechanism of lignans biosynthesis. However, the genetic background of lignan biosynthesis in plants is well characterized. We attempted to put together a regulatory mosaic based on current knowledge describing miRNA-mediated regulation of genes, enzymes, or transcription factors involved in this biosynthesis process. At the same time, we would like to underline the fact that further research is necessary to improve our understanding of the miRNAs regulating plant lignan biosynthesis by exploitation of current approaches for functional identification of miRNAs.