Primary transcript of miR858 encodes regulatory peptide and controls flavonoid biosynthesis and development in Arabidopsis

miR397 regulates cadmium stress response by coordinating lignin polymerization in the root exodermis in Kandelia obovata

Secondary lignification of the root exodermis of Kandelia obovata is crucial for its response to adversity such as high salinity and anaerobic environment, and this lignification is also effective in blocking cadmium transport to the roots. However, how the differences in lignification of root exodermis at different developmental stages respond to Cd stress and its regulatory mechanisms have not been revealed. In this study, after analyzing the root structure and cell wall thickness using a Phenom scanning electron microscope as well as measuring cadmium content in the root cell wall, we found that the exodermis of young and mature roots of K. obovata responded to Cd stress through the polymerization of different lignin monomers, forming two different mechanisms: chelation and blocking. Through small RNA sequencing, RLM-5'-RACE and dual luciferase transient expression system, we found that miR397 targets and regulates KoLAC4/17/7 expression. The expression of KoLAC4/17 promoted the accumulation of guaiacyl lignin during lignification and enhanced the binding of cadmium to the cell wall. Meanwhile, KoLAC7 expression promotes the accumulation of syringyl lignin during lignification, which enhances the obstruction of cadmium and improves the tolerance to cadmium. These findings enhance our understanding of the molecular mechanisms underlying the differential lignification of the root exodermis of K. obovata in response to cadmium stress, and provide scientific guidance for the conservation of mangrove forests under heavy metal pollution.

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.

Genome-Wide Identification and Functional Analysis of Salvia miltiorrhiza MicroRNAs Reveal the Negative Regulatory Role of Smi-miR159a in Phenolic Acid Biosynthesis

MicroRNAs (miRNAs) are a group of endogenous small non-coding RNAs in plants. They play critical functions in various biological processes during plant growth and development. Salvia miltiorrhiza is a well-known traditional Chinese medicinal plant with significant medicinal, economic, and academic values. In order to elucidate the role of miRNAs in S. miltiorrhiza, six small RNA libraries from mature roots, young roots, stems, mature leaves, young leaves and flowers of S. miltiorrhiza and one degradome library from mixed tissues were constructed. A total of 184 miRNA precursors, generating 137 known and 49 novel miRNAs, were genome-widely identified. The identified miRNAs were predicted to play diversified regulatory roles in plants through regulating 891 genes. qRT-PCR and 5' RLM-RACE assays validated the negative regulatory role of smi-miR159a in SmMYB62, SmMYB78, and SmMYB80. To elucidate the function of smi-miR159a in bioactive compound biosynthesis, smi-miR159a transgenic hairy roots were generated and analyzed. The results showed that overexpression of smi-miR159a caused a significant decrease in rosmarinic acid and salvianolic acid B contents. qRT-PCR analysis showed that the targets of smi-miR159a, including SmMYB62, SmMYB78, and SmMYB80, were significantly down-regulated, accompanied by the down-regulation of SmPAL1, SmC4H1, Sm4CL1, SmTAT1, SmTAT3, SmHPPR1, SmRAS, and SmCYP98A14 genes involved in phenolic acid biosynthesis. It suggests that smi-miR159a is a significant negative regulator of phenolic acid biosynthesis in S. miltiorrhiza.

Identification of miRNA858 long-loop precursors in seed plants

MicroRNAs (miRNAs) are a class of nonprotein-coding short transcripts that provide a layer of post-transcriptional regulation essential to many plant biological processes. MiR858, which targets the transcripts of MYB transcription factors, can affect a range of secondary metabolic processes. Although miR858 and its 187-nt precursor have been well studied in Arabidopsis (Arabidopsis thaliana), a systematic investigation of miR858 precursors and their functions across plant species is lacking due to a problem in identifying the transcripts that generate this subclass. By re-evaluating the transcript of miR858 and relaxing the length cut-off for identifying hairpins, we found in kiwifruit (Actinidia chinensis) that miR858 has long-loop hairpins (1,100 to 2,100 nt), whose intervening sequences between miRNA generating complementary sites were longer than all previously reported miRNA hairpins. Importantly, these precursors of miR858 containing long-loop hairpins (termed MIR858L) are widespread in seed plants including Arabidopsis, varying between 350 and 5,500 nt. Moreover, we showed that MIR858L has a greater impact on proanthocyanidin and flavonol levels in both Arabidopsis and kiwifruit. We suggest that an active MIR858L-MYB regulatory module appeared in the transition of early land plants to large upright flowering plants, making a key contribution to plant secondary metabolism.

MicroRNA-encoded regulatory peptides modulate cadmium tolerance and accumulation in rice

MicroRNAs (miRNAs) are small noncoding RNAs that play a vital role in plant responses to abiotic and biotic stresses. Recently, it has been discovered that some primary miRNAs (pri-miRNAs) encode regulatory short peptides called miPEPs. However, the presence of miPEPs in rice, and their functions in response to abiotic stresses, particularly stress induced by heavy metals, remain poorly understood. Here, we identified a functional small peptide (miPEP156e) encoded by pri-miR156e that regulates the expression of miR156 and its target SPL genes, thereby affecting miR156-mediated cadmium (Cd) tolerance in rice. Overexpression of miPEP156e led to decreased uptake and accumulation of Cd and reactive oxygen species (ROS) levels in plants under Cd stress, resulting in improved rice Cd tolerance, as observed in miR156-overexpressing lines. Conversely, miPEP156e mutants displayed sensitivity to Cd stress due to the elevated accumulation of Cd and ROS. Transcriptome analysis further revealed that miPEP156e improved rice Cd tolerance by modulating Cd transporter genes and ROS scavenging genes. Our study provides insights into the regulatory mechanism of miPEP156e in rice response to Cd stress and demonstrates the potential of miPEPs as an effective tool for improving crop abiotic stress tolerance.

What, where, and how: Regulation of translation and the translational landscape in plants

Translation is a crucial step in gene expression and plays a vital role in regulating various aspects of plant development and environmental responses. It is a dynamic and complex program that involves interactions between mRNAs, transfer RNAs, and the ribosome machinery through both cis- and trans-regulation while integrating internal and external signals. Translational control can act in a global (transcriptome-wide) or mRNA-specific manner. Recent advances in genome-wide techniques, particularly ribosome profiling and proteomics, have led to numerous exciting discoveries in both global and mRNA-specific translation. In this review, we aim to provide a "primer" that introduces readers to this fascinating yet complex cellular process and provide a big picture of how essential components connect within the network. We begin with an overview of mRNA translation, followed by a discussion of the experimental approaches and recent findings in the field, focusing on unannotated translation events and translational control through cis-regulatory elements on mRNAs and trans-acting factors, as well as signaling networks through 3 conserved translational regulators TOR, SnRK1, and GCN2. Finally, we briefly touch on the spatial regulation of mRNAs in translational control. Here, we focus on cytosolic mRNAs; translation in organelles and viruses is not covered in this review.

Light-dependent expression and accumulation of miR408-encoded peptide, miPEP408, is regulated by HY5 in Arabidopsis

Recent studies propose that primary transcripts of miRNAs (pri-miRNAs) contain small Open Reading Frames (ORFs) capable of encoding miRNA-encoded peptides (miPEPs). These miPEPs can function as transcriptional regulators for their corresponding pri-miRNAs, ultimately enhancing mature miRNA accumulation. Notably, pri-miR408 encodes the functional peptide miPEP408, regulating expression of miR408 and its target genes, providing plant tolerance to stresses. While miPEPs are crucial regulators, the factors governing them are have not been studied in detail. Here, we explored the light-dependent regulation of miPEP408 in Arabidopsis. Expression analysis during dark-light transitions revealed light-induced transcription and accumulation of the miPEP408. As the promoter of miR408 contains cis-acting elements responsible for binding to the bZIP-type transcription factor ELONGATED HYPOCOTYL5 (HY5), known for light-mediated regulation in plants, we studied its involvement in the regulation of miR408. Analysis of HY5 mutant (hy5-215), complemented line (HY5OX/hy5), and CONSTITUTIVE PHOTOMORPHOGENIC 1 mutant (cop1-4) plants supported HY5's positive regulation of miPEP408. Grafting and GUS assays further suggested the role of HY5 as a shoot-root mobile signal inducing light-dependent miPEP408 expression. This study underscores the regulatory impact of light on small peptides, exemplified by miPEP408, mediated by the key transcription factor HY5.

UDP-glucosyltransferase 71C4 controls the flux of phenylpropanoid metabolism to shape cotton seed development

Seeds play a crucial role in plant reproduction, making it essential to identify genes that affect seed development. In this study, we focused on UDP-glucosyltransferase 71C4 (UGT71C4) in cotton, a member of the glycosyltransferase family that shapes seed width and length, thereby influencing seed index and seed cotton yield. Overexpression of UGT71C4 results in seed enlargement owing to its glycosyltransferase activity on flavonoids, which redirects metabolic flux from lignin to flavonoid metabolism. This shift promotes cell proliferation in the ovule via accumulation of flavonoid glycosides, significantly enhancing seed cotton yield and increasing the seed index from 10.66 g to 11.91 g. By contrast, knockout of UGT71C4 leads to smaller seeds through activation of the lignin metabolism pathway and redirection of metabolic flux back to lignin synthesis. This redirection leads to increased ectopic lignin deposition in the ovule, inhibiting ovule growth and development, and alters yield components, increasing the lint percentage from 41.42% to 43.40% and reducing the seed index from 10.66 g to 8.60 g. Our research sheds new light on seed size development and reveals potential pathways for enhancing seed yield.

Biological Activity of Artificial Plant Peptides Corresponding to the Translational Products of Small ORFs in Primary miRNAs and Other Long "Non-Coding" RNAs

Generally, lncPEPs (peptides encoded by long non-coding RNAs) have been identified in many plant species of several families and in some animal species. Importantly, molecular mechanisms of the miPEPs (peptides encoded by primary microRNAs, pri-miRNAs) are often poorly understood in different flowering plants. Requirement for the additional studies in these directions is highlighted by alternative findings concerning positive regulation of pri-miRNA/miRNA expression by synthetic miPEPs in plants. Further extensive studies are also needed to understand the full set of their roles in eukaryotic organisms. This review mainly aims to consider the available data on the regulatory functions of the synthetic miPEPs. Studies of chemically synthesized miPEPs and analyzing the fine molecular mechanisms of their functional activities are reviewed. Brief description of the studies to identify lncORFs (open reading frames of long non-coding RNAs) and the encoded protein products is also provided.

Micropeptides: potential treatment strategies for cancer

Some noncoding RNAs (ncRNAs) carry open reading frames (ORFs) that can be translated into micropeptides, although noncoding RNAs (ncRNAs) have been previously assumed to constitute a class of RNA transcripts without coding capacity. Furthermore, recent studies have revealed that ncRNA-derived micropeptides exhibit regulatory functions in the development of many tumours. Although some of these micropeptides inhibit tumour growth, others promote it. Understanding the role of ncRNA-encoded micropeptides in cancer poses new challenges for cancer research, but also offers promising prospects for cancer therapy. In this review, we summarize the types of ncRNAs that can encode micropeptides, highlighting recent technical developments that have made it easier to research micropeptides, such as ribosome analysis, mass spectrometry, bioinformatics methods, and CRISPR/Cas9. Furthermore, based on the distribution of micropeptides in different subcellular locations, we explain the biological functions of micropeptides in different human cancers and discuss their underestimated potential as diagnostic biomarkers and anticancer therapeutic targets in clinical applications, information that may contribute to the discovery and development of new micropeptide-based tools for early diagnosis and anticancer drug development.

Small but mighty: Peptides regulating abiotic stress responses in plants

Throughout evolution, plants have developed strategies to confront and alleviate the detrimental impacts of abiotic stresses on their growth and development. The combat strategies involve intricate molecular networks and a spectrum of early and late stress-responsive pathways. Plant peptides, consisting of fewer than 100 amino acid residues, are at the forefront of these responses, serving as pivotal signalling molecules. These peptides, with roles similar to phytohormones, intricately regulate plant growth, development and facilitate essential cell-to-cell communications. Numerous studies underscore the significant role of these small peptides in coordinating diverse signalling events triggered by environmental challenges. Originating from the proteolytic processing of larger protein precursors or directly translated from small open reading frames, including microRNA (miRNA) encoded peptides from primary miRNA, these peptides exert their biological functions through binding with membrane-embedded receptor-like kinases. This interaction initiates downstream cellular signalling cascades, often involving major phytohormones or reactive oxygen species-mediated mechanisms. Despite these advances, the precise modes of action for numerous other small peptides remain to be fully elucidated. In this review, we delve into the dynamics of stress physiology, mainly focusing on the roles of major small signalling peptides, shedding light on their significance in the face of changing environmental conditions.

Transcriptional regulation of flavonol biosynthesis in plants

Flavonols are a class of flavonoids that play a crucial role in regulating plant growth and promoting stress resistance. They are also important dietary components in horticultural crops due to their benefits for human health. In past decades, research on the transcriptional regulation of flavonol biosynthesis in plants has increased rapidly. This review summarizes recent progress in flavonol-specific transcriptional regulation in plants, encompassing characterization of different categories of transcription factors (TFs) and microRNAs as well as elucidation of different transcriptional mechanisms, including direct and cascade transcriptional regulation. Direct transcriptional regulation involves TFs, such as MYB, AP2/ERF, and WRKY, which can directly target the key flavonol synthase gene or other early genes in flavonoid biosynthesis. In addition, different regulation modules in cascade transcriptional regulation involve microRNAs targeting TFs, regulation between activators, interaction between activators and repressors, and degradation of activators or repressors induced by UV-B light or plant hormones. Such sophisticated regulation of the flavonol biosynthetic pathway in response to UV-B radiation or hormones may allow plants to fine-tune flavonol homeostasis, thereby balancing plant growth and stress responses in a timely manner. Based on orchestrated regulation, molecular design strategies will be applied to breed horticultural crops with excellent health-promoting effects and high resistance.

miR397b-LAC2 module regulates cadmium stress response by coordinating root lignification and copper homeostasis in Arabidopsis thaliana

Non-essential heavy metal cadmium (Cd) is toxic to plants and animals. Cadmium affects plant photosynthesis, respiration, and causes water imbalance and may lead to plant death. Cadmium induces toxicity by interfering with the essential metal copper (Cu) homeostasis, which affects plant nutrition. Though root lignin biosynthesis is positively regulated by Cd stress, the underlying mechanisms promoting lignin accumulation and controlling Cd-induced Cu limitation responses are unclear. Here, we elucidated the role of Cu-responsive microRNA (miR397b) in Arabidopsis thaliana plants for Cd stress by targeting the LACCASE2 (LAC2) gene. This study demonstrated the fundamental mechanism of miR397b-mediated Cd stress response by enhancing the lignin content in root tissues. We developed miR397b over-expressing plants, which showed considerable Cd stress tolerance. Plants with knockdown function of LAC2 also showed significant tolerance to Cd stress. miR397b overexpressing and lac2 mutant plants showed root reduction, higher biomass and chlorophyll content, and significantly lower Reactive Oxygen Species (ROS). This study demonstrated the miR397b-mediated Cd stress response in Arabidopsis by enhancing the lignin content in root tissues. We conclude that modulation in miR397b can be potentially used for improving plants for Cd tolerance and Cu homeostasis.

Mutation in shoot-to-root mobile transcription factor, ELONGATED HYPOCOTYL 5, leads to low nicotine levels in tobacco

Tobacco remains one of the most commercially important crops due to the parasympathomimetic alkaloid nicotine used in cigarettes. Most genes involved in nicotine biosynthesis are expressed in root tissues; however, their light-dependent regulation has not been studied. Here, we identified the ELONGATED HYPOCOTYL 5 homolog, NtHY5, from Nicotiana tabacum and demonstrated that NtHY5 could complement the Arabidopsis thaliana hy5 mutant at molecular, morphological and biochemical levels. We report the development of CRISPR/Cas9-based knockout mutant plants of tobacco, NtHY5CR, and show down-regulation of the nicotine and phenylpropanoid pathway genes leading to a significant reduction in nicotine and flavonol content, whereas NtHY5 overexpression (NtHY5OX) plants show the opposite effect. Grafting experiments using wild-type, NtHY5CR, and NtHY5OX indicated that NtHY5 moves from shoot-to-root to regulate nicotine biosynthesis in the root tissue. Shoot HY5, directly or through enhancing expression of the root HY5, promotes nicotine biosynthesis by binding to light-responsive G-boxes present in the NtPMT, NtQPT and NtODC promoters. We conclude that the mobility of HY5 from shoot-to-root regulates light-dependent nicotine biosynthesis. The CRISPR/Cas9-based mutants developed, in this study; with low nicotine accumulation in leaves could help people to overcome their nicotine addiction and the risk of death.

Molecular mechanism of miRNA mediated biosynthesis of secondary metabolites in medicinal plants

Plant secondary metabolites are important raw materials for the pharmaceutical industry, and their biosynthetic processes are subject to diverse and precise regulation by miRNA. The identification of miRNA molecules in medicinal plants and exploration of their mechanisms not only contribute to a deeper understanding of the molecular genetic mechanisms of plant growth, development and resistance to stress, but also provide a theoretical basis for elucidating the pharmacological effects of authentic medicinal materials and constructing bioreactors for the synthesis of medicinal secondary metabolite components. This paper summarizes the research reports on the discovery of miRNA in medicinal plants and their regulatory mechanisms on the synthesis of secondary metabolites by searching the relevant literature in public databases. It summarizes the currently discovered miRNA and their functions in medicinal plants, and summarizes the molecular mechanisms regulating the synthesis and degradation of secondary metabolites. Furthermore, it provides a prospect for the research and development of medicinal plant miRNA. The compiled information contributes to a comprehensive understanding of the research progress on miRNA in medicinal plants and provides a reference for the industrial development of related secondary metabolite biosynthesis.

MicroRNAs constitute an additional layer in plant response to simultaneous bio- and abiotic stresses as exemplified by UV-B radiation and flg22-treatment on Arabidopsis thaliana

Plants are confronted with various environmental stresses and develop sophisticated adaptive mechanisms. Our previous work demonstrated that the crosstalk of flg22 and ultraviolet (UV)-B-induced signalling cascades reprograms the expression of flavonol pathway genes (FPGs), benefiting plant defence responses. Although several transcription factors have been identified to be involved in this crosstalk, the underlying mechanism is largely unclear. Here, we analyzed microRNAs (miRNAs) and identified 126, 129 and 113 miRNAs with altered abundances compared to untreated control in flg22-, UV-B- and flg22/UV-B-treated seedlings, respectively. Two distinct modules were identified: The first consists of 10 miRNAs repressed by UV-B but up-regulated by flg22, and the second with five miRNAs repressed by flg22 but up-regulated by UV-B. In Arabidopsis, the knockdown of miR858a, a representative of module I, increased the abundance of CHS (a marker gene for FPGs), whereas its overexpression reduced CHS. Conversely, knockout of miR164b from module II decreased CHS and its overexpression increased CHS transcript levels. These data suggest a decisive role of miRNAs in the crosstalk. In the next, we described the interaction between miR858a and its target MYB111 (a positive regulator of FPGs) from module I in detail. We showed that MYB111 was profoundly post-transcriptionally regulated by miR858a during the crosstalk, whose expression was specifically but antagonistically controlled by UVR8- and FLS2-mediated signallings. Moreover, transcriptional monitoring using the GUS reporter gene demonstrates that miRNA-mediated posttranscriptional regulation is the main driving force in reprogramming the expression of FPGs and regulates plant adaptation to multiple concurrent environmental stresses.

Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis

A crucial step in functional genomics is identifying actively translated ORFs and linking them to biological functions. The challenge lies in identifying short ORFs, as their identification is greatly influenced by data quality and depth. Here, we improved the coverage of super-resolution Ribo-seq in Arabidopsis (Arabidopsis thaliana), revealing uncharacterized translation events for nuclear, chloroplastic, and mitochondrial genes. Assisted by a transcriptome assembly, we identified 7,751 unconventional translation events, comprising 6,996 upstream ORFs (uORFs) and 209 downstream ORFs on annotated protein-coding genes, as well as 546 ORFs in presumed noncoding RNAs. Proteomic data confirmed the production of stable proteins from some of these unannotated translation events. We present evidence of active translation from primary transcripts of trans-acting small interfering RNAs (TAS1-4) and microRNAs (pri-MIR163 and pri-MIR169) and periodic ribosome stalling supporting cotranslational decay. Additionally, we developed a method for identifying extremely short uORFs, including 370 minimum uORFs (AUG-stop), and 2,921 tiny uORFs (2 to 10 amino acids) and 681 uORFs that overlap with each other. Remarkably, these short uORFs exhibit strong translational repression as do longer uORFs. We also systematically discovered 594 uORFs regulated by alternative splicing, suggesting widespread isoform-specific translational control. Finally, these prevalent uORFs are associated with numerous important pathways. In summary, our improved Arabidopsis translational landscape provides valuable resources to study gene expression regulation.

The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling

Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent an emerging class of regulators, operating directly in the form of small interfering RNAs (siRNAs), microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). These ncRNAs exert control at various levels, including transcription, post-transcription, translation, and epigenetic. Furthermore, they interact with each other, contributing to a variety of biological processes and mechanisms associated with stress resilience. This review primarily concentrates on the recent advancements in plant ncRNAs, delineating their functions in growth and development across various organs such as root, leaf, seed/endosperm, and seed nutrient development. Additionally, this review broadens its scope by examining the role of ncRNAs in response to environmental stresses such as drought, salt, flood, heat, and cold in plants. This compilation offers updated information and insights to guide the characterization of the potential functions of ncRNAs in plant growth, development, and stress resilience in future research.

Multi-omics analysis of small RNA, transcriptome, and degradome to identify putative miRNAs linked to MeJA regulated and oridonin biosynthesis in Isodon rubescens

Isodon rubescens has garnered much attention due to its anti-tumor or anti-cancer properties. However, little is known about the molecular mechanism of oridonin biosynthesis leveraging the regulatory network between small RNAs and mRNAs. In this study, the regulatory networks of miRNAs and targets were examined by combining mRNA, miRNA, and degradome. A total of 348 miRNAs, including 287 known miRNAs and 61 novel miRNAs, were identified. Among them, 51 miRNAs were significantly expressed, and 36 miRNAs responded to MeJA. A total of 3066 target genes were associated with 228 miRNAs via degradome sequencing. Multi-omics analysis demonstrated that 27 miRNA-mRNA pairs were speculated to be involved in MeJA regulation, and 36 miRNA-mRNA pairs were hypothesized to be involved in the genotype-dependence of I. rubescens. Furthermore, 151 and 7 miRNA-mRNA modules were likely engaged in oridonin biosynthesis as identified by psRNATarget and degradome sequencing, respectively. Some miRNA-mRNA modules were confirmed via RT-qPCR. Moreover, miRNAs targeting plant hormone signal transduction pathway genes were identified, such as miR156, miR167, miR393, and PC-3p-19822_242. Collectively, our results demonstrate for the first time that miRNAs are identified in I. rubescens, and laid a solid foundation for further research on the molecular mechanism of oridonin biosynthesis mediated by miRNA.

Advances in regulatory mechanism(s) and biotechnological approaches to modulate nicotine content in tobacco

More than 8 million deaths are caused by tobacco-related diseases every year. A staggering 1.2 million of those fatalities occur due to second-hand smoke exposure among non-smokers, but more than 7 million are due to direct tobacco use among smokers. Nicotine acts as the key ingredient triggering the addiction. The United States Food and Drug Administration (FDA) has classified more than 90 chemical components of tobacco and related smoke as hazardous or potentially hazardous leading to cancer, cardiovascular, respiratory, and reproductive disorders. Hence, reducing nicotine content has been the foremost objective to reduce health and death risks. Therefore, various biotechnological approaches for developing tobacco varieties with low nicotine concentrations are urgently required for the welfare of humankind. In recent years, numerous advancements have been made in nicotine-based tobacco research, suggesting regulatory components involved in nicotine biosynthesis and developing nicotine-less tobacco varieties through biotechnological approaches. This review highlights the various regulatory components and major approaches used to modulate nicotine content in tobacco cultivars.

Non-Mature miRNA-Encoded Micropeptide miPEP166c Stimulates Anthocyanin and Proanthocyanidin Synthesis in Grape Berry Cells

The phenylpropanoid and flavonoid pathways exhibit intricate regulation, not only influenced by environmental factors and a complex network of transcription factors but also by post-transcriptional regulation, such as silencing by microRNAs and miRNA-encoded micropeptides (miPEPs). VviMYBC2-L1 serves as a transcriptional repressor for flavonoids, playing a crucial role in coordinating the synthesis of anthocyanin and proanthocyanidin. It works in tandem with their respective transcriptional activators, VviMYBA1/2 and VviMYBPA1, to maintain an equilibrium of flavonoids. We have discovered a miPEP encoded by miR166c that appears to target VviMYBC2-L1. We conducted experiments to test the hypothesis that silencing this transcriptional repressor through miPEP166c would stimulate the synthesis of anthocyanins and proanthocyanidins. Our transcriptional analyses by qPCR revealed that the application of exogenous miPEP166c to Gamay Fréaux grape berry cells resulted in a significant upregulation in flavonoid transcriptional activators (VviMYBA1/2 and VviMYBPA1) and structural flavonoid genes (VviLDOX and VviDFR), as well as genes involved in the synthesis of proanthocyanidins (VviLAR1 and VviANR) and anthocyanins (VviUFGT1). These findings were supported by the increased enzyme activities of the key enzymes UFGT, LAR, and ANR, which were 2-fold, 14-fold, and 3-fold higher, respectively, in the miPEP166c-treated cells. Ultimately, these changes led to an elevated total content of anthocyanins and proanthocyanidins.

MiRNAs differentially expressed in vegetative and reproductive organs of Marchantia polymorpha - insights into their expression pattern, gene structures and function

MicroRNAs regulate gene expression affecting a variety of plant developmental processes. The evolutionary position of Marchantia polymorpha makes it a significant model to understand miRNA-mediated gene regulatory pathways in plants. Previous studies focused on conserved miRNA-target mRNA modules showed their critical role in Marchantia development. Here, we demonstrate that the differential expression of conserved miRNAs among land plants and their targets in selected organs of Marchantia additionally underlines their role in regulating fundamental developmental processes. The main aim of this study was to characterize selected liverwort-specific miRNAs, as there is a limited knowledge on their biogenesis, accumulation, targets, and function in Marchantia. We demonstrate their differential accumulation in vegetative and generative organs. We reveal that all liverwort-specific miRNAs examined are encoded by independent transcriptional units. MpmiR11737a, MpmiR11887 and MpmiR11796, annotated as being encoded within protein-encoding genes, have their own independent transcription start sites. The analysis of selected liverwort-specific miRNAs and their pri-miRNAs often reveal correlation in their levels, suggesting transcriptional regulation. However, MpmiR11796 shows a reverse correlation to its pri-miRNA level, suggesting post-transcriptional regulation. Moreover, we identify novel targets for selected liverwort-specific miRNAs and demonstrate an inverse correlation between their expression and miRNA accumulation. In the case of one miRNA precursor, we provide evidence that it encodes two functional miRNAs with two independent targets. Overall, our research sheds light on liverwort-specific miRNA gene structure, provides new data on their biogenesis and expression regulation. Furthermore, identifying their targets, we hypothesize the potential role of these miRNAs in early land plant development and functioning.

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.

LncRNAs exert indispensable roles in orchestrating the interaction among diverse noncoding RNAs and enrich the regulatory network of plant growth and its adaptive environmental stress response

With the advent of advanced sequencing technologies, non-coding RNAs (ncRNAs) are increasingly pivotal and play highly regulated roles in the modulation of diverse aspects of plant growth and stress response. This includes a spectrum of ncRNA classes, ranging from small RNAs to long non-coding RNAs (lncRNAs). Notably, among these, lncRNAs emerge as significant and intricate components within the broader ncRNA regulatory networks. Here, we categorize ncRNAs based on their length and structure into small RNAs, medium-sized ncRNAs, lncRNAs, and circle RNAs. Furthermore, the review delves into the detailed biosynthesis and origin of these ncRNAs. Subsequently, we emphasize the diverse regulatory mechanisms employed by lncRNAs that are located at various gene regions of coding genes, embodying promoters, 5'UTRs, introns, exons, and 3'UTR regions. Furthermore, we elucidate these regulatory modes through one or two concrete examples. Besides, lncRNAs have emerged as novel central components that participate in phase separation processes. Moreover, we illustrate the coordinated regulatory mechanisms among lncRNAs, miRNAs, and siRNAs with a particular emphasis on the central role of lncRNAs in serving as sponges, precursors, spliceosome, stabilization, scaffolds, or interaction factors to bridge interactions with other ncRNAs. The review also sheds light on the intriguing possibility that some ncRNAs may encode functional micropeptides. Therefore, the review underscores the emergent roles of ncRNAs as potent regulatory factors that significantly enrich the regulatory network governing plant growth, development, and responses to environmental stimuli. There are yet-to-be-discovered roles of ncRNAs waiting for us to explore.

The Characterization of R2R3-MYB Genes in Ammopiptanthus nanus Uncovers That the miR858-AnaMYB87 Module Mediates the Accumulation of Anthocyanin under Osmotic Stress

R2R3-MYB transcription factors (TFs) participate in the modulation of plant development, secondary metabolism, and responses to environmental stresses. Ammopiptanthus nanus, a leguminous dryland shrub, tolerates a high degree of environmental stress, including drought and low-temperature stress. The systematic identification, structural analysis, evolutionary analysis, and gene profiling of R2R3-MYB TFs under cold and osmotic stress in A. nanus were performed. Up to 137 R2R3-MYB TFs were identified and clustered into nine clades, with most A. nanus R2R3-MYB members belonging to clade VIII. Tandem and segmental duplication events drove the expansion of the A. nanus R2R3-MYB family. Expression profiling revealed that multiple R2R3-MYB genes significantly changed under osmotic and cold stress conditions. MiR858 and miR159 targeted 88 R2R3-MYB genes. AnaMYB87, an miR858-targeted clade VIII R2R3-MYB TF, was up-regulated under both osmotic and cold stress. A transient expression assay in apples showed that the overexpression of AnaMYB87 promoted anthocyanin accumulation. A luciferase reporter assay in tobacco demonstrated that AnaMYB87 positively affected the transactivation of the dihydroflavonol reductase gene, indicating that the miR858-MYB87 module mediates anthocyanin accumulation under osmotic stress by regulating the dihydroflavonol reductase gene in A. nanus. This study provides new data to understand the roles of R2R3-MYB in plant stress responses.

Rose long noncoding RNA lncWD83 promotes flowering by modulating ubiquitination of the floral repressor RcMYC2L

Long noncoding RNAs (lncRNAs) play important roles in various signaling pathways in vascular plants. However, the crosstalk between lncRNAs and E3 ubiquitin ligases has been barely reported. In this study, we demonstrate that the lncRNA lncWD83 from rose (Rosa chinensis) 'Old blush' activates flowering by modulating the ubiquitination of the floral repressor MYC2 LIKE (RcMYC2L). Flowering was substantially delayed in rose by virus-induced gene silencing of lncWD83. In an in vitro pull-down assay, lncWD83 associated with PLANT U-BOX PROTEIN 11 (PUB11), a U-box-containing E3 ubiquitin ligase. Seedlings with knocked down RcPUB11 transcripts phenocopied the later-flowering phenotype of lncWD83-silenced seedlings. RcMYC2L physically interacted with RcPUB11 and was ubiquitinated in an RcPUB11-dependent manner in vitro. Accordingly, silencing RcMYC2L fully reversed the later-flowering phenotype resulting from RcPUB11 knockdown. Furthermore, RcMYC2L bound to G-box-related motifs in the FLOWERING LOCUS T (RcFT) promoter and repressed its transcription. However, RcPUB11 alleviated this repression of RcFT expression via proteasomal degradation of RcMYC2L, and lncWD83 enhanced this degradation by associating with RcPUB11. Therefore, lncWD83 promotes flowering by modulating the ubiquitination of the floral repressor RcMYC2L in rose plants. These findings reveal a distinct regulatory mechanism for an lncRNA in facilitating ubiquitin-mediated proteolysis to regulate rose flowering.

Light regulation of the biosynthesis of phenolics, terpenoids, and alkaloids in plants

Biosynthesis of specialized metabolites (SM), including phenolics, terpenoids, and alkaloids, is stimulated by many environmental factors including light. In recent years, significant progress has been made in understanding the regulatory mechanisms involved in light-stimulated SM biosynthesis at the transcriptional, posttranscriptional, and posttranslational levels of regulation. While several excellent recent reviews have primarily focused on the impacts of general environmental factors, including light, on biosynthesis of an individual class of SM, here we highlight the regulation of three major SM biosynthesis pathways by light-responsive gene expression, microRNA regulation, and posttranslational modification of regulatory proteins. In addition, we present our future perspectives on this topic.

PEP444c encoded within the MIR444c gene regulates microRNA444c accumulation in barley

MicroRNAs are small, noncoding RNA molecules that regulate the expression of their target genes. The MIR444 gene family is present exclusively in monocotyledons, and microRNAs444 from this family have been shown to target certain MADS-box transcription factors in rice and barley. We identified three barley MIR444 (MIR444a/b/c) genes and comprehensively characterised their structure and the processing pattern of the primary transcripts (pri-miRNAs444). Pri-microRNAs444 undergo extensive alternative splicing, generating functional and nonfunctional pri-miRNA444 isoforms. We show that barley pri-miRNAs444 contain numerous open reading frames (ORFs) whose transcripts associate with ribosomes. Using specific antibodies, we provide evidence that selected ORFs encoding PEP444a within MIR444a and PEP444c within MIR444c are expressed in barley plants. Moreover, we demonstrate that CRISPR-associated endonuclease 9 (Cas9)-mediated mutagenesis of the PEP444c-encoding sequence results in a decreased level of PEP444 transcript in barley shoots and roots and a 5-fold reduced level of mature microRNA444c in roots. Our observations suggest that PEP444c encoded by the MIR444c gene is involved in microRNA444c biogenesis in barley.

Shining in the dark: the big world of small peptides in plants

Small peptides represent a subset of dark matter in plant proteomes. Through differential expression patterns and modes of action, small peptides act as important regulators of plant growth and development. Over the past 20 years, many small peptides have been identified due to technical advances in genome sequencing, bioinformatics, and chemical biology. In this article, we summarize the classification of plant small peptides and experimental strategies used to identify them as well as their potential use in agronomic breeding. We review the biological functions and molecular mechanisms of small peptides in plants, discuss current problems in small peptide research and highlight future research directions in this field. Our review provides crucial insight into small peptides in plants and will contribute to a better understanding of their potential roles in biotechnology and agriculture.

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.

An insight into the roles of regulatory ncRNAs in plants: An abiotic stress and developmental perspective

Different environmental cues lead to changes in physiology, biochemistry and molecular status of plant's growth. Till date, various genes have been accounted for their role in regulating plant development and response to abiotic stress. Excluding genes that code for a functional protein in a cell, a large chunk of the eukaryotic transcriptome consists of non-coding RNAs (ncRNAs) which lack protein coding capacity but are still functional. Recent advancements in Next Generation Sequencing (NGS) technology have led to the unearthing of different types of small and large non-coding RNAs in plants. Non-coding RNAs are broadly categorised into housekeeping ncRNAs and regulatory ncRNAs which work at transcriptional, post-transcriptional and epigenetic levels. Diverse ncRNAs play different regulatory roles in nearly all biological processes including growth, development and response to changing environments. This response can be perceived and counteracted by plants using diverse evolutionarily conserved ncRNAs like miRNAs, siRNAs and lncRNAs to participate in complex molecular regimes by activating gene-ncRNA-mRNA regulatory modules to perform the downstream function. Here, we review the current understanding with a focus on recent advancements in the functional studies of the regulatory ncRNAs at the nexus of abiotic stresses and development. Also, the potential roles of ncRNAs in imparting abiotic stress tolerance and yield improvement in crop plants are also discussed with their future prospects.

The role of flavonols in insect resistance and stress response

Plants are sessile organisms and must adapt to various environmental changes, especially from stress conditions. Synthesis of secondary metabolites by the plant is one of the adaptive mechanisms against stress to provide resistance. Among several secondary metabolites, flavonols, a subgroup of flavonoids, are one of the most widely distributed in the plant kingdom. These molecules work as antioxidants, reduce reactive oxygen species (ROS) in plants, and cause detrimental effects on insect growth on feeding. Despite the great interest in flavonol function leading to insect tolerance and stress response, the detailed mechanisms related to these specific functions have yet to be studied. In this review, we have summarized the role of flavonols in plant defense against insects and different abiotic stresses and possible mechanisms involved in these functions.

The eTM-miR858-MYB62-like module regulates anthocyanin biosynthesis under low-nitrogen conditions in Malus spectabilis

The anthocyanin content increases in Malus spectabilis leaves under low-nitrogen conditions. Noncoding RNAs are indicated to play key regulatory roles in anthocyanin biosynthesis. However, the functional roles of noncoding RNAs in anthocyanin biosynthesis under low-nitrogen conditions remain elusive. In this study, miR858 was screened as a key regulator of anthocyanin biosynthesis under low-nitrogen conditions through whole-transcriptome sequencing. Then, we used miR858 as an entry point to explore the regulatory network of lncRNA-miRNA-mRNA by dual-luciferase reporter assays and GUS histochemical staining assays, as well as to identify the mechanism of this regulatory network in anthocyanin biosynthesis by both transient and stable transformation experiments in Malus. MiR858 overexpression increased total anthocyanin content. MiR858 acted by negatively regulating its target gene, MsMYB62-like, under the low-nitrogen condition. MsMYB62-like inhibited the expression of MsF3'H, thereby negatively regulating anthocyanin biosynthesis. In addition, eTM858-1 and eTM858-2 were identified as endogenous target mimics of miR858 that bind to miR858 to prevent cleavage of MsMYB62-like and thereby negatively regulate anthocyanin biosynthesis. The results clarify the mechanism through which the eTM-miR858-MYB62-like module regulates anthocyanin biosynthesis in Malus under low-nitrogen conditions.

microRNA408 and its encoded peptide regulate sulfur assimilation and arsenic stress response in Arabidopsis

MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in regulating various developmental and biological processes. The expression of miRNAs is differentially modulated in response to various biotic and abiotic stresses. Recent findings have shown that some pri-miRNAs encode small regulatory peptides known as microRNA-encoded peptides (miPEPs). miPEPs regulate the growth and development of plants by modulating corresponding miRNA expression; however, the role of these peptides under different stress conditions remains unexplored. Here, we report that pri-miR408 encodes a small peptide, miPEP408, that regulates the expression of miR408, its targets, and associated phenotype in Arabidopsis. We also report that miR408, apart from Plantacyanin (ARPN) and Laccase3 (LAC3), targets a glutathione S-transferase (GSTU25) that plays a role in sulfur assimilation and exhibits a range of detoxification activities with the environmental pollutant. Plants overexpressing miR408 showed severe sensitivity under low sulfur (LS), arsenite As(III), and LS + As(III) stress, while miR408 mutants developed using the CRISPR/Cas9 approach showed tolerance. Transgenic lines showed phenotypic alteration and modulation in the expression of genes involved in the sulfur reduction pathway and affect sulfate and glutathione accumulation. Similar to miR408 overexpressing lines, the exogenous application of synthetic miPEP408 and miPEP408OX lines led to sensitivity in plants under LS, As(III), and combined LS + As(III) stress compared to the control. This study suggests the involvement of miR408 and miPEP408 in heavy metal and nutrient deficiency responses through modulation of the sulfur assimilation pathway.

Unveiling the secrets of non-coding RNA-encoded peptides in plants: A comprehensive review of mining methods and research progress

Non-coding RNAs (ncRNAs) are not conventionally involved in protein encoding. However, recent findings indicate that ncRNAs possess the capacity to code for proteins or peptides. These ncRNA-encoded peptides (ncPEPs) are vital for diverse plant life processes and exhibit significant potential value. Despite their importance, research on plant ncPEPs is limited, with only a few studies conducted and less information on the underlying mechanisms, and the field remains in its nascent stage. This manuscript provides a comprehensive overview of ncPEPs mining methods in plants, focusing on prediction, identification, and functional analysis. We discuss the strengths and weaknesses of various techniques, identify future research directions in the ncPEPs domain, and elucidate the biological functions and agricultural application prospects of plant ncPEPs. By highlighting the immense potential and research value of ncPEPs, we aim to lay a solid foundation for more in-depth studies in plant science.

The Classification, Molecular Structure and Biological Biosynthesis of Flavonoids, and Their Roles in Biotic and Abiotic Stresses

With the climate constantly changing, plants suffer more frequently from various abiotic and biotic stresses. However, they have evolved biosynthetic machinery to survive in stressful environmental conditions. Flavonoids are involved in a variety of biological activities in plants, which can protect plants from different biotic (plant-parasitic nematodes, fungi and bacteria) and abiotic stresses (salt stress, drought stress, UV, higher and lower temperatures). Flavonoids contain several subgroups, including anthocyanidins, flavonols, flavones, flavanols, flavanones, chalcones, dihydrochalcones and dihydroflavonols, which are widely distributed in various plants. As the pathway of flavonoid biosynthesis has been well studied, many researchers have applied transgenic technologies in order to explore the molecular mechanism of genes associated with flavonoid biosynthesis; as such, many transgenic plants have shown a higher stress tolerance through the regulation of flavonoid content. In the present review, the classification, molecular structure and biological biosynthesis of flavonoids were summarized, and the roles of flavonoids under various forms of biotic and abiotic stress in plants were also included. In addition, the effect of applying genes associated with flavonoid biosynthesis on the enhancement of plant tolerance under various biotic and abiotic stresses was also discussed.

Regulatory miPEP Open Reading Frames Contained in the Primary Transcripts of microRNAs

This review aims to consider retrospectively the available data on the coding properties of pri-microRNAs and the regulatory functions of their open reading frames (ORFs) and the encoded peptides (miPEPs). Studies identifying miPEPs and analyzing the fine molecular mechanisms of their functional activities are reviewed together with a brief description of the methods to identify pri-miRNA ORFs and the encoded protein products. Generally, miPEPs have been identified in many plant species of several families and in a few animal species. Importantly, molecular mechanisms of the miPEP action are often quite different between flowering plants and metazoan species. Requirement for the additional studies in these directions is highlighted by alternative findings concerning negative or positive regulation of pri-miRNA/miRNA expression by miPEPs in plants and animals. Additionally, the question of how miPEPs are distributed in non-flowering plant taxa is very important for understanding the evolutionary origin of such micropeptides. Evidently, further extensive studies are needed to explore the functions of miPEPs and the corresponding ORFs and to understand the full set of their roles in eukaryotic organisms. Thus, we address the most recent integrative views of different genomic, physiological, and molecular aspects concerning the expression of miPEPs and their possible fine functions.

The Essentials on microRNA-Encoded Peptides from Plants to Animals

Primary transcripts of microRNAs (pri-miRNAs) were initially defined as long non-coding RNAs that host miRNAs further processed by the microRNA processor complex. A few years ago, however, it was discovered in plants that pri-miRNAs actually contain functional open reading frames (sORFs) that translate into small peptides called miPEPs, for microRNA-encoded peptides. Initially detected in Arabidopsis thaliana and Medicago truncatula, recent studies have revealed the presence of miPEPs in other pri-miRNAs as well as in other species ranging from various plant species to animals. This suggests that miPEP numbers remain largely underestimated and that they could be a common signature of pri-miRNAs. Here we present the most recent advances in miPEPs research and discuss how their discovery has broadened our vision of the regulation of gene expression by miRNAs, and how miPEPs could be interesting tools in sustainable agriculture or the treatment of certain human diseases.

Identification and function of miRNA-mRNA interaction pairs during lateral root development of hemi-parasitic Santalum album L. seedlings

Sandalwood (Santalum album L.) is a hemi-parasitic tree species famous for its santalol and santalene, which are extracted from its heartwood and roots. The ability to understand root functionality within its branched root system would benefit the regulation of sandalwood growth and enhance the commercial value of sandalwood. Phenotypic and anatomical evidence in this study indicated that seed germination stage 4 (SG4) seemed pivotal for lateral root (LR) morphogenesis. Small RNA (sRNA) high-throughput sequencing of root tissues at three sub-stages of SG4 (lateral root primordia initiation (LRPI), lateral root primordia development (LRPD), and lateral root primordia emergence (LRPE)) was performed to identify microRNAs (miRNAs) associated with LR development. A total of 135 miRNAs, including 70 differentially expressed miRNAs (DEMs), were screened. Ten DEMs were selected to investigate transcript abundance in different organs or developmental stages. Among 100 negative DEM-mRNA interaction pairs, four targets (Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8) were selected for studying cleavage sites by 5' RLM-RACE validation. The expression mode of the four miRNA-mRNA pairs was investigated after indole-3-acetic acid (IAA) treatment. IAA enhanced the abundance of homeobox-leucine-zipper protein 32 (HOX32), laccase 12 (LAC12), myeloblastosis86 (MYB86), and pectin methylesterase inhibitor6 (PMEI6) target transcripts by reducing the expression of Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8 in the first 10 min. A schematic model of miRNA-regulated LR development is proposed for this hemi-parasitic species. This novel genetic information for improving sandalwood root growth and development may allow for the cultivation of fast-growing and high-yielding plantations.

Plant microProteins and miPEPs: Small molecules with much bigger roles

The plant science community has identified various regulatory components involved in gene expression. With the advancement of approaches and technologies, new layers of gene regulation have been identified, which play essential roles in fine-tuning biological processes. In this area, recently, small peptides emerged as key regulators in gene regulation to control developmental and physiological processes in plants. Various small peptides have also been identified and characterized to elucidate their roles. A class of small peptides, microProteins (miPs), have been shown to contain at least a protein-protein interaction domain with the potential to regulate multi-domain proteins by becoming a part of protein complexes. Recent studies suggest that some pri-miRNAs encode peptides (miPEPs), which are essential components in plant growth and development. This review provides updates about these small peptides, in general, summarizing their potential role in gene regulation and possible mechanism(s) in plants. We also propose that in-depth research on newly identified plant peptides in crops help to provide solutions enabling sustainable agriculture and food production.

MicroRNA: noncoding but still coding, another example of self-catalysis

MicroRNAs (miRNAs) are known to interact with specific mRNAs to regulate gene expression at the post-transcriptional level by cleaving/repressing the translation process. MiRNA-mediated regulation of gene expression has become an interesting area of research on biological processes like growth, development, and stress responses. Studies suggest that some of the noncoding RNAs possess short open reading frames (ORFs) that code for micropeptides (miPEPs) having a regulatory function. Dual functions of some MIR genes are being deciphered, wherein the gene is transcribed into a longer transcript having a stem-loop structure and a shorter alternatively spliced transcript with no stem-loop. While the longer transcript is processed into miRNA, the shorter one is translated into miPEP. The miPEP enhances the transcription/production of the pri-miRNA from which it originates. Regulatory action of miPEP being species-specific, synthetic miPEP being is tested for exogenous application on crop plant to improve stress tolerance/agronomic performance. Deployment of the miPEP-mediated regulatory function might be a promising strategy to modulated miRNA-facilitated regulation of gene/trait of interest towards developing climate-resilient crops. In this review, we describe the newly identified and verified function of the MIR gene in the coding of miPEPs along with the comparison of the features of miRNA and miPEP in plant. We also discuss about their potential role in crop improvement and some of the yet unanswered question about miPEP.

vvi-miPEP172b and vvi-miPEP3635b increase cold tolerance of grapevine by regulating the corresponding MIRNA genes

As a kind of small molecular weight proteins, many peptides have been discovered, including peptides encoded by pri-miRNA (miPEPs). Similar as traditional phytohormone or signaling molecular, these peptides participate in numerous plant growth processes. MicroRNAs (miRNAs) play an important regulatory role in plant stress response. While the roles of miPEPs in response to abiotic stress has not been studied now. In this study, to explore whether miPEPs could contribute to low temperature (4ºC) tolerance of plants, the expression pattern of 23 different vvi-MIRs were analyzed by qRT-PCR in 'Thompson Seedless' (Vitis vinifera) plantlets under cold stress (4ºC) firstly, and vvi-MIR172b and vvi-MIR3635b which showed an elevated expression levels were selected to identify miPEPs. Through transient expression, one small open reading frame (sORF) in each of the two pri-miRNAs could increase the expression of corresponding vvi-MIR, and the amino acid sequences of sORFs were named vvi-miPEP172b and vvi-miPEP3635b, respectively. The synthetic vvi-miPEP172b and vvi-miPEP3635b were applied to the grape plantlets, and the tissue culture plantlets exhibited a higher cold tolerance compared with the control groups. These results revealed the effective roles of miPEPs in plant cold stress resistance for the first time, providing a theoretical basis for the future application of miPEPs to agricultural production.

From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants

The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.

What Do We Know about Barley miRNAs?

Plant miRNAs are powerful regulators of gene expression at the post-transcriptional level, which was repeatedly proved in several model plant species. miRNAs are considered to be key regulators of many developmental, homeostatic, and immune processes in plants. However, our understanding of plant miRNAs is still limited, despite the fact that an increasing number of studies have appeared. This systematic review aims to summarize our current knowledge about miRNAs in spring barley (Hordeum vulgare), which is an important agronomical crop worldwide and serves as a common monocot model for studying abiotic stress responses as well. This can help us to understand the connection between plant miRNAs and (not only) abiotic stresses in general. In the end, some future perspectives and open questions are summarized.

Identification of Key Genes during Ethylene-Induced Adventitious Root Development in Cucumber (Cucumis sativus L.)

Ethylene (ETH), as a key plant hormone, plays critical roles in various processes of plant growth and development. ETH has been reported to induce adventitious rooting. Moreover, our previous studies have shown that exogenous ETH may induce plant adventitious root development in cucumber (Cucumis sativus L.). However, the key genes involved in this process are still unclear. To explore the key genes in ETH-induced adventitious root development, we employed a transcriptome technique and revealed 1415 differentially expressed genes (DEGs), with 687 DEGs up-regulated and 728 DEGs down-regulated. Using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, we further identified critical pathways that were involved in ETH-induced adventitious root development, including carbon metabolism (starch and sucrose metabolism, glycolysis/gluconeogenesis, citrate cycle (TCA cycle), oxidative phosphorylation, fatty acid biosynthesis, and fatty acid degradation), secondary metabolism (phenylalanine metabolism and flavonoid biosynthesis) and plant hormone signal transduction. In carbon metabolism, ETH reduced the content of sucrose, glucose, starch, the activity of sucrose synthase (SS), sucrose–phosphate synthase (SPS) and hexokinase (HK), and the expressions of CsHK2, pyruvate kinase2 (CsPK2), and CsCYP86A1, whereas it enhanced the expressions of β-amylase 1 (CsBAM1) and β-amylase 3 (CsBAM3). In secondary metabolism, the transcript levels of phenylalanine ammonia-lyase (CsPAL) and flavonoid 3′-monooxygenase (CsF3′M) were negatively regulated, and that of primary-amine oxidase (CsPAO) was positively regulated by ETH. Additionally, the indole-3-acetic acid (IAA) content and the expressions of auxin and ETH signaling transduction-related genes (auxin transporter-like protein 5 (CsLAX5), CsGH3.17, CsSUAR50, and CsERS) were suppressed, whereas the abscisic acid (ABA) content and the expressions of ABA and BR signaling transduction-related genes (CsPYL1, CsPYL5, CsPYL8, BRI1-associated kinase 1 (CsBAK1), and CsXTH3) were promoted by ETH. Furthermore, the mRNA levels of these genes were confirmed by real-time PCR (RT-qPCR). These results indicate that genes related to carbon metabolism, secondary metabolite biosynthesis, and plant hormone signaling transduction are involved in ETH-induced adventitious root development. This work identified the key pathways and genes in ETH-induced adventitious rooting in cucumber, which may provide new insights into ETH-induced adventitious root development and will be useful for investigating the molecular roles of key genes in this process in further studies.

Pervasive translation of small open reading frames in plant long non-coding RNAs

Long non-coding RNAs (lncRNAs) are primarily recognized as non-coding transcripts longer than 200 nucleotides with low coding potential and are present in both eukaryotes and prokaryotes. Recent findings reveal that lncRNAs can code for micropeptides in various species. Micropeptides are generated from small open reading frames (smORFs) and have been discovered frequently in short mRNAs and non-coding RNAs, such as lncRNAs, circular RNAs, and pri-miRNAs. The most accepted definition of a smORF is an ORF containing fewer than 100 codons, and ribosome profiling and mass spectrometry are the most prevalent experimental techniques used to identify them. Although the majority of micropeptides perform critical roles throughout plant developmental processes and stress conditions, only a handful of their functions have been verified to date. Even though more research is being directed toward identifying micropeptides, there is still a dearth of information regarding these peptides in plants. This review outlines the lncRNA-encoded peptides, the evolutionary roles of such peptides in plants, and the techniques used to identify them. It also describes the functions of the pri-miRNA and circRNA-encoded peptides that have been identified in plants.

Natural variation in the transcription factor REPLUMLESS contributes to both disease resistance and plant growth in Arabidopsis

When attacked by pathogens, plants need to reallocate energy from growth to defense to fend off the invaders, frequently incurring growth penalties. This phenomenon is known as the growth-defense tradeoff and is orchestrated by a hardwired transcriptional network. Altering key factors involved in this network has the potential to increase disease resistance without growth or yield loss, but the mechanisms underlying such changes require further investigation. By conducting a genome-wide association study (GWAS) of leaves infected by the hemi-biotrophic bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000, we discovered that the Arabidopsis transcription factor REPLUMLESS (RPL) is necessary for bacterial resistance. More importantly, RPL functions in promoting both disease resistance and growth. Transcriptome analysis revealed a cluster of genes in the GRETCHEN HAGEN 3 (GH3) family that were significantly upregulated in rpl mutants, leading to the accumulation of indole-3-acetic acid-aspartic acid (IAA-Asp). Consistent with this observation, transcripts of virulence effector genes were activated by IAA-Asp accumulated in the rpl mutants. We found that RPL protein could directly bind to GH3 promoters and repress their expression. RPL also repressed flavonol synthesis by directly repressing CHI expression and thus activated the auxin transport pathway, which promotes plant growth. Therefore, RPL plays an important role in plant immunity and functions in the auxin pathway to optimize Arabidopsis growth and defense.

MicroRNAs: emerging regulators in horticultural crops

Horticulture is one of the oldest agricultural practices with great popularity throughout the world. Horticultural crops include fruits, vegetables, ornamental plants, as well as medicinal and beverage plants. They are cultivated for food, specific nutrition, and medical use, or for aesthetic pleasure. MicroRNAs (miRNAs), which constitute a major class of endogenous small RNAs in plants, affect a multitude of developmental and physiological processes by imparting sequence specificity to gene regulation. Over the past decade, tens of thousands of miRNAs have been identified in more than 100 horticultural crops and their critical roles in regulating quality development of diverse horticultural crops have been demonstrated. Here, we review how miRNAs have emerged as important regulators and promising tools for horticultural crop improvement.

Roles of microRNAs in abiotic stress response and characteristics regulation of plant

MicroRNAs (miRNAs) are a class of non-coding endogenous small RNAs (long 20-24 nucleotides) that negatively regulate eukaryotes gene expression at post-transcriptional level via cleavage or/and translational inhibition of targeting mRNA. Based on the diverse roles of miRNA in regulating eukaryotes gene expression, research on the identification of miRNA target genes has been carried out, and a growing body of research has demonstrated that miRNAs act on target genes and are involved in various biological functions of plants. It has an important influence on plant growth and development, morphogenesis, and stress response. Recent case studies indicate that miRNA-mediated regulation pattern may improve agronomic properties and confer abiotic stress resistance of plants, so as to ensure sustainable agricultural production. In this regard, we focus on the recent updates on miRNAs and their targets involved in responding to abiotic stress including low temperature, high temperature, drought, soil salinity, and heavy metals, as well as plant-growing development. In particular, this review highlights the diverse functions of miRNAs on achieving the desirable agronomic traits in important crops. Herein, the main research strategies of miRNAs involved in abiotic stress resistance and crop traits improvement were summarized. Furthermore, the miRNA-related challenges and future perspectives of plants have been discussed. miRNA-based research lays the foundation for exploring miRNA regulatory mechanism, which aims to provide insights into a potential form of crop improvement and stress resistance breeding.