COP1 E3 ligase protects HYL1 to retain microRNA biogenesis

Proteolytic control of the RNA silencing machinery

Studies in plants were often pioneering in the field of RNA silencing and revealed a broad range of small RNA (sRNA) categories. When associated with ARGONAUTE (AGO) proteins, sRNAs play important functions in development, genome integrity, stress responses, and antiviral immunity. Today, most of the protein factors required for the biogenesis of sRNA classes, their amplification through the production of double-stranded RNA, and their function in transcriptional and posttranscriptional regulation have been identified. Nevertheless, and despite the importance of RNA silencing, we still know very little about their posttranslational regulation. This is in stark contrast with studies in metazoans, where different modifications such as prolyl hydroxylation, phosphorylation, sumoylation, ubiquitylation, and others have been reported to alter the activity and stability of key factors, such as AGO proteins. Here, we review current knowledge of how key components of the RNA silencing machinery in plants are regulated during development and by microbial hijacking of endogenous proteases.

HYL1's multiverse: A journey through miRNA biogenesis and beyond canonical and non-canonical functions of HYL1

A delicate balance in gene expression, a process highly controlled by post-transcriptional gene silencing mediated by miRNAs, is vital during plant growth and responses to stress. Within the miRNA biogenesis pathway, HYL1 is one of the most important proteins, initially recognized for its role as a cofactor of DCL1. Yet, HYL1's functions extend beyond miRNA processing, encompassing transcriptional regulation and protein translation between other recently discovered functions. This review comprehensively examines our current knowledge of HYL1 functions in plants, looking at its structure, the complex biochemistry behind it, and its involvement in a variety of cellular processes. We also explored the most compelling open questions regarding HYL1 biology and the further perspectives in its study. Unraveling HYL1 functional details could better understand how plants grow, face environmental stresses, and how the miRNA pathway adapts its outcome to the plant growing conditions.

The spliceosome-associated protein CWC15 promotes miRNA biogenesis in Arabidopsis

MicroRNAs (miRNAs) play a key role in regulating gene expression and their biogenesis is precisely controlled through modulating the activity of microprocessor. Here, we report that CWC15, a spliceosome-associated protein, acts as a positive regulator of miRNA biogenesis. CWC15 binds the promoters of genes encoding miRNAs (MIRs), promotes their activity, and increases the occupancy of DNA-dependent RNA polymerases at MIR promoters, suggesting that CWC15 positively regulates the transcription of primary miRNA transcripts (pri-miRNAs). In addition, CWC15 interacts with Serrate (SE) and HYL1, two key components of microprocessor, and is required for efficient pri-miRNA processing and the HYL1-pri-miRNA interaction. Moreover, CWC15 interacts with the 20 S proteasome and PRP4KA, facilitating SE phosphorylation by PRP4KA, and subsequent non-functional SE degradation by the 20 S proteasome. These data reveal that CWC15 ensures optimal miRNA biogenesis by maintaining proper SE levels and by modulating pri-miRNA levels. Taken together, this study uncovers the role of a conserved splicing-related protein in miRNA biogenesis.

JANUS, a spliceosome-associated protein, promotes miRNA biogenesis in Arabidopsis

MicroRNAs (miRNAs) are important regulators of genes expression. Their levels are precisely controlled through modulating the activity of the microprocesser complex (MC). Here, we report that JANUS, a homology of the conserved U2 snRNP assembly factor in yeast and human, is required for miRNA accumulation. JANUS associates with MC components Dicer-like 1 (DCL1) and SERRATE (SE) and directly binds the stem-loop of pri-miRNAs. In a hypomorphic janus mutant, the activity of DCL1, the numbers of MC, and the interaction of primary miRNA transcript (pri-miRNAs) with MC are reduced. These data suggest that JANUS promotes the assembly and activity of MC through its interaction with MC and/or pri-miRNAs. In addition, JANUS modulates the transcription of some pri-miRNAs as it binds the promoter of pri-miRNAs and facilitates Pol II occupancy of at their promoters. Moreover, global splicing defects are detected in janus. Taken together, our study reveals a novel role of a conserved splicing factor in miRNA biogenesis.

Tailed-Hoogsteen Triplex DNA Silver Nanoclusters Emit Red Fluorescence upon Target miRNA Sensing

MicroRNAs (miRNAs) are small RNA molecules, typically 21-22 nucleotides in size, which play a crucial role in regulating gene expression in most eukaryotes. Their significance in various biological processes and disease pathogenesis has led to considerable interest in their potential as biomarkers for diagnosis and therapeutic applications. In this study, a novel method for sensing target miRNAs using Tailed-Hoogsteen triplex DNA-encapsulated Silver Nanoclusters (DNA/AgNCs) is introduced. Upon hybridization of a miRNA with the tail, the Tailed-Hoogsteen triplex DNA/AgNCs exhibit a pronounced red fluorescence, effectively turning on the signal. It is successfully demonstrated that this miRNA sensor not only recognized target miRNAs in total RNA extracted from cells but also visualized target miRNAs when introduced into live cells, highlighting the advantages of the turn-on mechanism. Furthermore, through gel-fluorescence assays and small-angle X-ray scattering (SAXS) analysis, the turn-on mechanism is elucidated, revealing that the Tailed-Hoogsteen triplex DNA/AgNCs undergo a structural transition from a monomer to a dimer upon sensing the target miRNA. Overall, the findings suggest that Tailed-Hoogsteen triplex DNA/AgNCs hold great promise as practical sensors for small RNAs in both in vitro and cell imaging applications.

Hyponastic Leaves 1 Interacts with RNA Pol II to Ensure Proper Transcription of MicroRNA Genes

Hyponastic Leaves 1 (HYL1) [also known as Double-stranded RNA-Binding protein 1 (DRB1)] is a double-stranded RNA-binding protein involved in microRNA (miRNA) processing in plants. It is a core component of the Microprocessor complex and enhances the efficiency and precision of miRNA processing by the Dicer-Like 1 protein. In this work, we report a novel function of the HYL1 protein in the transcription of miRNA (MIR) genes. HYL1 colocalizes with RNA polymerase II and affects its distribution along MIR genes. Moreover, proteomic experiments revealed that the HYL1 protein interacts with many transcription factors. Finally, we show that the action of HYL1 is not limited to MIR genes and impacts the expression of many other genes, a majority of which are involved in plastid organization. These discoveries indicate HYL1 as an additional player in gene regulation at the transcriptional level, independent of its role in miRNA biogenesis.

RNA Polymerase III-Dependent BoNR8 and AtR8 lncRNAs Contribute to Hypocotyl Elongation in Response to Light and Abscisic Acid

Hypocotyl elongation is inhibited by light and promoted by darkness. The plant hormone abscisic acid (ABA) also inhibits hypocotyl elongation. However, details of the molecular mechanism that regulates the integrated effects of light and ABA signaling on hypocotyl elongation remain unclear. Long non-coding RNAs (lncRNAs; >200 nt) do not encode proteins but play many physiological roles in organisms. Until now, only a few lncRNAs related to hypocotyl elongation have been reported. The lncRNAs BoNR8 (272 nt) and AtR8 (259 nt), both of which are transcribed by RNA polymerase III, are homologous lncRNAs that are abundantly present in cabbage and Arabidopsis, respectively. These lncRNAs shared 77% sequence identity, and their predicted RNA secondary structures were similar; the non-conserved nucleotides in both sequences were positioned mainly in the stem-loop regions of the secondary structures. A previous study showed that BoNR8 regulated seed germination along with ABA and that AtR8 may be involved in innate immune function in Arabidopsis. Our results show that the expression levels of BoNR8 and AtR8 were differentially affected by light and ABA and that overexpression (OX) of both BoNR8 and AtR8 in Arabidopsis regulated hypocotyl elongation depending on light and ABA.. The expression levels of light-related genes PHYB, COP1, HY5 and PIF4 and ABA-related genes ABI3 and ABI5 were altered in the AtR8-OX and BoNR8-OX lines, and, in an ABI3-defective mutant, hypocotyl elongation was greatly increased under dark condition with the addition of ABA. These results indicate that BoNR8 and AtR8 regulate hypocotyl elongation together with ABI3 and key downstream light signaling genes.

Light-Dependent Regulatory Interactions between the Redox System and miRNAs and Their Biochemical and Physiological Effects in Plants

Light intensity and spectrum play a major role in the regulation of the growth, development, and stress response of plants. Changes in the light conditions affect the formation of reactive oxygen species, the activity of the antioxidants, and, consequently, the redox environment in the plant tissues. Many metabolic processes, thus the biogenesis and function of miRNAs, are redox-responsive. The miRNAs, in turn, can modulate various components of the redox system, and this process is also associated with the alteration in the intensity and spectrum of the light. In this review, we would like to summarise the possible regulatory mechanisms by which the alterations in the light conditions can influence miRNAs in a redox-dependent manner. Daily and seasonal fluctuations in the intensity and spectral composition of the light can affect the expression of miRNAs, which can fine-tune the various physiological and biochemical processes due to their effect on their target genes. The interactions between the redox system and miRNAs may be modulated by light conditions, and the proposed function of this regulatory network and its effect on the various biochemical and physiological processes will be introduced in plants.

HOS15 represses flowering by promoting GIGANTEA degradation in response to low temperature in Arabidopsis

Flowering is the primary stage of the plant developmental transition and is tightly regulated by environmental factors such as light and temperature. However, the mechanisms by which temperature signals are integrated into the photoperiodic flowering pathway are still poorly understood. Here, we demonstrate that HOS15, which is known as a GI transcriptional repressor in the photoperiodic flowering pathway, controls flowering time in response to low ambient temperature. At 16°C, the hos15 mutant exhibits an early flowering phenotype, and HOS15 acts upstream of photoperiodic flowering genes (GI, CO, and FT). GI protein abundance is increased in the hos15 mutant and is insensitive to the proteasome inhibitor MG132. Furthermore, the hos15 mutant has a defect in low ambient temperature-mediated GI degradation, and HOS15 interacts with COP1, an E3 ubiquitin ligase for GI degradation. Phenotypic analyses of the hos15 cop1 double mutant revealed that repression of flowering by HOS15 is dependent on COP1 at 16°C. However, the HOS15-COP1 interaction was attenuated at 16°C, and GI protein abundance was additively increased in the hos15 cop1 double mutant, indicating that HOS15 acts independently of COP1 in GI turnover at low ambient temperature. This study proposes that HOS15 controls GI abundance through multiple modes as an E3 ubiquitin ligase and transcriptional repressor to coordinate appropriate flowering time in response to ambient environmental conditions such as temperature and day length.

Role of plant microRNAs and their corresponding pathways in fluctuating light conditions

In recent years, it has been established that microRNAs (miRNAs) are critical for various plant physiological regulations in numerous species. Next-generation sequencing technologies have aided to our understandings related to the critical role of miRNAs during environmental stress conditions and plant development. Light influences not just miRNA accumulation but also their biological activities via regulating miRNA gene transcription, biosynthesis, and RNA-induced silencing complex (RISC) activity. Light-regulated routes, processes, and activities can all be affected by miRNAs. Here, we will explore how light affects miRNA gene expression and how conserved and novel miRNAs exhibit altered expression across different plant species in response to variable light quality. Here, we will mainly discuss recent advances in understanding how miRNAs are involved in photomorphogenesis, and photoperiod-dependent plant biological processes such as cell proliferation, metabolism, chlorophyll pigment synthesis and axillary bud growth. The review concludes by presenting future prospects via hoping that light-responsive miRNAs can be exploited in a better way to engineer economically important crops to ensure future food security.

The plant FYVE domain-containing protein FREE1 associates with microprocessor components to repress miRNA biogenesis

FYVE domain protein required for endosomal sorting 1 (FREE1), originally identified as a plant-specific component of the endosomal sorting complex required for transport (ESCRT) machinery, plays diverse roles either in endosomal sorting in the cytoplasm or in transcriptional regulation of abscisic acid signaling in the nucleus. However, to date, a role for FREE1 or other ESCRT components in the regulation of plant miRNA biology has not been discovered. Here, we demonstrate a nuclear function of FREE1 as a cofactor in miRNA biogenesis in plants. FREE1 directly interacts with the plant core microprocessor component CPL1 in nuclear bodies and disturbs the association between HYL1, SE and CPL1. Inactivation of FREE1 in the nucleus increases the binding affinity between HYL1, SE, and CPL1 and causes a transition of HYL1 from the inactive hyperphosphorylated version to the active hypophosphorylated form, thereby promoting miRNA biogenesis. Our results suggest that FREE1 has evolved as a negative regulator of miRNA biogenesis and provides evidence for a link between FYVE domain-containing proteins and miRNA biogenesis in plants.

Independent Responses of Photosynthesis and Plant Morphology to Alterations of PIF Proteins and Light-Dependent MicroRNA Contents in Arabidopsis thaliana pif Mutants Grown under Lights of Different Spectral Compositions

The effects of the quality of light on the content of phytochrome interacting factors (PIFs) such as PIF3, PIF4 and PIF5, as well as the expression of various light-dependent microRNAs, in adult Arabidopsis thaliana pif mutant plants (pif4, pif5, pif3pif5, pif4pif5, pif3pif4pif5) were studied. We demonstrate that under blue light, the pif4 mutant had maximal expression of most of the studied microRNAs (miR163, miR319, miR398, miR408, miR833) when the PIF4 protein in plants was reduced. This finding indicates that the PIF4 protein is involved in the downregulation of this group of microRNAs. This assumption is additionally confirmed by the fact that under the RL spectrum in pif5 mutants, practically the same miRNAs decrease expression against the background of an increase in the amount of PIF4 protein. Unlike the WT and other mutants, the pif4 mutant responded to the BL spectrum not only by activating the expression of light-dependent miRNAs, but also by a significant increase in the expression of transcription factors and key light signalling genes. These molecular reactions do not affect the activity of photosynthesis but may be involved in the formation of a light quality-dependent phenotype.

COP1 mutation causes low leaf temperature under various abiotic stresses in Arabidopsis thaliana

Stomata are microscopic pores on epidermal cells of leaves and stems that regulate water loss and gas exchange between the plant and its environment. Constitutive photomorphogenic 1 (COP1) is an E3 ubiquitin ligase that is involved in plant growth and development and multiple abiotic stress responses by regulating the stability of various target proteins. However, little is known about how COP1 controls stomatal aperture and leaf temperature under various environmental conditions. Here, we show that COP1 participates in leaf temperature and stomatal closure regulation under normal and stress conditions in Arabidopsis. Leaf temperature of cop1 mutants was relatively lower than that of wild type (WT) under drought, salt, and heat stress and after abscisic acid (ABA), CaCl2, and H2O2 treatments. However, leaf temperature was generally higher in both WT and cop1 mutants after abiotic stress and chemical treatment than that of untreated WT and cop1 mutants. Stomatal aperture was wider in cop1 mutants than that in WT under all conditions tested, although the extent of stomatal closure varied between WT and cop1 mutants. Under dark conditions, leaf temperature was also lower in cop1 mutants than that in WT. Expression of the genes encoding ABA receptors, ABA biosynthesis proteins, positive regulators of stomatal closure and heat tolerance, and ABA-responsive proteins was lower in cop1 mutants that that in WT. In addition, expression of respiration-related genes was lower in cop1 mutants that that in WT. Taken together, the data provide evidence that mutations in COP1 lead to wider stomatal aperture and higher leaf temperature under normal and stress conditions, indicating that leaf temperature is highly correlated with stomatal aperture.

Arabidopsis AAR2, a conserved splicing factor in eukaryotes, acts in microRNA biogenesis

In yeast and humans, AAR2 is involved in pre-messenger RNA (pre-mRNA) splicing through regulating U5 snRNP assembly. This study shows that Arabidopsis AAR2 promotes microRNA (miRNA) accumulation in addition to its conserved role in pre-mRNA splicing. AAR2 is associated with the microprocessor component HYL1 and promotes its dephosphorylation to produce the active form in miRNA biogenesis. The study also reveals a previously unknown role of HYL1 in causing the degradation of the primary precursors to miRNAs (pri-miRNAs) and a role of AAR2 in protecting pri-miRNAs from HYL1-depedent degradation. Taken together, our findings provide insights into the role of a conserved splicing factor in miRNA biogenesis in plants.

MicroRNAs (miRNAs) play an essential role in plant growth and development, and as such, their biogenesis is fine-tuned via regulation of the core microprocessor components. Here, we report that Arabidopsis AAR2, a homolog of a U5 snRNP assembly factor in yeast and humans, not only acts in splicing but also promotes miRNA biogenesis. AAR2 interacts with the microprocessor component hyponastic leaves 1 (HYL1) in the cytoplasm, nucleus, and dicing bodies. In aar2 mutants, abundance of nonphosphorylated HYL1, the active form of HYL1, and the number of HYL1-labeled dicing bodies are reduced. Primary miRNA (pri-miRNA) accumulation is compromised despite normal promoter activities of MIR genes in aar2 mutants. RNA decay assays show that the aar2-1 mutation leads to faster degradation of pri-miRNAs in a HYL1-dependent manner, which reveals a previously unknown and negative role of HYL1 in miRNA biogenesis. Taken together, our findings reveal a dual role of AAR2 in miRNA biogenesis and pre-messenger RNA splicing.

Effects of acute intravenous lipopolysaccharide administration on the plasma lipidome and metabolome in lactating Holstein cows experiencing hyperlipidemia

INTRODUCTION

The effects of lipopolysaccharides (i.e., endotoxin; LPS) on metabolism are poorly defined in lactating dairy cattle experiencing hyperlipidemia.

OBJECTIVES

Our objective was to explore the effects of acute intravenous LPS administration on metabolism in late-lactation Holstein cows experiencing hyperlipidemia induced by intravenous triglyceride infusion and feed restriction.

METHODS

Ten non-pregnant lactating Holstein cows (273 ± 35 d in milk) were administered a single bolus of saline (3 mL of saline; n [Formula: see text] 5) or LPS (0.375 [Formula: see text]g of LPS/kg of body weight; n [Formula: see text] 5). Simultaneously, cows were intravenously infused a triglyceride emulsion and feed restricted for 16 h to induce hyperlipidemia in an attempt to model the periparturient period. Blood was sampled at routine intervals. Changes in circulating total fatty acid concentrations and inflammatory parameters were measured. Plasma samples were analyzed using untargeted lipidomics and metabolomics.

RESULTS

Endotoxin increased circulating serum amyloid A, LPS-binding protein, and cortisol concentrations. Endotoxin administration decreased plasma lysophosphatidylcholine (LPC) concentrations and increased select plasma ceramide concentrations. These outcomes suggest modulation of the immune response and insulin action. Lipopolysaccharide decreased the ratio of phosphatidylcholine to phosphatidylethanomanine, which potentially indicate a decrease in the hepatic activation of phosphatidylethanolamine N-methyltransferase and triglyceride export. Endotoxin administration also increased plasma concentrations of pyruvic and lactic acids, and decreased plasma citric acid concentrations, which implicate the upregulation of glycolysis and downregulation of the citric acid cycle (i.e., the Warburg effect), potentially in leukocytes.

CONCLUSION

Acute intravenous LPS administration decreased circulating LPC concentrations, modified ceramide and glycerophospholipid concentrations, and influenced intermediary metabolism in dairy cows experiencing hyperlipidemia.

Emerging roles of the ubiquitin-proteasome pathway in enhancing crop yield by optimizing seed agronomic traits

Ubiquitin-proteasome pathway has the potential to modulate crop productivity by influencing agronomic traits. Being sessile, the plant often uses the ubiquitin-proteasome pathway to maintain the stability of different regulatory proteins to survive in an ever-changing environment. The ubiquitin system influences plant reproduction, growth, development, responses to the environment, and processes that control critical agronomic traits. E3 ligases are the major players in this pathway, and they are responsible for recognizing and tagging the targets/substrates. Plants have a variety of E3 ubiquitin ligases, whose functions have been studied extensively, ranging from plant growth to defense strategies. Here we summarize three agronomic traits influenced by ubiquitination: seed size and weight, seed germination, and accessory plant agronomic traits particularly panicle architecture, tillering in rice, and tassels branch number in maize. This review article highlights some recent progress on how the ubiquitin system influences the stability/modification of proteins that determine seed agronomic properties like size, weight, germination and filling, and ultimately agricultural productivity and quality. Further research into the molecular basis of the aforementioned processes might lead to the identification of genes that could be modified or selected for crop development. Likewise, we also propose advances and future perspectives in this regard.

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

The present review highlights the regulatory roles of microRNAs in plant secondary metabolism and focuses on different bioengineering strategies to modulate secondary metabolite content in plants. MicroRNAs (miRNAs) are the class of small endogenous, essential, non-coding RNAs that riboregulate the gene expression involved in various biological processes in most eukaryotes. MiRNAs has emerged as important regulators in plants that function by silencing target genes through cleavage or translational inhibition. These miRNAs plays an important role in a wide range of plant biological and metabolic processes, including plant development and various environmental response controls. Several important plant secondary metabolites like alkaloids, terpenoids, and phenolics are well studied for their function in plant defense against different types of pests and herbivores. Due to the presence of a wide range of biological and pharmaceutical properties of plant secondary metabolites, it is important to study the regulation of their biosynthetic pathways. The contribution of miRNAs in regulating plant secondary metabolism is not well explored. Recent advancements in molecular techniques have improved our knowledge in understanding the molecular function of genes, proteins, enzymes, and small RNAs involved in different steps of secondary metabolic pathways. In the present review, we have discussed the recent progress made on miRNA biogenesis, its regulation, and highlighted the current research developed in the field of identification, analysis, and characterizations of various miRNAs that regulate plant secondary metabolism. We have also discussed how different bioengineering strategies such as artificial miRNA (amiRNA), endogenous target mimicry, and CRISPR/Cas9 could be utilized to enhance the secondary metabolite production in plants.

In Arabidopsis thaliana, RNA-Induced Silencing Complex-Loading of MicroRNAs Plays a Minor Regulatory Role During Photomorphogenesis Except for miR163

The shift of dark-grown seedlings to the light leads to substantial reprogramming of gene expression, which results in dramatic developmental changes (referred to as de-etiolation or photomorphogenesis). MicroRNAs (miRNAs) regulate most steps of plant development, thus miRNAs might play important role in transcriptional reprogramming during de-etiolation. Indeed, miRNA biogenesis mutants show aberrant de-etiolation. Previous works showed that the total miRNA expression pattern (total miRNAome) is only moderately altered during photomorphogenesis. However, a recent study has shown that plant miRNAs are present in two pools, biologically active miRNAs loaded to RISC (RNA-induced silencing complex-loaded) form while inactive miRNAs accumulate in duplex form upon organ formation. To test if RISC-loading efficiency is changed during photomorphogenesis. we compared the total miRNAome and the RISC-loaded miRNAome of dark-grown and de-etiolated Arabidopsis thaliana seedlings. miRNA sequencing has revealed that although regulated RISC-loading is involved in the control of active miRNAome formation during de-etiolation, this effect is moderate. The total miRNAomes and the RISC-loaded miRNAomes of dark-grown and de-etiolated plants are similar indicating that most miRNAs are loaded onto RISC with similar efficiency in dark and light. Few miRNAs were loaded onto RISC with different efficiency and one miRNA, miR163, was RISC-loaded much more effectively in light than in dark. Thus, our results suggest that although RISC-loading contributes significantly to the control of the formation of organ-specific active miRNA pools, it plays a limited role in the regulation of active miRNA pool formation during de-etiolation. Regulated RISC-loading strongly modifies the expression of miRNA163, could play a role in the fine-tuning of a few other miRNAs, and do not modify the expression of most miRNAs.

RNA-binding proteins and their role in translational regulation in plants

Translation is a fundamental process for life that needs to be finely adapted to the energetical, developmental and environmental conditions; however, the molecular mechanisms behind such adaptation are not yet fully understood. By directly recognizing and binding to cis-elements present in their target mRNAs, RBPs govern all post-transcriptional regulatory processes. They orchestrate the balance between mRNA stability, storage, decay, and translation of their client mRNAs, playing a crucial role in the modulation of gene expression. In the last years exciting discoveries have been made regarding the roles of RBPs in fine-tuning translation. In this review, we focus on how these RBPs recognize their targets and modulate their translation, highlighting the complex and diverse molecular mechanisms implicated. Since the repertoire of RBPs keeps growing, future research promises to uncover new fascinating means of translational modulation, and thus, of gene expression.

Dynamic Phosphorylation of miRNA Biogenesis Factor HYL1 by MPK3 Involving Nuclear-Cytoplasmic Shuttling and Protein Stability in Arabidopsis

MicroRNAs (miRNAs) are one of the prime regulators of gene expression. The recruitment of hyponastic leaves 1 (HYL1), a double-stranded RNA binding protein also termed as DRB1, to the microprocessor complex is crucial for accurate primary-miRNA (pri-miRNA) processing and the accumulation of mature miRNA in Arabidopsis thaliana. In the present study, we investigated the role of the MAP kinase-mediated phosphorylation of AtHYL1 and its sub-cellular activity. AtMPK3 specifically phosphorylates AtHYL1 at the evolutionarily conserved serine-42 present at the N-terminal regions and plays an important role in its nuclear-cytosolic shuttling. Additionally, we identified that AtHYL1 is cleaved by trypsin-like proteases into an N-terminal fragment, which renders its subcellular activities. We, for the first time, report that the dimerization of AtHYL1 not only takes place in the nucleus, but also in the cytosol, and the C-terminal of AtHYL1 has a role in regulating its stability, as well as its subcellular localization. AtHYL1 is hyper-phosphorylated in mpk3 mutants, leading to higher stability and reduced degradation. Our data show that AtMPK3 is a negative regulator of AtHYL1 protein stability and that the AtMPK3-induced phosphorylation of AtHYL1 leads to its protein degradation.

Plastid retrograde regulation of miRNA expression in response to light stress

BACKGROUND

MicroRNAs (miRNAs) are a class of endogenous noncoding RNAs that play a pivotal role in the regulation of plant development and responses to the surrounding environment. Despite the efforts made to elucidate their function in the adaptation of plants to many abiotic and biotic stresses, their role in high light (HL) stress is still vague. HL stress often arises upon plant exposure to full sunlight. Subsequent changes in nuclear gene expression are triggered by chloroplast-derived retrograde signals.

RESULTS

In this study, we show that HL is involved in miRNA-dependent regulation in Arabidopsis thaliana rosettes. Microtranscriptomic screening revealed a limited number of miRNAs reacting to HL. To explain the miRNA regulation mechanisms at the different biogenesis stages, chemical and genetic approaches were applied. First, we tested the possible role of plastoquinone (PQ) redox changes using photosynthetic electron transport chain inhibitors. The results suggest that increased primary transcript abundance (pri-miRNAs) of HL-regulated miRNAs is dependent on signals upstream of PQ. This indicates that such signals may originate from photosystem II, which is the main singlet oxygen (¹O₂) source. Nevertheless, no changes in pri-miRNA expression upon a dark-light shift in the conditional fluorescent (flu) mutant producing ¹O₂ were observed when compared to wild-type plants. Thus, we explored the ¹O₂ signaling pathway, which is initiated independently in HL and is related to β-carotene oxidation and production of volatile derivatives, such as β-cyclocitral (β-CC). Pri-miRNA induction by β-CC, which is a component of this ¹O₂ pathway, as well as an altered response in the methylene blue sensitivity 1 (mbs1) mutant support the role of ¹O₂ signaling in miRNA regulation.

CONCLUSIONS

We show that light stress triggers changes in miRNA expression. This stress response may be regulated by reactive oxygen species (ROS)-related signaling. In conclusion, our results link ROS action to miRNA biogenesis, suggesting its contribution to inconsistent pri- and mature miRNA dynamics.

PRP4KA phosphorylates SERRATE for degradation via 20S proteasome to fine-tune miRNA production in Arabidopsis

Phosphorylation can quickly switch on/off protein functions. Here, we reported pre-mRNA processing 4 kinase A (PRP4KA), and its paralogs interact with Serrate (SE), a key factor in RNA processing. PRP4KA phosphorylates at least five residues of SE in vitro and in vivo. Hypophosphorylated, but not hyperphosphorylated, SE variants could readily rescue se phenotypes in vivo. Moreover, hypophosphorylated SE variants had stronger binding affinity to microprocessor component HYL1 and were more resistant to degradation by 20S proteasome than hyperphosphorylated counterparts. Knockdown of the kinases enhanced the accumulation of hypophosphorylated SE. However, the excessive SE interfered with the assembly and function of SE-scaffolded macromolecule complexes, causing the se-like defects in the mutant and wild-type backgrounds. Thus, phosphorylation of SE via PRP4KA can quickly clear accumulated SE to secure its proper amount. This study provides new insight into how protein phosphorylation regulates miRNA metabolism through controlling homeostasis of SE accumulation in plants.

Mechanisms of MicroRNA Biogenesis and Stability Control in Plants

MicroRNAs (miRNAs), a class of endogenous, non-coding RNAs, which is 20-24 nucleotide long, regulate the expression of its target genes post-transcriptionally and play critical roles in plant normal growth, development, and biotic and abiotic stresses. In cells, miRNA biogenesis and stability control are important in regulating intracellular miRNA abundance. In addition, research on these two aspects has achieved fruitful results. In this review, we focus on the recent research progress in our understanding of miRNA biogenesis and their stability control in plants.

The positive feedback regulatory loop of miR160-Auxin Response Factor 17-HYPONASTIC LEAVES 1 mediates drought tolerance in apple trees

Drought stress tolerance is a complex trait regulated by multiple factors. Here, we demonstrate that the miRNA160-Auxin Response Factor 17 (ARF17)-HYPONASTIC LEAVES 1 module is crucial for apple (Malus domestica) drought tolerance. Using stable transgenic plants, we found that drought tolerance was improved by higher levels of Mdm-miR160 or MdHYL1 and by decreased levels of MdARF17, whereas reductions in MdHYL1 or increases in MdARF17 led to greater drought sensitivity. Further study revealed that modulation of drought tolerance was achieved through regulation of drought-responsive miRNA levels by MdARF17 and MdHYL1; MdARF17 interacted with MdHYL1 and bound to the promoter of MdHYL1. Genetic analysis further suggested that MdHYL1 is a direct downstream target of MdARF17. Importantly, MdARF17 and MdHYL1 regulated the abundance of Mdm-miR160. In addition, the Mdm-miR160-MdARF17-MdHYL1 module regulated adventitious root development. We also found that Mdm-miR160 can move from the scion to the rootstock in apple and tomato (Solanum lycopersicum), thereby improving root development and drought tolerance of the rootstock. Our study revealed the mechanisms by which the positive feedback loop of Mdm-miR160-MdARF17-MdHYL1 influences apple drought tolerance.

HYL1-CLEAVAGE SUBTILASE 1 (HCS1) suppresses miRNA biogenesis in response to light-to-dark transition

HYPONASTIC LEAVES 1 (HYL1)-CLEAVAGE SUBTILASE 1 (HCS1) is a novel negative regulator of microRNA (miRNA) biogenesis that degrades HYL1 in the cytoplasm. Furthermore, cytoplasm CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) E3 ligase inhibit HCS1-mediated HYL1 degradation. The COP1-HYL1-HCS1 network may integrate two essential cellular pathways: the miRNA-biogenetic pathway and light signaling pathway. Our finding suggests a regulatory pathway in the miRNA-biogenetic system.

The core plant microprocessor consists of DICER-LIKE 1 (DCL1), SERRATE (SE), and HYPONASTIC LEAVES 1 (HYL1) and plays a pivotal role in microRNA (miRNA) biogenesis. However, the proteolytic regulation of each component remains elusive. Here, we show that HYL1-CLEAVAGE SUBTILASE 1 (HCS1) is a cytoplasmic protease for HYL1-destabilization. HCS1-excessiveness reduces HYL1 that disrupts miRNA biogenesis, while HCS1-deficiency accumulates HYL1. Consistently, we identified the HYL1^K154A mutant that is insensitive to the proteolytic activity of HCS1, confirming the importance of HCS1 in HYL1 proteostasis. Moreover, HCS1-activity is regulated by light/dark transition. Under light, cytoplasmic CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) E3 ligase suppresses HCS1-activity. COP1 sterically inhibits HCS1 by obstructing HYL1 access into the catalytic sites of HCS1. In contrast, darkness unshackles HCS1-activity for HYL1-destabilization due to nuclear COP1 relocation. Overall, the COP1-HYL1-HCS1 network may integrate two essential cellular pathways: the miRNA-biogenetic pathway and light signaling pathway.

Serrate-Associated Protein 1, a splicing-related protein, promotes miRNA biogenesis in Arabidopsis

MicroRNAs (miRNAs) are essential regulators of gene expression in metazoans and plants. In plants, most miRNAs are generated from primary miRNA transcripts (pri-miRNAs), which are processed by the Dicer-like 1 (DCL1) complex along with accessory proteins. Serrate-Associated Protein 1 (SEAP1), a conserved splicing-related protein, has been studied in human and yeast. However, the functions of SEAP1 in plants remain elusive. Lack of SEAP1 results in embryo lethality and knockdown of SEAP1 by an artificial miRNA (amiR^SEAP1 ) causes pleiotropic developmental defects and reduction in miRNA accumulation. SEAP1 associates with the DCL1 complex, and may promote the interaction of the DCL1 complexes with pri-miRNAs. SEAP1 also enhances pri-miRNA accumulation, but does not affect pri-miRNA transcription, suggesting it may indirectly or directly stabilize pri-miRNAs. In addition, SEAP1 affects the splicing of some pri-miRNAs and intron retention of messenger RNAs at global levels. Our findings uncover both conserved and novel functions of SEAP1 in plants. Besides the role as a splicing factor, SEPA1 may promote miRNA biogenesis by positively modulating pri-miRNA splicing, processing and/or stability.

SUMOylation of different targets fine-tunes phytochrome signaling

Plants monitor their surrounding ambient light environment by specialized photoreceptor proteins. Among them, phytochromes monitor red and far-red light. These molecules perceive photons, undergo a conformational change, and regulate diverse light signaling pathways, resulting in the mediation of key developmental and growth responses throughout the whole life of plants. Posttranslational modifications of the photoreceptors and their signaling partners may modify their function. For example, the regulatory role of phosphorylation has been investigated for decades by using different methodological approaches. In the past few years, a set of studies revealed that ubiquitin-like short protein molecules, called small ubiquitin-like modifiers (SUMOs) are attached reversibly to different members of phytochrome signaling pathways, including phytochrome B, the dominant receptor of red light signaling. Furthermore, SUMO attachment modifies the action of the target proteins, leading to altered light signaling and photomorphogenesis. This review summarizes recent results regarding SUMOylation of various target proteins, the regulation of their SUMOylation level, and the physiological consequences of SUMO attachment. Potential future research directions are also discussed.

MicroRNAs: Tiny, powerful players of metal stress responses in plants

Metal contamination of the environment is a widespread problem threatening sustainable and safe crop production. Physio-biochemical and molecular mechanisms of plant responses to metal exposure have been studied to establish the best possible agronomical or biotechnological methods to tackle metal contamination. Metal stress tolerance is regulated by several molecular effectors among which microRNAs are one of the key master regulators of plant growth and stress responses in plants. MicroRNAs are known to coordinate multitude of plant responses to metal stress through antioxidant functions, root growth, hormonal signalling, transcription factors and metal transporters. The present review discusses integrative functions of microRNAs in the regulation of metal stress in plants, which will be useful for engineering stress tolerance traits for improved plant growth and productivity in metal stressed situations.

Cytoplasmic HYL1 modulates miRNA-mediated translational repression

MicroRNAs (miRNAs) control various biological processes by repressing target mRNAs. In plants, miRNAs mediate target gene repression via both mRNA cleavage and translational repression. However, the mechanism underlying this translational repression is poorly understood. Here, we found that Arabidopsis thaliana HYPONASTIC LEAVES1 (HYL1), a core component of the miRNA processing machinery, regulates miRNA-mediated mRNA translation but not miRNA biogenesis when it localized in the cytoplasm. Cytoplasmic HYL1 localizes to the endoplasmic reticulum and associates with ARGONAUTE1 (AGO1) and ALTERED MERISTEM PROGRAM1. In the cytoplasm, HYL1 monitors the distribution of AGO1 onto polysomes, binds to the mRNAs of target genes, represses their translation, and partially rescues the phenotype of the hyl1 null mutant. This study uncovered another function of HYL1 and provides insight into the mechanism of plant gene regulation.

Post-transcriptional regulation of seed dormancy and germination: Current understanding and future directions

Seed dormancy is a developmental checkpoint that prevents mature seeds from germinating under conditions that are otherwise favorable for germination. Temperature and light are the most relevant environmental factors that regulate seed dormancy and germination. These environmental cues can trigger molecular and physiological responses including hormone signaling, particularly that of abscisic acid and gibberellin. The balance between the content and sensitivity of these hormones is the key to the regulation of seed dormancy. Temperature and light tightly regulate the transcription of thousands of genes, as well as other aspects of gene expression such as mRNA splicing, translation, and stability. Chromatin remodeling determines specific transcriptional outputs, and alternative splicing leads to different outcomes and produces transcripts that encode proteins with altered or lost functions. Proper regulation of chromatin remodeling and alternative splicing may be highly relevant to seed germination. Moreover, microRNAs are also critical for the control of gene expression in seeds. This review aims to discuss recent updates on post-transcriptional regulation during seed maturation, dormancy, germination, and post-germination events. We propose future prospects for understanding how different post-transcriptional processes in crop seeds can contribute to the design of genotypes with better performance and higher productivity.

Regulation of pri-MIRNA processing: mechanistic insights into the miRNA homeostasis in plant

miRNAs in plant plays crucial role in controlling proper growth, development and fitness by modulating the expression of their target genes. Therefore to modulate the expression of any stress/development related gene specifically, it is better to modulate expression of the miRNA that can target that gene. To modulate the expression level of miRNA, it is prerequisite to uncover the underlying molecular mechanism of its biogenesis. The biogenesis pathway consists of two major steps, transcription of MIR gene to pri-MIRNA and processing of pri-MIRNA into mature miRNA via sequential cleavage steps. Both of these pathways are tightly controlled by several different factors involving structural and functional molecules. This review is mainly focused on different aspects of pri-MIRNA processing mechanism to emphasize on the fact that to modulate the level of a miRNA in the cell only over-expression or knock-down of that MIR gene is not always sufficient rather it is also crucial to take processing regulation into consideration. The data collected from the recent and relevant literatures depicts that processing regulation is controlled by several aspects like structure and size of the pri-MIRNA, presence of introns in MIR gene and their location, interaction of processing factors with the core components of processing machinery etc. These detailed information can be utilized to figure out the particular point which can be utilized to modulate the expression of the miRNA which would ultimately be beneficial for the scientist and researcher working in this field to generate protocol for engineering plant with improved yield and stress tolerance.

Light-stabilized FHA2 suppresses miRNA biogenesis through interactions with DCL1 and HYL1

The precise regulation of microRNA (miRNA) biogenesis is crucial for plant development, which requires core microprocessors and many fine tuners to coordinate their miRNA processing activity/specificity in fluctuating cellular environments. During de-etiolation, light triggers a dramatic accumulation of core microprocessors and primary miRNAs (pri-miRNAs) but decreases pri-miRNA processing activity, resulting in relatively constant miRNA levels. The mechanisms underlying these seemingly contradictory regulatory changes remain unclear. In this study, we identified forkhead-associated domain 2 (FHA2) as a light-stabilized suppressor of miRNA biogenesis. We found that FHA2 deficiency increased the level of mature miRNAs, accompanied by a reduction in pri-miRNAs and target mRNAs. Biochemical assays showed that FHA2 associates with the core microprocessors DCL1, HYL1, and SE, forming a complex to suppress their pri-miRNA processing activity. Further analyses revealed that FHA2 promotes HYL1 binding but inhibits the binding of DCL1-PAZ-RNase-RNA-binding domains (DCL1-PRR) to miRNAs, whereas FHA2 does not directly bind to these RNAs. Interestingly, we found that FHA2 protein is unstable in the dark but stabilized by light during de-etiolation. Consistently, disruption of FHA led to defects in light-triggered changes in miRNA expression and reduced the survival rate of de-etiolated seedlings after prolonged light deprivation. Collectively, these data suggest that FHA2 is a novel light-stabilized suppressor of miRNA biogenesis and plays a role in fine-tuning miRNA processing during de-etiolation.

Uncovering a novel function of the CCR4-NOT complex in phytochrome A-mediated light signalling in plants

Phytochromes are photoreceptors regulating growth and development in plants. Using the model plant Arabidopsis, we identified a novel signalling pathway downstream of the far-red light-sensing phytochrome, phyA, that depends on the highly conserved CCR4-NOT complex. CCR4-NOT is integral to RNA metabolism in yeast and animals, but its function in plants is largely unknown. NOT9B, an Arabidopsis homologue of human CNOT9, is a component of the CCR4-NOT complex, and acts as negative regulator of phyA-specific light signalling when bound to NOT1, the scaffold protein of the complex. Light-activated phyA interacts with and displaces NOT9B from NOT1, suggesting a potential mechanism for light signalling through CCR4-NOT. ARGONAUTE 1 and proteins involved in splicing associate with NOT9B and we show that NOT9B is required for specific phyA-dependent alternative splicing events. Furthermore, association with nuclear localised ARGONAUTE 1 raises the possibility that NOT9B and CCR4-NOT are involved in phyA-modulated gene expression.

Place a seedling on a windowsill, and soon you will notice the fragile stem bending towards the glass to soak in the sun and optimize its growth. Plants can ‘sense’ light thanks to specialized photoreceptor molecules: for instance, the phytochrome A is responsible for detecting weak and ‘far-red’ light from the very edge of the visible spectrum. Once the phytochrome has been activated, this message is relayed to the rest of the plant through an intricate process that requires other molecules.

The CCR4-NOT protein complex is vital for all plants, animals and fungi, suggesting that it was already present in early life forms. Here, Schwenk et al. examine whether CCR4-NOT could have acquired a new role in plants to help them respond to far-red light.

Scanning the genetic information of the plant model Arabidopsis thaliana revealed that the gene encoding the NOT9 subunit of CCR4-NOT had been duplicated in plants during evolution. NOT9B, the protein that the new copy codes for, has a docking site that can attach to both phytochrome A and CCR4-NOT. When NOT9B binds phytochrome A, it is released from the CCR4-NOT complex: this could trigger a cascade of reactions that ultimately changes how A. thaliana responds to far-red light. Plants that had not enough or too much NOT9B were respectively more or less responsive to that type of light, showing that the duplication of the gene coding for this subunit had helped plants respond to certain types of light.

The findings by Schwenk et al. illustrate how existing structures can be repurposed during evolution to carry new roles. They also provide a deeper understanding of how plants optimize their growth, a useful piece of information in a world where most people rely on crops as their main source of nutrients.

Recent advances in the regulation of plant miRNA biogenesis

MicroRNAs (miRNAs) are essential non-coding riboregulators of gene expression in plants and animals. In plants, miRNAs guide their effector protein named ARGONAUTE (AGO) to find target RNAs for gene silencing through target RNA cleavage or translational inhibition. miRNAs are derived from primary miRNA transcripts (pri-miRNAs), most of which are transcribed by the DNA-dependent RNA polymerase II. In plants, an RNase III enzyme DICER-LIKE1-containing complex processes pri-miRNAs in the nucleus into miRNAs. To ensure proper function of miRNAs, plants use multiple mechanisms to control miRNA accumulation. On one hand, pri-miRNA levels are controlled through transcription and stability. On the other hand, the activities of the DCL1 complex are regulated by many protein factors at transcriptional, post-transcriptional and post-translational levels. Notably, recent studies reveal that pri-miRNA structure/sequence features and modifications also play important roles in miRNA biogenesis. In this review, we summarize recent progresses on the mechanisms regulating miRNA biogenesis.

The apple MdCOP1-interacting protein 1 negatively regulates hypocotyl elongation and anthocyanin biosynthesis

BACKGROUND

In plants, CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) is a key negative regulator in photoperiod response. However, the biological function of COP1-interacting protein 1 (CIP1) and the regulatory mechanism of the CIP1-COP1 interaction are not fully understood.

RESULTS

Here, we identified the apple MdCIP1 gene based on the Arabidopsis AtCIP1 gene. Expression pattern analysis showed that MdCIP1 was constitutively expressed in various tissues of apple, and responded to stress and hormone signals at the transcriptional level. Ectopic expression of MdCIP1 complemented the phenotypes of the Arabidopsis cip1 mutant, and MdCIP1 inhibited anthocyanin biosynthesis in apple calli. In addition, the biochemical assay demonstrated that MdCIP1 could interact with MdCOP1 protein by their coiled-coil domain, and MdCIP1-OX/cop1-4 had a similar phenotype in photomorphogenesis with the cop1-4 mutant, suggesting that COP1 is epistatic to CIP1. Furthermore, the transient transformation assay indicated that MdCIP1 repressed anthocyanin biosynthesis in an MdCOP1-mediated pathway.

CONCLUSION

Take together, this study finds that MdCIP1 acts as a repressor in regulating hypocotyl elongation and anthocyanin biosynthesis through MdCOP1 in apple.

Illuminating the COP1/SPA Ubiquitin Ligase: Fresh Insights Into Its Structure and Functions During Plant Photomorphogenesis

CONSTITUTIVE PHOTOMORPHOGENIC 1 functions as an E3 ubiquitin ligase in plants and animals. Discovered originally in Arabidopsis thaliana, COP1 acts in a complex with SPA proteins as a central repressor of light-mediated responses in plants. By ubiquitinating and promoting the degradation of several substrates, COP1/SPA regulates many aspects of plant growth, development and metabolism. In contrast to plants, human COP1 acts as a crucial regulator of tumorigenesis. In this review, we discuss the recent important findings in COP1/SPA research including a brief comparison between COP1 activity in plants and humans.

Effect of red light on photosynthetic acclimation and the gene expression of certain light signalling components involved in the microRNA biogenesis in the extremophile Eutrema salsugineum

The photosynthetic acclimation of extremophile Eutrema salsugineum plants to red light (RL) (14 days, 150 μmol photons m^-2 s^-1, 660 nm) and the expression of the key photoreceptor apoprotein genes, transcription factors (TFs) and associated with phytochrome system MIR (microRNA) genes were studied. RL exposure induced an increase in the content of anthocyanin and total phenolic compounds and the level of Chls was decreased. The photosystem 2 electron transport rate and the number of open reaction centres (q_L) were not changed in RL plants, however, the levels of non-photochemical quenching (NPQ) and the regulated quantum yield of non-photochemical quenching Y(NPQ) were significantly higher in the RL plants. The rate of CO₂ uptake was decreased by almost 1.4-fold but the respiration and transpiration rates, as well as the stomatal conductance were not changed in the RL plants. An increase in the expression of the photoreceptor apoprotein genes PHYA, PHYB and PHYC, the TF genes PIF4, PIF5 and miR395, miR408, miR165 and decreases in the levels of the transcripts of the TF gene HY5 and miR171, miR157, and miR827 were detected. The acclimation effect of photosynthetic apparatus to RL was accompanied by an increase of pigment content such as total phenolic compounds and carotenoids and it is due to the changes in the expression of the apoprotein phytochrome genes PHYA, PHYB, PHYC and phytochrome signalling TFs (PIF4, PIF5 and HY5) as well as MIR genes associated with phytochrome system.

Strontium stress disrupts miRNA biogenesis by reducing HYL1 protein levels in Arabidopsis

Strontium (Sr) is an emerging environmental pollutant that has become a major global concern after the nuclear accident at the Fukushima Daiichi Nuclear Power Plant in 2011. Although many studies have demonstrated the harmful effects of Sr on plant growth and development at the physiological level, knowledge regarding how plants sense and respond to Sr stress at the molecular level is limited. Recent studies have suggested that microRNAs (miRNAs) function as key regulators of plant growth and development as well as in the responses of plants to environmental stresses, including salinity, drought, cold, nutrient starvation, and heavy metals. In this study, we examined the global expression profile of miRNAs under Sr stress using small RNA sequencing analysis in Arabidopsis to better understand the molecular basis of plant responses to Sr stress. To identify specific Sr-responsive miRNAs, we performed comparative miRNA expression profiling analysis using control, CaCl₂-, and SrCl₂-treated seedlings. Compared to the control treatment, the expressions of most miRNAs were considerably decreased in the Sr-treated seedlings. However, under Sr stress, the expressions of primary miRNAs (pri-miRNAs) and their target genes were significantly increased; the protein levels of HYPONASTIC LEAVES 1 (HYL1), one of the core components of the microprocessor complex, were strongly reduced despite the increased HYL1 mRNA expression. In addition, hyl1-2 mutant plants were shown to be more sensitive to Sr stress than wild-type plants. Collectively, our results strongly suggested that Sr stress may be associated with the disruption of miRNA biogenesis by reducing the protein level of HYL1, which is required to maintain proper growth and development for plants. Our findings further indicated that some miRNAs may play important roles in plant responses to Sr stress.

MAC5, an RNA-binding protein, protects pri-miRNAs from SERRATE-dependent exoribonuclease activities

MAC5 is a component of the conserved MOS4-associated complex. It plays critical roles in development and immunity. Here we report that MAC5 is required for microRNA (miRNA) biogenesis. MAC5 interacts with Serrate (SE), which is a core component of the microprocessor that processes primary miRNA transcripts (pri-miRNAs) into miRNAs and binds the stem-loop region of pri-miRNAs. MAC5 is essential for both the efficient processing and the stability of pri-miRNAs. Interestingly, the reduction of pri-miRNA levels in mac5 is partially caused by XRN2/XRN3, the nuclear-localized 5'-to-3' exoribonucleases, and depends on SE. These results reveal that MAC5 plays a dual role in promoting pri-miRNA processing and stability through its interaction with SE and/or pri-miRNAs. This study also uncovers that pri-miRNAs need to be protected from nuclear RNA decay machinery, which is connected to the microprocessor.

Dual function of HYPONASTIC LEAVES 1 during early skotomorphogenic growth in Arabidopsis

Seeds germinating underground display a specific developmental programme, termed skotomorphogenesis, to ensure survival of the emerging seedlings until they reach the light. They rapidly elongate the hypocotyl and maintain the cotyledons closed, forming a hook with the hypocotyl in order to protect apical meristematic cells from mechanical damage. Such crucial events for the fate of the seedling are tightly regulated and although some transcriptional regulators and phytohormones are known to be implicated in this regulation, we are still far from a complete understanding of these biological processes. Our work provides information on the diverse roles in skotomorphogenesis of the core components of microRNA biogenesis in Arabidopsis, HYL1, DCL1, and SE. We show that hypocotyl elongation is promoted by all these components, probably through the action of specific miRNAs. Hook development also depends on these proteins however, remarkably, HYL1 exerts its role in an opposite way to DCL1 and SE. Interestingly, we found that a specific HYL1 domain involved in protein-protein interaction is required for this function. Genetic evidences also point to the phosphorylation status of HYL1 as important for this function. We propose that HYL1 help maintain the hook closed during early skotomorphogenesis in a microprocessor-independent manner by repressing the activity of HY5, the transcriptional master regulator that triggers light responses. This work uncovers a previously unnoticed link between components of the miRNA biogenesis machinery, the skotomorphogenic growth, and hook development in Arabidopsis.

Light Triggers the miRNA-Biogenetic Inconsistency for De-etiolated Seedling Survivability in Arabidopsis thaliana

The shift of dark-grown seedlings into light causes enormous transcriptome changes followed by a dramatic developmental transition. Here, we show that microRNA (miRNA) biogenesis also undergoes regulatory changes during de-etiolation. Etiolated seedlings maintain low levels of primary miRNAs (pri-miRNAs) and miRNA processing core proteins, such as Dicer-like 1, SERRATE, and HYPONASTIC LEAVES 1, whereas during de-etiolation both pri-miRNAs and the processing components accumulate to high levels. However, the levels of most miRNAs do not notably increase in response to light. To reconcile this inconsistency, we demonstrated that an unknown suppressor decreases miRNA-processing activity and light-induced SMALL RNA DEGRADING NUCLEASE 1 shortens the half-life of several miRNAs in de-etiolated seedlings. Taken together, these data suggest a novel mechanism, miRNA-biogenetic inconsistency, which accounts for the intricacy of miRNA biogenesis during de-etiolation. This mechanism is essential for the survival of de-etiolated seedlings after long-term skotomorphogenesis and their optimal adaptation to ever-changing light conditions.

Beyond the darkness: recent lessons from etiolation and de-etiolation studies

The state of etiolation is generally defined by the presence of non-green plastids (etioplasts) in plant tissues that would normally contain chloroplasts. In the commonly used dark-grown seedling system, etiolation is coupled with a type of growth called skotomorphogenesis. Upon illumination, de-etiolation occurs, marked by the transition from etioplast to chloroplast, and, at the seedling level, a switch to photomorphogenic growth. Etiolation and de-etiolation systems are therefore important for understanding both the acquisition of photosynthetic capacity during chloroplast biogenesis and plant responses to light-the most relevant signal in the life and growth of the organism. In this review, we discuss recent discoveries (within the past 2-3 years) in the field of etiolation and de-etiolation, with a particular focus on post-transcriptional processes and ultrastructural changes. We further discuss ambiguities in definitions of the term 'etiolation', and benefits and biases of common etiolation/de-etiolation systems. Finally, we raise several open questions and future research possibilities.

Keep calm and carry on: miRNA biogenesis under stress

MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression. Their biogenesis relies on the cleavage of longer precursors by a nuclear localized processing machinery. The evolutionary preference of plant miRNAs to silence transcription factors turned these small molecules into key actors during growth and adaptive responses. Furthermore, during their life cycle plants are subject to changes in the environmental conditions surrounding them. In order to face these changes, plants display unique adaptive capacities based on an enormous developmental plasticity, where miRNAs play central roles. Many individual miRNAs have been shown to modulate the plant response to different environmental cues and stresses. In the last few years, increasing evidence has shown that not only individual genes encoding miRNAs but also the miRNA pathway as a whole is subject to regulation in response to external stimulus. In this review, we discuss the current knowledge about the miRNA pathway. We dissect the pathway to analyze the events leading to the generation of these small RNAs and emphasize the regulation of core components of the miRNA biogenesis machinery.

SMA1, a homolog of the splicing factor Prp28, has a multifaceted role in miRNA biogenesis in Arabidopsis

MicroRNAs (miRNAs) are a class of small non-coding RNAs that repress gene expression. In plants, the RNase III enzyme Dicer-like (DCL1) processes primary miRNAs (pri-miRNAs) into miRNAs. Here, we show that SMALL1 (SMA1), a homolog of the DEAD-box pre-mRNA splicing factor Prp28, plays essential roles in miRNA biogenesis in Arabidopsis. A hypomorphic sma1-1 mutation causes growth defects and reduces miRNA accumulation correlated with increased target transcript levels. SMA1 interacts with the DCL1 complex and positively influences pri-miRNA processing. Moreover, SMA1 binds the promoter region of genes encoding pri-miRNAs (MIRs) and is required for MIR transcription. Furthermore, SMA1 also enhances the abundance of the DCL1 protein levels through promoting the splicing of the DCL1 pre-mRNAs. Collectively, our data provide new insights into the function of SMA1/Prp28 in regulating miRNA abundance in plants.

Plant microRNAs: Biogenesis, Homeostasis, and Degradation

MicroRNAs (miRNAs), a class of endogenous, tiny, non-coding RNAs, are master regulators of gene expression among most eukaryotes. Intracellular miRNA abundance is regulated under multiple levels of control including transcription, processing, RNA modification, RNA-induced silencing complex (RISC) assembly, miRNA-target interaction, and turnover. In this review, we summarize our current understanding of the molecular components and mechanisms that influence miRNA biogenesis, homeostasis, and degradation in plants. We also make comparisons with findings from other organisms where necessary.

Micromanagement of Developmental and Stress-Induced Senescence: The Emerging Role of MicroRNAs

MicroRNAs are short (19⁻24-nucleotide-long), non-coding RNA molecules. They downregulate gene expression by triggering the cleavage or translational inhibition of complementary mRNAs. Senescence is a stage of development following growth completion and is dependent on the expression of specific genes. MicroRNAs control the gene expression responsible for plant competence to answer senescence signals. Therefore, they coordinate the juvenile-to-adult phase transition of the whole plant, the growth and senescence phase of each leaf, age-related cellular structure changes during vessel formation, and remobilization of resources occurring during senescence. MicroRNAs are also engaged in the ripening and postharvest senescence of agronomically important fruits. Moreover, the hormonal regulation of senescence requires microRNA contribution. Environmental cues, such as darkness or drought, induce senescence-like processes in which microRNAs also play regulatory roles. In this review, we discuss recent findings concerning the role of microRNAs in the senescence of various plant species.

The analogous and opposing roles of double-stranded RNA-binding proteins in bacterial resistance

The Arabidopsis plasma membrane-localized resistance protein RPM1 is degraded upon the induction of the hypersensitive response (HR) triggered in response to its own activation or that of other unrelated resistance (R) proteins. We investigated the role of RPM1 turnover in RPM1-mediated resistance and showed that degradation of RPM1 is not associated with HR or resistance mediated by this R protein. Likewise, the runaway cell death phenotype in the lsd1 mutant was not associated with RPM1 degradation and did not alter RPM1-derived resistance. RPM1 stability and RPM1-mediated resistance were dependent on the double-stranded RNA binding (DRB) proteins 1 and 4. Interestingly, the function of DRB1 in RPM1-mediated resistance was not associated with its role in pre-miRNA processing. The DRB3 and DRB5 proteins negatively regulated RPM1-mediated resistance and a mutation in these completely or partially restored resistance in the drb1, drb2, and drb4 mutant backgrounds. Conversely, plants overexpressing DRB5 showed attenuated RPM1-mediated resistance. A similar role for DRBs in basal and R-mediated resistance suggests that these proteins play a general role in bacterial resistance.

The Plant microRNA Pathway: The Production and Action Stages

Plant microRNAs are an endogenous class of small regulatory RNA central to the posttranscriptional regulation of gene expression in plant development and environmental stress adaptation or in response to pathogen challenge. The plant microRNA pathway is readily separated into two distinct stages: (1) the production stage, which is localized to the plant cell nucleus and where the microRNA small RNA is processed from a double-stranded RNA precursor transcript, and (2) the action stage, which is localized to the plant cell cytoplasm and where the mature microRNA small RNA is loaded into an effector complex and is used by the complex as a sequence specificity guide to direct expression repression of target genes harboring highly complementary microRNA target sequences. Historical research indicated that the plant microRNA pathway was a highly structured, almost linear pathway requiring a small set of core machinery proteins. However, contemporary research has demonstrated that the plant microRNA pathway is highly dynamic, and to allow for this flexibility, a large and highly functionally diverse set of machinery proteins is now known to be required. For example, recent research has shown that plant microRNAs can regulate target gene expression via a translational repression mechanism of RNA silencing in addition to the standard messenger RNA cleavage-based mechanism of RNA silencing: a mode of RNA silencing originally assigned to all plant microRNAs. Using Arabidopsis thaliana as our model system, here we report on both the core and auxiliary sets of machinery proteins now known to be required for both microRNA production and microRNA action in plants.

Revealing of MicroRNA Involved Regulatory Gene Networks on Terpenoid Biosynthesis in Camellia sinensis in Different Growing Time Points

Tea, made from leaves of Camellia sinensis, has long been consumed worldwide for its unique taste and aroma. Terpenoids play important roles not only in tea beverage aroma formation, but also in the productivity and quality of tea plantation due to their significant contribution to light harvesting pigments and phytohormones. To date, however, the regulation of terpenoid synthase genes remains unclear. Herein, the analyses of metabolomics, sRNAs, degradome, and transcriptomics were performed and integrated for identifying key regulatory miRNA-target circuits on terpenoid biosynthesis in leaf tissues over five different months in which the amount of terpenoids in tea leaves varies greatly. Four classes of miRNA-TF pairs that might play a central role in the regulation of terpenoid biosynthesis were also uncovered. Ultimately, a hypothetical model was proposed that mature miRNAs maintained by light regulator at both the transcriptional and posttranscriptional levels negatively regulate the targets to control terpenoid biosynthesis.