Overexpression of miR172 suppresses the brassinosteroid signaling defects of bak1 in Arabidopsis

Genome-Wide Identification of the Rehmannia glutinosa miRNA Family and Exploration of Their Expression Characteristics Caused by the Replant Disease Formation-Related Principal Factor

Background/Objectives: Rehmannia glutinosa, a highly valuable medicinal plant in China, is encountering severe replant disease. Replant disease represents a complex stress driven by multiple principal factors (RDFs), including allelochemicals, microbes, and their interactions. miRNAs are recognized as key regulators of plant response to stresses; however, their specific roles within RDFs are not entirely clear. Methods: This study builds six RDF treatments, comprising R. glutinosa continuously planted (SP), normally planted (NP), and NP treated with ferulic acid (FA), Fusarium oxysporum (FO), and a combination of FA with FO (FAFO). sRNA-seq technology was used to identify crucial miRNAs in response to diverse RDFs. Results: In total, 30 sRNA datasets were generated from the SP, NP, FA, FO, and FAFO samples. A total of 160 known and 41 novel miRNAs (RgmiRNAs) were identified in the R. glutinosa genome based on the sRNA database. Abundance analysis revealed that RgmiRNAs in SP exhibited a distinct expression profile in comparison with others. Of these, 124, 86, 86, and 90 RgmiRNAs were differentially expressed in SP, FA, FO, and FAFO compared with NP. Target analysis indicated that RgmiRNAs downregulated in both SP and RDFs impede the organism growth of R. glutinosa. RgmiRNAs upregulated in SP can disrupt root formation and nutrient metabolism, in which, two RgmiR398 were uniquely expressed in SP. It was confirmed to target RgCSD genes. The expression patterns of RgmiR398 and RgCSD indicated that replant disease induces the oxidative damage of R. glutinosa through RgmiR398. Conclusions:RgmiRNA profiling under RDFs provides a theoretical basis for the further clarification of RgmiRNA function in replant disease.

miR394 modulates brassinosteroid signaling to regulate hypocotyl elongation in Arabidopsis

The interplay between microRNAs (miRNAs) and phytohormones allows plants to integrate multiple internal and external signals to optimize their survival of different environmental conditions. Here, we report that miR394 and its target gene LEAF CURLING RESPONSIVENESS (LCR), which are transcriptionally responsive to BR, participate in BR signaling to regulate hypocotyl elongation in Arabidopsis thaliana. Phenotypic analysis of various transgenic and mutant lines revealed that miR394 negatively regulates BR signaling during hypocotyl elongation, whereas LCR positively regulates this process. Genetically, miR394 functions upstream of BRASSINOSTEROID INSENSITIVE2 (BIN2), BRASSINAZOLEs RESISTANT1 (BZR1), and BRI1-EMS-SUPPRESSOR1 (BES1), but interacts with BRASSINOSTEROID INSENSITIVE1 (BRI1) and BRI1 SUPRESSOR PROTEIN (BSU1). RNA-sequencing analysis suggested that miR394 inhibits BR signaling through BIN2, as miR394 regulates a significant number of genes in common with BIN2. Additionally, miR394 increases the accumulation of BIN2 but decreases the accumulation of BZR1 and BES1, which are phosphorylated by BIN2. MiR394 also represses the transcription of PACLOBUTRAZOL RESISTANCE1/5/6 and EXPANSIN8, key genes that regulate hypocotyl elongation and are targets of BZR1/BES1. These findings reveal a new role for a miRNA in BR signaling in Arabidopsis.

Investigating the effect of drought stress and methanol spraying on the influential genes in the Calvin cycle and photorespiration of rapeseed (Brassica napus)

Due to global warming and changes in precipitation patterns, many regions are prone to permanent drought. Rapeseed (Brassica napus ) is one of the main sources of edible oils worldwide, and its production and yield are affected by drought. In this study, gene expression alterations under drought stress are investigated with bioinformatics studies to examine evolutionary relations of conserved motifs structure and interactions among Calvin cycle and photorespiration pathways key genes in drought-tolerant (SLM046) and drought-sensitive (Hayola308) genotypes of rapeseed. Investigating the conservation and evolutionary relationships revealed high conservation in motifs of FBPase, PRK, GlyK and NADP-ME enzymes. The analysis of protein interactions showed the correlation between FTRC, FBPase1, PRKX1, GlyKX2 and NADP-ME4 genes. Furthermore, in rapeseed, for the GlyKX2 and NADP-ME4 genes, four microRNAs of the miR172 family and four members of the miR167 family were identified as post-transcriptional regulators, respectively. The expression of ferredoxin thioredoxin reductase, fructose-1,6-bisphosphatase genes, phosphoribulokinase, glycerate kinase and malic enzyme 4 genes in the two rapeseed genotypes were evaluated by real-time qPCR method under 72h of drought stress and methanol foliar application. As a result, the highest expression levels of FTRC, PRKX1, GlyKX2, NADP-ME4 and FBPase1 were observed in methanol foliar application on the SLM046 genotype at 24h. In contrast, in methanol foliar application on the Hayola308 genotype, the highest expression levels of FTRC, PRKX1, GlyKX2, NADP-ME4 and FBPase1 were observed 8h after the treatment. Our study illustrated that methanol foliar application enhanced plant tolerance under drought stress.

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.

Coordinated regulation of vegetative phase change by brassinosteroids and the age pathway in Arabidopsis

Vegetative phase change in plants is regulated by a gradual decline in the level of miR156 and a corresponding increase in the expression of its targets, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes. Gibberellin (GA), jasmonic acid (JA), and cytokinin (CK) regulate vegetative phase change by affecting genes in the miR156-SPL pathway. However, whether other phytohormones play a role in vegetative phase change remains unknown. Here, we show that a loss-of-function mutation in the brassinosteroid (BR) biosynthetic gene, DWARF5 (DWF5), delays vegetative phase change, and the defective phenotype is primarily attributable to reduced levels of SPL9 and miR172, and a corresponding increase in TARGET OF EAT1 (TOE1). We further show that GLYCOGEN SYNTHASE KINASE3 (GSK3)-like kinase BRASSINOSTEROID INSENSITIVE2 (BIN2) directly interacts with and phosphorylates SPL9 and TOE1 to cause subsequent proteolytic degradation. Therefore, BRs function to stabilize SPL9 and TOE1 simultaneously to regulate vegetative phase change in plants.

Feedback Inhibition Might Dominate the Accumulation Pattern of BR in the New Shoots of Tea Plants (Camellia sinensis)

Brassinosteroid (BR), a kind of polyhydroxylated steroid hormone, plays an important role in physiological and biochemical processes in plants. Studies were mainly focused on BR signaling and its exogenous spraying to help enhance crop yields. Few research studies are centered on the accumulation pattern of BR and its mechanism. Yet, it is crucial to unlock the mystery of the function of BR and its cross action with other hormones. Tea (Camellia sinensis (L.) O. Kuntze) is one of the important economic crops in some countries, and new shoots are the raw materials for the preparation of various tea products. Different concentrations of exogenous BR were reported to have different effects on growth and development. New shoots of tea plants can thus be considered a valuable research object to study the accumulation pattern of BR. In this study, the quantity of five BR components (brassinolide, 28-norbrassinolide, 28-homobrassinolide, castasterone, and 28-norcastasterone) in different tissues of tea plants, including buds (Bud), different maturity of leaves (L1, L2), and stems (S1, S2) were determined by UPLC-MS/MS. A total of 15 cDNA libraries of the same tissue with three repetitions for each were constructed and sequenced. The BR-accumulation pattern and gene expression pattern were combined together for weighted gene co-expression network analysis (WGCNA). BR-accumulation-relative genes were then screened using two methods, based on the K.in value and BR biosynthetic pathway (ko00905), respectively. The result showed that photosynthesis-related genes and CYP450 family genes were actively involved and might play important roles in BR accumulation and/or its accumulation pattern. First and foremost, feedback inhibition was more likely to dominate the accumulation pattern of BR in the new shoots of tea plants. Moreover, three conserved miRNAs with their target transcriptional factors and target mRNAs had been figured out from negative correlation modules that might be strongly linked to the BR-accumulation pattern. Our study provided an experimental basis for the role of BR in tea plants. The excavation of genes related to the accumulation pattern of BR provided the possibility of cross-action studies on the regulation of BR biosynthesis and the study between BR and other hormones.

Comprehensive Identification and Profiling of miRNAs Involved in Terpenoid Synthesis of Gleditsia sinensis Lam

Gleditsia sinensis Lam. is a tree with worldwide distribution and important economic and medicinal values; its pods contain terpenoids including gleditsioside, thiamine, and brassinosteroids. However, thus far, there are few studies on the terpenoid regulation of G. sinensis at the molecular level. microRNA (miRNA) is a class of small RNAs with conserved and crucial roles in the regulation of diverse biological processes during plant growth and development. To identify the miRNAs of G. sinensis and evaluate their involvement in terpenoid synthesis, this investigation quantified the content changes in saponins in pods at three developmental stages: May (pod-setting stage), July (elongation stage), and September (browning stage), and then we performed genome-wide miRNA profiles during the three development stages of the G. sinensis pods. A total of 351 conserved miRNAs belonging to 216 families were identified, among which 36 conserved miRNAs exist specifically in legumes. Through target analysis, 708 unigenes were predicted to be candidate targets of 37 differentially expressed miRNAs. The targets of miR838-3p and miR2093-5p were involved in the derived branches of monoterpenes and gleditsioside, in brassinosteroid biosynthesis (BRB), and in indole alkaloid biosynthesis (IAB). Intriguingly, the targets of miR829-3p.1 were predicted to take part in thiamine biosynthesis, and the targets of miR4414b and miR5037a were involved in the main process of cytokinin synthesis. The corresponding targets participated in BRB, IAB, and terpenoid backbone biosynthesis, which were enriched significantly, suggesting that miR2093-5p, miR4414b, miR5037a, miR829-3p.1, and miR838-3p play indispensable roles in the regulation of triterpenoid saponin and monoterpenoid biosynthesis. To date, this is the first report of miRNA identification in G. sinensis and miRNA expression profiles at different developmental stages of G. sinensis pods, which provides a basis for further uncovering the molecular regulation of terpenoid synthesis in G. sinensis and new insights into the role of miRNAs in legumes.

miRNAs as key regulators via targeting the phytohormone signaling pathways during somatic embryogenesis of plants

Somatic embryogenesis is the regeneration of embryos from the somatic cell via dedifferentiation and redifferentiation without the occurrence of fertilization. A complex network of genes regulates the somatic embryogenesis process. Especially, microRNAs (miRNAs) have emerged as key regulators by affecting phytohormone biosynthesis, transport and signal transduction pathways. miRNAs are small, non-coding small RNA regulatory molecules involved in various developmental processes including somatic embryogenesis. Several types of miRNAs such as miR156, miR157, miR 159, miR 160, miR165, miR166, miR167, miR390, miR393 and miR396 have been reported to intricate in regulating somatic embryogenesis via targeting the phytohormone signaling pathways. Here we review current research progress on the miRNA-mediated regulation involved in somatic embryogenesis via regulating auxin, ethylene, abscisic acid and cytokinin signaling pathways. Further, we also discussed the possible role of other phytohormone signaling pathways such as gibberellins, jasmonates, nitric oxide, polyamines and brassinosteroids. Finally, we conclude by discussing the expression of miRNAs and their targets involved in somatic embryogenesis and possible regulatory mechanisms cross talk with phytohormones during somatic embryogenesis.

Crosstalk of the Brassinosteroid Signalosome with Phytohormonal and Stress Signaling Components Maintains a Balance between the Processes of Growth and Stress Tolerance

Brassinosteroids (BRs) are a class of phytohormones, which regulate various processes during plant life cycle. Intensive studies conducted with genetic, physiological and molecular approaches allowed identification of various components participating in the BR signaling—from the ligand perception, through cytoplasmic signal transduction, up to the BR-dependent gene expression, which is regulated by transcription factors and chromatin modifying enzymes. The identification of new components of the BR signaling is an ongoing process, however an emerging view of the BR signalosome indicates that this process is interconnected at various stages with other metabolic pathways. The signaling crosstalk is mediated by the BR signaling proteins, which function as components of the transmembrane BR receptor, by a cytoplasmic kinase playing a role of the major negative regulator of the BR signaling, and by the transcription factors, which regulate the BR-dependent gene expression and form a complicated regulatory system. This molecular network of interdependencies allows a balance in homeostasis of various phytohormones to be maintained. Moreover, the components of the BR signalosome interact with factors regulating plant reactions to environmental cues and stress conditions. This intricate network of interactions enables a rapid adaptation of plant metabolism to constantly changing environmental conditions.

Identification of exosome-like nanoparticle-derived microRNAs from 11 edible fruits and vegetables

Edible plant-derived exosome-like nanoparticles (EPDELNs) are novel naturally occurring plant ultrastructures that are structurally similar to exosomes. Many EPDELNs have anti-inflammatory properties. MicroRNAs (miRNAs) play a critical role in mediating physiological and pathological processes in animals and plants. Although miRNAs can be selectively encapsulated in extracellular vesicles, little is known about their expression and function in EPDELNs. In this study, we isolated nanovesicles from 11 edible fruits and vegetables and subjected the corresponding EPDELN small RNA libraries to Illumina sequencing. We identified a total of 418 miRNAs-32 to 127 per species-from the 11 EPDELN samples. Target prediction and functional analyses revealed that highly expressed miRNAs were closely associated with the inflammatory response and cancer-related pathways. The 418 miRNAs could be divided into three classes according to their EPDELN distributions: 26 "frequent" miRNAs (FMs), 39 "moderately present" miRNAs (MPMs), and 353 "rare" miRNAs (RMs). FMs were represented by fewer miRNA species than RMs but had a significantly higher cumulative expression level. Taken together, our in vitro results indicate that miRNAs in EPDELNs have the potential to regulate human mRNA.