Secondary Metabolic Pathways Research Articles

Deletion of bZIP Transcription Factor PratfA Reveals Specialized Metabolites Potentially Regulating Stress Response in Penicillium raistrickii.

Fungal secondary metabolism (SM) is highly correlated with physiological processes that are typically regulated by pleiotropic regulators. In this study, we purposefully altered PratfA, a crucial regulator associated with oxidative stress in Penicillium raistrickii CGMCC 3.1066. After the knockout of PratfA, a novel polyketide (PK) raistrilide A (1) and the known nonribosomal peptide (NRP) tunicoidine (2) subsequently disappeared. Notably, compound 1 is a rare octaketone derivative and contains two unsubstituted cis-double bonds, demonstrating its unique biosynthetic mechanism. The knockout of PratfA resulted in the disappearance of 1-2 and greatly increased the susceptibility of ΔPratfA mutant strain to oxidative stress, rendering it nearly impossible to survive in such environments. At present, the OE⸬PratfA strain showed no phenotypic or oxidative stress sensitivity differences compared to the wild-type strain. Our findings highlight that the oxidative-stress-related transcription factor (TF) PratfA influences SM pathways in P. raistrickii. The manipulation of regulatory factors can guide the discovery of novel natural products (NPs).

Genome-Wide Identification of the Uridine Diphosphate Glucotransferase Gene Family and Expression Profiling Analysis in the Stem Development of Prunus mume

Prunus mume, a traditional ornamental species native to China, is highly valued for both its captivating weeping variety and economic value. The glycosylation of metabolites, which is mediated by UDP-glycosyltransferases (UGTs), is essential for the regulation of secondary metabolic pathways in plants. Here, we systematically identified and analyzed the UGTs in P. mume. A total of 182 PmUGTs were identified using genomic data and categorized into 16 distinct subfamilies (A–P). All PmUGTs were distributed unevenly across the eight chromosomes, with clear evidence of tandem duplication. Additionally, synteny analysis revealed a close evolutionary relationship between P. mume and Prunus persica. A promoter cis-acting element analysis indicated that PmUGTs may respond to light, hormones, and external stresses. A heatmap analysis revealed that PmUGTs had specific expression patterns across different tissues, under various hormone treatments, and in different developmental stages of stem lignification. Notably, qRT-PCR verification showed significant differences in PmUGT163 expression between straight and weeping stems, underscoring its role in regulating plant architecture formation. Taken together, our study elucidates the evolutionary trajectory of PmUGTs and lays the groundwork for the further validation of the candidate genes involved in plant architectural formation.

Germination and False Germination Increase the Levels of Bioactive Steroidal Saponins in Oats.

The health benefits of oats, particularly their enhanced nutritional and bioactive properties when sprouted, are well-documented. However, changes in steroidal saponins during germination and false germination are lacking. This study explored the influence of various temperatures (20, 25, and 30 °C) and durations (1, 3, 5, and 7 days) on the steroidal saponin profiles in both germinated and false-germinated oats and assessed their anti-inflammatory activities. The findings revealed that germination at 20 °C for 7 days significantly increased the total steroidal saponin content to 3265.54 μg/g, doubling its original concentration. Notably, avenacoside E (AVE-E), the most potent anti-inflammatory steroidal saponin in oats, increased by an impressive 21-fold from 64.02 to 1421.35 μg/g, becoming the predominant saponin following germination. Furthermore, the hydrolysis of sugar moieties and enzymatic synthesis of steroidal saponins were proposed as plausible secondary metabolic pathways during germination and false germination. This research provides the first evidence that germination and false germination can significantly enhance the steroidal saponin levels in oats and their anti-inflammatory properties, with germination proving more effective than false germination, highlighting the potential of these methods to further enhance the health benefits of oats.

Chemical composition and insecticidal activity of Mentha rotundifolia and Chrysanthemum coronarium essential oils against the tomato leaf miner, Tuta absoluta

Tuta absoluta is one of the most destructive pests of tomatoes. Chemical insecticides used to control this leafminer harm all organisms, increasing the risk to public health and the environment. Developing natural alternatives, such as bioinsecticides formulated from essential plant oils, is a key strategy to address this problem. These volatile compounds, derived from the secondary metabolic pathways of plants, exhibit targeted activity against specific pest species. Their use is consistent with an environmentally responsible framework that reduces adverse impacts on ecosystems, protects non-target organisms, safeguards human health, and enhances the efficacy of integrated crop management systems. This study aims to determine the chemical composition of the essential oils (EOs) of from round leaf mint (Mentha rotundifolia) and crown chrysanthemum (Chrysanthemum coronarium) and to evaluate their toxicity to T. absoluta larvae in-vitro. The chemical composition of EOs obtained by steam distillation from the leaves of the plants was analyzed by gas chromatography coupled with mass spectrometry (GC-MS). Indeed, 77 volatile compounds representing 98.19% of the total oil of M. rotundifolia, including cyclobutane acetonitrile, 1-methyl-2-(1-methyl ethenyl)-, terpinene-4-ol, p-menthane, germacrene D, caryophyllene and myrcene, were the main compounds. However, farnesene, myrcene, eugenol, germacrene D, phytol, and pinene were significant components among 69 compounds representing 95.39% of the total oil of C. coronarium. Results showed that the EOs were toxic to the different larval stages. According to the Finney method, concentrations 2.88 and 1.07% are the LC50 of M. rotundifolia and C. coronarium oils, which induce 50% mortality of T. absoluta within 7 days of exposure. Statistical analysis of in-vitro tests showed that both EOs had a similar level of insecticidal efficacy by contact. The overall results showed that the oils used have been shown to have an important insecticidal effect and can be used as a source of biological and natural treatment against tomato leafminer (TLM).

Drimane-type sesquiterpenoids and triterpenoids from the whole plant of Limonium sinense with their antiproliferative and anti-inflammatory activities.

Saline-tolerant medicinal plants possess novel chemical constituents with high bioactivity because of their unique secondary metabolic pathways. Limonium sinense, an aquatic plant found in the coastal wetlands of the Yellow River Delta, was collected and studied in the present work. Ten drimane-type sesquiterpenoids and four triterpenoids, including six new ones (sinenseines A-F), were isolated from a whole plant of L. sinense for the first time. Their structures, including the absolute configurations, were determined by analyzing the comprehensive spectroscopic data. In addition, twelve terpenoids, including nine sesquiterpenoids, were identified using UPLC-MS/MS and GNPS methods. All isolates were evaluated for their antiproliferative and anti-inflammatory activities. Compounds 2-4, 6, 13, and 14 showed moderate anti-tumor effects on A549, H1299, HepG2 and A2780 cells with IC50 values ranging from 35.2 ± 2.0 to 90.5 ± 3.1 μM. Furthermore, compound 1 exhibited significant anti-inflammatory activity with an IC50 value of 8.3 ± 1.2 μM against NO production in LPS-induced RAW 264.7 macrophages.

Transcriptomic and metabolomic responses of maize under conventional and biodegradable microplastic stress

AbstractThe increasing accumulation of microplastics in agricultural soils potentially threatens crop safety and quality. However, studies regarding the molecular mechanisms underlying the effects of conventional and biodegradable microplastics on plant growth remain limited. Herein, we estimated the effects of biodegradable polybutylene adipate terephthalate, poly (butylene succinate), polylactic acid, and conventional non‐biodegradable polyethylene and polystyrene microplastics (at a concentration of 1% [w/w]) on the growth and physiological performance of maize (Zea mays L.). In addition, we studied the molecular mechanisms underlying the effects of these microplastics on maize. Exposure to microplastics induced the production of antioxidant enzymes and antioxidants at varying levels in the maize. While the maize antioxidant systems were induced against biodegradable microplastic exposure, maize photosynthesis was relatively more important for conventional microplastic treatments. Additionally, metabolomics and transcriptomic analyses revealed that the pathways of secondary metabolite biosynthesis, photosynthesis, energy metabolism, and carbohydrate metabolism were regulated by biodegradable and conventional microplastics. Specifically, microplastics induced the plant hormone signal transduction and mitogen‐activated protein kinase signaling pathways. Our results further indicated that microplastics could impact the plant through changing the soil environmental variables or altering the soil microbial communities. This study provides a molecular‐scale perspective on the responses of crops to microplastic contamination, and these findings will contribute to the ecological risk assessment of biodegradable and conventional microplastics.

Integrated metabolomic and transcriptomic analysis reveals the role of root phenylpropanoid biosynthesis pathway in the salt tolerance of perennial ryegrass

Perennial ryegrass (Lolium perenne) is a widely cultivated forage and turf grass species. Salt stress can severely damage the growth of grass plants. The genome-wide molecular mechanisms of salt tolerance have not been well understood in perennial grass species. In this study, the salt sensitive genotype P1 (PI265351, Chile) and the salt tolerant genotype P2 (PI368892, Algeria) of perennial ryegrass were subjected to 200 mM NaCl, and transcriptomics and metabolomics analyses were performed. A total of 5,728 differentially expressed genes (DEGs) were identified through pairwise comparisons. Antioxidant enzyme encoding genes (LpSOD1, LpCAT1), ion channel gene LpCaC1 and transcription factors (LpERFs, LpHSF1 and LpMYB1) were significantly upregulated in P2, suggesting their involvement in regulating expression of salt-responsive genes for salt tolerance. Functional analysis of DEGs revealed that biosynthesis of secondary metabolites, carbohydrate metabolism and signal transduction were the main pathways in response to salt stress. Weighted gene co-expression network analysis (WGCNA) based on RNA-Seq data showed that membrane transport and ABC transporters were significantly correlated with salt tolerance-related traits. The combined transcriptomics and metabolomics analysis demonstrated that the phenylpropanoid biosynthesis pathway was a major secondary metabolic pathway in the salt response of perennial ryegrass. Especially, the tolerant genotype P2 had greater amounts of upregulated phenylpropanoids, flavonoids and anthocyanins and higher expressions of relevant genes in the pathway than the sensitive genotype P1, indicating a role of phenylpropanoid biosynthesis for perennial ryegrass to adapt to salt stress. The results provided insights into the molecular mechanisms of perennial ryegrass adaptation to salinity and laid a base for genetic improvement of salt tolerance in perennial grass species.

Metabolomics-based analysis of nitric oxide regulation of ginseng herb quality.

Ginsenosides, the primary active ingredients in Panax ginseng, are secondary metabolites. However, their content varies significantly across batches due to differences in environmental conditions and production methods. Ecological stress can increase the levels of reactive oxygen species (ROS) in plants, and ROS can enhance secondary metabolism. Nitric oxide (NO) can promote the production of O2 ·- and H2O2. This study utilized physiological and non-targeted metabolomics to investigate how NO regulates ginseng quality and how P. ginseng adapts to adversity. Sodium nitroprusside (SNP, an NO donor) at 0.5 mmol·L-1 significantly increased ROS levels, with O2 ·- increasing by 64.3% (P < 0.01) and H2O2 by 79.2% (P < 0.01). Nitric oxide influenced P. ginseng metabolism, with 24 metabolites showing significant differences. Rotenone, lactic acid, and gluconic acid, which are involved in ROS metabolism, increased significantly, whereas tyrosine decreased. Metabolites involved in secondary metabolic pathways, including campesterol, ginsenosides Rh1, Rb1, Rc, Rd, Rg3, phenylalanine, and tryptophan, increased markedly, whereas 2,3-oxidosqualene, glucose 1-phosphate, ferulic acid, and pyrogallol decreased. Isocitric acid, succinic acid, and 3-isopropylmalic acid, associated with respiratory metabolism, showed significant increases, but pyruvic acid decreased. Finally, 18:0 Lyso PC and 9-hydroxy-10E,12Z-octadecadienoic acid, linked to cell membrane protection, increased significantly, and mannose and raffinose decreased. Sodium nitroprusside enhances the physiological resilience of P. ginseng under stress and improves its quality. © 2024 Society of Chemical Industry.

Effect of co-inoculations of Saccharomyces cerevisiae and grape endophytes on the fermentation property, organic acid, and volatile aroma compounds.

Grape endophytic fungi (EFFs) have rich secondary metabolic pathways that can synthesize bioactive substances and various enzymes, which may contribute to the improvement of wine quality. In order to investigate the effect of EFFs on fermentation characteristics and chemical components, fermentations by co-inoculations of Saccharomyces cerevisiae and five EFF strains at different concentrations were performed in this study. It was found that EFFs affected the fermentation rate and are related to the genus of EFFs and inoculation amount. Among them, strains RH48 and RH34 facilitated the fermentation process at an optimal concentration of 3.5g/L. Strain RH34 had acid-increasing potential and effectively increased malic and succinic acid contents. In terms of volatile aroma compounds, CS13 3.5g/L and RH34 3.5g/L treatment showed significant enhancement of acetate esters content by 91.04% and 61.34%, respectively, whereas RH48 3.5g/L and CS13 3.5g/L showed significant enhancement of fatty acid ethyl ester content by 52.14% and 48.45%, respectively. In addition, strain CS13 at 3.5g/L also significantly increased the content of terpenes, higher alcohols, and aromatic compounds, showing great potential in improving the aroma quality (floral, fruity, etc.) of wine. The results of the present study may be useful for the innovation of wine fermentation aids and the improvement of wine quality.

Establishing a comprehensive web-based analysis platform for Nicotiana benthamiana genome and transcriptome.

Nicotiana benthamiana has long served as a crucial plant material extensively used in plant physiology research, particularly in the field of plant pathology, because of its high susceptibility to plant viruses. Additionally, it serves as a production platform to test vaccines and other valuable substances. Among its approximately 3.1 Gb genome, 57 583 genes have been annotated within a 61 Mb region. We created a comprehensive and easy-to-use platform to use transcriptomes for modern annotation. These tools allow to visualize gene expression profiles, draw molecular evolutionary phylogenetic trees of gene families, perform functional enrichment analyses, and facilitate output downloads. To demonstrate their utility, we analyzed the gene expression profiles of enzymes within the nicotine biosynthesis pathway, a secondary metabolic pathway characteristic of the Nicotiana genus. Using the developed tool, expression profiles of the nicotine biosynthesis pathway genes were generated. The expression patterns of eight gene groups in the pathway were strongly expressed in the roots and weakly expressed in leaves and flowers of N. benthamiana. The results were consistent with the established gene expression profiles in Nicotiana tabacum and provided insights into gene family composition and expression trends. The compilation of this database tool can facilitate genetic analysis of N. benthamiana in the future.

The use of silver nanoparticles against aflatoxin contamination in crops – mechanism, challenges and future scope

Abstract Certain Aspergillus spp. release harmful byproducts known as aflatoxins. These carcinogenic toxins contaminate crops, such as groundnut, maize, and rice. This contamination poses a significant health risk and economic burden. Current control methods have limitations. This review explores the potential of silver nanoparticles (AgNPs) as a novel strategy to mitigate aflatoxin contamination (AC). The review highlights the advantages of AgNPs, such as (1) antimicrobial properties against Aspergillus flavus and Aspergillus parasiticus, the aflatoxin producers; (2) effectiveness at concentrations that do not inhibit fungal growth, potentially reducing aflatoxin production; and (3) potential for eco-friendly synthesis using plant extracts. The review also discusses the potential drawbacks of AgNPs viz. (a) environmental concerns regarding accumulation and impact on beneficial soil microbes; and (b) cytotoxicity towards various organisms, requiring further research on safety. Studies suggest AgNPs can inhibit aflatoxin synthesis by disrupting the transcription of aflatoxin biosynthesis genes, damaging the fungal cell membrane and causing leakage of cellular components, and interfering with the secondary metabolism pathway. The review concludes that AgNPs offer a promising approach for aflatoxin control. However, further research is needed to address cytotoxicity concerns and optimise their safe and effective application in agricultural settings.

A Comprehensive Metagenome Study Identifies Distinct Biological Pathways in Asthma Patients: An In-Silico Approach.

Asthma is a multifactorial disease with phenotypes and several clinical and pathophysiological characteristics. Besides innate and adaptive immune responses, the gut microbiome generates Treg cells, mediating the allergic response to environmental factors and exposure to allergens. Because of the complexity of asthma, microbiome analysis and other precision medicine methods are now widely regarded as essential elements of efficient disease therapy. An in-silico pipeline enables the comparative taxonomic profiling of 16S rRNA metagenomic profiles of 20 asthmatic patients and 15 healthy controls utilizing QIIME2. Further, PICRUSt supports downstream gene enrichment and pathway analysis, inferring the enriched pathways in a diseased state. A significant abundance of the phylum Proteobacteria, Sutterella, and Megamonas is identified in asthma patients and a diminished genus Akkermansia. Nasal samples reveal a high relative abundance of Mycoplasma in the nasal samples. Further, differential functional profiling identifies the metabolic pathways related to cofactors and amino acids, secondary metabolism, and signaling pathways. These findings support that a combination of bacterial communities is involved in mediating the responses involved in chronic respiratory conditions like asthma by exerting their influence on various metabolic pathways.

Elucidating ligand interactions and small-molecule activation in the pyrrolnitrin biosynthetic enzyme PrnB.

Pyrrolnitrin, a potent antifungal compound originally discovered in Pseudomonas strains, is biosynthesized through a secondary metabolic pathway involving four key enzymes. Central to this process is PrnB, a heme enzyme that catalyzes the complex transformation of 7-Cl-L-tryptophan. Despite its structural similarity to indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase and its classification within the histidine-ligated heme-dependent aromatic oxygenase superfamily, PrnB has remained relatively unexplored due to the challenges in reconstituting its invitro activity. In this work, we investigated the interactions of PrnB from different strains with its substrates, substrate analogs, and small molecules using various biophysical and biochemical techniques. Our spectroscopic data reveal that the substrate amino group directly coordinates with the heme in both oxidized and reduced enzyme forms. This binding conformation was further confirmed by X-ray crystallography of enzyme-ligand binary complexes. The amine ligation inhibits H2O2 and CN- from interacting with the ferric heme but does not notably impact •NO binding or O2 activation by the ferrous heme. Stopped-flow spectroscopy showed the formation of heme-based oxidants similar to those reported in indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase when PrnB was exposed to H2O2 or O2. However, these intermediates lacked catalytic activity, and PrnB was inactive when coupled with common redox systems under various conditions. This suggests that PrnB operates through a catalytic mechanism distinct from other heme-dependent aromatic oxygenases and most heme enzymes. Our study provides new insights into ligand binding and small-molecule activation mechanisms of PrnB, highlighting its unique functionality and distinguishing it from existing paradigms in heme catalysis.

Enhanced reactive oxygen species and metabolism are involved in the reduction of tribenuron-methyl residues in Tartary buckwheat mutants

Tartary buckwheat, known for its rapid growth, short growth cycles, and adaptability, is cultivated worldwide, particularly in East Asia and Eastern Europe. However, weed infestations severely impact yield and quality, and the absence of effective herbicides poses a considerable challenge to Tartary buckwheat production. To address this, we used ethyl methane sulfonate (EMS) mutagenesis to create a mutant population of Tartary buckwheat seeds. We applied a targeted screening process using the herbicide tribenuron-methyl (TM) to select mutants with reduced sensitivity to the herbicide. Integrative analysis of transcriptomic and metabolomic data indicated that TM primarily inhibited photosynthesis and amino acid biosynthesis pathways in sensitive plants, leading to toxicity. Conversely, resistant plants could reduce the toxic effects of TM on Tartary buckwheat by increasing antioxidant enzyme activity and enhancing secondary metabolic pathways such as flavonoid biosynthesis. TM also upregulated the expression of a gene encoding uridine diphosphate glucuronic acid transferase-like (FtUGT79L). Overexpression of FtUGT79L in Arabidopsis substantially increased total flavonoid content and improved the resistance of Arabidopsis to TM at the seedling and adult stages. The study provides insights into innovative approaches for breeding herbicide-resistant Tartary buckwheat germplasm and serves as an important reference for the development of herbicide-resistant varieties of other crops.

Molecular Functional and Transcriptome Analysis of Arabidopsis thaliana Overexpression BrBBX21 from Zicaitai (Brassica rapa var. purpuraria).

B-box transcription factors (TFs) in plants are essential for circadian rhythm regulation, abiotic stress responses, hormonal signaling pathways, secondary metabolism, photomorphogenesis, and anthocyanin formation. Here, by blasting the AtBBX21 gene sequence, we identified a total of 18 BBX21 genes from five distinct Brassica species (Arabidopsis thaliana, Brassica rapa, Brassica oleracea, Brassica napus, and Brassica juncea). The BrBBX21-1 gene is most closely linked to the AtBBX21 gene based on phylogeny and protein sequence similarities. The BrBBX21-1 gene, which encodes a polypeptide of 319 amino acids, was identified from Zicaitai (Brassica rapa ssp. purpuraria) and functionally characterized. BrBBX21-1 was localized within the nucleus, and its overexpression in Arabidopsis augmented anthocyanin accumulation in both leaves and seeds. We further performed an RNA-seq analysis between the BrBBX21-OE and WT A. thaliana to identify the key regulators involved in anthocyanin accumulation. In detail, a total of 7583 genes demonstrated differential expression, comprising 4351 that were upregulated and 3232 that were downregulated. Out of 7583 DEGs, 81 F-box protein genes and 9 B-box protein genes were either up- or downregulated. Additionally, 7583 differentially expressed genes (DEGs) were associated with 109 KEGG pathways, notably including plant hormone signal transduction, the biosynthesis of secondary metabolites, metabolic pathways, glutathione metabolism, and starch and sucrose metabolism, which were considerably enriched. A transcriptome analysis led us to identify several structural genes, including DFRA, GSTF12, UGT75C1, FLS1, CHI1, 4CL3, and PAL1, and transcription factors, MYB90, TT8, and HY5, that are regulated by the overexpression of the BrBBX21-1 gene and involved in anthocyanin biosynthesis. Altogether, these findings demonstrate the beneficial regulatory function of BrBBX21-1 in anthocyanin accumulation and offer valuable information about the basis for breeding superior Brassica crops.

Multi-omics analysis reveals the positive impact of differential chloroplast activity during in vitro regeneration of barley.

Existence of potent in vitro regeneration system is a prerequisite for efficient genetic transformation and functional genomics of crop plants. In this study, two contrasting cultivars differencing in their in vitro regeneration efficiency were identified. Tissue culture friendly cultivar Golden Promise (GP) and tissue culture resistant DWRB91(D91) were selected as contrasting cultivars to investigate the molecular basis of regeneration efficiency through multiomics analysis. Transcriptomics analysis revealed 1487 differentially expressed genes (DEGs), in which 795 DEGs were upregulated and 692 DEGs were downregulated in the GP-D91 transcriptome. Genes encoding proteins localized in chloroplast and involved in ROS generation were upregulated in the embryogenic calli of GP. Moreover, proteome analysis by LC-MS/MS revealed 3062 protein groups and 16,989 peptide groups, out of these 1586 protein groups were differentially expressed proteins (DEPs). Eventually, GC-MS based metabolomics analysis revealed the higher activity of plastids and alterations in key metabolic processes such as sugar metabolism, fatty acid biosynthesis, and secondary metabolism. TEM analysis also revealed differential plastid development. Higher accumulation of sugars, amino acids and metabolites corresponding to lignin biosynthesis were observed in GP as compared to D91. A comprehensive examination of gene expression, protein profiling and metabolite patterns unveiled a significant increase in the genes encompassing various functions, such as ion homeostasis, chlorophyll metabolic process, ROS regulation, and the secondary metabolic pathway.

Transcriptome Analysis Reveals the Crucial Role of Phenylalanine Ammonia-Lyase in Low Temperature Response in Ammopiptanthus mongolicus.

Background: Ammopiptanthus mongolicus is a rare temperate evergreen shrub with high tolerance to low temperature, and understanding the related gene expression regulatory network can help advance research on the mechanisms of plant tolerance to abiotic stress. Methods: Here, time-course transcriptome analysis was applied to investigate the gene expression network in A. mongolicus under low temperature stress. Results: A total of 12,606 differentially expressed genes (DEGs) were identified at four time-points during low temperature stress treatment, and multiple pathways, such as plant hormones, secondary metabolism, and cell membranes, were significantly enriched in the DEGs. Trend analysis found that the expression level of genes in cluster 19 continued to upregulate under low temperatures, and the genes in cluster 19 were significantly enriched in plant hormone signaling and secondary metabolic pathways. Based on the transcriptome data, the expression profiles of the genes in abscisic acid, salicylic acid, and flavonoid metabolic pathways were analyzed. It was found that biosynthesis of abscisic acid and flavonoids may play crucial roles in the response to low temperature stress. Furthermore, members of the phenylalanine ammonia-lyase (PAL) family in A. mongolicus were systematically identified and their structures and evolution were characterized. Analysis of cis-acting elements showed that the PAL genes in A. mongolicus were closely related to abiotic stress response. Expression pattern analysis showed that PAL genes responded to various environmental stresses, such as low temperature, supporting their involvement in the low temperature response in A. mongolicus. Conclusions: Our study provides important data for understanding the mechanisms of tolerance to low temperatures in A. mongolicus.

Identification of the new allele ptc1-2 and analysis of the regulatory role of PTC1 gene in rice anther development

Anther development involves a series of important biological events that are precisely regulated by many genes. Although several important genes involved in rice anther development have been identified, the regulatory network involved in tapetal development and pollen wall formation is still largely unclear. PERSISTENT TAPETAL CELL 1 (PTC1) encodes a PHD-Finger protein, which plays a critical role in the regulation of tapetal cell death and pollen development in rice. Here, we report the isolation and characterization of a new allele ptc1-2 with 2-base deletion in the third exon, causing the absent of the PHD domain due to the sequence change. Cytological analysis revealed delayed tapetal PCD, defective pollen exine formation and abnormal ubisch bodies development. Transcriptome analysis revealed that genes related to pollen wall formation (secondary metabolism, phenylalanine synthesis, and cutin and wax biosynthesis pathways), cell death (cysteine and methionine metabolism and DNA repair pathways), and carbohydrate synthesis (starch and sucrose metabolism pathways) were significantly altered in ptc1-2 mutant. A total of 13 reported anther development genes exhibited significant expression changes in the ptc1-2 mutant. Yeast two-hybrid and BiFC analyses showed that PTC1 could interact with API5, an inhibitor of apoptosis, and the citrin-binding enzyme EDT1. This work is helpful in deepening the understanding of the regulatory network of male reproductive development in rice.

Balancing Growth and Defense: Nanoselenium and Melatonin in Tea (Camellia sinensis) Protection against Glufosinate.

Current crop stress resistance research suggests that the prominent stimulants nanoselenium (NSe) and melatonin (MT) might improve tea safety, quality, and stress resistance induced by the widely used nonselective herbicide glufosinate (GLU). Their biofortification effects on tea growth, antioxidant activity, and secondary metabolism pathways response to GLU remain unclear. Here, NSe, MT, and their combination NSe-MT effectively reduced 26.6-50.9% GLU and its metabolites in tea seedlings, balanced the photosystem, enhanced antioxidant defenses, and optimized reactive oxygen species scavenging mechanisms. Further, GLU-induced inhibition of glutamine synthetase (11.2-34.0%), ammonium toxicity (55.0-64.7%), and nitrogen metabolism disorders were alleviated. Stimulants exhibited different preferences in the accumulation of l-theanine (8.4-47%), gamma-aminobutyric acid (10.3-41.7%), and catechins (13.1-73.1%, excluding ECG), thereby influencing tea quality. Transcriptomic and metabolomic analyses validated that NSe-MT had a more pronounced impact on tender tea leaves than individual stimulant treatments. All stimulants reduced GLU-induced excessive jasmonic acid (29.8-50.5%) production and signaling responses, revealing their significance in crop physiological activities under herbicide or nitrogen stress. The reduction in aromatic amino acids helped mitigate GLU's interference with phenylpropanoid biosynthesis, leading to inhibited lignin production but enhanced nutritional flavonoid levels, such as catechins. NSe and NSe-MT demonstrated promising potential as herbicide safeners. These findings provided insights into GLU detoxification mechanisms in other nontarget crops as well.

The Effects of FR and UVA Irradiation Timing on Multi-Omics of Purple Lettuce in Plant Factories

The synergistic application of far-red (FR) and ultraviolet A (UVA) irradiation presents a promising approach for enhancing growth and the enrichment of secondary metabolites in plants. However, prolonged exposure to these combined light qualities imposes significant stress on plants, hindering their development. Therefore, an initial period of FR irradiation to promote plant growth, followed by a subsequent period of UVA irradiation to enhance the accumulation of plant quality, constitutes a viable strategy. Our study, focusing on purple lettuce, aims to elucidate the response mechanisms of the lettuce leaf under standard white light in commercial production, with the addition of different durations of FR and UVA irradiation, and to explore the complex dynamic changes at the multi-omics level. The results indicate that the duration of FR exposure is crucial in determining biomass-related phenotypes such as fresh weight, while the duration of UVA exposure significantly influences the accumulation of phenotypic markers like anthocyanins. At the transcriptional level, the most extensive transcriptional regulation was observed when FR was applied throughout the entire growth period, and UVA was applied eight days before harvest, significantly impacting pathways such as MAPK signaling cascades, plant hormone signal transduction, photosynthetic processes, and the biosynthesis of secondary metabolites. Metabolomic analysis corroborated the transcriptomic findings, with particular emphasis on antioxidant activity, photoprotection, and defense mechanisms. Our comprehensive analysis suggests that short-term UVA irradiation prior to harvest, based on full growth period FR irradiation, is feasible. The combined application of FR and UVA irradiation fine-tunes plant growth, developmental trajectories, and stress responses by modulating light signals, hormonal signals, and secondary metabolic pathways. These findings not only reveal the adaptive mechanisms of plants to fluctuating light environments but also provide a scientific basis for optimizing light management strategies in controlled plant production systems and precision agriculture.