Biosynthesis Pathway Research Articles

Photosystem rearrangements, photosynthetic efficiency, and plant growth in far red-enriched light.

Arabidopsis plants were grown in white light (400-700 nm) or in white light supplemented with far-red (FR) light peaking at 730 nm. FR-enriched light induced the typical shade avoidance syndrome characterized by enhanced length of seedling hypocotyl and leaf petiole. FR supplementation also caused a noticeable decrease in the carotenoid and chlorophyll content that was attributable to a block of pigment accumulation during plant development. The carotenoid decrease resulted from a downregulation of their biosynthesis pathway rather than carotenoid degradation. The losses of photosynthetic pigments are part of structural and functional rearrangements of the photosynthetic apparatus. The plastoquinone pool was chronically more oxidized in plants acclimated to white + FR light compared to white light-grown plants. Growth in FR-enriched light was associated with a higher photochemical efficiency of PSII compared to growth in white light and with a substantial increase in root and shoot biomass production. Light distribution between the photosystems was modified in favor of PSII by an increase in the PSII/PSI ratio and an inhibition of state transitions. Neither LHCII abundance nor nonphotochemical energy dissipation in the PSII chlorophyll antennae were modified significantly by the addition of FR light. A PSI supercomplex, not previously observed in Arabidopsis, was specifically found in plants grown in FR-enriched light. This large PSI complex contains a supplementary Lhca1-4 dimer, leading to a total of 6 LHCI antennae instead of 4 in the canonical PSI. Through those photosystem rearrangements and the synergistic interaction with white light, FR light is photosynthetically active and can boost photosynthesis and plant growth.

The association between metabolite profiles and impaired bone microstructure in adult growth hormone deficient rats.

Adult growth hormone deficiency (AGHD) is associated with an increased risk of fractures and impaired bone microstructure. Understanding the metabolic changes accompanying bone deterioration in AGHD might provide insights into mechanisms behind molecular changes and develop new biomarkers or nutritional strategies for bone destruction. Our study aimed to investigate the association between altered metabolite patterns and impaired bone microstructure in adult rats with growth hormone deficiency. Thirty seven-week-aged adult Lewis dwarf homozygous (dw/dw) rats (five females and five males), and adult Lewis dwarf heterozygous (dw/ +) rats (five females and five males) rats were compared. Micro-computed tomography (Micro-CT) was used to examine the bone's microstructure. Hematoxylin and eosin (H&E) staining were used to quantify the histological characteristics. Liquid chromatography-mass spectrometry untargeted serum metabolomic analysis was applied in the study. ELISA was used to measure serum bone turnover markers and IGF-1 levels. Adult dw/dw rats exhibited great reductions in trabecular volume bone density (Tb.vBMD), bone volume/total volume (BV/TV), and cortical thickness (Ct. Th) compared with adult dw/ + rats (all p values < 0.05), indicating significant impairment in bone microstructure. The serum metabolite profiles revealed substantial differences between the dw/dw rats and dw/ + rats. A total of 134 differential metabolites in positive ion mode and 49 differential metabolites in negative mode were identified. Five metabolites, including Lysophosphatidylcholine(LPC) 20:3, LPC22:6, LPC22:4, cortisol and histamine levels were upregulated in dw/dw rats. The steroid hormone biosynthesis and bile secretion pathways were the main perturbed metabolic pathways. There were significant associations between differential metabolites and the impaired bone microstructure parameters, indicating that the selected metabolites might serve as potential biomarkers for deteriorated bone microstructure in AGHD. Adult dw/dw rats exhibit impaired bone microstructure and distinct serum metabolic profiles, and the altered metabolites were significantly associated with bone microstructure destruction. This provides a new insight into understanding the mechanism of bone deterioration in AGHD patients from a metabolic perspective.

Integrated Metabolomics and Transcriptomics Provide Key Molecular Insights into Floral Stage-Driven Flavonoid Pathway in Safflower

Safflower (Carthamus tinctorius L.) is a traditional Chinese medicinal herb renowned for its high flavonoid content and significant medicinal value. However, the dynamic changes in safflower petal flavonoid profiles across different flowering phases present a challenge in optimizing harvest timing and medicinal use. To enhance the utilization of safflower, this study conducted an integrated transcriptomic and metabolomic analysis of safflower petals at different flowering stages. Our findings revealed that certain flavonoids were more abundant during the fading stage, while others peaked during full bloom. Specifically, seven metabolites, including p-coumaric acid, naringenin chalcone, naringenin, dihydrokaempferol, apigenin, kaempferol, and quercetin, accumulated significantly during the fading stage. In contrast, dihydromyricetin and delphinidin levels were notably reduced. Furthermore, key genes in the flavonoid biosynthesis pathway, such as 4CL, DFR, and ANR, exhibited up-regulated expression with safflower’s flowering progression, whereas CHI, F3H, and FLS were down-regulated. Additionally, exposure to UV-B stress at full bloom led to an up-regulation of flavonoid content and altered the expression of key flavonoid biosynthetic genes over time. This study not only elucidates the regulatory mechanisms underlying flavonoid metabolism in safflower but also provides insights for maximizing its medicinal and industrial applications.

Engineered production of 5-aminolevulinic acid in recombinant Escherichia coli BL21.

5-aminolevulinic acid (ALA) is a non-protein amino acid that has been widely used in the fields of medicine and agriculture. This study aims to engineer the C5 pathway of the ALA biosynthesis in Escherichia coli BL21 to enhance ALA production. The ALA synthase genes gltX, hemA, and hemL were overexpressed in E. coli BL21 to lead to the increase in the production of ALA. The sRNA RyhB was also overexpressed to downregulate the expression of ALA dehydratase to reduce the downstream bioconversion of ALA to porphobilinogen. Next, the gene arcA was knocked out by CRISPR-Cas9 technology to open the TCA cycle to promote the respiratory metabolism of the strain to reduce the feedback inhibition of heme to ALA. The fermentation conditions of the engineered strain were optimized by response surface experiments. The time-course analysis of the ALA production was carried out in a 1 L shake flask. Through these efforts, the production of ALA in engineered strain reached 2953 mg/L in a 1 L shake flask. This study contributes to the industrial production of ALA by the engineered E. coli in the future.

Structural variation reshapes population gene expression and trait variation in 2,105 Brassica napus accessions.

Although individual genomic structural variants (SVs) are known to influence gene expression and trait variation, the extent and scale of SV impact across a species remain unknown. In the present study, we constructed a reference library of 334,461 SVs from genome assemblies of 16 representative morphotypes of neopolyploid Brassica napus accessions and detected 258,865 SVs in 2,105 resequenced genomes. Coupling with 5 tissue population transcriptomes, we uncovered 285,976 SV-expression quantitative trait loci (eQTLs) that associate with altered expression of 73,580 genes. We developed a pipeline for the high-throughput joint analyses of SV-genome-wide association studies (SV-GWASs) and transcriptome-wide association studies of phenomic data, eQTLs and eQTL-GWAS colocalization, and identified 726 SV-gene expression-trait variation associations, some of which were verified by transgenics. The pervasive SV impact on how SV reshapes trait variation was demonstrated with the glucosinolate biosynthesis and transport pathway. The study highlighting the impact of genome-wide and species-scale SVs provides a powerful methodological strategy and valuable resources for studying evolution, gene discovery and breeding.

Discovery of potential natural therapeutics targeting cell wall biosynthesis in multidrug-resistant Enterococcus faecalis: a computational perspective.

Identifying therapeutic inhibitors of crucial enzymes involved in the peptidoglycan biosynthesis pathway is pivotal for developing new treatments against multidrug-resistant Enterococcus faecalis V583. MurM, an essential enzyme in this pathway, plays a significant role in the bacterium's cell wall synthesis, making it an attractive druggable target for novel antimicrobial strategies. This study explored the potential of natural compounds as inhibitors of MurM, aiming to discover promising drug candidates that could serve as the foundation for future therapeutic development. The three-dimensional structure of MurM was predicted, optimized, and its binding pocket was analyzed by comparing it with related structures. Over 4,70,000 natural compounds from the COCONUT database were subjected to virtual high-throughput screening (vHTS). The top lead candidates were selected based on their Lipinski's profile, ADME profile, toxicity profile, estimated binding free energy (ΔG) and estimated inhibition constant (Ki). Interaction pattern analysis was used to evaluate the non-covalent interactions between the inhibitors and key residues in MurM's binding pocket. Molecular dynamics simulations were performed over 300 ns to assess the structural stability and impact of these inhibitors on MurM's enzyme. Three lead compounds-CNP0056520, CNP0126952, and CNP0248480-were identified and prioritized with estimated ΔG ranging from - 9.35 to -7.9kcal/mol. Molecular dynamics simulations revealed minimal impact on MurM's overall structure and dynamics, with the candidate inhibitors forming stable protein-ligand complexes. These interactions were supported by several non-covalent interactions between the candidate inhibitors and key residues within MurM's binding pocket. These findings suggest that the identified natural product candidates could serve as promising inhibitors of MurM, potentially leading to novel therapeutics targeting cell wall biosynthesis in multidrug-resistant E. faecalis.

Methyl jasmonate improves rubber production and quality in Lactuca Serriola.

The increase in demand for natural rubber has led to the search for alternative sources. Lactuca serriola is emerging as a promising candidate, as the quality of the natural rubber it produces is comparable to that of the Pará Rubber Plant, Hevea brasiliensis. This study examines the effect of methyl jasmonate (MeJA), a known elicitor, on the expression of key rubber biosynthesis pathway genes (HMGR1, HMGS1, CPT2, and SRPP1) in the latex of L. serriola plants. The expression levels of these genes increased significantly after the foliar application of 200 and 400 µM MeJA. The highest relative expression level for HMGR1, HMGS1, CPT2 and SRPP1 was 3.74, 18.56, 11.91and 16.59 fold respectively. Furthermore, the rubber content in L. serriola showed a significant rise post-treatment compared to the control with increasing the level of MeJA (6.19%, 7.24% and 7.85% which correspond to 0, 200 and 400 µM). Gel permeation chromatography revealed an augmentation in the molecular weight of extracted natural rubber from treated plants. Samples treated with 400 µM of MeJA had the highest molecular weight (1570 kg mol-1) compared to control (1186 kg mol-1). This study has demonstrated that MeJA, through the regulation of rubber biosynthesis genes, is capable of enhancing the quality and quantity of natural rubber extracted from alternative sources, such as L. serriola.

Integrative multi-omics analysis of chilling stress in pumpkin (Cucurbita moschata).

Pumpkin (Cucurbita moschata) is an important vegetable crop that often suffers from low-temperature stress during growth. However, the molecular mechanism involved in its response to chilling stress remains unknown. In this study, we comprehensively investigated the effect of chilling stress in pumpkin seedlings by conducting physiological, transcriptomic, and metabolomic analyses. Under chilling stress, there was an overall increase in relative electrical conductivity, along with malondialdehyde, soluble sugar, and soluble protein contents, but decreased superoxide dismutase and peroxidase activities and chlorophyll contents in seedling leaves compared with controls. Overall, 5,780 differentially expressed genes (DEGs) and 178 differentially expressed metabolites (DEMs) were identified under chilling stress. Most DEGs were involved in plant hormone signal transduction and the phenylpropanoid biosynthesis pathway, and ERF, bHLH, WRKY, MYB, and HSF transcription factors were induced. Metabolomic analysis revealed that the contents of salicylic acid (SA), phenylalanine, and tyrosine increased in response to chilling stress. The findings indicated that the SA signaling and phenylpropanoid biosynthesis pathways are key to regulating the responses to chilling stress in pumpkins. Overall, our study provides valuable insights into the comprehensive response of C. moschata to chilling stress, enriching the theoretical basis of this mechanism and facilitating the development of molecular breeding strategies for pumpkin tolerance to chilling stress.

Gut microbiota and metabolomics unveil the mechanisms of Lomatogonium rotatum in ameliorating visceral fat and serum lipids in high-fat diet-induced obese mice

Lomatogonium rotatum (LR) is a folk medicinal herb traditionally used as a lipid-lowering and anti-obesity agent; but its pharmacological mechanism is unclear. In this study, we assessed the alterations of LR on gut microbes and serum metabolites in obese mice and their associated mechanisms of modulation on visceral fat and serum lipid by integrating gut microbiota and metabolomics analyses. Mice were fed a high-fat diet (HFD) to generate obesity and were then given LR and Orlistat orally at different doses (0.18, 0.9, 1.8 g/kg for LR and 0.048 g/kg for Orlistat) for a duration of 9 weeks. The impact of LR on weight loss was assessed through the examination of fat deposition, serum lipid indices, liver indices, and HE pathohistology. The effects of LR on gut microbiota and serum metabolites in obese mice were then investigated by 16S rRNA sequencing technology and untargeted metabolomics, and correlation analysis was performed. LR significantly reduced body weight, feed intake, Lee’s index, visceral fat accumulation, serum TG, TC, AST and ALT, and elevated serum HDL levels in obese mice. In addition, 16S rRNA sequencing results indicated that the LR intervention remodeled microbial diversity and composition, increased the relative abundance of gut microbes Bacteroidetes and Porphyromonadaceae in HFD-induced obese mice, and decreased the Deferribacteres, Firmicutes and the Firmicutes/Bacteroidetes ratio. Correlation analyses showed that LR regulation of L-tyrosine and hesperetin metabolism, as well as alterations in the metabolic pathways of Phenylalanine, tyrosine and tryptophan biosynthesis, were associated with the changes in abundance of Bacteroidetes, Firmicutes, Porphyromonadaceae and Deferribacteres. Our study demonstrated that LR has lipid lowering and visceral fat reduction effects and its function may be closely related to the improvement of the gut microbiota and its associated metabolites.

Antioxidative and Cytoprotective Effects of Rosa Roxburghii and Metabolite Changes in Oxidative Stress-Induced HepG2 Cells Following Rosa Roxburghii Intervention

Rosa Roxburghii (RR), a traditional Chinese medicinal fruit, is rich in bioactive substances that make it a potential natural antioxidant resource. This research aimed to study the antioxidant properties of RR by in vitro experiments and through intracellular assessment in H2O2-induced HepG2 cells. A non-targeted metabolic analysis was conducted to indicate changes in intracellular and extracellular metabolites. Differential metabolites and metabolic pathways were explored using PCA, PLS-DA, and KEGG pathway analysis. The results showed that RR rich in bioactive substances exhibited a significant antioxidative property in vitro and intracellularly. This property may be achieved by scavenging free radicals, increasing the activity of catalase (CAT), glutathione peroxidase (GSH-Px), superoxide dismutase (SOD), and the levels of bicinchoninic acid (BCA) while reducing the reactive oxygen species (ROS) generation. This study identified 13 differential metabolites intracellularly and 7 extracellularly, among which the key differential metabolites included D-glucopyranose, D-mannose, fructose, citric acid, malic acid, cholesterol, and cholestenone. These key metabolites primarily regulated glucose-related metabolism, the citrate cycle, and the primary bile acid biosynthesis pathway in H2O2-induced HepG2 cells. These findings provide potential application evidence of RR in the development of natural resources for functional foods.

Unveiling Key Genes and Unique Transcription Factors Involved in Secondary Cell Wall Formation in Pinus taeda

Pinus taeda is a key timber species, and extensive research has been conducted on its wood formation. However, a comprehensive investigation into the biosynthetic pathways of lignin, cellulose, and hemicellulose in P. taeda is lacking, resulting in an incomplete understanding of secondary cell wall (SCW) formation in this species. In this study, we systematically analyzed transcriptomic data from previously published sources and constructed detailed pathways for lignin, cellulose, and hemicellulose biosynthesis. We identified 188 lignin-related genes and 78 genes associated with cellulose and hemicellulose biosynthesis. An RT-qPCR highlighted 15 key lignin biosynthesis genes and 13 crucial genes for cellulose and hemicellulose biosynthesis. A STEM analysis showed that most essential enzyme-coding genes clustered into Profile 14, suggesting their significant role in SCW formation. Additionally, we identified seven NAC and six MYB transcription factors (TFs) from atypical evolutionary clades, with distinct expression patterns from those of the previously characterized NAC and MYB genes, indicating potentially unique functions in SCW formation. This research provides the first comprehensive overview of lignin, cellulose, and hemicellulose biosynthetic genes in P. taeda and underscores the importance of non-canonical NAC and MYB TFs, laying a genetic foundation for future studies on SCW regulatory mechanisms.

A pearl millet plasma membrane protein, PgPM19, facilitates seed germination through the negative regulation of abscisic acid-associated genes under salinity stress in Arabidopsis thaliana.

The pearl millet gene PgPM19 inhibits seed dormancy by negatively regulating the ABA biosynthesis and ABA signaling pathways in response to salinity stress in Arabidopsis. Abscisic acid (ABA) plays a pivotal role in orchestrating plant stress responses and development. However, how the ABA signal is transmitted in response to stresses remains primarily uncertain, particularly in monocotyledonous plants. In this study, PgPM19, a gene whose expression is induced by drought, salinity, heat, and ABA in both leaf and root tissues, was isolated from pearl millet. The expression of PgPM19 in yeast cells did not influence their growth when subjected to mannitol, sorbitol, or NaCl stress. However, Arabidopsis plants overexpressing PgPM19 (PgPM19_OE plants) exhibited increased germination rates, greater fresh weights and longer roots under salinity stress during germination, compared to wild-type (WT) plants. Conversely, the pm19L1 (SALK_075435) mutant, featuring a transfer DNA insertion in a closely related PgPM19 homolog (AT1G04560) in Arabidopsis, demonstrated reduced germination rates and smaller fresh weights under salinity-stressed condition than did WT and PgPM19_OE plants. A pivotal ABA biosynthesis gene, NCED3, ABA signaling pathway genes, such as PYL6 and SnRK2.7, alongside downstream ABI genes and stress-responsive genes RAB28 and RD29, were downregulated in PgPM19_OE plants, as evidenced by both transcriptome analysis and quantitative reverse transcription-PCR. These findings raise the possibility that PgPM19 is involved in regulating seed germination by mediating ABA biosynthesis and signaling pathway in response to salinity stress in Arabidopsis. This study contributes to a better understanding of PgPM19 in response to salinity stress and establishes a foundation for unraveling the crosstalk of stress responses and ABA in Arabidopsis and other plant species.

The Effects of Lead and Cross-Talk Between Lead and Pea Aphids on Defence Responses of Pea Seedlings

The main goal of this study was to investigate the effect of lead (Pb) at various concentrations, as an abiotic factor, and the cross-talk between Pb and pea aphid (Acyrthosiphon pisum (Harris)) (Hemiptera: Aphididae), as a biotic factor, on the defence responses of pea seedlings (Pisum sativum L. cv. Cysterski). The analysis of growth parameters for pea seedlings demonstrated that Pb at a low concentration, i.e., 0.025–0.0625 mM Pb(NO3)2, caused a hormesis effect, i.e., stimulation of seedling growth, whereas Pb at higher concentrations, i.e., 0.01–0.325 mM Pb(NO3)2, inhibited growth, which manifested as the inhibition of length and fresh biomass. The differences in the level of the main defence-related phytohormones, such as abscisic acid (ABA), jasmonic acid (JA) and salicylic acid (SA), and indole-3-acetic acid (IAA)—an auxin stimulating plant cell growth—depended on the dose of Pb, aphid infestation and direct contact of the stress factor with the organ. A high accumulation of soluble sugars in the organs of pea seedlings both at sublethal doses and hormetic doses at early experimental time points was observed. At 0 h and 24 h of the experiment, the hormetic doses of Pb significantly stimulated invertase activities, especially in the roots. Moreover, an increase was observed in the pisatin concentration in pea seedlings growing in the presence of different concentrations of Pb and in the case of cross-talk between Pb and A. pisum in relation to the control. Additionally, a significant induction of the expressions of isoflavone synthase (IFS) and 6α-hydroxymaackiain 3-O-methyltransferase (HMM) genes, which participate in the regulation of the pisatin biosynthesis pathway, in pea seedlings growing under the influence of sublethal 0.5 mM Pb(NO3)2 and hormetic 0.075 mM Pb(NO3)2 doses of Pb was noted. The obtained results showed that the response of P. sativum seedlings depends on the Pb dose applied, direct contact of the stress factor with the organ and the duration of contact.

Design, Synthesis, and Biological Studies of C-5-Substituted Diazenyl Derivatives of Uracil as Potent and Selective Antileishmanial Agents Targeting Uridine Biosynthesis Pathway Enzymes.

Herein, we describe the design and synthesis of a series of C-5-substituted diazenyl derivatives of uracil, exhibiting selective and potent antileishmanial but not antibacterial or antifungal activity. The formation of the substituted derivatives was confirmed by using FTIR, 1H, 13C NMR, and HRMS analysis. Among all of the sets of tested compounds, only three [4a, 6b, and 8b] showed the highest activity against Leishmania donovani (LD) promastigote and amastigote models of LD infections. Further, the cytotoxicity assays performed using three different cell lines, Vero cells, J774 cells, and THP1 cells, along with erythrocyte hemolysis assay showed the highest biocompatibility for the 4a, making it a lead compound for further biological assays. The LD cell death associated with 4a was not linked with ergosterol depletion, a common mechanism of action of antileishmanial drugs like amphotericin B (AmB). However, the LD cell death in the presence of 4a was reversed significantly through supplementation of uridine monophosphate (UMP), indicating the specific role of uridine biosynthesis pathway as the target of 4a. Furthermore, the in silico studies predicted ornithine monophosphate decarboxylase enzyme (OMPDCase) from LD as the plausible target for 4a. The proteomics analysis showed stronger downregulation of the aforementioned OMPDCase and also for a few other enzymes that are involved in the UMP biosynthesis pathway. This indicates that OMPDCase and other enzymes that regulate the UMP biosynthesis may be the target of 4a. Overall, the C-5-substituted diazenyl derivatives of uracil are presented here as novel and potent antileishmanial agents that can be used for treating visceral leishmaniasis (VL) wherein at present drug resistance and side effects of existing drugs demand a look for safer alternatives.

Impact of nitrogen rates on biosynthesis pathways: A comparative study of diterpene synthases in clerodane diterpenoids and enzymes in benzylisoquinoline alkaloids

Tinospora sagittata is rich in secondary metabolites used in traditional medicine. However, environmental factors impact key enzymes in metabolite synthesis, highlighting the need for improved growth conditions. This study employs transcriptomics and metabolomics to assess nitrogen's impact on enzymes in secondary metabolites biosynthesis pathways. The gene expressions of berberine bridge enzymes (BBEs) like TsBBE2 had peak expression in low nitrogen treatments (A0 and A1) but were absent in higher nitrogen treatments (A2 and A3). Similar trends were observed for other enzymes such as (S)-scoulerine 9-O-methyltransferase (TsCMT3), Tetrahydroberberine oxidase (TsSTOX), and Columbamine O-methyltransferase (TsCoCOMT2-4) in response to nitrogen levels. In examining gene families related to diterpene synthases (diTPS), 1-deoxyxylulose 5-phosphate synthase (TsDXR1) expression increased with higher nitrogen fertilizer, while TsDXR2 peaked at maximal nitrogen levels. Geranylgeranyl diphosphate synthase (TsGGPP3 and TsGGPP5) decreased with nitrogen levels. (−)-kolavenyl diphosphate synthase (KPS) genes had higher expression in treatments, while ent-kaurene synthase (KSL) genes, especially TsKSL1 and TsKSL2, showed higher expression in control conditions with lower nitrogen fertilizer. Metabolite analysis confirmed more upregulated compounds in A3 compared to A0. These findings have practical implications for agriculture and pharmaceuticals, highlighting the link between nitrogen fertilization and specialized metabolism in medicinal plants.

Competitive action network of polyamines metabolic and ethylene biosynthesis pathways in gibberellin-induced parthenocarpic berries during grape fruit setting

Polyamines (PAs) and ethylene are involved in the modulation of plant growth and development. However, their roles in fruit-set, especially in exogenous gibberellin (GA3)-induced grape parthenocarpic berries, and the related competitive action mode are poorly understood. For this, we, here performed their content determination, bioinformatics and expression pattern analysis of genes to identify the key ones in the competitive network of polyamines metabolic and ethylene biosynthesis (PMEB) pathways. The content of putrescine (Put) significantly increased; while 1-aminocyclopropanecarboxylic acid (ACC) sharply decreased during the fruit-set process of GA3-induced grape parthenocarpic seedless berries. Totally, twenty-five genes in PMEB pathways, including 20 polyamines metabolic (PM) genes and 5 ethylene biosynthesis (EB) ones were identified in grape, of which 8 PM and 2 EB genes possessed the motifs responsive to phytohormone GA. The expression levels of most PMEB genes kept changing during grape fruit-set generating a competitive action mode of GA3-mediated two metabolic fluxes toward PAs and ethylene synthesis. Exogenous GA3 might enhance grape fruit-set of parthenocarpic berries via up-regulation of VvSAMS4, VvSAMDC1/2, VvODC1, VvSPDS1, and VvPAO1 to promote PAs accumulation, whereby repressing the ethylene synthesis by down-regulation of VvACS1 and VvACO2. Our findings provide novel insights into GA3-mediated competitive inhibition of ethylene by PAs to promote the fruit-set of parthenocarpic berries in grape, which has important implications for molecular breeding of seedless grape with high fruit-setting rate.

Proteomic analysis identified proteins that are differentially expressed in the flavonoid and carotenoid biosynthetic pathways of Camellia Nitidissima flowers

BackgroundCamellia nitidissima Chi is a popular ornamental plant because of its golden flowers, which contain flavonoids and carotenoids. To understand the regulatory mechanism of golden color formation, the metabolites of C. nitidissima petals at five different developmental stages were detected, a proteome map of petals was first constructed via tandem mass tag (TMT) analysis, and the accuracy of the sequencing data was validated via parallel reaction monitoring (PRM).ResultsNineteen color components were detected, and most of these components were carotenoids that gradually accumulated, while some metabolites were flavonoids that were gradually depleted. A total of 97,647 spectra were obtained, and 6,789 quantifiable proteins were identified. Then, 1,319 differentially expressed proteins (DEPs) were found, 55 of which belong to the flavonoid and carotenoid pathways, as revealed by pairwise comparisons of protein expression levels across the five developmental stages. Notably, most DEPs involved in the synthesis of flavonoids, such as phenylalanine ammonium lyase and 4-coumarate-CoA ligase, were downregulated during petal development, whereas DEPs involved in carotenoid synthesis, such as phytoene synthase, 1-deoxy-D-xylulose-5-phosphate synthase, and β-cyclase, tended to be upregulated. Furthermore, protein‒protein interaction (PPI) network analysis revealed that these 55 DEPs formed two distinct PPI networks closely tied to the flavonoid and carotenoid synthesis pathways. Phytoene synthase and chalcone synthase exhibited extensive interactions with numerous other proteins and displayed high connectivity within the PPI networks, suggesting their pivotal biological functions in flavonoid and carotenoid biosynthesis.ConclusionProteomic data on the flavonoid and carotenoid biosynthesis pathways were obtained, and the regulatory roles of the DEPs were analyzed, which provided a theoretical basis for further understanding the golden color formation mechanism of C. nitidissima.

Decoding eggplant fruit: Multi-omics profiling of caffeoyl-CoA-3-OMT expression

Eggplant (Solanum melongena L.) is a rich source of health-promoting phenolic acids, mainly chlorogenic acid (CGA), and trace elements. CGA has been shown to have antioxidant, anti-inflammatory, neuroprotective, cardioprotective, anticancer, and antidiabetic properties. The natural genome of eggplants contains essential genes for beneficial traits like drought tolerance, disease resistance, and high concentrations of medicinal substances. Transcriptomic analysis of eggplant overexpressing the hydroxycinnamoyl CoA quinate hydroxycinnamoyl transferase (HQT) gene revealed upregulation of 2165 genes, including three similar to HQT and cinnamate-4-hydroxylase (C4H). Sequence similarity analysis showed homology to caffeoyl-CoA O-methyltransferases, key enzymes in the phenylpropanoid pathway leading to CGA biosynthesis. Gene ontology and KEGG pathway analysis identified 5 highly upregulated glycosyltransferase family 43 genes (650.3-fold change). Glycosyltransferases like UDP-glucose:cinnamate glucosyltransferase and cinnamate-glucose 4′-O-glucosyltransferase are crucial for CGA production in eggplant. qRT-PCR validated the potential upregulation of HQT and C4H in transgenic eggplants. Comparative analysis revealed eggplant has the highest CGA content (5–8.1 g/kg dry weight) among vegetables, with foliar CGA acting as a natural insecticide. CGA offers antioxidant, hypoglycemic, antiviral, and hepatoprotective benefits to humans. This study highlights the role of HQT and C4H in elevating the medicinal properties of eggplant through CGA biosynthesis pathway engineering.

Spatially heterogeneous lipid dysregulation in tuberculous meningitis

Tuberculous (TB) meningitis is the deadliest form of extrapulmonary TB which disproportionately affects children and immunocompromised individuals. Studies in pulmonary TB have shown that Mycobacterium tuberculosis can alter host lipid metabolism to evade the immune system. Cholesterol lowering drugs (i.e., statins) reduce the risk of infection, making them a promising host-directed therapy in pulmonary TB. However, the effect of M. tuberculosis infection on the young or adult brain lipidome has not been studied. The brain is the second-most lipid-rich organ, after adipose tissue, with a temporally and spatially heterogeneous lipidome that changes from infancy to adulthood. The young, developing brain in children may be uniquely vulnerable to alterations in lipid composition and homeostasis, as perturbations in cholesterol metabolism can cause developmental disorders leading to intellectual disabilities. To begin to understand the alterations to the brain lipidome in pediatric TB meningitis, we utilized our previously published young rabbit model of TB meningitis and applied mass spectrometry (MS) techniques to elucidate spatial differences. We used matrix assisted laser desorption/ionization-MS imaging (MALDI-MSI) and complemented it with region-specific liquid chromatography (LC)-MS/MS developed to identify and quantify sterols and oxysterols difficult to identify by MALDI MSI. MALDI-MSI revealed several sphingolipids, glycerolipids and glycerophospholipids that were downregulated in brain lesions. LC-MS/MS revealed the downregulation of cholesterol, several sterol intermediates along the cholesterol biosynthesis pathway and enzymatically produced oxysterols as a direct result of M. tuberculosis infection. However, oxysterols produced by oxidative stress were increased in brain lesions. Together, these results demonstrate significant spatially regulated brain lipidome dysregulation in pediatric TB meningitis.

Exploring Brazilian Natural Products as Potential Bioactive Compounds against Trypanosoma cruzi by Targeting Squalene Synthase

Introduction: Chagas disease is a neglected disease caused by the protozoan Trypanosoma cruzi that affects 7 million people worldwide. The current treatment is limited due to safety and efficacy issues. Therefore, the search for new antiparasitic drugs is fundamental. The enzyme squalene synthase (SQS) is an attractive therapeutic target since it participates in the ergosterol biosynthesis pathway. Objective: In the present study, we explored the Brazilian biodiversity to search for potential inhibitors of T. cruzi SQS (TcSQS) using ligand and structure-based virtual screening strategies. Materials and Methods: A virtual screening was performed within the NUBBE database, with more than 2,200 natural products (NP) or semisynthetic derivatives from the Brazilian biodiversity. Molecular docking and ADMET predictions were then performed. Results: A set of 12 NP showed interactions with TcSQS like those observed by known inhibitors and shared literature evidence that supports the predicted activity. Conclusion: Three compounds (flavonoids) showed good ADMET properties as potential inhibitors of TcSQS.