Amino Acid Biosynthesis Research Articles

Crystal Structures of Arabidopsis thaliana Acetohydroxyacid Synthase in Complex with the Herbicide Triasulfuron and Two Analogues with Herbicidal Activity in Field Trials.

Triasulfuron is a commercial herbicide of the sulfonylurea family. This compound targets acetohydroxyacid synthase (AHAS, E.C. 2.2.1.6), the first enzyme in the branched chain amino acid biosynthesis pathway. Here, we have determined crystal structures of Arabidopsis thaliana AHAS (AtAHAS) in complex with triasulfuron and two newly designed herbicidal compounds, identified as FMO and CMO, showing that their binding modes are subtly different. Kinetic studies showed all three compounds exhibit varying Ki values, 0.192 ± 0.013 μM for triasulfuron, 0.086 ± 0.013 μM for FMO, and 1.448 ± 0.058 μM for CMO, but all are strong time-dependent accumulative inhibitors of AtAHAS. Apart from triasulfuron being a powerful herbicide with application rates of 10-15 g/ha in wheat fields, CMO and FMO are also herbicidal at 7.5-30 g/ha for barnyard grass. This study emphasizes that accumulative inhibition is an important factor that contributes to herbicidal activity.

Mapping the proteomic landscape and anti-inflammatory role of Streptococcus parauberis extracellular vesicles

Bacterial extracellular vesicles (BEVs) are nanoscale membrane-bound structures involved in intercellular communication and transport of bioactive molecules. In this study, we described the proteomic insight and anti-inflammatory activity of Streptococcus parauberis BEVs (SpEVs). Proteomics analysis of SpEVs identified 6209 distinct peptides and 1039 proteins. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated enrichment in pathways related to the biosynthesis of aminoacyl tRNA, amino acids, and secondary metabolites. Based on the predicted protein-protein interactions, we discovered key immunological proteins such as IL12A, IL12B, IL8, CD28, and NF-κB between SpEVs and human proteins. Functionally, SpEVs exhibit strong anti-inflammatory activity in LPS-stimulated Raw 264.7 cells by reducing the production of key inflammatory mediators. These include nitric oxide (NO), reactive oxygen species (ROS), inflammatory cytokines such as TNFα and IL6, as well as inflammation-related proteins like inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). qRT-PCR and immunoblotting results clearly indicate that SpEVs modulate the NF-κB and MAPK pathways to induce anti-inflammatory activity. Furthermore, in vivo experiments with zebrafish larvae demonstrated that SpEVs treatment reduced the NO and ROS production with minimal cell mortality. Finally, we validated the anti-inflammatory activity of SpEVs in vivo by systematically assessing the inhibition of NO production, reduction in ROS generation, prevention of cell death, and modulation of NF-κB and MAPK signaling pathways. In conclusion, SpEVs contain rich in unique proteins that play crucial roles in mediating anti-inflammatory effects.

7286 Higher Order Associations Linking Tryptophan, Kynurenine, And Tyrosine As Serum Markers Of Glucocorticoid Downstream Action In Adipose Tissue

Abstract Disclosure: K. Bennett: None. T. Garner: None. D. Chantzichristos: Speaker; Self; Sanofi, Takeda. P. Jansson: None. A. Stevens: None. G. Johannsson: Consulting Fee; Self; Novo Nordisk, Shire, AstraZeneca. Speaker; Self; Novo Nordisk, Pfizer, Inc.. Introduction: Treatment of Adrenal Insufficiency (AI) by glucocorticoid (GC) replacement therapy is mainly guided by clinical judgement, as there is no biomarker of GC action to individualise its dosage. Hypergraphs are networks modelling higher order associations (HOAs), which are interactions between more than two ‘omic elements. The aim of this study was to use hypergraphs to identify serum markers that reflect the action of GCs in adipose tissue (AT). Methods: In a randomised, cross-over trial, 10 patients with primary AI received saline i.v. (GC withdrawal), or circadian infusion of hydrocortisone (GC exposure), with > 2 weeks apart. After 26 hours (8AM), AT biopsy and PBMCs were collected for transcriptomic analysis, and abdominal subcutaneous microdialysis and PBMCs were collected for metabolomic profiling using LC/MS. Hypergraph models were generated to integrate serum and AT transcriptomics and metabolomics, identifying clusters of putatively causally linked metabolites which could represent serum markers of downstream GC action in AT. Hypergraph structure was assessed in AT and serum using entropy to infer associations within pre-defined metabolic pathways. Differences in entropy between the interventions was measured using Bayes Factor. Univariate ROC curve analysis was used to calculate AUCs for the serum markers. Results: In AT dialysate, 22 metabolites were identified as significantly different between GC exposure and withdrawal states. These included metabolites found in lipolysis and proteolysis pathways, such as acyl carnitines, lysophosphatidylcholines, fatty acids, and peptide derivatives. Nine metabolites were significantly different between the interventions in the serum. DEGs in AT (n=2048) were found to be enriched in metabolic pathways. Hypergraphs were used to refine clusters in the serum based on their HOAs with AT differentially expressed genes and metabolites. Tryptophan, Kynurenine, and Tyrosine clustered together, demonstrating a relationship between their expression in serum, and the metabolomic and transcriptomic profile of AT. These HOAs were shared with cortisol in the exposure intervention, but not in GC withdrawal, suggesting GC dependent regulation. All 3 metabolites had AUC-ROCs > 0.8, with Kynurenine performing the best at 0.86. Tissue specific differences were seen in the entropy of metabolic pathways between GC exposure and withdrawal, with similar changes seen in lipid and proteolysis pathways, but no difference seen in serum in carbohydrate and amino acid biosynthesis. Conclusions: During near physiological exposure, we identified changes to hypergraph structure and metabolite concentrations in lipid, protein, and carbohydrate pathways in AT and serum, compared to GC withdrawal. Hypergraph integration of multi-omic data identified tryptophan, kynurenine, and tyrosine as potential serum markers reflecting GC action in AT. Presentation: 6/3/2024

Effects of phosphate-solubilizing bacteria Aspergillus flavus AF-LRH1 on promoting phosphorus solubilization, wheat growth and soil heavy metal remediation

Increasing nutrient supply level and eliminating pollution risk are essential to promote farmland soil use. In the soil-plant nutrition cycle, phosphorus is a limiting nutrient, toxic metals such as Cd and Pb are stress threats. Utilizing microorganisms as a bio-amendment could be a viable approach to enhance the cycling of soil phosphorus nutrients and immobilize Cd and Pb in the soil. This study involved the isolation of Aspergillus flavus AF-LRH1, a phosphate solubilizing fungal strain from soil. The strain exhibited the capacity to solubilize calcium phosphate, attaining a phosphorus concentration of 220.73 mg L−1 in the medium. High performance liquid chromatography analysis showed that AF-LRH1 produced a combination of organic acids (tartaric acid 260.7 mg L−1, fumaric acid 0.8 mg L−1, citric acid 911.9 mg L−1) to dissolve Ca3(PO4)2 by providing H+ ions. AF-LRH1 also utilizes NH4+ for the biosynthesis of amino acids and releases protons, which facilitate the dissolution of insoluble Ca3(PO4)2 and calcium phytate. Through these processes, calcium phosphate is partly converted into hydroxyapatite because of biological solubilization. AF-LRH1 strain showed the capability to recover phosphorus from various types of sludge-based solid residue by increasing the solubility of insoluble phosphate compounds for plant nutrient supply. In addition, the combining addition of AF-LRH1 strain and phosphate-containing amendments (calcium phosphate, sludge ash and biochar) benefited the decontamination of Pb and Cd contaminated soil. This finding confirmed the AF-LRH1 could be a promising environmental-friendly biofertilizer suitable for agricultural applications and bioremediation of heavy metal contaminated soil.

Mechanism of enhanced salt tolerance in Saccharomyces cerevisiae by CRZ1 overexpression

Achieving high-gravity fermentation in the industrial production of fuel ethanol, and enhancing the fermentation efficiency of high-salt raw materials, such as waste molasses, can significantly reduce wastewater output and process costs. Therefore, the development of hyperosmotic-tolerant industrial Saccharomyces cerevisiae strains, capable of resisting high-salt stress, offers both environmental and economic benefits. Our previous study highlighted the potential of CRZ1 overexpression as a strategy to improve the yeast strain’s resistance to high-salt stress, however, the underlying molecular mechanisms remain unexplored. The fermentation capabilities of the CRZ1-overexpressing strain, KCR3, and its parental strain, KF7, were evaluated under condition of 1.25 M NaCl at 35 °C. Compared to KF7, KCR3 showed an 81% increase in glucose consumption (129.25 ± 0.83 g/L) and a 105% increase in ethanol production (47.59 ± 0.93 g/L), with a yield of 0.37 g/g. Comparative transcriptomic analysis showed that under high-salt stress, KCR3 exhibited significantly upregulated expression of genes associated with ion transport, stress response, gluconeogenesis, and the utilization of alternative carbon sources, while genes related to glycolysis and the biosynthesis of ribosomes, amino acids, and fatty acids were notably downregulated compared to KF7. Crz1 likely expands its influence by regulating the expression of numerous transcription factors, thereby impacting genes involved in multiple aspects of cellular function. The study revealed the regulatory mechanism of Crz1 under high-salt stress, thereby providing guidance for the construction of salt-tolerant strains.

Integrated PacBio SMRT and Illumina sequencing uncovers transcriptional and physiological responses to drought stress in whole-plant Nitraria tangutorum.

Nitraria tangutorum Bobr., a prominent xerophytic shrub, exhibits remarkable adaptability to harsh environment and plays a significant part in preventing desertification in northwest China owing to its exceptional drought and salinity tolerance. To investigate the drought-resistant mechanism underlying N. tangutorum, we treated 8-week-old seedlings with polyethylene glycol (PEG)-6000 (20%, m/m) to induce drought stress. 27 samples from different tissues (leaves, roots and stems) of N. tangutorum at 0, 6 and 24h after drought stress treatment were sequenced using PacBio single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing to obtain a comprehensive transcriptome. The PacBio SMRT sequencing generated 44,829 non-redundant transcripts and provided valuable reference gene information. In leaves, roots and stems, we identified 1162, 2024 and 232 differentially expressed genes (DEGs), respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that plant hormone signaling and mitogen-activated protein kinase (MAPK) cascade played a pivotal role in transmitting stress signals throughout the whole N. tangutorum plant following drought stress. The interconversion of starch and sucrose, as well as the biosynthesis of amino acid and lignin, may represent adaptive strategies employed by N. tangutorum to effectively cope with drought. Transcription factor analysis showed that AP2/ERF-ERF, WRKY, bHLH, NAC and MYB families were mainly involved in the regulation of drought response genes. Furthermore, eight physiological indexes, including content of proline, hydrogen peroxide (H2O2), malondialdehyde (MDA), total amino acid and soluble sugar, and activities of three antioxidant enzymes were all investigate after PEG treatment, elucidating the drought tolerance mechanism from physiological perspective. The weighted gene co-expression network analysis (WGCNA) identified several hub genes serve as key regulator in response to drought through hormone participation, ROS cleavage, glycolysis, TF regulation in N. tangutorum. These findings enlarge genomic resources and facilitate research in the discovery of novel genes research in N. tangutorum, thereby establishing a foundation for investigating the drought resistance mechanism of xerophyte.

Genomic characterization and proteomic analysis of Bacillus amyloliquefaciens in response to lignin

This study examined the lignin degradation characteristics of Bacillus amyloliquefaciens MN-13. Specifically, whole-genome sequencing and comparative proteomic analysis were performed to investigate the responses of the MN-13 strain to lignin. A maximum lignin removal of 38.0 % was achieved after 36 h of inoculation in mineral salt medium with 0.2 g/L alkaline lignin, under the following conditions: the carbon to nitrogen ratio C/N = 1/1; inoculum size 6 %; addition of glucose as an exogenous carbon source. When the MN-13 strain was inoculated into mineral salt medium with and without lignin, respectively, 831 differentially expressed proteins were identified, 404 of which were up-regulated and 427 were down-regulated. Enrichment analysis revealed that up-regulated proteins were associated with microbial metabolism in diverse environment, biosynthesis of amino acids, and pathways related to energy production, including carbon metabolism, pyruvate metabolism, the TCA cycle etc. Genomic analysis revealed that the MN-13 strain possesses many ligninolytic enzymes and aromatics degradation pathway, including benzoate degradation and aminobenzoate degradation etc. Taken together, the proteomic and genomic analyses indicated that the meta-cleavage pathway of catechol, including benzoate degradation, etc., is the main lignin degradation pathway. These findings provide new insight into lignin degradation mediated by B. amyloliquefaciens.

Regulating role of Pleurotus ostreatus insoluble dietary fiber in high fat diet induced obesity in rats based on proteomics and metabolomics analyses

This study aims to reveal the effects of Pleurotus ostreatus insoluble dietary fiber (POIDF) on liver protein and cecal metabolites in obese rats and its potential mechanism by intestinal microbes. It was found that POIDF contained the structural characteristics of cellulose and hemicellulose, as well as amorphous diffraction peaks. POIDF could reduce the body weight and organ index of obese rats, regulate dyslipidemia, and improve the pathological changes of liver and epididymis fat. Further experimental results showed that POIDF could regulate the abundance of bacteria related to lipid metabolism, and maintain intestinal homeostasis. The metabolomics results showed that the fatty acyls pathway in the cecum contents was the pathway with the highest concentration of small molecule metabolites. POIDF supplementation regulated the expression of liver key proteins, as well as biosynthesis of amino acids, steroid biosynthesis, arachidonic acid metabolism and PPAR signaling pathway. Omics association analysis found that POIDF could further regulate liver proteins and their signaling pathways, regulate the levels of fatty acyls and amino acid metabolites in the gut and the enrichment of related pathways, and play a therapeutic or preventive role in obesity after degradation by intestinal microbiota.

Serum-Derived Extracellular Vesicles for the Treatment of Severe Ocular Surface Disease

PurposeAutologous serum is widely used for the treatment of severe ocular surface disease with mixed efficacy. Extracellular vesicles (EVs) are small membrane bound structures present in all body fluids, including serum. This study compared the proteomic, metabolomic, and inflammatory cytokine composition of serum-derived EVs (SDEVs) to that of the soluble free protein fraction and the subsequent capacity of SDEVs to induce corneal epithelial cell migration and inflammation. MethodsSDEVs were isolated from human serum using size exclusion chromatography. SDEVs were analyzed using nanoparticle tracking analysis, transmission electron microscopy, and western blotting. The effects of SDEVs on corneal epithelial cell migration were tested using a standard scratch assay. Inflammatory cytokines in SDEVs and the free protein fraction were quantified using a microarray. A mutli-omics approach was further used to define SDEV cargo. The ability of SDEVs to modulate inflammation in corneal epithelial cells was quantified using ELISAs. ResultsWestern blot and TEM confirmed the presence of SDEVs. Proinflammatory cytokines, along with complement proteins and TGF-β, were decreased in SDEVs compared to serum. Metabolites present in SDEVs were mostly involved in amino acid biosynthesis, the TCA cycle and oxidative phosphorylation. SDEVs exhibited pro-migratory effects similar to serum however, SDEVs did not induce secretion of IL-6 or IL-8. ConclusionsSDEVs exhibit reduced levels of pro-inflammatory cytokines while retaining the beneficial wound healing properties of serum. Unlike serum, SDEVs do not induce inflammation. SDEVs may represent an alternative option for patients with severe ocular surface disease where traditional autologous serum has failed.

Multiomics approach discloses lipids and metabolites profiles associated to Parkinson's disease stages and applied therapies

Profiling circulating lipids and metabolites in Parkinson's disease (PD) patients could be useful not only to highlight new pathways affected in PD condition but also to identify sensitive and effective biomarkers for early disease detection and potentially effective therapeutic interventions. In this study we adopted an untargeted omics approach in three groups of patients (No L-Dopa, L-Dopa and DBS) to disclose whether long-term levodopa treatment with or without deep brain stimulation (DBS) could reflect a characteristic lipidomic and metabolomic signature at circulating level. Our findings disclosed a wide up regulation of the majority of differentially regulated lipid species that increase with disease progression and severity. We found a relevant modulation of triacylglycerols and acyl-carnitines, together with an altered profile in adiponectin and leptin, that can differentiate the DBS treated group from the others PD patients. We found a highly significant increase of exosyl ceramides (Hex2Cer) and sphingoid bases (SPB) in PD patients mainly in DBS group (p < 0.0001), which also resulted in a highly accurate diagnostic performance. At metabolomic level, we found a wide dysregulation of pathways involved in the biosynthesis and metabolism of several amino acids. The most interesting finding was the identification of a specific modulation of L-glutamic acid in the three groups of patients. L-glutamate levels increased slightly in No L-Dopa and highly in L-Dopa patients while decreased in DBS, suggesting that DBS therapy might have a beneficial effect on the glutamatergic cascade. All together, these data provide novel insights into the molecular and metabolic alterations underlying PD therapy and might be relevant for PD prediction, diagnosis and treatment.

Rubisco supplies pyruvate for the 2-C-methyl-D-erythritol-4-phosphate pathway.

RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (Rubisco) produces pyruvate in the chloroplast through β-elimination of the aci-carbanion intermediate1. Here we show that this side reaction supplies pyruvate for isoprenoid, fatty acid and branched-chain amino acid biosynthesis in photosynthetically active tissue. 13C labelling studies of intact Arabidopsis plants demonstrate that the total carbon commitment to pyruvate is too large for phosphoenolpyruvate to serve as a precursor. Low oxygen stimulates Rubisco carboxylase activity and increases pyruvate production and flux through the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway, which supplies the precursors for plastidic isoprenoid biosynthesis2,3. Metabolome analysis of mutants defective in phosphoenolpyruvate or pyruvate import and biochemical characterization of isolated chloroplasts further support Rubisco as the main source of pyruvate in chloroplasts. Seedlings incorporated exogenous,13C-labelled pyruvate into MEP pathway intermediates, while adult plants did not, underscoring the developmental transition in pyruvate sourcing. Rubisco β-elimination leading to pyruvate constituted 0.7% of the product profile in in vitro assays, which translates to 2% of the total carbon leaving the Calvin-Benson-Bassham cycle. These insights solve the "pyruvate paradox"4, improve the fit of metabolic models for central metabolism and connect the MEP pathway directly to carbon assimilation.

Transcriptional and genetic characteristic of chimera pea generation via double ethyl methanesulfonate-induced mutation revealed by transcription analysis.

Ethyl methanesulfonate (EMS)-induced mutagenesis is a prominent method for generating plant mutants, often resulting in chimera plants; however, their transcriptional and genetic characteristic remain elusive. In this investigation, chimera pea (Pisum sativum L.) specimens, labeled GY1 and GY2, exhibiting a distinctive phenotype with yellow and green leaves were meticulously cultivated via sequential double EMS mutagenesis. The observed color disparity between the yellow and green leaves was attributed to a significant reduction in chlorophyll content coupled with heightened lutein levels in both chimeric variants. Transcriptome profiling revealed the enrichment of differentially expressed genes in both GY1 and GY2, specifically implicating Kyoto Encyclopedia of Genes and Genomes pathways linked to amino acid biosynthesis and ribosome development, alongside Gene Ontology (GO) biological processes linked with stress response mechanisms. Few structural genes associated with chlorophyll and lutein biosynthesis exhibited discernible differential expression. Despite these functional similarities, distinctive nuances were evident between specimens, with GY1 exhibiting enrichment in GO pathways related to chloroplast development and GY2 showing enrichment for ribosome development pathways. Single-nucleotide polymorphism (SNP) analysis uncovered a shared pool of 599 and 598 polymorphisms in the yellow and green leaves of GY1 and GY2, respectively, likely stemming from the initial EMS mutagenesis step. Further investigation revealed an increased number of unique SNPs in the yellow leaves following the second EMS application, whereas the green leaves exhibited sparse and unique SNP occurrences, suggestive of potential evasion from secondary mutagenesis. This inherent genetic variability underpins the mechanism underlying the formation of chimera plants. Predominant base mutations induced by EMS were characterized by G/A and C/T transitions, constituting 74.1% of the total mutations, aligning with established EMS mutation induction paradigms. Notably, genes encoding the eukaryotic translation initiation factor eIIso4G and the ubiquitin ligase RKP, known to modulate leaf color in model plants, harbored two SNPs in the yellow leaves of both GY1 and GY2, implicating their putative role in the yellow leaf phenotype. Collectively, this study provides novel insights into the transcriptional and genetic characteristics of chimera plants via EMS-induced mutagenesis.

Structurally diverse phenylpropanoyl phloroglucinol derivatives from Mallotus philippensis and their anti-bacterial activities

Fifteen undescribed phenylpropanoyl phloroglucinol derivatives featuring modified isoprenyl and/or geranyl units (1–15), in conjunction with thirteen known analogues (16–28), were obtained from the glandular hairs of the fruit of Mallotus philippensis. Meanwhile, fourteen pairs of new enantiomers [(±)-1–9, (±)-11–15] were further resolved by chiral purification. Their structures were determined by comprehensive spectroscopic analyses, single-crystal X-ray diffraction experiments and quantum chemical calculations. Bioactivity evaluation showed that compound 17 exhibited significant anti-bacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) with MIC of 6 μg/mL, while compounds 3, 4, 8 and 18 displayed moderate effects with MIC of 24, 12, 24, and 12 μg/mL, respectively. The KEGG enrichment analysis of 17 revealed that the phosphotransferase system (PTS) pathway was significantly enriched. In addition, compound 17 was found to affect the amino acids biosynthesis and amino acids/carbohydrate metabolism, and the qRT-PCR verified the accuracy of the transcriptome analysis.

Transcriptome and Metabolome Analyses Reveal the Molecular Mechanisms of Albizia odoratissima’s Response to Drought Stress

Albizia odoratissima is a deciduous tree species belonging to the family Leguminosae. It is widely distributed in the southern subtropical and tropical areas of China and has important ecological and economic value. The growth and metabolic processes of A. odoratissima are affected by drought stress, but the molecular mechanisms remain unknown. Therefore, this study investigated the physicochemical properties, gene expression, and metabolites of A. odoratissima seedlings under drought stress. The results show that, in leaves of A. odoratissima seedlings, drought stress reduced the moisture content, chlorophyll content, photosynthetic efficiency, superoxide dismutase (SOD) activity, and gibberellin (GA) and indoleacetic acid (IAA) contents while increasing the catalase (CAT) and peroxidase (POD) activities and malondialdehyde (MDA), proline, soluble sugar, and soluble protein contents. Within the CK5 (Day 5 of control group) vs. T5 (Day 5 of drought treatment), CK10 vs. T10, CK15 vs. T15, and CK20 vs. T20 groups (CK: control group; T: drought treatment), a total of 676 differentially expressed genes (DEGs) were upregulated and 518 DEGs were downregulated, and a total of 228 and 143 differential accumulation metabolites (DAMs) were identified in the CK10 vs. T10 and CK20 vs. T20 groups. These were mainly involved in the amino acid and alkaloid metabolism pathways in the leaves of the A. odoratissima seedlings. In the amino acid and alkaloid biosynthesis pathways, the relative expression levels of the AoproA (Aod04G002740, ORTHODONTIC APPLIANCE), AoOAT (Aod07G015970, ORNITHINE-OXO-ACID TRANSAMINASE), and AoAOC3 (Aod12G005010/08G003360/05G023920/08G003000/08G003010, AMINE OXIDASE COPPER CONTAINING 3) genes increased, which concurrently promoted the accumulation of arginine, proline, piperine, cadaverine, and lysine. Furthermore, some key transcription factors in the response to drought were identified in the leaves using the weighted gene co-expression network analyses (WGCNA) method. These findings reveal that A. odoratissima seedlings respond to drought stress by improving the capacities of the antioxidant system and secondary metabolism.

Physiological and proteomic responses of Posidonia oceanica to phytotoxins of invasive Caulerpa species

The invasive green algae Caulerpa taxifolia (M. Vahl) C. Agardh, 1817 and Caulerpa cylindracea Sonder, 1845 are widely diffused in the Mediterranean Sea, where they compete for space with the endemic seagrass Posidonia oceanica (Linnaeus) Delile, 1813, a keystone species in Mediterranean marine biodiversity. The present study aims to explore the possible effects of bioactive metabolites from the invasive algae on the seagrass, which may imply an allelopathic action. In particular, the study focuses on the effects of the algal alkaloid caulerpin and the sesquiterpene caulerpenyne. Changes in leaf growth, chlorophyll content, and leaf protein expression of P. oceanica genets under treatments were evaluated after 28 days of cultivation in mesocosms. Caulerpenyne strongly inhibited the growth of adult leaves and the formation of new ones, while inducing the elongation of the intermediate leaves and increased total chlorophyll content; on the contrary, caulerpin did not significantly influence leaf growth and the formation of new ones. A total of 107 differentially accumulated proteins common to the two treatments were also identified using the proteomic approach. Both molecules induced cells to maintain homeostasis, enhancing the amino acid metabolism or fatty acid biosynthesis. Despite these disruptions, P. oceanica demonstrated a more efficient response to stress induced by caulerpin, stimulating the biosynthesis of essential amino acids to maintain cellular homeostasis and mitigate damage caused by reactive oxygen species (ROS). Overall, obtained results supports the possible role of caulerpenyne, and not caulerpin, as an effector in allelopathic interactions among invasive Caulerpa species and P. oceanica in the Mediterranean.

Transcriptomic and Metabolomic Profiling of Root Tissue in Drought-Tolerant and Drought-Susceptible Wheat Genotypes in Response to Water Stress.

Wheat is the most widely grown crop in the world; its production is severely disrupted by increasing water deficit. Plant roots play a crucial role in the uptake of water and perception and transduction of water deficit signals. In the past decade, the mechanisms of drought tolerance have been frequently reported; however, the transcriptome and metabolome regulatory network of root responses to water stress has not been fully understood in wheat. In this study, the global transcriptomic and metabolomics profiles were employed to investigate the mechanisms of roots responding to water stresses using the drought-tolerant (DT) and drought-susceptible (DS) wheat genotypes. The results showed that compared with the control group, wheat roots exposed to polyethylene glycol (PEG) had 25941 differentially expressed genes (DEGs) and more upregulated genes were found in DT (8610) than DS (7141). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs of the drought-tolerant genotype were preferably enriched in the flavonoid biosynthetic process, anthocyanin biosynthesis and suberin biosynthesis. The integrated analysis of the transcriptome and metabolome showed that in DT, the KEGG pathways, including flavonoid biosynthesis and arginine and proline metabolism, were shared by differentially accumulated metabolites (DAMs) and DEGs at 6 h after treatment (HAT) and pathways including alanine, aspartate, glutamate metabolism and carbon metabolism were shared at 48 HAT, while in DS, the KEGG pathways shared by DAMs and DEGs only included arginine and proline metabolism at 6 HAT and the biosynthesis of amino acids at 48 HAT. Our results suggest that the drought-tolerant genotype may relieve the drought stress by producing more ROS scavengers, osmoprotectants, energy and larger roots. Interestingly, hormone signaling plays an important role in promoting the development of larger roots and a higher capability to absorb and transport water in drought-tolerant genotypes.

A novel effect of sulforaphane on promoting mouse granulosa cells proliferation via the NRF2–TKT pathway

IntroductionGranulosa cells (GCs) is essential for maintaining follicular development. Follicle-stimulating Hormone (FSH) has been demonstrated to effectively promote GCs proliferation, driving the establishment of various superovulation techniques for animal husbandry. However, these techniques face challenges, such as high costs, hormonal imbalances, and an increased risk of early ovarian dysfunction. Therefore, it is important to investigate new methods to improve GCs proliferation. ObjectivesThis study aimed to investigate the effect of sulforaphane (SFN) on ovarian GCs proliferation and the underlying mechanisms. MethodsA comparative transcriptomic analysis of ovaries from the control, SFN, and FSH groups was conducted to identify the primary factors contributing to high proliferative capacity. The role of SFN in the regulation of cell proliferation has been examined in mouse ovarian GCs. Gene interference, overexpression, CUT&TAG technology, and transcriptome analyses were performed to elucidate the underlying mechanisms of the nuclear factor E2-related factor 2 (NRF2)–transketolase (TKT) axis in mediating GCs proliferation. ResultsOur research revealed a previously unknown function of SFN, an isothiocyanate of plant origin that is prevalent in cruciferous vegetables, in facilitating the proliferation of mouse ovarian GCs. The efficacy of SFN in enhancing GCs proliferation is similar to that of FSH. At the mechanistic level, SFN promotes NRF2 to transport to the nucleus, which subsequently activates the key enzyme of the non-oxidative pentose phosphate pathway TKT. This activation is instrumental in generating ribose 5-phosphate, a critical precursor for amino acid and nucleotide biosynthesis that underpins the proliferation of GCs. ConclusionCollectively, our findings delineate a novel pathway by which SFN, through the NRF2-TKT axis, enhances the nucleotide pool and thereby supports the proliferation of mouse GCs, presenting novel avenues for exploration in reproductive biology and agricultural sciences.

Thymus algeriensis essential oil: Phytochemical investigation, bactericidal activity, synergistic effect with colistin, molecular docking, and dynamics analysis against Gram-negative bacteria resistant to colistin

Due to the increasing resistance prevalence to the last line of antibiotics, such as colistin, and the rising threat of multi-drug resistant bacteria, it is crucial to find alternative therapeutic options. The current study focuses on evaluating antibacterial activities alone and in combination with colistin of Thymus algeriensis essential oil (TA-EO) against colistin-resistant Klebsiella pneumoniae, Pseudomonas aeruginosa, and Escherichia coli co-harboring mcr-1 gene. GC/MS was used to determine the chemical composition of TA-EO. Disc diffusion and microdilution techniques were used to evaluate the antimicrobial activities of TA-EO. Synergism between colistin and TA-EO was evaluated by checkerboard assay. The major compounds of TA-EO were docked with known enzymes involved in resistance to colistin, as well as the biosynthesis of peptidoglycan and amino acids. GC/MS revealed that TA-EO was of carvacrol chemotype (67.94 %). The TA-EO showed remarkable antibacterial activities against all Gram-negative bacterial strains, with the diameter of inhibition zones varied between 30 and 50 mm and a ratio MBC/MIC equal to 1 for the vast majority of bacterial isolates. Interestingly, the checkerboard showed synergism between TA-EO and colistin against colistin-resistant Escherichia coli co-harboring mcr-1 gene (FICI˂1) and reduced the MIC of colistin by 16- to 512-fold and those of TA-EO by 4- to 16-fold. The docking study demonstrated that carvacrol had high binding free energies against MCR-1, a phosphoethanolamine transferase extracellular domain, and its catalytic domain implicated in resistance to colistin, and undecaprenyl pyrophosphate synthase in complex with magnesium which is involved in bacterial peptidoglycan biosynthesis. The molecular dynamics study for 100-ns also revealed the stability of the MCR-1/carvacrol complex with a constant surface area over the simulation. These results support using carvacrol or TA-EO as a bactericidal agent, either alone or in combination with colistin, to treat infections caused by colistin-resistant Gram-negative bacteria.

Transcriptomic and proteomic analysis of resistance to matrine in Oedaleus asiaticus (Orthoptera: Oedipodidae)

In order to determine the specific genes and proteins that are affected by matrine and play a role in regulating metabolism in the locust species Oedaleus asiaticus, we conducted RNA-seq, proteomic sequencing, and bioinformatics analyses on third-instar nymphs. These nymphs were divided into two groups: one group was grown under normal conditions, while the other group was treated with matrine. The purpose of this investigation was to gain insight into the molecular mechanisms underlying matrine resistance. Genes and proteins that exhibited differential expression were identified and subjected to analysis using bioinformatics software. The DESeq analysis revealed a total of 743 transcripts that were differentially expressed (DETs). Among these, 208 transcripts were up-regulated, and 535 were downregulated in ZO/ZCK. The iTRAQ discovered that 34 and 65 proteins were, respectively, up- and down-regulated in ZO/ZCK. Additionally, enrichment studies based on Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed. The KEGG and GO analysis of the DEGs suggested the essential roles of matrine treatment in the regulation of O. asiaticus, especially via the biosynthesis of amino acids, glycolysis/gluconeogenesis, iInsulin signaling pathway and MAPK signaling pathway. The findings demonstrated that matrine exerted control of the growth of O. asiaticus via modulating the synthesis of metabolism and biosynthesis. Increased expression of detoxifying enzymes was observed, which may be related to matrine detoxification. These findings provide a basis for better comprehension of the molecular mechanism behind the regulation of development mediated by matrine in Asian locust hoppers.

Integrated miRNA and mRNA Transcriptome Analysis Reveals Regulatory Mechanisms in the Response of Winter Brassica rapa to Drought Stress.

Drought is a major abiotic stress factor that reduces agricultural productivity. Understanding the molecular regulatory network of drought response in winter rape is of great significance for molecular Brassica rapa. In order to comprehensively analyze the network expression of DEGs and DEMIs in winter rape under drought stress, in this study we used Longyou 7 as the experimental material to identify DEGs and DEMIs related to drought stress by transcriptome and miRNA sequencing. A total of 14-15 key differential mRNA genes related to drought stress and biological stress were screened out under different treatments in the three groups. and 32 differential miRNAs were identified through targeted regulatory relationships, and the mRNA expression of 20 target genes was negatively regulated by the targeting regulatory relationship. It is mainly enriched in starch and sucrose metabolism, carbon metabolism and other pathways. Among them, gra-MIR8731-p3_2ss13GA18GA regulated the expression of multiple mRNAs in the three treatments. miRNA is mainly involved in the drought resistance of Chinese cabbage winter rape by regulating the expression of target genes, such as starch and sucrose metabolism, amino acid biosynthesis, and carbon metabolism. These miRNAs and their target genes play an indispensable role in winter rapeseed drought stress tolerance regulation.