Metabolism Biosynthesis Research Articles

Dissection of genetic architecture for desirable traits in sugarcane by integrated transcriptomics and metabolomics

Sugarcane is an important sugar and energy crop. Breeding varieties with high yield and sugar, strong stress tolerance, as well as beneficial for mechanized harvesting are the goal of sugarcane breeder. In the present study, transcriptomics and metabolomics were conducted to explore the molecular basis for outstanding performance of five elite varieties GT42, GT44, LC05-136, YZ08-1609, and YZ05-51, along with the cross-parent CP72-1210 compared to ROC22. Transcriptomics revealed a total of 18,353 differentially expressed genes (DEGs) and several regulatory pathways, including carbon fixation, starch and sucrose metabolism, phenylpropanoids biosynthesis, flavonoid biosynthesis, cysteine and methionine metabolism, as well as zeatin biosynthesis. Expression patterns of genes involved in these pathways confirmed their role in determining the agronomic traits. Besides, metabolomics disclosed 175 differentially accumulated metabolites (DAMs), including specific metabolites of amino acids and secondary metabolites. Furthermore, conjoint analysis of transcriptomics and metabolomics highlighted the manipulation of 113 genes led to changed levels of 20 metabolites associated with carbon fixation, sucrose accumulation, phytohormone response and secondary metabolism. Finally, we depicted here a blueprint outlining the genetic basis underlying the desirable traits in sugarcane. This study will accelerate the dissection of the molecular basis for sugarcane traits and provide targets for molecular breeding.

Natural High Strontium Mineral Water Might Reduce Liver Protein Synthesis: A Non-Targeted Metabolomics Study in Rats.

Strontium-rich mineral water (strontium > 0.20mg/L) is the second largest type of mineral water on commercial drinking water market. Exposure to high levels of strontium through drinking water or soil may interfere with calcium metabolism and increase the risk of cardiovascular and skeletal diseases, but no in-depth mechanism has been disclosed to date. Data on liver metabolic alterations in rats resulted from drinking natural high strontium mineral water (strontium 26.06mg/L, SrHW) or tap water (filtered by activated carbon, strontium 0.49mg/L, TW) for 3months were obtained and analyzed with non-targeted metabolomics strategy. Compared with rats drinking TW, those drinking SrHW showed a significant change in 36 liver metabolites. Among them, 33 liver metabolites (including 14 amino acids, 6 carbohydrates, 4 short-chain fatty acids, 4 organic acids, 2 phenylpropanoic acids, 1 fatty acid, 1 peptide, and 1 bile acid) were down-regulated, and 3 (hydroxyphenyllactic acid, propionylcarnitine and S-adenosine homocysteine) were up-regulated. Metabolic pathway analysis showed that aminoacyl-tRNA biosynthesis, valine, leucine and isoleucine biosynthesis, and alanine, aspartate and glutamate metabolism are most impacted. Furthermore, the serum prealbumin content also significantly decreased in rats drinking SrHW. Therefore, changes in liver metabolites and serum protein levels suggested that high concentration of strontium in water was associated with decreased liver protein synthesis; changes in liver metabolites suggested that high strontium was associated with decreased lipid levels. In conclusion, high strontium in water may exert a negative effect on protein synthesis, and further study on the dose-response relationship is necessary.

Whole-Genome Bisulfite Sequencing (WGBS) Analysis of Gossypium hirsutum under High-Temperature Stress Conditions

Background: DNA methylation is an important part of epigenetic regulation and plays an important role in the response of plants to adverse stress. Methods: In this study, whole-genome bisulfite sequencing (WGBS) was performed on the high-temperature-resistant material Xinluzao 36 and the high-temperature-sensitive material Che 61–72 at 0 h and 12 h under high-temperature stress conditions. Results: The results revealed that the Gossypium hirsutum methylation levels of CG and CHG (H = A, C, or T) decreased after the high-temperature stress treatment, and the methylation level of the A subgenome was significantly greater than that of the D subgenome. The methylation level of CHH increased, and the methylation level of CHH in the D subgenome was significantly greater than that in the A subgenome after high-temperature stress treatment. The methylation density of CG is lower than that of CHG and CHH, and the methylation density of the middle region of chromosomes is greater than that of both ends, which is opposite to the distribution density of genes. There were 124 common differentially methylated genes in the CG, CHG, and CHH groups, and 5130 common DEGs and differentially methylated genes were found via joint analysis with RNA-seq; these genes were significantly enriched in the biosynthesis of plant hormones, thiamine metabolism, glutathione metabolism, and tyrosine metabolism pathways. DNA methylation did not affect the expression of many genes (accounting for 85.68% of the differentially methylated genes), DNA methylation-promoted gene expression was located mainly in the downstream region of the gene or gene body, and the expression of inhibitory genes was located mainly in the upstream region of the gene. Conclusions: This study provides a theoretical basis for further exploration of the gene expression and functional regulatory mechanism of G. hirsutum DNA methylation under high-temperature stress conditions.

Targeted metabolomics of muscle amino acid profles and hepatic transcriptomics analyses in grass carp (Ctenopharyngodon idellus) fed with broad beans

While tissue amino acid compositions reflect that of the dietary protein source, and the liver orchestrates amino acid metabolism. In this study, we investigated the muscle amino acid profiles in ordinary and crisp grass carp. The 22 amino acids were measured, and seventeen showed significant concentration differences. To understand the molecular mechanisms behind changes, we analyzed the liver transcriptome, and the 2519 differentially expressed genes (DEGs) were identified, with 1156 up-regulated and 1363 down-regulated genes. DEGs were enriched in ribosome-related biological processes. KEGG pathway analysis showed enrichment in tryptophan metabolism, lysine degradation, valine, leucine and isoleucine degradation, galactose metabolism, and glutathione metabolism with up-regulated genes, arginine and proline metabolism, arginine biosynthesis and alanine, aspartate, amino sugar and nucleotide sugar metabolism, N-Glycan biosynthesis and glutamate metabolism with down-regulated genes. A protein-protein interaction network with 260 nodes and 249 edges was constructed, and 3 modules were extracted. The top 10 hub genes with close connections to other nodes were ITM1, STT3B, SEL1L, UGGT1, MLEC, IL1B, ALG5, KRTCAP2, NFKB2, and IRAK3. In summary, this study identified candidate genes and focused on amino acid and glycan metabolism pathways, providing a reference for further investigation into liver amino acid metabolism in grass carp fed with broad beans.

RCC1 regulation of subcellular protein localization via Ran GTPase drives pancreatic ductal adenocarcinoma growth

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy, with limited therapeutic options. Here, we evaluated the role of regulator of chromosome condensation 1 (RCC1) in PDAC. RCC1 functions as a guanine exchange factor for GTP-binding nuclear protein Ran (Ran) GTPase and is involved in nucleocytoplasmic transport. RCC1 RNA expression is elevated in PDAC tissues compared to normal pancreatic tissues and correlates with poor prognosis. RCC1 silencing by RNAi and CRISPR-Cas9 knockout (KO) results in reduced proliferation in 2-D and 3-D cell cultures. RCC1 knockdown (KD) reduced migration and clonogenicity, enhanced apoptosis, and altered cell cycle progression in human PDAC and murine cells from LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx1-Cre (KPC) tumors. Mechanistically, RCC1 KO shows widespread transcriptomic alterations including regulation of PTK7, a co-receptor of the Wnt signaling pathway. RCC1 KD disrupted subcellular Ran localization and the Ran gradient. Nuclear and cytosolic proteomics revealed altered subcellular proteome localization in Rcc1 KD KPC-tumor-derived cells and several altered metabolic biosynthesis pathways. In vivo, RCC1 KO cells show reduced tumor growth potential when injected as sub-cutaneous xenografts. Finally, RCC1 KD sensitized PDAC cells to gemcitabine chemotherapy treatment. This study reveals the role of RCC1 in pancreatic cancer as a novel molecular vulnerability that could be exploited to enhance therapeutic response.

Environmentally Relevant Concentrations of S-6PPD-Quinone Caused More Serious Hepatotoxicity Than R-Enantiomer and Racemate in Oncorhynchus mykiss.

6PPD-quinone (6PPD-Q) is frequently detected in various environmental media, and the environmentally relevant concentrations can be fatal to Oncorhynchus mykiss. Notably, 6PPD-Q has two enantiomers (S-6PPD-Q and R-6PPD-Q). In this study, O. mykiss was separately exposed to each enantiomer and racemate of 6PPD-Q for 96 h at environmentally relevant concentrations, and livers were collected. Effects on the biochemical, pathological, and ultrastructural changes were assessed, and metabolomics was conducted to elucidate the potential hepatotoxicity mechanism. Compared with the control treatment, the levels of catalase (CAT, all treatments except for 0.1 μg/L rac-6PPD-Q), and glutathione-S-transferase (GST, all treatments) significantly declined. Hepatocyte space became smaller, nuclear morphology changed, and nucleolysis occurred. Mitochondrial malformation and vesicle-like structure dilation of the endoplasmic reticulum (ER) were observed in the hepatocytes, which was most serious after S-6PPD-Q exposure. Some amino acid metabolism, folate biosynthesis, taurine and hypotaurine metabolism and purine metabolism were disturbed, consistent with mitochondrial dysfunction and ER stress. The differential metabolites were in the order of S-6PPD-Q (216) > rac-6PPD-Q (88) > R-6PPD-Q (56). Thus, 6PPD-Q-induced hepatic mitochondrial dysfunction and ER stress, causing metabolic disturbance and oxidative stress might be the toxic mechanism of 6PPD-Q in O. mykiss liver, and S-6PPD-Q effects were the most serious.

Transcriptomic and metabolomic investigations of methyl jasmonate-mediated enhancement of low temperature stress resistance in Cassia obtusifolia L.

Low temperature stress negatively impacts plant growth and development, reducing crop yields by disrupting metabolite production and accumulation. Cassia obtusifolia L., a widely cultivated medicinal plant in subtropical regions, is particularly vulnerable to such stress. Methyl jasmonate (MeJA) regulates plant growth, defense mechanisms, and secondary metabolite production. This study investigated how C. obtusifolia responds to low temperature stress under MeJA treatment using transcriptomic and metabolomic approaches. MeJA treatment upregulated several transcription factor families, including APE/ERF-ERF, WRKY, NAC, and MYB-related, which modulated the plant's response to cold stress. These transcription factors influenced the expression of genes involved in glycolysis, sugar metabolism, and amino acid pathways, contributing to the plant's adaptive responses. Differentially expressed genes were associated with key metabolic processes such as flavonoid biosynthesis, ribosome function, glycolysis/gluconeogenesis, and sugar metabolism. Using H-NMR and LC-MS techniques, we observed that MeJA induced the accumulation of sugars and amino acids in the leaves of C. obtusifolia seedlings under cold stress, while levels of three flavonoid compounds Isoliquiritigenin, Kaempferol-7-O-glucoside, and Phloretin significantly decreased. Enrichment analysis indicated that MeJA modulates the biosynthetic pathways of these compounds in a dose-dependent manner. Integrating metabolomic and transcriptomic data further elucidated alterations in the flavonoid biosynthetic network and other metabolic pathways under low temperature stress. These findings offer insights into the molecular mechanisms underlying flavonoid synthesis and other metabolic adjustments in C. obtusifolia under MeJA treatment.

Metabolic Response in the Gill Tissue of Juvenile Black-Shelled Pearl Oyster (Pinctada fucata martensii) under Salinity Stress

Salinity significantly affects shellfish metabolism and growth. In this study, we evaluated the characterization of metabolomic differences in the juvenile black-shelled pearl oyster, Pinctada fucata martensii, under 15‰ (LSG), 25‰ (CG), and 35‰ (HSG) salinity conditions. Non-targeted metabolomics analyses revealed that salinity stress altered the metabolism of pearl oyster. A total of 229 significant differential metabolites (SDMs) were identified between LSG and CG via an in-house MS2 database, 241 SDMs were identified between LSG and HSG, and 50 SDMs were identified between CG and HSG. The pathway analysis showed that 21 metabolic pathways were found between LSG and CG, such as arginine and proline metabolism, glycerophospholipid metabolism, and pentose and glucuronide interconversion. A total of 23 metabolic pathways were obtained between LSG and HSG, such as aspartate, alanine, and glutamate metabolism. Only aminoacyl-tRNA biosynthesis, cysteine and methionine metabolism, and biotin metabolism were enriched between CG and HSG. A further integrated analysis suggested that amino acid metabolism might participate in osmoregulation and energy metabolism to respond to salinity stress in P. f. martensii, and the metabolic pathways differed under varying salinity stress conditions. In addition, low salinity stress might promote apoptosis in pearl oysters. Altogether, these results clarify the salinity tolerance mechanism of pearl oysters.

GC–MS metabolomics of French lettuce (Lactuca Sativa L. var capitata) leaves exposed to bisphenol A via the hydroponic media

IntroductionBisphenol A (BPA), an organic compound used to produce polycarbonate plastics and epoxy resins, has become a ubiquitous contaminant due to its high-volume production and constant release to the environment. Plant metabolomics can trace the stress effects induced by environmental contaminants to the variation of specific metabolites, making it an alternative way to study pollutants toxicity to plants. Nevertheless, there is an important knowledge gap in metabolomics applications in this area.ObjectiveEvaluate the influence of BPA in French lettuce (Lactuca Sativa L. var capitata) leaves metabolic profile by gas chromatography coupled to mass spectrometry (GC–MS) using a hydroponic system.MethodsLettuces were cultivated in the laboratory to minimize biological variation and were analyzed 55 days after sowing (considered the plant’s adult stage). Hexanoic and methanolic extracts with and without derivatization were prepared for each sample and analyzed by GC–MS.ResultsThe highest number of metabolites was obtained from the hexanoic extract, followed by the derivatized methanolic extract. Although no physical differences were observed between control and contaminated lettuce leaves, the multivariate analysis determined a statistically significant difference between their metabolic profiles. Pathway analysis of the most affected metabolites showed that galactose metabolism, starch and fructose metabolism and steroid biosynthesis were significantly affected by BPA exposure.ConclusionsThe preparation of different extracts from the same sample permitted the determination of metabolites with different physicochemical properties. BPA alters the leaves energy and membrane metabolism, plant growth could be affected at higher concentrations and exposition times.

Antimicrobial properties of essential oil extracted from Schizonepeta annua against methicillin-resistant Staphylococcus aureus via membrane disruption

Schizonepeta annua (Pall.) Schischk. has long been traditionally employed in China for its anti-inflammatory, antimicrobial, and soothing properties. This study evaluates the antibacterial properties of essential oil extracted from Schizonepeta annua (SEO) and oregano (OEO) against methicillin-resistant Staphylococcus aureus (MRSA). SEO and OEO demonstrated substantial antibacterial efficacy, with SEO exhibiting significantly enhanced antibacterial activity due to its complex composition. Mechanistic investigations revealed that both essential oils disrupt bacterial membrane integrity and biosynthetic pathways, leading to the extrusion of intracellular contents. Metabolomic analyses using GC-Q-TOF-MS highlighted SEO's selective targeting of bacterial membranes, while non-targeted metabolomics indicated significant effects on MRSA's amino acid metabolism and aminoacyl-tRNA biosynthesis. These findings suggest that SEO causes considerable damage to MRSA cell membranes and affects amino acid metabolism, supporting its traditional use and highlighting its potential in treating infections. Our results offer robust theoretical support for SEO's role as an antimicrobial agent and establish a solid foundation for its practical application in combating multidrug-resistant infections.

Serum metabolism-transcriptomics investigated into the immunity of whey protein isolate-galacto-oligosaccharide conjugates after dynamic high-pressure microfluidics pretreatment

The objective of this study was to investigate the immunomodulatory effects of whey protein isolate (WPI)-galacto-oligosaccharide conjugates following dynamic high-pressure microfluidics pretreatment (DHPM) in cyclophosphamide-induced immunosuppressed mice. DHPM facilitated the conjugation of WPI and galacto-oligosaccharide, and inhibited the generation of fluorescent advanced glycation end products (AGEs) and pentosidine. The conjugates demonstrated a significant immune recovery effect on CTX-induced immunosuppressed mice, as evidenced by the enhancement of IgG antibody levels (from 3.5 to 4.1) and the reduction of the levels of immunosuppressive effector factors TGF-β (from 148.1 to 111.2) and IFN-γ (from 34.4 to 17.9). Furthermore, the conjugates exhibited a notable ability to repair histological lesion in the spleen of CTX-induced immunosuppressed mice. Spleen transcriptomics revealed that the Marco, Klrc3 and Cd209b genes were associated with the immune enhancement activity of the conjugates. Metabolomic analysis identified arginine biosynthesis, sphingolipid metabolism, alanine, aspartate and glutamate metabolism, and phenylalanine, tyrosine and tryptophan biosynthesis as key pathways in the immune enhancement activity of the conjugates. Metabolomics combined with transcriptomics indicated the importance of macrophage activation in the restoration of immunosuppressed mice’s immunity by the conjugates. Therefore, the improvement in immunity observed with WPI-galacto-oligosaccharide conjugates may be related to the activation of macrophages.

Longitudinal changes of serum metabolomic profile after laparoscopic sleeve gastrectomy in obesity.

Bariatric surgery induces significant weight loss, increases insulin sensitivity, and improves dyslipidemia. As one of the most widely performed bariatric surgeries, laparoscopic sleeve gastrectomy (LSG) is thought to improve the metabolic profile along with weight loss. The objective of this study was to evaluate longitudinal changes in the serum metabolite levels after LSG and elucidate the underlying mechanisms of metabolic improvement. Clinical metabolic parameters and serum samples were collected preoperatively and at 1, 3, and 6 months postoperatively from nine patients with obesity undergoing LSG. Serum metabolites were measured using a non-targeted metabolic liquid chromatography-mass spectrometry method. During the 1, 3, and 6 months postoperative follow-up, the body mass index, HOMA-IR, and liver fat content showed a gradual descending trend. A total of 328 serum metabolites were detected, and 38 were differentially expressed. The up-regulated metabolites were mainly enriched in ketone body metabolism, alpha-linolenic acid and linoleic acid metabolism, pantothenate and CoA biosynthesis, glycerolipid metabolism, and fructose and mannose degradation, while the down-regulated metabolites were closely related to caffeine metabolism, oxidation of branched-chain fatty acids, glutamate metabolism, and homocysteine degradation. Notably, nine metabolites (oxoglutarate, 2-ketobutyric acid, succinic acid semialdehyde, phthalic acid, pantetheine, eicosapentaenoate, 3-hydroxybutanoate, oxamic acid, and dihydroxyfumarate) showed persistent differential expression at 1, 3, and 6 months follow-up. Some were found to be significantly associated with weight loss, insulin resistance improvement, and liver fat content reduction. This finding may provide a new perspective for revealing novel biomarkers and mechanisms of metabolic improvement in obesity and related comorbidities.

Integrative transcriptome and metabolome analysis reveals the mechanism of fulvic acid alleviating drought stress in oat.

Drought stress inhibits oat growth and yield. The application of fulvic acid (FA) can improve the drought resistance of oats, but the corresponding molecular mechanism of FA-mediated drought resistance remains unclear. Here, we studied the effects of FA on the drought tolerance of oat leaves through physiological, transcriptomic, and metabolomics analyses, and identified FA-induced genes and metabolites related to drought tolerance. Physiological analysis showed that under drought stress, FA increased the relative water and chlorophyll contents of oat leaves, enhanced the activity of antioxidant enzymes (SOD, POD, PAL, CAT and 4CL), inhibited the accumulation of malondialdehyde (MDA), hydrogen peroxide (H2O2) and dehydroascorbic acid (DHA), reduced the degree of oxidative damage in oat leaves, improved the drought resistance of oats, and promoted the growth of oat plants. Transcriptome and metabolite analyses revealed 652 differentially expressed genes (DEGs) and 571 differentially expressed metabolites (DEMs) in FA-treated oat leaves under drought stress. These DEGs and DEMs are involved in a variety of biological processes, such as phenylspropanoid biosynthesis and glutathione metabolism pathways. Additionally, FA may be involved in regulating the role of DEGs and DEMs in phenylpropanoid biosynthesis and glutathione metabolism under drought stress. In conclusion, our results suggest that FA promotes oat growth under drought stress by attenuating membrane lipid peroxidation and regulating the antioxidant system, phenylpropanoid biosynthesis, and glutathione metabolism pathways in oat leaves. This study provides new insights into the complex mechanisms by which FA improves drought tolerance in crops.

Molecular and physiological mechanisms of aging are distinct in the cardiac right and left ventricles

AbstractAging is the primary risk factor for heart disease, the leading global cause of death. Right ventricular (RV) function predicts survival in several age‐related clinical contexts, yet no therapies directly improve RV function, in large part due to a poor mechanistic understanding of RV aging and how it is distinct from the widely studied left ventricle (LV). To address this gap, we comprehensively quantified RV functional and morphological remodeling with age. We further aimed to identify molecular mechanisms of RV aging thus we performed RNAseq on RV and LV from male and female young (4 months) and aged (19–21 months) C57BL6 mice. Contrary to the concentric hypertrophic remodeling and diastolic dysfunction that occurs in the LV, the aging RV underwent eccentric remodeling with significant dilation and impaired systolic function. Transcriptomic data were also consistent with ventricle‐specific aging, with few genes (13%) similarly shared between ventricles with aging. KEGG analysis identified shared aging genes in inflammatory and immune cell pathways that were confirmed by flow cytometry that demonstrated higher percent of GR1+ myeloid cells in both ventricles. Unique RV aging genes enriched in the biosynthesis of saturated fatty acids, PPAR signaling, and butanoate metabolism, and we identified putative novel RV‐specific aging genes. Together, we suggest that the RV and LV are unique cardiac chambers that undergo distinct remodeling with age. These robust differences may explain why therapies designed from LV‐based studies fail to improve RV function and suggest that future efforts emphasizing ventricular differences may elucidate new therapies for healthy cardiac aging.

Transcriptome analysis of inflorescence embryogenesis in Festuca Glauca

In this study, RNA-seq was employed for transcriptome sequencing at four developmental stages of normal (L) and embryogenic (X) Festuca glauca ‘Elijah Blue’ inflorescences to analyze and identify the metabolic pathways and regulatory genes associated with inflorescence embryogenesis, thereby facilitating the understanding of the molecular mechanisms of inflorescence embryogenesis in Festuca glauca. The results revealed a total of 50,733 differentially expressed genes (DEGs) between the control (L) and embryogenic (X) samples at different developmental stages. Among them, 19,640 (38.71 %) were upregulated and 31,093 (61.29 %) were downregulated. A total of 2585 DEGs were expressed in both stage 1 (L1-vs-X1) and stage 4 (L4-vs-X4). Gene Ontology (GO) analysis revealed that the DEGs in these stages were mainly enriched in processes related to photosynthetic membranes, chloroplasts, activity of DNA-binding transcription factors, components of ribosomal structure, reactions involving oxidized compounds, and photosynthesis; while Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the DEGs in these stages were mainly enriched in pathways such as plant-pathogen interactions, plant hormone signal transduction, phenylpropanoid biosynthesis, ribosomes, and galactose metabolism. The top families containing differentially expressed transcription factors (DETFs) in these stages included ERF, bHLH, MYB-related, NAC, and WRKY. A total of 39 and 29 DETFs associated with embryogenesis were identified in the L1-vs-X1 and L4-vs-X4 stages, respectively. Additionally, 79 and 110 embryogenesis-related genes were identified in the plant hormone signal transduction metabolic pathway in the L1-vs-X1 and L4-vs-X4 stages, respectively.

Comparative Metabolomics Reveals Changes in the Metabolic Pathways of Ampicillin- and Gentamicin-Resistant Staphylococcus aureus.

Antibiotic resistance is a major global challenge requiring new treatments and a better understanding of the bacterial resistance mechanisms. In this study, we compared ampicillin-resistant (R-AMP) and gentamicin-resistant (R-GEN) Staphylococcus aureus strains with a sensitive strain (ATCC6538) using metabolomics. We identified 109 metabolites; 28 or 31 metabolites in R-AMP or R-GEN differed from those in ATCC6538. Moreover, R-AMP and R-GEN were enriched in five and four pathways, respectively. R-AMP showed significantly up-regulated amino acid metabolism and down-regulated energy metabolism, whereas R-GEN exhibited an overall decrease in metabolism, including carbohydrate, energy, and amino acid metabolism. Furthermore, the activities of the metabolism-related enzymes pyruvate dehydrogenase and TCA cycle dehydrogenases were inhibited in antibiotic-resistant bacteria. Significant decreases in NADH and ATP levels were also observed. In addition, the arginine biosynthesis pathway, which is related to nitric oxide (NO) production, was enriched in both antibiotic-resistant strains. Enhanced NO synthase activity in S. aureus promoted NO production, which further reduced reactive oxygen species, mediating the development of bacterial resistance to ampicillin and gentamicin. This study reveals that bacterial resistance affects metabolic profile, and changes in energy metabolism and arginine biosynthesis are important factors leading to drug resistance in S. aureus.

Impact of camptothecin exposures on the development and larval midgut metabolomic profiles of Spodoptera frugiperda

Spodoptera frugiperda is an economic agricultural pest that has invaded many countries around the world and caused huge losses in grain production. Camptothecin (CPT) is one of the botanical compounds with insecticidal activity and has the potential for pest control. However, the effects of CPT on development and metabolism of S. frugiperda remain unknown. In this study, we have investigated the adverse effects of 1.0 and 5.0 mg/kg CPT exposures on the growth and development of S. frugiperda. Our results found that 1.0 and 5.0 mg/kg CPT treatments altered the parameters of the life cycle, including inducing larval mortality, altering the weight of larvae, pupae, and adults, the larval duration, and decreasing the pupation rate and emergence rate. In addition, comparative metabolomics analysis was performed in the larval midgut of S. frugiperda to explore the toxicity mechanism of CPT. A total of 261 and 348 differential metabolites were identified in the groups with 1.0 and 5.0 mg/kg CPT treatments, respectively. Further analysis found that pantothenate and CoA biosynthesis, sulfur relay system, selenocompound metabolism, and fatty acid biosynthesis pathways were significantly altered by 5.0 mg/kg CPT exposure. Our results provided new insight into the toxicological mechanisms of CPT against S. frugiperda and laid the foundation for the field application of CPT in pest control.

Assembly and functional profile of rhizosphere microbial community during the Salix viminalis-AMF remediation of polycyclic aromatic hydrocarbon polluted soils

Arbuscular mycorrhizal fungi (AMF) are positive to the phytoremediation by improving plant biomass and soil properties. However, the role of AM plants to the remediation of polycyclic aromatic hydrocarbons (PAHs) is yet to be widely recognized, and the impact of AM plants to indigenous microbial communities during remediation remains unclear. In this work, a 90-day study was conducted to assess the effect of AMF-Salix viminalis on the removal of PAHs, and explore the impact to the microbial community composition, abundance, and function. Results showed that AMF-Salix viminalis effectively enhanced the removal of benzo[a]pyrene, and enriched more PAH-degrading bacteria, consisting of Actinobacteria, Chloroflexi, Sphingomonas, and Stenotrophobacter, as well as fungi including Basidiomycota, Pseudogymnoascus, and Tomentella. For gene function, AM willow enhanced the enrichment of genes involved in amino acid synthesis, aminoacyl-tRNA biosynthesis, and cysteine and methionine metabolism pathways. F. mosseae inoculation had a greater effect on alpha- and beta-diversity of microbial genes at 90 d. Additionally, AMF inoculation significantly increased the soil microbial biomass carbon and organic matter concentration. All together, the microbial community assembly and function shaped by AM willow promoted the dissipation of PAHs. Our results support the effectiveness of AM remediation and contribute to reveal the enhancing-remediation mechanism to PAHs using multi-omics data.

Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants.

The naturally selected fungal crop (Leucoagaricus gongylophorus) farmed by leafcutter ants shows striking parallels with artificially selected plant crops domesticated by humans (e.g. polyploidy, engorged nutritional rewards, and dependence on cultivation). To date, poorly resolved L. gongylophorus genome assemblies based on short-read sequencing have constrained hypotheses about how millions of years under cultivation by ants shaped the fungal crop genome and potentially drove domestication. We use PacBio HiFi sequencing of L. gongylophorus from the leafcutter ant Atta colombica to identify 18 putatively novel biosynthetic gene clusters that likely cemented life as a cultivar (e.g. plant fragment degradation, ant-farmer communication, and antimicrobial defense). Comparative analyses with cultivated and free-living fungi showed genomic signatures of stepwise domestication transitions: (i) free-living to ant-cultivated: loss of genes conferring stress response and detoxification; (ii) hyphal food to engorged nutritional rewards: expansions of genes governing cellular homeostasis, carbohydrate metabolism, and siderophore biosynthesis; and (iii) detrital provisioning to freshly cut plant fragments: gene expansions promoting cell wall biosynthesis, fatty acid metabolism, and DNA repair. Comparisons across L. gongylophorus fungi farmed by 3 leafcutter ant species highlight genomic signatures of exclusively vertical clonal propagation and widespread transposable element activity. These results show how natural selection can shape domesticated cultivar genomes toward long-term ecological resilience of farming systems that have thrived across millennia.

Chlorpyrifos degradation by Shewanella oneidensis MR-1: Characteristics and mechanism analysis

This study conducted a series of experiments to investigate the degradation performance and mechanism of chlorpyrifos (CPF) degradation by Shewanella oneidensis MR-1 (S. oneidensis MR-1). The results showed that the S. oneidensis MR-1 degradation CPF rate was maximized at a salinity of 10 g·L−1, 35 °C, pH 7, and an inoculum amount of 20 %. The simultaneous addition of anthraquinone sodium 2,6-disulfonate (AQDS) and goethite [FeO(OH)] were able to increase the degradation efficiency to 174.12 %. Further, SEM results showed the FeO(OH) surface might provide a dense reaction site for the degradation. XRD and FTIR analysis revealed the hydroxyl group participated in the degradation process. XPS analysis showed that the addition of AQDS and FeO(OH) promoted the conversion of Fe(III) to enhance the degradation of CPF. Meanwhile, metabolites analysis, indicated that S. oneidensis MR-1 regulated its antioxidant capacity by enhancing its amino acid metabolism and lipid biosynthesis to cope with CPF stress. This work could provide new insights for efficient CPF removal in the future.