Amino Acid Biosynthesis Pathways Research Articles

The effect of Polyethylene Terephthalate (PET) Microplastic stress on the composition and gene regulatory network of amino acid in Capsicum annuum

Polyethylene Terephthalate (PET) is a widely used plastic in daily life. The extensive accumulation of PET microplastics (PET-MPs) in the environment adversely affects plant growth in multiple ways. However, the impact of PET-MPs exposure on the plant metabolism and the underlying molecular mechanisms are largely unexplored. To address this gap, we employed metabolomics and transcriptomics combination analyses to investigate the effects of PET-MPs exposure, varying in particle size and concentration, on the amino acid content and composition in pepper, as well as the underlying genes regulatory network. A total of 282 amino acids and their derivatives were identified, including 8 essential amino acids. Significant changes in differentially accumulated amino acids (DAAs) and differentially expressed genes (DEGs) were observed across different treatments, indicating that PET-MPs exposure affects amino acid metabolism in peppers, with these effects closely related to the size and concentration of PET-MPs. Ten DAAs with significant variable importance were identified through OPLS-DA. Weighted gene co-expression network analysis (WGCNA) revealed that the red module was significantly correlated with most of the DAAs indicators, highlighting the essential roles of HMSI, BCAT, and 12 transcription factor (TF) genes in regulating amino acid synthesis under PET-MPs exposure. Furthermore, correlation and redundancy analysis (RDA) identified three candidate genes, HSMI, PROC, and FHM, involved in amino acid biosynthesis pathways. This study enhances our understanding of MPs pollution and provides novel insights into the impact of MPs on crop growth and nutrition.

Elucidating metabolic pathways through genomic analysis in highly heavy metal-resistant Halobacterium salinarum strains

The annotated and predicted genomes of five archaeal strains (AS1, AS2, AS8, AS11 and AS19), isolated from Sfax solar saltern sediments (Tunisia) and affiliated with Halobacterium salinarum, were performed by RAST webserver (Rapid Annotation using Subsystem Technology) and NCBI prokaryotic genome annotation pipeline (PGAP). The results showed the ability of strains to use a reduced semi-phosphorylative Entner-Doudoroff pathway for glucose degradation and an Embden-Meyerhof one for gluconeogenesis. They could use glucose, fructose, glycerol, and acetate as sole source of carbon and energy. ATP synthase, various cytochromes and aerobic respiration proteins were encoded. All strains showed fermentation capability through the arginine deiminase pathway and facultative anaerobic respiration using electron acceptors (Dimethyl sulfoxide and trimethylamine N-oxide). Several biosynthesis pathways for many amino acids were identified. Comparative and pangenome analyses between the strains and the well-studied halophilic archaea Halobacterium NRC-1 highlighted a notable dissimilarity. Besides, the strains shared a core genome of 1973 genes and an accessory genome of 767 genes. 129, 94, 67, 15 and 29 unique genes were detected in the AS1, AS2, AS8, AS11 and AS19 genomes, respectively. Most of these unique genes code for hypothetical proteins. The strains displayed plant-growth promoting characteristics under heavy metal stress (Ammonium assimilation, phosphate solubilization, chemotaxis, cell motility and production of indole acetic acid, siderophore and phenazine). Therefore, they could be used as a biofertilizer to promote plant growth. The genomes encoded numerous biotechnologically relevant genes responsible for vitamin biosynthesis, including cobalamin, folate, biotin, pantothenate, riboflavin, thiamine, menaquinone, nicotinate, and nicotinamide. The carotenogenetic pathway of the studied strains was also predicted. Consequently, the findings of this study contribute to a better understanding of the halophilic archaea metabolism providing valuable insights into their ecophysiology as well as relevant biotechnological applications.

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

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

Combined Transcriptomic and Metabolomic Analyses Reveal the Mechanisms by Which the Interaction Between Sulfur and Nitrogen Affects Garlic Yield and Quality

Nitrogen and sulfur are essential macronutrients in plant growth and development, and their interaction profoundly influences gene expression, metabolic activities, and adaptability in plants, directly affecting plant growth and yield. Garlic (Allium sativum L.) is a crop of significant economic and medicinal value. However, despite the critical role of the nitrogen–sulfur interaction in garlic’s adaptability, yield, and quality, the specific mechanisms underlying these effects remain unclear. In this study, transcriptomic and metabolomic analyses were employed to investigate the effects of combined sulfur and nitrogen application on garlic bulb tissues. The results show that the combined application of sulfur and nitrogen significantly increased the diameter and weight of garlic bulbs by 14.96% and 35.47%, respectively. The content of alliin increased by 28.48%, while the levels of abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), and gibberellin (GA) increased by 15.82%, 12.94%, 32.34%, and 48.13%, respectively. Additionally, the activities of alliinase, superoxide dismutase (SOD), and catalase (CAT) were enhanced by 7.93%, 4.48%, and 19.74%, respectively. Moreover, the application of sulfur and nitrogen significantly reduced the malondialdehyde (MDA) content and peroxidase (POD) activity in garlic bulbs by 29.66% and 9.42%, respectively, thereby improving garlic’s adaptability and growth potential. Transcriptomic analysis revealed differentially expressed genes in several key pathways, including plant hormone signal transduction, RNA degradation, glutathione metabolism, amino acid biosynthesis, and glycerophospholipid metabolism. Metabolomic analysis identified 80 differentially abundant metabolites primarily consisting of amino acids, indole carboxylic acids, and fatty acids. The integrated transcriptomic and metabolomic analyses highlighted the pivotal roles of glutathione metabolism, glycerophospholipid metabolism, and amino acid biosynthesis pathways in the synergistic effects of sulfur and nitrogen. This study not only provides critical scientific evidence for understanding the mechanisms underlying the nitrogen–sulfur interaction’s impact on the yield and quality of garlic but also offers a scientific basis for optimizing nutrient management strategies to enhance garlic yield and quality.

Exploring microbial diversity and functionality in Verdejo wine vinegar fermentation through LC-MS/MS analysis

The identification of microorganisms in vinegar production remains a challenge mainly, due to the difficulty of isolating and characterizing the microbiota involved. This implies that despite progress in understanding the composition and role of these microbial communities, there are still virtually unknown microorganisms in these environments. Metaproteomics reveals microbial diversity and behavior by analysis of proteins, offering precise insights into key moments and conditions in biological processes like acetification. This study consists of a thorough metaproteomic analysis during the elaboration of an innovative vinegar, Verdejo wine vinegar. Acetic acid fermentation occurred by submerged culture in an 8L automated Frings reactor operated in semi-continuous mode. LC-MS/MS identified 1626 proteins from 149 taxonomic groups, mainly Acetobacteraceae (1529), followed by yeast (47), lactic acid bacteria (29), and Archaea (21). Komagataeibacter (73.7%), Acetobacter (10.7%), Gluconacetobacter (1.7%), Novacetimonas (1.6%), and Gluconobacter (1.3%) were prevalent genera, with K. europaeus being the dominant species (56.7%). To our knowledge, this is the first metaproteomic approach to comprehensively address the study of so diverse microbial populations. GO Term analysis emphasized "heterocyclic compound binding" and "organic substance metabolic process", while analysis of protein-protein interactions identified key metabolic processes, such as amino acid biosynthesis, especially BCAAs, and crucial energetic pathways such as the TCA cycle. Stress response mechanisms, such as the dnaK-dnaJ-grpE and cl2p system, have been also highlighted. These analyses revealed the molecular and functional complexity of the acetification process, highlighting the critical importance of diverse metabolic routes in the adaptation of the microbiota members to the medium conditions. Overall, this study aims to characterize the microbiota driving Verdejo wine acetification and explore its composition, functions, and key metabolic processes.

Bone loss with aging is independent of gut microbiome in mice

Emerging evidence suggests a significant role of gut microbiome in bone health. Aging is well recognized as a crucial factor influencing the gut microbiome. In this study, we investigated whether age-dependent microbial change contributes to age-related bone loss in CB6F1 mice. The bone phenotype of 24-month-old germ-free (GF) mice was indistinguishable compared to their littermates colonized by fecal transplant at 1-month-old. Moreover, bone loss from 3 to 24-month-old was comparable between GF and specific pathogen-free (SPF) mice. Thus, GF mice were not protected from age-related bone loss. 16S rRNA gene sequencing of fecal samples from 3-month and 24-month-old SPF males indicated an age-dependent microbial shift with an alteration in energy and nutrient metabolism potential. An integrative analysis of 16S predicted metagenome function and LC-MS fecal metabolome revealed an enrichment of protein and amino acid biosynthesis pathways in aged mice. Microbial S-adenosyl methionine metabolism was increased in the aged mice, which has previously been associated with the host aging process. Collectively, aging caused microbial taxonomic and functional alteration in mice. To demonstrate the functional importance of young and old microbiome to bone, we colonized GF mice with fecal microbiome from 3-month or 24-month-old SPF donor mice for 1 and 8 months. The effect of microbial colonization on bone phenotypes was independent of the microbiome donors’ age. In conclusion, our study indicates age-related bone loss occurs independent of gut microbiome.

Regulatory mechanism of cysteine-dependent methionine biosynthesis in Bifidobacterium longum: insights into sulfur metabolism in gut microbiota

ABSTRACT Sulfur, a critical element for bacterial growth, is not directly utilized by bifidobacteria, rendering the sulfur-containing amino acid biosynthesis pathway, particularly for cysteine and methionine, poorly understood. This research identifies six genes involved in this pathway through re-annotation of the Bifidobacterium longum DJO10A genome. These genes play crucial roles in bioconversion processes essential for cysteine utilization, highlighting its significance in sulfur metabolism. Our study uncovers a novel regulatory mechanism of these pathways under varying cysteine concentrations. We demonstrate a dual-pathway mechanism for methionine biosynthesis: one directly utilizing cysteine (trans-sulfurylation pathway) and another utilizing H2S derived from cysteine degradation (direct sulfurylation pathway). This regulatory dual-pathway mechanism is contingent on environmental cysteine levels, with both pathways activated at low cysteine levels, while higher levels predominantly engage the H2S-utilizing pathway. This investigation not only advances our understanding of DJO10A’s metabolic capabilities but also underscores the bacterium’s adaptability through sophisticated regulatory mechanisms for sulfur-containing amino acid biosynthesis. The elucidation of these pathways provides valuable insights into the survival strategies of bifidobacteria in the gut environment, where sulfur sources can vary greatly. Through detailed genomic, transcriptional, and enzymatic analyses, this study significantly contributes to the field of microbiology, offering a foundation for future research on gut microbiota metabolic pathways and their implications for host health.

Comparative Metabolome and Transcriptome Analyses Reveal Molecular Mechanisms Involved in the Responses of Two Carex rigescens Varieties to Salt Stress.

Salt stress severely inhibits crop growth and production. The native turfgrass species Carex rigescens in northern China, exhibits extraordinary tolerance to multiple abiotic stresses. However, little is known about its specific metabolites and pathways under salt stress. To explore the molecular metabolic mechanisms under salt stress, we conducted metabolome analysis combined with transcriptome analysis of two varieties of Carex rigescens with differing salt tolerances: salt-sensitive Lvping NO.1 and salt-tolerant Lvping NO.2. After 5 days of salt treatment, 114 and 131 differentially abundant metabolites (DAMs) were found in Lvping NO.1 and Lvping NO.2, respectively. Among them, six amino acids involved in the amino acid biosynthesis pathway, namely, valine, phenylalanine, isoleucine, tryptophan, threonine, and serine, were accumulated after treatment. Furthermore, most DAMs related to phenylalanine biosynthesis, metabolism, and phenylpropanoid biosynthesis increased under salt stress in both varieties. The expression profiles of metabolism-associated genes were consistent with the metabolic profiles. However, genes including HCT, β-glucosidases, and F5H, and metabolite 4-hydroxycinnamic acid, of the two varieties may account for the differences in salt tolerance. Our study provides new insights into the mechanisms underlying salt tolerance in Carex rigescens and reveals potential metabolites and genes to improve crop resilience to saline environments.

Response and adaptation of Chlorella pyrenoidosa to 6PPD: Physiological and genetic mechanisms

The extensive contamination of the tire antidegradant N-(1,3-dimethylbutyl)-N′-phenyl-p-phenylenediamine (6PPD) in aquatic environments have raised concerns about its potential threats to aquatic organisms. Here, the responses of green algae Chlorella pyrenoidosa (C. pyrenoidosa) to 6PPD exposure were investigated for the first time. The growth of C. pyrenoidosa experienced three sequential phases, including inhibition, recovery and stimulation. Physiological and transcriptome analysis suggested that the growth inhibition was associated with the suppressed nitrogen assimilation and amino acid biosynthesis pathways, among which nitrate transporter (NRT) 2.1 was a key target of 6PPD. Molecular docking revealed the steadily binding of 6PPD to the substrate entry region of NRT 2.1 via hydrogen bonds and π − cation interaction, blocking the acquisition of extracellular inorganic nitrogen. Along with the removal of 6PPD through abiotic processes and biodegradation, an adaptive metabolic shift in cells not only facilitated growth recovery but also triggered a compensatory stimulation phase. With regard to microalgal adaptation, upregulated DNA replication and repair pathways served to maintain the integrity of the genetic information, enhanced photosynthesis cascades and central carbon metabolism improved carbon flux and energy conversion to microalgal biomass, recovered amino acid biosynthesis produced essential proteins for multiple metabolisms. The results provide new insights into microalgal molecular responses to 6PPD exposure, facilitating a better understanding of ecological consequences of 6PPD in the environment.

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.

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.

What's GABA got to do with it? A potential link between the microbiome, schizophrenia, and the endo-cannabinoid system

The microbiome has been linked to numerous neurological and psychiatric diseases, including schizophrenia. Nevertheless, correlating microbial perturbations to pathophysiological aspects of schizophrenia remains elusive, as study participants are typically medicated when sampled, complicating mechanistic investigation. Here we explored specific microbial and metabolic alterations in schizophrenia patients, while explicitly considering their medications. We recruited 30 patients and 14 healthy controls. Fecal and serum samples were collected for microbiota and (untargeted) metabolome characterization, respectively. While significant differences were detected between microbiome of controls and schizophrenia patients overall, patients not taking GABA-enhancing drugs had profiles similar to the control group. This pattern was preserved, but to a lesser extent, when comparing metabolomes. Several key metabolic pathways differed between patients and controls, even after filtering out those directly related to pharmaceuticals and their metabolism, and the citric acid cycle and amino acid biosynthesis pathways were enriched in the group prescribed antipsychotics without GABA-enhancers. Administration of exogenous GABA affected overall patient homeostasis, not just disease course, supporting our hypothesis that microbiota play a part in cognitive, emotional, and mental function, and that this role must be considered in the full context of an individual's state, including medication.

Analysis of the Mechanism of Wood Vinegar and Butyrolactone Promoting Rapeseed Growth and Improving Low-Temperature Stress Resistance Based on Transcriptome and Metabolomics.

Rapeseed is an important oil crop in the world. Wood vinegar could increase the yield and abiotic resistance of rapeseed. However, little is known about the underlying mechanisms of wood vinegar or its valid chemical components on rapeseed. In the present study, wood vinegar and butyrolactone (γ-Butyrolactone, one of the main components of wood vinegar) were applied to rapeseed at the seedling stage, and the molecular mechanisms of wood vinegar that affect rapeseed were studied by combining transcriptome and metabolomic analyses. The results show that applying wood vinegar and butyrolactone increases the biomass of rapeseed by increasing the leaf area and the number of pods per plant, and enhances the tolerance of rapeseed under low temperature by reducing membrane lipid oxidation and improving the content of chlorophyll, proline, soluble sugar, and antioxidant enzymes. Compared to the control, 681 and 700 differentially expressed genes were in the transcriptional group treated with wood vinegar and butyrolactone, respectively, and 76 and 90 differentially expressed metabolites were in the metabolic group. The combination of transcriptome and metabolomic analyses revealed the key gene-metabolic networks related to various pathways. Our research shows that after wood vinegar and butyrolactone treatment, the amino acid biosynthesis pathway of rapeseed may be involved in mediating the increase in rapeseed biomass, the proline metabolism pathway of wood vinegar treatment may be involved in mediating rapeseed's resistance to low-temperature stress, and the sphingolipid metabolism pathway of butyrolactone treatment may be involved in mediating rapeseed's resistance to low-temperature stress. It is suggested that the use of wood vinegar or butyrolactone are new approaches to increasing rapeseed yield and low-temperature resistance.

Mycobacterial Targets for Thiourea Derivatives: Opportunities for Virtual Screening in Tuberculosis Drug Discovery.

Tuberculosis (TB) remains a primary global health concern, necessitating the discovery and development of new anti-TB drugs, mainly to combat drug-resistant strains. In this context, thiourea derivatives have emerged as promising candidates in TB drug discovery due to their diverse chemical structures and pharmacological properties. This review aimed to explore this potential, identifying and exploring molecular targets for thiourea derivatives in Mycobacterium tuberculosis (Mtb) and the potential application of virtual screening techniques in drug discovery. We have compiled a comprehensive list of possible molecular targets of thiourea derivatives in Mtb. The enzymes are primarily involved in the biosynthesis of various cell wall components, including mycolic acids, peptidoglycans, and arabinans, or targets in the branched-chain amino acid biosynthesis (BCAA) pathway and detoxification mechanisms. We discuss the potential of these targets as critical constituents for the design of novel anti-TB drugs. Besides, we highlight the opportunities that virtual screening methodologies present in identifying potential thiourea derivatives that can interact with these molecular targets. The presented findings contribute to the ongoing efforts in TB drug discovery and lay the foundation for further research in designing and developing more effective treatments against this devastating disease.

Genomically recoded Escherichia coli with optimized functional phenotypes.

Genomically recoded organisms hold promise for many biotechnological applications, but they may exhibit substantial fitness defects relative to their non-recoded counterparts. We used targeted metabolic screens, genetic analysis, and proteomics to identify the origins of fitness impairment in a model recoded organism, Escherichia coli C321.∆A. We found that defects in isoleucine biosynthesis and release factor activity, caused by mutations extant in all K-12 lineage strains, elicited profound fitness impairments in C321.∆A, suggesting that genome recoding exacerbates suboptimal traits present in precursor strains. By correcting these and other C321.∆A-specific mutations, we engineered C321.∆A strains with doubling time reductions of 17% and 42% in rich and minimal medium, respectively, compared to ancestral C321. Strains with improved growth kinetics also demonstrated enhanced ribosomal non-standard amino acid incorporation capabilities. Proteomic analysis indicated that C321.∆A lacks the ability to regulate essential amino acid and nucleotide biosynthesis pathways, and that targeted mutation reversion restored regulatory capabilities. Our work outlines a strategy for the rapid and precise phenotypic optimization of genomically recoded organisms and other engineered microbes.

A methionine-choline-deficient diet induces nonalcoholic steatohepatitis and alters the lipidome, metabolome, and gut microbiome profile in the C57BL/6J mouse

The methionine-choline-deficient (MCD) diet-induced non-alcoholic steatohepatitis (NASH) in mice is a well-established model. Our study aims to elucidate the factors influencing liver pathology in the MCD mouse model by examining physiological, biochemical, and molecular changes using histology, molecular techniques, and OMICS approaches (lipidomics, metabolomics, and metagenomics). Male C57BL/6J mice were fed a standard chow diet, a methionine-choline-sufficient (MCS) diet, or an MCD diet for 10 weeks. The MCD diet resulted in reduced body weight and fat mass, along with decreased plasma triglyceride, cholesterol, glucose, and insulin levels. However, it notably induced steatosis, inflammation, and alterations in gene expression associated with lipogenesis, inflammation, fibrosis, and the synthesis of apolipoproteins, sphingolipids, ceramides, and carboxylesterases.Lipid analysis revealed significant changes in plasma and tissues: most ceramide non-hydroxy-sphingosine lipids significantly decreased in the liver and plasma but increased in the adipose tissue of MCD diet-fed animals. Oxidized glycerophospholipids mostly increased in the liver but decreased in the adipose tissue of the MCD diet-fed group. The gut microbiome of the MCD diet-fed group showed an increase in Firmicutes and a decrease in Bacteroidetes and Actinobacteria. Metabolomic profiling demonstrated that the MCD diet significantly altered amino acid biosynthesis, metabolism, and nucleic acid metabolism pathways in plasma, liver, fecal, and cecal samples. LC-MS data indicated higher total plasma bile acid intensity and reduced fecal glycohyodeoxycholic acid intensity in the MCD diet group. This study demonstrates that although the MCD diet induces hepatic steatosis, the mechanisms underlying NASH in this model differ from those in human NASH pathology.

Effect of varying temperature increases on the microbial community of Pleistocene and Holocene permafrost

The total area covered by permafrost has been continually decreasing over the past decades. This study investigates the effect of various temperature increases on the microbiome of permafrost sampled at the Cold Regions Research and Engineering Laboratory (CRREL) Permafrost Tunnel site in Fox, Alaska, USA, corresponding to the Holocene (around 8000 years before present (ybp)) and Pleistocene (around 36,000 ybp), respectively. The soil was subjected to two thawing time courses, with temperature increasing from −4 °C to either +4 °C or +25 °C, and total nucleic acid was extracted at each time point. Consistent with previous 16S rRNA amplicon sequencing studies on the Permafrost Tunnel, the Pleistocene was dominated by Clostridia, while the Holocene was mainly composed of Clostridia, Bacteroidia and Alphaproteobacteria at −4 °C. Thawing at +25 °C resulted in divergent microbial profiles for permafrost of both ages, with the Pleistocene becoming more similar to the active layer, while the Holocene was relatively less impacted. Prediction of metabolic function revealed that bacteria from the Holocene permafrost activated degradation pathways upon thawing at +25 °C, while bacteria from the Pleistocene were more involved in amino-acid biosynthesis pathways, suggesting different mechanisms of adaptation.

Transcriptome analysis of Pennisetum americanum × Pennisetum purpureum and Pennisetum americanum leaves in response to high-phosphorus stress

Excessive phosphorus (P) levels can disrupt nutrient balance in plants, adversely affecting growth. The molecular responses of Pennisetum species to high phosphorus stress remain poorly understood. This study examined two Pennisetum species, Pennisetum americanum × Pennisetum purpureum and Pennisetum americanum, under varying P concentrations (200, 600 and 1000 µmol·L− 1 KH2PO4) to elucidate transcriptomic alterations under high-P conditions. Our findings revealed that P. americanum exhibited stronger adaption to high-P stress compared to P. americanum× P. purpureum. Both species showed an increase in plant height and leaf P content under elevated P levels, with P. americanum demonstrating greater height and higher P content than P. americanum× P. purpureum. Transcriptomic analysis identified significant up- and down-regulation of key genes (e.g. SAUR, GH3, AHP, PIF4, PYL, GST, GPX, GSR, CAT, SOD1, CHS, ANR, P5CS and PsbO) involved in plant hormone signal transduction, glutathione metabolism, peroxisomes, flavonoid biosynthesis, amino acid biosynthesis and photosynthesis pathways. Compared with P. americanum× P. purpureum, P. americanum has more key genes in the KEGG pathway, and some genes have higher expression levels. These results contribute valuable insights into the molecular mechanisms governing high-P stress in Pennisetum species and offer implications for broader plant stress research.

Ectoine maintains the flavor and nutritional quality of broccoli during postharvest storage

The bacterial derived osmolyte ectoine has been shown to stabilize cell structure and function, a property that may help to extend the shelf life of broccoli. The impact of ectoine on broccoli stored for 4 d at 20 °C and 90% relative humidity was investigated. Results indicated that 0.20% ectoine treatment maintained the quality of broccoli, by reducing rate of respiration and ethylene generation, while increasing the levels of total phenolics, flavonoids, TSS, soluble protein, and vitamin C, relative to control. Headspace-gas chromatography–mass spectrometry, transcriptomic and metabolomic analyses revealed that ectoine stabilized aroma components in broccoli by maintaining level of volatile compounds and altered the expression of genes and metabolites associated with sulfur metabolism, as well as fatty acid and amino acid biosynthesis pathways. These findings provide a greater insight into how ectoine preserves the flavor and nutritional quality of broccoli, thus, extending its shelf life.

Multi-omic analysis reveals the effects of interspecific hybridization on the synthesis of seed reserve polymers in a Triticum turgidum ssp. durum × Aegilops sharonensis amphidiploid

BackgroundWheat grain endosperm is mainly composed of proteins and starch. The contents and the overall composition of seed storage proteins (SSP) markedly affect the processing quality of wheat flour. Polyploidization results in duplicated chromosomes, and the genomes are often unstable and may result in a large number of gene losses and gene rearrangements. However, the instability of the genome itself, as well as the large number of duplicated genes generated during polyploidy, is an important driving force for genetic innovation. In this study, we compared the differences in starch and SSP, and analyzed the transcriptome and metabolome among Aegilops sharonensis (R7), durum wheat (Z636) and amphidiploid (Z636×R7) to reveal the effects of polyploidization on the synthesis of seed reserve polymers.ResultsThe total starch and amylose content of Z636×R7 was significantly higher than R7 and lower than Z636. The gliadin and glutenin contents of Z636×R7 were higher than those in Z636 and R7. Through transcriptome analysis, there were 21,037, 2197, 15,090 differentially expressed genes (DEGs) in the three comparison groups of R7 vs Z636, Z636 vs Z636×R7, and Z636×R7 vs R7, respectively, which were mainly enriched in carbon metabolism and amino acid biosynthesis pathways. Transcriptome data and qRT-PCR were combined to analyze the expression levels of genes related to storage polymers. It was found that the expression levels of some starch synthase genes, namely AGP-L, AGP-S and GBSSI in Z636×R7 were higher than in R7 and among the 17 DEGs related to storage proteins, the expression levels of 14 genes in R7 were lower than those in Z636 and Z636×R7. According to the classification analysis of all differential metabolites, most belonged to carboxylic acids and derivatives, and fatty acyls were enriched in the biosynthesis of unsaturated fatty acids, niacin and nicotinamide metabolism, one-carbon pool by folate, etc.ConclusionAfter allopolyploidization, the expression of genes related to starch synthesis was down-regulated in Z636×R7, and the process of starch synthesis was inhibited, resulting in delayed starch accumulation and prolongation of the seed development process. Therefore, at the same development time point, the starch accumulation of Z636×R7 lagged behind that of Z636. In this study, the expression of the GSe2 gene in Z636×R7 was higher than that of the two parents, which was beneficial to protein synthesis, and increased the protein content. These results eventually led to changes in the synthesis of seed reserve polymers. The current study provided a basis for a greater in-depth understanding of the mechanism of wheat allopolyploid formation and its stable preservation, and also promoted the effective exploitation of high-value alleles.