Search Results (331)

Background/Objectives: tRNAs, tRNAomes, aminoacyl-tRNA synthetases (AARSs), the first proteins, ribosomes and the genetic code coevolved. We utilize sequence data to reconstruct key steps in establishing the first code on Earth. Methods: Networks were constructed to describe initial tRNAome and AARSome evolution. Results: tRNA-34 wobble and tRNA-37 modifications were necessary to evolve the code, as were additional tRNA modifications, so diverse tRNA modification enzymes (i.e., histidyl-tRNA -1 GTP synthase) are among the first proteins. tRNA-linked chemistry brought asparagine, glutamine, cysteine and possibly additional amino acids into the code. tRNA, tRNA modifications and tRNA-linked chemistry were core founding innovations for code evolution. Coevolution of AARSomes was also essential. Class II and class I AARSs have distinct folds but are nonetheless homologs by sequence. Early AARS enzymes folded around Zn motifs. Networks were generated for tRNAomes and AARSomes in ancient Archaea, because Archaea are the closest living organisms to the last universal common ancestor. Conclusions: The first code on Earth was surprisingly ordered, and the few apparent deviations from the regular order can yet be explained. Early in the evolution of the code, innovation was more strongly selected than accuracy. The code froze, however, because of evolving fidelity mechanisms. A historical record was documented in tRNA and in the genetic code structure and has been preserved in living organism sequences. AARSome structure describes the first code evolution more adequately than tRNAomes. Full article

The toxicity of copper (Cu) severely affects the growth and physiological metabolism of plants. 2-(3,4-Dichlorophenoxy) triethylamine (DCPTA) is a plant growth regulator known to enhance plant tolerance to various abiotic stresses; however, its specific role in mitigating Cu toxicity via cell wall modulation and nitrogen metabolism remains unclear. “Zhongnong 26” (Cucumis sativus L.) seedlings were subjected to a randomized block design with four treatments: control (CK), 0.25 mg/L DCPTA, 50 μM Cu, and 50 μM Cu + 0.25 mg/L DCPTA, with three biological replicates per treatment. The results indicated that DCPTA application significantly alleviated Cu-induced growth inhibition. Specifically, DCPTA improved root system architecture by markedly increasing total root length (68.8%), surface area (68.7%), and the number and length of secondary lateral roots (69.6%, 173.2%). Furthermore, DCPTA enhanced the biosynthesis of cell wall polysaccharides—including pectin (24.3%), hemicellulose 1 (22.4%), hemicellulose 2 (23.7%) and cellulose (33.1%) in roots. Fourier Transform Infrared (FTIR) spectroscopy analysis revealed that DCPTA modified functional groups (e.g., –OH, –COOH) within the cell wall, enhancing their metal-chelating capacity. Consequently, DCPTA promoted the immobilization of Cu in the root cell wall fractions (particularly pectin and HC2) and shifted Cu into less toxic, pectate- and protein-bound forms, thereby reducing its translocation to leaves. Additionally, DCPTA restored the activities of key nitrogen metabolism enzymes in leaves and roots. Compared with Cu treatment alone, nitrate reductase (NR) activity increased by 77.7% and 90.6%, while glutamine synthetase (GS) activity remained stable, and glutamate synthase (GOGAT) activity increased by 10.3% and 71.3% in leaves and roots, respectively. In conclusion, DCPTA enhances copper sequestration in roots by coordinating the regulation of root structure and cell wall strengthening (with an increase in pectin and hemicellulose content). This is crucial for protecting the nitrogen metabolism within the cells (including the enzymes that drive the nitrate–ammonium reduction pathway) to maintain metabolic balance under Cu stress. Full article

Alzheimer’s disease (AD) is increasingly recognized as a multisystem neurodegenerative disorder in which sensory dysfunction accompanies cognitive decline. As an accessible extension of the central nervous system, the retina provides a valuable window for investigating early neurodegenerative processes; however, the cellular mechanisms underlying AD-associated retinal pathology remain incompletely understood. Here, using the APP/PS1 mouse model, we systematically examined structural, functional, and glial alterations in the retina across disease stages. Despite robust age-dependent amyloid plaque accumulation in visual-related brain regions, no plaque-like β-amyloid (Aβ) deposits were detected in the retina even at advanced ages. Nevertheless, young APP/PS1 mice exhibited early thinning of inner retinal layers, impaired retinal electrophysiological responses, and reduced excitatory synaptic inputs to retinal ganglion cells (RGCs), preceding overt neuronal loss. These neuronal changes were accompanied by pronounced Müller glial activation, characterized by upregulation of gliosis markers and extensive morphological remodeling. Functional analyses further revealed dynamic alterations in glial homeostasis, including early elevation followed by age-dependent decline of glutamine synthetase activity, together with increased expression and disrupted perivascular polarity of aquaporin-4. Consistently, transcriptomic profiling of young AD retinas identified coordinated dysregulation of genes involved in amino acid metabolism, transport, and oxidative stress responses. Together, our findings identify Müller glial remodeling as an early feature of AD-associated retinal pathology that coincides with synaptic vulnerability of RGCs and occurs independently of local Aβ plaque deposition, highlighting retinal glia as potential early indicators and modulators of neurodegeneration. Full article

Cancer progression is influenced by the dynamic interplay between tumor cells and the surrounding stromal microenvironment. Therapy-induced senescence (TIS) of stromal fibroblasts represents a common outcome of anticancer treatments, contributing to tumor progression through the senescence-associated secretory phenotype (SASP). While SASP cytokines promote cancer malignancy, the contribution of secreted metabolites from senescent cells remains poorly understood. Here, we investigate the role of senescent stromal metabolism in regulating prostate and ovarian cancer cell invasion. Conditioned media (CM) from TIS-induced human prostate (HPFs) and ovarian fibroblasts (HOFs) promote enhanced invasion of cancer cells. Invasion is partially preserved after exposure to boiled CM, suggesting a role for heat-stable metabolic factors. Metabolomic profiling of senescent fibroblasts-derived CM reveals a significant increase in Glutamine (Gln) levels, identifying senescent stromal fibroblasts as a previously unrecognized source of extracellular Gln in the tumor microenvironment (TME). Exposure of cancer cells to senescent CM increases Gln uptake, together with upregulation of the transporter SLC1A5 and increased intracellular Gln. This metabolic adaptation is associated with increased malignant phenotype including epithelial-to-mesenchymal transition (EMT) and stemness features. Extracellular Gln depletion, pharmacological inhibition of glutaminase-1 (GLS1) in cancer cells, or Gln synthetase (GS) silencing in fibroblasts markedly impair senescent fibroblasts CM-induced invasion, EMT markers expression, and stemness features in cancer cells. Stromal-derived Gln is associated with increased cancer cell invasion through activation of a redox-dependent NRF2/ETS1 signaling axis. Analysis of patient-derived transcriptomic datasets further suggests chemotherapy-associated upregulation of Gln metabolism and ETS1 expression. These findings identify senescent stromal-derived Gln as a key metabolic driver of prostate and ovarian cancer aggressiveness and reveal a TIS-associated metabolic vulnerability that could be explored in future preclinical studies. Full article

Background: Apigenin, as a flavonoid, can be protective against oxidative damage in hypoxic events due to its antioxidant properties. Here, we have investigated the neuroprotective effects of apigenin in an ex vivo model of ischemic damage, using cerebellar slices from postnatal day (P)8–12 reporter mice to identify oligodendrocytes (SOX10-EGFP) and astrocytes (GFAP-EGFP). Methods: Apigenin (10 and 20 μM) was administered preventively at 60 min prior to and during inducing ischemic damage by oxygen and glucose deprivation (OGD); controls were maintained with glucose and normoxia (OGN). Results: OGD induced a marked retraction of oligodendroglial processes without reducing the oligodendrocyte number. This structural disruption was prevented by apigenin; notably, 10 μM apigenin blocked process retraction, whereas 20 μM did not, indicating a dose-dependent effect on the oligodendroglial morphology. Consistent with this, MBP and NF70 immunofluorescence analyses of axonal myelination demonstrated that OGD caused a significant loss of myelin sheaths, and this was prevented by pre-treatment with apigenin. In addition, apigenin prevented astrocyte reactivity induced by OGD, as assessed by increased GFAP-EGFP expression and decreased expression of glutamine synthetase. Moreover, immunofluorescence for calbindin indicated that apigenin protected Purkinje neurons from ischemic damage. Conclusions: These results demonstrate that apigenin is neuroprotective in ischemia and this is associated with modulation of astrocyte reactivity and maintenance of oligodendrocyte and myelin integrity. Full article

Temperature and nitrogen fertilizer are key environmental factors that significantly affect rice growth and grain quality. There remains a lack of systematic research on the effects of temperature and nitrogen fertilizer on carbon–nitrogen metabolism during grain-filling, and consequently on the taste quality of rice varieties with different taste characteristics. To bridge this gap, pot experiments were conducted under different temperature and nitrogen fertilizer conditions to investigate the changes in carbon and nitrogen metabolism and the quality of different high-quality and stable-taste rice varieties during the grain filling stage. Our research results indicate that high-temperature conditions inhibit both carbon and nitrogen metabolism; however, the variations differ among rice varieties with differing taste stability. Under both normal and high nitrogen levels, compared to Akita Komachi (AK), a variety with poor taste stability, Jikedao 606 (J 606), a variety with strong taste stability, maintained a certain photosynthetic capacity under high-temperature conditions, with smaller decreases in net photosynthetic rate and soil–plant analysis development values, declining by 4.30–5.59% and 4.30–5.59% respectively. The decline in the activities of nitrate reductase, glutamine synthetase, and glutamate synthase in nitrogen metabolism was relatively small; in comparison, the decrease in the activities of ADP-glucose pyrophosphorylase, granule-bound starch synthase, starch branching enzyme, and starch debranching enzyme in carbon metabolism was comparatively minor. The content of amylose and amylopectin in the grains was maintained, improving the milled rice rate and head rice rate, thereby ensuring strong stability of excellent sensory quality. Under both high-temperature and high-nitrogen conditions, the yields of the two rice varieties were maintained. In summary, variations exist in carbon and nitrogen metabolism among different rice varieties with stable excellent taste under varying temperature and nitrogen fertilizer conditions. These metabolic differences affect starch synthesis in the endosperm, ultimately influencing the stability of rice sensory quality. This study provides a theoretical basis for nitrogen fertilizer application under high-temperature conditions and the cultivation of rice varieties with excellent taste stability. Full article

Efficient microbial assimilation of high-concentration ammonium nitrogen and its conversion into value-added bioproducts represent a pivotal yet underexplored strategy for sustainable nitrogen management. Here, we report a newly isolated Bacillus velezensis strain, GY1, with a robust intrinsic capacity for simultaneous NH₄⁺-N assimilation and γ-polyglutamic acid (γ-PGA) biosynthesis. Under optimized conditions (37 °C, pH 7.0, C/N = 12:1), GY1 achieved 76.5% removal of ammonium nitrogen (400 mg/L) with negligible nitrite accumulation (<0.02 mg/L), indicating assimilation rather than nitrification. Transcriptomic analysis revealed a coordinated metabolic flux wherein the glutamine synthetase - glutamate synthase pathway GS-GOGAT pathway supplies glutamate for γ-PGA synthesis, while polymerization further facilitates ammonium sequestration via electrostatic interactions. GY1 produced up to 612.8 mg/L γ-PGA, and genetic overexpression of capB synchronized these pathways, enhancing both ammonium assimilation (87.4%) and γ-PGA yield (843.9 mg/L). Notably, this metabolic coupling remained resilient in complex substrates, achieving 68.8% ammonium removal and 220.7 mg/L γ-PGA production in untreated biogas slurry. Together, these findings establish GY1 as a metabolically robust platform linking nitrogen assimilation with biopolymer synthesis, offering a mechanistic framework for circular nitrogen economies. Full article

Salinity stress severely limits rice productivity and grain quality worldwide. Although exogenous foliar application of titanium dioxide nanoparticles (nano-TiO₂) has been reported to enhance crop stress tolerance, its regulatory roles in yield formation and grain quality in rice varieties with differing salt tolerance are not well understood. In the present study, two contrasting rice varieties, viz., Jingliangyou 3261 (JLY3261; salt-tolerant) and Yuxiangyouzhan (YXYZ; salt-sensitive), were applied with five nano-TiO₂ foliar application treatments—viz., CK: water spray; Ti1: 15 mg L⁻¹; Ti2: 30 mg L⁻¹; Ti3: 45 mg L⁻¹; and Ti4: 60 mg L⁻¹—at the jointing and panicle initiation stages. Plants were irrigated with 0.3% saltwater to simulate salt stress. The results showed that Ti2 and Ti3 treatments led to 8.59% and 14.80% increases in grain yield in JLY3261 and YXYZ, respectively, compared with CK. Ti2 and Ti3 treatments significantly increased the leaf area index, net photosynthetic rate, and aboveground biomass of both varieties at the heading stage. Meanwhile, the activities of antioxidant enzymes such as superoxide dismutase and peroxidase, as well as nitrogen metabolism enzymes including nitrate reductase and glutamine synthetase, were improved with a substantial reduction in malondialdehyde contents. Application of nano-TiO₂ upregulated the expression of ion transport-related genes such as OsSOSs, OsNHXs and OsHKTs, thus improving leaf K⁺ accumulation and reducing Na⁺ content to optimize the K⁺/Na⁺ ratio. In addition, Ti2 and Ti3 treatments improved the milled rice rate, head rice rate, and protein content, while they decreased the chalkiness degree of both rice cultivars. Principal component analysis showed that the aboveground biomass at the heading stage was a core evaluation index for both varieties. Overall, foliar application of 30–45 mg L⁻¹ nano-TiO₂ was found to be effective regarding growth and yield improvement in rice under saline conditions. This study provides a theoretical basis for agro-management strategies for rice cultivation in saline–alkaline soils. Full article

In the context of global climate change, the co-occurrence of salt and heat stress represents a major constraint to rice production, resulting in greater yield penalties than either stress alone. This study aimed to assess the effects of salt and heat stress on oxidative homeostasis, photosynthetic performance, carbon (C)–nitrogen (N) metabolism, and rice yield. The experiment comprised four treatments, i.e., control (CK), salt (irrigation with 3.9 dS m⁻¹ NaCl solution), heat (exposure to 36 °C/30 °C day/night for 5 days at panicle initiation), and combined salt + heat stress. Results showed that combined stress enhanced reactive oxygen species (ROS) accumulation (i.e., H₂O₂ content and O₂⁻ contents were 1.3 and 1.5 times higher than CK), and the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were increased by 64.6%, 69.5%, and 74.8% higher than CK. At the molecular level, salt + heat stress upregulated antioxidant defense-related genes, i.e., OsAPX2, OsSODCC1, and OsAPX1, while significantly downregulated ion homeostasis-related genes, i.e., OsSOSs, OsHKT1;3, OsHKT1;5, and OsNHX4, and photosynthesis-related genes, i.e., Ospsbo, OsRbcS2, and OsRbcS3, compared with CK. Furthermore, salt + heat stress reduced the activities of C-metabolism enzymes (sucrose phosphate synthase, sucrose synthase, and starch synthase) and N-metabolism enzymes (nitrate reductase, glutamine synthetase, and glutamate synthase), leading to 34.3% and 18.6% lower stem-sheath non-structural carbohydrate accumulation in stem sheath and its translocation rate, respectively, while total N accumulation decreased by 42.9%, as compared with CK. Ultimately, these cascading effects inhibited panicle development and reduced yield. The findings provide a theoretical basis for improving rice tolerance to combined abiotic stresses by targeting oxidative stress mitigation, photosynthetic protection, and key stress-responsive gene regulation. Full article

The incorporation of alfalfa into grass systems reduces reliance on nitrogen fertilizer application. Over two consecutive years, we investigated the regulation of carbon and nitrogen metabolism in grasses and productivity enhancement under four nitrogen application rates (0, 105, 210, and 315 kg·ha⁻¹) and five alfalfa incorporation levels (0%, 10%, 20%, 30%, and 40%); incorporation (%) refers strictly to seeding proportion (% of the monoculture seeding rate). Within the range of 20–30% alfalfa incorporation and 105–210 kg·ha⁻¹ nitrogen application, key physiological and biochemical parameters, except the net photosynthetic rate (P_n), reached their peak values compared to the N0A0 (no nitrogen and no alfalfa) treatment. Transpiration rate (T_r), intercellular CO₂ concentration (C_i), and stomatal conductance (G_s) increased by 43.64%, 40%, and 48.09%, respectively. P_n peaked under the N2A0 treatment (210 kg·ha⁻¹ nitrogen application and no alfalfa), increased by 65.63%. Nitrate reductase (NR), glutamine synthetase (GS), and ribulose-1,5-bisphosphate carboxylase (RuBisCO) activity increased by 154.60%, 112.39%, and 199.19%, respectively. Total sugar (TS) and protein production (YCP) increased by 122.22% and 145.17%, respectively. The entropy-weighted TOPSIS evaluation based on multi-objective assessment showed that the combination of 20% alfalfa incorporation with 105 kg N·ha⁻¹ application is an efficient model for enhancing forage productivity in the Horqin Sandy Land. Full article

Soybeans are highly susceptible to drought stress, which significantly impairs their growth and yield. Silicon (Si) supplementation has emerged as a promising strategy to mitigate drought-induced damage in plants. We investigated changes in the physiological and chloroplast proteomes in soybeans under drought stress, both with and without Si supplementation. Soybean plants were grown under controlled conditions and subjected to drought stress. The treatments included Si application (sodium silicate), sodium chloride control, and water control. Chloroplast proteins were extracted from control and Si-treated plants and analyzed using two-dimensional gel electrophoresis and mass spectrometry. Plants treated with Si showed improved drought tolerance, exhibiting reduced leaf rolling and wilting, while the control plants experienced significant wilting under drought conditions. Photosynthetic performance, measured by quantum efficiency of photosystem II and chlorophyll content, was better maintained in Si-supplemented plants under drought. However, stomatal conductance and transpiration were similarly reduced across all drought treatments. We detected 15 Si-responsive protein spots corresponding to 13 unique chloroplast proteins that were differentially expressed in response to Si supplementation. These identified proteins include those involved in photosynthesis, such as Rubisco activase isoforms, oxygen-evolving enhancer proteins, and PsbP domain-containing protein, as well as stress response proteins like dehydrin and 20 kDa chaperonin. Si treatment upregulated Rubisco activase isoforms, oxygen-evolving enhancer proteins, PsbP domain-containing protein, and 20 kDa chaperonin, which are typically reduced under drought. Si treatment maintained a higher glutamine synthetase level under drought stress. Gene ontology and KEGG pathway analyses revealed that Si-modulated proteins are associated with photosynthesis, energy metabolism, and nitrogen metabolism under drought stress. Our findings demonstrate that Si supplementation alleviates drought stress in soybean by preserving chloroplast function and enhancing the expression of photosynthetic proteins and enzymes, as well as key stress-responsive proteins. This research provides insights into the molecular mechanisms of Si-induced drought tolerance in soybeans and highlights potential targets for developing drought-resilient soybean cultivars. Full article

Glutamine synthetase, a critical enzyme catalyzing the conversion of glutamate and ammonia into glutamine, has been shown to influence sperm development in mammals. Here, we carried out functional analysis of Bombyx mori homolog of glutamine synthetase 1 (BmGS1) and screened its small-molecule inhibitor. RT-PCR and qPCR showed that BmGS1 was specifically expressed in the testis of the silkworm, with the highest expression in the moth stage. Subcellular localization revealed that the BmGS1 protein was localized in mitochondria and cytoplasm. Identification of upstream regulatory factors revealed that the expression of BmGS1 is positively regulated by the sex-related transcription factor Bmdsx. Virtual screening, molecular docking and MD simulations showed that the small molecule Ethylhexyl triazone (ET), as well as the known GS inhibitor L-Methionine -DL-sulfoximine (MSX), could be stably bound to BmGS1. Subsequently, site-specific mutation and fluorescence binding assays revealed that the putative key sites of ET binding to the protein were E79 and R265, and the putative key sites of MSX binding to the protein were E81, R245, and R286. Both in vitro and in vivo experiments demonstrated that inhibitor treatment significantly attenuated BmGS1 enzymatic activity. Inhibitor-injected silkworms showed reduced fertilization rates compared to control groups. Our findings raise BmGS1 as a potential target for silkworm sterility. Full article

Canopy ammonia (NH₃) exchange is a major contributor to agricultural NH₃ emissions and is closely linked to nitrogen-use efficiency. Glutamine synthetase (GS) mediates plant NH₃ assimilation, yet the specific roles of different GS isoenzymes in regulating wheat canopy NH₃ exchange remain unclear. This study aimed to clarify the functional differences of wheat TaGS isoenzymes in modulating canopy–atmosphere NH₃ exchange dynamics using two wheat cultivars (Yumai 49-198 and Xinong 509) under two nitrogen application levels (120 and 225 kg N ha⁻¹). Field experiments combined with FTIR-based NH₃ flux measurement, biochemical assays, and molecular analyses were conducted at anthesis and 16, 24, and 30 days after anthesis (DAA). Results showed that the leaf NH₃ compensation point, determined by apoplastic NH₄⁺ concentration, is a key factor influencing canopy NH₃ exchange. Leaf NH₃ sources exhibited distinct temporal specificity: photorespiration and nitrate reduction dominated at anthesis to 16 DAA, whereas nitrogenous compound degradation prevailed at 24–30 DAA. This temporal partitioning was highly coordinated with TaGS isoenzyme expression: TaGS2 was highest in early grain filling, potentially supporting assimilate NH₃ from photorespiration/nitrate reduction, while TaGS1;1 expression increased progressively, aligning with the scavenging of NH₃ from organic nitrogen degradation. These coordinated patterns suggest that the TaGS isoenzymes play differentiated roles in influencing wheat canopy NH₃ exchange. This study thus provides correlative insights that point to potential molecular targets for breeding nitrogen-efficient wheat cultivars and mitigating agricultural NH₃ emissions sustainably. Full article

Erysiphe corylacearum, the causal agent of powdery mildew in hazelnut (Corylus avellana L.), has become an emerging pathogen of concern in Italian hazelnut production requiring rapid and accurate detection to support timely disease management and phytosanitary measures. We developed and validated a field-deployable loop-mediated isothermal amplification (LAMP) assay for the specific detection of E. corylacearum and evaluated three primer sets targeting the Internal Transcribed Spacer (ITS) region, RNA polymerase II second largest subunit (rpb2), and glutamine synthetase (GS) genes; the GS-targeting Ecg set showed the highest sensitivity and specificity. The assay was shown to be sensitive down to 200 fg of fungal DNA, efficiently detected E. corylacearum from diluted crude leaf extracts, and produced results within half an hour, allowing the detection of latent infections before visible symptoms emerged. On-site validation with a portable LAMP instrument showed the assay’s suitability for field-deployable diagnosis and early-warning applications in hazelnut orchards. Full article

Water scarcity is a major constraint to upland rice production, and optimizing drought management to balance yield and quality is critical for sustainable agriculture. This study investigated the effects of three soil water potential (SWP) levels—0 kPa (control), −20 kPa (moderate drought), and −40 kPa (severe drought)—on grain quality, nitrogen metabolism, and endosperm structure in two upland rice varieties (Brazilian upland rice and Zhonghan 3). Compared with the control, moderate drought significantly improved grain quality: whole milled rice recovery increased by 5.3–7.8%, chalky grain rate decreased by 16.1–29.6%, amylose content declined by 8.65–12.19%, and glutelin content rose by 9.3–12.9%. Under moderate drought, nitrogen metabolism appeared to be upregulated, as indicated by increased activities of glutamine synthetase (GS, +18.6%) and glutamate dehydrogenase (GDH, +14.2%) and higher glutamate content (+21.4%) in Zhonghan 3, with similar but slightly attenuated responses in Brazilian upland rice. Moderate drought was associated with elevated glutelin accumulation and a more compact endosperm microstructure, suggesting a potential link between nitrogen metabolism and grain development. In contrast, severe drought impaired both grain quality and yield. Correlation analysis (n = 12) revealed that the GS/GDH ratio and glutelin content were significantly correlated with improved grain quality—positively with milled rice recovery (r = 0.58 * to 0.82 **, p < 0.05 or 0.01) and negatively with chalkiness, amylose content, and setback viscosity (r = −0.58 * to −0.93 **, p < 0.05 or 0.01). These findings indicate that maintaining SWP at −20 kPa represents a feasible strategy to enhance upland rice grain quality, offering a theoretical basis for water-saving, quality-oriented production systems. Full article