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Keywords = central carbon and nitrogen metabolism

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30 pages, 2017 KB  
Review
Post-Translational Control of Nitrate Reductase Under Elevated CO2 in Solanum lycopersicum: Carbon–Nitrogen Signaling and Photosynthetic Acclimation
by Abhishek Sahoo and Mukesh Meena
Plants 2026, 15(17), 2663; https://doi.org/10.3390/plants15172663 - 31 Aug 2026
Viewed by 356
Abstract
Rising atmospheric CO2 is altering carbon–nitrogen interactions in C3 crops, with tomato (Solanum lycopersicum L.) showing enhanced carbon assimilation but frequently reduced nitrogen acquisition and assimilation. Nitrate reductase (NR), the rate-limiting enzyme in nitrate reduction, plays a central role by [...] Read more.
Rising atmospheric CO2 is altering carbon–nitrogen interactions in C3 crops, with tomato (Solanum lycopersicum L.) showing enhanced carbon assimilation but frequently reduced nitrogen acquisition and assimilation. Nitrate reductase (NR), the rate-limiting enzyme in nitrate reduction, plays a central role by integrating nitrate assimilation with carbon metabolism and nitric oxide (NO) signaling. This review summarizes current knowledge of NR regulation in tomato under elevated CO2 (eCO2), focusing on post-translational mechanisms and their contribution to photosynthetic acclimation. Elevated CO2 modulates NR activity through interconnected changes in photorespiration, carbohydrate-mediated feedback, redox regulation, source–sink dynamics, and nitrogen availability. While eCO2 generally suppresses leaf nitrate assimilation by reducing photorespiratory support, root-zone CO2 enrichment can transiently stimulate root NR activity, highlighting tissue-specific regulation. Multi-omics studies further demonstrate extensive metabolic and molecular reprogramming affecting carbon skeleton supply, amino acid biosynthesis, and nitrogen assimilation. In addition, NR-dependent NO production links nitrogen metabolism with stomatal regulation through ABA-independent H2O2–NO signaling. Despite these advances, the roles of NR phosphorylation, 14-3-3 protein interactions, and redox-mediated regulation under eCO2 remain poorly understood. Overall, NR functions as a key metabolic and signaling hub coordinating carbon and nitrogen metabolism under future climate conditions. Understanding these regulatory mechanisms will facilitate strategies to improve nitrogen-use efficiency, sustain photosynthesis, and enhance tomato productivity under elevated atmospheric CO2 while identifying priorities for future physiological, molecular, and multi-omics research. Full article
(This article belongs to the Special Issue Photosynthesis, Nitrogen and Elevated CO2 in the Atmosphere)
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19 pages, 5702 KB  
Article
Mixed Exposure to Underground Air Pollutants and Metabolic Syndrome in Coal Miners: A Cross-Sectional Study Integrating Multi-Pollutant Models and Urinary Metabolomics
by Jia Wang, Shuying Chen, Chenyi Wang, Wenwen Li, Yuanjie Zou, Fenglin Zhu and Min Mu
Toxics 2026, 14(9), 746; https://doi.org/10.3390/toxics14090746 - 24 Aug 2026
Viewed by 304
Abstract
To investigate the associations between single and mixed exposure to air pollutants in underground coal mine environments and the risk of metabolic syndrome (MetS) among workers, we conducted a cross-sectional study. Multivariable logistic regression, Bayesian kernel machine regression (BKMR), and quantile-based g-computation (Qgcomp) [...] Read more.
To investigate the associations between single and mixed exposure to air pollutants in underground coal mine environments and the risk of metabolic syndrome (MetS) among workers, we conducted a cross-sectional study. Multivariable logistic regression, Bayesian kernel machine regression (BKMR), and quantile-based g-computation (Qgcomp) were used to evaluate the joint effects of mixed pollutant exposures and to identify the major contributing components. In addition, untargeted urinary metabolomics analysis was performed to explore the potential biological mechanisms. After adjusting for confounding factors, logistic regression analysis revealed that exposure to coal dust (CD), carbon monoxide (CO), carbon dioxide (CO2), and nitrogen dioxide (NO2) was associated with an increased risk of MetS. Furthermore, BKMR and Qgcomp models consistently indicated a significant positive association between mixed pollutant exposure and MetS risk, with CD and NO2 identified as the primary components with the strongest statistical contribution. CD exposure was mainly associated with central obesity and hypertension, whereas NO2 exposure was primarily linked to elevated blood glucose and triglyceride levels. MetS patients exhibited significant alterations in urinary metabolic profiles, with more than 113 differentially abundant metabolites identified. Notably, leukotrienes were positively correlated with NO2 exposure, while acylcarnitines were associated with CD exposure. Pathway enrichment analysis indicated significant disturbances in pyrimidine and arachidonic acid metabolism. These findings provide important evidence for developing comprehensive occupational health strategies in mining environments. Full article
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32 pages, 13732 KB  
Article
Integrated GWAS Candidate Prioritization, Moso Bamboo Transcriptome Screening and Diverse Bamboo Shoot Multi-Omics Reveal a Multi-Layer Framework for Bamboo Property Formation
by Chunze Xie, Jingjing Long, Tiansi Luo, Yidan Shi, Ruidong Lu, Yuanhang Wu, Senlong Zheng, Jiahe Li, Wei Zhang, Jiayu Liu, Wanyu Li, Zhixiang Xu, Feng Tian, Hong Zeng, Shoujin Cao, Peng Dang, Hanbin Wu and Song Sheng
Horticulturae 2026, 12(8), 1030; https://doi.org/10.3390/horticulturae12081030 - 18 Aug 2026
Viewed by 400
Abstract
Bamboo shoot development influences subsequent culm architecture and material properties, but the biological relevance of GWAS-derived candidates remains unclear. A stepwise candidate-prioritization strategy integrated 99 previously reported property-associated candidates with large-scale moso bamboo transcriptome screening, multi-species bamboo shoot transcriptome–metabolome data, and qRT-PCR analysis. [...] Read more.
Bamboo shoot development influences subsequent culm architecture and material properties, but the biological relevance of GWAS-derived candidates remains unclear. A stepwise candidate-prioritization strategy integrated 99 previously reported property-associated candidates with large-scale moso bamboo transcriptome screening, multi-species bamboo shoot transcriptome–metabolome data, and qRT-PCR analysis. The candidates were classified into three functional layers: environmental adaptation/stress signaling, carbohydrate metabolism/carbon allocation, and cell wall biosynthesis/remodeling. A rule-based ranking that balanced candidate representation across the three functional categories retained 44 genes for transcriptomic evaluation, of which 30 showed strong or moderate expression support across 90 comparisons. Cell wall biosynthesis/remodeling genes exhibited the broadest transcriptional responses, whereas carbohydrate- and regulatory-related genes provided complementary metabolic and upstream evidence. Correlation analysis across 24 matched shoot variables and 5059 metabolites prioritized PH02Gene17228, PH02Gene00247, and PH02Gene51360, which were associated with amino acid/nitrogen metabolism, hormone/signaling-like metabolites, and organic acid/central carbon metabolism, respectively. qRT-PCR analysis independently supported their expression patterns in developing bamboo shoots. These results support a working model in which regulatory signaling, carbon allocation, and cell wall remodeling jointly contribute to bamboo property-related variation. The prioritized genes provide targets for functional validation and may inform future marker development and molecular breeding aimed at improving bamboo culm quality and material properties. Full article
(This article belongs to the Section Genetics, Genomics, Breeding, and Biotechnology (G2B2))
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21 pages, 21904 KB  
Article
Effects of Dietary Protein and Starch Digestion Rates on Jejunal and Cecal Microbial Community States and Feed Efficiency in Raccoon Dogs
by Weixiao Nan, Runyu Jiang, Xing Duan, Sibo Chen, Shaochen Yu, Ruijia Deng, Yunxi Zhang, Daozhi Wang, Haoxuan Xu, Zhipeng Li and Huazhe Si
Animals 2026, 16(16), 2549; https://doi.org/10.3390/ani16162549 - 15 Aug 2026
Viewed by 322
Abstract
Feed efficiency remains a significant challenge in farmed raccoon dogs, and performance differences can occur even when diets are formulated with similar nutrient levels. Beyond nutrient concentrations, digestion kinetics can alter the timing of carbon and nitrogen availability along the gastrointestinal tract, thereby [...] Read more.
Feed efficiency remains a significant challenge in farmed raccoon dogs, and performance differences can occur even when diets are formulated with similar nutrient levels. Beyond nutrient concentrations, digestion kinetics can alter the timing of carbon and nitrogen availability along the gastrointestinal tract, thereby influencing microbial assembly in a segment-specific way. Twenty 2-month-old male raccoon dogs (Nyctereutes procyonoides) were divided into four dietary groups (n = 5) in a 2 × 2 factorial design. The design combined protein-source formulations containing either soybean cake or dried distillers grains with solubles and starch-source formulations based primarily on either extruded corn or high-amylose corn starch, representing relatively rapid and slow expected digestion characteristics, respectively. The purpose was to assess how digestion-rate synchronization affects jejunal and cecal microbiota structure and whether community state types (CSTs) link diet and feed efficiency. Growth performance varied modestly among treatments, with group B showing the lowest feed-to-gain ratio (F/G) and highest average daily gain (ADG). Starch source significantly affected ADG, while protein and protein × starch interaction influenced F/G. Microbiota profiles were strongly segment-dependent: the cecum had higher richness and diversity than the jejunum. Two-way analyses and Bray–Curtis ordinations showed that the jejunal community was primarily associated with the protein × starch interaction, whereas the cecal community was associated mainly with the protein-source factor and the protein × starch interaction. Network analysis revealed more complex and densely connected microbial communities in the cecum, with core genera occupying central positions. Dirichlet multinomial mixture modeling, performed independently for each intestinal segment, identified two jejunal community states (J-CST1 and J-CST2) and two cecal community states (C-CST1 and C-CST2). J-CST1 and J-CST2 represented alternative lactic acid bacteria-dominated configurations, with J-CST2 enriched in Lactobacillus and J-CST1 characterized by higher abundances of Streptococcus and Bacillus. C-CST2 was represented predominantly by samples from group B and was characterized by higher abundances of Segatella and taxa affiliated with Bacteroidota and Lachnospiraceae. Predicted functional profiles differed between CSTs, involving pathways related to carbohydrate, amino acid, lipid, and bile acid metabolism. Mediation analysis did not provide consistent evidence of significant indirect effects for J-CST membership, whereas C-CST membership was associated with significant estimated indirect effects on final body weight, ADG, and F/G. These findings suggest that dietary protein- and starch-source combinations with different expected digestion characteristics drive segment-specific microbial patterns. Supported by taxonomic, network and functional evidence, cecal CSTs act as an intermediate ecological phenotype that partially explains the variation in growth efficiency, highlighting hindgut community states as potential targets for personalized nutrition of raccoon dogs. Full article
(This article belongs to the Section Animal Nutrition)
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18 pages, 2839 KB  
Article
Characterization of a Novel Quorum Quencher Acinetobacter schindleri Strain XJ-10: AHL Degradation Capability, Metabolic Pathways and Its Role in Soft Rot Disease Biocontrol
by Xiaofang Luo, Hui Liu, Zhihao Wen, Wen-Juan Chen, Xinghui Fan, Mohamed A. Ghorab, Shaohua Chen and Yonglin Liao
Plants 2026, 15(16), 2439; https://doi.org/10.3390/plants15162439 - 11 Aug 2026
Viewed by 243
Abstract
Quorum sensing (QS) is critically involved in mediating microbial interactions and serves as a central regulatory mechanism in bacterial pathogenesis. As an emerging countermeasure, quorum quenching (QQ) suppresses QS-regulated virulence through enzymatic or chemical disruption of signal systems. N-acyl homoserine lactone (AHL), [...] Read more.
Quorum sensing (QS) is critically involved in mediating microbial interactions and serves as a central regulatory mechanism in bacterial pathogenesis. As an emerging countermeasure, quorum quenching (QQ) suppresses QS-regulated virulence through enzymatic or chemical disruption of signal systems. N-acyl homoserine lactone (AHL), an evolutionarily conserved QS signal, coordinates the pathogenicity of multiple plant pathogens, particularly Dickeya zeae, which causes soft rot disease in various crops and leads to substantial agricultural losses. In this study, the QQ strain Acinetobacter schindleri XJ-10 was evaluated for its capacity to degrade AHL and attenuate the pathogenicity of D. zeae EC1 in host plants. Notably, strain XJ-10 exhibited efficient AHL degradation at 0.2 mmol/L within 24 h, achieving a degradation efficiency of 98.80%. Subsequently, gas chromatography–mass spectrometry (GC-MS) analysis identified N-hexanoyl-L-homoserine lactone and propanamide as key intermediates during AHL degradation, confirming complete mineralization to CO2 and H2O. Based on the structural characterization of AHL and its intermediates, the metabolic pathway within strain XJ-10 was proposed. The degradation pathway initiates with the hydrolysis of the ester ring of N-hexanoyl-L-homoserine lactone, generating N-hexanoyl-L-homoserine. Subsequent carbon–nitrogen bond scission is predicted to yield N-cyclohexyl-propanamide, which is further catabolized to produce hexanamide and propanamide. Furthermore, strain XJ-10 exhibited biocontrol activity against soft rot disease affecting potato (Solanum tuberosum), radish (Raphanus sativus), and Chinese cabbage (Brassica rapa subsp. pekinensis), as its crude enzyme extract effectively reduced disease incidence and severity in planta. While strain XJ-10 showed no detectable acylase activity, it exhibited significant degradation activity against AHL, suggesting a distinct QQ mechanism. Collectively, these findings broaden the scope of QQ-based biocontrol strategies and enhance mechanistic insights into managing bacterial diseases through QS modulation. Full article
(This article belongs to the Special Issue Biological Control of Phytopathogen-Associated Plant Diseases)
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22 pages, 808 KB  
Review
Amino Acid Metabolic Remodeling in Bivalves Under Environmental Stress: Roles, Mechanisms, and Implications for Bivalve Health—A Review
by Yichen Lin, Wei Chen, Jixing Peng, Xinnan Zhao, Yan Di, Mengmeng Guo, Yanfang Zhao, Haiyan Wu, Guanchao Zheng, Qianqian Geng and Zhijun Tan
Fishes 2026, 11(8), 460; https://doi.org/10.3390/fishes11080460 - 6 Aug 2026
Viewed by 389
Abstract
Climate change and increasing instability in coastal marine environments have intensified stressors such as elevated temperature, hypoxia, salinity variation, and pollutant exposure, posing major challenges to the survival, health, and culture performance of bivalves. As economically important aquaculture species and key components of [...] Read more.
Climate change and increasing instability in coastal marine environments have intensified stressors such as elevated temperature, hypoxia, salinity variation, and pollutant exposure, posing major challenges to the survival, health, and culture performance of bivalves. As economically important aquaculture species and key components of coastal ecosystems, bivalves are highly sensitive to environmental fluctuations, making their metabolic responses highly relevant to both physiological adaptation and aquaculture sustainability. Increasing evidence indicates that metabolic remodeling is an important adaptive strategy supporting bivalve tolerance to environmental stress, with amino acid metabolic remodeling emerging as one of its most sensitive and functionally important components. This review summarizes the major response patterns, key pathways, and potential regulatory mechanisms of amino acid metabolism in bivalves under different stress conditions. Different environmental stressors induce distinct yet integrated shifts in amino acid metabolism, including enhanced catabolism, carbon–nitrogen redistribution, osmotic regulation, and antioxidant defense, thereby supporting energy homeostasis and physiological stress tolerance in bivalves. By highlighting amino acid metabolic remodeling as a central mechanism of bivalve adaptation to environmental stress, this review provides insights into adaptive responses, metabolite-based indicators for monitoring aquaculture environments and bivalve health, and management strategies for improving resilience in bivalve aquaculture. Full article
(This article belongs to the Special Issue Genomic Selection, Genome-Wide Association and Omics in Aquaculture)
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18 pages, 4267 KB  
Article
Trade-Offs and Driving Factors of Microbial Carbon and Nitrogen Use Efficiency in Typical Forest Ecosystems of Funiu Mountain
by Yadong Xu, Yiran Lai, Luotong Zhao, Shujuan Guo and Tianfu Han
Microorganisms 2026, 14(7), 1580; https://doi.org/10.3390/microorganisms14071580 - 20 Jul 2026
Viewed by 423
Abstract
Soil microbial carbon use efficiency (CUE) and nitrogen use efficiency (NUE) are fundamental parameters governing organic matter turnover in terrestrial ecosystems, yet how forest type-driven variation in litter quality propagates through the litter–soil–microbe continuum to regulate these efficiencies remains poorly resolved. Across three [...] Read more.
Soil microbial carbon use efficiency (CUE) and nitrogen use efficiency (NUE) are fundamental parameters governing organic matter turnover in terrestrial ecosystems, yet how forest type-driven variation in litter quality propagates through the litter–soil–microbe continuum to regulate these efficiencies remains poorly resolved. Across three forest types in the Funiu Mountains, central China—a Larix gmelinii (LG) plantation, a Quercus aliena var. acuteserrata (QA) secondary forest, and a mixed Quercus aliena var. acutiserrata and Pinus armandii (QP) forest—we quantified litter chemistry, soil physicochemical properties, microbial biomass, extracellular enzyme activities, and microbial nutrient use efficiencies (MUE: NUE, and phosphorus use efficiency, PUE) derived from a modified saturation kinetics model. Principal coordinate analysis revealed significant multivariate differentiation among forest types across litter, soil, microbial biomass, and enzyme modules (Adonis R2 = 0.198–0.427; all p < 0.05). Compared with LG and QA, QP exhibited a pronounced stoichiometric imbalance: it supported the highest litter organic carbon and total nitrogen, the lowest lignin-to-cellulose ratio, the largest soil C and N pools (SOC and STN), and the greatest microbial biomass carbon (MBC). However, despite this resource-rich environment, microbial biomass C:N:P ratios exhibited constrained variation, while soil C:P (SCP) and N:P ratios (SNP) in QP reached extreme values (112.3 and 7.25, respectively), generating severe stoichiometric imbalance. Vector analysis indicated that all forests were under relative nitrogen limitation (vector angle < 45°), with QP showing the strongest limitation (41.6 ± 0.4°). Critically, QP exhibited the highest NUE (0.47 ± 0.03) but the lowest CUE (0.95 ± 0.01), and CUE and NUE were nearly perfectly negatively correlated across all sites (R = −0.98, p < 0.001). Random forest analysis identified extracellular enzyme stoichiometry as the dominant proximate predictor of MUE. Partial least squares structural equation modeling (GOF = 0.673–0.674; R2 = 0.592–0.603) revealed that litter and soil properties had no significant direct effects on CUE or NUE; instead, soil nutrients exerted strong indirect association through a cascade—soil → microbial biomass → enzyme activity—with opposite total effects on CUE (−0.731, p < 0.001) versus NUE (+0.755, p < 0.001). These findings reveal that the same soil nutrient enrichment that accompanies mixed-species afforestation drives divergent microbial metabolic responses—suppressing CUE while promoting NUE—through a shared cascading structure, with implications for predicting soil carbon and nutrient retention under shifting forest compositions. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 3rd Edition)
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17 pages, 4559 KB  
Article
Trifluoromethanesulfonamide Induces Male Sterility Through Systemic Metabolic Reprogramming and Anther-Specific Proline Deficiency
by Yuka Sekiguchi, Yan Gao, Hiromitsu Tabeta, Muneo Sato, Masami Yokota Hirai, Nasrein Mohamed Kamal and Takayoshi Ishii
Int. J. Mol. Sci. 2026, 27(12), 5554; https://doi.org/10.3390/ijms27125554 - 19 Jun 2026
Viewed by 597
Abstract
Chemical hybridization agents (CHAs) enable efficient, large-scale hybrid seed production, yet their mechanisms remain poorly understood. Understanding how CHAs induce male sterility at the metabolic level is important for both basic pollen biology and crop breeding. Here, we performed integrated metabolomic analyses to [...] Read more.
Chemical hybridization agents (CHAs) enable efficient, large-scale hybrid seed production, yet their mechanisms remain poorly understood. Understanding how CHAs induce male sterility at the metabolic level is important for both basic pollen biology and crop breeding. Here, we performed integrated metabolomic analyses to investigate the metabolic basis of the action of trifluoromethanesulfonamide (TFMSA) across multiple species and tissues. TFMSA treatment induced systemic metabolic reprogramming across species, prominently affecting amino acid metabolism, central carbon metabolism, and one-carbon metabolism. Although individual metabolite responses varied among species, pathway-level analyses consistently revealed coordinated modulation of carbon–nitrogen metabolic networks. In reproductive tissues, TFMSA induced tissue-specific metabolic changes. In cowpea anthers, proline was the only metabolite significantly altered and was strongly depleted, whereas in floral tissues several amino acids, including phenylalanine and tyrosine, were accumulated. Pathway analysis revealed altered amino acid metabolism, suggesting that systemic metabolic responses accompanied the proline reduction in anthers. These findings indicate that TFMSA induces male sterility through coordinated metabolic reprogramming across tissues and species, leading to depletion of key metabolites required for pollen development. This study provides a metabolic framework for understanding CHA-induced male sterility and highlights TFMSA as a powerful tool for probing metabolic regulation of pollen development. Full article
(This article belongs to the Section Molecular Plant Sciences)
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29 pages, 9857 KB  
Article
Network Structure Explained the Differences in the Response of Soil Bacterial Community Structure and Functional Structure to Afforestation Types
by Zhenlu Qiu, Jin Liu, Hui Gao, Suying Dong, Xiaojin Zang, Wenxin Kang and Jing Shu
Forests 2026, 17(6), 702; https://doi.org/10.3390/f17060702 - 16 Jun 2026
Viewed by 489
Abstract
This study used 16S rDNA high-throughput sequencing and Faprotax functional prediction to analyze the effects of different artificial forests (coniferous forest, conifer–broad-leaved mixed forest, broad-leaved forest) in the Fanggan ecological restoration area of North China on soil bacterial community composition and functional characteristics [...] Read more.
This study used 16S rDNA high-throughput sequencing and Faprotax functional prediction to analyze the effects of different artificial forests (coniferous forest, conifer–broad-leaved mixed forest, broad-leaved forest) in the Fanggan ecological restoration area of North China on soil bacterial community composition and functional characteristics and, based on network topology features, analyzed the potential influencing pathways. Planting broad-leaved forests significantly increased soil bacterial α-diversity indices (ACE, Chao1, Shannon) and induced the greatest heterogeneity in both community and functional composition. Soil bacteria exhibit significant differences in taxonomic structure across forest types but not in functional structure. The classification network and functional network of broad-leaved forests are more complex than those of coniferous and mixed forests, with the former having more nodes and edges, as well as higher weighted degree and betweenness centrality. Zi-Pi analysis indicates that high-abundance taxa involved in carbon and nitrogen cycles dominate the keystone taxa of the taxonomic network, while low-abundance pathogenic, urea-decomposing, and trace element metabolism functional groups dominate the keystone groups of the functional network. Redundancy analysis further revealed that soil available potassium concentration, pH, and tree species composition (importance values of Pinus tabulaeformis and Populus davidiana) were the principal determinants of bacterial functional structure. Collectively, broad-leaved forests achieve higher network robustness via elevated network complexity and functional redundancy, whereas coniferous forests might rely on functional convergence and modular integration to cope with resource limitation. These results indicate that network traits mediate the distinct responses of bacterial communities and their functional potentials, offering practical references for vegetation restoration in limestone mountain areas. Full article
(This article belongs to the Section Forest Soil)
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17 pages, 2636 KB  
Article
The Role of ATG8 in Promoting Lipid Accumulation in the Oleaginous Fungus Mucor circinelloides During Nitrogen Limitation
by Hequn Li, Hongjuan Yuan, Bushra Iqbal, Tianyu Wang, Zhen Wang and Huaiyuan Zhang
J. Fungi 2026, 12(6), 410; https://doi.org/10.3390/jof12060410 - 4 Jun 2026
Viewed by 670
Abstract
Autophagy is a central cellular process that recycles intracellular components and supplies precursors for biosynthesis. As a key regulator of autophagosome formation, autophagy-related protein 8 (ATG8) plays an essential role in macromolecular degradation and in the availability of lipid precursors. However, whether enhanced [...] Read more.
Autophagy is a central cellular process that recycles intracellular components and supplies precursors for biosynthesis. As a key regulator of autophagosome formation, autophagy-related protein 8 (ATG8) plays an essential role in macromolecular degradation and in the availability of lipid precursors. However, whether enhanced autophagic flux promotes lipid accumulation in oleaginous fungi remains unclear. In this study, atg8-1 and atg8-2 were homologously overexpressed in the oleaginous fungus Mucor circinelloides to evaluate their roles in lipid biosynthesis. The engineered strains McATG8-1T2 and McATG8-2T2 showed significantly increased total fatty acid (TFA) contents (32.9% and 32.5%), representing improvements of 15.0% and 13.7% compared with the control. γ-Linolenic acid levels were also elevated to 16.9% and 16.5%, relative increases of 25.2% and 22.0%, respectively. RT-qPCR analysis revealed coordinated upregulation of genes involved in autophagy, central carbon metabolism, lipid biosynthesis, and the pentose phosphate pathway. Ethanolamine supplementation further enhanced lipid accumulation, increasing TFA contents by 12.2–14.6%. In addition, inhibition of target of rapamycin complex 1 using rapamycin produced a strong synergistic effect with atg8 overexpression, leading to substantial lipid increases under nitrogen-limited and nitrogen-rich conditions. Collectively, these findings demonstrated that ATG8-mediated autophagy enhanced lipid accumulation and acted as a key determinant of lipid synthesis flux. Full article
(This article belongs to the Section Fungal Cell Biology, Metabolism and Physiology)
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37 pages, 21678 KB  
Article
From Pathway Tracing to Actionable Targets: Integrative Mendelian Randomization and Experimental Triangulation Map Metabolic Pathways Across Ovarian Cancer Histotypes
by Xinqi Wang, Haoyu Wang, Siyuan Hu, Wenyi Zhang, Huiyu Chen, Ying Shen, Hongyang Xue and Li Hong
Int. J. Mol. Sci. 2026, 27(11), 5043; https://doi.org/10.3390/ijms27115043 - 2 Jun 2026
Viewed by 797
Abstract
Ovarian cancer (OC) comprises multiple histotypes with distinct mechanisms, molecular features, and clinical behavior. We used Mendelian randomization (MR) to map histotype-stratified metabolic pathways and connect them to drug targets, establishing a translatable target–metabolic node–histotype risk chain. We built a multi-stage MR framework [...] Read more.
Ovarian cancer (OC) comprises multiple histotypes with distinct mechanisms, molecular features, and clinical behavior. We used Mendelian randomization (MR) to map histotype-stratified metabolic pathways and connect them to drug targets, establishing a translatable target–metabolic node–histotype risk chain. We built a multi-stage MR framework using Integrative Epidemiology Unit (IEU) OpenGWAS summary statistics. After screening 1400 plasma metabolites against overall ovarian cancer in UK Biobank and Ovarian Cancer Association Consortium (OCAC) with KEGG enrichment, we traced a prespecified amino acid/energy–nitrogen axis using histotype-stratified univariable MR and pathway-restricted multivariable MR. We then performed cis drug-target MR for PPARG, DPP4, ABCC8/KCNJ11, and SLC5A2, integrated triangulation, colocalization, and mediation analyses, and experimentally interrogated the prioritized PPARG/ABCC8-KCNJ11–lactate–invasive mucinous ovarian cancer (IMOC) triangle. Screening nominated 55 and 72 metabolites in UK Biobank and OCAC, respectively (IVW p < 0.05), highlighting amino-acid nitrogen and central-carbon metabolism. Univariable Mendelian randomization (UVMR) showed marked heterogeneity: alanine increased low-grade serous ovarian cancer (LGSOC) risk, glutamate was protective for endometrioid OC, and lactate-related traits most consistently implicated the low-grade/borderline serous lineage. In multivariable Mendelian randomization (MVMR), tryptophan and lactate levels emerged as independent risk nodes for serous low-grade plus low malignant potential (LG + LMP). Drug-target MR prioritized PPARG as protective (OR = 0.18) and ABCC8/KCNJ11 as risk-increasing (OR = 7.50) for IMOC, with opposite target → lactate effects supporting a directionally symmetric target–lactate–IMOC triangle. Experimental perturbation in mucinous ovarian cancer models produced concordant reciprocal changes in lactate and malignant phenotypes, extending this triangle biologically. This integrative MR framework delineates histotype-specific metabolic drivers and links them to actionable targets, providing a roadmap from genetic prioritization to mechanistic and translational validation. Full article
(This article belongs to the Section Molecular Endocrinology and Metabolism)
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21 pages, 2967 KB  
Article
5-Aminolevulinic Acid Drives Coordinated Astaxanthin and Lipid Accumulation in Green Alga Chromochloris zofingiensis
by Jinrui Gao, Zhongliang Sun, Bin Liu, Yu Zhang and Liqin Sun
Foods 2026, 15(10), 1768; https://doi.org/10.3390/foods15101768 - 17 May 2026
Viewed by 379
Abstract
Chromochloris zofingiensis, a photosynthetic microalga, has attracted considerable attention due to its ability to simultaneously accumulate lipids and astaxanthin. However, the induction of lipid and secondary metabolite biosynthesis by abiotic stress is typically accompanied by growth inhibition, resulting in a trade-off between [...] Read more.
Chromochloris zofingiensis, a photosynthetic microalga, has attracted considerable attention due to its ability to simultaneously accumulate lipids and astaxanthin. However, the induction of lipid and secondary metabolite biosynthesis by abiotic stress is typically accompanied by growth inhibition, resulting in a trade-off between metabolite accumulation and biomass production. In recent years, phytohormones have emerged as an effective strategy for regulating microalgal metabolism, owing to their high specificity and low effective dosage. In this study, 5-aminolevulinic acid (5-ALA) was applied under nitrogen-deficient conditions, and its effects on growth, photosynthesis, lipid metabolism, and carotenoid biosynthesis were systematically evaluated through integrated physiological, biochemical, and transcriptomic analyses. The results showed that 5-ALA had no significant effect on biomass accumulation or photosynthetic performance. However, at 2 μM, 5-ALA exhibited the strongest promotive effect on lipid and astaxanthin accumulation, with total fatty acids (TFA) and triacylglycerol (TAG) contents increasing by 13.3% and 25.7%, respectively, and total carotenoids and astaxanthin contents increasing by 15.6% and 17.2%, respectively. Under semi-continuous cultivation, TAG and astaxanthin productivities were enhanced by 13.9% and 22.9%, reaching 164 mg L−1 d−1 and 2.15 mg L−1 d−1, respectively. Transcriptomic analysis revealed that 5-ALA induced only limited transcriptional changes but enhanced glycolysis, central carbon metabolism, and nitrogen recycling, thereby increasing the supply of carbon precursors and energy. Notably, no significant transcriptional changes were observed in the carotenoid biosynthesis pathway, indicating that the enhanced accumulation of total carotenoids and astaxanthin was likely driven by increased metabolic flux. In terms of lipid metabolism, the upregulation of pathways involved in the conversion of membrane lipids into TAG, together with the downregulation of TAG degradation pathways and enhanced carbon flux, collectively promoted TAG accumulation. Overall, this study demonstrates that supplementation with 2 μM 5-ALA provides a practical and cost-effective strategy for the efficient co-production of lipids and astaxanthin in C. zofingiensis. Full article
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22 pages, 3313 KB  
Article
Improved Water Use Efficiency in Rice During Drought–Rewatering Cycles: Insights from Transcriptomics and Metabolomics
by Han Qiao, Xianzhi Deng, Xin Wang, Yufan Zhang, Jiateng Ma and Liangsheng Shi
Agronomy 2026, 16(10), 975; https://doi.org/10.3390/agronomy16100975 - 14 May 2026
Cited by 1 | Viewed by 490
Abstract
Alternate wetting and drying (AWD) is a crucial water-saving irrigation strategy in rice production, yet its regulatory mechanisms during drought–rewatering cycles remain unclear, particularly across recovery stages. Using a polyethylene glycol (PEG-6000) hydroponic system, we analyzed physiological, metabolomic, and transcriptomic responses of Oryza [...] Read more.
Alternate wetting and drying (AWD) is a crucial water-saving irrigation strategy in rice production, yet its regulatory mechanisms during drought–rewatering cycles remain unclear, particularly across recovery stages. Using a polyethylene glycol (PEG-6000) hydroponic system, we analyzed physiological, metabolomic, and transcriptomic responses of Oryza sativa L. ssp. japonica under control, continuous drought, and rewatering treatments. The net photosynthetic rate (Pn) recovered within one day after rewatering, and subsequently exceeded control levels, indicating a photosynthetic compensatory effect. In contrast, instantaneous water-use efficiency (WUE) showed only a transient increase before declining thereafter and remaining lower than under continuous drought, revealing an asynchronous recovery in which carbon assimilation precedes the recovery of transpiration. Metabolomic analysis indicated a shift from drought-induced accumulation to recovery-driven metabolic reprogramming, with coordinated up-regulation of central carbon metabolism and chlorophyll biosynthesis. Decreases in citrate, malate, and glutamate suggested their sustained utilization to support nitrogen assimilation and chlorophyll synthesis. Transcriptomic data further revealed large-scale reprogramming during late recovery, including up-regulation of nitrogen assimilation genes (e.g., NIA, NiR), linking carbon–nitrogen coordination with photosynthetic compensation. Overall, these results demonstrate that stage-specific integration of physiological recovery, metabolic restructuring, and transcriptional regulation underlies AWD-induced efficiency and identify early rewatering as a critical window for optimizing WUE. Full article
(This article belongs to the Section Plant-Crop Biology and Biochemistry)
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27 pages, 10837 KB  
Article
LED Light Intensity Regulates Nitrogen Assimilation Enzyme Activity and Metabolic Responses in Iceberg and Leaf Lettuce (Lactuca sativa L.)
by Nga T. T. Nguyen, Nasratullah Habibi, Naveedullah Sediqui, Oliveira Leonardo de Almeida, Maryam Dabirimirhosseinloo, Naoki Terada, Atsushi Sanada and Kaihei Koshio
Plants 2026, 15(9), 1321; https://doi.org/10.3390/plants15091321 - 25 Apr 2026
Cited by 2 | Viewed by 710
Abstract
Light availability is a key environmental factor regulating nitrogen assimilation, carbon metabolism, and nutritional quality in leafy vegetables grown in controlled environments. However, how practical lighting regimes used in plant factories with artificial lighting (PFALs) influence the coordination between nitrogen assimilation and central [...] Read more.
Light availability is a key environmental factor regulating nitrogen assimilation, carbon metabolism, and nutritional quality in leafy vegetables grown in controlled environments. However, how practical lighting regimes used in plant factories with artificial lighting (PFALs) influence the coordination between nitrogen assimilation and central carbon metabolism across different lettuce cultivar types remains insufficiently understood. This study investigated how moderate differences in photosynthetic photon flux density (PPFD) influence nitrogen metabolism and metabolic coordination in hydroponically cultivated lettuce. Two cultivars representing contrasting morphological types, iceberg lettuce (‘Celebration’) and leaf lettuce (‘Sunny’), were grown under LED light intensities of 150 and 200 µmol·m−2·s−1. Nitrate, nitrite, and ammonium concentrations were measured together with the activities of nitrate reductase (NRA) and nitrite reductase (NiRA), as well as ascorbic acid content. Metabolomic profiling was additionally performed to characterize broader metabolic responses. Higher light intensity enhanced nitrate reduction capacity in both cultivars, but the resulting patterns of nitrogen accumulation were strongly genotype-dependent. The leaf lettuce cultivar ‘Sunny’ exhibited increased NRA and reduced nitrate accumulation under higher light intensity, whereas the iceberg lettuce cultivar ‘Celebration’ accumulated more nitrate under the same conditions. Ammonium responses further suggested differences in downstream nitrogen assimilation processes. Elevated light intensity also increased ascorbic acid levels in both cultivars. Metabolomic analysis revealed contrasting cultivar-specific shifts in central carbon metabolism, particularly involving soluble sugars and tricarboxylic acid cycle intermediates, indicating differential coordination between carbon metabolism and nitrogen utilization. Overall, these findings demonstrate that moderate changes in light intensity within the practical PFAL cultivation range can significantly influence the integration of carbon and nitrogen metabolism in lettuce. Importantly, cultivar-specific physiological traits determine how these metabolic responses translate into nitrate accumulation and nutritional quality in controlled-environment production systems. Full article
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21 pages, 5166 KB  
Article
Glycine Betaine-Induced Metabolic Responses Under Heat and Cold Stress in Passiflora edulis f. flavicarpa
by Leonardo de Almeida Oliveira, Nga Thi Thu Nguyen, Darel Kenth Solde Antesco, Maryam Dabirimirhosseinlo, Naoki Terada, Atsushi Sanada and Kaihei Koshio
Int. J. Mol. Sci. 2026, 27(9), 3811; https://doi.org/10.3390/ijms27093811 - 24 Apr 2026
Cited by 1 | Viewed by 657
Abstract
Temperature extremes represent a major constraint for the cultivation of yellow passion fruit (Passiflora edulis Sims f. flavicarpa), a tropical crop increasingly exposed to heat waves and chilling events under climate change. Glycine betaine (GB) is a widely studied osmoprotectant in [...] Read more.
Temperature extremes represent a major constraint for the cultivation of yellow passion fruit (Passiflora edulis Sims f. flavicarpa), a tropical crop increasingly exposed to heat waves and chilling events under climate change. Glycine betaine (GB) is a widely studied osmoprotectant in plants, yet its influence on metabolic responses of passion fruit under contrasting temperature stresses remains poorly characterized. This study investigated the effects of exogenous GB on primary metabolite profiles of passion fruit seedlings subjected to heat (25, 35, and 45 °C) and cold (25, 15, and 5 °C) conditions. Seedlings were treated with GB (100 mM) or left untreated, and leaf metabolites were quantified using GC–MS-based metabolomics. Heat exposure was associated with pronounced changes in amino acids, organic acids, sugars, polyamines, and γ-aminobutyric acid (GABA), while GB-treated plants showed altered levels of proline, GABA, polyamines, and selected tricarboxylic acid intermediates. Under cold conditions, several amino acids and organic acids decreased, whereas soluble sugars accumulated, particularly in GB-treated plants. Principal component analysis revealed distinct metabolic configurations under heat and cold treatments and indicated that GB modified metabolite profiles in a stress-dependent manner rather than restoring control-like states. These findings describe how GB is associated with shifts in central carbon and nitrogen metabolism under contrasting temperature regimes, providing a metabolomic perspective on stress-related metabolic adjustments in passion fruit. Full article
(This article belongs to the Special Issue Abiotic Stress in Plants, 2nd Edition)
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