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Keywords = central carbon metabolism

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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
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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14 pages, 16503 KB  
Review
Breaking the Growth–Defense Trade-Off: bHLH Transcription Factors as Integrators of Development, Metabolism, and Yield in Artemisia annua
by Mingyuan Yuan and Fei Zhou
Genes 2026, 17(8), 883; https://doi.org/10.3390/genes17080883 - 29 Jul 2026
Viewed by 224
Abstract
Artemisinin, a sesquiterpene lactone produced by Artemisia annua, is synthesized and stored predominantly in glandular secretory trichomes (GSTs). Despite substantial advances in elucidating its biosynthetic pathway and transcriptional regulation, a key challenge remains: how developmental processes, hormone signaling, and metabolic pathways are [...] Read more.
Artemisinin, a sesquiterpene lactone produced by Artemisia annua, is synthesized and stored predominantly in glandular secretory trichomes (GSTs). Despite substantial advances in elucidating its biosynthetic pathway and transcriptional regulation, a key challenge remains: how developmental processes, hormone signaling, and metabolic pathways are coordinately integrated to overcome the trade-off between trichome density, metabolic flux, and vegetative biomass, which ultimately limits whole-plant yield. Recent studies have identified basic helix–loop–helix (bHLH) transcription factors (TFs) as central integrative hubs in this network. AabHLH113 functions as a convergence node linking jasmonic acid (JA) and abscisic acid (ABA) signaling to activate core biosynthetic genes. AaMYC3 bridges development and metabolism by promoting GST initiation via AaHD1 while enhancing pathway flux and cooperating with other bHLH factors to amplify amorpha-4,11-diene synthase (ADS) and artemisinic aldehyde delta-11(13) reductase (DBR2) expression. Extending this regulation to the whole-plant level, AaSPATULA coordinates GST formation with photosynthetic capacity, carbon assimilation, and biomass accumulation. Here, we propose a unified framework in which bHLH TFs integrate hormone signaling, trichome development, metabolic flux, and carbon allocation into a coherent regulatory system. We further discuss implications for next-generation metabolic engineering and highlight future directions, including multi-omics-guided, multi-target editing of regulatory hubs. This developmental–metabolic integration framework provides a conceptual basis for optimizing artemisinin production and improving high-value metabolite biosynthesis in other trichome-bearing plants. Full article
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14 pages, 3412 KB  
Article
Metabolic Reprogramming During Heat Stress and Short-Term Recovery in Oudemansiella raphanipes Revealed by Integrated Metabolomics and Transcriptomics
by Yangyang Peng, Jianhao Wang, Lingjun Xu, Nan Liao, Yan Hai, Zitian Xiao, Jiang Xu and Ming Liu
J. Fungi 2026, 12(8), 557; https://doi.org/10.3390/jof12080557 - 28 Jul 2026
Viewed by 184
Abstract
Temperature constrains stable mycelial growth and production of Oudemansiella raphanipes, but its molecular response to heat stress followed by recovery remains insufficiently resolved. We integrated untargeted LC-MS metabolomics and RNA sequencing to compare control mycelia maintained at 28 °C (HPJZ28) with mycelia [...] Read more.
Temperature constrains stable mycelial growth and production of Oudemansiella raphanipes, but its molecular response to heat stress followed by recovery remains insufficiently resolved. We integrated untargeted LC-MS metabolomics and RNA sequencing to compare control mycelia maintained at 28 °C (HPJZ28) with mycelia exposed to 42 °C for 6 h and then allowed to recover at 28 °C for 2 h (HPJZ42-R). Metabolomic and transcriptomic profiles separated clearly between the two conditions, indicating broad post-heat recovery-associated molecular remodeling. Most differential metabolites were lower in HPJZ42-R, whereas a smaller subset accumulated, suggesting selective metabolic reorganization rather than generalized activation. Transcriptome analysis identified extensive gene-expression remodeling, with 1081 upregulated and 1878 downregulated genes in the HPJZ28 versus HPJZ42-R comparison. Pathway-level analyses implicated central carbon metabolism, lipid metabolism, amino acid metabolism, peroxisome-related processes, and calcium signaling. Because the sampling design included a recovery period and a single post-stress time point, integrated gene–metabolite correlations are interpreted as exploratory associations rather than evidence of direct regulatory coupling. These results provide species-level multi-omics evidence for the post-heat recovery state of O. raphanipes and identify candidate pathways for future functional and physiological validation. Full article
(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 3rd Edition)
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39 pages, 4271 KB  
Review
Natural Product-Derived Carbon Dots in Neurodegenerative Diseases: Advances in Blood–Brain-Barrier-Related Delivery, Neuroprotection, and Theranostics
by Kaixin Song, Xiang Gu, Na Sun, Rujia Xie, Ziyan Chen, Zili Wang, Ya Li and Lei Meng
Biology 2026, 15(15), 1235; https://doi.org/10.3390/biology15151235 - 25 Jul 2026
Viewed by 426
Abstract
The mechanisms underlying neurodegenerative diseases (NDDs) involve multiple pathological processes, such as abnormal protein aggregation, oxidative stress, neuroinflammation, mitochondrial dysfunction, and the disruption of neurovascular unit homeostasis. The blood–brain barrier (BBB) restricts drug exposure in the brain, posing a significant challenge for central [...] Read more.
The mechanisms underlying neurodegenerative diseases (NDDs) involve multiple pathological processes, such as abnormal protein aggregation, oxidative stress, neuroinflammation, mitochondrial dysfunction, and the disruption of neurovascular unit homeostasis. The blood–brain barrier (BBB) restricts drug exposure in the brain, posing a significant challenge for central nervous system delivery and for improving therapeutic efficacy. In recent years, carbon dots derived from natural products (CDs) have emerged as candidate materials for brain delivery and theranostic applications due to their small size, modifiable surfaces, fluorescence-tracking capability, and potential neuroprotective activity. This narrative review summarizes their sources, physicochemical characteristics, biological basis, interactions with the BBB, delivery strategies, neuroprotective effects, and imaging applications. Current evidence suggests that these CDs can alleviate oxidative stress and inflammatory responses, influence abnormal protein aggregation, and support drug delivery and fluorescence tracking in certain cellular and animal models. However, BBB permeability, brain fluorescence signals, brain parenchymal exposure, and therapeutic efficacy represent distinct levels of evidence and should not be considered interchangeable. Future studies should focus on strengthening material standardization, ensuring batch-to-batch consistency, characterizing absorption, distribution, metabolism, and excretion (ADME), conducting long-term safety assessments, and validating using humanized BBB models. Full article
(This article belongs to the Special Issue Neurodegeneration: Pathways and Mechanisms)
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13 pages, 3072 KB  
Article
A GATA2 Transcription Factor Negatively Regulates CoFBA Expression and Fructose-1,6-Bisphosphate Accumulation in Cocos nucifera
by Zijia Liu, Qikai Zhang, Qiaoyu Huang, Dan Feng, Jixin Zou and Dongdong Li
Horticulturae 2026, 12(8), 914; https://doi.org/10.3390/horticulturae12080914 - 24 Jul 2026
Viewed by 207
Abstract
Coconut (Cocos nucifera L.) is an important tropical horticultural crop valued for its edible endosperm with high oil content. However, the molecular mechanisms governing carbon partitioning and the regulation of glycolytic genes during endosperm development remain largely unclear. Fructose-1,6-bisphosphate aldolase (FBA), a [...] Read more.
Coconut (Cocos nucifera L.) is an important tropical horticultural crop valued for its edible endosperm with high oil content. However, the molecular mechanisms governing carbon partitioning and the regulation of glycolytic genes during endosperm development remain largely unclear. Fructose-1,6-bisphosphate aldolase (FBA), a key enzyme in glycolysis, plays a central role in carbohydrate metabolism, yet its transcriptional regulatory mechanisms in coconut have not been elucidated. In this study, the CoFBA promoter (proFBA) was isolated and used for yeast one-hybrid screening, leading to the identification of a GATA transcription factor, CoGATA2. Subcellular localization analysis confirmed that CoGATA2 is localized in the nucleus. Yeast one-hybrid assays, electrophoretic mobility shift assays (EMSA), and transient expression in coconut protoplasts demonstrated that CoGATA2 directly binds to a proFBA fragment containing the predicted GATA motif and represses CoFBA expression. Moreover, virus-induced gene silencing (VIGS) of CoGATA2 in coconut callus resulted in significant upregulation of CoFBA expression and increased fructose-1,6-bisphosphate (FBP) levels. Collectively, these findings demonstrate that CoGATA2 functions as a transcriptional repressor of CoFBA and that this regulation correlates with altered FBP levels in coconut callus. However, the precise mechanism by which FBP accumulation occurs and its relationship to glycolytic flux require further investigation. This study provides new insights into the transcriptional regulation of a key glycolytic gene in coconut and offers a foundation for future efforts to manipulate carbon partitioning in this important horticultural crop. Full article
(This article belongs to the Special Issue Multi-Omics-Driven Breeding for Tropical Horticultural Crops)
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24 pages, 6713 KB  
Article
Antifungal Efficacy and Mechanisms of Methyleugenol from Asarum Essential Oil Against Rhizoctonia solani Causing Ginseng Damping-Off Disease
by Rui Zhang, Xiaolin Chen, Xueqian Yan, Zhongliang Yang, Dandan Zhang, Yingping Wang and Baohui Lu
Agriculture 2026, 16(14), 1547; https://doi.org/10.3390/agriculture16141547 - 20 Jul 2026
Viewed by 361
Abstract
Damping-off disease caused by Rhizoctonia solani is a devastating soilborne disease that poses a serious threat to sustainable ginseng (Panax ginseng) production. In an effort to develop environmentally friendly control alternatives, we investigated the volatile constituents of Asarum heterotropoides essential oil [...] Read more.
Damping-off disease caused by Rhizoctonia solani is a devastating soilborne disease that poses a serious threat to sustainable ginseng (Panax ginseng) production. In an effort to develop environmentally friendly control alternatives, we investigated the volatile constituents of Asarum heterotropoides essential oil using GC-MS in 2023 and identified methyleugenol as the predominant bioactive component, accounting for 21.32% of the total volatile fraction. Mycelial growth rate assays demonstrated that methyleugenol exerted pronounced antifungal activity against R. solani, with EC50 and EC90 values of 60 mg/L and 800 mg/L, respectively. Treatment at 0.1 mg/mL resulted in 51% growth inhibition after 4 days of incubation. To elucidate the underlying mechanisms of action, R. solani mycelia exposed to 0.1 mg/mL methyleugenol were harvested at 4 and 6 days post-treatment for integrated transcriptomic and untargeted metabolomic profiling. Transcriptome analysis revealed 1444 and 1157 significantly downregulated genes at 4 and 6 days, respectively, with 836 genes consistently repressed at both time points. GO and KEGG enrichment analyses indicated that these persistently suppressed genes were predominantly associated with protein processing in the endoplasmic reticulum, protein export, tyrosine metabolism, and peroxisome biogenesis. Metabolomic profiling identified 95 differentially accumulated metabolites that were commonly reduced across both time points, with KEGG pathway enrichment highlighting significant suppression of starch and sucrose metabolism and galactose metabolism pathways central to carbon source utilization. Integrative transcriptome–metabolome correlation analysis further uncovered three key transcription factors (gene-RDB_LOCUS74145, gene-RDB_LOCUS26344, and gene-RDB_LOCUS52181) implicated in the regulation of carbohydrate metabolism and tricarboxylic acid cycle-related metabolite production. Collectively, our findings indicate that methyleugenol suppresses R. solani growth through a multi-target mechanism involving impairment of carbon source metabolism, disruption of protein processing and secretion, and attenuation of cellular energy supply. These results provide a mechanistic foundation for the development of botanical fungicide-based strategies for the green management of ginseng damping-off disease. Full article
(This article belongs to the Section Crop Protection, Diseases, Pests and Weeds)
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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 304
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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26 pages, 13978 KB  
Article
Transcriptome-and Metabolome-Based Mechanisms of High-Temperature Adaptation in Triploid Rainbow Trout (Oncorhynchus mykiss)
by Shuchen Huang, Changzhong Li, Ying Yang, Tianxiu Liang, Xin Xie, Jingjing Zhang, Zhaonan Li, Jin Li and Yanxia Chen
Biology 2026, 15(14), 1194; https://doi.org/10.3390/biology15141194 - 20 Jul 2026
Viewed by 398
Abstract
High-temperature stress poses a critical challenge to cold-water aquaculture; however, the size-associated molecular mechanisms underlying thermal adaptation in triploid rainbow trout (Oncorhynchus mykiss) remain poorly understood. Here, we integrated transcriptomic and metabolomic profiling of liver tissues, which plays central role in [...] Read more.
High-temperature stress poses a critical challenge to cold-water aquaculture; however, the size-associated molecular mechanisms underlying thermal adaptation in triploid rainbow trout (Oncorhynchus mykiss) remain poorly understood. Here, we integrated transcriptomic and metabolomic profiling of liver tissues, which plays central role in energy metabolism and stress integration, from three body-weight classes—small (0.8 kg ± 0.18 kg), medium (1.5 kg ± 0.22 kg), and large (2.5 kg ± 0.31 kg)—sampled under peak summer heat stress (20.5 °C). Transcriptomic analysis identified 974, 570, and 862 group-specific differentially expressed genes, respectively, revealing a non-linear, size-associated transcriptional pattern. Genes assigned to the ribosome pathway were significantly enriched in comparisons involving MLA and SLA relative to LLA, but not between SLA and MLA, whereas carbon metabolism and amino acid biosynthesis were enriched exclusively in smaller fish, indicating a higher catabolic burden under heat stress. Metabolomic profiling identified 1123 metabolites, with lipids accounting for 45.06%, and showed size-specific enrichments in biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, arachidonic acid metabolism, and pathways related to necroptosis. Integrative analysis revealed that in smaller fish, pla2g1b and gpx4a coordinately regulate the accumulation of prostaglandin H2 and 16(R)-HETE, forming a regulatory network with ferroptosis-related genes acsl4a and hmox1a; concurrently, chka, lpin1, and phospholipase A2 members drive extensive membrane phospholipid remodeling. The observed negative correlation between hsd17b3 expression and 7α-hydroxytestosterone levels suggests size-associated steroid-mediated energy repartitioning. Collectively, smaller fish undergo extensive transcriptional and metabolic reprogramming with heightened activation of cell death pathways, whereas larger fish maintain greater thermal buffering capacity. These findings provide molecular targets for size-stratified thermal management and selective breeding in rainbow trout aquaculture. Full article
(This article belongs to the Section Genetics and Genomics)
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36 pages, 1243 KB  
Review
Hexokinase 2 and Carbohydrate Metabolism: A Multifaceted Metabolic Hub
by Roman Maslanka, Justyna Folta, Magdalena Lubińska, Łukasz Słota and Renata Zadrag-Tecza
Genes 2026, 17(7), 823; https://doi.org/10.3390/genes17070823 - 19 Jul 2026
Viewed by 377
Abstract
Hexokinase 2 (Hxk2p) is a key enzyme in glucose metabolism but also acts as a central regulator linking glucose-dependent signaling with cellular physiology in Saccharomyces cerevisiae. Beyond its catalytic function in glycolysis, Hxk2p acts as a regulator of carbon catabolite repression, influencing [...] Read more.
Hexokinase 2 (Hxk2p) is a key enzyme in glucose metabolism but also acts as a central regulator linking glucose-dependent signaling with cellular physiology in Saccharomyces cerevisiae. Beyond its catalytic function in glycolysis, Hxk2p acts as a regulator of carbon catabolite repression, influencing the expression of genes required for the utilization of alternative carbon sources and mitochondrial activity. Accumulating evidence indicates that deletion of HXK2 triggers a systemic, multidirectional reprogramming of cellular metabolism and physiology that mimics calorie restriction conditions even in nutrient-rich environments. This widespread metabolic reconfiguration involves a fundamental shift from a rapid fermentative mode to an energy-efficient respiratory state, including the redistribution of carbon flux between glycolysis, the pentose phosphate pathway, and respiration. These changes are associated with alterations in ATP homeostasis, biosynthetic capacity, redox balance, and proteostasis. Crucially, because of its implications in genomic regulation, the absence of Hxk2p induces global transcriptional remodelling, whereby the expression of genes involved in respiratory and alternative carbon source metabolism is derepressed, while the expression of glycolytic and biosynthetic genes is downregulated. Ultimately, these pleiotropic adaptations work synergistically, affecting cellular fitness and increasing cell reproductive potential. Therefore, Hxk2p integrates metabolic and signaling pathways that link carbon source utilization with cellular growth, cell cycle, energy homeostasis, and stress responses. This review summarizes current knowledge on Hxk2p function in carbohydrate metabolism, with particular emphasis on its regulatory roles and their implications for gene expression, cellular physiology, and proliferation capacity. Full article
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23 pages, 3432 KB  
Review
Research Advances in Plant Pyruvate Kinase
by Ruixiao Peng, Fudeng Huang, Yong He, Junfeng Xu, Ying Zhu, Mengyun Ren, Yuanyuan Hao and Zhihong Tian
Int. J. Mol. Sci. 2026, 27(14), 6346; https://doi.org/10.3390/ijms27146346 - 17 Jul 2026
Viewed by 248
Abstract
Pyruvate kinase (PK) is the terminal rate-limiting enzyme of glycolysis and occupies a central position in plant energy metabolism and carbon skeleton allocation. Plant PK isoenzymes comprise the cytosolic pyruvate kinase (PKc) and the plastidic pyruvate kinase (PKp), which differ markedly in gene [...] Read more.
Pyruvate kinase (PK) is the terminal rate-limiting enzyme of glycolysis and occupies a central position in plant energy metabolism and carbon skeleton allocation. Plant PK isoenzymes comprise the cytosolic pyruvate kinase (PKc) and the plastidic pyruvate kinase (PKp), which differ markedly in gene origin, protein structure, subcellular localization, and physiological function, exhibiting independent evolutionary histories and functional diversification. Recent studies have revealed that PKc possesses dynamic subcellular distribution, allowing it to shuttle among the cytosol, mitochondria, and nucleus, where it participates in stress responses and epigenetic regulation through protein–protein interactions. PKp is localized to plastids and connects carbon metabolism with lipid biosynthesis and the methylerythritol phosphate (MEP) pathway by supplying pyruvate, thereby playing critical roles in seed development and oil accumulation. This review comprehensively summarizes recent advances in plant PKc and PKp concerning protein structure and subunit composition, tissue-specific expression, subcellular localization, protein interaction networks, activity regulation, and their effects on plant growth, development, and stress responses. In addition, phylogenetic tree, motif, and domain analyses of pyruvate kinase genes from Oryza sativa (rice), Glycine max (soybean), Gossypium hirsutum (cotton), Solanum tuberosum (potato), Arachis hypogaea (peanut), and Arabidopsis thaliana, as well as promoter cis-element analyses, are performed. This review aims to provide theoretical references for crop quality improvement and stress-resilient breeding. Full article
(This article belongs to the Section Molecular Plant Sciences)
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14 pages, 2474 KB  
Article
Fecal Microbiota of the Bobcat (Lynx rufus) in a Temperate Forest of Central Mexico
by Leslie M. Montes-Carreto, Jimena Herandi Espinal-Cárdenas, Hanya D. Arellano-Hernández, José Antonio Guerrero and Esperanza Martinez-Romero
Ecologies 2026, 7(3), 68; https://doi.org/10.3390/ecologies7030068 - 15 Jul 2026
Viewed by 929
Abstract
Carnivores harbor gut microbial communities adapted to protein and fat-rich diets. These microbial communities play an important role in amino acid degradation and bile acid metabolism. The bobcat (Lynx rufus) spans diverse North America habitats, yet its gut microbiota across regions [...] Read more.
Carnivores harbor gut microbial communities adapted to protein and fat-rich diets. These microbial communities play an important role in amino acid degradation and bile acid metabolism. The bobcat (Lynx rufus) spans diverse North America habitats, yet its gut microbiota across regions remains under characterized. Here, we characterized the fecal microbiota of bobcats from a high-elevation temperate forest in central Mexico (Chichinautzin Biological Corridor) using 16S rRNA gene amplicon sequencing (V3–V4 region). Comparisons with previously published studies were used only to place our findings in the context of the available literature. In total, 632 amplicon sequence variants (ASVs) were recovered from 10 samples. A total of 35 bacterial families and 58 genera were identified. The most abundant genera included Clostridium, Fusobacterium, Bacteroides, and Phocaeicola. Several samples were dominated by genera such as Pseudomonas, Blautia, Ammoniphilus, Alloprevotella, and Hafnia, indicating marked among-sample variability. Functional prediction suggested that pathways related to ABC transporters, purine and pyrimidine metabolism, ribosomal functions, two-component systems, amino acid metabolism, and central carbon metabolism were among the most represented inferred functional categories. These predictions should be regarded as exploratory and hypothesis-generating, providing an overview of the potential metabolic capabilities of the fecal microbiota inferred from 16S rRNA gene data. Full article
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20 pages, 4227 KB  
Article
Simultaneous Disruption of Phosphate and Carbon Signaling Regulators Enables Adaptive Gene Expression Through Non-Cognate Phosphorylation of PhoP
by Jae-Yong Park, Wael Abdel-Fattah and F. Marion Hulett
Biology 2026, 15(14), 1138; https://doi.org/10.3390/biology15141138 - 13 Jul 2026
Viewed by 391
Abstract
The PhoP–PhoR two-component system (TCS) controls transcription of the Pho regulon in response to inorganic phosphate limitation in Bacillus subtilis. In addition to its role in phosphate homeostasis, increasing evidence suggests that central metabolic pathways influence Pho regulon activity. Here, we investigated [...] Read more.
The PhoP–PhoR two-component system (TCS) controls transcription of the Pho regulon in response to inorganic phosphate limitation in Bacillus subtilis. In addition to its role in phosphate homeostasis, increasing evidence suggests that central metabolic pathways influence Pho regulon activity. Here, we investigated the mechanism underlying phosphate-independent activation of the Pho regulon in a ccpA mutant lacking the global regulator of CCR. Gene expression analyses demonstrated strong glucose-dependent induction of Pho regulon genes in the absence of both CcpA and the cognate histidine kinase PhoR. Using PhosTag gel electrophoresis analysis and a phoasphoablative mutation in phoP (D53A), we detected early PhoP phosphorylation and determined that Pho regulon activation requires a phosphorylatable form of PhoP, even when the cognate histidine kinase phoR gene was deleted. Because PhoR can phosphorylate non-cognate response regulator YycF, we examined whether the essential YycFG signaling system contributes to PhoP activation. Co-immunoprecipitation and in vitro phosphorylation assays confirmed a direct interaction between PhoP and YycG and demonstrated in vitro PhoP phosphorylation by YycG. Taken together, we propose a model in which CcpA limits excessive PhoP accumulation to preserve signaling specificity and prevent aberrant activation through non-cognate kinases. Furthermore, our study reveals a previously unrecognized link between carbon catabolite repression and phosphate starvation signaling and demonstrates another crosstalk between two-component signal transduction systems in the Gram-positive bacterium, B. subtilis. Full article
(This article belongs to the Section Biochemistry and Molecular Biology)
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31 pages, 5139 KB  
Article
Spatiotemporal Patterns, Driving Factors, and Low-Carbon Mitigation of Land-Use Carbon Emissions in the Tarim Basin Oasis Urban Agglomeration (Arid Northwest China)
by Yuying Wang and Jiangling Hu
Sustainability 2026, 18(14), 6982; https://doi.org/10.3390/su18146982 - 8 Jul 2026
Viewed by 293
Abstract
Against the backdrop of global climate change and carbon neutrality strategies, land use carbon emissions have become a prominent topic amid regional efforts toward low-carbon transformation. However, existing studies on land-use carbon emissions have predominantly focused on humid and economically developed regions, while [...] Read more.
Against the backdrop of global climate change and carbon neutrality strategies, land use carbon emissions have become a prominent topic amid regional efforts toward low-carbon transformation. However, existing studies on land-use carbon emissions have predominantly focused on humid and economically developed regions, while the unique carbon metabolism pathways of arid oasis–desert ecosystems, which are characterized by extremely low environmental carrying capacity and high sensitivity to land-use disturbance, remain largely unexplored. This study takes the oasis urban cluster in the Tarim Basin in southern Xinjiang Uygur Autonomous Region as the research object. This region belongs to a typical oasis–desert composite ecosystem, with a simple structure and low environmental carrying capacity (reflected by sparse vegetation cover < 20%, annual precipitation < 100 mm, extremely limited water resources, and high sensitivity to land disturbance). Its carbon metabolism pathway (i.e., the dynamic balance between carbon sources and sinks induced by land-use change) is fundamentally different from that in humid areas, and thus merits dedicated investigation. This study selects the period from 2000 to 2020 as the research period, which completely covers the acceleration period of urbanization and agricultural expansion in the Tarim Basin oasis urban cluster since the advancement of China’s Western Development Initiative. The data have a temporal resolution of 5 years (samples in 2000, 2005, 2010, 2015, 2020) and a spatial resolution of 30 m for land use and prefecture level for socio-economic indicators. Based on this, to fill the above-mentioned research gap, a research framework integrating the carbon emission coefficient accounting method, landscape pattern index, spatial autocorrelation analysis and geographic detector is adopted. Specifically, this study aims to systematically quantify the spatio-temporal evolution of land use carbon emissions and identify the most robust driving factors in the Tarim Basin oasis urban cluster by integrating multiple models, an approach that has not been previously applied to arid oasis regions. The research results show: (1) Based on the carbon emission coefficient method, total carbon emissions increased from 1.4455 million tons to 22.364 million tons, following a ‘slow-then-fast’ trajectory. In terms of temporal evolution, the study period can be further divided into three sub-stages: 2000–2005 (slow diffusion, with emission center skewed toward the northern energy-intensive zone), 2005–2015 (rapid restructuring, characterized by a ‘unipolar surge’ in Aksu and spread to the central oasis belt), and 2015–2020 (high-intensity stabilization, forming a cross-regional emission belt). Meanwhile, the land use structure has undergone a significant transformation. Construction land and cultivated land have continued to expand, while ecological land has significantly shrunk, resulting in a complex transformation pattern of oasis–desert ecotone. (2) The overall landscape became increasingly fragmented and diversified, the integrity of ecological space was damaged, and the regional carbon sink function was weakened. (3) The spatial autocorrelation analysis indicates that the spatial distribution of carbon emissions shows a heterogeneous pattern, forming a high-emission concentration area centered around Aksu-Bayingol. However, the global Moran’s I index is negative (such as −0.171 in 2020, p > 0.05), suggesting that carbon emissions have not formed a significant spatial clustering. (4) Carbon emissions are dominated by human and economic factors, and the interaction of factors is significant. The geographic detector identifies population density (average q value 0.904) and the proportion of construction land (average q value 0.858) as the key determinants of spatial variation in carbon emissions, reflecting the sensitive response of the human-nature system of arid zones to the urbanization process. These findings not only clarify the spatio-temporal features and driving forces of land use carbon emissions in the Tarim Basin oasis urban cluster, but also provide a replicable analytical framework for carbon-emission research in other arid and semi-arid regions worldwide. Based on these findings, we discuss the unique driving mechanisms of carbon emissions in arid regions, conclude that construction land expansion and population density are the dominant factors, and recommend a three-tier zoning governance system (carbon source control zone, carbon sink enhancement zone, coordinated development zone) for low-carbon spatial planning in arid areas. Full article
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29 pages, 3974 KB  
Review
Choline and Its Companions: Inter-Related Roles of Choline and B Vitamins in Fetal Development and Offspring Health
by Emma J. Derbyshire
Nutrients 2026, 18(14), 2218; https://doi.org/10.3390/nu18142218 - 8 Jul 2026
Viewed by 616
Abstract
Background/Objectives: Previous publications have primarily examined the individual roles of nutrients during fetal development. However, growing evidence suggests that one-carbon (1C) metabolism nutrients, including choline and key B vitamins, act synergistically within interconnected metabolic pathways that modulate epigenetic regulation and may have [...] Read more.
Background/Objectives: Previous publications have primarily examined the individual roles of nutrients during fetal development. However, growing evidence suggests that one-carbon (1C) metabolism nutrients, including choline and key B vitamins, act synergistically within interconnected metabolic pathways that modulate epigenetic regulation and may have implications for the health of future generations. Methods: This narrative integrative review examined evidence relating to the roles of choline and B vitamins (B1, B2, B6, folate (B9) and B12) in fetal development and offspring health. Peer-reviewed literature was identified through PubMed, Science Direct and Semantic Scholar. Results: Current evidence indicates that periconceptional and maternal intake and status of 1C metabolism nutrients are associated with DNA methylation processes involved in developmental programming and the risk of non-communicable diseases (NCDs) in childhood and adulthood. Habitual intakes of several 1C metabolism nutrients are frequently below recommended levels during pregnancy and lactation, particularly for choline and folate. Inadequate intakes, each contributing differently to 1C metabolism, may disrupt 1C metabolic pathways and alter DNA methylation patterns during critical windows of fetal programming. Homocysteine metabolism is intricately linked to 1C metabolism and is modulated by choline and B vitamins. Collectively, these pathways have potential implications for the health of the next generation, including effects on growth, neural tube closure, brain development and increased susceptibility to diseases later in life, e.g., cardiovascular disease, diabetes, obesity and other chronic conditions. Adequate maternal intakes of choline and B vitamins may help mitigate the ‘early life origin’ of certain NCDs by promoting healthy neurodevelopment, reducing inflammation, and regulating central metabolic pathways. Conclusions: Greater awareness of the roles and importance of 1C metabolism nutrients, including choline and key B vitamins (B1, B2, B6, folate and B12), during the early life course is warranted. Furthermore, there is also a need for organizations and policy makers to formalize intake recommendations for 1C metabolism nutrients beyond the individualized simplicity of folate/folic acid, and to extend this to include other methyl-donor nutrients with epigenetic effects, such as choline and key B vitamins, given their interconnected roles in 1C metabolism and fetal development. Full article
(This article belongs to the Special Issue Early Life Nutrition and Neurocognitive Development)
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23 pages, 21293 KB  
Article
Low-Temperature Stress Impairs Reproductive Performance and Olfactory Behaviors in Tuta absoluta via Metabolic and Transcriptional Changes
by Bo Feng, Chuanhong Feng, Zhigang Yang, Genyun Liang, Liping Xiong, Xi Yang, Jiatao Huang, Tao Hu, Lingzhi Huang, Yong Yin and Kaidi Zheng
Insects 2026, 17(7), 706; https://doi.org/10.3390/insects17070706 - 7 Jul 2026
Viewed by 541
Abstract
Low temperature critically pressures insect pest distributions and population dynamics; however, integrated understanding of cold stress responses in invasive pests, particularly at the adult stage, remains limited. Here, we investigated the integrated physiological, biochemical, metabolomic and transcriptomic responses of Tuta absoluta (Meyrick, 1917) [...] Read more.
Low temperature critically pressures insect pest distributions and population dynamics; however, integrated understanding of cold stress responses in invasive pests, particularly at the adult stage, remains limited. Here, we investigated the integrated physiological, biochemical, metabolomic and transcriptomic responses of Tuta absoluta (Meyrick, 1917) exposed to control (CT: 25 °C), moderate cold stress (MCS: 15 °C) and severe cold stress (SCS: 5 °C) conditions. Our results revealed that low-temperature stress impaired T. absoluta emergence, survival, fecundity and egg hatching in a stress intensity-dependent manner. Also, low temperature reduced the olfactory-mediated host-seeking behaviors of T. absoluta females. The biochemical analyses revealed depletion of triglycerides, glycogen and Na+/K+-ATPase activity alongside compensatory trehalose accumulations, while antioxidant enzyme activities (SOD, POD, CAT) were differentially modulated indicating progressive oxidative defense impairment under low temperature. Untargeted metabolomic profiling identified extensive differential metabolite accumulations, revealing systematic dysregulation of alkaloid biosynthesis, amino acid metabolism and central carbon metabolic pathways. Transcriptomic analysis identified several differentially expressed genes (DEGs) enriched in thermogenesis, oxidative phosphorylation, MAPK signaling and neurodegeneration-associated pathways. Furthermore, integrative transcriptome–metabolome analysis revealed coordinated gene–metabolite regulatory networks scaling systematically with cold stress intensity. These findings advance our mechanistic understanding of thermal stress adaptations in T. absoluta and may contribute to the development of climate-informed pest management strategies. Full article
(This article belongs to the Section Insect Physiology, Reproduction and Development)
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