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Summary: The shape of rice grains not only determines the thousand‐grain weight but also correlates closely with the grain quality.Here we identified an ultra‐large grain accession (ULG) with a thousand‐grain weight exceeding 60 g. The integrated analysis of QTL, BSA, de novo genome assembled, transcription sequencing, and gene editing was conducted to dissect the molecular basis of the ULG formation.The ULG pyramided advantageous alleles from at least four known grain‐shaping genes, OsLG3, OsMADS1, GS3, GL3.1, and one novel locus, qULG2‐b, which encoded a leucine‐rich repeat receptor‐like kinase. The collective impacts of OsLG3, OsMADS1, GS3, and GL3.1 on grain size were confirmed in transgenic plants and near‐isogenic lines. The transcriptome analysis identified 112 genes cooperatively regulated by these four genes that were prominently involved in photosynthesis and carbon metabolism. By leveraging the pleiotropy of these genes, we enhanced the grain yield, appearance, and stress tolerance of rice var. SN265.Beyond showcasing the pyramiding of multiple grain size regulation genes that can produce ULG, our study provides a theoretical framework and valuable genomic resources for improving rice variety by leveraging the pleiotropy of grain size regulated genes. [ABSTRACT FROM AUTHOR]

Graphene oxide (GO), beyond its specialized industrial applications, is rapidly gaining prominence as a nanomaterial for modern agriculture. However, its specific effects on seed priming for salinity tolerance and yield formation in crops remain elusive. Under both pot-grown and field-grown conditions, this study combined physiological indices with transcriptomics and metabolomics to investigate how GO affects seed germination, seedling salinity tolerance, and peanut pod yield. Peanut seeds were firstly treated with 400 mg L⁻¹ GO (termed GO priming). At seed germination stage, GO-primed seeds exhibited higher germination rate and percentage of seeds with radicals breaking through the testa. Meanwhile, omics analyses revealed significant enrichment in pathways associated with carbon and nitrogen metabolisms in GO-primed seeds. At seedling stage, GO priming contributed to strengthening plant growth, enhancing photosynthesis, maintaining the integrity of plasma membrane, and promoting the nutrient accumulation in peanut seedlings under 200 mM NaCl stress. Moreover, GO priming increased the activities of antioxidant enzymes, along with reduced the accumulation of reactive oxygen species (ROS) in response to salinity stress. Furthermore, the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) of peanut seedlings under GO priming were mainly related to photosynthesis, phytohormones, antioxidant system, and carbon and nitrogen metabolisms in response to soil salinity. At maturity, GO priming showed an average increase in peanut pod yield by 12.91% compared with non-primed control. Collectively, our findings demonstrated that GO plays distinguish roles in enhancing seed germination, mitigating salinity stress, and boosting pod yield in peanut plants via modulating multiple physiological processes. [ABSTRACT FROM AUTHOR]

The potential of Euglena gracilis for carbon sequestration offers significant opportunities in the capture and utilization of carbon dioxide (CO2 ). In this study, a mutant LE-ZW of E. gracilis, capable of efficient growth and carbon sequestration, was obtained through ultraviolet mutagenesis combined with high carbon acclimation. Subsequently, the potential of LE-ZW for carbon assimilation was systematically analyzed. The results demonstrated that the cell density of the LE-ZW was 1.33 times that of the wild type and its carbon sequestration efficiency was 6.67 times that of the wild type when cultured at an optimal CO2 concentration of 5% until day 10. At this time, most key enzyme genes associated with the photosystem membrane protein complex, photosynthetic electron transport chain, antenna protein, and carbon fixation were up-regulated in mutant LE-ZW. Furthermore, after 10  days of culture under 10% CO2, the cell density and carbon sequestration efficiency of LE-ZW reached 1.10 times and 1.54 times of that under 5% CO2, respectively. Transcriptome analysis revealed significant up-regulation of key enzyme genes associated with carbon fixation, central carbon metabolism, and photosynthesis in LE-ZW under a 10% CO2 concentration. Physiological indices such as the amount of oxygen evolution, the values of Fv/Fm, the expression levels of photosynthetic protein genes and the enzyme activity of key enzymes related to photosynthetic carbon assimilation were corroborated by transcriptome data, elucidating that the mutant LE-ZW exhibited augmented photosynthetic carbon sequestration capacity and metabolic activity, thereby demonstrating robust adaptability to a high-carbon environment. This research contributes to a deeper understanding of the carbon assimilation mechanism in photosynthetic protists under elevated CO2 concentrations. [ABSTRACT FROM AUTHOR]

Background: Clostridium autoethanogenum is an acetogenic bacterium that autotrophically converts carbon monoxide (CO) and carbon dioxide (CO2) gases into bioproducts and fuels via the Wood–Ljungdahl pathway (WLP). To facilitate overall carbon capture efficiency, the reaction stoichiometry requires supplementation of hydrogen at an increased ratio of H2:CO to maximize CO2 utilization; however, the molecular details and thus the ability to understand the mechanism of this supplementation are largely unknown. Results: In order to elucidate the microbial physiology and fermentation where at least 75% of the carbon in ethanol comes from CO2, we established controlled chemostats that facilitated a novel and high (11:1) H2:CO uptake ratio. We compared and contrasted proteomic and metabolomics profiles to replicate continuous stirred tank reactors (CSTRs) at the same growth rate from a lower (5:1) H2:CO condition where ~ 50% of the carbon in ethanol is derived from CO2. Our hypothesis was that major changes would be observed in the hydrogenases and/or redox-related proteins and the WLP to compensate for the elevated hydrogen feed gas. Our analyses did reveal protein abundance differences between the two conditions largely related to reduction–oxidation (redox) pathways and cofactor biosynthesis, but the changes were more minor than we would have expected. While the Wood–Ljungdahl pathway proteins remained consistent across the conditions, other post-translational regulatory processes, such as lysine-acetylation, were observed and appeared to be more important for fine-tuning this carbon metabolism pathway. Metabolomic analyses showed that the increase in H2:CO ratio drives the organism to higher carbon dioxide utilization resulting in lower carbon storages and accumulated fatty acid metabolite levels. Conclusions: This research delves into the intricate dynamics of carbon fixation in C. autoethanogenum, examining the influence of highly elevated H2:CO ratios on metabolic processes and product outcomes. The study underscores the significance of optimizing gas feed composition for enhanced industrial efficiency, shedding light on potential mechanisms, such as post-translational modifications (PTMs), to fine-tune enzymatic activities and improve desired product yields. [ABSTRACT FROM AUTHOR]

Background: Proliferative hepatocellular carcinomas (HCCs) is a class of aggressive tumors with poor prognosis. We aimed to construct a computed tomography (CT)-based radiomics nomogram to predict proliferative HCC, stratify clinical outcomes and explore the tumor microenvironment. Methods: Patients with pathologically diagnosed HCC following a hepatectomy were retrospectively collected from two medical centers. A CT-based radiomics nomogram incorporating radiomics model and clinicoradiological features to predict proliferative HCC was constructed using the training cohort (n = 184), and validated using an internal test cohort (n = 80) and an external test cohort (n = 89). The predictive performance of the nomogram for clinical outcomes was evaluated for HCC patients who underwent surgery (n = 201) or received transarterial chemoembolization (TACE, n = 104). RNA sequencing data and histological tissue slides from The Cancer Imaging Archive database were used to perform transcriptomics and pathomics analysis. Results: The areas under the receiver operating characteristic curve of the radiomics nomogram to predict proliferative HCC were 0.84, 0.87, and 0.85 in the training, internal test, and external test cohorts, respectively. The radiomics nomogram could stratify early recurrence-free survivals in the surgery outcome cohort (hazard ratio [HR] = 2.25; P < 0.001) and progression-free survivals in the TACE outcome cohort (HR = 2.21; P = 0.03). Transcriptomics and pathomics analysis indicated that the radiomics nomogram was associated with carbon metabolism, immune cells infiltration, TP53 mutation, and heterogeneity of tumor cells. Conclusion: The CT-based radiomics nomogram could predict proliferative HCC, stratify clinical outcomes, and measure a pro-tumor microenvironment. [ABSTRACT FROM AUTHOR]

Nitrogen (N) nutrition impacts on primary carbon metabolism and can lead to changes in δ13C of respired CO2. However, uncertainty remains as to whether (1) the effect of N nutrition is observed in all species, (2) N source also impacts on respired CO2 in roots and (3) a metabolic model can be constructed to predict δ13C of respired CO2 under different N sources. Here, we carried out isotopic measurements of respired CO2 and various metabolites using two species (spinach, French bean) grown under different NH4+:NO3− ratios. Both species showed a similar pattern, with a progressive 13C‐depletion in leaf‐respired CO2 as the ammonium proportion increased, while δ13C in root‐respired CO2 showed little change. Supervised multivariate analysis showed that δ13C of respired CO2 was mostly determined by organic acid (malate, citrate) metabolism, in both leaves and roots. We then took advantage of nonstationary, two‐pool modelling that explained 73% of variance in δ13C in respired CO2. It demonstrates the critical role of the balance between the utilisation of respiratory intermediates and the remobilisation of stored organic acids, regardless of anaplerotic bicarbonate fixation by phosphoenolpyruvate carboxylase and the organ considered. [ABSTRACT FROM AUTHOR]

This research assesses the aboveground matter accumulation and Fv/Fm ratios (maximum quantum efficiency of PSII) in young plants (5 months old) of Agave mapisaga and Agave salmiana grown under greenhouse conditions. This study also evaluated changes in the relative abundance of several different metabolites (sugars, free amino acids, and soluble phenols) during the major daily phases (I, III, and IV) of Crassulacean acid metabolism (CAM). These two species were also investigated to determine if differences in these parameters were evident with respect to their geographical origins (i.e. Metepec, Tlajomulco, and Tlaxiaca, in the state of Hidalgo, Mexico). Differences in shoot mass (0.51−0.82 g plant−1), water content (75−93%), fructose (4−27 μmol g−1), glucose (57−73 μmol g−1), sucrose (10−30 μmol g−1), free amino acids (5−25 μmol g−1), soluble phenolics (0.7−3.5 μmol g−1), and Fv/Fm ratios (0.75−0.80) were evident between plants with different origins. Specifically, at the end of Phase I compared to Phase IV, the results showed significant reductions in dry matter (up to 3.3%) and also reductions in fructose/sucrose. Relative amino acid concentrations were lowest in Phase III (8.8 μmol g−1) compared to Phase I (16 μmol g−1). These are novel observations, since all these changes and the biochemical and physiological performance in the CAM phases have not been previously determined in Agave plants differing in their geographical origins. The morphological and physiological adaptations of Agave species, including the Classulacean acid metabolism (CAM), allow plants to develop in arid and semi-arid environments. Four diel phases have been described in CAM plants that regulate carbon metabolism, growth and yield. The hypothesis is that in early-development plants from seeds, growing under greenhouse conditions, of each genotype's physiological responses, including growth and metabolites concentrations, vary among CAM phases because of the species of Agave and the seed provenance. [ABSTRACT FROM AUTHOR]

Acinetobacter lwoffii is widely considered to be a harmful bacterium that is resistant to medicines and disinfectants. A. lwoffii NL1 degrades phenols efficiently and shows promise as an aromatic compound degrader in antibiotic-contaminated environments. To gain a comprehensive understanding of A. lwoffii, the first genome-scale metabolic model of A. lwoffii was constructed using semi-automated and manual methods. The iNX811 model, which includes 811 genes, 1071 metabolites, and 1155 reactions, was validated using 39 unique carbon and nitrogen sources. Genes and metabolites critical for cell growth were analyzed, and 12 essential metabolites (mainly in the biosynthesis and metabolism of glycan, lysine, and cofactors) were identified as antibacterial drug targets. Moreover, to explore the metabolic response to phenols, metabolic flux was simulated by integrating transcriptomics, and the significantly changed metabolism mainly included central carbon metabolism, along with some transport reactions. In addition, the addition of substances that effectively improved phenol degradation was predicted and validated using the model. Overall, the reconstruction and analysis of model iNX811 helped to study the antimicrobial systems and biodegradation behavior of A. lwoffii. [ABSTRACT FROM AUTHOR]

Summary: Plants express diverse nutrient use and acquisition traits, but it is unclear how trait combinations at the species level are constrained by phylogeny, trait coordination, or trade‐offs in resource investment. One trait – nitrogen (N) fixation – is assumed to correlate with other traits and used to define plant functional groups, despite potential confounding effects of phylogeny.We quantified growth, carbon metabolism, fixation rate, root phosphatase activity (RPA), mycorrhizal colonization, and leaf and root morphology/chemistry across 22 species of fixing and nonfixing tropical Fabaceae trees under common conditions.Belowground trait variation was high even among closely related species, and most traits displayed a phylogenetic signal, including N‐fixation rate and nodule biomass. Across species, we observed strong positive correlations between physiological traits such as RPA and root respiration. RPA increased ~ fourfold per unit increase in fixation, supporting the debated hypothesis that N‐fixers 'trade' N for phosphatases to enhance phosphorus acquisition. Specific root length and root N differed between functional groups, though for other traits, apparent differences became nonsignificant after accounting for phylogenetic nonindependence.We conclude that evolutionary history, trait coordination, and fixation ability contribute to nutrient trait expression at the species level, and recommend explicitly considering phylogeny in analyses of functional groupings. [ABSTRACT FROM AUTHOR]

• Lumichrome is a growth promoting substance, its mechanism of action is unknown. • Proteomic analysis indicated that lumichrome promotes Arabidopsis thaliana growth through enhancing multiple aspects of the photosynthetic process. • Lumichrome alters carbon partitioning away from starch synthesis to favour sucrose and reducing sugars. Lumichrome, a novel bacterial molecule derived from Sinorhizobium meliloti, plays a crucial role in enhancing plant growth, particularly by increasing photosynthesis and influencing carbon metabolism. Through its impact on gene expression, it has been found to promote turgor-driven growth and ethylene-related delay leaf senescence. In line with previous studies, the current study revealed that treating Arabidopsis thaliana with lumichrome suggested the activation of jasmonate-related signals that delayed leaf senescence. Decreased AOC2 levels, together with the high levels of ABR protein, suggested delayed light and dark-induced leaf senescence. This, along with an increase in chlorophyll content, may possibly be attributed to the enhancement of optimal light absorption, energy conversion, and electron transfer capacity of active PSII reactions. In addition, the increased expression of MPH2 and ATPD subunits might have contributed to a better PSII repair, maintenance of proper photosynthetic function under changing light, and increased ATP synthase activity, ultimately resulting in higher photosynthesis efficiency. Moreover, the increased expression of TRX-M1, TRX-M4, plastid PRX-IIE, and cytosolic APX1 proteins could have improved the ability of treated plants to counteract ROS at PSII and PSI, leading to a better CO 2 assimilation rate and plant growth. Subsequently, increased FBA8 could have directed the fixed carbon partitioning into the cytosolic glycolysis pathway. Altogether, these changes may have contributed to increased growth through higher levels of sucrose and reducing sugars. [ABSTRACT FROM AUTHOR]

Rivers efficiently collect, process, and transport terrestrial‐derived carbon. River ecosystem metabolism is the primary mechanism for processing carbon. Diel cycles of dissolved oxygen (DO) have been used for decades to infer river ecosystem metabolic rates, which are routinely used to predict metabolism of carbon dioxide (CO2) with uncertainties of the assumed stoichiometry ranging by a factor of 4. Dissolved inorganic carbon (DIC) has been less used to directly infer metabolism because it is more difficult to quantify, involves the complexity of inorganic carbon speciation, and as shown in this study, likely requires a two‐station approach. Here, we developed DIC metabolism models using single‐ and two‐station approaches. We compared metabolism estimates based on simultaneous DO and DIC monitoring in the Upper Clark Fork River (USA), which also allowed us to estimate ecosystem‐level photosynthetic and respiratory quotients (PQE and RQE). We observed that metabolism estimates from DIC varied more between single‐ and two‐station approaches than estimates from DO. Due to carbonate buffering, CO2 is slower to equilibrate with the atmosphere compared to DO, likely incorporating a longer distance of upstream heterogeneity. Reach‐averaged PQE ranged from 1.5 to 2.0, while RQE ranged from 0.8 to 1.5. Gross primary production from DO was larger than that from DIC, as was net ecosystem production by 100mmolm−2d−1$$ 100\kern0.5em \mathrm{mmol}\kern0.5em {\mathrm{m}}^{-2}\kern0.5em {\mathrm{d}}^{-1} $$. The river was autotrophic based on DO but heterotrophic based on DIC, complicating our understanding of how metabolism regulated CO2 production. We suggest future studies simultaneously model metabolism from DO and DIC to understand carbon processing in rivers. [ABSTRACT FROM AUTHOR]

Background: Astragalus cicer L. is a perennial rhizomatous legume forage known for its quality, high biomass yield, and strong tolerance to saline-alkaline soils. Soil salinization is a widespread environmental pressure. To use A. cicer L. more scientifically and environmentally in agriculture and ecosystems, it is highly important to study the molecular response mechanism of A. cicer L. to salt stress. Results: In this study, we used RNA-seq technology and weighted gene coexpression network analysis (WGCNA) were performed. The results showed 4 key modules were closely related to the physiological response of A. cicer. L. to salt stress. The differentially expressed genes (DEGs) of key modules were mapped into the KEGG database, and found that the most abundant pathways were the plant hormone signal transduction pathway and carbon metabolism pathway. The potential regulatory networks of the cytokinin signal transduction pathway, the ethylene signal transduction pathway, and carbon metabolism related pathways were constructed according to the expression pathways of the DEGs. Seven hub genes in the key modules were selected and distributed among these pathways. They may involved in the positive regulation of cytokinin signaling and carbon metabolism in plant leaves, but limited the positive expression of ethylene signaling. Thus endowing the plant with salt tolerance in the early stage of salt stress. Conclusions: Based on the phenotypic and physiological responses of A. cicer L. to salt stress, this study constructed the gene coexpression network of potential regulation to salt stress in key modules, which provided a new reference for exploring the response mechanism of legumes to abiotic stress. [ABSTRACT FROM AUTHOR]

Endemic fermented vegetables play a crucial role in local cuisine and culture, with traditionally fermented raw green vegetables such as gundruk being a popular practice in North Bengal and Sikkim, India. However, there is a gap in the microbial profiling of these vegetables. This study aimed to explore the diversity of dominant bacterial populations in fermented leafy vegetables using both culture-dependent and culture-independent methods. In addition to isolating bacteria using conventional methods, we conducted phenotypic and biochemical characterization, community DNA isolation, and amplicon sequencing. We also introduced a new approach in bioinformatics analysis: reverse ecology, which analyzes complementation and competition among participant microbes. In conventional culture-dependent techniques, LAB genera such as Lactobacillus, Enterococcus, Leuconostoc, and Pediococcus have been identified as predominant consortia, whereas metagenomic analysis revealed that the microbiome of fermented dried leafy vegetables was mainly composed of Firmicutes, Proteobacteria, Actinobacteria, Bacteroides, and Planctomycetes at the phylum level. Within the Lactobacillaceae family, predominant types included Lactobacillus, Lactococcus, Pediococcus, Leuconostoc, Enterococcus, Vagococcus, Weissella, and Carnobacterium. The microbial metabolism revealed key pathways, such as carbon metabolism, glycolysis, gluconeogenesis, and glyoxylate. Aromatic amino acid degradation, fatty acid metabolism, amino sugar metabolism, nucleotide sugar metabolism, and biosynthesis of nucleotide sugar pathways were also active. The competition index among microbes and human metabolic data was low (0.32-0.44), indicating minimal competition for nutrition. Complementation indices between bacteria and humans were high (0.76-0.88), suggesting a beneficial impact of gundruk microbial populations on human health. [ABSTRACT FROM AUTHOR]

Industrial biotechnology heavily relies on the microbial conversion of carbohydrate substrates derived from sugar- or starch-rich crops. This dependency poses significant challenges in the face of a rising population and food scarcity. Consequently, exploring renewable, non-competing carbon sources for sustainable bioprocessing becomes increasingly important. Ethanol, a key C2 feedstock, presents a promising alternative, especially for producing acetyl-CoA derivatives. In this review, we offer an in-depth analysis of ethanol's potential as an alternative carbon source, summarizing its distinctive characteristics when utilized by microbes, microbial ethanol metabolism pathway, and microbial responses and tolerance mechanisms to ethanol stress. We provide an update on recent progress in ethanol-based biomanufacturing and ethanol biosynthesis, discuss current challenges, and outline potential research directions to guide future advancements in this field. The insights presented here could serve as valuable theoretical support for researchers and industry professionals seeking to harness ethanol's potential for the production of high-value products. Highlight: Highlights the characteristics of ethanol as a carbon source in bioprocessing. Summarizes microbial ethanol metabolism, stress responses, and tolerance mechanisms. Reviews recent progress in ethanol-based biomanufacturing and ethanol biosynthesis. [ABSTRACT FROM AUTHOR]

BACKGROUND RESULTS CONCLUSION Saccharomyces cerevisiae is a fungus widely used in the food industry and biofuel industry, whereas it is usually exposed to high sugar stress during the fermentation process. Ca2+ is a key second messenger of the cell, it can regulate cell metabolism. The present study investigated the effect of the Ca2+ signal on the activity of key enzymes of carbon metabolism and related gene expression in yeast under high sugar fermentation.The expression of genes encoding hexokinase was up‐regulated in the high sugar environment, the activity of hexokinase was increased, glucose transmembrane transport capacity was enhanced, the ability of glucose to enter into glycolytic metabolism was increased, and the expression of genes related to pentose phosphate metabolism, glycerol metabolism and trehalose metabolism was up‐regulated in the high glucose with Ca2+ group.Ca2+ signal regulates the cellular metabolism of glycerol and trehalose and optimizes the allocation of carbon flow by regulating the key enzymes and related gene expression to enhance the resistance of yeast to high sugar stress. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Background: Salvia miltiorrhiza Bunge, a significant and widely used medicinal herb, is also recognized in the US Pharmacopoeia as a dietary supplement. However, the decline in yield and quality limits its further development as a traditional herbal medicine. Therefore, a deeper understanding of how synthetic communities (SynCom) affect the quality and yield of S. miltiorrhiza and the underlying mechanisms is necessary. Results: In this study, we selected S. miltiorrhiza as the research subject and designed two synthetic communities (SynCom 1 and SynCom 2) using five endophytic fungi without significantly growth-promoting effect. We conducted both greenhouse and field experiments to investigate their impact on the yield and quality of the herbal plants. Greenhouse experiments confirmed that SynCom 1 significantly increased the biomass of S. miltiorrhiza, whereas SynCom 2 had the opposite effect. Field experiments further demonstrated that the application of SynCom 1 promoted photosynthesis and enhanced carbon and nitrogen metabolism, steady and markedly promoted plant growth, and thus increased S. miltiorrhiza yield compared to the uninoculated. In contrast, SynCom 2 inhibited yield but increased the content of the main active components. Un-targeted metabolomics analysis showed that SynCom 1 mainly promoted tricarboxylic acid cycle and nitrogen assimilation process to increase yield, and SynCom 2 mainly increase substrate content in the salvianolic acid and tanshinone synthesis pathways to improve quality. Conclusion: These beneficial qualities exhibited by SynComs composed of fungi without apparent growth-promoting abilities represent an untapped resource that can be leveraged to enhance crop productivity. This opens up new research avenues for precision manipulation of plant microbiomes. Highlights: The Synthetic communities with non-growth promoting fungi promote the growth and quality of Salvia miltiorrhiza Bge. SynCom 1 promoted tricarboxylic acid cycle and nitrogen assimilation process to increase yield. SynCom 2 increase substrate content in the salvianolic acid and tanshinone synthesis pathways to improve quality. The SynComs possess the potential to be applied to field planting and promote medicine food homology plant development as well. The addition of distant species changes the interaction pattern among closely related species. [ABSTRACT FROM AUTHOR]

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight in rice. Polyhydroxyalkanoates (PHAs) consitute a diverse group of biopolyesters synthesized by bacteria under nutrient-limited conditions. The phaC gene is important for PHA polymerization. We investigated the effects of phaC gene mutagensis in Xoo strain PXO99A. The phaC gene knock-out mutant exhibited reduced swarming ability relative to that of the wild-type. Under conditions where glucose was the sole sugar source, extracellular polysaccharide (EPS) production by ΔphaC declined by 44.8%. ΔphaC showed weak hypersensitive response (HR) induction in the leaves of non-host Nicotiana tabacum, concomitant with downregulation of hpa1 gene expression. When inoculated in rice leaves by the leaf-clipping method, ΔphaC displayed reduced virulence in terms of lesion length compared with the wild-type strain. The complemented strain showed no significant difference from the wild-type strain, suggesting that the deletion of phaC in Xoo induces significant alterations in various physiological and biological processes. These include bacterial swarming ability, EPS production, transcription of hrp genes, and glucose metabolism. These changes are intricately linked to the energy utilization and virulence of Xoo during plant infection. These findings revealed involvement of phaC in Xoo is in the maintaining carbon metabolism by functioning in the PHA metabolic pathway. [ABSTRACT FROM AUTHOR]

Organic management enhances the formation of distinct and stable soil microbial communities, however, its influence on the temporal recovery of microbiome and multifunctionality of sterilized soil remains poorly understood. We used amplicon sequencing and metagenomic sequencing to investigate the effects of microbial communities in long‐term organic and conventional managed soils on restoring soil microbiome and functionality. We calculated multifunctionality of soils at days 30 and 90 of recolonization using the averaging approach. Results showed that organic management (O) significantly increased alpha diversity, niche width and network complexity of microbial community compared to conventional management (C). The alpha diversity, niche width and network complexity of microbial community in soils with organic soil suspension were significantly increased compared to conventional management at days 30 and 90 of recolonization. Soil multifunctionality of sterilized organic managed soil inoculated with organic soil suspension (OO) was 14.6% to 70.6% higher than that of the rest treatments. Macrogenomic analysis revealed that O significantly enriched functional pathways of ABC transporters, carbon metabolism, biosynthesis of amino acids, two‐component and nitrogen metabolism as well as most of the functional genes for carbon degradation, carbon fixation, nitrogen cycling and phosphorus cycles compared to C. These functional pathways and genes were also significantly enriched in soils with organic soil suspension at day 30 and 90 of recolonization. Furthermore, alpha diversity, niche width, network complexity, functional pathways and functional genes of microbiome correlated positively with soil multifunctionality. Synthesis and applications. Our results emphasize the importance of organic management induced changes in diversity, network complexity, and functionality of microbial communities for promoting recovery to soil microbial and functional losses, providing the theoretical basis for sustainable impact of organic management in agronomic production on soil microbiome and function. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Introduction: Salt stress is a major abiotic stress that affects crop growth and productivity. Choline Chloride (CC) has been shown to enhance salt tolerance in various crops, but the underlying molecularmechanisms in rice remain unclear. Methods: To investigate the regulatory mechanism of CC-mediated salt tolerance in rice, we conducted morpho-physiological, metabolomic, and transcriptomic analyses on two rice varieties (WSY, salt-tolerant, and HHZ, saltsensitive) treated with 500 mg·L-1 CC under 0.3% NaCl stress. Results: Our results showed that foliar application of CC improved morphophysiological parameters such as root traits, seedling height, seedling strength index, seedling fullness, leaf area, photosynthetic parameters, photosynthetic pigments, starch, and fructose content under salt stress, while decreasing soluble sugar, sucrose, and sucrose phosphate synthase levels. Transcriptomic analysis revealed that CC regulation combined with salt treatment induced changes in the expression of genes related to starch and sucrose metabolism, the citric acid cycle, carbon sequestration in photosynthetic organs, carbon metabolism, and photosynthetic antenna proteins in both rice varieties. Metabolomic analysis further supported these findings, indicating that photosynthesis, carbon metabolism, and carbon fixation pathways were crucial in CC-mediated salt tolerance. Discussion: The combined transcriptomic and metabolomic data suggest that CC treatment enhances rice salt tolerance by activating distinct transcriptional cascades and phytohormone signaling, alongwithmultiple antioxidants and uniquemetabolic pathways. These findings provide a basis for further understanding the mechanisms of metabolite synthesis and gene regulation induced by CC in rice in response to salt stress, and may inform strategies for improving crop resilience to salt stress. [ABSTRACT FROM AUTHOR]

The dramatic decrease in atmospheric CO2 concentration during Oligocene was proposed as directly linked to C4 evolution. However, it remains unclear how the decreased CO2 concentration directly facilitate C4 evolution, besides its role as a selection pressure. We conducted a systematic transcriptomics and metabolomics analysis under short-term low CO2 condition and found that Arabidopsis grown under this condition showed 1) increased expression of most genes encoding C4-related enzymes and transporters; 2) increased expression of genes involved in photorespiration and pathways related to carbon skeleton generation for ammonium refixation; 3) increased expression of genes directly involved in ammonium refixation. Furthermore, we found that in vitro treatment of leaves with NH4 + induced a similar pattern of changes in C4 related genes and genes involved in ammonium refixation. These data support the view that Arabidopsis grown under short-term low CO2 conditions rewired its metabolism to supply carbon skeleton for ammonium recycling, during which process the expression of C4 genes were up-regulated as a result of a hitchhiking process. This study provides new insights into the adaptation of the C3 model plant Arabidopsis under low CO2 conditions and suggests that low CO2 can facilitate the evolution of C4 photosynthesis beyond the commonly assumed role of being a selection pressure. [ABSTRACT FROM AUTHOR]

In the relay intercropping system of maize/sweet potato, the growth of the sweet potatoes is seriously limited by weak light stress in the early stage due to shade from maize plants. However, it is not clear how the weak light affects sweet potatoes and causes tuberous root loss. By setting two light intensity levels (weak light = 30% transmittance of normal light), this study evaluated the responses of two sweet potato cultivars with different tolerances to weak light in a field-based experiment and examined the divergence of gene expression related to light and photosynthesis in a pot-based experiment. The results showed that under weak light, the anatomic structure of functional leaves changed, and the leaf thickness decreased by 39.98% and 17.32% for Yuhongxinshu-4 and Wanshu-7, respectively. The ratio of S/R increased, and root length, root superficial area, and root volume all decreased. The photosynthetic enzyme rubisco was weakened, and the net photosynthetic rate (Pn) declined as well. The level of gene expression in Wanshu-7 was higher than that of Yuhongxinshu-4. The KEGG analysis showed that differentially expressed genes from the two cultivars under weak-light stress used the same enrichment pathway, mainly via glutathione metabolism and flavonoid biosynthesis. After full light levels were restored, the differentially expressed genes were all enriched in pathways such as photosynthesis, photosynthetic pigment synthesis, and carbon metabolism. These findings indicated that weak light changed the plant morphology, photosynthetic physiology and gene expression levels of sweet potatoes, which eventually caused losses in the tuberous root yield. The more light-sensitive cultivar (Wanshu-7) had stronger reactions to weak light. This study provides a theoretical basis and strategy for breeding low-light-tolerant varieties and improving relay intercropping production in sweet potatoes. [ABSTRACT FROM AUTHOR]

Astragalus polysaccharide‐containing 3D‐printed scaffold shows great potential in traumatic skin repair. This study aimed to investigate its repairing effect and to combine it with proteomic technology to deeply resolve the related protein expression changes. Thirty SD rats were divided randomly into three groups (n = 10 per group): the sham‐operated group, the model group and the scaffold group. Subsequently, we conducted a comparative analysis on trauma blood perfusion, trauma healing rate, histological changes, the expression of the YAP/TAZ signalling pathway and angiogenesis‐related factors. Additionally, neonatal skin tissues were collected for proteomic analysis. The blood perfusion volume and wound healing recovery in the scaffold group were better than that in the model group (p < 0.05). The protein expression of STAT3, YAP, TAZ and expression of vascular‐related factor A (VEGFA) in the scaffold group was higher than that in the model group (p < 0.05). Proteomic analysis showed that there were 207 differential proteins common to the three groups. Mitochondrial function, immune response, redox response, extracellular gap and ATP metabolic process were the main groups of differential protein changes. Oxidative phosphorylation, metabolic pathway, carbon metabolism, calcium signalling pathway, etc. were the main differential metabolic pathway change groups. Astragalus polysaccharide‐containing 3D‐printed scaffold had certain reversals of protein disorder. The Astragalus polysaccharide‐containing 3D‐printed scaffold may promote the VEGFs by activating the YAP/TAZ signalling pathway with the help of STAT3 into the nucleus, accelerating early angiogenesis of the trauma, correcting the protein disorder of the trauma and ultimately realizing the repair of the wound. [ABSTRACT FROM AUTHOR]

17β-Estradiol (E2) is a novel micro-pollutant that is widely distributed in aquatic sediments and has a universal toxicological effect on aquatic organisms. However, its ecological impact on aquatic microorganisms is not yet clear. In this study, we designed a simulation system for oligotrophic water deposition in the laboratory, analyzed the impact of different concentrations of E2 pollution on the carbon metabolism activity (carbon gas emission rate) of water microorganisms. Based on high-throughput sequencing results, we revealed the impact of E2 pollution on the community structure succession and metabolic function of bacteria, archaea, and methanogens in the simulated system, explored the impact mechanism of E2 pollution on microbial carbon metabolism in water bodies. Our results suggested that E2 significantly impacts the bacterial and archaeal community rather than the methanogen community, thereby indirectly inhibiting methane production. The achievements will bridge the theoretical gap between estrogen metabolism and carbon metabolism in sedimentary environments and contribute to enriching the ecological toxicology theory of steroid estrogen. [ABSTRACT FROM AUTHOR]

Background: Streptococcus suis is an important zoonotic pathogen. Biofilm formation largely explains the difficulty in preventing and controlling S. suis. However, little is known about the molecular mechanism of S. suis biofilm formation. Results: In this study, transcriptomic and metabolomic analyses of S. suis in biofilm and planktonic states were performed to identify key genes and metabolites involved in biofilm formation. A total of 789 differential genes and 365 differential metabolites were identified. By integrating transcriptomics and metabolomics, five main metabolic pathways were identified, including amino acid pathway, nucleotide metabolism pathway, carbon metabolism pathway, vitamin and cofactor metabolism pathway, and aminoacyl-tRNA biosynthesis metabolic pathway. Conclusions: These results provide new insights for exploring the molecular mechanism of S. suis biofilm formation. [ABSTRACT FROM AUTHOR]

Edible fungi cultivation serves as an efficient biological approach to transforming agroforestry byproducts, particularly Korshinsk peashrub (KP) branches into valuable mushroom (Lentinus edodes) products. Despite the widespread use of KP, the molecular mechanisms underlying its regulation of mushroom development remain largely unknown. In this study, we conducted a combined analysis of transcriptome and metabolism of mushroom fruiting bodies cultivated on KP substrates compared to those on apple wood sawdust (AWS) substrate. Our aim was to identify key metabolic pathways and genes that respond to the effects of KP substrates on mushrooms. The results revealed that KP induced at least a 1.5-fold increase in protein and fat content relative to AWS, with 15% increase in polysaccharide and total sugar content in mushroom fruiting bodies. There are 1196 differentially expressed genes (DEGs) between mushrooms treated with KP relative to AWS. Bioinformatic analysis show significant enrichments in amino acid metabolic process, oxidase activity, malic enzyme activity and carbon metabolism among the 698 up-regulated DEGs induced by KP against AWS. Additionally, pathways associated with organic acid transport and methane metabolism were significantly enriched among the 498 down-regulated DEGs. Metabolomic analysis identified 439 differentially abundant metabolites (DAMs) in mushrooms treated with KP compared to AWS. Consistent with the transcriptome data, KEGG analysis on metabolomic dataset suggested significant enrichments in carbon metabolism, alanine, aspartate and glutamate metabolism among the up-regulated DAMs by KP. In particular, some DAMs were enhanced by 1.5-fold, including D-glutamine, L-glutamate, glucose and pyruvate in mushroom samples treated with KP relative to AWS. Targeted metabolomic analysis confirmed the contents of DAMs related to glutamate metabolism and energy metabolism. In conclusion, our findings suggest that reprogrammed carbon metabolism and oxidoreductase pathways act critical roles in the enhanced response of mushroom to KP substrates. [ABSTRACT FROM AUTHOR]

Introduction: Soil microbial functional traits are key indicators of soil microbial ecological traits; however, how mixing patterns of Chinese fir and broadleaved trees drive soil microbial functional trait variation at the aggregate scale and how soil microbial functional traits are linked to soil fertility factors have largely not been determined. Methods: In this study, soil from the 0-20 cm depths in three Chinese fir plantations was collected, and the soil samples were separated into >2 mm (large macro-aggregate), 0.25-2 mm (macro-aggregate) and <0.25 mm (microaggregate) by complying with an optimal moisture sieving procedure. The metabolic activities, functional diversity and different carbon sources utilization characteristics of the soil microorganisms were determined by the Biolog Eco microplate method. Results: In all Chinese fir plantations, micro-aggregates (<0.25 mm) consistently exhibited the highest levels of microbial metabolic activity, a more uniform carbon source utilisation capacity, and the highest microbial diversity. Microaggregates also showed elevated levels of soil organic carbon (OC), total nitrogen (TN), total phosphorus (TP), and higher ratios of C/N and C/P compared to large macro-aggregates and macro-aggregates, indicating that micro-aggregates contain more resources available to soil microorganisms. Soil OC, TN, and TP content were enhanced by integration with Michelia macclurei, suggesting that this combination promotes relatively favourable soil conditions for microbial growth and multiplication. This, in turn, promotes microbial metabolic activity. Furthermore, redundancy and correlation analyses showed that soil OC, TN, and TP were identified as principal determinants of soil microbial functional properties in Chinese fir plantations. Discussion: In summary, mixed cultivation and aggregate size influenced microbial functional properties via soil nutrient alterations. Consequently, adopting a mixed cultivation approach of Chinese fir and broadleaved trees is advocated in the subtropical regions of Guangxi. Employing a diversity of tree species, including M. macclurei, is recommended for optimal soil quality preservation. [ABSTRACT FROM AUTHOR]

Aims Carbon source is a necessary nutrient for bacterial strain growth. In industrial production, the cost of using different carbon sources varies greatly. Moreover, the complex environment in space may cause metabolic a series of changes in the strain, and this method has been successfully applied in some basic research. To date, space mutagenesis is still limited number of studies, particularly in carbon metabolism of probiotics. Methods and results HG-R7970-41 was isolated from bacterium suspension (Probio-M9) after space flight, which can produce capsular polysaccharide after space mutagenesis. Phenotype Microarray (PM) was used to evaluated the metabolism of HG-R7970-41 in 190 single carbon sources. RNA sequencing and total protein identification of two strains revealed their different carbon metabolism mechanisms. PM results demonstrated the metabolism of 10 carbon sources were different between Probio-M9 and HG-R7970-41. Transcriptomic and proteomic analyses revealed that this change in carbon metabolism of HG-R7970-41 mainly related to changes in phosphorylation and the glycolysis pathway. Based on the metabolic mechanism of different carbon sources and related gene cluster analysis, we found that the final metabolic activities of HG-R7970-41 and Probio-M9 were mainly regulated by PTS-specific membrane embedded permease, carbohydrate kinase and two rate-limiting enzymes (phosphofructokinase and pyruvate kinase) in the glycolysis pathway. The expanded culture test also confirmed that HG-R7970-41 had different metabolic characteristics from original strain. Conclusions These results suggested that space environment could change carbon metabolism of Probio-M9. The new isolate (HG-R7970-41) showed a different carbon metabolism pattern from the original strain mainly by the regulation of two rate-limiting enzymes. [ABSTRACT FROM AUTHOR]

Phloroglucinol (1,3,5-trihydroxybenzene) is a key intermediate in the degradation of polyphenols such as flavonoids and hydrolysable tannins and can be used by certain bacteria as a carbon and energy source for growth. The identification of enzymes that participate in the fermentation of phloroglucinol to acetate and butyrate in Clostridia was recently reported. In this study, we present the discovery and characterization of a novel metabolic pathway for phloroglucinol degradation in the bacterium Collinsella sp. zg1085, from marmot respiratory tract. In both the Clostridial and Collinsella pathways, phloroglucinol is first reduced to dihydrophoroglucinol by the NADPH-dependent phloroglucinol reductase (PGR), followed by ring opening to form (S)-3-hydroxy-5-oxohexanoate by a Mn2+-dependent dihydrophloroglucinol cyclohydrolase (DPGC). In the Collinsella pathway, (S)-3-hydroxy-5-oxohexanoate is then cleaved to form malonate semialdehyde and acetone by a newly identified aldolase (HOHA). Finally, a NADP+-dependent malonate-semialdehyde dehydrogenase converts malonate semialdehyde to CO2 and acetyl-CoA, an intermediate in carbon and energy metabolism. Recombinant expression of the Collinsella PGR, DPGC, and HOHA in E. coli enabled the conversion of phloroglucinol into acetone, providing support for the proposed pathway. Experiments with Olsenella profusa, another bacterium containing the gene cluster of interest, show that the PGR, DPGC, HOHA, and MSDH are induced by phloroglucinol. Our findings add to the variety of metabolic pathways for the degradation of phloroglucinol, a widely distributed phenolic compound, in the anaerobic microbiome. [ABSTRACT FROM AUTHOR]

Low temperatures during germination inhibit seed growth, lead to small and weak seedlings, and significantly reduce the wheat yield. Alleviating the adverse effects of low temperature on wheat seed germination is highly important for achieving high and stable wheat yields. In this study, Tongmai 6 (insensitive) and Zhengmai 113 (sensitive), which have different low-temperature sensitivities during germination were treated with low temperature during germination. The transcriptome, metabolome and physiological data revealed that low temperature decreased the germination rate, downregulated the expression of a large number of genes involved in regulating glycometabolism, and inhibited carbon, nitrogen (especially amino acids) and energy metabolism in the seeds. Arginine content increased at low temperature, and its increase in the low-temperature-tolerant variety was significantly greater than that in the sensitive variety. Arginine priming experiment showed that treatment with an appropriate concentration of arginine improved the seed germination rate. The conversion of starch to soluble sugar significantly increased under exogenous arginine conditions, the content of key metabolites in energy metabolism increased, and the utilization of ATP in the seeds increased. Taken together, arginine priming increased seed germination at low temperature by relieving inhibition of seed carbon and nitrogen metabolism and improving seed energy metabolism. [ABSTRACT FROM AUTHOR]

Folate-mediated one-carbon metabolism (FOCM) plays an important role in colorectal carcinogenesis. Previous studies have assessed the role of folate-mediated one-carbon metabolism (FOCM)-related gene-diet interaction in the aetiology of colorectal cancer (CRC), however, the results remained inconclusive. Thus, this study aimed to investigate dietary factors and genetic variants related to FOCM, as well as potential nutrient-gene and nutrient-lifestyle interactions, on CRC risk. This observational study included 229 patients diagnosed with CRC and 229 age- and sex-matched subjects as controls from a population-based bowel cancer screening program. Conditional logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (95%CI) for CRC risk. A Bonferroni-corrected threshold of α = 0.005 was considered significant, and P values less than 0.05 were considered to be suggestive of an association. After Bonferroni correction, a high dietary intake of betaine was associated with a decreased risk of CRC in the adjusted model (OR, 95% CI: 0.21, 0.10–0.40, P < 0.001). Two SNPs, rs1476413 and rs17824591, exhibited significant gene-diet interactions with total choline ad vitamin B12 intakes, respectively, in adjusted models (total choline, tertile 3 vs. 1, OR, 95% CI: 0.25, 0.11–0.66, Pinteraction = 0.012; vitamin B12, tertile 2 vs. tertile 1, OR, 95% CI: 2.48, 1.04-5.00, Pinteraction = 0.003). These findings suggest that betaine intake and interactions between some dietary factors and variants in MTHFR and MTHFD1 genes have an influence on CRC risk in the population studied. If these results are confirmed, specific nutritional intervention strategies could be designed. [ABSTRACT FROM AUTHOR]

Summary: Glycosyltransferases (GTs) are enzymes that transfer sugars to various targets. They play important roles in diverse biological processes, including photosynthesis, cell motility, exopolysaccharide biosynthesis, and lipid metabolism; however, their involvement in regulating carbon metabolism in Synechocystis sp. PCC 6803 has not been reported.We identified a novel GT protein, Slr1064, involved in carbon metabolism. The effect of slr1064 deletion on the growth of Synechocystis cells and functional mechanisms of Slr1064 on carbon metabolism were thoroughly investigated through physiological, biochemistry, proteomic, and metabolic analyses.We found that this GT, which is mainly distributed in the membrane compartment, is essential for the growth of Synechocystis under heterotrophic and mixotrophic conditions, but not under autotrophic conditions. The deletion of slr1064 hampers the turnover rate of Gap2 under mixotrophic conditions and disrupts the assembly of the PRK/GAPDH/CP12 complex under dark culture conditions. Additionally, UDP‐GlcNAc, the pivotal metabolite responsible for the O‐GlcNAc modification of GAPDH, is downregulated in the Δslr1064.Our work provides new insights into the role of GTs in carbon metabolism in Synechocystis and elucidate the mechanism by which carbon metabolism is regulated in this important model organism. [ABSTRACT FROM AUTHOR]

Drought stress is a critical environmental factor that significantly impacts plant growth and productivity. However, the transcriptome analysis of differentially expressed genes in response to drought stress in Camellia oleifera Abel. is still unclear. This study analyzed the transcriptome sequencing data of C. oleifera under drought treatments. A total of 20,674 differentially expressed genes (DEGs) were identified under drought stress, with the number of DEGs increasing with the duration of drought. Specifically, 11,793 and 18,046 DEGs were detected after 8 and 15 days of drought treatment, respectively, including numerous upregulated and downregulated genes. Gene Ontology (GO) enrichment analysis showed that the DEGs were primarily involved in various biological processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that carbon metabolism, glyoxylate and dicarboxylate metabolism, proteasome, glycine, serine, and threonine metabolism were the main affected pathways. Among the DEGs, 376 protein kinases, 42 proteases, 168 transcription factor (TF) genes, and 152 other potential functional genes were identified, which may play significant roles in the drought response of C. oleifera. The expression of relevant functional genes was further validated using quantitative real-time PCR (qRT-PCR). These findings contribute to the comprehension of drought tolerance mechanisms in C. oleifera and bolster the identification of drought-resistant genes for molecular breeding purposes. [ABSTRACT FROM AUTHOR]

Recombinant protein production in Komagataella phaffi (K. phaffi), a widely utilized host organism, can be optimized by enhancing the metabolic flux in the central carbon metabolism pathways. The methanol utilization pathway (MUT) during methanol-based growth plays a crucial role in providing precursors and energy for cell growth and development. This study investigated the impact of boosting the methanol dissimilation pathway, a branch of MUT that plays a vital role in detoxifying formaldehyde and providing energy in the form of NADH, in K. phaffi. This was achieved by integrating two orthologous genes from Hansenula polymorpha into the K. phaffi genome: formaldehyde dehydrogenase (HpFLD) and formate dehydrogenase (HpFMDH). The HpFLD and HpFMDH genes were isolated from the Hansenula polymorpha genome and inserted under the regulation of the pAOX1 promoter in the genome of recombinant K. phaffi that already contained a single copy of model protein genes (eGFP or EGII). The expression levels of these model proteins were assessed through protein activity assays and gene expression analysis. The findings revealed that while both orthologous genes positively influenced model protein production, HpFMDH exhibited a more pronounced upregulation in expression compared to HpFLD. Co-expression of both orthologous genes demonstrated synergistic effects, resulting in approximately a twofold increase in the levels of the model proteins detected. This study provides valuable insights into enhancing the production capacity of recombinant proteins in K. phaffi. [ABSTRACT FROM AUTHOR]

Photorespiration, caused by oxygenation of the enzyme Rubisco, is considered a wasteful process, because it reduces photosynthetic carbon gain, but it also supplies amino acids and is involved in amelioration of stress. Here, we show that a sudden increase in photorespiratory activity not only reduced carbon acquisition and production of sugars and starch, but also affected diurnal dynamics of amino acids not obviously involved in the process. Flux calculations based on diurnal metabolite profiles suggest that export of proline from leaves increases, while aspartate family members accumulate. An immense increase is observed for turnover in the cyclic reaction of glutamine synthetase/glutamine-oxoglutarate aminotransferase (GS/GOGAT), probably because of increased production of ammonium in photorespiration. The hpr1-1 mutant, defective in peroxisomal hydroxypyruvate reductase, shows substantial alterations in flux, leading to a shift from the oxoglutarate to the aspartate family of amino acids. This is coupled to a massive export of asparagine, which may serve in exchange for serine between shoot and root. [ABSTRACT FROM AUTHOR]

Nitrogen is the primary nutrient for plants. Low nitrogen generally affects plant growth and fruit quality. Melon, as an economic crop, is highly dependent on nitrogen. However, the response mechanism of its self-rooted and grafted seedlings to low-nitrogen stress has not been reported previously. Therefore, in this study, we analyzed the transcriptional differences between self-rooted and grafted seedlings under low-nitrogen stress using fluorescence characterization and RNA-Seq analysis. It was shown that low-nitrogen stress significantly inhibited the fluorescence characteristics of melon self-rooted seedlings. Analysis of differentially expressed genes showed that the synthesis of genes related to hormone signaling, such as auxin and brassinolide, was delayed under low-nitrogen stress. Oxidative stress response, involved in carbon and nitrogen metabolism, and secondary metabolite-related differentially expressed genes (DEGs) were significantly down-regulated. It can be seen that low-nitrogen stress causes changes in many hormonal signals in plants, and grafting can alleviate the damage caused by low-nitrogen stress on plants, ameliorate the adverse effects of nitrogen stress on plants, and help them better cope with environmental stresses. [ABSTRACT FROM AUTHOR]

β-Alanine is a versatile amino acid with wide-range industrial applications, but its production from glucose has been limited by a low yield. This study addresses this challenge by developing efficient Escherichia coli strains with modified carbon metabolism as microbial cell factories and implementing a two-stage fermentation strategy. The introduction of aspartate decarboxylase (PanDE56S/I88M) facilitates the conversion of aspartate to β-alanine, while the overexpression of key enzymes such as phosphoenolpyruvate carboxylase and aspartate dehydrogenase increases the carbon flow from phosphoenolpyruvate to aspartate. To mitigate oxidative stress, the glutathione cycle was enhanced by overexpressing BtuE and Gor. In a bioreactor, the optimized strain achieved β-alanine production of 71.7 g/L with a yield of 1.0 mol/mol glucose, reaching a peak of 1.29 mol/mol. Notably, the utilization of acetate as a carbon feedstock enabled the production of 50 g/L of β-alanine with a 0.33 mol/mol acetate yield, showcasing the potential for sustainable production. This research offers valuable insights into improving the carbon yield in β-alanine production, which is of great importance for industrial applications. [ABSTRACT FROM AUTHOR]

Ganoderma lingzhi, a species of white rot fungus, possesses the highest abundance of lignocellulose-degrading enzymes among these fungi, as well as a relatively high carbon conversion rate. Corn straw, as an important sustainable resource, is used as a substrate for the liquid culture of G. lingzhi. However, little is known about the genes encoding the lignocellulose degradation and polysaccharide and triterpenoid biosynthetic pathways involved in this process. This paper employs transcriptomics to uncover the key genes involved in lignocellulose degradation and the synthesis of polysaccharides and triterpenoids during the liquid fermentation of G. lingzhi using corn straw as the substrate, as well as their associations. Carbohydrate-Active enzymes analysis of differential genes in the sequencing results was used to analyze the genes related to lignocellulose degradation. Among these, 43 core genes encoding CAZymes were obtained after 0 to 5 days of fermentation, and 25 core genes encoding CAZymes were obtained after 5 to 12 days of fermentation. The differential expression levels of DN3690_c0_g1 (EGL), DN3627_c0_g2 (XYN), DN4778_c0_g1 (XYN), DN2037_c0_g1 (LACC), and DN277_c2_g1 (MnP) were used to identify the key genes. The polysaccharide synthesis metabolic pathway favored mannitol synthesis, and the expression of triterpene precursor-metabolizing enzyme genes revealed higher expression levels of key enzyme genes such as ACAT, HMGS, and MPK. A correlation clustering analysis of genes related to lignocellulose degradation, polysaccharide, and triterpene anabolism during liquid fermentation showed that lignocellulose degradation genes mainly influenced arabinose and mannitol anabolism, as well as the synthesis of triterpene precursors. [ABSTRACT FROM AUTHOR]

This study took Nanchang as a research object and established an urban carbon metabolism process model based on carbon flow and an urban carbon metabolism analogy model based on Kleiber's law. The ecological relationship between land types and their changes caused by carbon flow in the process of land use change was studied by applying the ecological network analysis (ENA), and whether the relationship between urban carbon metabolism and the scale of construction land was consistent with the biometabolic law by using the panel data model. The results showed that the net carbon flow in Nanchang continued to show negative values from 2000 to 2020, and the mean value of the mutualism index (M ) was less than 1, both factors indicating a negative impact of land use change. Exploitation and control relationships were the most major ecological relationships, dominated by urban land. The β values of the carbon metabolism models for rural settlements and other construction land were less than 1, implying an analogous relationship between carbon metabolism and biometabolism for both. The study provides a scientific foundation for national and local governments to formulate carbon emission reduction policies and plan low-carbon land use patterns. [ABSTRACT FROM AUTHOR]

Corynebacterium glutamicum (C. glutamicum) has become industrially important in producing glutamic acid and lysine since its discovery and has been the subject of proteomics and central carbon metabolism studies. The proteome changes depending on environmental conditions, nutrient availability, and stressors. Post-translational modification (PTMs), such as phosphorylation, methylation, and glycosylation, alter the function and activity of proteins, allowing them to respond quickly to environmental changes. Proteomics techniques, such as mass spectrometry and two-dimensional gel electrophoresis, have enabled the study of proteomes, identification of proteins, and quantification of the expression levels. Understanding proteomes and central carbon metabolism in microorganisms provides insight into their physiology, ecology, and biotechnological applications, such as biofuels, pharmaceuticals, and industrial enzyme production. Several attempts have been made to create efficient production strains to increase productivity in several research fields, such as genomics and proteomics. In addition to amino acids, C. glutamicum is used to produce vitamins, nucleotides, organic acids, and alcohols, expanding its industrial applications. Considerable information has been accumulated, but recent research has focused on proteomes and central carbon metabolism. The development of genetic engineering technologies, such as CRISPR-Cas9, has improved production efficiency by allowing precise manipulation of the metabolic pathways of C. glutamicum. In addition, methods for designing new metabolic pathways and developing customized strains using synthetic biology technology are gradually expanding. This review is expected to enhance the understanding of C. glutamicum and its industrial potential and help researchers identify research topics and design studies. [ABSTRACT FROM AUTHOR]

Gluconobacter oxydans (Go) and Brettanomyces bruxellensis (Bb) are detrimental micro-organisms compromising wine quality through the production of acetic acid and undesirable aromas. Non-Saccharomyces yeasts, like Metschnikowia species, offer a bioprotective approach to control spoilage micro-organisms growth. Antagonist effects of forty-six Metschnikowia strains in a co-culture with Go or Bb in commercial grape juice were assessed. Three profiles were observed against Go: no effect, complete growth inhibition, and intermediate bioprotection. In contrast, Metschnikowia strains exhibited two profiles against Bb: no effect and moderate inhibition. These findings indicate a stronger antagonistic capacity against Go compared to Bb. Four promising Metschnikowia strains were selected and their bioprotective impact was investigated at lower temperatures in Chardonnay must. The antagonistic effect against Go was stronger at 16 °C compared to 20 °C, while no significant impact on Bb growth was observed. The bioprotection impact on Saccharomyces cerevisiae fermentation has been assessed. Metschnikowia strains' presence did not affect the fermentation time, but lowered the fermentation rate of S. cerevisiae. An analysis of central carbon metabolism and volatile organic compounds revealed a strain-dependent enhancement in the production of metabolites, including glycerol, acetate esters, medium-chain fatty acids, and ethyl esters. These findings suggest Metschnikowia species' potential for bioprotection in winemaking and wine quality through targeted strain selection. [ABSTRACT FROM AUTHOR]

Background: Cell energy metabolism controls the activation and function of dendritic cells (DCs). Inflammatory dendritic epidermal cells (IDECs) in skin lesions of atopic dermatitis (AD) express high-affinity IgE receptor (FceRI) and toll-like receptor 2 (TLR2), which mediate the generation and maintenance of inflammation. However, cellular energy metabolism and effector function of IDECs mediated by FceRI and TLR2 have not been fully elucidated. Methods: IDECs in vitro were treated with TLR2 agonist Pam3CSK4 and anti-IgE alone or in combination for 24 h. Further, we analyzed the expression of cell surface activation markers, production of inflammatory factors, and cellular energy metabolism profiles of IDECs by using flow cytometry, multiplex assay, RNA sequencing, targeted energy metabolism, and seahorse assays. Results: Compared to the unstimulated or anti-IgE groups, Pam3CSK4 alone or combined with anti-IgE groups significantly increased the expression of CD80, CD83, and CD86 on IDECs, but did not affect the expression of the above markers in the anti-IgE group. The release of inflammatory cytokines increased in the Pam3CSK4 alone or combined with anti-IgE groups, while there was a weak increasing trend in the anti-IgE group. The glycolysis/gluconeogenesis pathway of carbon metabolism was affected in all treatment groups. Furthermore, compared to the control group, we found a decrease in pyruvic acid, upregulation of PFKM, downregulation of FBP1, and increase in extracellular lactate, glycolysis rate, and glycolysis capacity after all treatments, while there was no difference between each treatment group. However, there was no difference in glycolytic reserve and mitochondrial basic and maximum respiration among all groups. Conclusion: Our results indicate that glycolysis of IDECs may be activated through FceRI and TLR2 to upregulate inflammatory factors, suggesting that danger signals from bacteria or allergens might evoke an inflammatory response from AD through the glycolysis pathway [ABSTRACT FROM AUTHOR]

The analysis of the differences in metabolic profiles between naturally Ophiocordyceps sinensis (NO) and cultivated Ophiocordyceps sinensis (CO) is an essential process for the medicinal value mining of Ophiocordyceps sinensis. Non-targeted metabolomics was used to compare the differences in metabolite composition and abundance between NO and CO. Total metabolite composition found that NO is rich in organic acids and derivatives, and CO is rich in lipids and lipid-like molecules. HCA found that organooxygen compounds, cinchona alkaloid, and fatty acyls had different abundances in NO and CO. The variable importance in projection value and quantitative analysis of metabolites found that NO was rich in l-iditol, malate, linoleic acid, and oleic acid; CO is rich in sucrose, perseitol, hydroquinidine, nonanoic acid, 1-hydroxy-2-naphthoic acid, hymol-β-d-glucoside, and gly-his-lys. these compounds have the potential to be biomarkers of NO and CO. KEGG enrichment analysis showed that ascorbate and aldarate metabolism, carbon metabolism, pyrimidine metabolism, and fatty acid biosynthesis were the most different metabolic pathways between NO and CO. Therefore, the analysis of the characteristics of NO and CO metabolites has reference value for finding their different medicinal functions. [ABSTRACT FROM AUTHOR]

Pathogenic bacteria's metabolic adaptation for survival and proliferation within hosts is a crucial aspect of bacterial pathogenesis. Here, we demonstrate that citrate, the first intermediate of the tricarboxylic acid (TCA) cycle, plays a key role as a regulator of gene expression in Staphylococcus aureus. We show that citrate activates the transcriptional regulator CcpE and thus modulates the expression of numerous genes involved in key cellular pathways such as central carbon metabolism, iron uptake and the synthesis and export of virulence factors. Citrate can also suppress the transcriptional regulatory activity of ferric uptake regulator. Moreover, we determined that accumulated intracellular citrate, partly through the activation of CcpE, decreases the pathogenic potential of S. aureus in animal infection models. Therefore, citrate plays a pivotal role in coordinating carbon metabolism, iron homeostasis, and bacterial pathogenicity at the transcriptional level in S. aureus, going beyond its established role as a TCA cycle intermediate. Author summary: Citrate is the first intermediate of the TCA cycle, and its classic role is as a participant in metabolic reactions. In this study, we explored the non-metabolic role of citrate in Staphylococcus aureus. The results suggested that citrate can influence central carbon metabolism, iron homeostasis and the expression of virulence factors by modulating the regulatory activity of the catabolite control protein E (CcpE) and ferric uptake regulator (Fur). For instance, we revealed a new axis, named citrate-CcpE-pycA, was responsible for controlling the endogenous biosynthesis of aspartate, which likely resulted in changes in metabolic adaptation in the host and influenced the pathogenesis of this important human pathogen. Thus, citrate serves as a key signaling molecule for the modulation of gene expression in S. aureus. [ABSTRACT FROM AUTHOR]

Pyruvate:quinone oxidoreductase (PQO) is a flavin‐containing peripheral membrane enzyme catalyzing the decarboxylation of pyruvate to acetate and CO2 with quinone as an electron acceptor. Here, we investigate PQO activity in Corynebacterium glutamicum, examine purified PQO, and describe the crystal structure of the native enzyme and a truncated version. The specific PQO activity was highest in stationary phase cells grown in complex medium, lower in cells grown in complex medium containing glucose or acetate, and lowest in cells grown in minimal acetate‐medium. A similar pattern with about 30‐fold higher specific PQO activities was observed in C. glutamicum with plasmid‐bound pqo expression under the control of the tac promoter, indicating that the differences in PQO activity are likely due to post‐transcriptional control. Continuous cultivation of C. glutamicum at dilution rates between 0.05 and 0.4 h−1 revealed a negative correlation between PQO activity and growth rate. Kinetic analysis of PQO enzymes purified from cells grown in complex or in minimal acetate‐medium revealed substantial differences in specific activity (72.3 vs. 11.9 U·mg protein−1) and turnover number (kcat: 440 vs. 78 s−1, respectively), suggesting post‐translational modifications affecting PQO activity. Structural analysis of PQO revealed a homotetrameric arrangement very similar to the Escherichia coli pyruvate oxidase PoxB except for the C‐terminal membrane binding domain, which exhibited a conformation markedly different from its PoxB counterpart. A truncated PQO variant lacking 17 C‐terminal amino acids showed higher affinity to pyruvate and was independent of detergent activation, highlighting the importance of the C‐terminus for enzyme activation and lipid binding. [ABSTRACT FROM AUTHOR]

The mechanisms governing gene regulation in domestic Yuzhong pigeon breast muscle development remain largely elusive. Here, we conducted a comparative analysis using Iso-seq and RNA-seq data from domestic Yuzhong pigeons and European meat pigeons to uncover signaling pathways and genes involved in breast muscle development. The Iso-seq data from domestic Yuzhong pigeons yielded 131,377,075 subreads, resulting in 16,587 non-redundant high-quality full-length transcripts post-correction. Furthermore, utilizing pfam, CPC, PLEK, and CPAT, we predicted 5575, 4973, 2333, and 4336 lncRNAs, respectively. Notably, several genes potentially implicated in breast muscle development were identified, including tropomyosin beta chain, myosin regulatory light chain 2, and myosin binding protein C. KEGG enrichment analysis revealed critical signaling pathways in breast muscle development, spanning carbon metabolism, biosynthesis of amino acids, glycolysis/gluconeogenesis, estrogen signaling, PI3K-AKT signaling, protein processing in the endoplasmic reticulum, oxidative phosphorylation, pentose phosphate pathway, fructose and mannose metabolism, and tight junctions. These findings offer insights into the biological processes driving breast muscle development in domestic Yuzhong pigeon, contributing to our understanding of this complex phenomenon. [ABSTRACT FROM AUTHOR]

SUMMARY BILE ACID: SODIUM SYMPORTER FAMILY PROTEIN 2 (BASS2) is localized within chloroplast membranes, facilitating the translocation of pyruvate and Na+ from the cytosol to the plastid, where pyruvate supports isopentenyl diphosphate (IPP) synthesis via the methylerythritol phosphate pathway in C3 plants. Nevertheless, the biological function of BASS2 in C4 plants has not been well defined. This study unveils a previously unidentified role of PvBASS2 in Na+ and pyruvate transport in seashore paspalum (Paspalum vaginatum), a halophytic C4 grass, indicating a specific cellular function within this plant species. Data showed that overexpression of PvBASS2 in seashore paspalum attenuated salt tolerance, whereas its RNAi lines exhibited enhanced salt resistance compared to wild‐type plants, suggesting a negative regulatory role of PvBASS2 in seashore paspalum salt tolerance. The constitutive overexpression of PvBASS2 was also found to reduce salt tolerance in Arabidopsis. Further study revealed that PvBASS2 negatively regulates seashore paspalum salt tolerance, possibly due to elevated Na+/K+ ratio, disrupted chloroplast structure, and reduced photosynthetic efficiency following exposure to salinity. Importantly, our subsequent investigations revealed that modulation of PvBASS2 expression in seashore paspalum influenced carbon dioxide assimilation, intermediary metabolites of the tricarboxylic acid cycle, and enzymatic activities under salinity treatment, which in turn led to alterations in free amino acid concentrations. Thus, this study reveals a role for BASS2 in the C4 plant seashore paspalum and enhances our comprehension of salt stress responses in C4 plants. [ABSTRACT FROM AUTHOR]

Bacteria of the phylum Planctomycetota have received much attention over the years due to their unique cell biology and potential for biotechnological application. Within the phylum, bacteria of the class Phycisphaerae have been found in a multitude of environmental datasets. However, only a few species have been brought into culture so far and even enrichments are scarce. Therefore, very little is known about their lifestyle, which has hindered efforts to estimate their environmental relevance. Here, we analysed all medium- and high-quality Phycisphaerae genomes represented in the genome taxonomy database to learn more about their physiology. We combined automatic and manual annotation efforts to provide a bird's eye view of their diverse energy metabolisms. Contrasting previous reports, we did not find indications for the presence of genes for anaerobic ammonium oxidation in any Phycisphaerae genome. Instead, we found that many members of this class are adapted to a facultative anaerobic or strictly fermentative lifestyle and may be specialized in the breakdown of carbon compounds produced by other organisms. Based on these findings, we provide a practical overview of organic carbon substrates predicted to be utilized by Phycisphaerae families. [ABSTRACT FROM AUTHOR]

Cyanobacteria are the only prokaryotes capable of performing oxygenic photosynthesis. Many cyanobacterial strains can live in different trophic modes, ranging from photoautotrophic and heterotrophic to mixotrophic growth. However, the regulatory mechanisms allowing a flexible switch between these lifestyles are poorly understood. As anabolic fixation of CO2 in the Calvin-Benson-Bassham (CBB) cycle and catabolic sugar-degradation pathways share intermediates and enzymatic capacity, a tight regulatory network is required to enable simultaneous opposed metabolic fluxes. The Entner-Doudoroff (ED) pathway was recently predicted as one glycolytic route, which cooperates with other pathways in glycogen breakdown. Despite low carbon flux through the ED pathway, metabolite analyses of mutants deficient in the ED pathway revealed a distinct phenotype pointing at a strong regulatory impact of this route. The small Cp12 protein downregulates the CBB cycle in darkness by inhibiting phosphoribulokinase and glyceraldehyde 3-phosphate dehydrogenase. New results of metabolomic and redox level analyses on strains with Cp12 variants extend the known role of Cp12 regulation towards the acclimation to external glucose supply under diurnal conditions as well as to fluctuations in CO2 levels in the light. Moreover, carbon and nitrogen metabolism are closely linked to maintain an essential C/N homeostasis. The small protein PirC was shown to be an important regulator of phosphoglycerate mutase, which identified this enzyme as central branching point for carbon allocation from CBB cycle towards lower glycolysis. Altered metabolite levels in the mutant DpirC during nitrogen starvation experiments confirm this regulatory mechanism. The elucidation of novel mechanisms regulating carbon allocation at crucial metabolic branching points could identify ways for targeted redirection of carbon flow towards desired compounds, and thus help to further establish cyanobacteria as green cell factories for biotechnological applications with concurrent utilization of sunlight and CO2. [ABSTRACT FROM AUTHOR]

In our research, we utilized six small-fruited pepper germplasms as materials, selected cotyledons with the petiole and hypocotyls as explants, and conducted in vitro regeneration studies. Our outcomes specify that the most suitable explant is cotyledon with the petiole, and the suitable genotype is HNUCA341. The optimal medium for inducing and elongating adventitious buds for this genotype is Murashige and Skoog medium (MS) + 9.12 μM Zeatin (ZT) + 0.57 μM 3-Indoleacetic acid (IAA), with a bud induction rate of 44.4%. The best rooting induction medium is MS + 1.14 μM IAA, with a rooting rate of 86.7%. Research on the addition of exogenous hormones has revealed that the induction speed of buds in small-fruited pepper (HNUCA341) in the combination of ZT and IAA hormones (abbreviated as ZI) is quicker, and the induction effect is better. The histological observations indicate that ZI treatment accelerates the initiation of explant division and differentiation, causing a shorter duration of vascular-bundle tissue production. The plant hormone signaling pathway was significantly enriched by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, including ARR9 (LOC107843874, LOC107843885), ARR4 (LOC107848380, LOC107862455), AHK4 (LOC107870540), AHP1 (LOC107839518), LAX2 (LOC107846008), SAUR36 (LOC107852624), IAA8 (LOC107841020), IAA16 (LOC107839415), PYL4 (LOC107843441), and PYL6 (LOC107871127); these significantly enriched genes may be associated with in vitro regeneration. In addition, the carbon metabolism pathway and plant mitogen-activated protein kinase (MAPK) signaling pathway are also significantly enriched in KEGG. The results of the Gene Ontology (GO) analysis revealed that differentially expressed genes related to carbon metabolism and fixation, photosynthesis and MAPK signaling pathways were upregulated under ZI treatment. It was found that they might be associated with enhanced regeneration in vitro. Furthermore, we also screened out differentially expressed transcription factors, primarily from the MYB, bHLH, AP2/ERF, and NAC families. Overall, our work accumulated important data for the in-depth analysis of the molecular mechanism of in vitro regeneration of pepper, and provides valuable germplasm for establishing an efficient stable pepper genetic-transformation system based on tissue culture. [ABSTRACT FROM AUTHOR]