Carbon Metabolism Research Articles

Metagenomic Analysis: Alterations of Soil Microbial Community and Function due to the Disturbance of Collecting Cordyceps sinensis

Soil microorganisms are critical to the occurrence of Cordyceps sinensis (Chinese Cordyceps), a medicinal fungi used in Traditional Chinese Medicine. The over-collection of Chinese Cordyceps has caused vegetation degradation and impacted the sustainable occurrence of Cordyceps. The effects of Chinese Cordyceps collection on soil microorganisms have not been reported. Metagenomic analysis was performed on the soil of collecting and non-collecting areas of production and non-production areas, respectively. C. sinensis collection showed no alteration in alpha-diversity but significantly affected beta-diversity and the community composition of soil microorganisms. In Cordyceps production, Thaumarchaeota and Crenarchaeota were identified as the dominant archaeal phyla. DNA repair, flagellar assembly, propionate metabolism, and sulfur metabolism were affected in archaea, reducing the tolerance of archaea in extreme habitats. Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Nitrospirae were identified as the dominant bacterial phyla. The collection of Chinese Cordyceps enhanced the bacterial biosynthesis of secondary metabolites and suppressed ribosome and carbon metabolism pathways in bacteria. A more complex microbial community relationship network in the Chinese Cordyceps production area was found. The changes in the microbial community structure were closely related to C, N, P and enzyme activities. This study clarified soil microbial community composition and function in the Cordyceps production area and established that collection clearly affects the microbial community function by altering microbial community structure. Therefore, it would be important to balance the relationship between cordyceps production and microbiology.

Phosphorus limitation regulates the responses of microbial carbon metabolism to long-term combined additions of nitrogen and phosphorus in a cropland

Microorganisms play central roles in the decomposition and retention of soil organic carbon (SOC), but how nutrient addition in intensively managed croplands influences microbial C metabolism remains uncertain. Here, we investigated the effects of coupled phosphorus (P) and nitrogen (N) additions on microbial respiration, growth rate, C use efficiency (CUE), and biomass turnover time in a continuously managed Zea mays cropland, by combining an 18-year field fertilization experiment with the 18O–H2O labeling approach. Results showed that adding P at 50 and 100 kg P ha−1, combined with 150 kg N ha−1, increased respiration by 109% and 50.7%, increased growth rate by 207% and 135%, and increased CUE from approximately 0.26 without P addition to around 0.33 and 0.35, respectively. Conversely, adding N at varying rates (0, 100, 150, and 250 kg N ha−1), combined with 50 kg P ha−1, generated variable responses. These findings underscore the significance of P as the primary limiting element for microbial metabolism in this system. Ecoenzyme stoichiometry analysis further revealed that P addition decreased microbial P vs. N limitation, as well as decreased relative C limitation. In total, changes in P vs. N limitation with P and N additions accounted for 39.6% of the variation in microbial respiration, and in conjunction with relative C limitation, co-explained 51.4% of variations in growth rate and 44.0% of variations in CUE. Furthermore, our investigation identified positive associations of CUE with the activities of N and P-acquiring enzymes, but not with SOC. These results demonstrate flexible responses of microbial C metabolism to long-term anthropogenic N and P additions, highlighting their dependence on soil nutrient limitation. Consequently, optimizing the P-to-N fertilization ratio to alleviate relative P and C limitations may maximize microbial C assimilation and SOC retention in agroecosystems.

Ecological adaptations of amphibians to environmental changes along an altitudinal gradient (Case Study: Bufo gargarizans) from phenotypic and genetic perspectives

BackgroundOrganisms have evolved a range of phenotypic and genetic adaptations to live in different environments along an altitudinal gradient. Herein, we studied the widely distributed Chinese toad, Bufo gargarizans, as a model and used an integrated phenotype-genotype approach to assess adaptations to different altitudinal environments.ResultsComparison of populations from four altitudes (50 m, 1200 m, 2300 m, and 3400 m) showed more effective defenses among high-altitude toads. These included thickened epidermis, more epidermal capillaries and granular glands, greater gland size in skin, and higher antioxidant enzyme activities in plasma. High-altitude toads also showed increased erythrocytes and hematocrit and elevated hemoglobin concentration, potentially improving oxygen delivery. Elevated altitude led to a metabolic shift from aerobic to anaerobic metabolism, and high-altitude populations favored carbohydrates over fatty acids to fuel for energy metabolism. Differentially expressed genes were associated with adaptive phenotypic changes. For instance, expression of genes associated with fatty acid metabolism showed greater suppression at high altitude (3400 m), consistent with decreased flux of β-hydroxybutyric acid and lower free fatty acids levels. Moreover, down-regulation of genes involved in carbon metabolism processes at high altitude (3400 m) were coincident with reduced TCA cycle flux. These results suggest that high-altitude toads adopt a metabolic suppression strategy for survival under harsh environmental conditions. Moreover, the hypoxia-inducible factor signaling cascade was activated at high altitude.ConclusionsCollectively, these results advance our comprehension of adaptation to high-altitude environments by revealing physiological and genetic mechanisms at work in Chinese toads living along altitudinal gradients.

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

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

Pretreated polystyrene is degraded by a microbial consortium enriched from wetland plastic waste

The biodegradation of polystyrene (PS), a type of plastic with aromatic rings in its polymer chain, is a critical environmental goal worldwide. Microbial degradation of PS has been reported, but the underlying mechanisms are poorly understood. Here, we constructed a microcosm wetland containing PS plastic. We isolated six highly efficient PS plastic–degrading bacterial strains and created a microbial consortium (MCs) consisting of these strains. After a 30-day incubation period, MCs-treated PS exhibited hallmarks of degradation, including –CO– formation, reduced hydrophobicity, surface porosity, and 20 % weight loss. The efficiency of PS degradation was enhanced by using a combination of physical-chemical pretreatment and biological methods, increasing the microbial degradation rate by 20 %. Antioxidant 2246 (C23H32O2) was detected in the culture supernatant via GC-MS. Metatranscriptomic sequencing analysis provided insight into the possible metabolic pathway of PS degradation by the composite bacteria. We identified 31 highly expressed genes encoding proteins that function in carbon metabolism pathways and 34 unique proteases which catalyze the cleavage of long polymer chains. The resulting small molecules are absorbed and further degraded intracellularly by enzymes such as coenzyme synthase, hydratase, transferase, carboxylase, and dehydrogenase. These findings lay the foundation for the efficient and sustainable degradation of PS.

Protein and lysine improvement harnessed by a signal chain of red light-emitting diode light in Chlorella pyrenoidosa

Microalgae are emerging as a novel single-cell protein source that can substitute traditional plant protein feeds. In this investigation, lysine and protein accumulation in Chlorella pyrenoidosa were significantly enhanced under red light-emitting diode light, addressing challenge of limiting amino acid in plant proteins. The study employed targeted metabolomics, HPLC, and qRT-PCR to validate the light-induced pathway triggering lysine biosynthesis. Specifically, the pathway involves Ca2+-CaM as an intermediary in signal transduction, which directly inhibits PEPC activity. This inhibition directs a significant carbon flux towards central carbon metabolism, resulting in increased pyruvate levels—a critical precursor for lysine biosynthesis via the diaminopimelate pathway. Ultimately, the content of protein and lysine under red light increased by 36.02 % and 99.56 %, respectively, compared to those under white light. These findings provide a novel orientation for the precise regulation of lysine accumulation in microalgae, and moreover lay a solid theoretical foundation for producing microalgal proteins.

Novel motif associated with carbon catabolite repression in two major Gram-positive pathogen virulence regulatory proteins.

Carbon catabolite repression (CCR) is a widely conserved regulatory process that ensures enzymes and transporters of less-preferred carbohydrates are transcriptionally repressed in the presence of a preferred carbohydrate. This phenomenon can be regulated via a CcpA-dependent or CcpA-independent mechanism. The CcpA-independent mechanism typically requires a transcriptional regulator harboring a phosphotransferase regulatory domain (PRD) that interacts with phosphotransferase system (PTS) components. PRDs contain a conserved histidine residue that is phosphorylated by the PTS-associated HPr-His15~P protein. PRD-containing regulators often harbor additional domains that resemble PTS-associated EIIB protein domains with a conserved cysteine residue that can be phosphorylated by cognate PTS components. We noted that Mga, the PRD-containing central virulence regulator of Streptococcus pyogenes, has an EIIBGat domain containing a cysteine that, based on the presence of a similar motif in glycerol kinase, could be a target for phosphorylation. Using site-directed mutagenesis, we constructed phospho-ablative and phospho-mimetic substitutions of this cysteine and found that these substitutions modify the CCR of the Rgg2/3 quorum-sensing system. Moreover, we provide genetic evidence that the phospho-donor of this cysteine residue is likely to be ManL, the EIIA/B subunit of the mannose PTS system. Interestingly, a structurally distinct virulence gene regulator, PrfA of Listeria monocytogenes, harbors a similar cysteine-containing motif, and phospho-ablative and phospho-mimetic substitutions of the cysteine-altered CCR of PrfA-dependent virulence gene expression. Collectively, our data suggest that phosphorylation of a cysteine within the shared novel motif in Mga and PrfA may be a heretofore missing link between cellular metabolism and virulence.IMPORTANCEIn this study, we identified a novel cysteine-containing motif within the amino acid sequence of two structurally distinct transcriptional regulators of virulence in two Gram-positive pathogens that appears to link carbon metabolism with virulence gene expression. The results also highlight the potential post-translational modification of cysteine in bacterial species, a rare and understudied modification.

Comparative metabolomic analysis of spaghetti meat and wooden breast in broiler chickens: unveiling similarities and dissimilarities.

Spaghetti meat (SM) and wooden breast (WB) are emerging myopathies in the breast meat of fast-growing broiler chickens. The purpose of the study was to investigate the metabolomic differences between normal (N), SM, and WB fillets 24h postmortem. Eight chicken breasts for each experimental group were collected from a commercial processing plant. Supernatant from tissue homogenates were subjected to ultra-performance liquid chromatographytandem mass spectrometry (UPLC-MS) analysis. A total of 3,090 metabolites were identified in the chicken breast meat. The comparison of WB and N showed 850 differential metabolites (P < 0.05), and the comparison of SM and N displayed 617 differential metabolites. The comparison of WB and SM showed 568 differential metabolites. The principal component analysis (PCA) plots showed a distinct separation between SM and N and between WB and N except for one sample, but SM and WB were not distinctly separated. Compared to N, 15-Hydroxyeicosatetraenoic acid (15-HETE) increased, and D-inositol-4-phosphate decreased in both SM and WB, indicating that cellular homeostasis and lipid metabolism can be affected in SM and WB. The abundance of nicotinamide adenine dinucleotide (NAD) + hydrogen (H) (NADH) was exclusively decreased between SM and N (P < 0.05). Purine metabolism was upregulated in SM and WB compared to N with a greater degree of upregulation in WB than SM. Folic acid levels decreased in SM and WB compared to N (P < 0.05). Steroid hormone biosynthesis was downregulated in SM compared to N (P < 0.05). Carbon metabolism was downregulated in SM and WB compared to N with greater degree of downregulation in WB than SM (P < 0.05). These data suggest both shared and unique metabolic alterations in SM and WB, indicating commonalities and differences in their underlying etiologies and meat quality traits. Dietary supplementation of deficient nutrients, such as NADH, folic acids, etc. and modulation of altered pathways in SM and WB would be strategies to reduce the incidence and severity of SM and WB.

A preliminary study of carbon dioxide and methane emissions from patchy tropical seagrass meadows in Thailand.

Seagrass meadows are a significant blue carbon sink due to their ability to store large amounts of carbon within sediment. However, the knowledge of global greenhouse gas (GHG) emissions from seagrass meadows is limited, especially from meadows in the tropical region. Therefore, in this study, CO2 and CH4 emissions and carbon metabolism were studied at a tropical seagrass meadow under various conditions. CO2 and CH4 emissions and carbon metabolism were measured using benthic chambers deployed for 18 h at Koh Mook, off the southwest coast of Thailand. The samples were collected from areas of patchy Enhalus acoroides, Thalassia hemprichii, and bare sand three times within 18 h periods of incubation: at low tide at 6 pm (t0), at low tide at 6 am (t1), and at high tide at noon (t2). Seagrass meadows at Koh Mook exhibited varying CO2 and CH4 emissions across different sampling areas. CO2 emissions were higher in patchy E. acoroides compared to patchy T. hemprichii and bare sand areas. CH4 emissions were only detected in vegetated areas (patchy E. acoroides and T. hemprichii) and were absent in bare sand. Furthermore, there were no significant differences in net community production across sampling areas, although seagrass meadows were generally considered autotrophic. Koh Mook seagrass meadows contribute only slightly to GHG emissions. The results suggested that the low GHG emissions from Koh Mook seagrass meadows do not outweigh their role as significant carbon sinks, with a value 320 t CO2 -eq. This study provided baseline information for estimating GHG emissions in seagrass meadows in Thailand.

Histone-like transcription factor Hfl1p in Candida albicans harmonizes nuclear and mitochondrial genomic network in regulation of energy metabolism and filamentation development

ABSTRACT Candida albicans is an opportunistic fungal pathogen known for surviving in various nutrient-limited conditions within the host and causing infections. Our prior research revealed that Hfl1p, an archaeal histone-like or Hap5-like protein, is linked to mitochondrial ATP generation and yeast-hyphae morphogenesis. However, the specific roles of Hfl1p in these virulence behaviours, through its function in the CBF/NF-Y complex or as a DNA polymerase II subunit, remain unclear. This study explores Hfl1p’s diverse functions in energy metabolism and morphogenesis. By combining proteomic analysis and phenotypic evaluations of the hfl1Δ/hfl1Δ mutant with ChIP data, we found that Hfl1p significantly impacts mitochondrial DNA-encoded CI subunits, the tricarboxylic acid (TCA) cycle, and morphogenetic pathways. This influence occurs either independently or alongside other transcription factors recognizing a conserved DNA motif (TAXXTAATTA). These findings emphasize Hfl1p’s critical role in linking carbon metabolism and mitochondrial respiration to the yeast-to-filamentous form transition, enhancing our understanding of C. albicans’ metabolic adaptability during morphological transition, an important pathogenic trait of this fungus. This could help identify therapeutic targets by disrupting the relationship between energy metabolism and cell morphology in C. albicans.

Physiological and gene expression response mechanisms of dehydration process in Cinnamomum cassia (L.) J. Presl seeds.

A critical factor in the storability of recalcitrant seeds is their moisture content (MC), but its effect on the viability of Cinnamomum cassia (L.) J. Presl (C. cassia) seeds is not fully understood. Measured the germination rate, starch and soluble sugar content, and transcriptome of 8 seed samples with different MC obtained by low-temperature drying method. It was found that the germination rate was significantly negatively correlated with MC. The lethal MC was around 15.6%. During the dehydration process, there was a significant increase in the content of soluble sugars and starch. Transcriptome analysis was performed on CK, W3, W6 showed a total of 62.78 Gb of clean data. Among the 30,228 Unigenes, 28,195 were successfully annotated. In the three comparative groups (CK and W3, CK and W6, W3 and W6), 6,842, 7,640, and 11,628 differentially expressed genes (DEGs) were obtained, respectively. These DEGs were found to be involved in a variety of metabolic pathways, including carbon metabolism, amino acid biosynthesis, starch and sucrose metabolism, glycolysis/gluconeogenesis, and nucleotide and amino sugar metabolism. A total of 1,416 common genes were identified among all three comparison groups. Furthermore, among all the DEGs, a total of 71 transcription factor families were identified, with the C2H2 transcription factor family having the highest number of genes. This ground-breaking study sheds light on the physiological response and gene expression profiles of C. cassia seeds after undergoing dehydration treatment, which will provide valuable insights for further research and understanding of this process.

Anti-echinococcal effect of metformin in advanced experimental cystic echinococcosis: reprogrammed intermediary carbon metabolism in the parasite.

Metformin, a safe biguanide derivative with antiproliferative properties, has shown antiparasitic efficacy against the Echinococcus larval stage. Hence, we assessed the efficacy of a dose of 250 mg kg-1 day-1 in experimental models of advanced CE, at 6 and 12 months post-infection with oral and intraperitoneal administration, respectively. At this high dose, metformin reached intracystic concentrations between 0.7 and 1.7 mM and triggered Eg-TOR inhibition through AMPK activation by AMP-independent and -dependent mechanisms, which are dependent on drug dose. Cystic metformin uptake was controlled by increased expression of organic cation transporters in the presence of the drug. In both experimental models, metformin reduced the weight of parasite cysts, altered the ultrastructural integrity of their germinal layers, and reduced the intracystic availability of glucose, limiting the cellular carbon and energy charge and the proliferative capacity of metacestodes. This glucose depletion in the parasite was associated with a slight increase in cystic uptake of 2-deoxiglucose and the transcriptional induction of GLUT genes in metacestodes. In this context, drastic glycogen consumption led to increased lactate production and altered intermediary metabolism in treated metacestodes. Specifically, the fraction of reducing soluble sugars decreased twofold, and the levels of non-reducing soluble sugars, such as sucrose and trehalose, were modified in both cystic fluid and germinal cells. Taken together, our findings highlight the relevance of metformin as a promising candidate for CE treatment and warrant further research to improve the therapeutic conditions of this chronic zoonosis in humans.

H-NOX Influences Biofilm Formation, Central Metabolism, and Quorum Sensing in Paracoccus denitrificans.

The transition from planktonic to biofilm growth in bacteria is often accompanied by greater resistance to antibiotics and other stressors, as well as distinct alterations in physical traits, genetic activity, and metabolic restructuring. In many species, the heme nitric oxide/oxygen binding proteins (H-NOX) play an important role in this process, although the signaling mechanisms and pathways in which they participate are quite diverse and largely unknown. In Paracoccus denitrificans, deletion of the hnox gene results in a severe biofilm-deficient phenotype. Quantitative proteomics was used to assemble a comprehensive data set of P. denitrificans proteins showing altered abundance of those involved in several important metabolic pathways. Further, decreased levels of pyruvate and elevated levels of C16 homoserine lactone were detected for the Δhnox strain, associating the biofilm deficiency with altered central carbon metabolism and quorum sensing, respectively. These results expand our knowledge of the important role of H-NOX signaling in biofilm formation.

Exogenous glutathione (GSH/GSSG) promoted the synthesis of patchoulol and pogostone, main active components of Pogostemon cablin (Patchouli)

Glutathione redox pair (GSH/GSSG) is the main characterizing substance that regulates the redox balance in cells and affects several physiological processes, such as plant metabolism, antioxidants, and detoxification. Pogostemon cablin was treated with different concentrations of reduced glutathione (GSH) and oxidized glutathione (GSSG), and it was found that 2 mM GSH and 4 mM GSSG treatments promoted the synthesis of patchoulol and pogostone. A total of 6620 significant differentially expressed gene were identified by transcriptome analysis. KEGG analysis showed that DEGs were mainly enriched in metabolic pathways, secondary metabolite biosynthesis, carbon metabolism, and phytohormone signaling pathways; 388 DEGs in the 2 mM GSH (11d) group, and 254 DEGs in the 4 mM GSSG (11d) group, were related to the biosynthesis of secondary metabolites. Further analysis by Gene Set Enrichment Analysis (GSEA) revealed that there were 139 and 83 DEGs associated with terpene synthesis between the two treatment groups, respectively, and the expression of key genes in the synthesis pathway (11 HMGR, 4 DXR, 2 GPPS, and 8 PTS) was up-regulated, which may be the result of transcription factors regulating their expression. The present study preliminarily showed that glutathione redox pair induced the expression of genes related to the terpene biosynthesis pathway, thereby promoting the biosynthesis of patchoulol and pogostone, which provides a reference basis for the technique of regulating and controlling the content of medicinal constituents of patchouli.

Characteristics of Myocardial Structure and Central Carbon Metabolism during the Early and Compensatory Stages of Cardiac Hypertrophy.

Cardiac hypertrophy is a classical forerunner of heart failure and myocardial structural and metabolic remodeling are closely associated with cardiac hypertrophy. We aim to investigate the characteristics of myocardial structure and central carbon metabolism of cardiac hypertrophy at different stages. Using echocardiography and pathological staining, early and compensatory cardiac hypertrophy were respectively defined as within 7 days and from 7 to 14 days after transverse aortic constriction (TAC) in mice. Among mass-spectrometry-based metabolomics, we identified 45 central carbon metabolites. Differential metabolite analysis showed that six metabolites, including citrate, cis-aconitate and so on, decreased significantly on day 1 after TAC. Ten metabolites, including l-lactate, (S)-2-hydroxyglutarate and so on, were obviously changed on days 10 and 14. Pathway analysis showed that these metabolites were involved in seven metabolic pathways, including carbohydrates, amino acids and so on. Western blot showed the expression of ATP-citrate lyase, malate dehydrogenase 1 and lactate dehydrogenase A in myocardium changed markedly on day 3, while the phosphorylation level of AMP-activated protein kinase did not show significantly difference. We hope our research will promote deeper understanding and early diagnosis of cardiac hypertrophy in clinical practice. All raw data were deposited in MetaboLights (MTBLS10555).

Uncovering malate dehydrogenase: structure, function and role in disease.

Malate dehydrogenases (MDHs) have been extensively studied since the 1960s due to their key roles in carbon metabolism and pathways such as redox balance and lipid synthesis. Recently, there has been renewed interest in these enzymes with the discovery of their role in the metabolic changes that occur during cancer and a widespread community of undergraduate teaching laboratories addressing MDH research questions, the Malate Dehydrogenase CUREs Community (MCC). This special issue describes different facets of MDH, including its physiological role, its structure-function relationships, its regulation through post-translational modifications, and perspectives on its evolutionary history. There are two human isoforms: a cytoplasmic isoform that carries out formation of NAD+ for glycolysis, and a mitochondrial isoform that plays a major role in the citric acid cycle. Although the sequences of these two isoforms vary, the structures of the enzymes are similar, and studies suggest that each isoform may form complexes with other enzymes in common pathways. Experimental and theoretical advances have helped to characterize the post-translational modifications of MDH, allowing us to ask more complex questions involving the regulation of the enzyme and substrate promiscuity in the context of cancer. Additionally, there are many unresolved questions on the role of malate dehydrogenase in other organisms, especially in parasites. The review articles in this issue seek to shed light on the latest advances in our understanding of MDH and highlight areas for future studies.

Biomarkers and pathways in autism spectrum disorder: An individual meta-analysis based on proteomic and metabolomic data.

The utilization of biomarkers for the diagnosis and management of autism spectrum disorders (ASD) remains a relatively unexplored frontier in clinical practice. Proteomics and metabolomics are important tools for revealing key biomarkers and evaluating biological pathways in ASD. We conducted an individual meta-analysis to compare the consistency of biomarkers of ASD from central nervous system (brain and cerebrospinal fluid), circulatory system (blood), and non-invasive samples (urine, saliva, and faeces) and performed pathway enrichment analyses to identify pathways enriched in ASD. After screening 926 proteomics and 619 metabolomics articles, we collected data from 10 studies involving 940 differential proteins and 16 studies assessing a total of 748 differential metabolites. In brain tissue, blood, and urine of ASD cases and controls, flotillin-2 (FLOT2), apolipoprotein E (ApoE), and EH domain-containing protein 3 (EHD3) exhibit differential expression, while vinculin (VCL) displays variations in saliva, blood, and urine. Similarly, in case-control studies, gelsolin (GSN) shows differential expression in brain tissue, saliva, and urine, and malate dehydrogenase 2 (MDH2) in brain tissue, blood, and saliva. Hippuric acid and salicyluric acid were simultaneously found in the brain, blood, urine, and faeces. In terms of pathways, glycolysis/gluconeogenesis, carbon metabolism, and glutathione metabolism were enriched in the brain as well as in saliva or urine. In our study, we identified six shared protein and two metabolic markers in central nervous system, circulatory system, and non-invasive samples, underscoring their potential value for ASD diagnosis and management, warranting further research.

A LysR-type regulator influencing swimming motility, galactose utilization, and virulence in Ralstonia solanacearum GMI1000

BackgroundLysR-type transcriptional regulators (LTTRs) are one of the largest families of regulators in prokaryotic organism, which help the bacterium adapt to diverse conditions by controlling a wide array of regulons, encompassing genes responsible for nitrogen and carbon fixation, oxidative stress response, bacterial virulence, and the breakdown of diverse compounds. Ralstonia solanacearum strain GMI1000 possesses 80 LTTR genes, yet the precise roles and functional contributions of only three of these LTTRs have been conclusively established among the total. In this work, our group reveal a novel LTTR member LysR7 (RS_RS02375) that exerts multiple regulatory roles in motility, carbon metabolism and virulence.ResultsIn this investigation, an in-frame deletion mutant ΔlysR7 and a complemented strain CΔlysR7 were prepared. The mutant ΔlysR7 had increased swimming motility on semi-soft medium and showed a reduced replication rate in nutrient-rich medium and in planta. Moreover, ΔlysR7 was unable to grow on nutrient-limited medium, supplemented with galactose as a single carbon resource. RT-qPCR analysis and GUS activity detection indicated that the expression of lysR7 was induced in the presence of galactose. The mutant ΔlysR7 caused weaker wilt disease on either Solanum lycopersicum or Capsicum annuum plants compared to both wild type GMI1000 and CΔlysR7. Transcriptome analysis revealed that 12 upregulated and 8 downregulated differentially expressed genes (DEGs) in ΔlysR7 were restored in CΔlysR7 relative to wild type. In particular, the expression of hrpG, a key gene responsible for type III secretion system, was downregulated. KEGG analysis revealed that, except for lysR7 gene, the 19 DEGs were most enriched in microbial metabolism in diverse environments and metabolic pathways.ConclusionsThe data indicate that LysR7 regulates multiple processes in association with motility, galactose metabolism and virulence in R. solanacearum. The study offers valuable evidence to understand comprehensive regulatory mechanisms mediated by LTTR family members in R. solanacearum.Graphical

Optimizing roof-harvested rainwater storage: Impact of dissolved oxygen regime on self-purification and quality dynamics

Roof-harvested rainwater presents a promising, unconventional, and sustainable water resource for both potable and non-potable uses. However, there is a significant gap in understanding the quality evolution of stored rainwater under varying dissolved oxygen conditions and its suitability for various applications. This study investigated the evolution of rainwater quality under three distinct storage conditions: aerated, open, and sealed. Additionally, the microbial community and metabolic functions were analyzed to systematically evaluate the self-purification performance over long-term storage durations. The results indicate that aerated storage enhances microbial carbon metabolism, leading to a degradation rate of 54.4 %. Sealed and open storage conditions exhibited primary organic matter degradation during the early and late stages, respectively. Roof-rainwater harvesting (RRWH) systems showed limited denitrification activity across all three dissolved oxygen conditions. The maximum accumulation of NO3-N during the storage period reached 5.23 mg/L. In contrast, sealed storage demonstrated robust self-purification performance, evidenced by a comprehensive coefficient of 15.83 calculated by Streeter-Phelps model. These findings provide valuable insights into the mechanisms governing rainwater quality changes under various storage conditions, emphasizing the necessity for developing effective management strategies for the storage and utilization of roof-harvested rainwater.

Unravelling the molecular regulation network of carbon metabolism and lipid metabolism during seed development in Akebia trifoliata via integrated multi-omics analysis

Akebia trifoliata is a medicinal plant with high oil content and broad pharmacological effects. To investigate the regulatory mechanisms of key metabolic pathways during seed development, we conducted an integrated multi-omics analysis, including transcriptomics, proteomics, and metabolomics, exploring the dynamic changes in carbon and lipid metabolism. Metabolomics analysis revealded that glucose and sucrose levels decreased, while glycolytic intermediate phosphoenolpyruvate and fatty acids increased with seed development, indicating a shift in carbon flux towards fatty acid synthesis. Integrated transcriptomic and proteomic analyses showed that 70 days after flowering, the expression levels of genes and proteins associated with carbon and fatty acid metabolism were upregulated, suggesting an increased energy demand. Additionally, LEC2, LEC1, WRI1, FUS3, and ABI3 were identified as vital regulators of lipid synthesis. By constructing a multi-omics co-expression network, we identified hub genes such as aroE, GAPDH, KCS, TPS, and hub proteins like PGM, PDH, ENO, PFK, PK, ACCase, SAD, PLC, and OGDH that play critical regulatory roles in seed lipid synthesis. This study provides new ideas for the molecular basis of lipid synthesis in Akebia trifoliata seeds and can facilitate future research on the genetic improvement through molecular-assisted breeding.