The relationship between gut microbiota and depressive disorder has become a research focus in recent years. Within the microbiota-gut-brain axis, the gut microbiota influences the onset and progression of depressive disorder primarily through the tryptophan metabolic pathway. Tryptophan, an essential amino acid in humans, is subject to dual regulation by intestinal microorganisms, which modulate its metabolic balance via inflammatory stimulation and microbial metabolite production. In depression, excessive activation of the kynurenine branch of tryptophan metabolism leads to the accumulation of proinflammatory and neurotoxic metabolites, thereby exacerbating neuroinflammation in the brain. Intervention studies indicate that the antidepressant-like effects of probiotics and traditional Chinese medicine are associated with remodeling of the gut microbiota, restoration of tryptophan metabolic balance, and alleviation of neuroinflammation. Furthermore, targeted inhibition of kynurenine 3-monooxygenase can mitigate neuroinflammation by regulating microglial activity, thus improving depressive-like behaviors. In summary, the metabolite-inflammation axis represents a central node in the interaction regulation between tryptophan metabolism and the microbiota-gut-brain axis. This provides a theoretical foundation for developing novel therapeutic strategies targeting depression through modulation of gut microbiota-mediated tryptophan metabolism.
Tryptophan/metabolism* ; Gastrointestinal Microbiome/physiology* ; Humans ; Depressive Disorder/microbiology* ; Probiotics/therapeutic use* ; Brain/metabolism* ; Kynurenine/metabolism* ; Metabolic Networks and Pathways ; Animals ; Medicine, Chinese Traditional

The metabolic reactions in cells, whether spontaneous or enzyme-catalyzed, form a highly complex metabolic network closely related to cellular physiological metabolic activities. The reconstruction of cellular physiological metabolic network models aids in systematically elucidating the relationship between genotype and growth phenotype, providing important computational biology tools for precisely characterizing cellular physiological metabolic activities and green biomanufacturing. This paper systematically introduces the latest research progress in different types of cellular physiological metabolic network models, including genome-scale metabolic models (GEMs), kinetic models, and enzyme-constrained genome-scale metabolic models (ecGEMs). Additionally, our paper discusses the advancements in the automated construction of GEMs and strategies for condition-specific GEM modeling. Considering artificial intelligence offers new opportunities for the high-precision construction of cellular physiological metabolic network models, our paper summarizes the applications of artificial intelligence in the development of kinetic models and enzyme-constrained models. In summary, the high-quality reconstruction of the aforementioned cellular physiological metabolic network models will provide robust computational support for future research in quantitative synthetic biology and systems biology.
Metabolic Networks and Pathways/physiology* ; Models, Biological ; Artificial Intelligence ; Systems Biology ; Kinetics ; Cell Physiological Phenomena ; Computational Biology ; Synthetic Biology ; Humans

To explore the renal metabolic markers relavant to the renal toxicity of diethylnitrosamine and the metabolic pathways involved in the renal metabolic markers.
 Methods: Nineteen Sprague Dawley rats were assigned into 2 groups: A normal control group (n=9) and a diethylnitrosamine (DEN) administration group (n=10). The rats in the normal control group were given sterilized water for free drinking. The rats in the DEN administration group were given 0.1 mg/mL DEN solution for free drinking. After 18 weeks, the kidney tissues were collected and tested for nuclear magnetic resonance detection and pathological examination.
 Results: The content of kidneys metabolites in the rats with the DEN administration was changed significantly. The levels of alanine, taurine, pyruvate, acetate, and choline were significantly reduced compared with rat in the normal control group, while the levels of creatine, glycine, TMAO, methionine, proline, lactate, valine, leucine and isoleucine were significantly increased.
 Conclusion: Metabolicomics studies have revealed significant differences in five metabolic pathways, including valine, leucine and isoleucine biosynthesis, glycine serine and threonine metabolism, pyruvate metabolism, glycolysis or gluconeogenesis, cysteine and methionine metabolism.
Alkylating Agents ; toxicity ; Animals ; Diethylnitrosamine ; toxicity ; Glycine ; Kidney ; drug effects ; physiology ; Metabolic Networks and Pathways ; drug effects ; Rats ; Rats, Sprague-Dawley

T cells are an important adaptive immune response arm that mediates cell-mediated immunity. T cell metabolism plays a central role in T cell activation, proliferation, differentiation, and effector function. Specific metabolic programs are tightly controlled to mediate T cell immune responses, and alterations in T cell metabolism may result in many immunological disorders. In this review, we will summarize the main T cell metabolic pathways and the important factors participating in T cell metabolic programming during T cell homeostasis, differentiation, and function.
Animals ; Cell Physiological Phenomena ; Humans ; Immunity, Cellular ; physiology ; Metabolic Networks and Pathways ; immunology ; T-Lymphocytes ; immunology ; metabolism

PURPOSE: Our previous high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry study identified bladder cancer (BCA)-specific urine metabolites, including carnitine, acylcarnitines, and melatonin. The objective of the current study was to determine which metabolic pathways are perturbed in BCA, based on our previously identified urinary metabolome. MATERIALS AND METHODS: A total of 135 primary BCA samples and 26 control tissue samples from healthy volunteers were analyzed. The association between specific urinary metabolites and their related encoding genes was analyzed. RESULTS: Significant alterations in the carnitine-acylcarnitine and tryptophan metabolic pathways were detected in urine specimens from BCA patients compared to those of healthy controls. The expression of eight genes involved in the carnitine-acylcarnitine metabolic pathway (CPT1A, CPT1B, CPT1C, CPT2, SLC25A20, and CRAT) or tryptophan metabolism (TPH1 and IDO1) was assessed by RT-PCR in our BCA cohort (n=135). CPT1B, CPT1C, SLC25A20, CRAT, TPH1, and IOD1 were significantly downregulated in tumor tissues compared to normal bladder tissues (p<0.05 all) of patients with non-muscle invasive BCA, whereas CPT1B, CPT1C, CRAT, and TPH1 were downregulated in those with muscle invasive BCA (p<0.05), with no changes in IDO1 expression. CONCLUSION: Alterations in the expression of genes associated with the carnitine-acylcarnitine and tryptophan metabolic pathways, which were the most perturbed pathways in BCA, were determined.
Aged ; Biomarkers/metabolism ; Carcinoma, Transitional Cell/genetics/*metabolism/pathology ; Carnitine/*analogs & derivatives/genetics/metabolism ; Case-Control Studies ; Female ; Humans ; Male ; Metabolic Networks and Pathways/*physiology ; Middle Aged ; RNA, Messenger/metabolism ; Real-Time Polymerase Chain Reaction ; Urinary Bladder Neoplasms/genetics/*metabolism/pathology

BACKGROUNDThe mechanism of the neural injury caused by chronic intermittent hypoxia (CIH) that characterizes obstructive sleep apnea syndrome (OSAS) is not clearly known. The purpose of this study was to investigate whether P2X7 receptor (P2X7R) is responsible for the CIH-induced neural injury and the possible pathway it involves.

METHODSEight-week-old male C57BL/6 mice were used. For each exposure time point, eight mice divided in room air (RA) and IH group were assigned to the study of P2X7R expression. Whereas in the 21 days-Brilliant Blue G (BBG, a selective P2X7R antagonist) study, 48 mice were randomly divided into CIH group, BBG-treated CIH group, RA group and BBG-treated RA group. The hippocampus P2X7R expression was determined by Western blotting and real-time polymerase chain reaction (PCR). The spatial learning was analyzed by Morris water maze. The nuclear factor kappa B (NFκB) and NADPH oxidase 2 (NOX2) expressions were analyzed by Western blotting. The expressions of tumor necrosis factor α, interleukin 1β (IL-β), IL-18, and IL-6 were measured by real-time PCR. The malondialdehyde and superoxide dismutase levels were detected by colorimetric method. Cell damage was evaluated by Hematoxylin and Eosin staining and Terminal Transferase dUTP Nick-end Labeling method.

RESULTSThe P2X7R mRNA was elevated and sustained after 3-day IH exposure and the P2X7R protein was elevated and sustained after 7-day IH exposure. In the BBG study, the CIH mice showed severer neuronal cell damage and poorer performance in the behavior test. The increased NFκB and NOX2 expressions along with the inflammation injury and oxidative stress were also observed in the CIH group. BBG alleviated CIH-induced neural injury and consequent functional deficits.

CONCLUSIONSThe P2X7R antagonism attenuates the CIH-induced neuroinflammation, oxidative stress, and spatial deficits, demonstrating that the P2X7R is an important therapeutic target in the cognition deficits accompanied OSAS.

Animals ; Disease Models, Animal ; Hypoxia ; Male ; Metabolic Networks and Pathways ; Mice ; Mice, Inbred C57BL ; Purinergic P2 Receptor Antagonists ; pharmacology ; Receptors, Purinergic P2X7 ; analysis ; physiology ; Rosaniline Dyes ; pharmacology ; Sleep Apnea, Obstructive ; metabolism

Biotin is an important micronutrient that serves as an essential enzyme cofactor. Bacteria obtain biotin either through de novo synthesis or by active uptake from exogenous sources. Mycobacteria are unusual amongst bacteria in that their primary source of biotin is through de novo synthesis. Here we review the importance of biotin biosynthesis in the lifecycle of Mycobacteria. Genetic screens designed to identify key metabolic processes have highlighted a role for the biotin biosynthesis in bacilli growth, infection and survival during the latency phase. These studies help to establish the biotin biosynthetic pathway as a potential drug target for new anti-tuberculosis agents.
Biotin ; biosynthesis ; Carbon-Carbon Ligases ; metabolism ; Carrier Proteins ; metabolism ; Cell Membrane ; metabolism ; Coenzymes ; metabolism ; Fatty Acids ; biosynthesis ; Genes, Bacterial ; Genome, Bacterial ; Metabolic Networks and Pathways ; Molecular Structure ; Mycobacterium Infections ; microbiology ; Mycobacterium tuberculosis ; genetics ; metabolism ; pathogenicity ; physiology ; Virulence

The exploitation of microbial manufacture process (MMP) in industrial biotechnology requires a comprehensive understanding and an efficient modification of microorganism physiology. The availability of genome sequences and accumulation of -omics data allow us to understand of microbial physiology at the systems level, and genome-scale metabolic model (GSMM) represents a valuable framework for integrative analysis of metabolism of microorganisms. Genome scale metabolic models are reconstructed based on a combination of genome sequence and the more detailed biochemical knowledge, and these reconstructed models can be used for analyzing and simulating the operation of metabolism in response to different perturbations. Here we describe the reconstruction protocols for GSMM in further detail and provide the perspective of GSMM.
Biotechnology ; methods ; Genetic Engineering ; Genomics ; methods ; Industrial Microbiology ; Metabolic Networks and Pathways ; physiology ; Models, Biological

A large and growing number of complete genomes from diverse species open tremendous opportunities for getting deep insights into cell metabolism. This increased understanding strongly supports engineering of cell metabolism for microbial production. In spite of the recent progress, a large fraction of genes in most of the available genomes remain incorrectly or imprecisely annotated. In this paper we review some of the new comparative genomics techniques used to reconstruct regulatory and metabolic networks from genomic data, reveal gaps in current knowledge, and identify previously uncharacterized genes. The application will be discussed by using a recent example-reconstruction of xylose utilization pathway in Clostridium acetobutylicum.
Bacteria ; genetics ; metabolism ; Clostridium acetobutylicum ; genetics ; metabolism ; Comparative Genomic Hybridization ; Genetic Engineering ; Genome, Bacterial ; Genomics ; methods ; Metabolic Networks and Pathways ; physiology ; Xylose ; metabolism

Dozens of genome-scale metabolic networks have been reconstructed by integrating information from various databases on genes, proteins, metabolites and validated by experiment data from the literature. The reconstructed networks can be used to quantitatively investigate the interactions between components of a biological system at a system level. Such theoretical study could help us understand the organization principle of the large scale network and thus provide guidance to strain optimization through metabolic engineering technology. In this review, we evaluate the methods for the reconstruction, analysis and application of genome-scale metabolic networks. The difficulties and perspectives on this emerging research field are also discussed.
Biotechnology ; methods ; Genetic Engineering ; Genomics ; methods ; Industrial Microbiology ; Metabolic Networks and Pathways ; physiology