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Possible purine catabolic pathway in E. coli.

Possible purine catabolic pathway in E. coli.

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Escherichia coli is not known to utilize purines, other than adenine and adenosine, as nitrogen sources. We reinvestigated purine catabolism because a computer analysis suggested several potential ς54-dependent promoters within a 23-gene cluster whose products have homology to purine catabolic enzymes. Our results did not provide conclusive evidenc...

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... another molybdenum-containing protein of the xanthine oxidase family. (This family is described in more detail below.) The products of genes b2873 and b2879 show homology to allantoinase, and the product of b2883 shows homology to allantoate amidohydrolase. These enzymes can be organized into a pathway similar to that found in other organisms (Fig. 3). The only enzymes of the proposed pathway not identified in the cluster were a potential uricase and a potential ureidoglycolate dehydrogenase. We will present evi- dence below that suggests that E. coli contains a uricase activ- ...
Context 2
... as the sole nitrogen source in anaerobically grown E. coli (5). Cusa et al. (5) showed that E. coli contains allantoinase, allantoate amidohydrolase, and ureidoglycolate dehydrogenase, which collectively catalyze the conversion of allantoin to oxaluric acid. Such a metabolism implies that E. coli possesses most of the enzymes of purine catabolism (Fig. 3). The inability to use purines aerobically might be due to inadequate transport, weak promoters, or the absence of ap- propriate ...

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... Among them, β2microglobulin (M11870-3), apolipoprotein E (M34203-3), ATP synthesis protein (M7709-26) promote the metabolic process, which is inhibited by NADH ubiquinone oxidoreductase chain 4L (M10880-9), somatostatin-28 (M3130-58), ATP synthetase f (0) complex C1 (M7668-64), necrosis induced Phytophthora protein (M8414-05), and prions (M9074-86). The metabolic pathways of D-glyceric acid include pentose phosphate pathway (map00030) (Cusa et al., 1999), glycine, serine and threonine metabolism (map00260) (Xi et al., 2000) glycolipid metabolism (map00561) (Yew & Gerlt, 2002), glyoxylate metabolism (map00630) (Kouril et al., 2013) and methane metabolism (map00680) (Bursy et al., 2007). With the increase of storage time, the percentage of D-glyceric acid increased, which indicated that thioredoxin (M11722-8) and β2-microglobulin (M11870-3) were beneficial to the production of metabolites. ...
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Abstract This study aims to investigate experimentally the influence of microbial bacterial proteins on microbial metabolites in the chilled storage of Tan Sheep meat based on the surface enhanced laser desorption/ionization-time of flight-mass spectrometry (SELDI-TOF-MS) and gas chromatography-time of flight-mass spectrometry (GC-TOF MS). The correlation analysis of differentially abundant proteins and differential metabolites detected simultaneously in different storage periods has been carried out by heatmap analysis. The results show that 30 differential expressed metabolites were statistically significant. These metabolites were identified as potential spoilage biomarkers. Among of them, 25 differential expressed metabolites can be matched to KEGG metabolic pathways. cyano-amino-acid pathway, pentose phosphate pathway, histidine pathway, purine metabolic pathways, lanine, aspartic acid and glutamate pathway were highly active. Therefore, the differentially abundant proteins contents of microbiology in metabolism can lead to differential effects on metabolic pathways.
... Escherichia-Shigella were overrepresented in the high uric acid group. Xi et al. (2000) demonstrated that these bacteria could secrete xanthine deaminase, which can convert hypoxanthine and xanthine into uric acid. In line with our findings, Mendez-Salazar et al. (2021) also revealed Escherichia-Shigella enrichment in gout patients. ...
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Diabetes mellitus is a metabolic disease closely related to a disordered gut microbiome. Diabetic patients usually suffer from various metabolic disorders, such as increased serum uric acid levels. Although serum uric acid levels depend partially on intestine excretion, the relationship between uric acid and gut microbiome in diabetic patients remains unknown. We collected a total of 126 fecal samples from diabetic patients for 16S ribosomal RNA gene amplicon sequencing and recorded clinical data. We analyzed the correlation between clinical indicators and gut microbiota of diabetic patients using Spearman analysis. Since uric acid was the most prominent one, we classified diabetic patients based on their uric acid levels to find the microbiome associated with uric acid disturbance. We constructed Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway profiles using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to identify variations between the different groups. Among all the clinical indicators, uric acid had the strongest correlation with gut microbiota. First, we divided the patients into three groups according to their uric acid levels. The two low uric acid groups were similar, while the elevated uric acid group had significant differences in gut microbiota and metabolic pathways. The elevated uric acid group had a significantly lower gut microbiota diversity. At the genus level, this group had remarkably higher Escherichia–Shigella amounts and notably lower Faecalibacterium , Oscillospiraceae_UCG−002 , and Oscillospiraceae_UCG−005 amounts. The gut microbiota of the high uric acid group was predicted to be enriched in metabolism, human diseases, and lipopolysaccharide biosynthesis. Since the two low uric acid groups were similar, we regrouped and matched the abnormal uric acid patients with normal uric acid patients. The differences in gut microbiota and metabolic pathways related to nucleotide metabolism became more significant. The serum uric acid levels were associated with gut microbiome changes. This might be related to uric acid metabolism by gut microbes. Our study indicates that targeting the gut microbiome could help manage elevated uric acid levels.
... This process enables gut bacteria to obtain carbon and nitrogen. Hualin Xi et al. revealed that bacterial lineages belonging to Escherichia-Shigella, which were enriched among tophaceous gout patients in our study, might contribute to purine salvage by inducing the xanthine dehydrogenase activity (Xi et al. 2000). They also proposed that this action may allow these bacteria to obtain nitrogen as a means of survival. ...
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Objective To evaluate the taxonomic composition of the gut microbiome in gout patients with and without tophi formation, and predict bacterial functions that might have an impact on urate metabolism. Methods Hypervariable V3–V4 regions of the bacterial 16S rRNA gene from fecal samples of gout patients with and without tophi (n = 33 and n = 25, respectively) were sequenced and compared to fecal samples from 53 healthy controls. We explored predictive functional profiles using bioinformatics in order to identify differences in taxonomy and metabolic pathways. Results We identified a microbiome characterized by the lowest richness and a higher abundance of Phascolarctobacterium , Bacteroides , Akkermansia , and Ruminococcus_gnavus_group genera in patients with gout without tophi when compared to controls. The Proteobacteria phylum and the Escherichia-Shigella genus were more abundant in patients with tophaceous gout than in controls. Fold change analysis detected nine genera enriched in healthy controls compared to gout groups ( Bifidobacterium, Butyricicoccus, Oscillobacter, Ruminococcaceae_UCG_010, Lachnospiraceae_ND2007_group, Haemophilus, Ruminococcus_1, Clostridium_sensu_stricto_1, and Ruminococcaceae_UGC_013 ). We found that the core microbiota of both gout groups shared Bacteroides caccae , Bacteroides stercoris ATCC 43183 , and Bacteroides coprocola DSM 17136 . These bacteria might perform functions linked to one-carbon metabolism, nucleotide binding, amino acid biosynthesis, and purine biosynthesis. Finally, we observed differences in key bacterial enzymes involved in urate synthesis, degradation, and elimination. Conclusion Our findings revealed that taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.
... Some microorganisms, e.g., Klebsiella pneumoniae can utilize purines as carbon or nitrogen source (Tyler, 1978). E. coli can utilize purines as nitrogen source (Xi et al., 2000). This major down-regulation in nucleotide metabolism might suggest that E. coli is using nucleotides as nitrogen source instead of using them as building blocks for DNA and RNA. ...
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Palladium (Pd), due to its unique catalytic properties, is an industrially important heavy metal especially in the form of nanoparticles. It has a wide range of applications from automobile catalytic converters to the pharmaceutical production of morphine. Bacteria have been used to biologically produce Pd nanoparticles as a new environmentally friendly alternative to the currently used energy-intensive and toxic physicochemical methods. Heavy metals, including Pd, are toxic to bacterial cells and cause general and oxidative stress that hinders the use of bacteria to produce Pd nanoparticles efficiently. In this study, we show in detail the Pd stress-related effects on E. coli. Pd stress effects were measured as changes in the transcriptome through RNA-Seq after 10 min of exposure to 100 μM sodium tetrachloropalladate (II). We found that 709 out of 3,898 genes were differentially expressed, with 58% of them being up-regulated and 42% of them being down-regulated. Pd was found to induce several common heavy metal stress-related effects but interestingly, Pd causes unique effects too. Our data suggests that Pd disrupts the homeostasis of Fe, Zn, and Cu cellular pools. In addition, the expression of inorganic ion transporters in E. coli was found to be massively modulated due to Pd intoxication, with 17 out of 31 systems being affected. Moreover, the expression of several carbohydrate, amino acid, and nucleotide transport and metabolism genes was vastly changed. These results bring us one step closer to the generation of genetically engineered E. coli strains with enhanced capabilities for Pd nanoparticles synthesis.
... In most species, including mammals, plants, and bacteria, allantoin is a major metabolic intermediate. Urate oxidase (uricase) converts uric acid [3], which is a degradation product of nucleic acids [4], to uric acid [5][6][7]. It's popular in toothpaste [8], mouthwash [9], and other oral health items [10], as well as shampoos, lipsticks, anti-acne products [11], sun care products, and clarifying lotions, as well as other cosmetic and pharmaceutical products [12]. Since uric acid is the end product of purine metabolism in humans [13], allantoin can only be produced by non-enzymatic processes involving reactive oxygen species, making it a good biomarker for oxidative stress in chronic illnesses [14] and ageing [15,16]. ...
Article
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Objective: Special, effective high pressure liquid chromatography method has been developed for the simultaneous quantification of Allantoin and Permethrin. Methods: By using Waters HPLC e-2695 quaternary pump with a PDA detector of 2998 instrument the chromatographic separation of Allantoin and Permethrin was achieved on the column of Symmetry C18 (150x4.6 mm, 3.5 µm) using an isocratic elution with a buffer containing 0.1percent ortho phosphoric acid and acetonitrile at a rate of 40:60 as a mobile phase with a flow rate of 1 ml/min at ambient temperature. A detector wavelength of 226 nm utilizing the PDA detector were given in the instrumental settings. The linearity was studied between the concentration range of 1-15 µg/ml of Allantoin and 25-375 µg/ml of Permethrin were injected with a run time of 6 min. As a part of method validation the parameters like specificity, linearity, accuracy, ruggedness, robustness were determined and the results were found to be within the allowable limit. Validation of the proposed method was carried out according to an International Conference on Harmonization (ICH) guidelines. Results: LOD and LOQ for the two active ingredients were established with respect to test concentration. The plotted calibration curves were linear with a regression coefficient of R2>0.999, indicates that the linearity was with in the limit. As a part of method validation the parameters like specificity, linearity, accuracy, ruggedness, robustness were determined and the results were found to be within the allowable limit. Conclusion: The method developed was found to be applicable to routine analysis and to be used for the measurement of both active pharmaceutical ingredients (i. e, Allantoin and Permethrin). Since, there is no HPLC method reported in the literature for the estimation of Allantoin and Permethrin, there is a need to develop quantitative methods under different conditions to achieve improvement in specificity, selecivity etc.
... This data is further supported by the lower cell number of ETEC after the co-culture. Similarly, di-peptide gln-gln involved in ETEC acid resistance [79] and arabinosylhypoxanthine involved in the purine metabolism, E. coli cellular growth, and virulence in mixed culture [80,81] were seen in higher abundance in the co-culture group. This may reflect an initial defensive response of ETEC to CP9 in the co-culture. ...
Article
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Microbial life in extreme environments, such as deserts and deep oceans, is thought to have evolved to overcome constraints of nutrient availability, temperature, and suboptimal hygiene environments. Isolation of probiotic bacteria from such niche may provide a competitive edge over traditional probiotics. Here, we tested the survival, safety, and antimicrobial effect of a recently isolated and potential novel strain of Bacillus subtilis (CP9) from desert camel in vitro. Antimicrobial assays were performed via radial diffusion, agar spot, and co-culture assays. Cytotoxic analysis was performed using pig intestinal epithelial cells (IPEC-J2). Real time-PCR was performed for studying the effect on ETEC virulence genes and metabolomic analysis was performed using LC-MS. The results showed that CP9 cells were viable in varied bile salts and in low pH environments. CP9 showed no apparent cytotoxicity in IPEC-J2 cells. CP9 displayed significant bactericidal effect against Enterotoxic E. coli (ETEC), Salmonella Typhimurium, and Methicillin-resistant Staphylococcus aureus (MRSA) in a contact inhibitory fashion. CP9 reduced the expression of ETEC virulent genes during a 5 h co-culture. Additionally, a unique emergent metabolic signature in co-culture samples was observed by LC-MS analysis. Our findings indicate that CP9 exhibits a strong antibacterial property and reveals potential mechanisms behind.
... Purine breakdown is also upregulated in these conditions. E. coli does not generally metabolism purines as a nitrogen source, though it can catabolise certain purines to supply intermediates for other biological processes (Xi et al. 2000). The increase in amino acid synthesis demands more components which the cells could be supplying by breaking down purines such as adenosine. ...
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Deriving new value from waste streams is a central aim of the circular bioeconomy. In this study we investigate whether chemically defined spent media (CDSM) waste from cell culture bioprocess can be effectively recycled and used as a feed in microbial fermentation to produce new recombinant protein products. Our results show that 1) CDSM supplemented with 2% glycerol supported a specific growth rate of E. coli cultures equivalent to that achieved using a nutritionally rich media (LB) used as a baseline reference. 2) The amount of recombinant protein produced following induction in an expression screen was approximately two-fold higher in the CDSM fed cultures than that of baseline. 3) Mass spectrometry analysis of the proteome of E. coli cultures fed in CDSM revealed a greater or lesser differential protein expression pattern depending on supplementation conditions. Further, in a 16 hr fermentation the optimised CDSM-fed culture delivered a protein yield of more than double that achieved by the baseline media. We conclude that spent cell culture media, which represents millions of litres of waste generated by the bioprocessing industry annually, has the potential to be a valuable feed resource for the production of recombinant proteins in secondary microbial fermentation.
... Among the oxidoreductases that require bis-molybdopterin guanine dinucleotide is formate dehydrogenase (FDH) [31] used by the in silico cell when the primary carbon source is a derivative of formate, glycine, or a purine. FDH is also required for the catabolism of urate [32,33]. Adenosyl-cobalamin is computationally required for growth only when the carbon or nitrogen source is ethanolamine, as adenosyl-cobalamin in an essential cofactor for ethanolamine ammonia-lyase, the first step of ethanolamine catabolism. ...
Article
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Sustaining a robust metabolic network requires a balanced and fully functioning proteome. In addition to amino acids, many enzymes require cofactors (coenzymes and engrafted prosthetic groups) to function properly. Extensively validated resource allocation models, such as genome-scale models of metabolism and gene expression (ME-models), have the ability to compute an optimal proteome composition underlying a metabolic phenotype, including the provision of all required cofactors. Here we apply the ME-model for Escherichia coli K-12 MG1655 to computationally examine how environmental conditions change the proteome and its accompanying cofactor usage. We found that: (1) The cofactor requirements computed by the ME-model mostly agree with the standard biomass objective function used in models of metabolism alone (M-models); (2) ME-model computations reveal non-intuitive variability in cofactor use under different growth conditions; (3) An analysis of ME-model predicted protein use in aerobic and anaerobic conditions suggests an enrichment in the use of peroxyl scavenging acids in the proteins used to sustain aerobic growth; (4) The ME-model could describe how limitation in key protein components affect the metabolic state of E . coli . Genome-scale models have thus reached a level of sophistication where they reveal intricate properties of functional proteomes and how they support different E . coli lifestyles.
... Xdh participates in purine salvage where it converts hypoxanthine to xanthine, thereby favoring the conversion of adenine to guanine (Fig. 1B). Xdh also initiates purine degradation by converting xanthine to urate, which is ultimately degraded to ammonia and CO 2 (Xi, Schneider and Reitzer 2000). Ralstonia solanacearum encodes the requisite enzymes for complete purine degradation and it can use xanthine as a nitrogen source (Lundgren et al. 2015). ...
Article
The stringent response involves accumulation of (p)ppGpp, and it ensures that survival is prioritized. Production of (p)ppGpp requires purine synthesis, and upregulation of an operon that encodes the purine salvage enzyme xanthine dehydrogenase (Xdh) has been observed during stringent response in some bacterial species, where direct binding of ppGpp to a TetR-family transcription factor is responsible for increased xdh gene expression. We show here that the plant pathogen Ralstonia solanacearum has a regulatory system in which the LysR-family transcription factor XanR controls expression of the xan operon; this operon encodes Xdh as well as other enzymes involved in purine salvage, which favor accumulation of xanthine. XanR bound upstream of the xan operon, a binding that was attenuated on addition of either ppGpp or cyclic di-guanosine monophosphate (c-di-GMP). Using a reporter in which enhanced green fluorescent protein (EGFP) is expressed under control of a modified xan promoter, XanR was shown to repress EGFP production. Our data suggest that R. solanacearum features a regulatory mechanism in which expression of genes encoding purine salvage enzymes is controlled by a transcription factor that belongs to a different protein family, yet performs similar regulatory functions.
... In many organisms, adenosine nucleotides degradation II degrades the nucleotide form (AMP) to urate and downwards, generating carbon, nitrogen, and energy [13,14]. The key enzyme in this pathway, adenosine deaminase, is widely classified in human tissues. ...
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Zucker Diabtic Fatty rats is a common model used for the studies related to type 2 diabetes. Metabolomics, proven by previous studies, can be used for the prediction of phenotype. This investigation held untargeted metabolomics analysis on the serum metabolites of the Zucker Diabetic Fatty rats, intended to gain insights in the study of the pathology of type 2 diabetes. LCMS method (liquid chromatography coupled with mass spectrometry) is an analytical chemistry technique used to separate and purify complex mixtures. After identifying metabolites using MS2 library spectrum matching, this investigation used Metabo Analyst to compare fatty rats and lean rats. Lastly, by applying over representation analysis, we identified seven metabolic pathways that are important for humans, which assists in discovery of therapeutic targets and the developments of diabetes biomarkers.