Metabolic adaptations in higher animals. V. The study of metabolic pathways by means of metabolic adaptations.
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Acclimatization↗
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Modelling and analysis of metabolic pathways.
Modelling and analysis of metabolic pathways has received an increasing amount of attention over the past few years. Progress has been made in many aspects such as the identification of rate-controlling steps, applications of optimization principles, and stoichiometric analyses. In addition, the scope of modelling has also expanded. These efforts have led to an improved understanding of metabolic pathways and have facilitated their manipulation.
Bacteria↗
Studies on metabolic pathways of cyanate in rats.
Metabolic pathways of cyanate in rats were studied by means of measurements of cyanate, carbamyl phosphate and S-carbamyl group. Approximately 30-50% of cyanate administered to rats (0.5 mmol/kg body weight) was found in buffered gastric contents, and was also detected as ammonia liberated by acid hydrolysis. However, the gastric excretion of cyanate was a temporary phenomenon just after cyanate administration. Biliary and urinary excretion of cyanate and acid-soluble S-carbamyl group are minor metabolic pathways.
Animals↗
Tissue-specific regulation of metabolic pathways through the transcriptional coactivator PGC1-alpha.
Metabolic pathways are controlled at different levels in response to environmental or hormonal stimuli. This control is achieved, at least in part, at the transcriptional level of gene expression. The regulation of gene expression is executed by specific transcription factors, but there is another level of regulation by a set of proteins that modulate these factors called transcriptional coactivators. In mammals, one of the most characterized examples of regulation of metabolic pathways by transcriptional coactivators is peroxisome proliferator-activated receptors gamma (PPARgamma) coactivator-1 alpha (PGC-1alpha). PGC-1alpha is activated by signals that control energy and nutrient homeostasis. Notably, PGC-1alpha induces and coordinates gene expression that stimulates mitochondrial biogenesis and a thermogenic program in brown fat, fiber-type switching in skeletal muscle, and metabolic pathways linked to the fasted response in the liver. PGC-1alpha activates gene expression through specific interaction with transcription factors that bind to the promoters of metabolic genes. These transcription factors can be ubiquitous such as the nuclear respiratory factors or tissue-enriched factors such as PPARgamma (brown fat), hepatocyte nuclear factor (HNF4alpha) (liver and pancreas) and muscle enhancer factor (MEF2s). The fact that PGC-1alpha controls important metabolic pathways in several tissues suggests that it can be a therapeutic target for antiobesity or diabetes drugs.
Animals↗
Topics in Xenobiochemistry: do metabolic pathways exist for xenobiotics? The micro-metabolism hypothesis.
1. The relevance of the concept of 'the metabolic pathway' for the understanding of xenobiotic metabolism is discussed in the light of advances in modern analytical methods that have enabled the detection and identification of minor metabolites present at ever lower concentrations. 2. A model is suggested where the overall metabolic fate of a xenobiotic is the sum of all the possible metabolic reactions permitted by the solution chemistry of the compound modulated by factors such as the metabolizing enzyme complement of the organism, the affinity of those enzymes for the xenobiotic substrates and the probabilities of all of these processes. 3. In this probabilistic, rather than deterministic, system, the resulting proportions of particular metabolites will, therefore, depend on the sums of the probabilities of particular biotransformation reactions occurring and the stability (chemical or metabolic) of the resulting metabolite. 4. In this model, all the potential metabolic possibilities that could result for any individual xenobiotic will occur to some extent. However, in actuality, many of the resulting metabolites will be produced or excreted in such small quantities as to defy ready detection with current methods.
Animals↗
Metabolism of aminopyrine and derivatives in man: in vivo study of monomorphic and polymorphic metabolic pathways.
1. The main metabolic pathways involved in the biodisposition of aminopyrine have been monitored in vivo in 60 healthy volunteers by measuring the amount of parent drug and metabolites recovered in the urine 24 h after oral administration of 250 mg aminopyrine. 2. The amount of metabolites in the 24-h urine was (mean +/- SD of 60 individuals): unchanged aminopyrine, 0.2 +/- 0.2 mg; methyl aminoantipyrine, 4.5 +/- 2.8 mg; formyl aminoantipyrine, 18.5 +/- 10.1 mg; aminoantipyrine, 9.2 +/- 6.6 mg; and acetyl aminoantipyrine, 31.8 +/- 21.1 mg. 3. Large interindividual differences (12-200-fold changes) are present in all the metabolic steps involved in aminopyrine biotransformation. These differences are not related to gender, intake of caffeine or alcohol, or known drug-metabolizing polymorphisms such as those involved in debrisoquine or mephenytoin metabolism. In contrast, smoking resulted in a decrease in the N(4)-demethylation ratio (p = 0.011). 4. The interindividual differences followed an apparently normal distribution in the N(4)- and N(2)-dimethylation and formylation pathways (p > 0.1). In contrast, acetylation follows a polymorphic distribution (p < 0.03), with an apparent antimode ratio close to 4. With the exception of the acetylation pathway, all of the metabolic ratios correlated between themselves (p < 0.001).
Administration, Oral↗
[Development of targeted chemoradiotherapy for malignant melanoma by exploitation of metabolic pathway].
Malignant melanoma cell possesses a unique metabolic pathway which consists of conversion of tyrosine, an essential amino acid, to dopa and subsequently to dopaquinone in the presence of tyrosinase to form melanin, the end product of the metabolic pathway. This tyrosinase-mediated melanin biosynthesis occurs within normal melanocyte and its transformed cell, malignant melanoma cell. It is in general highly elevated in malignant melanoma cells compared to normal melanocytes. The objective of our research is to develop targeted therapeutic approach for malignant melanoma by utilizing this unique metabolic pathway in the presence of tyrosinase. Specifically we have synthesized sulpher homologue of tyrosine, cysteinylphenol and its amine derivative, cysteaminylphenol (CAP) and subsequently its N-acetyl and N-propionyl derivatives (N-acetyl and N-propionyl-CAP). These synthetic compounds are good tyrosinase substrates and possess high lipophilicity and penetration through the plasma membrane into melanoma cells. Our in vivo and in vitro studies using these synthetic compounds revealed following findings: (1) CAP and its derivatives possess selective cytotoxicity to human neoplastic cells, in particular tyrosinase-positive melanoma cells; (2) N-Acetyl-CAP and N-propionyl-CAP possess both cytostatic and cytocidal effect; (3) These synthetic compounds provide irreversible DNA damage to melanoma cells with high tyrosinase activity; (4) However, there is no irreversible DNA damage to non-pigmented, tyrosinase negative cells; (5) Pharmacological effect of CAP appears to be related to oxidative stress; (6) Radio-labelled CAP derivatives showed selective incorporation into melanin-forming melanoma cells; (7) This selective cytotoxicity can occur in non-melanin forming cells after transfection of human tyrosinase cDNA, resulting cytocidal effect. All these findings clearly indicate that our synthetic compounds which are good substrates of human tyrosinase can provide basis for the development of targeted chemotherapy and/or chemoradiotherapy. In addition the transfection of human tyrosinase cDNA will provide the rational approach for developing the targeted gene therapy to non-melanoma cells.
Animals↗
Synergistic heterozygosity: disease resulting from multiple partial defects in one or more metabolic pathways.
Inborn errors of metabolism show considerable variation in the severity of symptoms. This is often ascribed to the differential effects of specific mutations on gene/enzyme function; however, such genotype/phenotype correlations are usually imprecise. In addition, in some patients with clinical and biochemical findings consistent with a defect in a particular metabolic pathway, it is ultimately impossible to arrive at a precise enzymatic diagnosis. In this situation, we have increasingly been identifying concurrent partial defects in more than one pathway, or at multiple steps in one pathway. In this study, we present the clinical, biochemical, and molecular findings from several patients showing multiple partial defects in energy metabolism. These patients show clinical symptoms consistent with a defect in the affected pathways even though they do not have a complete deficiency in any one enzyme. We hypothesize that such patients are exhibiting clinically significant reductions in energy metabolism related to the compound effects of these partial defects, a phenomenon we term "synergistic heterozygosity." Based on the frequencies of known disorders of energy metabolism, we propose that this may represent a previously unrecognized, relatively common mechanism of disease of potentially great clinical relevance.
AMP Deaminase↗
Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways.
Chemoheterotrophic bacteria use a few central metabolic pathways for carbon catabolism and energy production as well as for the generation of the main precursors for anabolic reactions. All sources of carbon and energy are converted to intermediates of these central pathways and then further metabolized. While the regulation of genes encoding enzymes used to introduce specific substrates into the central metabolism has already been studied to some detail, much less is known about the regulation of the central metabolic pathways. In this study, we investigated the responses of the Bacillus subtilis transcriptome to the presence of glucose and analyzed the role of the pleiotropic transcriptional regulator CcpA in these responses. We found that CcpA directly represses genes involved in the utilization of secondary carbon sources. In contrast, induction by glucose seems to be mediated by a variety of different mechanisms. In the presence of glucose, the genes encoding glycolytic enzymes are induced. Moreover, the genes responsible for the production of acetate from pyruvate with a concomitant substrate-level phosphorylation are induced by glucose. In contrast, the genes required for the complete oxidation of the sugar (Krebs cycle, respiration) are repressed if excess glucose is available for the bacteria. In the absence of glucose, the genes of the Krebs cycle as well as gluconeogenic genes are derepressed. The genes encoding enzymes of the pentose phosphate pathway are expressed both in the presence and the absence of glucose, as suggested by the central role of this pathway in generating anabolic precursors.
Acetates↗
The structure of the metabolic pathways involved in the metabolism of neurotransmitters, with emphasis on the gamma-aminobutyrate system.
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Acetylcholine↗
[Effect of an estrogen-progestin contraceptive preparation on the enzymatic acitivity of the pentosephosphate carbohydrate metabolic pathway and nucleic acid metabolic indices].
The effect of a long-term (14 days) combined introduction of mestranol and noiethinodrel in contraceptive doses on the activity of pentosophosphate routes enzymes of the carbohydrates metabolism, that of acid and basic ribonucleases and on the level of summary nucleinic acids in the uterus and liver in sexually mature female-rats was studied. It was found that the concentration of summary nucleinic acids in the tissues increases under the effect of the drug, the oxidative reactions enzymes become more active, while the activity of non-oxidative reactions enzymes of the pentosophosphate route and of acid and basic endoribonucleases in inhibited.
Animals↗
Flux analysis of microbial metabolic pathways using a visual programming environment.
This paper describes the use of a visual programming environment (LabVIEW) for the flux analysis of metabolic pathways. Representations of metabolic pathways are constructed in software from individual reaction elements (icons) which are linked together to indicate potential flux routes. Off-line bioprocess data are then used to supply the inputs and outputs to the metabolic pathway and the pathway fluxes are calculated. The metabolic system can be modelled at different levels of complexity and new pathways can be inserted into existing models. To illustrate this, flux analyses are performed on three Escherichia coli mutants with metabolic pathway deletions and insertions. The first analysis looks at organic acid production and the second at the effect of the presence in E. coli of an engineered pathway for toluene degradation.
Acetates↗
Directed evolution of metabolic pathways.
The modification of cellular metabolism is of biotechnological and commercial significance because naturally occurring metabolic pathways are the source of diverse compounds used in fields ranging from medicine to bioremediation. Directed evolution is the experimental improvement of biocatalysts or cellular properties through iterative genetic diversification and selection procedures. The creation of novel metabolic functions without disrupting the balanced intracellular pool of metabolites is the primary challenge of pathway manipulation. The introduction of coordinated changes across multiple genetic elements, in conjunction with functional selection, presents an integrated approach for the modification of metabolism with benign physiological consequences. Directed evolution formats take advantage of the dynamic structures of genomes and genomic sub-structures and their ability to evolve in multiple directions in response to external stimuli. The elucidation, design and application of genome-restructuring mechanisms are key elements in the directed evolution of cellular metabolic pathways.
Biotechnology↗
In vivo studies of intrahepatic metabolic pathways.
In vivo studies of liver metabolism have long been limited to measurement by the balance technique or isotope dilution method of the amounts of substrates taken up or produced by the liver. New methods, based mainly on the use of stable isotopes, now allow important data to be obtained on intrahepatic metabolic pathways. Nuclear magnetic resonance and chemical biopsy of glucuronic acid by acetaminophen facilitate the study of glycogen metabolism. Chemical biopsies of liver glutamine by phenylacetate and of cytosolic acetylCoA by sulfamethoxazole provide important data respectively on Krebs cycle activity and gluconeogenesis and on lipogenesis and cholesterol synthesis. Mass isotopomer distribution analysis of molecules synthesised during infusion of 13C-labelled precursors allows an estimation of in vivo gluconeogenesis as well as cholesterol synthesis and lipogenesis. Finally, these metabolic pathways can be studied through the incorporation of deuterium from deuterated water in glucose, fatty acids and cholesterol. All these non-invasive techniques allow investigations to be undertaken in human beings to study the nutritional and hormonal regulation of liver metabolism in normal subjects and in pathological situations.
Biopsy↗
MPW: the Metabolic Pathways Database.
The Metabolic Pathwasy Database (MPW) (www.biobase.com/emphome.html/homepage. html.pags/pathways.html) a derivative of EMP (www.biobase.com/EMP) plays a fundamental role in the technology of metabolic reconstructions from sequenced genomes under the PUMA (www.mcs.anl.gov/home/compbio/PUMA/Production/ ReconstructedMetabolism/reconstruction.html), WIT (www.mcs.anl.gov/home/compbio/WIT/wit.html ) and WIT2 (beauty.isdn.msc.anl.gov/WIT2.pub/CGI/user.cgi) systems. In October 1997, it included some 2800 pathway diagrams covering primary and secondary metabolism, membrane transport, signal transduction pathways, intracellular traffic, translation and transcription. In the current public release of MPW (beauty.isdn.mcs.anl.gov/MPW), the encoding is based on the logical structure of the pathways and is represented by the objects commonly used in electronic circuit design. This facilitates drawing and editing the diagrams and makes possible automation of the basic simulation operations such as deriving stoichiometric matrices, rate laws, and, ultimately, dynamic models of metabolic pathways. Individual pathway diagrams, automatically derived from the original ASCII records, are stored as SGML instances supplemented by relational indices. An auxiliary database of compound names and structures, encoded in the SMILES format, is maintained to unambiguously connect the pathways to the chemical structures of their intermediates.
Databases, Factual↗
HinCyc: a knowledge base of the complete genome and metabolic pathways of H. influenzae.
We present a methodology for predicting the metabolic pathways of an organism from its genomic sequence by reference to a knowledge base of known metabolic pathways. We applied these techniques to the genome of H. influenzae by reference to the EcoCyc knowledge base to predict which of 81 metabolic pathways of E. coli are found in H. influenzae. The resulting prediction is a complex hypothesis that is presented in computer form as HinCyc: an electronic encyclopedia of the genes and metabolic pathways of H. influenzae. HinCyc connects the predicted genes, enzymes, enzyme-catalyzed reactions, and biochemical pathways in a WWW-accessible knowledge base to allow scientists to explore this complex hypothesis.
Computer Communication Networks↗
2-Hydroxypenta-2,4-dienoate metabolic pathway genes in a strong polychlorinated biphenyl degrader, Rhodococcus sp. strain RHA1.
A gram-positive polychlorinated biphenyl (PCB) degrader, Rhodococcus sp. strain RHA1, metabolizes biphenyl through the 2-hydroxypenta-2,4-dienoate (HPD) and benzoate metabolic pathways. The HPD metabolic pathway genes, the HPD hydratase (bphE1), 4-hydroxy-2-oxovalerate aldolase (bphF1), and acetaldehyde dehydrogenase (acylating) (bphG) genes, were cloned from RHA1. The deduced amino acid sequences of bphGF1E1 have 30 to 58% identity with those of the HPD metabolic pathway genes of gram-negative bacteria. The order of these genes, bphG-bphF1-bphE1, differs from that of the HPD metabolic pathway genes, bphE-bphG-bphF, in gram-negative degraders of PCB, phenol, and toluene. Reverse transcription-PCR experiments indicated that the bphGF1E1 genes are inducibly cotranscribed in cells grown on biphenyl and ethylbenzene. Primer extension analysis revealed that the transcriptional initiation site exists within the bphR gene located adjacent to and upstream of bphG, which is deduced to code a transcriptional regulator. The respective enzyme activities of bphGF1E1 gene products were detected in Rhodococcus erythropolis IAM1399 carrying a bphGF1E1 plasmid. The insertional inactivation of the bphE1, bphF1, and bphG genes resulted in the loss of the corresponding enzyme activities and diminished growth on both biphenyl and ethylbenzene. Severe growth interference was observed during growth on biphenyl. The growth defects were partially restored by the introduction of plasmids containing the respective intact genes. These results indicated that the cloned bphGF1E1 genes are not only responsible for the primary metabolism of HPD during growth on both biphenyl and ethylbenzene but are also involved in preventing the accumulation of unexpected toxic metabolites, which interfere with the growth of RHA1.
Aldehyde Oxidoreductases↗
An integrated modeling-experimental strategy for the analysis of metabolic pathways.
An inherent problem in studying the behavior of a metabolic pathway is the impossibility of developing a complete, detailed model that includes all the cellular processes that have an impact on the set of fluxes in such a pathway. Lacking this, one requires some means of modeling the interactions between a metabolic pathway and other cellular processes for the purpose of analyzing pathway characteristics within the cell (e.g., determining sensitivity coefficients for various steps in the pathway) with a minimal amount of time and effort. A general framework is developed for studying these issues in a rigorous manner. Using this framework, detailed knowledge about a metabolic pathway (i.e., a set of rate expressions for steps in the pathway) can be combined with the results from a relatively simple set of experiments in order to obtain estimates for the sensitivity of the pathway to enzyme activities, inhibition constants, and other parameters that determine the pathway's behavior, while accounting for the pathway's interaction with the rest of the cellular metabolism. A model system representing amino acid production is used to illustrate the problem and to provide results based on computational experiments. The modeling strategy described here should be useful in genetic design to improve pathway fluxes and metabolic network selectivity.
Amino Acids↗