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Acid Pathway (acid + pathway)
Kinds of Acid Pathway Selected AbstractsStimulation, Monitoring, and Analysis of Pathway Dynamics by Metabolic Profiling in the Aromatic Amino Acid PathwayBIOTECHNOLOGY PROGRESS, Issue 6 2004M. Oldiges Using a concerted approach of biochemical standard preparation, analytical access via LC-MS/MS, glucose pulse, metabolic profiling, and statistical data analysis, the metabolism dynamics in the aromatic amino acid pathway has been stimulated, monitored, and analyzed in different tyrosine-auxotrophic l -phenylalanine-producing Escherichiacoli strains. During the observation window from ,4 s (before) up to 27 s after the glucose pulse, the dynamics of the first five enzymatic reactions in the aromatic amino acid pathway was observed by measuring intracellular concentrations of 3-deoxy- d -arabino-heptulosonate 7-phosphate DAH(P), 3-dehydroquinate (3-DHQ), 3-dehydroshikimate (3-DHS), shikimate 3-phosphate (S3P), and shikimate (SHI), together with the pathway precursors phosphoenolpyruvate (PEP) and P5P, the lumped pentose phosphate pool as an alternative to the nondetectable erythrose 4-phosphate (E4P). Provided that a sufficient fortification of the carbon flux into the pathway of interest is ensured, respective metabolism dynamics can be observed. On the basis of the intracellular pool measurements, the standardized pool velocities were calculated, and a simple, data-driven criterion-called "pool efflux capacity" (PEC)-is derived. Despite its simplifying system description, the criterion managed to identify the well-known AroB limitation in the E. coli strain A (genotype ,( pheA tyrA aroF)/pJF119EH aroFfbrpheAfbramp) and it also succeeded to identify AroL and AroA (in strain B, genotype ,( pheA tyrA aroF)/pJF119EH aroFfbrpheAfbraroB amp) as promising metabolic engineering targets to alleviate respective flux control in subsequent l -Phe producing strains. Furthermore, using of a simple correlation analysis, the reconstruction of the metabolite sequence of the observed pathway was enabled. The results underline the necessity to extend the focus of glucose pulse experiments by studying not only the central metabolism but also anabolic pathways. [source] Expression profiling of Wilms tumors reveals new candidate genes for different clinical parametersINTERNATIONAL JOURNAL OF CANCER, Issue 8 2006B. Zirn Abstract Wilms tumor is the most frequent renal neoplasm in children, but our understanding of its genetic basis is still limited. We performed cDNA microarray experiments using 63 primary Wilms tumors with the aim of detecting new candidate genes associated with malignancy grade and tumor progression. All tumors had received preoperative chemotherapy as mandated by the SIOP protocol, which sets this study apart from related approaches in the Unites States that are based on untreated samples. The stratification of expression data according to clinical criteria allowed a rather clear distinction between different subsets of Wilms tumors. Clear-cut differences in expression patterns were discovered between relapse-free as opposed to relapsed tumors and tumors with intermediate risk as opposed to high risk histology. Several differentially expressed genes, e.g.TRIM22, CENPF, MYCN, CTGF, RARRES3 and EZH2, were associated with Wilms tumor progression. For a subset of differentially expressed genes, microarray data were confirmed by real-time RT-PCR on the original set of tumors. Interestingly, we found the retinoic acid pathway to be deregulated at different levels in advanced tumors suggesting that treatment of these tumors with retinoic acid may represent a promising novel therapeutic approach. © 2005 Wiley-Liss, Inc. [source] Fructose and glucose mediates enterotoxin production and anaerobic metabolism of Bacillus cereus ATCC14579TJOURNAL OF APPLIED MICROBIOLOGY, Issue 3 2009O. Ouhib-Jacobs Abstract Aims:, To determine the effects of carbohydrates on Bacillus cereus ATCC14579T anaerobic metabolism and enterotoxin production in amino acids rich medium. Methods and Results:,Bacillus cereus anaerobic growth on different carbohydrates (glucose, fructose, sucrose or glucose,fructose mixture) was examined in synthetic mMOD medium under continuous cultures (, = 0·2 h,1). Fermentation end-products, flux partitioning at each key branch points of the mixed acid pathway and consumption or production of amino acids were determined. On both fructose and sucrose, ATP production was favoured via acetate production from acetyl-CoA. In addition, amino acids present in the growth medium showed significant variations with high consumption of serine and net production of glutamate and alanine on some or all sugars. Enterotoxins Hbl and Nhe production was high during growth on fructose (or mixtures involving a fructose moiety). Conclusions:, Fructose was identified as a key sugar influencing anaerobic metabolism and toxin production of B. cereus. Significance and Impact of the Study:, The physiological differences associated with the fermentation of the various carbohydrates clearly modify toxinogenesis indicating that the risk of foodborne pathogens is to some extent dependent upon the prevailing nutritional environment. [source] Conversion of Th17-type into Th2-type inflammation by acetyl salicylic acid via the adenosine and uric acid pathway in the lungALLERGY, Issue 9 2010H.-G. Moon To cite this article: Moon H-G, Tae Y-M, Kim Y-S, Gyu Jeon S, Oh S-Y, Song Gho Y, Zhu Z, Kim Y-K. Conversion of Th17-type into Th2-type inflammation by acetyl salicylic acid via the adenosine and uric acid pathway in the lung. Allergy 2010; 65: 1093,1103. Abstract Background:, Allergen-specific T-cell responses orchestrate airway inflammation, which is a characteristic of asthma. Recent evidence suggests that noneosinophilic asthma can be developed by mixed Th1 and Th17 cell responses when exposed to lipopolysaccharide (LPS)-containing allergens. Objective:, To evaluate the therapeutic or adverse effects of acetyl salicylic acid (ASA) on the expression of Th1-type and Th17-type inflammation induced by airway exposure to LPS-containing allergens. Methods:, Th1 + Th17 asthma and Th2 asthma mouse models were generated by intranasal sensitization with ovalbumin (OVA) and LPS and intraperitoneal sensitization with OVA and alum, respectively. Therapeutic or adverse effects were evaluated after allergen challenge using pharmacologic and transgenic approaches. Results:, Lung infiltration of eosinophils was enhanced in OVA/LPS-sensitized mice by ASA treatment, which was accompanied by the enhanced production of eotaxin. These changes were associated with the down-regulation of Th17 cell response, which was partly dependent on adenosine receptor A1 and A3 subtypes, but up-regulation of allergen-specific IL-13 production from T cells. Lung inflammation induced by LPS-containing allergen was markedly reduced in IL-13-deficient mice in the context of ASA treatment, but not without ASA. Meanwhile, adenosine levels in the lung were enhanced by ASA treatment. Moreover, lung infiltration of eosinophils induced by ASA treatment was reversed by co-treatment of a xanthine oxidase inhibitor (allopurinol). Conclusion:, These findings suggest that ASA changes Th17-type into Th2-type inflammation mainly via the adenosine and uric acid metabolic pathway in the lung. [source] Progress in type II dehydroquinase inhibitors: From concept to practiceMEDICINAL RESEARCH REVIEWS, Issue 2 2007Concepción González-Bello Abstract Scientists are concerned by an ever-increasing rise in bacterial resistance to antibiotics, particularly in diseases such as malaria, toxoplasmosis, tuberculosis, and pneumonia, where the currently used therapies become progressively less efficient. It is therefore necessary to develop new, safe, and more efficient antibiotics. Recently, the existence of the shikimic acid pathway has been demonstrated in certain parasites such as the malaria parasite. These types of parasites cause more than a million casualties per year, and their effects are particularly strong in people with a compromised immune system such as HIV patients. In such cases it is possible that inhibitors of this pathway could be active against a large variety of microorganisms responsible for the more opportunistic infections in HIV patients. Interest in this pathway has resulted in the development of a wide variety of inhibitors for the enzymes involved. This review covers recent progress made in the development of inhibitors of the third enzyme of this pathway, i.e., the type II dehydroquinase. The X-ray crystal structures of several dehydroquinases (Streptomyces coelicolor, Mycobacterium tuberculosis, etc.) with an inhibitor bound in the active site have recently been solved. These complexes identified a number of key interactions involved in inhibitor binding and have shed light on several aspects of the catalytic mechanism. These crystal structures have also proven to be a useful tool for the design of potent and selective enzyme inhibitors, a feature that will also be discussed. © 2006 Wiley Periodicals, Inc. Med Res Rev [source] Allyl isothiocyanate as a cancer chemopreventive phytochemicalMOLECULAR NUTRITION & FOOD RESEARCH (FORMERLY NAHRUNG/FOOD), Issue 1 2010Yuesheng Zhang Abstract Allyl isothiocyanate (AITC), which occurs in many common cruciferous vegetables, is widely and often frequently consumed by humans. Besides antimicrobial activity against a wide spectrum of pathogens, it showed anticancer activity in both cultured cancer cells and animal models, although the underlining mechanisms remain largely undefined. Bioavailability of AITC is extremely high, as nearly 90% of orally administered AITC is absorbed. AITC absorbed in vivo is metabolized mainly through the mercapturic acid pathway and excreted in urine. Available data suggest that urinary concentrations of AITC equivalent are at least ten times higher than in the plasma, and tissue levels of AITC equivalent in the urinary bladder were 14,79 times higher than in other organs after oral AITC administration to rats. These findings suggest that AITC may be most effective in the bladder as a cancer chemopreventive compound. AITC at high-dose levels also exhibit a low degree of cytotoxicity and genotoxicity in animal studies, but such adverse effects are unlikely in humans exposed to dietary levels of AITC. Overall, AITC exhibits many desirable attributes of a cancer chemopreventive agent, and further studies are warranted in order to elucidate its mechanism of action and to assess its protective activity in humans. [source] Glyphosate applied at low doses can stimulate plant growthPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 4 2008Edivaldo D Velini Abstract BACKGROUND:Glyphosate blocks the shikimic acid pathway, inhibiting the production of aromatic amino acids and several secondary compounds derived from these amino acids. Non-target plants can be exposed to low doses of glyphosate by herbicide drift of spray droplets and contact with treated weeds. Previous studies have reported that low doses of glyphosate stimulate growth, although these data are very limited. The objective of this study was to determine the effects of low glyphosate doses on growth of a range of plant species. RESULTS:Growth of maize, conventional soybean, Eucalyptus grandis Hill ex Maiden, Pinus caribea L. and Commelia benghalensis L. was enhanced by 1.8,36 g glyphosate ha,1. Growth of glyphosate-resistant soybean was unaffected by any glyphosate dose from 1.8 to 720 g AE ha,1. The optimum doses for growth stimulation were distinct for plant species and tissue evaluated. The greatest stimulation of growth was observed for C. benghalensis and P. caribea. Shikimic acid levels in tissues of glyphosate-treated soybean and maize were measured and found to be elevated at growth-stimulating doses. CONCLUSION:Subtoxic doses of glyphosate stimulate the growth of a range of plant species, as measured in several plant organs. This hormesis effect is likely to be related to the molecular target of glyphosate, since the effect was not seen in glyphosate-resistant plants, and shikimate levels were enhanced in plants with stimulated growth. Copyright © 2008 Society of Chemical Industry [source] Stimulation, Monitoring, and Analysis of Pathway Dynamics by Metabolic Profiling in the Aromatic Amino Acid PathwayBIOTECHNOLOGY PROGRESS, Issue 6 2004M. Oldiges Using a concerted approach of biochemical standard preparation, analytical access via LC-MS/MS, glucose pulse, metabolic profiling, and statistical data analysis, the metabolism dynamics in the aromatic amino acid pathway has been stimulated, monitored, and analyzed in different tyrosine-auxotrophic l -phenylalanine-producing Escherichiacoli strains. During the observation window from ,4 s (before) up to 27 s after the glucose pulse, the dynamics of the first five enzymatic reactions in the aromatic amino acid pathway was observed by measuring intracellular concentrations of 3-deoxy- d -arabino-heptulosonate 7-phosphate DAH(P), 3-dehydroquinate (3-DHQ), 3-dehydroshikimate (3-DHS), shikimate 3-phosphate (S3P), and shikimate (SHI), together with the pathway precursors phosphoenolpyruvate (PEP) and P5P, the lumped pentose phosphate pool as an alternative to the nondetectable erythrose 4-phosphate (E4P). Provided that a sufficient fortification of the carbon flux into the pathway of interest is ensured, respective metabolism dynamics can be observed. On the basis of the intracellular pool measurements, the standardized pool velocities were calculated, and a simple, data-driven criterion-called "pool efflux capacity" (PEC)-is derived. Despite its simplifying system description, the criterion managed to identify the well-known AroB limitation in the E. coli strain A (genotype ,( pheA tyrA aroF)/pJF119EH aroFfbrpheAfbramp) and it also succeeded to identify AroL and AroA (in strain B, genotype ,( pheA tyrA aroF)/pJF119EH aroFfbrpheAfbraroB amp) as promising metabolic engineering targets to alleviate respective flux control in subsequent l -Phe producing strains. Furthermore, using of a simple correlation analysis, the reconstruction of the metabolite sequence of the observed pathway was enabled. The results underline the necessity to extend the focus of glucose pulse experiments by studying not only the central metabolism but also anabolic pathways. [source] Understanding the Key Factors that Control the Inhibition of Type,II Dehydroquinase by (2R)-2-Benzyl-3-dehydroquinic AcidsCHEMMEDCHEM, Issue 10 2010Antonio Peón Abstract The binding mode of several substrate analogues, (2R)-2-benzyl-3-dehydroquinic acids 4, which are potent reversible competitive inhibitors of type,II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway, has been investigated by structural and computational studies. The crystal structures of Mycobacterium tuberculosis and Helicobacter pylori DHQ2 in complex with one of the most potent inhibitor, p -methoxybenzyl derivative 4,a, have been solved at 2.40,Å and 2.75,Å, respectively. This has allowed the resolution of the M.,tuberculosis DHQ2 loop containing residues 20,25 for the first time. These structures show the key interactions of the aromatic ring in the active site of both enzymes and additionally reveal an important change in the conformation and flexibility of the loop that closes over substrate binding. The loop conformation and the binding mode of compounds 4,b,d has been also studied by molecular dynamics simulations, which suggest that the benzyl group of inhibitors 4 prevent appropriate orientation of the catalytic tyrosine of the loop for proton abstraction and disrupts its basicity. [source] Nanomolar Competitive Inhibitors of Mycobacterium tuberculosis and Streptomyces coelicolor Type,II DehydroquinaseCHEMMEDCHEM, Issue 2 2007Verónica F. Abstract Isomeric nitrophenyl and heterocyclic analogues of the known inhibitor (1S,3R,4R)-1,3,4-trihydroxy-5-cyclohexene-1-carboxylic acid have been synthesized and tested as inhibitors of M.,tuberculosis and S.,coelicolor type,II dehydroquinase, the third enzyme of the shikimic acid pathway. The target compounds were synthesized by a combination of Suzuki and Sonogashira cross-coupling and copper(I)-catalyzed 2,3-dipolar cycloaddition reactions from a common vinyl triflate intermediate. These studies showed that a para -nitrophenyl derivative is almost 20-fold more potent as a competitive inhibitor against the S.,coelicolor enzyme than that of M.,tuberculosis. The opposite results were obtained with the meta isomer. Five of the bicyclic analogues reported herein proved to be potent competitive inhibitors of S.,coelicolor dehydroquinase, with inhibition constants in the low nanomolar range (4,30,nM). These derivatives are also competitive inhibitors of the M.,tuberculosis enzyme, but with lower affinities. The most potent inhibitor against the S.,coelicolor enzyme, a 6-benzothiophenyl derivative, has a Ki value of 4,nM,over 2000-fold more potent than the best previously known inhibitor, (1R,4R,5R)-1,5-dihydroxy-4-(2-nitrophenyl)cyclohex-2-en-1-carboxylic acid (8,,M), making it the most potent known inhibitor against any dehydroquinase. The binding modes of the analogues in the active site of the S.,coelicolor enzyme (GOLD,3.0.1), suggest a key , -stacking interaction between the aromatic rings and Tyr,28, a residue that has been identified as essential for enzyme activity. [source] Linking Pneumocystis jiroveci sulfamethoxazole resistance to the alleles of the DHPS gene using functional complementation in Saccharomyces cerevisiaeCLINICAL MICROBIOLOGY AND INFECTION, Issue 5 2010R. Moukhlis Clin Microbiol Infect 2010; 16: 501,507 Abstract Curative and prophylactic therapy for Pneumocystis jiroveci pneumonia relies mainly on cotrimoxazole, an association of trimethoprim and sulfamethoxazole (SMX). SMX inhibits the folic acid pathway through competition with para-aminobenzoic acid (pABA), one of the two substrates of the dihydropteroate synthase (DHPS), a key enzyme in de novo folic acid synthesis. The most frequent non-synonymous single nucleotide polymorphisms (SNPs) in P. jiroveci DHPS are seen at positions 165 and 171, the combination leading to four possible different genetic alleles. A number of reports correlate prophylaxis failure and mutation in the P. jiroveci DHPS but, because of the impossibility of reliably cultivating P. jiroveci, the link between DHPS mutation(s) and SMX susceptibility is not definitively proven. To circumvent this limitation, the yeast Saccharomyces cerevisiae was used as a model. The introduction of the P. jiroveci DHPS gene, with or without point mutations, directly amplified from a clinical specimen and cloned in a centromeric plasmid into a DHPS-deleted yeast strain, allowed a fully effective complementation. However, in the presence of SMX at concentrations >250 mg/L, yeasts complemented with the double mutated allele showed a lower susceptibility compared with strains complemented with either a single mutated allele or wild-type alleles. These results confirm the need for prospective study of pneumocystosis, including systematic determination of the DHPS genotype, to clarify further the impact of mutations on clinical outcome. Additionally, the S. cerevisiae model proves to be useful for the study of still uninvestigated biological properties of P. jiroveci. [source] Regulatory factor X4 variant 3: A transcription factor involved in brain development and disease,JOURNAL OF NEUROSCIENCE RESEARCH, Issue 16 2007Donghui Zhang Abstract Regulatory factor X4 variant 3 (RFX4_v3) is a recently identified transcription factor specifically expressed in the brain. Gene disruption in mice demonstrated that interruption of a single allele (heterozygous, +/,) prevented formation of the subcommissural organ (SCO), resulting in congenital hydrocephalus, whereas interruption of two alleles (homozygous, ,/,) caused fatal failure of dorsal midline brain structure formation. These mutagenesis studies implicated RFX4_v3 in early brain development as well as the genesis of the SCO. Rfx4_v3 deficiency presumably causes abnormalities in brain by altering the expression levels of many genes that are crucial for brain morphogenesis, such as the signaling components in the Wnt, bone morphogenetic protein, and retinoic acid pathways. RFX4_v3 might affect these critical signaling pathways in brain development. Cx3cl1, a chemokine gene highly expressed in brain, was identified as a direct target for RFX4_v3, indicating that RFX4_v3 possesses trans -acting activity to stimulate gene expression. Rfx4_v3 is highly expressed in the suprachiasmatic nucleus and might be involved in regulating the circadian clock. One haplotype in RFX4_v3 gene is linked to a higher risk of bipolar disorder, suggesting that this protein might contribute to the pathogenesis of the disease. This Mini-Review describes our current knowledge about RFX4_v3, an important protein that appears to be involved in many aspects of brain development and disease. © 2007 Wiley-Liss, Inc. [source] Arachidonic acid activation of intratumoral steroid synthesis during prostate cancer progression to castration resistanceTHE PROSTATE, Issue 3 2010Jennifer A. Locke Abstract BACKGROUND De novo androgen synthesis and subsequent androgen receptor (AR) activation has recently been shown to contribute to castration-resistant prostate cancer (CRPC) progression. Herein we provide evidence that fatty acids (FA) can trigger androgen synthesis within steroid starved prostate cancer (CaP) tumor cells. METHODS Tumoral FA and steroid levels were assessed by GC,MS and LC,MS, respectively. Profiles of genes and proteins involved in FA activation of steroidogenesis were assessed by fluorescence microscopy, immunohistochemistry, microarray expression profiling and Western blot analysis. RESULTS In human CaP tissues the levels of proteins responsible for FA activation of steroid synthesis were observed to be altered during progression to CRPC. Further investigating this mechanism in LNCaP cells, we demonstrate that specific FA, arachidonic acid, is synthesized in an androgen-dependent and AR-mediated manner. Arachidonic acid is known to induce steroidogenic acute regulatory protein (StAR) in steroidogenic cells. When bound to hormone sensitive lipase (HSL), StAR shuttles free cholesterol into the mitochondria for downstream conversion into androgens. We show that arachidonic acid induces androgen production in steroid starved LNCaP cells coincidently in the same conditions that HSL and StAR are predominantly localized in the mitochondria. Furthermore, their activities are verified by a functional increase in mitochondrial uptake of cholesterol in this steroid starved environment. CONCLUSIONS We propose that this characterized arachidonic acid induced steroidogenesis mechanism significantly contributes to the activation of AR in CRPC progression and therefore recommend that fatty acid pathways be targeted therapeutically in progressing CaP. Prostate 70: 239,251, 2010. © 2009 Wiley-Liss, Inc. [source] | ||||||||||||||||