PubMed

Related Articles Changes in urinary metabolic profile after oral administration of curcuma extract in rats. J Pharm Biomed Anal. 2014 Nov;100:348-56 Authors: Dall'Acqua S, Stocchero M, Clauser M, Boschiero I, Ndoum E, Schiavon M, Mammi S, Schievano E Abstract The diffusion of phytochemicals in health promoting products is growing, but studies related to their effects on healthy subjects are still lacking despite the large consumption of natural products as nutraceuticals or food supplements. In many cases, research supports the in vitro antioxidant activity of phytochemicals, but the health claims attributed to the final marketed nutraceutical products have dubious scientific foundation. Also, studies focussed on the definition of their biological targets and mechanisms of action can be useful to assess their efficacy and safety. In this study, the effect of oral administration of 80mg/kg of Curcuma longa Linn. extract to 12 healthy rats over 25 days was evaluated by monitoring the changes of urinary composition. 24-h urine was collected during the animal experiment and the composition was analyzed by (1)H NMR and HPLC-MS. The two datasets were studied individually through a metabolomic approach and the multivariate analysis revealed significant differences between the control and the treated group. Curcumin levels were also measured in 24-h urine samples by HPLC-MS. Both the (1)H NMR and the HPLC-MS dataset showed that the administration of 80mg/kg of Curcuma longa extract to healthy animals induces changes in urinary composition. Decreased allantoin urinary levels can be considered a partial demonstration of the in vivo effect of curcumin on oxidative stress in a healthy animal model. PMID: 25200426 [PubMed - indexed for MEDLINE]

Related Articles Genomics of ageing in twins. Proc Nutr Soc. 2014 Nov;73(4):526-31 Authors: Mangino M Abstract Ageing is a complex multifactorial process, reflecting the progression of all degenerative pathways within an organism. Due to the increase of life expectancy, in recent years, there is a pressing need to identify early-life events and risk factors that determine health outcomes in later life. So far, genetic variation only explains ~20-25 % of the variability of human survival to age 80+. This clearly implies that other factors (environmental, epigenetic and lifestyle) contribute to lifespan and the rate of healthy ageing within an individual. Twin studies in the past two decades proved to be a very powerful tool to discriminate the genetic from the environmental component. The aim of this review is to describe the basic concepts of the twin study design and to report some of the latest studies in which high-throughput technologies (e.g. genome/epigenome-wide assay, next generation sequencing, MS metabolic profiling) combined with the classical twin design have been applied to the analysis of novel 'omics' to further understand the molecular mechanisms of human ageing. PMID: 24984159 [PubMed - indexed for MEDLINE]

Related Articles [Preliminary study on the discrimination of oral mucosa pathogens Saccharomyces with metabonomics method]. Hua Xi Kou Qiang Yi Xue Za Zhi. 2013 Jun;31(3):291-3, 299 Authors: Li M, Zhang X, Si Q Abstract OBJECTIVE: To evaluate the feasibility of identifying oral mucosa pathogenic bacteria by comparing the metabolic profiling of Saccharomyces and try to find a convenient and rapid way to discriminate oral micro-organisms. METHODS: Saccharomyces albicans ATCC 10231 and Saccharomyces tropicalis ATCC 13803 and Saccharomyces glabrata ATCC 15126 were respectively inoculated in sabouraud medium. The growth quantity were measured periodically by a spectrophotometer. And the growth curves of the inoculated bacteria were completed. The culture solutions in stationary phases of the three bacteria were respectively tested with 'H-nuclear magnetic resonance(1H-NMR) spectroscopy. The data of 1H-NMR spectroscopy results were analyzed by principal components analysis (PCA). RESULTS: The PCA showed respectively a obvious clustering phenomena and the points of every two groups' data stayed separately. Therefore, the NMR-based metabonomics profiles could discriminate the three kinds of mucosa pathogenic bacteria. CONCLUSION: The metabonomics can be expected to be a kind of promising useful method in quick discrimination of oral pathogenic bacteria. PMID: 23841304 [PubMed - indexed for MEDLINE]

Keratotic follicular plugs with calcifications in Conradi-Hünermann-Happle syndrome: histologic, biochemical and genetic testing correlation. Br J Dermatol. 2015 Jun 15; Authors: Leclerc-Mercier S, Dufernez F, Fraitag S, Coulombe J, Dompmartin A, Barreau M, Bozon D, Lamazière A, Bonnefont JP, Khalifa E, Bodemer C, Hadj-Rabia S Abstract Conradi-Hünermann-Happle Syndrome (CHH, chondrodysplasia punctata type 2, MIM#302960), is an extremely rare X-linked dominant disorder of cholesterol metabolism which is usually lethal in male fetuses. Phenotypic expression is variable.(1, 2) The classical phenotype associates skeletal defects (cranio-facial anomalies, short stature, shortened asymmetric limbs associated with epiphyseal stippling), ocular anomalies (congenital cataract, microphtalmia) and skin lesions. At birth, transient ichthyosiform erythroderma is reported followed by linear ichthyosis on Blaschko lines (Figure 1A). Follicular atrophoderma reminiscent of "orange peel" skin occurs in later life (Figure 1B). This article is protected by copyright. All rights reserved. PMID: 26075358 [PubMed - as supplied by publisher]

Inborn Errors of Metabolism: Advances in Diagnosis and Therapy. JAMA Pediatr. 2015 Jun 15; Authors: Vernon HJ Abstract Inborn errors of metabolism (IEMs) are a large class of genetic disorders characterized by disruption of cellular biochemical functions. Although individual IEMs are rare, collectively they represent a large and diverse class of genetic conditions, with new disorders and disease mechanisms being described regularly. Advances in the understanding of the molecular and biochemical etiologies of many IEMs via modalities such as whole-exome sequencing and metabolomics have led to significant progress in detection and treatment in recent years. In this review, we examine the current state of newborn screening for IEMs, recent advances in therapy for IEMs (including glutaric aciduria type I, urea cycle disorders, mitochondrial disorders, and lysosomal storage disorders), and opportunities for further exploration and discovery. PMID: 26075348 [PubMed - as supplied by publisher]

Widening our gaze of red blood storage haze: a role for metabolomics. Transfusion. 2015 Jun;55(6):1139-42 Authors: Zimring JC PMID: 26074173 [PubMed - in process]

A peaklet-based generic strategy for the untargeted analysis of comprehensive two-dimensional gas chromatography mass spectrometry data sets. J Chromatogr A. 2015 Jun 3; Authors: Egert B, Weinert CH, Kulling SE Abstract Comprehensive two-dimensional gas chromatography mass spectrometry (GC×GC-MS) is a well-established key technology in analytical chemistry and increasingly used in the field of untargeted metabolomics. However, automated processing of large GC×GC-MS data sets is still a major bottleneck in untargeted, large-scale metabolomics. For this reason we introduce a novel peaklet-based alignment strategy. The algorithm is capable of an untargeted deterministic alignment exploiting a density based clustering procedure within a time constrained similarity matrix. Exploiting minimal (1)D and (2)D retention time shifts between peak modulations, the alignment is done without the need for peak merging which also eliminates the need for linear or nonlinear retention time correction procedures. The approach is validated in detail using data of urine samples from a large human metabolomics study. The data was acquired by a Shimadzu GCMS-QP2010 Ultra GC×GC-qMS system and consists of 512 runs, including 312 study samples and 178 quality control sample injections, measured within a time period of 22 days. The final result table consisted of 313 analytes, each of these being detectable in at least 75% of the study samples. In summary, we present an automated, reliable and fully transparent workflow for the analysis of large GC×GC-qMS metabolomics data sets. PMID: 26074098 [PubMed - as supplied by publisher]

Influence of HEK293 metabolism on the production of viral vectors and vaccine. Vaccine. 2015 Jun 11; Authors: Petiot E, Cuperlovic-Culf M, Shen CF, Kamen A Abstract Mammalian cell cultures are increasingly used for the production of complex biopharmaceuticals including viral vectors and vaccines. HEK293 is the predominant cell line used for the transient expression of recombinant proteins and a well-established system for the production of viral vectors. Understanding metabolic requirements for high productivity in HEK293 cells remains an important area of investigation. Many authors have presented approaches for increased productivity through optimization of cellular metabolism from two distinct perspectives. One is a non-targeted approach, which is directed to improving feeding strategies by addition of exhausted or critical substrates and eventually removal of toxic metabolites. Alternatively, a targeted approach has attempted to identify specific targets for optimization through better understanding of the cellular metabolism under different operating conditions. This review will present both approaches and their successes with regards to improvement of viral production in HEK293 cells outlining the key relations between HEK293 cell metabolism and viral vector productivity. Also, we will summarize the current knowledge on HEK293 metabolism indicating remaining issues to address and problems to resolve to maximize the productivity of viral vectors in HEK293 cells. PMID: 26073013 [PubMed - as supplied by publisher]

A Metabolomic Approach to Understanding the Metabolic Link between Obesity and Diabetes. Mol Cells. 2015 Jun 15; Authors: Park S, Sadanala KC, Kim EK Abstract Obesity and diabetes arise from an intricate interplay between both genetic and environmental factors. It is well recognized that obesity plays an important role in the development of insulin resistance and diabetes. Yet, the exact mechanism of the connection between obesity and diabetes is still not completely understood. Metabolomics is an analytical approach that aims to detect and quantify small metabolites. Recently, there has been an increased interest in the application of metabolomics to the identification of disease biomarkers, with a number of well-known biomarkers identified. Metabolomics is a potent approach to unravel the intricate relationships between metabolism, obesity and progression to diabetes and, at the same time, has potential as a clinical tool for risk evaluation and monitoring of disease. Moreover, metabolomics applications have revealed alterations in the levels of metabolites related to obesity-associated diabetes. This review focuses on the part that metabolomics has played in elucidating the roles of metabolites in the regulation of systemic metabolism relevant to obesity and diabetes. It also explains the possible metabolic relation and association between the two diseases. The metabolites with altered profiles in individual disorders and those that are specifically and similarly altered in both disorders are classified, categorized and summarized. PMID: 26072981 [PubMed - as supplied by publisher]

Related Articles Antiandrogenic therapy with finasteride attenuates cardiac hypertrophy and left ventricular dysfunction. Circulation. 2015 Mar 24;131(12):1071-81 Authors: Zwadlo C, Schmidtmann E, Szaroszyk M, Kattih B, Froese N, Hinz H, Schmitto JD, Widder J, Batkai S, Bähre H, Kaever V, Thum T, Bauersachs J, Heineke J Abstract BACKGROUND: In comparison with men, women have a better prognosis when experiencing aortic valve stenosis, hypertrophic cardiomyopathy, or heart failure. Recent data suggest that androgens like testosterone or the more potent dihydrotestosterone contribute to the development of cardiac hypertrophy and failure. Therefore, we analyzed whether antiandrogenic therapy with finasteride, which inhibits the generation of dihydrotestosterone by the enzyme 5-α-reductase, improves pathological ventricular remodeling and heart failure. METHODS AND RESULTS: We found a strongly induced expression of all 3 isoforms of the 5-α-reductase (Srd5a1 to Srd5a3) in human and mouse hearts with pathological hypertrophy, which was associated with increased myocardial accumulation of dihydrotestosterone. Starting 1 week after the induction of pressure overload by transaortic constriction, mice were treated with finasteride for 2 weeks. Cardiac function, hypertrophy, dilation, and fibrosis were markedly improved in response to finasteride treatment in not only male, but also in female mice. In addition, finasteride also very effectively improved cardiac function and mortality after long-term pressure overload and prevented disease progression in cardiomyopathic mice with myocardial Gαq overexpression. Mechanistically, finasteride, by decreasing dihydrotestosterone, potently inhibited hypertrophy and Akt-dependent prohypertrophic signaling in isolated cardiac myocytes, whereas the introduction of constitutively active Akt blunted these effects of finasteride. CONCLUSIONS: Finasteride, which is currently used in patients to treat prostate disease, potently reverses pathological cardiac hypertrophy and dysfunction in mice and might be a therapeutic option for heart failure. PMID: 25632043 [PubMed - indexed for MEDLINE]

Related Articles Comparative metabolite profiling of two rice genotypes with contrasting salt stress tolerance at the seedling stage. PLoS One. 2014;9(9):e108020 Authors: Zhao X, Wang W, Zhang F, Deng J, Li Z, Fu B Abstract BACKGROUND: Rice is sensitive to salt stress, especially at the seedling stage, with rice varieties differing remarkably in salt tolerance (ST). To understand the physiological mechanisms of ST, we investigated salt stress responses at the metabolite level. METHODS: Gas chromatography-mass spectrometry was used to profile metabolite changes in the salt-tolerant line FL478 and the sensitive variety IR64 under a salt-stress time series. Additionally, several physiological traits related to ST were investigated. RESULTS: We characterized 92 primary metabolites in the leaves and roots of the two genotypes under stress and control conditions. The metabolites were temporally, tissue-specifically and genotype-dependently regulated under salt stress. Sugars and amino acids (AAs) increased significantly in the leaves and roots of both genotypes, while organic acids (OAs) increased in roots and decreased in leaves. Compared with IR64, FL478 experienced greater increases in sugars and AAs and more pronounced decreases in OAs in both tissues; additionally, the maximum change in sugars and AAs occurred later, while OAs changed earlier. Moreover, less Na+ and higher relative water content were observed in FL478. Eleven metabolites, including AAs and sugars, were specifically increased in FL478 over the course of the treatment. CONCLUSIONS: Metabolic responses of rice to salt stress are dynamic and involve many metabolites. The greater ST of FL478 is due to different adaptive reactions at different stress times. At early salt-stress stages, FL478 adapts to stress by decreasing OA levels or by quickly depressing growth; during later stages, more metabolites are accumulated, thereby serving as compatible solutes against osmotic challenge induced by salt stress. PMID: 25265195 [PubMed - indexed for MEDLINE]

Related Articles A multienzyme complex channels substrates and electrons through acetyl-CoA and methane biosynthesis pathways in Methanosarcina. PLoS One. 2014;9(9):e107563 Authors: Lieber DJ, Catlett J, Madayiputhiya N, Nandakumar R, Lopez MM, Metcalf WW, Buan NR Abstract Multienzyme complexes catalyze important metabolic reactions in many organisms, but little is known about the complexes involved in biological methane production (methanogenesis). A crosslinking-mass spectrometry (XL-MS) strategy was employed to identify proteins associated with coenzyme M-coenzyme B heterodisulfide reductase (Hdr), an essential enzyme in all methane-producing archaea (methanogens). In Methanosarcina acetivorans, Hdr forms a multienzyme complex with acetyl-CoA decarbonylase synthase (ACDS), and F420-dependent methylene-H4MPT reductase (Mer). ACDS is essential for production of acetyl-CoA during growth on methanol, or for methanogenesis from acetate, whereas Mer is essential for methanogenesis from all substrates. Existence of a Hdr:ACDS:Mer complex is consistent with growth phenotypes of ACDS and Mer mutant strains in which the complex samples the redox status of electron carriers and directs carbon flux to acetyl-CoA or methanogenesis. We propose the Hdr:ACDS:Mer complex comprises a special class of multienzyme redox complex which functions as a "biological router" that physically links methanogenesis and acetyl-CoA biosynthesis pathways. PMID: 25232733 [PubMed - indexed for MEDLINE]

Related Articles Allele compensation in tip60+/- mice rescues white adipose tissue function in vivo. PLoS One. 2014;9(5):e98343 Authors: Gao Y, Hamers N, Rakhshandehroo M, Berger R, Lough J, Kalkhoven E Abstract Adipose tissue is a key regulator of energy homestasis. The amount of adipose tissue is largely determined by adipocyte differentiation (adipogenesis), a process that is regulated by the concerted actions of multiple transcription factors and cofactors. Based on in vitro studies in murine 3T3-L1 preadipocytes and human primary preadipocytes, the transcriptional cofactor and acetyltransferase Tip60 was recently identified as an essential adipogenic factor. We therefore investigated the role of Tip60 on adipocyte differentiation and function, and possible consequences on energy homeostasis, in vivo. Because homozygous inactivation results in early embryonic lethality, Tip60+/- mice were used. Heterozygous inactivation of Tip60 had no effect on body weight, despite slightly higher food intake by Tip60+/- mice. No major effects of heterozygous inactivation of Tip60 were observed on adipose tissue and liver, and Tip60+/- displayed normal glucose tolerance, both on a low fat and a high fat diet. While Tip60 mRNA was reduced to 50% in adipose tissue, the protein levels were unaltered, suggesting compensation by the intact allele. These findings indicate that the in vivo role of Tip60 in adipocyte differentiation and function cannot be properly addressed in Tip60+/- mice, but requires the generation of adipose tissue-specific knock out animals or specific knock-in mice. PMID: 24870614 [PubMed - indexed for MEDLINE]

Related Articles The potential biomarker panels for identification of Major Depressive Disorder (MDD) patients with and without early life stress (ELS) by metabonomic analysis. PLoS One. 2014;9(5):e97479 Authors: Ding X, Yang S, Li W, Liu Y, Li Z, Zhang Y, Li L, Liu S Abstract OBJECTIVE: The lack of the disease biomarker to support objective laboratory tests still constitutes a bottleneck in the clinical diagnosis and evaluation of major depressive disorder (MDD) and its subtypes. We used metabonomic techniques to screen the diagnostic biomarker panels from the plasma of MDD patients with and without early life stress (ELS) experience. METHODS: Plasma samples were collected from 25 healthy adults and 46 patients with MDD, including 23 patients with ELS and 23 patients without ELS. Furthermore, gas chromatography/mass spectrometry (GC/MS) coupled with multivariate statistical analysis was used to identify the differences in global plasma metabolites among the 3 groups. RESULTS: The distinctive metabolic profiles exist either between healthy subjects and MDD patients or between the MDD patients with ELS experience (ELS/MDD patients) and the MDD patients without it (non-ELS/MDD patients), and some diagnostic panels of feature metabolites' combination have higher predictive potential than the diagnostic panels of differential metabolites. CONCLUSIONS: These findings in this study have high potential of being used as novel laboratory diagnostic tool for MDD patients and it with ELS or not in clinical application. PMID: 24870353 [PubMed - indexed for MEDLINE]

Related Articles Combined systems approaches reveal highly plastic responses to antimicrobial peptide challenge in Escherichia coli. PLoS Pathog. 2014 May;10(5):e1004104 Authors: Kozlowska J, Vermeer LS, Rogers GB, Rehnnuma N, Amos SB, Koller G, McArthur M, Bruce KD, Mason AJ Abstract Obtaining an in-depth understanding of the arms races between peptides comprising the innate immune response and bacterial pathogens is of fundamental interest and will inform the development of new antibacterial therapeutics. We investigated whether a whole organism view of antimicrobial peptide (AMP) challenge on Escherichia coli would provide a suitably sophisticated bacterial perspective on AMP mechanism of action. Selecting structurally and physically related AMPs but with expected differences in bactericidal strategy, we monitored changes in bacterial metabolomes, morphological features and gene expression following AMP challenge at sub-lethal concentrations. For each technique, the vast majority of changes were specific to each AMP, with such a plastic response indicating E. coli is highly capable of discriminating between specific antibiotic challenges. Analysis of the ontological profiles generated from the transcriptomic analyses suggests this approach can accurately predict the antibacterial mode of action, providing a fresh, novel perspective for previous functional and biophysical studies. PMID: 24789011 [PubMed - indexed for MEDLINE]

Related Articles Systems medicine: a new approach to clinical practice. Arch Bronconeumol. 2014 Oct;50(10):444-51 Authors: Cardinal-Fernández P, Nin N, Ruíz-Cabello J, Lorente JA Abstract Most respiratory diseases are considered complex diseases as their susceptibility and outcomes are determined by the interaction between host-dependent factors (genetic factors, comorbidities, etc.) and environmental factors (exposure to microorganisms or allergens, treatments received, etc.) The reductionist approach in the study of diseases has been of fundamental importance for the understanding of the different components of a system. Systems biology or systems medicine is a complementary approach aimed at analyzing the interactions between the different components within one organizational level (genome, transcriptome, proteome), and then between the different levels. Systems medicine is currently used for the interpretation and understanding of the pathogenesis and pathophysiology of different diseases, biomarker discovery, design of innovative therapeutic targets, and the drawing up of computational models for different biological processes. In this review we discuss the most relevant concepts of the theory underlying systems medicine, as well as its applications in the various biological processes in humans. PMID: 24397963 [PubMed - indexed for MEDLINE]

Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments. Bioinformatics. 2015 Jun 15;31(12):i161-i170 Authors: Yamanishi Y, Tabei Y, Kotera M Abstract MOTIVATION: Recent advances in mass spectrometry and related metabolomics technologies have enabled the rapid and comprehensive analysis of numerous metabolites. However, biosynthetic and biodegradation pathways are only known for a small portion of metabolites, with most metabolic pathways remaining uncharacterized. RESULTS: In this study, we developed a novel method for supervised de novo metabolic pathway reconstruction with an improved graph alignment-based approach in the reaction-filling framework. We proposed a novel chemical graph alignment algorithm, which we called PACHA (Pairwise Chemical Aligner), to detect the regioisomer-sensitive connectivities between the aligned substructures of two compounds. Unlike other existing graph alignment methods, PACHA can efficiently detect only one common subgraph between two compounds. Our results show that the proposed method outperforms previous descriptor-based methods or existing graph alignment-based methods in the enzymatic reaction-likeness prediction for isomer-enriched reactions. It is also useful for reaction annotation that assigns potential reaction characteristics such as EC (Enzyme Commission) numbers and PIERO (Enzymatic Reaction Ontology for Partial Information) terms to substrate-product pairs. Finally, we conducted a comprehensive enzymatic reaction-likeness prediction for all possible uncharacterized compound pairs, suggesting potential metabolic pathways for newly predicted substrate-product pairs. CONTACT: maskot@bio.titech.ac.jp. PMID: 26072478 [PubMed - as supplied by publisher]

The Caenorhabditis elegans lipidome A primer for lipid analysis in Caenorhabditis elegans. Arch Biochem Biophys. 2015 Jun 10; Authors: Witting M, Schmitt-Kopplin P Abstract Lipids play important roles in biology, ranging from building blocks of membranes to signaling lipids. The nematode and model organism Caenorhabditis elegans has been used to explore lipid metabolism and several techniques for their analysis have been employed. These techniques include different possibilities ranging from visualization of lipid droplets, analysis of total fatty acids to analysis of complex lipids using lipidomics approaches. Lipidomics evolved from metabolomics, the latest off-spring of the "omics"-technologies and aims to characterize the lipid content of a given organism or system. Although being an extensively studied model organism, only a few applications of lipidomics to C. elegans have been reported to far, but the number is steadily increasing with more applications expected in the near future. This review gives an overview on the C. elegans lipidome, lipid classes it contains and ways to analyze them. It serves as primer for scientists interested in studying lipids in this model organism and list methods used so far and what information can be derived from them. Lastly, challenges and future (methodological) research directions, together with new methods potentially useful for C. elegans lipid research are discussed. PMID: 26072113 [PubMed - as supplied by publisher]

Related Articles Multi-level systems biology modeling characterized the atheroprotective efficiencies of modified dairy fats in a hamster model. Am J Physiol Heart Circ Physiol. 2015 Jun 12;:ajpheart.00032.2015 Authors: Martin JC, Berton A, Ginies C, Bott R, Scheercousse P, Saddi A, Gripois D, Landrier JF, Dalemans D, Alessi MC, Delplanque B Abstract We assessed the atheroprotective efficiency of modified dairy fats in hyperlipidemic hamsters. A systems biology approach was implemented to reveal and quantify the dietary fat-related components of the disease. Three modified dairy fats (40% energy) were prepared from regular butter by mixing with a plant oil mixture, by removing cholesterol alone or by removing cholesterol in combination with reducing saturated fatty acids. A plant oil mixture with regular butter was used as the control diet. The atherosclerosis severity (aortic cholesteryl-ester level) was higher in the regular butter-fed hamsters than in the other four groups (P < 0.05). Eighty-seven of the 1666 variables measured from multi-platform analysis were found to be strongly associated with the disease. When aggregated into 10 biological clusters combined into a multivariate predictive equation, these 87 variables explained 81% of the disease variability. The biological cluster "regulation of lipid transport and metabolism" appeared central to atherogenic development relative to diets. The "vitamin E metabolism" cluster was the main driver of atheroprotection with the best performing transformed dairy fat. Under conditions that promote atherosclerosis, the impact of dairy fats on atherogenesis could be greatly ameliorated by technological modifications. Our modeling approach allowed for identifying and quantifying the contribution of complex factors to atherogenic development in each dietary setup. PMID: 26071539 [PubMed - as supplied by publisher]

Related Articles Phenolic amides are potent inhibitors of de novo nucleotide biosynthesis. Appl Environ Microbiol. 2015 Jun 12; Authors: Pisithkul T, Jacobson TB, O'Brien TJ, Stevenson DM, Amador-Noguez D Abstract An outstanding challenge towards efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using E. coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we show that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to: 1) rapid buildup of 5-phosphoribosylpyrophosphate (PRPP), a key precursor in nucleotide biosynthesis; 2) rapid decrease in the levels of pyrimidine biosynthetic intermediates; and 3) long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using (13)C-sugars and (15)N-ammonia demonstrated that carbon and nitrogen flux into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help develop strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals. PMID: 26070680 [PubMed - as supplied by publisher]