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Metabolites, Volume 3, Issue 1 (March 2013), Pages 1-203

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Research

Jump to: Review

Open AccessArticle The Metabolic Interplay between Plants and Phytopathogens
Metabolites 2013, 3(1), 1-23; doi:10.3390/metabo3010001
Received: 8 October 2012 / Revised: 18 December 2012 / Accepted: 31 December 2012 / Published: 8 January 2013
Cited by 4 | PDF Full-text (904 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Plant diseases caused by pathogenic bacteria or fungi cause major economic damage every year and destroy crop yields that could feed millions of people. Only by a thorough understanding of the interaction between plants and phytopathogens can we hope to develop strategies [...] Read more.
Plant diseases caused by pathogenic bacteria or fungi cause major economic damage every year and destroy crop yields that could feed millions of people. Only by a thorough understanding of the interaction between plants and phytopathogens can we hope to develop strategies to avoid or treat the outbreak of large-scale crop pests. Here, we studied the interaction of plant-pathogen pairs at the metabolic level. We selected five plant-pathogen pairs, for which both genomes were fully sequenced, and constructed the corresponding genome-scale metabolic networks. We present theoretical investigations of the metabolic interactions and quantify the positive and negative effects a network has on the other when combined into a single plant-pathogen pair network. Merged networks were examined for both the native plant-pathogen pairs as well as all other combinations. Our calculations indicate that the presence of the parasite metabolic networks reduce the ability of the plants to synthesize key biomass precursors. While the producibility of some precursors is reduced in all investigated pairs, others are only impaired in specific plant-pathogen pairs. Interestingly, we found that the specific effects on the host’s metabolism are largely dictated by the pathogen and not by the host plant. We provide graphical network maps for the native plant-pathogen pairs to allow for an interactive interrogation. By exemplifying a systematic reconstruction of metabolic network pairs for five pathogen-host pairs and by outlining various theoretical approaches to study the interaction of plants and phytopathogens on a biochemical level, we demonstrate the potential of investigating pathogen-host interactions from the perspective of interacting metabolic networks that will contribute to furthering our understanding of mechanisms underlying a successful invasion and subsequent establishment of a parasite into a plant host. Full article
(This article belongs to the Special Issue Metabolic Network Models)
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Open AccessArticle Absolute Configuration of the New 3-epi-cladocroic Acid from the Mediterranean Sponge Haliclona fulva
Metabolites 2013, 3(1), 24-32; doi:10.3390/metabo3010024
Received: 26 November 2012 / Revised: 16 December 2012 / Accepted: 31 December 2012 / Published: 14 January 2013
Cited by 2 | PDF Full-text (121 KB) | HTML Full-text | XML Full-text
Abstract
The marine sponge Haliclona fulva (previously described as Reniera fulva) is widespread in the Mediterranean Sea. The chemical study of the sponge led to the isolation and identification of a new compound: 3-epi-cladocroic acid (1) alongside the previously reported cladocroic acid (2) [...] Read more.
The marine sponge Haliclona fulva (previously described as Reniera fulva) is widespread in the Mediterranean Sea. The chemical study of the sponge led to the isolation and identification of a new compound: 3-epi-cladocroic acid (1) alongside the previously reported cladocroic acid (2) and some other known compounds previously isolated. The structure was fully determined on the basis of extensive analysis by 1D and 2D NMR, as well as GC-MS/MS. The absolute configuration was determined by comparison of the experimental electronic circular dichroism (ECD) spectra with theoretically calculated spectra; these results may be extended to other asymetric cyclopropane carboxylic acids. Full article
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Open AccessArticle Metabonomic Response to Milk Proteins after a Single Bout of Heavy Resistance Exercise Elucidated by 1H Nuclear Magnetic Resonance Spectroscopy
Metabolites 2013, 3(1), 33-46; doi:10.3390/metabo3010033
Received: 13 November 2012 / Revised: 18 December 2012 / Accepted: 21 January 2013 / Published: 30 January 2013
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Abstract
In the present study, proton NMR-based metabonomics was applied on femoral arterial plasma samples collected from young male subjects (milk protein n = 12 in a crossover design; non-caloric control n = 8) at different time intervals (70, 220, 370 min) after [...] Read more.
In the present study, proton NMR-based metabonomics was applied on femoral arterial plasma samples collected from young male subjects (milk protein n = 12 in a crossover design; non-caloric control n = 8) at different time intervals (70, 220, 370 min) after heavy resistance training and intake of either a whey or calcium caseinate protein drink in order to elucidate the impact of the protein source on post-exercise metabolism, which is important for muscle hypertrophy. Dynamic changes in the post-exercise plasma metabolite profile consisted of fluctuations in alanine, beta-hydroxybutyrate, branched amino acids, creatine, glucose, glutamine, glutamate, histidine, lipids and tyrosine. In comparison with the intake of a non-caloric drink, the same pattern of changes in low-molecular weight plasma metabolites was found for both whey and caseinate intake. However, the study indicated that whey and caseinate protein intake had a different impact on low-density and very-low-density lipoproteins present in the blood, which may be ascribed to different effects of the two protein sources on the mobilization of lipid resources during energy deficiency. In conclusion, no difference in the effects on low-molecular weight metabolites as measured by proton NMR-based metabonomics was found between the two protein sources. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Application)
Open AccessArticle Characterisation of the Metabolites of 1,8-Cineole Transferred into Human Milk: Concentrations and Ratio of Enantiomers
Metabolites 2013, 3(1), 47-71; doi:10.3390/metabo3010047
Received: 19 November 2012 / Revised: 16 January 2013 / Accepted: 21 January 2013 / Published: 30 January 2013
Cited by 5 | PDF Full-text (450 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
1,8-Cineole is a widely distributed odorant that also shows physiological effects, but whose human metabolism has hitherto not been extensively investigated. The aim of the present study was, thus, to characterise the metabolites of 1,8-cineole, identified previously in human milk, after the [...] Read more.
1,8-Cineole is a widely distributed odorant that also shows physiological effects, but whose human metabolism has hitherto not been extensively investigated. The aim of the present study was, thus, to characterise the metabolites of 1,8-cineole, identified previously in human milk, after the oral intake of 100 mg of this substance. Special emphasis was placed on the enantiomeric composition of the metabolites since these data may provide important insights into potential biotransformation pathways, as well as potential biological activities of these substances, for example on the breastfed child. The volatile fraction of the human milk samples was therefore isolated via Solvent Assisted Flavour Evaporation (SAFE) and subjected to gas chromatography-mass spectrometry (GC-MS). The absolute concentrations of each metabolite were determined by matrix calibration with an internal standard, and the ratios of enantiomers were analysed on chiral capillaries. The concentrations varied over a broad range, from traces in the upper ng/kg region up to 40 µg/kg milk, with the exception of the main metabolite α2-hydroxy-1,8-cineole that showed concentrations of 100–250 µg/kg. Also, large inter- and intra-individual variations were recorded for the enantiomers, with nearly enantiomerically pure α2-hydroxy- and 3-oxo-1,8-cineole, while all other metabolites showed ratios of ~30:70 to 80:20. Full article
Open AccessArticle Metabolic Changes in Synechocystis PCC6803 upon Nitrogen-Starvation: Excess NADPH Sustains Polyhydroxybutyrate Accumulation
Metabolites 2013, 3(1), 101-118; doi:10.3390/metabo3010101
Received: 20 December 2012 / Revised: 28 January 2013 / Accepted: 30 January 2013 / Published: 6 February 2013
Cited by 13 | PDF Full-text (568 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Polyhydroxybutyrate (PHB) is a common carbon storage polymer among heterotrophic bacteria. It is also accumulated in some photoautotrophic cyanobacteria; however, the knowledge of how PHB accumulation is regulated in this group is limited. PHB synthesis in Synechocystis sp. PCC 6803 is [...] Read more.
Polyhydroxybutyrate (PHB) is a common carbon storage polymer among heterotrophic bacteria. It is also accumulated in some photoautotrophic cyanobacteria; however, the knowledge of how PHB accumulation is regulated in this group is limited. PHB synthesis in Synechocystis sp. PCC 6803 is initiated once macronutrients like phosphorus or nitrogen are limiting. We have previously reported a mutation in the gene sll0783 that impairs PHB accumulation in this cyanobacterium upon nitrogen starvation. In this study we present data which explain the observed phenotype. We investigated differences in intracellular localization of PHB synthase, metabolism, and the NADPH pool between wild type and mutant. Localization of PHB synthase was not impaired in the sll0783 mutant; however, metabolome analysis revealed a difference in sorbitol levels, indicating a more oxidizing intracellular environment than in the wild type. We confirmed this by directly measuring the NADPH/NADP ratio and by altering the intracellular redox state of wild type and sll0783 mutant. We were able to physiologically complement the mutant phenotype of diminished PHB synthase activity by making the intracellular environment more reducing. Our data illustrate that the NADPH pool is an important factor for regulation of PHB biosynthesis and metabolism, which is also of interest for potential biotechnological applications. Full article
(This article belongs to the Special Issue Metabolism in Phototrophic Prokaryotes and Algae)
Open AccessArticle Isolation and Expression of a cDNA Encoding Methylmalonic Aciduria Type A Protein from Euglena gracilis Z
Metabolites 2013, 3(1), 144-154; doi:10.3390/metabo3010144
Received: 27 December 2012 / Revised: 6 February 2013 / Accepted: 7 February 2013 / Published: 18 February 2013
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Abstract
In animals, cobalamin (Cbl) is a cofactor for methionine synthase and methylmalonyl-CoA mutase (MCM), which utilizes methylcobalamin and 5′-deoxyadenosylcobalamin (AdoCbl), respectively. The cblA complementation class of inborn errors of Cbl metabolism in humans is one of three known disorders that affect AdoCbl [...] Read more.
In animals, cobalamin (Cbl) is a cofactor for methionine synthase and methylmalonyl-CoA mutase (MCM), which utilizes methylcobalamin and 5′-deoxyadenosylcobalamin (AdoCbl), respectively. The cblA complementation class of inborn errors of Cbl metabolism in humans is one of three known disorders that affect AdoCbl synthesis. The gene responsible for cblA has been identified in humans (MMAA) as well as its homolog (meaB) in Methylobacterium extorquens. Recently, it has been reported that human MMAA plays an important role in the protection and reactivation of MCM in vitro. However, the physiological function of MMAA is largely unknown. In the present study, we isolated the cDNA encoding MMAA from Euglena gracilis Z, a photosynthetic flagellate. The deduced amino acid sequence of the cDNA shows 79%, 79%, 79% and 80% similarity to human, mouse, Danio rerio MMAAs and M. extorquens MeaB, respectively. The level of the MCM transcript was higher in Cbl-deficient cultures of E. gracilis than in those supplemented with Cbl. In contrast, no significant differences were observed in the levels of the MMAA transcript under the same two conditions. No significant difference in MCM activity was observed between Escherichia coli that expressed either MCM together with MMAA or expressed MCM alone. Full article
(This article belongs to the Special Issue Metabolism in Phototrophic Prokaryotes and Algae)
Open AccessArticle Knowledge Discovery in Spectral Data by Means of Complex Networks
Metabolites 2013, 3(1), 155-167; doi:10.3390/metabo3010155
Received: 6 December 2012 / Revised: 5 February 2013 / Accepted: 5 March 2013 / Published: 11 March 2013
Cited by 2 | PDF Full-text (556 KB) | HTML Full-text | XML Full-text
Abstract
In the last decade, complex networks have widely been applied to the study of many natural and man-made systems, and to the extraction of meaningful information from the interaction structures created by genes and proteins. Nevertheless, less attention has been devoted to [...] Read more.
In the last decade, complex networks have widely been applied to the study of many natural and man-made systems, and to the extraction of meaningful information from the interaction structures created by genes and proteins. Nevertheless, less attention has been devoted to metabonomics, due to the lack of a natural network representation of spectral data. Here we define a technique for reconstructing networks from spectral data sets, where nodes represent spectral bins, and pairs of them are connected when their intensities follow a pattern associated with a disease. The structural analysis of the resulting network can then be used to feed standard data-mining algorithms, for instance for the classification of new (unlabeled) subjects. Furthermore, we show how the structure of the network is resilient to the presence of external additive noise, and how it can be used to extract relevant knowledge about the development of the disease. Full article
(This article belongs to the Special Issue Data Processing in Metabolomics)
Open AccessArticle Gas-Chromatography Mass-Spectrometry (GC-MS) Based Metabolite Profiling Reveals Mannitol as a Major Storage Carbohydrate in the Coccolithophorid Alga Emiliania huxleyi
Metabolites 2013, 3(1), 168-184; doi:10.3390/metabo3010168
Received: 1 February 2013 / Revised: 1 March 2013 / Accepted: 1 March 2013 / Published: 11 March 2013
Cited by 6 | PDF Full-text (372 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Algae are divergent organisms having a wide variety of evolutional histories. Although most of them share photosynthetic activity, their pathways of primary carbon metabolism are rather diverse among species. Here we developed a method for gas chromatography-mass spectroscopy (GC-MS) based metabolite profiling [...] Read more.
Algae are divergent organisms having a wide variety of evolutional histories. Although most of them share photosynthetic activity, their pathways of primary carbon metabolism are rather diverse among species. Here we developed a method for gas chromatography-mass spectroscopy (GC-MS) based metabolite profiling for the coccolithophorid alga Emiliania huxleyi, which is one of the most abundant microalgae in the ocean, in order to gain an overview of the pathway of primary metabolism within this alga. Following method optimization, twenty-six metabolites could be detected by this method. Whilst most proteogenic amino acids were detected, no peaks corresponding to malate and fumarate were found. The metabolite profile of E. huxleyi was, however, characterized by a prominent accumulation of mannitol reaching in excess of 14 nmol 106 cells−1. Similarly, the accumulation of the 13C label during short term H13CO3 feeding revealed a massive redistribution of label into mannitol as well as rapid but saturating label accumulation into glucose and several amino acids including aspartate, glycine and serine. These results provide support to previous work suggesting that this species adopts C3 photosynthesis and that mannitol functions as a carbon store in E. huxleyi. Full article
(This article belongs to the Special Issue Metabolism in Phototrophic Prokaryotes and Algae)
Open AccessArticle Characterization of Flavan-3-ols and Expression of MYB and Late Pathway Genes Involved in Proanthocyanidin Biosynthesis in Foliage of Vitis bellula
Metabolites 2013, 3(1), 185-203; doi:10.3390/metabo3010185
Received: 25 December 2012 / Revised: 4 February 2013 / Accepted: 7 March 2013 / Published: 19 March 2013
Cited by 3 | PDF Full-text (2281 KB) | HTML Full-text | XML Full-text
Abstract
Proanthocyanidins (PAs) are fundamental nutritional metabolites in different types of grape products consumed by human beings. Although the biosynthesis of PAs in berry of Vitis vinifera has gained intensive investigations, the understanding of PAs in other Vitis species is limited. In this [...] Read more.
Proanthocyanidins (PAs) are fundamental nutritional metabolites in different types of grape products consumed by human beings. Although the biosynthesis of PAs in berry of Vitis vinifera has gained intensive investigations, the understanding of PAs in other Vitis species is limited. In this study, we report PA formation and characterization of gene expression involved in PA biosynthesis in leaves of V. bellula, a wild edible grape species native to south and south-west China. Leaves are collected at five developmental stages defined by sizes ranging from 0.5 to 5 cm in length. Analyses of thin layer chromatography (TLC) and high performance liquid chromatography-photodiode array detector (HPLC-PAD) show the formation of (+)-catechin, (−)-epicatechin, (+)-gallocatechin and (−)-epigallocatechin during the entire development of leaves. Analyses of butanol-HCl boiling cleavage coupled with spectrometry measurement at 550 nm show a temporal trend of extractable PA levels, which is characterized by an increase from 0.5 cm to 1.5 cm long leaves followed by a decrease in late stages. TLC and HPLC-PAD analyses identify cyanidin, delphinidin and pelargonidin produced from the cleavage of PAs in the butanol-HCl boiling, showing that the foliage PAs of V. bellula include three different types of extension units. Four cDNAs, which encode VbANR, VbDFR, VbLAR1 and VbLAR2, respectively, are cloned from young leaves. The expression patterns of VbANR and VbLAR2 but not VbLAR1 and VbDFR follow a similar trend as the accumulation patterns of PAs. Two cDNAs encoding VbMYBPA1 and VbMYB5a, the homologs of which have been demonstrated to regulate the expression of both ANR and LAR in V. vinifera, are also cloned and their expression profiles are similar to those of VbANR and VbLAR2. In contrast, the expression profiles of MYBA1 and 2 homologs involved in anthocyanin biosynthesis are different from those of VbANR and VbLAR2. Our data show that both ANR and LAR branches are involved in PA biosynthesis in leaves of V. bellula. Full article
(This article belongs to the Special Issue Metabolomics in Plant Metabolic Engineering)

Review

Jump to: Research

Open AccessReview Recent Applications of Metabolomics Toward Cyanobacteria
Metabolites 2013, 3(1), 72-100; doi:10.3390/metabo3010072
Received: 20 December 2012 / Revised: 23 January 2013 / Accepted: 23 January 2013 / Published: 4 February 2013
Cited by 19 | PDF Full-text (1291 KB) | HTML Full-text | XML Full-text
Abstract
Our knowledge on cyanobacterial molecular biology increased tremendously by the application of the “omics” techniques. Only recently, metabolomics was applied systematically to model cyanobacteria. Metabolomics, the quantitative estimation of ideally the complete set of cellular metabolites, is particularly well suited to mirror [...] Read more.
Our knowledge on cyanobacterial molecular biology increased tremendously by the application of the “omics” techniques. Only recently, metabolomics was applied systematically to model cyanobacteria. Metabolomics, the quantitative estimation of ideally the complete set of cellular metabolites, is particularly well suited to mirror cellular metabolism and its flexibility under diverse conditions. Traditionally, small sets of metabolites are quantified in targeted metabolome approaches. The development of separation technologies coupled to mass-spectroscopy- or nuclear-magnetic-resonance-based identification of low molecular mass molecules presently allows the profiling of hundreds of metabolites of diverse chemical nature. Metabolome analysis was applied to characterize changes in the cyanobacterial primary metabolism under diverse environmental conditions or in defined mutants. The resulting lists of metabolites and their steady state concentrations in combination with transcriptomics can be used in system biology approaches. The application of stable isotopes in fluxomics, i.e. the quantitative estimation of carbon and nitrogen fluxes through the biochemical network, has only rarely been applied to cyanobacteria, but particularly this technique will allow the making of kinetic models of cyanobacterial systems. The further application of metabolomics in the concert of other “omics” technologies will not only broaden our knowledge, but will also certainly strengthen the base for the biotechnological application of cyanobacteria. Full article
(This article belongs to the Special Issue Metabolism in Phototrophic Prokaryotes and Algae)
Open AccessReview Exometabolomics Approaches in Studying the Application of Lignocellulosic Biomass as Fermentation Feedstock
Metabolites 2013, 3(1), 119-143; doi:10.3390/metabo3010119
Received: 12 October 2012 / Revised: 13 December 2012 / Accepted: 28 January 2013 / Published: 11 February 2013
Cited by 6 | PDF Full-text (604 KB) | HTML Full-text | XML Full-text
Abstract
Lignocellulosic biomass is the future feedstock for the production of biofuel and bio-based chemicals. The pretreatment-hydrolysis product of biomass, so-called hydrolysate, contains not only fermentable sugars, but also compounds that inhibit its fermentability by microbes. To reduce the toxicity of hydrolysates as [...] Read more.
Lignocellulosic biomass is the future feedstock for the production of biofuel and bio-based chemicals. The pretreatment-hydrolysis product of biomass, so-called hydrolysate, contains not only fermentable sugars, but also compounds that inhibit its fermentability by microbes. To reduce the toxicity of hydrolysates as fermentation media, knowledge of the identity of inhibitors and their dynamics in hydrolysates need to be obtained. In the past decade, various studies have applied targeted metabolomics approaches to examine the composition of biomass hydrolysates. In these studies, analytical methods like HPLC, RP-HPLC, CE, GC-MS and LC-MS/MS were used to detect and quantify small carboxylic acids, furans and phenols. Through applying targeted metabolomics approaches, inhibitors were identified in hydrolysates and their dynamics in fermentation processes were monitored. However, to reveal the overall composition of different hydrolysates and to investigate its influence on hydrolysate fermentation performance, a non-targeted metabolomics study needs to be conducted. In this review, a non-targeted and generic metabolomics approach is introduced to explore inhibitor identification in biomass hydrolysates, and other similar metabolomics questions. Full article
(This article belongs to the Special Issue Metabolomics in Metabolic Engineering)

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