scholarly journals Comparative metabolomics of Phialemonium curvatum as an omnipotent fungus cultivated on crude palm oil versus glucose

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Arief Izzairy Zamani ◽  
Susann Barig ◽  
Sarah Ibrahim ◽  
Hirzun Mohd. Yusof ◽  
Julia Ibrahim ◽  
...  
Keyword(s):  
Carbon Source ◽  
Organic Acids ◽  
Vegetable Oil ◽  
Carbon Metabolism ◽  
Sole Carbon Source ◽  
Carbon Sources ◽  
Tca Cycle ◽  
Central Carbon Metabolism ◽  
Targeted Metabolomics ◽  
Central Carbon

Abstract Background Sugars and triglycerides are common carbon sources for microorganisms. Nonetheless, a systematic comparative interpretation of metabolic changes upon vegetable oil or glucose as sole carbon source is still lacking. Selected fungi that can grow in acidic mineral salt media (MSM) with vegetable oil had been identified recently. Hence, this study aimed to investigate the overall metabolite changes of an omnipotent fungus and to reveal changes at central carbon metabolism corresponding to both carbon sources. Results Targeted and non-targeted metabolomics for both polar and semi-polar metabolites of Phialemonium curvatum AWO2 (DSM 23903) cultivated in MSM with palm oil (MSM-P) or glucose (MSM-G) as carbon sources were obtained. Targeted metabolomics on central carbon metabolism of tricarboxylic acid (TCA) cycle and glyoxylate cycle were analysed using LC–MS/MS-TripleQ and GC–MS, while untargeted metabolite profiling was performed using LC–MS/MS-QTOF followed by multivariate analysis. Targeted metabolomics analysis showed that glyoxylate pathway and TCA cycle were recruited at central carbon metabolism for triglyceride and glucose catabolism, respectively. Significant differences in organic acids concentration of about 4- to 8-fold were observed for citric acid, succinic acid, malic acid, and oxaloacetic acid. Correlation of organic acids concentration and key enzymes involved in the central carbon metabolism was further determined by enzymatic assays. On the other hand, the untargeted profiling revealed seven metabolites undergoing significant changes between MSM-P and MSM-G cultures. Conclusions Overall, this study has provided insights on the understanding on the effect of triglycerides and sugar as carbon source in fungi global metabolic pathway, which might become important for future optimization of carbon flux engineering in fungi to improve organic acids production when vegetable oil is applied as the sole carbon source.

scholarly journals Metabolic Changes Induced by Deletion of Transcriptional Regulator GCR2 in Xylose-Fermenting Saccharomyces cerevisiae

2020 ◽  
Vol 8 (10) ◽  
pp. 1499
Author(s):  
Minhye Shin ◽  
Soo Rin Kim
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Carbon Source ◽  
Pentose Phosphate Pathway ◽  
Carbon Metabolism ◽  
Transcriptional Regulator ◽  
Central Carbon Metabolism ◽  
Pentose Phosphate ◽  
Metabolic Changes ◽  
Regulatory Systems ◽  
Central Carbon

Glucose repression has been extensively studied in Saccharomyces cerevisiae, including the regulatory systems responsible for efficient catabolism of glucose, the preferred carbon source. However, how these regulatory systems would alter central metabolism if new foreign pathways are introduced is unknown, and the regulatory networks between glycolysis and the pentose phosphate pathway, the two major pathways in central carbon metabolism, have not been systematically investigated. Here we disrupted gcr2, a key transcriptional regulator, in S. cerevisiae strain SR7 engineered to heterologously express the xylose-assimilating pathway, activating genes involved in glycolysis, and evaluated the global metabolic changes. gcr2 deletion reduced cellular growth in glucose but significantly increased growth when xylose was the sole carbon source. Global metabolite profiling revealed differential regulation of yeast metabolism in SR7-gcr2Δ, especially carbohydrate and nucleotide metabolism, depending on the carbon source. In glucose, the SR7-gcr2Δ mutant showed overall decreased abundance of metabolites, such as pyruvate and sedoheptulose-7-phosphate, associated with central carbon metabolism including glycolysis and the pentose phosphate pathway. However, SR7-gcr2Δ showed an increase in metabolites abundance (ribulose-5-phosphate, sedoheptulose-7-phosphate, and erythrose-4-phosphate) notably from the pentose phosphate pathway, as well as alteration in global metabolism when compared to SR7. These results provide insights into how the regulatory system GCR2 coordinates the transcription of glycolytic genes and associated metabolic pathways.

scholarly journals The Functional Structure of Central Carbon Metabolism in Pseudomonas putida KT2440

2014 ◽  
Vol 80 (17) ◽  
pp. 5292-5303 ◽  
Author(s):  
Suresh Sudarsan ◽  
Sarah Dethlefsen ◽  
Lars M. Blank ◽  
Martin Siemann-Herzberg ◽  
Andreas Schmid
Keyword(s):  
Pseudomonas Putida ◽  
Carbon Metabolism ◽  
Carbon Sources ◽  
Central Carbon Metabolism ◽  
Transcriptional Level ◽  
Regulation Mechanism ◽  
Central Metabolism ◽  
Content Type ◽  
Central Carbon ◽  
Definition Of

ABSTRACTWhat defines central carbon metabolism? The classic textbook scheme of central metabolism includes the Embden-Meyerhof-Parnas (EMP) pathway of glycolysis, the pentose phosphate pathway, and the citric acid cycle. The prevalence of this definition of central metabolism is, however, equivocal without experimental validation. We address this issue using a general experimental approach that combines the monitoring of transcriptional and metabolic flux changes between steady states on alternative carbon sources. This approach is investigated by using the model bacteriumPseudomonas putidawith glucose, fructose, and benzoate as carbon sources. The catabolic reactions involved in the initial uptake and metabolism of these substrates are expected to show a correlated change in gene expressions and metabolic fluxes. However, there was no correlation for the reactions linking the 12 biomass precursor molecules, indicating a regulation mechanism other than mRNA synthesis for central metabolism. This result substantiates evidence for a (re)definition of central carbon metabolism including all reactions that are bound to tight regulation and transcriptional invariance. Contrary to expectations, the canonical Entner-Doudoroff and EMP pathwayssensu strictoare not a part of central carbon metabolism inP. putida, as they are not regulated differently from the aromatic degradation pathway. The regulatory analyses presented here provide leads on a qualitative basis to address the use of alternative carbon sources by deregulation and overexpression at the transcriptional level, while rate improvements in central carbon metabolism require careful adjustment of metabolite concentrations, as regulation resides to a large extent in posttranslational and/or metabolic regulation.

scholarly journals A Functional cra Gene Is Required forSalmonella enterica Serovar Typhimurium Virulence in BALB/c Mice

2000 ◽  
Vol 68 (6) ◽  
pp. 3772-3775 ◽  
Author(s):  
James H. Allen ◽  
Maryjane Utley ◽  
Han van den Bosch ◽  
Piet Nuijten ◽  
Maarten Witvliet ◽  
...  
Keyword(s):  
Carbon Metabolism ◽  
Salmonella Enterica ◽  
Protein A ◽  
Carbon Sources ◽  
Central Carbon Metabolism ◽  
Central Carbon ◽  
Serovar Typhimurium ◽  
Gluconeogenic Substrates

ABSTRACT A minitransposon mutant of Salmonella enterica serovar Typhimurium SR-11, SR-11 Fad−, is unable to utilize gluconeogenic substrates as carbon sources and is avirulent and immunogenic when administered perorally to BALB/c mice (M. J. Utley et al., FEMS Microbiol. Lett., 163:129–134, 1998). Here, evidence is presented that the mutation in SR-11 Fad− that renders the strain avirulent is in the cra gene, which encodes the Cra protein, a regulator of central carbon metabolism.

scholarly journals Dissection of Central Carbon Metabolism of Hemoglobin-ExpressingEscherichia coli by 13C Nuclear Magnetic Resonance Flux Distribution Analysis in Microaerobic Bioprocesses

2001 ◽  
Vol 67 (2) ◽  
pp. 680-687 ◽  
Author(s):  
Alexander D. Frey ◽  
Jocelyne Fiaux ◽  
Thomas Szyperski ◽  
Kurt Wüthrich ◽  
James E. Bailey ◽  
...  
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Carbon Metabolism ◽  
Tca Cycle ◽  
Central Carbon Metabolism ◽  
Distribution Analysis ◽  
E Coli ◽  
13C Nuclear Magnetic Resonance ◽  
Central Carbon ◽  
Nuclear Magnetic

ABSTRACT Escherichia coli MG1655 cells expressingVitreoscilla hemoglobin (VHb), Alcaligenes eutrophus flavohemoprotein (FHP), the N-terminal hemoglobin domain of FHP (FHPg), and a fusion protein which comprises VHb and theA. eutrophus C-terminal reductase domain (VHb-Red) were grown in a microaerobic bioreactor to study the effects of low oxygen concentrations on the central carbon metabolism, using fractional13C-labeling of the proteinogenic amino acids and two-dimensional [13C, 1H]-correlation nuclear magnetic resonance (NMR) spectroscopy. The NMR data revealed differences in the intracellular carbon fluxes between E. coli cells expressing either VHb or VHb-Red and cells expressingA. eutrophus FHP or the truncated heme domain (FHPg).E. coli MG1655 cells expressing either VHb or VHb-Red were found to function with a branched tricarboxylic acid (TCA) cycle. Furthermore, cellular demands for ATP and reduction equivalents in VHb- and VHb-Red-expressing cells were met by an increased flux through glycolysis. In contrast, in E. coli cells expressingA. eutrophus hemeproteins, the TCA cycle is running cyclically, indicating a shift towards a more aerobic regulation. Consistently, E. coli cells displaying FHP and FHPg activity showed lower production of the typical anaerobic by-products formate, acetate, and d-lactate. The implications of these observations for biotechnological applications are discussed.

scholarly journals Evidence for loss and adaptive reacquisition of alcoholic fermentation in an early-derived fructophilic yeast lineage

2017 ◽  
Author(s):  
Carla Gonçalves ◽  
Jennifer H. Wisecaver ◽  
Madalena Salema-Oom ◽  
Maria José Leandro ◽  
Xing-Xing Shen ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Carbon Metabolism ◽  
Alcoholic Fermentation ◽  
Carbon Sources ◽  
Central Carbon Metabolism ◽  
High Sugar ◽  
Central Carbon ◽  
Adaptive Nature

AbstractFructophily is a rare trait that consists in the preference for fructose over other carbon sources. Here we show that in a yeast lineage (theWickerhamiella/Starmerella, W/S clade) formed by fructophilic species thriving in the floral niche, the acquisition of fructophily is part of a wider process of adaptation of central carbon metabolism to the high sugar environment. Coupling comparative genomics with biochemical and genetic approaches, we show that the alcoholic fermentation pathway was profoundly remodeled in the W/S clade, as genes required for alcoholic fermentation were lost and subsequently re-acquired from bacteria through horizontal gene transfer. We further show that the reinstated fermentative pathway is functional and that an enzyme required for sucrose assimilation is also of bacterial origin, reinforcing the adaptive nature of the genetic novelties identified in the W/S clade. This work shows how even central carbon metabolism can be remodeled by a surge of HGT events.

Central carbon metabolism of Leishmania parasites

Parasitology ◽  
2010 ◽  
Vol 137 (9) ◽  
pp. 1303-1313 ◽  
Author(s):  
ELEANOR C. SAUNDERS ◽  
DAVID P. DE SOUZA ◽  
THOMAS NADERER ◽  
MARIJKE F. SERNEE ◽  
JULIE E. RALTON ◽  
...  
Keyword(s):  
Carbon Metabolism ◽  
Drug Targets ◽  
Carbon Sources ◽  
Central Carbon Metabolism ◽  
Mammalian Host ◽  
Insect Vector ◽  
Carbon Utilization ◽  
Central Carbon ◽  
Host Infection

SUMMARYLeishmania spp. are sandfly-transmitted protozoa parasites that cause a spectrum of diseases in humans. Many enzymes involved in Leishmania central carbon metabolism differ from their equivalents in the mammalian host and are potential drug targets. In this review we summarize recent advances in our understanding of Leishmania central carbon metabolism, focusing on pathways of carbon utilization that are required for growth and pathogenesis in the mammalian host. While Leishmania central carbon metabolism shares many features in common with other pathogenic trypanosomatids, significant differences are also apparent. Leishmania parasites are also unusual in constitutively expressing most core metabolic pathways throughout their life cycle, a feature that may allow these parasites to exploit a range of different carbon sources (primarily sugars and amino acids) rapidly in both the insect vector and vertebrate host. Indeed, recent gene deletion studies suggest that mammal-infective stages are dependent on multiple carbon sources in vivo. The application of metabolomic approaches, outlined here, are likely to be important in defining aspects of central carbon metabolism that are essential at different stages of mammalian host infection.

scholarly journals Metabolic Flux Ratio Analysis of Genetic and Environmental Modulations of Escherichia coli Central Carbon Metabolism

1999 ◽  
Vol 181 (21) ◽  
pp. 6679-6688 ◽  
Author(s):  
Uwe Sauer ◽  
Daniel R. Lasko ◽  
Jocelyne Fiaux ◽  
Michel Hochuli ◽  
Ralf Glaser ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Carbon Metabolism ◽  
Metabolic Flux ◽  
Flux Ratio ◽  
Tca Cycle ◽  
Central Carbon Metabolism ◽  
E Coli ◽  
Chemostat Cultures ◽  
Central Carbon ◽  
Pep Carboxykinase

ABSTRACT The response of Escherichia coli central carbon metabolism to genetic and environmental manipulation has been studied by use of a recently developed methodology for metabolic flux ratio (METAFoR) analysis; this methodology can also directly reveal active metabolic pathways. Generation of fluxome data arrays by use of the METAFoR approach is based on two-dimensional13C-1H correlation nuclear magnetic resonance spectroscopy with fractionally labeled biomass and, in contrast to metabolic flux analysis, does not require measurements of extracellular substrate and metabolite concentrations. METAFoR analyses of E. coli strains that moderately overexpress phosphofructokinase, pyruvate kinase, pyruvate decarboxylase, or alcohol dehydrogenase revealed that only a few flux ratios change in concert with the overexpression of these enzymes. Disruption of both pyruvate kinase isoenzymes resulted in altered flux ratios for reactions connecting the phosphoenolpyruvate (PEP) and pyruvate pools but did not significantly alter central metabolism. These data indicate remarkable robustness and rigidity in central carbon metabolism in the presence of genetic variation. More significant physiological changes and flux ratio differences were seen in response to altered environmental conditions. For example, in ammonia-limited chemostat cultures, compared to glucose-limited chemostat cultures, a reduced fraction of PEP molecules was derived through at least one transketolase reaction, and there was a higher relative contribution of anaplerotic PEP carboxylation than of the tricarboxylic acid (TCA) cycle for oxaloacetate synthesis. These two parameters also showed significant variation between aerobic and anaerobic batch cultures. Finally, two reactions catalyzed by PEP carboxykinase and malic enzyme were identified by METAFoR analysis; these had previously been considered absent in E. colicells grown in glucose-containing media. Backward flux from the TCA cycle to glycolysis, as indicated by significant activity of PEP carboxykinase, was found only in glucose-limited chemostat culture, demonstrating that control of this futile cycle activity is relaxed under severe glucose limitation.

scholarly journals Toward a Genome Scale Sequence Specific Dynamic Model of Cell-Free Protein Synthesis inEscherichia coli

2017 ◽  
Author(s):  
Nicholas Horvath ◽  
Michael Vilkhovoy ◽  
Joseph A. Wayman ◽  
Kara Calhoun ◽  
James Swartz ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Organic Acids ◽  
Carbon Metabolism ◽  
Protein Production ◽  
Central Carbon Metabolism ◽  
Free Protein ◽  
E Coli ◽  
Central Carbon ◽  
Genome Scale ◽  
Cell Free Protein Synthesis

AbstractCell-free protein expression systems have become widely used in systems and synthetic biology. In this study, we developed an ensemble of dynamicE. colicell-free protein synthesis (CFPS) models. Model parameters were estimated from a training dataset for the cell-free production of a protein product, chloramphenicol acetyltransferase (CAT). The dataset consisted of measurements of glucose, organic acids, energy species, amino acids, and CAT. The ensemble accurately predicted these measurements, especially those of the central carbon metabolism. We then used the trained model to evaluate the optimality of protein production. CAT was produced with an energy efficiency of 12%, suggesting that the process could be further optimized. Reaction group knockouts showed that protein productivity and the metabolism as a whole depend most on oxidative phosphorylation and glycolysis and gluco-neogenesis. Amino acid biosynthesis is also important for productivity, while the overflow metabolism and TCA cycle affect the overall system state. In addition, the translation rate is shown to be more important to productivity than the transcription rate. Finally, CAT production was robust to allosteric control, as was most of the network, with the exception of the organic acids in central carbon metabolism. This study is the first to use kinetic modeling to predict dynamic protein production in a cell-freeE. colisystem, and should provide a foundation for genome scale, dynamic modeling of cell-freeE. coliprotein synthesis.

scholarly journals Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Carla Gonçalves ◽  
Jennifer H Wisecaver ◽  
Jacek Kominek ◽  
Madalena Salema Oom ◽  
Maria José Leandro ◽  
...  
Keyword(s):  
Carbon Metabolism ◽  
Alcoholic Fermentation ◽  
Carbon Sources ◽  
Central Carbon Metabolism ◽  
Yeast Gene ◽  
Ample Evidence ◽  
High Sugar ◽  
Central Carbon ◽  
Bacterial Genes ◽  
Horizontal Acquisition

Fructophily is a rare trait that consists of the preference for fructose over other carbon sources. Here, we show that in a yeast lineage (the Wickerhamiella/Starmerella, W/S clade) comprised of fructophilic species thriving in the high-sugar floral niche, the acquisition of fructophily is concurrent with a wider remodeling of central carbon metabolism. Coupling comparative genomics with biochemical and genetic approaches, we gathered ample evidence for the loss of alcoholic fermentation in an ancestor of the W/S clade and subsequent reinstatement through either horizontal acquisition of homologous bacterial genes or modification of a pre-existing yeast gene. An enzyme required for sucrose assimilation was also acquired from bacteria, suggesting that the genetic novelties identified in the W/S clade may be related to adaptation to the high-sugar environment. This work shows how even central carbon metabolism can be remodeled by a surge of HGT events.

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