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ABSTRACT Metabolic engineering strategies applied over the last two decades to produce shikimate (SA) in Escherichia coli have resulted in a battery of strains bearing many expression systems. However, the effects that these systems have on the host physiology and how they impact the production of SA are still not well understood. In this work we utilized an engineered E. coli strain to determine the consequences of carrying a vector that promotes SA production from glucose with a high-yield but that is also expected to impose a significant cellular burden. Kinetic comparisons in fermentors showed that instead of exerting a negative effect, the sole presence of the plasmid increased glucose consumption without diminishing the growth rate. By constitutively expressing a biosynthetic operon from this vector, the more active glycolytic metabolism was exploited to redirect intermediates toward the production of SA, which further increased the glucose consumption rate and avoided excess acetate production. Fluxomics and metabolomics experiments revealed a global remodeling of the carbon and energy metabolism in the production strain, where the increased SA production reduced the carbon available for oxidative and fermentative pathways. Moreover, the results showed that the production of SA relies on a specific setup of the pentose phosphate pathway, where both its oxidative and non-oxidative branches are strongly activated to supply erythrose-4-phosphate and balance the NADPH requirements. This work improves our understanding of the metabolic reorganization observed in E. coli in response to the plasmid-based expression of the SA biosynthetic pathway. Biotechnol. Bioeng. 2017;114: 1319-1330. © 2017 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

In prominent gut Bacteroides strains, sophisticated strategies have been evolved to achieve the complete degradation of dietary polysaccharides such as xylan, which is one of the major components of the plant cell wall. Polysaccharide Utilization Loci (PULs) consist of gene clusters encoding different proteins with a vast arsenal of functions, including carbohydrate binding, transport and hydrolysis. Transport is often attributed to TonB-dependent transporters, although major facilitator superfamily (MFS) transporters have also been identified in some PULs. However, until now, few of these transporters have been biochemically characterized. Here, we targeted a PUL-like system from an uncultivated Bacteroides species that is highly prevalent in the human gut metagenome. It encodes three glycoside-hydrolases specific for xylo-oligosaccharides, a SusC/SusD tandem homolog and a MFS transporter. We combined PUL rational engineering, metabolic and transcriptional analysis in Escherichia coli to functionally characterize this genomic locus. We demonstrated that the SusC and the MFS transporters are specific for internalization of linear xylo-oligosaccharides of polymerization degree up to 3 and 4 respectively. These results were strengthened by the study of growth dynamics and transcriptional analyses in response to XOS induction of the PUL in the native strain, Bacteroides vulgatus. [ABSTRACT FROM AUTHOR]

Metabolic control in Escherichia coli is a complex process involving multilevel regulatory systems but the involvement of post-transcriptional regulation is uncertain. The post-transcriptional factor CsrA is stated as being the only regulator essential for the use of glycolytic substrates. A dozen enzymes in the central carbon metabolism (CCM) have been reported as potentially controlled by CsrA, but its impact on the CCM functioning has not been demonstrated. Here, a multiscale analysis was performed in a wild-type strain and its isogenic mutant attenuated for CsrA (including growth parameters, gene expression levels, metabolite pools, abundance of enzymes and fluxes). Data integration and regulation analysis showed a coordinated control of the expression of glycolytic enzymes. This also revealed the imbalance of metabolite pools in the csrA mutant upper glycolysis, before the phosphofructokinase PfkA step. This imbalance is associated with a glucose-phosphate stress. Restoring PfkA activity in the csrA mutant strain suppressed this stress and increased the mutant growth rate on glucose. Thus, the carbon storage regulator system is essential for the effective functioning of the upper glycolysis mainly through its control of PfkA. This work demonstrates the pivotal role of post-transcriptional regulation to shape the carbon metabolism. [ABSTRACT FROM AUTHOR]

ABSTRACT The growing demand for 13C-metabolic flux analysis (13C-MFA) in the field of metabolic engineering and systems biology is driving the need to rationalize expensive and time-consuming 13C-labeling experiments. Experimental design is a key step in improving both the number of fluxes that can be calculated from a set of isotopic data and the precision of flux values. We present IsoDesign, a software that enables these parameters to be maximized by optimizing the isotopic composition of the label input. It can be applied to 13C-MFA investigations using a broad panel of analytical tools (MS, MS/MS, 1H NMR, 13C NMR, etc.) individually or in combination. It includes a visualization module to intuitively select the optimal label input depending on the biological question to be addressed. Applications of IsoDesign are described, with an example of the entire 13C-MFA workflow from the experimental design to the flux map including important practical considerations. IsoDesign makes the experimental design of 13C-MFA experiments more accessible to a wider biological community. IsoDesign is distributed under an open source license at http://metasys.insa-toulouse.fr/software/isodes/ Biotechnol. Bioeng. 2014;111: 202-208. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Adaptive metabolic behavior of photoautotrophic microorganisms toward genetic and environmental perturbations can be interpreted in a quantitative depiction of carbon flow through a biochemical reaction network using isotopic non-stationary 13C-metabolic flux analysis (INST 13C-MFA). To evaluate 13C-metabolic flux maps for Chlamydomonas reinhardtii, an original experimental framework was designed allowing rapid, reliable collection of high-quality isotopomer data against time. It involved (i) a short-time 13C labeling injection device based on mixing control in a torus-shaped photobioreactor with plug-flow hydrodynamics allowing a sudden step-change in the 13C proportion in the substrate feed and (ii) a rapid sampling procedure using an automatic fast filtration method coupled to a manual rapid liquid nitrogen quenching step. 13C-substrate labeling enrichment was controlled through the total dissolved inorganic carbon concentration in the pulsed solution. First results were obtained from steady-state continuous culture measurements allowing the characterization of the kinetics of label incorporation into light-limited growing cells cultivated in a photobioreactor operating at the maximal biomass productivity for an incident photon flux density of 200 µmol m−2 s−1. 13C label incorporation was measured for 21 intracellular metabolites using IC-MS/MS in 58 samples collected across a labeling experiment duration of 7 min. The fastest labeling rate was observed for 2/3-phosphoglycerate with an apparent isotopic stationary state reached after 300 s. The labeling rate was consistent with the optimized mixing time of about 4.9 s inside the reactor and the shortest reliable sampling period assessed at 5 s. Biotechnol. Bioeng. 2012; 109: 3030-3040. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Respiring Saccharomyces cerevisiae cells respond to a sudden increase in glucose concentration by a pronounced drop of their adenine nucleotide content ([ATP]+[ADP]+[AMP]=[AXP]). The unknown fate of ‘lost’ AXP nucleotides represented a long-standing problem for the understanding of the yeast's physiological response to changing growth conditions. Transient accumulation of the purine salvage pathway intermediate, inosine, accounted for the apparent loss of adenine nucleotides. Conversion of AXPs into inosine was facilitated by AMP deaminase, Amd1, and IMP-specific 5′-nucleotidase, Isn1. Inosine recycling into the AXP pool was facilitated by purine nucleoside phosphorylase, Pnp1, and joint action of the phosphoribosyltransferases, Hpt1 and Xpt1. Analysis of changes in 24 intracellular metabolite pools during the respiro-fermentative growth transition in wild-type, amd1, isn1, and pnp1 strains revealed that only the amd1 mutant exhibited significant deviations from the wild-type behavior. Moreover, mutants that were blocked in inosine production exhibited delayed growth acceleration after glucose addition. It is proposed that interconversion of adenine nucleotides and inosine facilitates rapid and energy-cost efficient adaptation of the AXP pool size to changing environmental conditions. [ABSTRACT FROM AUTHOR]

Abstract: The deletion of the zwf gene encoding G6PDH activity led to restructuring of the carbon flux through central metabolism in Escherichia coli, though over-expression of this gene had only minor consequences for overall carbon flux. The modified carbon flux seen in the zwf deletion mutant enabled alternative routes of anabolic precursor formation and an adequate supply of NADPH synthesis via a modified TCA cycle to be generated so as to sustain growth rates comparable to the WT. [Copyright &y& Elsevier]

Investigates the pathways of polysaccharide biosynthesis in cells of the soil bacterium Sinorhizobium meliloti. Synthesis of internal and external polysaccharides; Contribution of the Entner-Duodoroff pathway to early steps of polysaccharide synthesis; Proposed carbohydrate metabolism scheme in S. meliloti.

Rat cerebellar and cortical astrocytes cultured for 15 or 35 days were incubated with [1-13C]glucose in the presence or absence of 4 mM exogenous glutamine and the release of 13C-enriched metabolites into cell media was studied by 13C-NMR spectroscopy. In the presence of exogenous glutamine, both cerebellar and cortical astrocytes consumed the amino acid. In contrast, a net production of glutamine occurred in the absence of the amino acid. Simultaneously, a release of 13C-enriched glutamine into cell media was observed and was higher in the presence than in the absence of exogenous glutamine. This demonstrated the occurrence of an isotopic-exchange process which may involve a futile cycle at the level of glutamine synthetase and glutaminase activities. The 13C-enrichment ratio between glutamine carbons C2 and C3 was close to 1 in the presence of exogenous glutamine whereas it was higher than 1 in its absence, indicating that pyruvate carboxylase was more active in the absence of glutamine. In addition to glutamine, alanine was synthesized and exported into the medium of both cerebellar and cortical astrocytes. In contrast, citrate was specifically produced by cortical astrocytes. Slight increases in alanine and glutamine productions were observed for cortical astrocyte cultures between 15 and 35 days, whereas the amino acid production by cerebellar astrocytes increased several-fold after 35 days compared with that at 15 days of culture. [ABSTRACT FROM AUTHOR]

Focuses on metabolic flux determination in C6 glioma cells using carbon-13 distribution upon [1-[sup13]C]glucose incubation. Distribution of the carbon-13 isotope at the different carbon positions of metabolites in cells fed with carbon-13 isotope-enriched substrates; Calculation of metabolic fluxes in a rat tumor cell line; Different metabolic characteristics of C6 cells and astrocytes.

The metabolism of [1-[sup13]C]glucose in rat cerebellum astrocytes and granule cells was investigated using [sup13]C- and [sup1]H-NMR spectroscopy. Near homogeneous primary cultures of each cell type were incubated with [1-[sup13]C]glucose, under the same conditions. Analysing the relative [sup13]C enrichments of metabolites in spectra of cell perchloric acid extracts, on the one hand, the [sup13]C-1H spin-coupling patterns in [sup1]H-NMR spectra of cell medium lactate and the [sup13]C-[sup13]C spin-coupling patterns in [sup13]C-NMR spectra of purified cell glutamate, on the other hand, showed significant differences, between the two cell types, in the activity of various metabolic ways. First, the carbon flux through the oxidative branch of the hexose monophosphate shunt, which leads to unenriched lactate, was found higher in granule cells than in astrocytes. Second, although the specific [sup13]C enrichment of lactate was higher in astrocytes than in granule cells, the fraction of [sup13]C-enriched acetyl-CoA entering the citric acid cycle was more than twice as high in granule cells as in astrocytes. Lactate C[sub3] and acetyl-CoA C[sub2] enrichments were very similar in granule cells, whereas acetyl-CoA C[sub2] enrichment was 60% lower than that of lactate C[sub3] in astrocytes. These results can be explained by the fact that granule cells used almost exclusively the exogenous glucose to fuel the citric acid cycle, whereas astrocytes used concomitantly glucose and other carbon sources. Last, in the case of granule cells, glutamate C[sub2] and C[sub3] enrichments were equivalent; the carbon flux through the pyruvate carboxylase route was evaluated to be around 15% of the carbon flux through the citrate synthetase route. In astrocytes, glutamate C[sub2] enrichment was higher than that of C[sub3], which could be explained by a pyruvate carboxylase activity much more active in these cells than in granule cells. [ABSTRACT FROM AUTHOR]