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Several pathways of central metabolism are activated under P-deficiency, these mainly include alternative metabolic routes that use pyrophosphate and prevent excessive P utilization.
A feasible mechanism involved in the lifespan extension conferred by prohibitin depletion is cellular signaling and the activation of alternative metabolic routes that will counter the mitochondrial defect.
One of the main consequences of this evolutionary pathway, i.e. gene duplication followed by evolutionary divergence, is the separation of metabolic routes that were originally fused in a single, common one.
These notions differ only slightly in their mathematical formulation (Klamt & Stelling, 2003; Papin et al., 2004): the main idea is to determine the set of elementary and independent metabolic routes that can occur in the metabolic model.
Observations falling in the second category allow for instance the selection of those metabolic routes that are compatible with the experimental observations, or help predict quantitative values for the fluxes.
Using this model, we have used in silico Flux Balance Analysis (FBA) to determine key metabolic routes that are essential for generating energy and biomass, thus creating a list of genes potentially essential for growth under laboratory conditions.
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Plants and many microorganisms synthesize folates de novo through a complex metabolic route that is now fully elucidated.
In this view, the mutational elimination of any one reaction might be readily compensated by an alternative metabolic route that is either already present in the genome or can be readily transferred into the genome through horizontal transfer.
The required enzymatic reaction(s) were added to the model based on one of the following 2 criteria: (i) the presence genes in the R. sphaeroides genome encoding the proteins potentially capable of catalyzing the new reaction(s) to be added; and (ii) if no putative enzymes were identified, the metabolic route that required the addition of the fewest reactions to iRsp1095 was selected.
Comparison of these metabolic routes reveals that photobiological conversion of CO2 to ethylene represents a carbon-negative process with a high demand for photosynthetically derived ATP and reducing equivalents, while heterotrophic ethylene production from hexose/pentose has no net cofactor input but still results in carbon loss.
The upregulation of this metabolic route indicated that rate-limiting glutathione precursors (glycine and cysteine) were generated by MPP+-exposed cells at accelerated rates.
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