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To obtain an overall picture of metabolic pathways responding to oxygen availability, gene set enrichment analysis was performed.
To obtain a general view of metabolic pathways responding to oxygen availability, we overlapped the fold change values obtained from the HvsN comparison of the producing strains with the map of S. cerevisiae core metabolism.
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Microalgal cellular growth and metabolic pathways respond in a highly dynamic way to environmental conditions, especially nutrient availability [ 21].
The only primary metabolic pathway responding similar to all stresses was nitrate assimilation, which was down-regulated.
This result suggests that high Flo11 levels may have metabolic impacts, either through sensing pathways responding to cell wall status or by indirectly changing the environment of individual cells from free-floating to being attached to substrates or other cells.
Constraint-based analysis using genome-scale metabolic reconstructions is a widely used computational tool for predicting how fluxes through microbial metabolic pathways will respond to changes in the culture environment or gene deletions/insertions [ 26, 27].
The produced TDP is incorporated into TDP-dependent enzymes that are up-regulated at the same time such as KGDH, PDH, TK, all of which are involved in the main metabolic pathways that respond to stress conditions in plants.
For example, both directed evolution and structure-based rational design approaches have been applied to modify scaffold [ 1] and regulatory [ 2] proteins to either increase reaction rates in metabolic pathways or respond to new input signals.
The circadian clock is fundamental in the regulation of metabolic processes; controlling expression of genes involved in metabolic pathways but also responding to metabolic cues [ 32].
Perturbed metabolic regions under aerobic conditions were predominantly in central metabolic pathways involved in responding to the changed NADH/NADPH demand and did not necessarily emphasize that glutamate dehydrogenase was the site of the genetic modification.
To identify metabolic pathways and processes responding to drought stress or recovery, expression changes in each functional category (MapMan bin) were compared to the overall responses across all genes (Wilcoxon rank sum tests, FDR = 0.05).
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