Senger2008 - Genome-scale metabolic network of Clostridium acetobutylicum (iCac802)

Senger2008 - Genome-scale metabolic network
of Clostridium acetobutylicum (iCac802)

This model is described in the article:

Genome-scale model for
Clostridium acetobutylicum: Part I. Metabolic network
resolution and analysis.

Senger RS, Papoutsakis ET.
Biotechnol. Bioeng. 2008 Dec; 101(5):
1036-1052
Abstract:

A genome-scale metabolic network reconstruction for
Clostridium acetobutylicum (ATCC 824) was carried out using a
new semi-automated reverse engineering algorithm. The network
consists of 422 intracellular metabolites involved in 552
reactions and includes 80 membrane transport reactions. The
metabolic network illustrates the reliance of clostridia on the
urea cycle, intracellular L-glutamate solute pools, and the
acetylornithine transaminase for amino acid biosynthesis from
the 2-oxoglutarate precursor. The semi-automated reverse
engineering algorithm identified discrepancies in reaction
network databases that are major obstacles for fully automated
network-building algorithms. The proposed semi-automated
approach allowed for the conservation of unique clostridial
metabolic pathways, such as an incomplete TCA cycle. A
thermodynamic analysis was used to determine the physiological
conditions under which proposed pathways (e.g., reverse partial
TCA cycle and reverse arginine biosynthesis pathway) are
feasible. The reconstructed metabolic network was used to
create a genome-scale model that correctly characterized the
butyrate kinase knock-out and the asolventogenic M5 pSOL1
megaplasmid degenerate strains. Systematic gene knock-out
simulations were performed to identify a set of genes encoding
clostridial enzymes essential for growth in silico.

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