Gonzalez2010_N_pharaonis_metabolism

This is metabolic network reconstruction of Natronomonas pharaonis
described in the article
Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis.

Gonzalez O, Oberwinkler T, Mansueto L, Pfeiffer F, Mendoza E, Zimmer R, Oesterhelt D. PLoS Comput Biol.
2010 Jun 3;6(6):e1000799. PMID: 20543878
, DOI: e1000799. doi:10.1371/journal.pcbi.1000799

Abstract:
Natronomonas pharaonis is an archaeon adapted to two extreme conditions: high salt concentration and alkaline pH. It has become one of the model organisms for the study of extremophilic life. Here, we present a genome-scale, manually curated metabolic reconstruction for the microorganism. The reconstruction itself represents a knowledge base of the haloalkaliphile's metabolism and, as such, would greatly assist further investigations on archaeal pathways. In addition, we experimentally determined several parameters relevant to growth, including a characterization of the biomass composition and a quantification of carbon and oxygen consumption. Using the metabolic reconstruction and the experimental data, we formulated a constraints-based model which we used to analyze the behavior of the archaeon when grown on a single carbon source. Results of the analysis include the finding that Natronomonas pharaonis, when grown aerobically on acetate, uses a carbon to oxygen consumption ratio that is theoretically near-optimal with respect to growth and energy production. This supports the hypothesis that, under simple conditions, the microorganism optimizes its metabolism with respect to the two objectives. We also found that the archaeon has a very low carbon efficiency of only about 35%. This inefficiency is probably due to a very low P/O ratio as well as to the other difficulties posed by its extreme environment.
This model was downloaded from the supplemetary materials to the article. To make this file valid SBML, some minor changes had to be done. The reaction Test_sink and empty lists were removed.
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