Characterization of Growth and Metabolism of the Haloalkaliphile Natronomonas pharaonis

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.

Control of fluxes in metabolic networks

“…The covered organisms include three archaea (Feist et al 2006;Gonzalez et al 2010;Satish Kumar et al 2011), five prokaryotes Nogales et al 2008;Zhang et al 2009;Orth et al 2011;Wodke et al 2013), and five eukaryotes (Duarte et al 2007;Andersen et al 2008;Quek and Nielsen 2008;Manichaikul et al 2009;Arnold and Nikoloski 2014).…”

Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

“…In 2008, they released the first manually curated GEM for Halobacterium salinarum R-1 ( i OG478) [13]. This was followed in 2010 by a new GEM for a haloalkaliphile, Natronomonas pharaonis ( i OG654) [25], which inherited significantly from the H. salinarum model. The only other nonmethanogenic archaeal GEM to our knowledge was independently constructed in 2012 for the Sulfolobus solfataricus by Ulas et al [26].…”

“…The metabolic network for the polyextremophile (high salt concentration and alkaline pH) Natronomonas pharaonis was developed [25] using the reconstruction for H. salinarum . The network is significantly larger, with nearly 30% more genes associated with reactions, mostly due to additional amino acid and carbon degradation pathways.…”

“…The authors measured the amino acid content to define the biomass composition and found, similar to H. salinarum , that it made up about 75% of organic mass [13, 25]. Perhaps the high protein content helps to compensate for the high osmolarity in which the organisms are grown.…”

“…Using experiments, they identified an acetate:oxygen ratio of about 1 : 2 and an ATP maintenance cost of ~30  μ mol/ΔOD·mL. A wide range of maintenance energies and acetate:oxygen ratios gave near optimal growth, indicating that growth of N. pharaonis is robust to environment and the biological objective is to maximize growth and energy production [25]. They found that the carbon incorporation was actually quite low (~35%).…”