Genome-Scale Reconstruction and Analysis of the Metabolic Network in the Hyperthermophilic Archaeon Sulfolobus Solfataricus

Abstract

We describe the reconstruction of a genome-scale metabolic model of the crenarchaeon Sulfolobus solfataricus, a hyperthermoacidophilic microorganism. It grows in terrestrial volcanic hot springs with growth occurring at pH 2–4 (optimum 3.5) and a temperature of 75–80°C (optimum 80°C). The genome of Sulfolobus solfataricus P2 contains 2,992,245 bp on a single circular chromosome and encodes 2,977 proteins and a number of RNAs. The network comprises 718 metabolic and 58 transport/exchange reactions and 705 unique metabolites, based on the annotated genome and available biochemical data. Using the model in conjunction with constraint-based methods, we simulated the metabolic fluxes induced by different environmental and genetic conditions. The predictions were compared to experimental measurements and phenotypes of S. solfataricus. Furthermore, the performance of the network for 35 different carbon sources known for S. solfataricus from the literature was simulated. Comparing the growth on different carbon sources revealed that glycerol is the carbon source with the highest biomass flux per imported carbon atom (75% higher than glucose). Experimental data was also used to fit the model to phenotypic observations. In addition to the commonly known heterotrophic growth of S. solfataricus, the crenarchaeon is also able to grow autotrophically using the hydroxypropionate-hydroxybutyrate cycle for bicarbonate fixation. We integrated this pathway into our model and compared bicarbonate fixation with growth on glucose as sole carbon source. Finally, we tested the robustness of the metabolism with respect to gene deletions using the method of Minimization of Metabolic Adjustment (MOMA), which predicted that 18% of all possible single gene deletions would be lethal for the organism.

Genome Sequencing of Sulfolobus sp. A20 from Costa Rica and Comparative Analyses of the Putative Pathways of Carbon, Nitrogen, and Sulfur Metabolism in Various Sulfolobus Strains

“…As revealed by the genome analysis of S. solfataricus P2, strain A20 lacks the classical Embden–Meyerhof–Parnas (EMP) and pentose phosphate pathways, since the genes encoding the homologs of the key enzymes in these pathways, i.e., phosphofructokinase in the former and glucose-6-phosphate dehydrogenase, 6-phosphogluconolactonase and 6-phosphogluconate dehydrogenase in the latter, are missing from the genomes (She et al, 2001; Ulas et al, 2012). Like other genome-sequenced Sulfolobus strains, strain A20 may utilize glucose through either the semi-phosphorylative or the non-phosphorylative-Entner-Doudoroff (ED) pathway, or both (Table 3).…”

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

“…This exciting progress allowed the unraveling of protein function in vivo and qualifies Archaea as model organisms for synthetic biology and systems biology (303,397,398). Thus, within the last years, the first genome-wide metabolic models, flux balance analysis (FBA), as well as first detailed reaction kinetic models were established for Archaea (338,(399)(400)(401)(402)(403)(404). These studies also analyzed the responses to different carbon sources and, often performed in combination with biochemical studies, revealed new, exciting, deeper insights into the regulation of metabolic networks at the transcript and protein levels.…”

“…Later, Sul. solfataricus was established as a systems biology organism; a genome-scale model was established; and flux balance analysis (FBA) in response to different carbon sources was performed (303,399).…”

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

“…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]. …”