title: Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function.
abstract: Decades of biochemical, bioinformatic, and sequencing data are currently being systematically compiled into genome-scale metabolic reconstructions (GEMs). Such reconstructions are knowledge-bases useful for engineering, modeling, and comparative analysis. Here we review the fifteen GEMs of archaeal species that have been constructed to date. They represent primarily members of the Euryarchaeota with three-quarters comprising representative of methanogens. Unlike other reviews on GEMs, we specially focus on archaea. We briefly review the GEM construction process and the genealogy of the archaeal models. The major insights gained during the construction of these models are then reviewed with specific focus on novel metabolic pathway predictions and growth characteristics. Metabolic pathway usage is discussed in the context of the composition of each organism's biomass and their specific energy and growth requirements. We show how the metabolic models can be used to study the evolution of metabolism in archaea. Conservation of particular metabolic pathways can be studied by comparing reactions using the genes associated with their enzymes. This demonstrates the utility of GEMs to evolutionary studies, far beyond their original purpose of metabolic modeling; however, much needs to be done before archaeal models are as extensively complete as those for bacteria.
authors.affiliation: Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
authors.forename: ShengShee
authors.identifier: 0000-0001-6927-4323
authors.initials: S
authors.lastname: Thor
authors.affiliation: Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
authors.forename: Joseph R
authors.identifier: 0000-0003-0989-5288
authors.initials: JR
authors.lastname: Peterson
authors.affiliation: Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, 1206 W Gregory Dr., Urbana, IL 61801, USA.
authors.forename: Zaida
authors.identifier: 0000-0001-9749-8367
authors.initials: Z
authors.lastname: Luthey-Schulten
mesh_terms: D019295:Computational Biology; D019605:Euryarchaeota / Q000378:metabolism*; D053858:Metabolic Networks and Pathways; D008954:Models, Biological