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Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function 时间:2017-09-06 16:16 来源:未知作者:admin 点击: 次 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.
1. Introduction
Since their discovery and classification in the late 1970s and early 1980s [1–5] archaea have garnered considerable interest, due in part to prevailing thoughts at the time that they lived primarily in extreme conditions, a property that results in unique cell physiology and metabolic characteristics [6]. Although the original classification of organisms was based on only thirteen sequences with only four representatives of archaea [2], the proposal of the three domains of life has been tested time and time again [6–10] and holds up well. Archaea have now been found to reside in essentially every terrestrial environment, and the unique natural capability of methane production among certain archaeal groups makes this domain of life remarkably novel.
Despite the significant progress in sequencing archaeal genomes, a systematic understanding of the metabolism of archaea is still lacking. This is especially true for peripheral metabolic pathways and mechanisms of adaptation to extreme environments [11]. It has often been noted that the environmental niches dominated by archaea constitute extremely stressful or even fatal homes for their bacterial cousins; thus, they have evolved unique coping mechanisms and optimized their metabolisms to salvage the energy that would otherwise be left unused in the environment. It has been proposed that adaptation to energy stress could be the primary factor driving the evolution of archaea [12]. The consequence would be that they have evolved specialized tolerance and metabolic capabilities unique to their environments which make them relatively inflexible to adaptation like their bacterial counterparts. It has been proposed that this inflexibility possibly results in tighter phylogenetic groups that directly represent less metabolic diversity [12]. Indeed, the evidence seems to support this hypothesis as only 89 genera of archaea have been identified in contrast to the over 1,400 bacterial genera. This fact should be exploitable by systems biology researchers as it means that information gained by one member of a taxon can largely be extended to other related members of the taxa.
For this reason, systematic databases of the metabolic properties of the archaea are highly desirable; the field of systems biology is uniquely positioned to provide useful insight into the diversity and evolution of metabolic capabilities. To date, fifteen genome-scale metabolic models (GEMs; one of the main products of systems biology research) have been constructed for ten archaeal species. However, these models represent primarily members of the Euryarchaeota with almost three-quarters representatives of methanogens. An examination of the phylogenetic tree demonstrates a lack of well-curated metabolic reconstructions in many of the archaeal taxa (see Figure 1).