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.

中文翻译：

---

古细菌的基因组规模代谢建模有助于深入了解代谢功能。

目前正在将数十年的生化，生物信息学和测序数据系统地汇编成基因组规模的代谢重建（GEM）。这样的重建是可用于工程，建模和比较分析的知识库。在这里，我们回顾了迄今已建成的15种古细菌GEM。它们主要代表Euryarchaeota成员，四分之三代表产甲烷菌。与对GEM的其他评论不同，我们特别关注古细菌。我们简要回顾了GEM的构建过程和古细菌模型的家谱。然后，将在构建这些模型期间获得的主要见解进行回顾，并特别关注新颖的代谢途径预测和生长特征。代谢途径的使用在每种生物的生物量组成及其比能和生长需求的背景下进行了讨论。我们展示了如何使用代谢模型研究古细菌中新陈代谢的演变。可以通过使用与它们的酶相关的基因比较反应来研究特定代谢途径的保守性。这证明了GEMs在进化研究中的用途，远远超出了它们对代谢建模的初衷。但是，要使古细菌模型像细菌模型那样广泛地完成，还需要做很多工作。可以通过使用与它们的酶相关的基因比较反应来研究特定代谢途径的保守性。这证明了GEMs在进化研究中的用途，远远超出了它们对代谢建模的初衷。但是，要使古细菌模型像细菌模型那样广泛地完成，还需要做很多工作。可以通过使用与它们的酶相关的基因比较反应来研究特定代谢途径的保守性。这证明了GEMs在进化研究中的用途，远远超出了它们对代谢建模的初衷。但是，要使古细菌模型像细菌模型那样广泛地完成，还需要做很多工作。