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Core and Panmetabolism in Escherichia coli

机译：大肠杆菌的核心代谢和全代谢

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Escherichia coli exhibits a wide range of lifestyles encompassing commensalism and various pathogenic behaviors which its highly dynamic genome contributes to develop. How environmental and host factors shape the genetic structure of E. coli strains remains, however, largely unknown. Following a previous study of E. coli genomic diversity, we investigated its diversity at the metabolic level by building and analyzing the genome-scale metabolic networks of 29 E. coli strains (8 commensal and 21 pathogenic strains, including 6 Shigella strains). Using a tailor-made reconstruction strategy, we significantly improved the completeness and accuracy of the metabolic networks over default automatic reconstruction processes. Among the 1,545 reactions forming E. coli panmetabolism, 885 reactions were common to all strains. This high proportion of core reactions (57%) was found to be in sharp contrast to the low proportion (13%) of core genes in the E. coli pangenome, suggesting less diversity of metabolic functions compared to that of all gene functions. Core reactions were significantly overrepresented among biosynthetic reactions compared to the more variable degradation processes. Differences between metabolic networks were found to follow E. coli phylogeny rather than pathogenic phenotypes, except for Shigella networks, which were significantly more distant from the others. This suggests that most metabolic changes in non-Shigella strains were not driven by their pathogenic phenotypes. Using a supervised method, we were yet able to identify small sets of reactions related to pathogenicity or commensalism. The quality of our reconstructed networks also makes them reliable bases for building metabolic models.
机译：大肠杆菌表现出广泛的生活方式，包括共生主义和各种病原行为，其高度动态的基因组有助于其发展。环境和宿主因素如何影响 E的遗传结构。然而，大肠杆菌菌株仍然未知。在先前对 E的研究之后。大肠杆菌的基因组多样性，我们通过建立和分析29个 E的基因组规模的代谢网络来研究其在代谢水平上的多样性。大肠埃希菌菌株（共8株共21株致病菌，其中6株志贺氏菌）。使用量身定制的重建策略，与默认的自动重建过程相比，我们显着提高了代谢网络的完整性和准确性。在形成 E的1,545个反应中。大肠杆菌全代谢，所有菌株共有885个反应。发现高比例的核心反应（57％）与 E中低比例的核心基因（13％）形成鲜明对比。大肠基因组研究表明，与所有基因功能相比，代谢功能的多样性较少。与降解过程相比，生物合成反应中的核心反应明显过多。发现代谢网络之间的差异遵循 E。除了志贺氏菌网络之外，大肠埃希菌系统发育而不是致病表型。这表明非志贺氏菌菌株的大多数代谢变化不是由其致病表型驱动的。使用一种有监督的方法，我们仍然能够识别出与致病性或共鸣有关的少量反应。我们重建网络的质量也使它们成为建立代谢模型的可靠基础。

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