Norsigian Charles J, Kavvas Erol, Seif Yara, Palsson Bernhard O, Monk Jonathan M
Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.
Front Genet. 2018 Apr 10;9:121. doi: 10.3389/fgene.2018.00121. eCollection 2018.
has become an urgent clinical threat due to the recent emergence of multi-drug resistant strains. There is thus a significant need to discover new therapeutic targets in this organism. One means for doing so is through the use of high-quality genome-scale reconstructions. Well-curated and accurate genome-scale models (GEMs) of would be useful for improving treatment options. We present an updated and improved genome-scale reconstruction of AYE, named iCN718, that improves and standardizes previous AYE reconstructions. iCN718 has 80% accuracy for predicting gene essentiality data and additionally can predict large-scale phenotypic data with as much as 89% accuracy, a new capability for an reconstruction. We further demonstrate that iCN718 can be used to analyze conserved metabolic functions in the A. baumannii core genome and to build strain-specific GEMs of 74 other strains from genome sequence alone. iCN718 will serve as a resource to integrate and synthesize new experimental data being generated for this urgent threat pathogen.
由于最近出现的多重耐药菌株，这已成为一个紧迫的临床威胁。因此，迫切需要在这种生物体中发现新的治疗靶点。一种实现此目的的方法是使用高质量的基因组规模重建。精心策划且准确的该生物体基因组规模模型（GEMs）将有助于改善治疗方案。我们展示了一个更新且改进的鲍曼不动杆菌AYE基因组规模重建，命名为iCN718，它改进并规范了先前的AYE重建。iCN718在预测基因必需性数据方面具有80%的准确率，此外还能以高达89%的准确率预测大规模表型数据，这是鲍曼不动杆菌重建的一项新能力。我们进一步证明，iCN718可用于分析鲍曼不动杆菌核心基因组中的保守代谢功能，并仅根据基因组序列构建其他74株鲍曼不动杆菌菌株的菌株特异性GEMs。iCN718将作为一种资源，用于整合和综合针对这种紧迫威胁病原体正在产生的新实验数据。
