Tran Jennifer Suzanne, Ward Ryan David, Iruegas-López Rubén, Ebersberger Ingo, Peters Jason Matthew
Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
PLoS Genet. 2025 Mar 28;21(3):e1011642. doi: 10.1371/journal.pgen.1011642. eCollection 2025 Mar.
The Gram-negative pathogen, Acinetobacter baumannii, poses a serious threat to human health due to its role in nosocomial infections that are resistant to treatment with current antibiotics. Despite this, our understanding of fundamental A. baumannii biology remains limited, as many essential genes have not been experimentally characterized. These essential genes are critical for bacterial survival and, thus, represent promising targets for drug discovery. Here, we systematically probe the function of essential genes by screening a CRISPR interference knockdown library against a diverse panel of chemical inhibitors, including antibiotics. We find that most essential genes show chemical-gene interactions, allowing insights into both inhibitor and gene function. For instance, knockdown of lipooligosaccharide (LOS) transport genes increased sensitivity to a broad range of chemicals. Cells with defective LOS transport showed cell envelope hyper-permeability that was dependent on continued LOS synthesis. Using phenotypes across our chemical-gene interaction dataset, we constructed an essential gene network linking poorly understood genes to well-characterized genes in cell division and other processes. Finally, our phenotype-structure analysis identified structurally related antibiotics with distinct cellular impacts and suggested potential targets for underexplored inhibitors. This study advances our understanding of essential gene and inhibitor function, providing a valuable resource for mechanistic studies, therapeutic strategies, and future key targets for antibiotic development.
革兰氏阴性病原体鲍曼不动杆菌对人类健康构成严重威胁，因为它在医院感染中发挥作用，且对目前的抗生素治疗具有耐药性。尽管如此，我们对鲍曼不动杆菌基本生物学的了解仍然有限，因为许多必需基因尚未经过实验表征。这些必需基因对细菌的生存至关重要，因此是有前景的药物发现靶点。在这里，我们通过针对包括抗生素在内的多种化学抑制剂筛选CRISPR干扰敲低文库，系统地探究必需基因的功能。我们发现大多数必需基因显示出化学-基因相互作用，从而能够深入了解抑制剂和基因的功能。例如，脂寡糖（LOS）转运基因的敲低增加了对多种化学物质的敏感性。LOS转运缺陷的细胞表现出细胞包膜超通透性，这依赖于持续的LOS合成。利用我们化学-基因相互作用数据集中的表型，我们构建了一个必需基因网络，将了解较少的基因与细胞分裂及其他过程中特征明确的基因联系起来。最后，我们的表型-结构分析确定了具有不同细胞影响的结构相关抗生素，并提出了未充分探索的抑制剂的潜在靶点。这项研究增进了我们对必需基因和抑制剂功能的理解，为机制研究、治疗策略以及抗生素开发的未来关键靶点提供了宝贵资源。
