Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan S4S 0A2, Canada.
Nucleic Acids Res. 2018 Oct 12;46(18):9684-9698. doi: 10.1093/nar/gky603.
We present the first high-resolution determination of transcriptome architecture in the priority pathogen Acinetobacter baumannii. Pooled RNA from 16 laboratory conditions was used for differential RNA-seq (dRNA-seq) to identify 3731 transcriptional start sites (TSS) and 110 small RNAs, including the first identification in A. baumannii of sRNAs encoded at the 3' end of coding genes. Most sRNAs were conserved among sequenced A. baumannii genomes, but were only weakly conserved or absent in other Acinetobacter species. Single nucleotide mapping of TSS enabled prediction of -10 and -35 RNA polymerase binding sites and revealed an unprecedented base preference at position +2 that hints at an unrecognized transcriptional regulatory mechanism. To apply functional genomics to the problem of antimicrobial resistance, we dissected the transcriptional regulation of the drug efflux pump responsible for chloramphenicol resistance, craA. The two craA promoters were both down-regulated >1000-fold when cells were shifted to nutrient limited medium. This conditional down-regulation of craA expression renders cells sensitive to chloramphenicol, a highly effective antibiotic for the treatment of multidrug resistant infections. An online interface that facilitates open data access and visualization is provided as 'AcinetoCom' (http://bioinf.gen.tcd.ie/acinetocom/).
我们首次对重要病原体鲍曼不动杆菌的转录组结构进行了高分辨率测定。将 16 种实验室条件下的混合 RNA 用于差异 RNA-seq（dRNA-seq），以鉴定 3731 个转录起始位点（TSS）和 110 个小 RNA，其中包括首次在鲍曼不动杆菌中鉴定出编码基因 3'端编码的 sRNA。大多数 sRNA 在测序的鲍曼不动杆菌基因组中是保守的，但在其他不动杆菌种中保守性较弱或不存在。TSS 的单核苷酸映射能够预测 -10 和 -35 RNA 聚合酶结合位点，并揭示了在位置 +2 处前所未有的碱基偏好，这暗示了一种未被识别的转录调控机制。为了将功能基因组学应用于抗菌药物耐药性问题，我们剖析了负责氯霉素耐药性的药物外排泵的转录调控，即 craA。当细胞转移到营养有限的培养基中时，两个 craA 启动子的表达均被下调了 >1000 倍。这种 craA 表达的条件下调使细胞对氯霉素敏感，氯霉素是治疗多药耐药感染的一种非常有效的抗生素。提供了一个在线界面，便于开放数据访问和可视化，称为“AcinetoCom”（http://bioinf.gen.tcd.ie/acinetocom/）。
