Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, 999077, China.
Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, Tianjin, 300457, China.
Nat Commun. 2019 Jul 3;10(1):2931. doi: 10.1038/s41467-019-10778-w.
The virulence of Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen, is regulated by many transcriptional factors (TFs) that control the expression of quorum sensing and protein secretion systems. Here, we report a genome-wide, network-based approach to dissect the crosstalk between 20 key virulence-related TFs. Using chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq), as well as RNA-seq, we identify 1200 TF-bound genes and 4775 differentially expressed genes. We experimentally validate 347 of these genes as functional target genes, and describe the regulatory relationships of the 20 TFs with their targets in a network that we call 'Pseudomonas aeruginosa genomic regulatory network' (PAGnet). Analysis of the network led to the identification of novel functions for two TFs (ExsA and GacA) in quorum sensing and nitrogen metabolism. Furthermore, we present an online platform and R package based on PAGnet to facilitate updating and user-customised analyses.
铜绿假单胞菌是一种革兰氏阴性机会性病原体，其毒力受到许多转录因子（TFs）的调控，这些转录因子控制着群体感应和蛋白分泌系统的表达。在这里，我们报告了一种基于基因组范围的网络方法，用于剖析 20 个关键毒力相关 TFs 之间的串扰。我们使用染色质免疫沉淀结合高通量测序（ChIP-seq）以及 RNA-seq，鉴定了 1200 个 TF 结合基因和 4775 个差异表达基因。我们通过实验验证了其中的 347 个基因作为功能靶基因，并在一个我们称之为“铜绿假单胞菌基因组调控网络”（PAGnet）的网络中描述了 20 个 TF 与其靶基因的调控关系。对网络的分析导致确定了两个 TFs（ExsA 和 GacA）在群体感应和氮代谢中的新功能。此外，我们还展示了一个基于 PAGnet 的在线平台和 R 包，以方便更新和用户自定义分析。
