An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosa

Hao Huang, Xiaolong Shao, Yingpeng Xie, Tingting Wang, Yingchao Zhang, Xin Wang () and Xin Deng ()
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Hao Huang: City University of Hong Kong
Xiaolong Shao: Nankai University
Yingpeng Xie: City University of Hong Kong
Tingting Wang: City University of Hong Kong
Yingchao Zhang: Nankai University
Xin Wang: City University of Hong Kong
Xin Deng: City University of Hong Kong

Nature Communications, 2019, vol. 10, issue 1, 1-13

Abstract: Abstract 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.

Date: 2019
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DOI: 10.1038/s41467-019-10778-w

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