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; Xin Deng

doi:10.1038/s41467-019-10778-w

Author(s)

Xiaolong Shao
Yingchao Zhang

Related Research Unit(s)

Detail(s)

Original language	English
Article number	2931
Journal / Publication	Nature Communications
Volume	10
Online published	3 Jul 2019
Publication status	Published - 2019

Link(s)

DOI	DOI https://doi.org/10.1038/s41467-019-10778-w Final Published version
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Attachment(s)	Documents 33799048.pdf Final Published version, 2.89 MB, PDF Publisher's Copyright Statement This full text is made available under CC-BY 4.0. https://creativecommons.org/licenses/by/4.0/
Link to Scopus	https://www.scopus.com/record/display.uri?eid=2-s2.0-85068379239&origin=recordpage
Permanent Link	https://scholars.cityu.edu.hk/en/publications/publication(fdca36e5-d589-4850-a1e3-fbb778d758e9).html

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.