An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosa
Year: 2019
Type: article
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.
Source: Nature Communications
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $5,200
Awards: Consensus molecular subtyping of pancreatic ductal adenocarcinoma and tumor-intrinsic regulatory network inference from deconvolved gene expression profiles, G3603521012, G3881707981, G5644275479, 调控丁香假单胞菌致病性的关键双组分系统的信号传导机理研究, Dissecting regulatory mechanisms underlying the poor prognosis colon cancer subtype, 双功能区染料敏化二氧化钛薄膜降解有机物研究, 一个新的蛋白酶系统RhpPC调控III型分泌系统的信号传导途径研究, Multi-omic molecular subtyping of ovarian high-grade serous carcinoma and multidimensional network inference for dissecting the mesenchymal subtype specific regulatory mechanisms
OpenAlex ID: W2953540547