Functional characterization of TetR-like transcriptional regulator PA3973 from Pseudomonas aeruginosa [RNA-seq]

Pseudomonas aeruginosa, a human opportunistic pathogen, is a common cause of nosocomial infections. Its ability to survive under different conditions relies on a complex regulatory network engaging transcriptional regulators controlling metabolic pathways and capabilities to efficiently use the available resources. P. aeruginosa PA3973 encodes a putative TetR family transcriptional regulator, with a helix-turn-helix motif involved in DNA binding. We applied transcriptome profiling (RNA-seq), and genome-wide identification of binding sites using ChIP-seq to unravel the biological role of PA3973. Overall design: Pseudomonas aeruginosa PAO1161 (leu-, r-, RifR) derivative of PAO1 was used in the experiment (Kawalek et al., 2020), as a control (reference) strain and Pseudomonas aeruginosa PAO1161 PA3973 deletion strain. To determine the impact of an increased PA3973 level on the transcriptome the RNA-seq analysis was performed on RNA isolated from Pseudomonas aeruginosa PAO1161/pKKB3.11 (lacIQ-tacp-PA3973) cultures grown under selection in L broth with 0.05 mM IPTG (hereafter referred to as PA3973+) as well as from Pseudomonas aeruginosa PAO1161 carrying pAMB9.37 (lacIQ-tacp) cells grown under selection with addition of 0.05 mM IPTG (empty vector control, hereafter called EV).Three independent biological replicates of total RNA were isolated for each strain from logarithmic (OD600 0.5) phase of planktonic culture grown on rich medium (L broth) at 37oC.