PA3027, a novel AraC-type transcriptional regulator activating genes of glycerolipid metabolism in Pseudomonas aeruginosa (PA3027 overexpression RNA-seq)

Pseudomonas aeruginosa encodes a large set of transcriptional regulators which allow to modulate and manage cellular metabolism to survive in variable environmental conditions, including the human body. The AraC family regulators are an abundant group of transcriptional regulators in bacteria, mostly acting as gene expression activators controlling diverse cellular functions e.g. carbon metabolism, stress response and virulence. PA3027 protein from P. aeruginosa has been classified in silico as a putative AraC-type transcriptional regulator. Comparative transcriptome analysis of P. aeruginosa PAO1161 overexpressing PA3027 versus empty vector control revealed a spectacular over 15-fold up-regulation of expression of pa3026-pa3024, PA3464 and PA3342 genes potentially involved in glycerolipid metabolism. Concomitantly, the ChIP-seq analysis using FLAG-PA3027 under mild overproduction conditions revealed at least 22 PA3027 binding sites in the PAO1161 genome, including promoter regions of genes showing a major increase in expression in response to PA3027 excess. The presented data showed that PA3027 acts as the transcriptional regulator in P. aeruginosa activating genes engaged in glycerolipid metabolism. Pseudomonas aeruginosa PAO1161 (leu-, r-, RifR) derivative of PAO1 was used in the experiment (Kawalek et al., 2020; BMC Genomics, 21:14). To determine the impact of an increased PA3027 level on the transcriptome the RNA-seq analysis was performed on RNA isolated from Pseudomonas aeruginosa PAO1161/ pKKB1.11 (lacIQ-tacp-PA3027) (hereafter referred to as PA3027) as well as from P. aeruginosa PAO1161 carrying pAMB9.37 (lacIQ-tacp) cells (empty vector control, hereafter called EV). Cells were grown under selection in L broth with 0.05 mM IPTG till reached the exponential phase of growth (OD600 0.5).The RNA was isolated from exponentially growing cultures (OD600 0.5). Three independent biological replicates of total RNA were isolated for each strain.