Comparison of the Pseudomonas aeruginosa PA2504 deficient strain and the PAO1161 wild type strain

Pseudomonas aeruginosa is an ubiquitous gram-negative bacterium that may colonize a wide range of organisms, including bacteria, plants, and animals. It is a human opportunistic pathogen which shows a great threat to immunocompromised patients. P. aeruginosa displays intrinsic resistance to many antibiotics, and has a high ability to develop novel mechanisms of resistance which forms a threat in hospital environments and makes it extremely hard to eradicate. Additionally over half of the genes of this bacteria have no described function, so it is urgent to search for proteins related to its pathogenicity and antibiotic resistance. The aim of this study was to characterise the P. aeruginosa PA2504 protein of unknown function. Basic phenotypic analysis did not indicate the role of PA2504 in the cell, thus, in order to recognize transcripts affected by the lack of PA2504 transcriptomes of the ?PA2504 and the wild-type PAO1161 strains were compared using high-throughput RNA sequencing (RNA-seq). Using qRT-PCR method we determined that the level of PA2504 transcript is higher in the stationary phase of growth as compared to the exponential phase of bacterial growth (Log2 FC = 2,77) thus the samples for the RNA-seq experiments were withdrawn from this phase of growth.The RNA-seq revealed that the expression of 42 transcripts was changed in the ?PA2504 mutant as compared to the parental PAO1161 strain and that the majority of them were connected to the sulphur transport/metabolism. Overall design: 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 effect of the lack of the PA2504 protein on the transcriptome, the RNA-seq analysis was performed on RNA isolated from Pseudomonas aeruginosa PAO1161 wild type strain control (later referred to as PAO1161) and the PAO1161 ?PA2504 strain (later reffered to as PA2504). The strains where grown in the L-broth rich medium in 37°C with shaking. The samples for the RNA extraction were withdrawn from the stationary phase of bacterial growth, after 18 h. Three independent biological replicates of total RNA were isolated for each strain.