Project description:To further characterize the organization of the transcriptional units and the global behaviour of the genomic island ICEclc in Pseudomonas knackmussii, we have employed Agilent DNA custom microarray in the 8X15K format.
Project description:To support our molecular hypothesis of the effect of rpoS and inrR genes over the activation of the ICEclc genome in Pseudomonas knackmussii B13, we have employed Agilent DNA custom microarray in the 8X15K format. ICEclc-specific gene expression in Pseudomonas knackmussii strain B13 was measured after 48 hours of stationary phase following a growth on 10mM 3-chlorobenzoate (3CBA) as sole carbon and energy source. Various genotypes were tested: wild type (strain nM-BM-078, in 5 replicates), inrR-/- (strain 2201, in triplicates), delta::rpoS (strain 2671, in triplicates).
Project description:To support our molecular hypothesis of the effect of rpoS and inrR genes over the activation of the ICEclc genome in Pseudomonas knackmussii B13, we have employed Agilent DNA custom microarray in the 8X15K format.
Project description:Pseudomonas aeruginosa is an opportunistic pathogen which causes acute and chronic infections that are difficult to treat. Comparative genomic analysis has showed a great genome diversity among P. aeruginosa clinical strains and revealed important regulatory traits during chronic adaptation. While current investigation of epigenetics of P. aeruginosa is still lacking, understanding the epigenetic regulation may provide biomarkers for diagnosis and reveal important regulatory mechanisms. The present study focused on characterization of DNA methyltransferases (MTases) in a chronically adapted P. aeruginosa clinical strain TBCF10839. Single-molecule real-time sequencing (SMRT-seq) was used to characterize the methylome of TBCF. RCCANNNNNNNTGAR and TRGANNNNNNTGC were identified as target motifs of DNA MTases, M.PaeTBCFI and M.PaeTBCFII, respectively.
Project description:Purpose of study was to investigate whole genome expression changes of a strain with deletion of the two-component system TctD-TctE and determine genes dysregulate relative to the parental wildtype to gain insight into possible regulatory targets of TctD-TctE. TctD-TctE is a two-component system in Pseudomonas aeruginosa that responds to and regulates uptake of tricarboxylic acids such as citric acid. It accomplishes this through derepression of the porin encoding the gene opdH, thereby regulating influx of citrate metabolites from the surrounding environment. Deletion of the tctED operon (ΔtctED) resulted in a reduced growth phenotype when citric acid is present in media. In the ΔtctED strain the presence of citric acid was found to have an inhibitory effect on growth. When the alternative carbon source arginine was present, wildtype levels of growth could not be restored. Static cultures of ΔtctED had low cell density in the presence of citric acid but maintained the same levels of biofilm formation compared to conditions when no citric acid was present. This suggests a dysregulation of biofilm formation in the presence of citric acid. In the ΔtctED strain there was also greater accumulation of tobramycin within the biofilm compared to the PA14 wildtype strain. Additionally, analysis of whole-genome expression found that multiple metabolic genes were dysregulated in ΔtctED. Here it is concluded that TctD-TctE is involved in biofilm tolerance to tobramycin in the presence of citrate metabolites.
