Escherichia coli K-12 Transcriptomics for Assessing the Mechanism of Action of High-Power Ultrasound

Abstract

An investigation into the mechanisms of action on bacteria involving exposure to stress factors was conducted in this study. The effects of ultrasound on Escherichia coli K-12 MG1655 and its isogenic mutant, ∆gadW, under high power ultrasound treatments (26 kHz) were screened and identified by analysing their transcriptome differences between primary and secondary sequential treatments using RNA-Seq. This also helped to assess any developed protection for cells between different generations. According to our results, 1825 genes of all tested conditions were expressed, playing different roles in the cell. The expression of these genes is associated with DNA damage, cell membrane integrity, and also metabolic effects. The studied strains also showed different differential expressed genes (DEGs), with some genes being directly responsible for defence mechanisms, while others play an indirect effect due to cell damage. A gradual decrease in the expression of the genes, as we moved from just one cycle of ultrasound treatment to sequential treatment, was evident from a heat map analysis of the results. Overall, E. coli K-12 builds a self-protection mechanism by increasing the expression of genes involved in the respiration for increased growth, and production of flagellum and pili. It can be concluded that high power ultrasound is a technology that triggers several different defence mechanisms which directly link to E. coli.

Keywords: E. coli K-12 mutants; GadW; RNA-Seq; sonochemistry; transcriptomics; ultrasound.

Figure 1

Venn diagrams for the negatively expressed DEGs of E. coli wild type over all treatments (a), E. coli ΔgadW (b) and of positively expressed DEGs of E. coli K-12 wild type (c), E. coli ΔgadW (d). The diagrams show the common DEGs between each treatment, together with the overall percentage. Experiment groups that were non-treated (i.e., pre-treatment of ultrasound) or treated with ultrasound were abbreviated as PT or US, respectively. US2 refers to the sequential ultrasound treatment on the same biological replicate.

Figure 2

Heat map showing the expression and phylogenetic tree of all the genes in relation to pre-treatment (PT), first ultrasound treatment (US), and sequential ultrasound treatment (US2). Legend is found on top of the diagram, where blue denotes down-regulation and red is up-regulation.