Modern transcriptomics is focused on probe – independent RNA sequencing (RNA-seq). Newest approaches enables simultaneous analysis of gene expression of host and pathogen. Concentration of 3mM of H2O2 used in this study works as an inducing agent for prophages, as presented previously, causing DNA damage and SOS response.
Presented study focused on transcriptomics of strains Escherichia coli MG1655 (NC_000913.3) and MG1655(933WΔtox) both grown in normal and stress conditions caused by H2O2. Total RNA was isolated from the samples collected in time 0 (OD600~0,1), after 1 and after 3 hours of experiment and send for RNA sequencing. Results of sequencing from particular samples were compared to visualize Differentially Expressed Gens (DEGs). In MG1655 strain in control experiment 14 different genes involved in response to stress were downregulated and 46 upregulated. During growth upon stress 12 different genes were downregulated and 48 upregulated. However these DEGS were not the same in both experiments. When strain MG1655(933WΔtox) was studied in normal conditions 32 different genes were downregulated and 42 upregulated. During prophage induction with H2O2 41 different genes were downregulated and 43 upregulated. When DEGs of both strains were compared 45 common genes were differentially expressed. Most interesting DEGs were cspC, cspG, ibpA, ibpB, dnaK, grpE, pspA, proX, dps, spy, yggE and ygiW. They are involved in response to temperature stimulus, heat shock, phage heat shock, response to osmotic stress, response to stress and resistance to peroxide. Expression of dnaK was downregulated at the beginning of induction of prophage and upregulated at the end in comparison to sample in time 0. Moreover expression of proX was changed during time of the induction from downregulation after 3h in comparison to 1h to upregulation after 3h in comparison to time 0. Level of expression of other genes differs either between strains or conditions of the experiment.

.