The study of EF4 mediated gene expression under tetracycline stress in two Escherichia coli strains

Purpose: We use the gene expression data to estimate the effects of tetracycline on gene expression and average ribosome density. Methods: The mRNAs were extracted with TRIzol reagent. The mRNAs were fragmented into 280 bp and the sequencing process was conducted on HiSeq 2500 platform. We use cutadapt, bowtie2, Plastid and DEseq2 software to analyze the expression levels of genes in two Escherichia coli strains. Results: The gene expression in EF4 knockout Escherichia coli strain was similar with BW25113 strain under normal condition. Under tetracycline treatment, many genes' expression were differentially regulated. Interestingly, we found that the gene expression of ribosomal proteins was up-regulated in WT strain comparing with EF4 knockout E. coli strain. Conclusions: Our results suggest that EF4 affects the average ribosome density and global gene expression in two Escherichia coli strain under tetracycline treatment. mRNA from WT and ΔEF4 strains and the two strains treated with tetracycline were fragmented and sequenced, in two replicates, using Illumina HiSeq 2500.