To compare the transcriptome of ompR null strains with wild-type strain of E. coli during acid or osmotic stress

In bacteria, one paradigm for signal transduction is the two-component regulatory system, consisting of a sensor kinase (usually a membrane protein) and a response regulator (usually a membrane protein) and a response regulator (usually a DNA binding protein). The EnvZ/OmpR two-component system in E. coli responds to osmotic stress and regulates expression of outer membrane proteins. Furthermore, bacteria were believed to regulate pH by acidifying after external acid stress, then immediately recovering. Using a pH-sensor in single living cells, we show that E. coli maintain an acidic cytoplasm. The osmotic stress transcription factor OmpR, was required. Thus, we set out to identify the OmpR targets under acid and osmotic stress. To identify OmpR targets under acid and osmotic stress conditions, we performed a microarray and compared the transcriptome of ompR null strains with wild-type strains of E. coli during acid or osmotic stress. E. coli strain was grown in MgM media at pH 5.6, 7.2 and 7.2 with 15% (w/v) sucrose to O.D ~0.6. The total RNA was isolated using an RNeasy mini kit (Qiagen) and proceeded for Microarray