Hfq Modulates the σ E -Mediated Envelope Stress Response and the σ 32 -Mediated Cytoplasmic Stress Response in Escherichia coli

Abstract

Hfq, a chaperone for small noncoding RNAs, regulates many processes in Escherichia coli, including the σ^S-mediated general stress response. Here we used microarray analysis to identify the changes in gene expression resulting from lack of Hfq. We identify several potential new targets for Hfq regulation, including genes encoding outer membrane proteins, enzymes, factors, and transporters. Many of these genes are involved in amino acid uptake and biosynthesis, sugar uptake and metabolism, and cell energetics. In addition, we find altered regulation of the σ^E- and σ³²-mediated stress responses, which we analyze further. We show that cells lacking Hfq induce the σ^E-mediated envelope stress response and are defective in σ^E-mediated repression of outer membrane proteins. We also show that the σ³²-mediated cytoplasmic stress response is repressed in cells lacking Hfq due to increased expression of DnaK. Furthermore, we show that cells lacking Hfq are defective in the “long-term adaptation” of σ³² to chronic chaperone overexpression. Together, our results indicate that Hfq may play a general role in stress response regulation in E. coli.