Hfq modulates the σE-mediated envelope stress response and the σ32-mediated cytoplasmic stress response in Escherichia coli

Hfq, a chaperone for small noncoding RNAs, regulates many processes in Escherichia coli, including the alpha(S)-smediated 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 alpha(E)- and alpha(32)-mediated stress responses, which we analyze further. We show that cells lacking Hfq induce the alpha(E)-mediated envelope stress response and are defective in alpha(E)-mediated repression of outer membrane proteins. We also show that the alpha(32)-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 alpha(32) to chronic chaperone overexpression. Together, our results indicate that Hfq may play a general role in stress response regulation in E. coli.