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

Eric Guisbert ,^1,, Virgil A. Rhodius,^2, Nidhi Ahuja,² Emily Witkin,² and Carol A. Gross^2,3*

Departments of Biochemistry and Biophysics,¹ Microbiology and Immunology,² Cell and Tissue Biology, University of California, San Francisco, California³

Received 8 August 2006/ Accepted 1 December 2006

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

Published ahead of print on 8 December 2006.

Supplemental material for this article may be found at http://jb.asm.org/.

E.G. and V.A.R. contributed equally to this study.

Present address: Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Chicago, Ill.

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