title: Hfq modulates the sigmaE-mediated envelope stress response and the sigma32-mediated cytoplasmic stress response in Escherichia coli.
abstract: Hfq, a chaperone for small noncoding RNAs, regulates many processes in Escherichia coli, including the sigma(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 sigma(E)- and sigma(32)-mediated stress responses, which we analyze further. We show that cells lacking Hfq induce the sigma(E)-mediated envelope stress response and are defective in sigma(E)-mediated repression of outer membrane proteins. We also show that the sigma(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 sigma(32) to chronic chaperone overexpression. Together, our results indicate that Hfq may play a general role in stress response regulation in E. coli.
authors.affiliation: Department of Biochemistry, University of California at San Francisco, San Francisco, CA 94158, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Guisbert
authors.forename: Virgil A
authors.initials: VA
authors.lastname: Rhodius
authors.forename: Nidhi
authors.initials: N
authors.lastname: Ahuja
authors.forename: Emily
authors.initials: E
authors.lastname: Witkin
authors.forename: Carol A
authors.initials: CA
authors.lastname: Gross
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D001425:Bacterial Outer Membrane Proteins / Q000235:genetics; D002462:Cell Membrane / Q000378:metabolism*; D018834:Chaperonin 60 / Q000502:physiology; D003593:Cytoplasm / Q000378:metabolism*; D004734:Energy Metabolism; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000502:physiology*; D006360:Heat-Shock Proteins / Q000502:physiology*; D035001:Host Factor 1 Protein / Q000502:physiology*; D012333:RNA, Messenger / Q000032:analysis; D012808:Sigma Factor / Q000502:physiology*; D014157:Transcription Factors / Q000502:physiology*
chemical_list: D000596:Amino Acids; D001425:Bacterial Outer Membrane Proteins; D018834:Chaperonin 60; D029968:Escherichia coli Proteins; D006360:Heat-Shock Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D012333:RNA, Messenger; D012808:Sigma Factor; D014157:Transcription Factors; C069774:heat-shock sigma factor 32; C063202:sporulation-specific sigma factors