title: pH dependence of the stress regulator DksA.
abstract: DksA controls transcription of genes associated with diverse stress responses, such as amino acid and carbon starvation, oxidative stress, and iron starvation. DksA binds within the secondary channel of RNA polymerase, extending its long coiled-coil domain towards the active site. The cellular expression of DksA remains constant due to a negative feedback autoregulation, raising the question of whether DksA activity is directly modulated during stress. Here, we show that Escherichia coli DksA is essential for survival in acidic conditions and that, while its cellular levels do not change significantly, DksA activity and binding to RNA polymerase are increased at lower pH, with a concomitant decrease in its stability. NMR data reveal pH-dependent structural changes centered at the interface of the N and C-terminal regions of DksA. Consistently, we show that a partial deletion of the N-terminal region and substitutions of a histidine 39 residue at the domain interface abolish pH sensitivity in vitro. Together, these data suggest that DksA responds to changes in pH by shifting between alternate conformations, in which competing interactions between the N- and C-terminal regions modify the protein activity.
authors: Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America; The Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America.
authors: Ran
authors: R
authors: Furman
authors: The Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America.
authors: Eric M
authors: EM
authors: Danhart
authors: Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America; The Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America.
authors: Monali
authors: M
authors: NandyMazumdar
authors: Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio, United States of America.
authors: Chunhua
authors: C
authors: Yuan
authors: The Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America.
authors: Mark P
authors: MP
authors: Foster
authors: Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America; The Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America.
authors: Irina
authors: I
authors: Artsimovitch
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D004926:Escherichia coli / Q000378:metabolism / Q000502:physiology*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism*; D006639:Histidine; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D011487:Protein Conformation; D055550:Protein Stability; D013312:Stress, Physiological
chemical_list: D029968:Escherichia coli Proteins; C090751:dksA protein, E coli; D006639:Histidine; D012321:DNA-Directed RNA Polymerases