Studies on the expression of 6S RNA from E. coli: involvement of regulators important for stress and growth adaptation.
The small bacterial 6S RNA has been recognized as a transcriptional regulator, facilitating the transition from exponential to stationary growth phase by preferentially inhibiting E sigma 70 RNA polymerase holoenzyme transcription. Consistent with this function, the cellular concentration of 6S RNA increases with stationary phase. We have studied the underlying mechanisms responsible for the growth phase-dependent differences in 6S RNA concentration. To this aim, we have analyzed the effects of the typical bacterial growth phase and stress regulators FIS, H-NS, LRP and StpA on 6S RNA expression. Measurements of 6S RNA accumulation in strains deficient in each one of these proteins support their contribution as potential regulators. Specific binding of the four proteins to DNA fragments containing 6S RNA promoters was demonstrated by gel retardation and DNase I footprinting. Moreover, in vitro transcription analysis with both RNA polymerase holoenzymes, E sigma 70 and E sigma 38, demonstrated a direct inhibition of 6S RNA transcription by H-NS, StpA and LRP, while FIS seems to act as a dual regulator. In vitro transcription in the presence of ppGpp indicates that 6S RNA promoters are not stringently regulated. Our results underline that regulation of 6S RNA transcription depends on a complex network, involving a set of bacterial regulators with general importance in the adaptation to changing growth conditions.
Neusser
Thomas
T
Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany.
Gildehaus
Nina
N
Wurm
Reinhild
R
Wagner
Rolf
R
D001483:Base Sequence; D018983:DNA Footprinting; D004268:DNA-Binding Proteins / Q000502:physiology; D012321:DNA-Directed RNA Polymerases / Q000502:physiology*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000502:physiology; D035021:Factor For Inversion Stimulation Protein / Q000502:physiology; D051756:Leucine-Responsive Regulatory Protein / Q000502:physiology; D018832:Molecular Chaperones / Q000502:physiology; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000502:physiology; D012329:RNA, Bacterial / Q000096:biosynthesis*; D022661:RNA, Untranslated; D012808:Sigma Factor / Q000502:physiology*; D014158:Transcription, Genetic / Q000187:drug effects
C411065:6S RNA; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D035021:Factor For Inversion Stimulation Protein; C501034:Fis protein, E coli; C497278:Lrp protein, E coli; D018832:Molecular Chaperones; D012329:RNA, Bacterial; D022661:RNA, Untranslated; D012808:Sigma Factor; C090104:StpA protein, E coli; D051756:Leucine-Responsive Regulatory Protein; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases