M. Krohn et R. Wagner, TRANSCRIPTIONAL PAUSING OF RNA-POLYMERASE IN THE PRESENCE OF GUANOSINE TETRAPHOSPHATE DEPENDS ON THE PROMOTER AND GENE SEQUENCE, The Journal of biological chemistry, 271(39), 1996, pp. 23884-23894
We have studied the response of the effector molecule guanosine 3',5'-
bisdiphosphate (ppGpp) on RNA polymerase pausing during in vitro trans
cription elongation. Pausing was followed during single round extensio
n of stalled ternary complexes excluding possible ppGpp effects on ini
tiation. The ppGpp dependences of early pausing sites within different
transcription systems controlled by promoters with known response to
enhanced ppGpp levels in vivo were quantitatively characterized. Trans
cription of stable RNAs and mRNA genes were analyzed. In addition, the
in vitro pausing behavior of two promoter variants directing the same
sequence but differing in their in vivo ppGpp sensitivity were compar
ed. In the presence of ppGpp we noted a slight general enhancement of
specific pauses in all transcription systems. However, genes known to
be un der stringent or growth rate control in vivo revealed a notably
stronger pausing enhancement. The sites of pausing are not changed by
the presence of ppGpp but appear to be sequence-specific. The effect o
f ppGpp on the extent of pausing depends on the particular promoter an
d closely adjacent sequences that the RNA polymerase has passed during
initiation. Pausing enhancement requires the presence of ppGpp during
elongation but not during initiation. The results underline the impor
tance of pausing for transcription regulation and offer a plausible ex
planation for inhibition of stable RNA expression under conditions of
elevated concentrations of ppGpp.