We have demonstrated that relA transcription is a target
for 6S RNA regulation, as first suggested by an expression
microarray experiment and confirmed by analysis of
promoter–lacZ fusions. Although the changes in relA
mRNA levels are modest, the changes are sufficient to
direct a corresponding change in ppGpp levels. In cells
lacking 6S RNA, maximum ppGpp levels are higher than in
wild-type cells during early stationary phase. However, in
both wild-type and 6S RNA null cells, the timing of initial
ppGpp accumulation appears to be similar, and ppGpp
levels are undetectable in long-term stationary phase
(.24 h). In wild-type cells, ppGpp accumulates when
RelA protein is activated in response to the presence of
uncharged tRNAs in the ribosome, as a signal that amino
acids are limiting. Later, in stationary phase, ppGpp levels
decrease again, in part driven by continued degradation
of ppGpp and a decrease in activation of RelA as the
translational capacity of the cell is reduced in response to
nutrient limitation (see Potrykus & Cashel, 2008). We
propose that 6S RNA does not alter the mechanism of
activation of RelA, nor the signals and molecules involved
in reducing ppGpp levels in later stationary phase. Instead,
6S RNA regulates the transcription of relA, thereby altering
the levels of RelA available to respond to these signals, and
leading to changes in the levels, but not the timing, of
ppGpp accumulation.