Previously, we reported that some of the promoters
examined here (i.e. livJ and hisG) were sensitive to 6S
RNA regulation during late stationary phase (16–24 h of
growth), and at that time it was presumed to be via direct
regulation (Cavanagh et al., 2008). In light of the above
observations that the effects of 6S RNA on these promoters
are likely to be indirect via changes in relA expression (and
ppGpp levels) during early stationary phase (6 h of
growth), we next revisited 6S RNA-dependent changes in
expression of these genes at later time frames. Of note,
previous work had shown that thrA, pheA and rrnBP1 are
not sensitive to 6S RNA in late stationary phase, whereas
livJ and hisG are sensitive, lending support to the
suggestion that there are 6S RNA effects on the
transcription of the first set of genes at later times
independent of those mediated through ppGpp in early
stationary phase. In addition, ppGpp levels are reduced to
background by 24 h of growth, decreasing the likelihood
that it is a major regulator at these later time frames in
stationary phase.