Here, we demonstrate that 6S RNA regulates the expression
of relA, which leads to changes in ppGpp levels during early
stationary phase, and thus adds another layer of regulation
to the complex network of responses that occur as cells
transition to less favourable growth conditions. We show
that 6S RNA-dependent changes in ppGpp levels during
early stationary phase (i.e. 6 h of growth) are sufficient to
lead to changes in the transcription of target genes such as
those involved in amino acid biosynthesis and rRNA.
Therefore, 6S RNA regulates transcription during this time
frame in spite of being at subsaturating levels for binding to
s70-RNAP. We also demonstrate that 6S RNA-dependent
changes in transcription in late stationary phase (.24 h)
are independent of ppGpp, thus revealing the diversity of
mechanisms for 6S RNA-dependent regulation of gene
expression during different times of cell growth and
survival.