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Taming feral promoters: comprehending their
complexity
Although most mechanistic studies of bacterial
transcription have focused on simple situations in which
a single transcription factor can activate or repress a
promoter, they likely do not provide a true reflection
of nature. Instead, the regulatory regions of many
bacterial genes are considerably more complex, including
multiple promoters and/or multiple binding sites for
multiple transcription factors. Furthermore, these
regulatory regions are bound by nucleoid proteins that
fold the genome into the highly compacted nucleoid.
As part of our attempt to understand how multiple RNA
polymerases, transcription factors, and nucleoid
proteins interact to ensure proper regulation, we have
been dissecting the extremely complex regulatory region
of acs, which encodes acetyl-CoA synthetase. This
high-affinity central metabolic enzyme provides the cell
with acetyl-CoA during periods of starvation.
The complex regulatory region that drives the
transcription of this key metabolic gene includes 3
promoters, 5 DNA sites for 3 distinct transcription
factors, and 7 DNA sites for 2 different nucleoid
proteins - all in less than 300-bp. Furthermore, this
region sits back-to-back and overlaps extensively with
the regulatory region that drives transcription of the
completely unrelated nrf operon. Using genetic
and biochemical approaches, we and our collaborators
(Drs. Douglas Browning and Stephen Busby of the
University of Birmingham (UK); Drs. Bianca Sclavi
and
Malcolm Buckle of the Ecole Normale Supérieure de
Cachan (Fra)) have dissected this complex regulatory
region, learning how the same DNA sequence can
independently regulate two divergent operons under
completely different environmental conditions, how
activation of transcription can co-depend upon two or
more activators, and how two different nucleoid proteins
can each inhibit transcription using two distinct and
independent mechanisms. Many of the lessons we have
learned appear to be universal.
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