Lecture 14 1
Reg. Networks are interlinked control systems; some are complex)
Not just 1 or 2 regulators affecting a single gene or
operon, but many transcripts.
Should NOT be understood as independent control circuits,
but rather a global network, affecting many different genes
- often unrelated genes
Definitions – steps of increasing complexity
Operons > Regulons > Modulons/Stimulons
Operon – a number of genes (often related in function) encoded
as a transcriptional unit AND transcriptionally co-regulated.
Typical of prokaryotes (polycistronic arrangement)
e.g. metabolic pathways (galETK, araBAD, lacZYA)
Regulon – organization of several independent operons,
controlled in a coordinated way. All share a common
Does not mean genes are always expressed in a parallel
manner (1. extent of reg varies AND 2. activation of one
operon/gene can be concurrent with repression of others
by same regulator. e.g. heat shock; SOS; Lrp) Lecture 14 2
Modulon – describes independent operons that belong to
different regulons but respond to a common regulator. A
regulatory level above a regulon. More global reg units.
e.g. metabolic genes encoding catabolic enzymes
regulated by CRP-cAMP. Regulated by regulator.
Stimulon – describes a collection of genes that respond to
a common stimulus independent of their regulatory
organization. Related by operation.
e.g. Heat Shock causes σH regulon induction. Lots of
other unrelated genes NOT under control of this σ factor
will be up- or down-regulated (activated or repressed), all
by different types of regulators but all responding to the
Can be studied using chip-on-chip. Chip has all the
transcripts of a certain bacteria. Probe with RNA extract of
your bacteria (same species as chip is for) under certain
conditions and see which genes are being activated. Can
chop up DNA, immunoprobe for your regulator. Take the
regulator + DNA regulator is bound to. Can then remove
protein and probe DNA on chip to see which genes the
regulator is controlling.
SOS Response: a regulon under control of LexA. Radman ‘74
One of the first clear networks of Tn regulation identified in
bacteria. Lecture 14 3
Straightforward logic; sophisticated circuitry; helps the cell
finely tune response. Lecture 14 4
Comprises a set of coordinated physiological responses
induced by DNA damage.
It induces > 20 different genes involved in different
mechanisms of DNA repair.
1. mismatch 2. recombinational 3. excision / error-prone
SOS expression involves 2 proteins, LexA and RecA
I. LexA – a typical Tn repressor – MW = 22.7 kDa
Each protein has 2 domains connected by a flexible hinge.
A. N terminal domain = AAs 1-84 = DNA-binding region
different but structurally related to a HTH.
B. C terminal domain = dimerization domain.
Proteins link together at C terminus to form a dimer.
A palindromic operator sequence (termed the SOS box) is
recognized by the dimeric repressor.
SOS box operons are found upstream of all genes in the SOS regulon.
Sometimes more than one operator can be found there
Operator positions relative to the promoters are variable:
e.g. uvrA – SOS box overlaps –35 hexamer Lecture 14 5
- uvrB or recA – SOS box located between –35 & -10
- sulA – overlaps –10
- uvrD – downstream of –10 promoter sequence
1. Different operator positions may indicate genes are not
regulated to the same extent.
2. Differences in SOS box sequences different affinities
for LexA dimer.
Both of these lead to
fine tuning the
Most SOS regulated
genes are expressed
at a low basal level in
the uninduced cell,
II. RecA. 37.8 kDa.
protein in cell
(also important in
For SOS, RecA
induction of genes
repressed by LexA. Lecture 14 6
In other words, LexA repression is relieved by proteolytic
cleavage of the LexA repressor proteins.
BUT, RecA is not a classical protease. Instead it facilitates
a latent capacity of LexA to AUTODIGEST
LexA cleavage leading to 2 fragments of similar size.
In the absence of DNA damage, LexA is perfectly stable;
even though normally there are 7000 copies of RecA / cell
When RecA senses DNA damage as a signal (& this is most
probably ssDNA regions resulting from various forms of DNA damage),
RecA stimulates LexA cleavage.
RecA is activated by single stranded DNA.
The RecA/ssDNA nucleoprotein filament is generated
when cell initially attempts to replicate damaged DNA.
RecA binding ssDNA results in activated RecA designated RecA*.
To mediate LexA cleavage, RecA* requires ATP, though
ATP hydrolysis to ADP is not requires for cleavage of
LexA by LexA. (binding of RecA to DNA???)
Activation of RecA is reversible & prevails as long as
inducing signal (ssDNA) is abund