A genetic switch with memory:
the lysis/lysogeny switch in
phage 
AMATH 882
Lecture 11, Feb. 12, 2013
Reference: A Genetic Switch, by Mark Ptashne
As an example of a genetic switch which can be
triggered by a transient stimulus, we consider the
case of phage .
Phage  is a bacteriophage -- a virus which infects
E. coli.
Phage Lambda: structure and infection
http://de.wikipedia.org/wiki/Bild:T4phage.jpg
http://fig.cox.miami.edu/Faculty/Dan
a/phage.jpg
Upon infection, the phage has two mechanisms
of action:
Lytic
Growth, in
which the
host’s
genetic
machinery is
used to
produce ~100
new phages,
and then the
host cell is
lysed
(broken).
Lysogeny, in
which the phage
chromosome is
integrated into the
host’s genome.
The phage then
dormantly infects
all progeny, as its
genome (called
the prophage) is
replicated when
the host divides.
The phage “chooses” between these two
mechanisms based on a “reading” of the host’s
behaviour. If the host is growing well the phage
lysogenizes the host and subsequently infects all
of its progeny. If the host is not growing well (e.g.
starving), the phage grows lytically - an 'abandon
ship' response.
This “decision” is based on a genetic switch.
The switch is composed of two genes and their
products:
Gene cI which codes for repressor
Gene cro which codes for Cro (control of
repressor and others)
These genes are adjacent to one another on the
phage genome:
PR (the right promoter) is the promoter for cro
PRM (repressor maintenance) is the promotor for cI
Both repressor and Cro regulate gene expression by
binding to the the right operator OR, which is divided
into three operator regions: OR1, OR2 and OR3
Repressor protein folds into two domains (labeled
amino (N) and carboxyl (C) for the two ends of the
polypeptide chain). The carboxyl domains associate
with one another, so that the protein is predominantly
present as a dimer.
These repressor dimers bind strongly to OR1 and
weakly to OR2 and OR3 (about ten times less affinity).
However, repressor
bound to OR1 binds
cooperatively to
repressor at OR2 greatly
increasing affinity for
that site.
The result: at low to mid
concentrations,
repressor is bound to
OR1 and OR2. Only at
much higher levels is it
also found bound to
OR3.
Effects of repressor binding:
repressor at OR1 inhibits Cro by blocking the binding site PR
Effects of repressor binding:
repressor at OR2 upregulates cI by binding to RNA
polymerase at PRM, increasing its affinity for the promoter
Thus at low-mid levels, repressor increases its own rate of
production (positive feedback)
Effects of repressor binding:
repressor at OR3 inhibits cI by blocking PRM.
Thus at high levels, repressor decreases its own rate of
production (negative feedback)
Conclusion: Repressor blocks production of Cro and
acts to maintain its own concentration at a particular
level. The result is a stable steady state -- repressor
high, Cro low.
Cro is a smaller protein than repressor, and folds into
a single domain. Like repressor, it is found mainly in
the form of a dimer.
Also like repressor, dimers of Cro bind to each
of the subregions of the right operator.
However, Cro's affinity for these operator
regions is opposite that of repressor. There are
no cooperative effects. Affinity for OR1 and OR2
is roughly equal, and is less than that for OR3.
Effects of Cro binding:
Cro at OR3 inhibits cI by blocking the binding site PRM
At higher concentrations, Cro inhibits its own
production by blocking RNA polyermase from PR. No
upregulation is needed since PR has a much higher
affinity for RNA polymerase than does PRM.
Conclusion: Cro blocks production of repressor and
acts to maintain its own concentration at a particular
level. The result is a stable steady state -- repressor
low, Cro high.
Summary:
System is bistable, with two stable steady states:
lysogeny: repressor levels are high, cro inactive,
levels of Cro low.
lysis: levels of Cro are high, cI inactive, levels of
repressor low. Cro then triggers production of other
phage genes needed to continue lytic growth.
Question: How does the phage switch from one
state to the other?
Hunger (or DNA damage, which can be induced in
the lab by exposure to ultraviolet light) causes an
increase in the activity of the bacterial (i.e. host)
protease RecA. (A protease is an enzyme which
degrades proteins). RecA cleaves repressor
rendering it unable to dimerize and hence inactive.
Once cleaved, repressor is unable to dimerize and so
is inactive -- it cannot bind to DNA to promote its own
production or to inhibit production of Cro.
The all-or-nothing, as
opposed to graded,
behaviour of this
induction by UV (or
hunger) is a direct
consequence of the
cooperativity in the
repressor mechanism.
A hypothetical analog
with no cooperativity
does not lead to the
same switch-like
behaviour.
Motivation: such genetic switches play a key role in
development (growth of a multicellular organism from
a single egg). An an egg divides, each cell receives
the same genetic content (i.e. identical copies of
DNA). What distinguishes different cell types is the
complement of genes which are expressed.
Cell differentiation occurs when a cell "chooses" to
express a certain gene profile. This "choice" is
typically based on signals from the environment.
These signals are often the result of gradients of
chemical messengers (morphogens), which have
been set up as part of development. A switch-like
response allows a gradient to set up differentiation
into a discrete number of cell types.
morphogen gradient
response of genetic network
differentiation into two distinct cell types