Positive feedback loops generate bistability

Positive feedback loops

generate bistability
Bởi:
TS. Nguyen Cuong

Autoregulation

Transcription of a gene is the process by which RNA polymerase (RNAp) produce

mRNA that corresponds to that gene’s coding sequence. The mRNA is then translated
into a protein. The transcription rate is controlled by the quality of RNAp-binding sites
on promoter, a regulatory region of DNA that precedes the gene. Whereas RNAp acts
on virtually all of the genes, changes in the expression of specific genes are due to
transcription factors, a kind of protein. Transcription factors affect the transcription
rate by binding specific sites in the promoters of the regulated genes. When bound,
they change the probability per unit time that RNAp binds the promoter and produces
an mRNA molecule. The transcription factors thus affect the rate at which RNAp
initiates transcription of the gene. The transcription factors can act as activators that
increase the transcription rate of a gene, or as repressors that reduce the transcription
rate. If the gene product P regulates its own transcription process, it would be called
autoregulation or autoregulatory protein. If protein P acts as an activator, then it is
a positive autoregulation. And if protein P acts as a repressor, then it is a negative
autoregulation. Figure 1

Schematic positive autoregulation.

Typically, transcription and translation processes, binding of transcription factor to

promoter and translating of mRNA to protein, occur much faster than protein
accumulation does. The former timescale is in order of second or minute. The later
timescale is in order of many minutes to hours. Thus, the production rate of a protein

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Positive feedback loops generate bistability

could be assumed in a quasi-steady-state description of promoter activity, transcription

factor binding-unbinding events.

The dynamics of protein P thus are described by its production rate kb + ksA(P) and
degradation/dilution rate kdP
dP
dt = kb + ksA(P) − kdP (eq1)

where P denotes the protein concentration. kb, ks, and kd are basal, maximal product
and degradation rates, respectively. The function A(P) represents autoregulation and
typically is a monotonic, S-shaped function. A useful function that describes many
real gene input functions is called Hill function. The Hill input function for positive
autoregulation is a curve that rises from zero and approaches a maximal saturated level

Pn
A(P) = (eq2)
Kn + Pn

where parameter K is activation coefficient with unit of concentration. It defines the

concentration of active X needed to significantly activate expression. The half-maximal
expression is reached, A(P) = 1 / 2 when P=X. The Hill coefficient n represents the
cooperativity of protein P on its own promoter. Typically, Hill coefficient n represents
the number of protein molecule in complex, it is monomer, dimer, trimer, … when
n=1, n=2, n=3, .., respectively. The Hill coefficient n governs the steepness of the input
function. If n=1, the Hill input function turns out to be the Michaelis-Menten function
which is a hyperbolic curve. With n>1, Hill function is a S-shaped function. And the
larger is n, the steeper the function. Typically, the input function are moderately steep,
with n=1-4. Figure 2

the input function A(P). With n=1, the Hill input function turns out to be the Michaelis-Menten
function which is a hyperbolic curve. With n>1, Hill function A(P) is a S-shaped function.

The activation coefficient K can be changed by mutations that alter the DNA sequence
of the binding site of P in the promoter of gene p. Even a change of a single DNA letter
in the binding site can strengthen or weaken the chemical bonds between transcription
factor and promoter and change K. The parameter K can also be varied if the position of
the binding site is changed. Similarly, the maximal activity ks can be tuned by mutations
in the RNA binding site or many other factors.

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Positive feedback loops generate bistability

The steady state concentration of protein P can be obtained by analytically or

numerically solving the equation dP/dt = 0, or equivalently using rate balance plot to
find out the steady state at intersection of production rate with degradation rate. The
former method gives out exact solution of steady state of P, while the later gives an
intuition of how the steady state of P depending on parameter changes. Here, the rate
balance plot is used to illustrate how the concentration of P changes according to the
parameters change, especially the maximal rate, ks, and activation coefficient K.

Without cooperativity, n=1, the feedback function A(P) simply is a hyperbolic curve.
The Figure 3A shows the plot of degradation rate, blue line, and production rate, red
lines, with maximal rate ks equally changing. The response curve of P corresponding
to intersection point of two rates with maximal rate changing is shown in Figure 3B. It
shows that the steady state of protein P concentration is increasing from basal activity,
P = kb / kd at ks = 0, with increment of ks. Initially, the steady state of protein P slowly
increases at small maximal rate, ks, then almost linearly increases at large maximal
rate, ks. The small maximal rate, ks, produces small concentration of protein P, at P<K,
the feedback function A(P) is weak or suppressed A(P) < 1 / 2. Thus, the steady state
of P, which is approximated by P ≈ (kb + ksA(P)) / kd, with A(P) < 1 / 2, slowly increases.
However, at the large enough maximal rate, ks, to produce protein P concentration larger
than activation coefficient, P>K, hence the feedback function A(P) reaches saturation,
A(P)~1, thus the steady state of P now is approximated by P ≈ (kb + ks) / kd linearly
increasing with maximal rate, ks.

Similarly, the Figure 3 C and D show rate plot and response curve, respectively. The
production P decreases quickly from maximal activity then reaches saturation at basal
activity as long as activation coefficient K increases (Figure 3D). The reasoning is
that, the larger activation coefficient K, the larger production is required to activate the
feedback function, A(P) > 1 / 2, the later activation of feedback function is (Figure 3C). If
the activation coefficient K is larger than maximal activity of production P, the product
P would be at low level since the feedback function is never activated.

(C)(A)(D)(B)

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Positive feedback loops generate bistability

The rate balance plots and bifurcation diagrams of autoregulation with Hill coefficient n=1. (A,
B) The rate balance plots and bifurcation diagrams of autoregulation, respectively, with respect
to maximal rate ks. (C, D) The rate balance plots and bifurcation diagrams of autoregulation,
respectively, with respect to activation coefficient K. Typically used parameters: kb = 0.1, kd = 1
, n = 3, ks = 1and K = 0.5.

With cooperativity of protein P at its promoter, n>1, the feedback function

A(P) = Pn / (Kn + Pn);n > 1 now is an S-shaped function. Thus production rate, kb + ksA(P),
is also an S-shaped curve. The production rate with respect to maximal rate ks is shown
in Figure 3A, red lines. The blue line is degradation rate, kdP. Now, there might be more
than one intersection, two or three intersections, between production and degradation
rates. Meaning that, the autoregulation could generate bistability, product P have two
stable steady states (filled circles) and one unstable steady state (unfilled circle) at a
certain range of parameters, Figure 4A and C. The product P can access those stable
steady states by tuning parameters. For instance, in Figure 4B, as maximal rate ks
increases, the product P is low until ks exceeds some critical value, k2s , at which point the
product P increases abruptly to a high value. Then if ks decreases, the product P does not
drop down until ks crosses another critical value, k1s . Notice that, for ks value between
k1s and k2s , the product P is bistable- that is, it has two stable steady state values (on the
upper and lower braches-the solid lines) separated by an unstable steady state (on the
intermediate branch – the dashed line). This sort of reversible bistability is also referred
as hysteresis.

(B)(C)(A)(D)

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Positive feedback loops generate bistability

The rate balance plots and bifurcation diagrams of autoregulation with Hill coefficient n>1. (A,
B) The production (red) and degradation (blue) rate plots and bifurcation diagrams of
autoregulation, respectively, with respect to maximal rate ks. (C, D) The production (red) and
degradation (blue) rate plots and bifurcation diagrams of autoregulation, respectively, with
respect to activation coefficient K. In rate balance plot, filled and un-filled circle represent
stable and unstable steady state, respectively. In bifurcation diagram, the solid and dashed lines
represent stable and unstable steady state, respectively. Typically used parameters: kb = 0.1,
kd = 1, n = 3, ks = 1and K = 0.5.

The signal-response curves in Figure 4B would be called ‘one-parameter bifurcation

diagram’. The parameter is maximal rate, ks. The steady state response, on the Y axis,
is concentration of P with respect to maximal rate, ks. At the critical points, k1s and k2s ,
the concentration of P changes abruptly from low to high concentration and vice versa.
Such points are called bifurcation points, in this case, ‘saddle –node bifurcation points -
SN’.

By tuning other parameter, such as activation coefficient K, the autoregulation also

could generate bistability as shown by one-parameter bifurcation diagram in Figure 4D.
The bistable region is in between K1 and K2, which are saddle –node bifurcation points.

In fact, the two parameters, maximal rate and activation coefficient, would be tuned
therefore the bistable region might changed accordingly. The Figure 5 shows bistable
region of autoregulation with changing of both parameters. The bistability disappears
through emergent of two saddle node points at the cusp when both of them are small.
As the activation coefficient K increases, the maximal rate also need to increases to
maintain the bistability. The reasoning is that, increasing of activation coefficient K
causes decrement of the concentration of P, thus the maximal rate should increase in
order to maintain the concentration of P.

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Positive feedback loops generate bistability

The two-parameter bifurcation diagram of autoregulation showing the region of bistability, the
region inside the cusp.

The reversible bistability or hysteresis of autoregulation has been well reported in many
experiments such as the lac-operon in bacteria, the activation of M-phase-promoting
factor in frog egg extracts, and the autocatalytic form.

Beside reversible bistability, the autoregulation could also generate irreversible

bistability, meaning that the concentration of product P changes abruptly and
irreversibly as parameter crosses a certain threshold. The irreversible bistability can be
achieved by introducing an additive term to the production rate, kb + ks1A(P) + ks2S, the
additive S term could be interpreted as an input signal or an additional transcription
factor binding gene promoter. Thus, the dynamics of product P now is
dP
dt = kb + ks1S + ks2A(P) − kdP (eq3)

In fact, one gene possibly is regulated by multiple transcription factors (refs). By

introducing additive transcription factor S, the autoregulation possibly generate
irreversible bistability. For instance, an example is shown in the Figure 6B, the
concentration of product P is low until the input signal S crosses a certain threshold S1,
at which point the product concentration increases abruptly to high level. Once jump
on, the concentration of P would never drop down even the input signal is washed
out, S=0. However, introducing an additional input signal S into production rate does
not guarantee irreversible bistability. Figure 6C, D show regions of mono stability (un-
shaded), reversible bistability (filled) and irreversible bistability (patterned) with respect
to ks and K, respectively.

The irreversible bistability is utilized in the processes characterized by a point-of-no-

return such as frog oocyte maturation in response to progesterone, the frog oocyte can
not returned to original state once matured; apoptosis is another decision that must be a
one-way switch.

(D)(C)(B)(A)

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Positive feedback loops generate bistability

The rate balance plots (A) and bifurcation diagrams (B) of autoregulation with additional
transcription factor S. The irreversible bistability could be generated by autoregulation.
Typically used parameters: kb = 0.1, ks1 = 0.1, ks = 1, kd = 1, n = 3, K = 0.5.

Auto-Phosphorylation

Proteins undergo a huge number of post translational modifications. However, only a

subset of these modifications is reversible, covalent modifications such as acetylation,
fatty acid acylation, glycosylation and phosphorylation. These modifications affect the
activity, life span, or cellular location of the modified proteins. Of the post translational
modifications mentioned above, phosphorylation is an important and ubiquitous one.
The phosphorylation reaction in the cell is a reversible one where kinases catalyze
the addition of the phosphoryl group and phosphatases catalyze the removal of the
phosphoryl group, Figure 7. Phosphorylation and dephosphorylation reactions under the
control of kinases and phosphatases, can occur in less than a second or over a span
of hours which makes this system ideal as a regulatory process. Phosphorylation and
dephosphorylation reactions can be part of a cascade of reactions which can amplify
a signal which has an extracellular origin such as hormones and growth factors. The
kinases and phosphatases are enzymes, a kind of protein.

Reversible phosphorylation of protein. Kinase E1 catalyzes the addition of phosphoryl group

(yellow circle) and phosphatase E2 catalyzes the removal of the phosphoryl group. In turn,
kinase E1 is regulated by phosphorylated protein P.

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Positive feedback loops generate bistability

The auto-phosphorylation protein, the protein is phosphorylated/dephosphorylated by

an enzyme and that enzyme is also phosphorylated/dephosphorylated by the protein,
have been reported in many other sources (fission, budding yeast cell cycle, .. refs).
The phosphorylation and dephosphorylation reactions of phosphorylation are typically
govern by the Michaelis-Menten equation. We assume the total protein concentration,
PT, is constantly produced and auto degraded. And the protein exists in two forms, free
form P and phosphorylated form P, thus P + P = PT. And assume that, the free form Pis
active form which is in our interest. Thus, dynamics of active form or free form P can
be described as the following,
dPT
dt = ksS − kdPT (eq4)

dP E(PT − P) P
dt = ksS + Vap K − Vip K − kdP (eq5)
ap + (PT − P) ip + P

dE P(1 − E) E
dt = Vae K
ae + (1 − E)
− Vie K
ie + E
(eq6)

The first and second terms on the right hand side of the first equation are production and
degradation rate of protein P with product rate ks and degradation rate kd, respectively.
The first and second terms on the right hand side of the second and the third equation are
dephosphorylation and phosphorylation reaction with maximal rate Vap, Vip, Vae, and
Vie, kinetic constant Kap, Kip, Kae, and Kie, respectively.

The Figure 8A shows the rate plots with assumption that the phosphorylation process
occurs much faster than protein synthesis, thus the total concentration PT is in
equilibrium state, PT = ksS / kd; and the enzyme E activation is much faster than that of P,
thus the enzyme E is also in equilibrium state, dE/dt = 0. The auto-phosphorylation is
also a positive feedback loop, so that it is able to generate bistability as shown in Figure
8A (rate balance plot) and B (bifurcation diagram plot).

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Positive feedback loops generate bistability

The rate balance plots (A), one parameter bifurcation diagrams (B) and two parameters
bifurcation diagram (C) of autophosphorylation with additional transcription factor S. The
reversible bistability could be generated by autophosphorylation. Red line and blue line
represent production and degradation rates, respectively. used parameters: ks=1ks=1 size 12{k
rSub { size 8{s} } =1} {}, kd=1kd=1 size 12{k rSub { size 8{d} } =1} {}, Vap=1Vap=1 size 12{V
rSub { size 8{ ital "ap"} } =1} {}, Vip=0.5Vip=0.5 size 12{V rSub { size 8{ ital "ip"} } =0 "." 5}
{}, Vae=1Vae=1 size 12{V rSub { size 8{ ital "ae"} } =1} {}, Vie=0.5Vie=0.5 size 12{V rSub {
size 8{ ital "ie"} } =0 "." 5} {}, Kap=Kip=Kae=Kie=0.01

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