Robustness in protein circuits:
adaptation in bacterial chemotaxis
Information in Biology 2008
Oren Shoval
1
Outline
• Noise is a part of life
• Overview of bacterial chemotaxis
• Internal mechanism of chemotaxis control
• The robust model of perfect adaptation
• Perfect adaptation and control theory
2
Outline
• Noise is a part of life
• Overview of bacterial chemotaxis
• Internal mechanism of chemotaxis control
• The robust model of perfect adaptation
• Perfect adaptation and control theory
3
Many biological processes are robust to
external and internal fluctuations
• Internal protein levels
vary significantly between
genetically identical cells
• Humans keep body Elowitz et al., Science, 2002
temperature at 36.7°
despite:
– External noise of
surrounding temperature
– Internal noise of body
weight, size, food intake
4
Sensitivity to noise is a measure of biological
system performance
• Sensitivity is the change in system output (Y)
due to changes in the internal parameter ()
% change output Y
SY ,
% change parameter
• Robustness means zero sensitivity
• For example, dependence of body
temperature on body weight:
Robust
% change Tbody
SY , 0
% change Weightbody
Savageau, Nature, 1971 5
Outline
• Noise is a part of life
• Overview of bacterial chemotaxis
• Internal mechanism of chemotaxis control
• The robust model of perfect adaptation
• Perfect adaptation and control theory
6
Chemotaxis: Bacteria can “swim” towards an
attractant and away from a repellent
Repellant Attractant
(poison) (food)
7
Swimming is done by a spiraling motor (flagella)
• Flagella can rotate in two directions:
Clock wise Counter clock wise
(advancing ~sec) (tumble ~0.1sec)
• Speed of about 50m/sec. Is this fast?
Organism Kilometers per hour Body lengths per second
Cheetah 111 25
Human - Michael Johnson 37.5 5.4
Bacteria 0.00018 25
8
Bacteria find their way up a nutrient gradient
by changing the tumbling rate
• Bacteria are too small to
measure gradient
• Gradient found by temporal
change during running
• Positive Lower Continue
Gradient tumbling in correct
rate direction
• Biased random walk
Berg, Nature, 1972
9
Automated analysis of the bacteria trails
enables extracting the chemotaxis parameters
Parameters:
• Mean free path
• Tumbling rate
Berg, Nature, 1972
10
Tumbling rate shows exact adaptation to
nutrient level
Steady state
tumbling rate
addition of nutrient
bacteria stop tumbling
Adaptation: slowly return to
a steady state tumbling
• Adaptation is commonly
found in sensory systems
• Adaptation is the focus of
Barkai’s paper Addition of attractant Adaptation
reduces tumbling
immediately
11
Adaptation increases the dynamic range of
sensors
• Adaptation keeps sensor sensitive to changes
regardless of average stimulus System unable to
Stimulus sense changes
level
Possible stimulus range
System dynamic range
• Bacteria without adaptation show <1% chemotaxis
ability
12
Outline
• Noise is a part of life
• Overview of bacterial chemotaxis
• Internal mechanism of chemotaxis control
• The robust model of perfect adaptation
• Perfect adaptation and control theory
13
Motor control by a two component system:
receptor and regulator
Receptor without an attractant Sensor Receptor
activity
level
Activate Y by adding a P more
P tumbling
Y-P binds to motor Y Y
Increase rate of tumbling Motor
Shorter runs Removal of P at
constant rate
14
An attractant inhibits the receptor, thus
reducing motor activity
Sugar
Adding attractant
Sensor Receptor
activity
Less receptor activity level
Less
Less Y-P is created P tumbling
Y Y
Reduced tumbling
Motor
Longer runs
Removal of P at
constant rate
Fast process (miliseconds)
15
Again:
Less sugar Shorter runs More sugar Longer runs
Sugar
Sensor Receptor Receptor
Sensor
activity activity
level level
more Less
P tumbling P tumbling
Y Y Y Y
Motor Motor
Removal of P at Removal of P at
constant rate constant rate
16
Adaptation is achieved by reactivating the
receptor
• Adding M (Methylation)
overcomes deactivation
due to sugar
M M
• R add M, B removes M Reactivation (R) Deactivation (B)
Negative
Sensor feedback
activity
level
Slow process (minutes)
17
The adaptation cycle:
Slow (minutes)
Fast (miliseconds)
18
Outline
• Noise is a part of life
• Overview of bacterial chemotaxis
• Internal mechanism of chemotaxis control
• The robust model of perfect adaptation
• Perfect adaptation and control theory
19
Is adaptation accuracy sensitive or robust to
internal protein levels?
• Example: If the level of protein R (reactivation)
changes by 20%, will we still have adaptation?
Two mechanisms for adaptation
20
Barkai proposed a robust model of adaptation
that depends on two assumptions
1. Methylation (R) works at
maximum rate (saturation)
2. Demethylation (B) occurs only on
activated receptors
CheR
Barkai, Nature, 1997
21
Let’s have fun with some equations
• The attractant governs the
active vs. inactive ratio:
Xm
*
( sugar)
Xm
• Methylation rate: CheR
d(Xm Xm)
*
R BX m
*
dt
• At steady state:
R
Xm
*
B
Adaptation is robust!
22
Experiments can measure the sensitivity of
chemotaxis parameters to internal protein level
• Alon experimentally varied the level of proteins that make up
chemotaxis
• Three parameters were extracted for each mutant:
Adaptation time
Steady state
tumbling Adaptation
precision
Alon et al., Nature, 1999
23
Experiments have proven that adaptation precision
is robust to variations in protein levels
x3 receptors
x50 CheR
x0.5 CheY
x12 CheB
x0 CheZ x0 CheZ
•Adaptation is precise in all cases
•Steady state tumbling rate and adaptation time change
Alon et al., Nature, 1999
24
Perfect adaptation is important, so the network
is designed to keep it robust
• Partial adaptation leads to <1% of wild-
type chemotaxis ability
However,
• Changing the tumbling frequency and
adaptation time does not affect
nonessential
chemotaxis ability features are
• Exact adaptation is displayed in taxis of sensitive to
many other bacterial species (B.
subtillis, R. sphaeroides)
protein levels
25
Outline
• Noise is a part of life
• Overview of bacterial chemotaxis
• Internal mechanism of chemotaxis control
• The robust model of perfect adaptation
• Perfect adaptation and control theory
26
Robust adaptation in chemotaxis is an
example of integral feedback control
r
b
A
Error
r bA b A r by
x
b
Yi et al., PNAS, 2001
27
Summary
• Biochemical networks need
to cope with noise
• Chemotaxis is the ability of
bacteria to swim towards an
attractant
• Chemotaxis adaptation is
robust to internal protein
levels
28