1. L17. Robustness in bacterial chemotaxis response
BME March 22, 2005
L17. Robustness in bacterial chemotaxis response
Lingchong You

2. Homework 1&2 graded; pick in office during office hours
No class March 24th. Instead, attend one or both of the following:
March 23, 3:00pm, 130 North Bldg, Richard Watanabe: “Integrating Compartmental Models and Genetics to Understand Glucose Tolerance”
March 24, 10am, CIEMAS auditorium B, Pak Kin Wong: “One In a Million” Bio-Nano- and Information Technologies for Controlling Complex Biological Systems

3. Groups & topics presentation order Name email: @duke.edu
Project topics 2
Blais, Pierre Emmanuel
peb5
Stochastic simulation of bistability 5
Chaudhry, Rajeev
rc16
circadian rhythms (with Ramlingam) 6
Chu, Edward William
ewc4
circadian rhythms (with peter)? 3
Donahoe, Casey D
cdd4
circadian rhythms (with Prangkio) 4
Hanson, Megan
mmh13
viral infection 8
Koreishi, Anjum Faruk
afk
cell cycle 7
Lee, Jiwon
jl54
cell-cell communication 1
Leung, Alan Tsun Lim
atl6
circadian rhythms 10
Novick, Paul Andrew
pan3
Prangkio, Panchika
pp9
circadian rhythms (with Donahoe)
Ramalingam, Sundhar
sr20
circadian rhythms (with Chaudhry) 9
Polikov, Vadim
vsp
cytokines

4. Project assistance
Week of 4/4-4/9; Each group must make ½ hr appointment with me to discuss your project progress.
Week of 4/12-4/15; No class. Optional appointments with me to assist with your projects

5. Tentative final presentation schedule (25 min/group, including Q&A)
Dates may change; you need to attend all presentations:
4/19: groups 1, 2, 3
4/21: 4, 5, 6
4/26: 7, 8, 9, 10
Project report due by 5/1 (both electronic & paper copies)

6. Brief review: network architecture  system property-
Negative feedback
(no time delay)
Homeostasis +
Positive feedback
Switch, bistability
When we examine network dynamics, there are two aspects involved. On one hand, we may have the knowledge of the underlying network. In this case, we can ask what the possible output from the network can be generated. Here are some elementary examples. If we have negative feedback, we can potentially generate a stable output (homeostasis) or oscillations, depending on whether there is time delay involved. If we have a positive feedback, we can then potentially generate switching behavior caused by bistability.
On the other hand, if we observe some system property, we can then guess what the underlying network structure maybe. In some cases, we know there are only a small number of network structures that can generate rate a certain behavior. For example, if we observe bistability, we know there must be a positive feedback involved. This perspective is useful, because it gives a new way of generating hypothesis, suggesting mechanisms or interactions to look for. -
Negative feedback
(+ long time delay)
Oscillations

7. Oscillator based on negative feedback only
Oscillator based on activator-inhibitor architecture

8. Robustness by communication
Coordination
Large numbers

9. Prototype: a population control circuit
extinction
No cell-cell
variations
AHL ? R R I
survival
luxR
luxI
ccdB
With cell-cell
variations
PluxI
CcdB
You et al, Nature (2004)

10. Typical simulation results

11. Typical dynamics in Top10F’ (pH=7; 34C)
OFF
Typical dynamics in Top10F’
(pH=7; 34C) ON
Population behavior
Stable regulation
Damped oscillations
Captured by model
Mutants arose after ~100 hrs ON
OFF

12. Long term monitoring of circuit dynamics
Balaggade, You et al. 2005, submitted

13. Robustness in bacterial chemotaxis
Fluorescent flagellar filaments of E. coli.

14. Random walk by E. coli
Berg, Physics Today, “Motile behavior of bacteria” (

15. Clockwise
Counter-clockwise
Run
Tumble

16. Attractant
(e.g. nutrient)
Repellent
(e.g. toxin)
Chemotaxis: reduction in tumbling frequency to drive swimming toward attractant

17. Input
regulation
Output

18. Perfect Adaptation in Bacterial Chemotaxis Signaling
Segall, J. E., Block, S. M. & Berg, H. E. Temporal comparisons in bacterial chemotaxis.
Proc. Natl. Acad. Sci. USA 83, (1986).
Adaptation precision =
Yss Y0
+ Asp

19. What’s the basis for perfect adaptation? Two explanations:
The kinetic parameters are fine-tuned.
E. g.: Spiro et al. A model of excitation and adaptation in bacterial chemotaxis. PNAS, 1997
Perfect adaptation is a robust property of the underlying network.
Barkai & Leibler 1997, Nature (Modeling)
Alon et al 1999, Nature (Experiment)

20. McAdams, et al 2004. Nat. Rev. Genetics

21. More simplified view R: CheR W: CheW A: CheA B: CheB Y: CheY
Y-p: phosphorylated CheY
Alon et al Nature

22. A two-state model Key reactions:
Binding and unbinding of the receptor complex to ligand
Methylation and demethylation of the complex
Each receptor complex may have several methylation sites
Phosphorylation and dephosphorylation of B
System activity (output): number of receptors in active form (different methylation states and occupancy of ligands affect the activity of each receptor state)
Barkai & Leibler 1997 Nature

23. Key assumptions
Input = ligand. Ligand binding and unbinding happens at the fastest time scale. Binding affinity is independent of receptor’s activity and its degree of methylation.
CheB only demethylates phosphorylated receptors.
CheR works at saturating level, or methylation of receptors follows a constant rate.
Demethylation is independent of ligand binding

24. Perfect adaptation:
Always returns to the same steady state
Barkai & Leibler 1997, Nature

25. Adaptation precision robust to perturbations

26. Adaptation time NOT robust

27. Experiment: perfect adaptation
No stimulation
Stimulated by attractant
(1mM L-aspartate)

28. Experimental measurements
Perfect adaptation
(Robust)
Highly variable adaptation time & s.s. tumbling frequency
Not robust

29. Changes in other parameters
Not robust
Robust
Also:
perfect adaptation precision
highly variant steady state levels and adaptation time

30. Summary
The adaptation precision of the E. coli chemotaxis network is highly robust to perturbations
Other system properties (steady state level or the adaptation time) are not robust.
In general, for many biological systems, only some system properties are robust to perturbations, but others are often sensitive

31. Why perfect adaptation
Possible reason:
Compensation for continued stimulation
“Preparation” for responding to further stimuli
Evidence:
Cells deficient in adaptation are poor in chemotaxis even if their steady state tumbling is similar to wild type
Cells capable of perfect adaptation are similar to WT in chemotaxis even if their steady state tumbling is quite different.

32. A highly simplified view of chemotaxis response
Input
Output
Tyson et al. Current Opinion in Cell Biology 2003, 15:221–231