1. Bacterial Chemotaxis Dr. Chrisantha Fernando Systems Biology Centre University of Birmingham, UK March 2007 Dr. Chrisantha Fernando Systems Biology Centre University of Birmingham, UK March 2007

2. Thanks to…  Uri Alon. The core of this lecture is based on a lecture given by Uri Alon, available at  http://www.weizmann.ac.il/mcb/UriAlon/ http://www.weizmann.ac.il/mcb/UriAlon/  Actually you can even here him giving the lecture in audio. I highly recommend it.  Uri Alon. The core of this lecture is based on a lecture given by Uri Alon, available at  http://www.weizmann.ac.il/mcb/UriAlon/ http://www.weizmann.ac.il/mcb/UriAlon/  Actually you can even here him giving the lecture in audio. I highly recommend it.

3. Rating 18: Neutrophil follows and kills bacteria

4. What is Chemotaxis? Rapid Response

6. Can’t measure spatial gradients! Difference in [chemical] too small to be detected

7. Runs and Tumbles Berg, Brown…, 1972

9. Due to Clockwise or Anti- Clockwise of Flagella Motor

10. Adaptation of tumbling frequency Well mixed reactor Measure tumbles Add attractant Add attractant EXACT Adaptation time

11. Exact Adaptation  The steady state tumbling frequency is independent of the attractant concentration.

12. Mechanism? 6 proteins control this computation. Adler. Clockwise/Anti-Clock Attractant binds 1000 receptors Receptor/Kinase CheY-P increases the prob. that motor turns clockwise, I.e producing tumbling. 30 binding sites for CheY on motor = Cooperativity. Kentner and Sourjik

14. Add attractant Attractant shuts off kinase CheY gets de-phosphorylated Tumbles decrease rapidly But how does adaptation occur, i.e increased tumbling again?

15. Adaptation Methylation can sensitize the detector This happens slowly, to an extent determined by two oppositely acting proteins.

16. CheR methylates and sensitizes CheB de-methylates and desensitizes CheB is activated by CheY-P, i.e. negative feedback loop.

18.  How robust is this circuit to change in protein concentration? Uri Alon asked whether it was “fine tuned” or “robust”. Behaviour Styles!

19. Experiments to alter protein levels in real bacteria.  Compute average tumbling frequency of population using image processing.  A variety of individual differences were found even in genetically identical organisms: “nervous” vs. “relaxed”.  Compute average tumbling frequency of population using image processing.  A variety of individual differences were found even in genetically identical organisms: “nervous” vs. “relaxed”.

21. Robust feature Not robust

23. Why is exact adaptation robust?  Adaptation time and tumbling frequency is not robust.  Mutants with only partial adaptation (no CheR and CheB) have 1% normal chemotaxis ability.  Hypothesis: Chemotaxis mechanism evolved so that exact adaptation was robust to variation in protein level changes.  Is it possible to have a good chemotaxis mechanism without exact adaptation?  Adaptation time and tumbling frequency is not robust.  Mutants with only partial adaptation (no CheR and CheB) have 1% normal chemotaxis ability.  Hypothesis: Chemotaxis mechanism evolved so that exact adaptation was robust to variation in protein level changes.  Is it possible to have a good chemotaxis mechanism without exact adaptation?

24. [Protein] is noisy  Sometimes only ~20 copies of a protein in a cell. This will vary due to noise in transcription and translation.  Imagine making a circuit that had to be robust to very unreliable and poorly specified electrical parts.  Sometimes only ~20 copies of a protein in a cell. This will vary due to noise in transcription and translation.  Imagine making a circuit that had to be robust to very unreliable and poorly specified electrical parts.

26. E EmEm EmEm = Output Active Inactive Input u + CheB + CheR 1.Tar complex (E) in methylated and unmethylated form 2.Ligand binds to methylated form only, and inactivates 3.We require a steady fixed active E m. 4.So, in proportion to [E m ] active, we destroy E m 5.This means, if [u] is increased, there is less E m, so less destruction of E m so, [E m ] again increases to its steady state. 6.Or, if [u] is decreased, [E m ] is increased, and so E m destruction rate increases so again reducing [E m ] to steady state.

27. Chemoattractant [Active receptor] Rate of de-methylation By CheB Binds to only Methylated receptors

29. Problems with Current Explanations  Explaining how the Tar complex can be so sensitive (high gain) over many orders of magnitude.

31. Dennis Bray : Outstanding Issues  http://www.pdn.cam.ac.uk/groups/comp- cell/Questions.html