1. VARIED STATE EXPRESSIONS Allen Lin Caltech iGEM 2008 Brainstorming

2. Why?  Currently standard to detect the expression of a gene: attach GPF in DNA so that it becomes transcribed and translated as part of a protein.  Can we be more creative?  What other types of expressions might bacteria be able to produce?

3. Why II?  Can we make the bacteria do something interesting when it’s in a particular state?  For example, make the bacteria have different phenotypes when It’s in different stages of mitosis ([cyclin]) Particular operons are active ([free repressor]) Certain enzyme pathways are activated

4. Actually…  These two goals are the same

5. For example….going off topic  What about have the bacteria make something when its in a particular state  Say, when a bacteria detects lactose, produces another compound  And have the bacteria sensitive to the second compound  … And migrate to the location to the first compound

6. Compound Detector and Remover  Bacteria start out in one location  Through random walk, spread across  When a bacterium detects a particular compound A, turns red and produces a compound B not normally produced by bacteria  Other bacteria in the region have heightened sensitivity to compound B in chemotaxis; when they detect it, turn green. And they migrate to the location of the initial bacteria. When they reach compound A, turn red + green, produce compound B, and digest compound A  Exponential effect, until compound A is completely digested. Then the bacteria are no longer red, and disperse through random walk.

7. No CheZ -> Stationary Cells Guiding Bacteria with Small Molecules and RNA Topp, S. and Gallivan, J.P. J. Am. Chem. Soc., 129, 21, 6807 - 6811, 2007, 10.1021/ja0692480

8. Use a RNA switch!

9. Theophylline presence -> mobility

10. Proof of concept

11. Problems  Bacteria are completely non-motile when compound theophylline not present  Is there a system in which chemotaxis is turned on by the presence of a compound, and not mobility is turned off by the lack of a compound?  Need a high concentration of output compound for it to diffuse and attract other bacteria

12. Having gone off-topic…  Instead of producing GFP when lac operon is transcribed, produce another compound that the bacteria secretes different phenotype  When bacteria sense this second compound, redirect normal chemotaxis scheme  Inputs -> different types of outputs

13. Uses  So this might be:  An efficient toxin clean up system  An infectious disease recognizer and fighter system  Anything in which don’t need a lot of resources to detect, but need a lot of resources to eliminate

14. Input -> Library of responses  Then that would be okay  And highly useful  Here, we have  Produce signaling compound  Produce change in mobility  What else can we do?  Produce different phenotype (ex. shiny)  Interrupt mitosis cycle  And more