Synthetic Biology Notes

General Terms
In vitro (within the glass) experimentation using a controlled environment (ex. Test tube/petri dish) In vivo (within the living) experimentation using a whole, living organism (e.g. animal ex vivo (out of the living) testing, clinical trials) experimentation/measurements done in or on tissue in an artificial environment outside the in silico performed on computer or viaorganism with the minimum alteration of computer simulation natural conditions

Ex vitro

Tabor 2009

A SYNTHETIC GENETIC EDGE DETECTION PROGRAM

System Mask filters light detected by bacteria bacteria/ lawn detects edges + gives visual output

Concept of Detection System Bacteria in dark produce signal (green circle) Signal diffuses Only bacteria in light respond to signal; Response = expression of visible reporter gene

Y = 0 when theres light. cell-cell communication NOT light box X AND (NOT Y) IF NOT light produce signal; IF signal AND NOT (NOT light) produce pigment;

inverter

light, no signal, no pigment light, signal, pigment No light, no signal, no pigment no light, signal, no pigment

phorphoryl OmpR group PCB

resp. reg.

light sensitive protein cph8 = [Cph1]+[EnvZ] Cph1 = photoreceptor domain of Synechocystis EnvZ = kinase domain of E.coli Inhibited with red light Requires phycocyanobilin (PCB) Covalently associated chromophore Produced from heme by genes ho1 and

Sensor
Phytochrome
Membrane bound extracellular sensor/photoreceptor Intracellular (response) regulator
Usu do not have DNA-binding domains Do not directly regulate gene expression

Fusion protein: phytochrome and EnvZ histidine kinase domain

Extracellular sensor Intracellular regulator

Photoreceptor Expression
PCB not produced in E.Coli Introduction of PCB synthesis genes Converts haem into PCB

Transduction Mechanism
Red light represses EnvZ auto-phosphorylation

Output
OmpR-P activates promoter linked to reporter gene lacZ reporter produce black compound

OmpR-P dependent ompC promoter

System Revisited

Light Canon