programmed cells: interfacing natural and engineered gene networks kobayashi, kærn, araki, chung,...
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Programmed cells: Interfacing natural and
engineered gene networks
Kobayashi, Kærn, Araki, Chung, Gardner, Cantor & Collins,( PNAS 2004).
You, Cox, Weiss & Arnold ( 2004 NATURE)
Noam Vardi
Transcription factors control gene expression
• Activators:
• Repressors
A B
A B
Activator A
RNA pol
RNA pol ON
Repressor A
RNA pol
OFF
Gene B
Gene B
inputoutput
chemo taxisFood gradient Direction of movement
Sugar
Metabolism
The composition of sugars in the environment
Activation of lac operon
Cells need to compute in order to survive
Sugar metabolism genes in E.coli
The lac genes are transcribed if and only if:
1. Absence of glucose
2. The relevant sugar is present
AND gate
Expression of alternative sugar genes
A modular programmed cell
input
engineered regulatory network
requirments
•the regulatory network can read the input
•The cell can read the output
Sensory
moduleoutput
Kobayashi, Kærn, Araki, Chung, Gardner, Cantor & Collins,( PNAS 2004).
The SOS pathway in E.coli
DNA damage
RecA
SOS repressor
SOS genes
UV radiation
Example 1 : interfacing the S.O.S pathway with a genetic switch
A genetic toggle switch
All or none reaction – when one promoter is ON , the second one is OFF
Each promoter is inhibited by the repressor transcribed from the opposite promoter
Phage lambda’s
Bi-stable system
A
Promoter A
B promoter B
Phage lambda toggle switch uses the E.coli SOS system
Lytic phase Lysogenic phase
DNA damage
RecAUV
radiation
Phage genes
OFF
Phage genes
ON
SOS
repressor
Interfacing the genetic switch with SOS pathway and an output module
regulatory module-
genetic switch
GFP*LP
output module - GFP
ON
DNA damage
SS DNA
UV RECA Sensory module-
SOS system
DNA
E.Coli cell
The system is applied using plasmidsPlasmid - an extra-chromosomal DNA molecule which is capable of replicating
GFP
output module
Regulatory module
Example 1 - results
Treating cells with UV
The genetic switch keep the system active long time after the S.O.S signal is gone and the DNA is repaired.
Possible application
Detecting DNA damage
Quorum sensing - the way bacteria communicate Quorum Sensing - a phenomenon whereby the accumulation of signaling molecules enable a single cell to sense the number of bacteria.
Vibrio fischeri.
Example 2 : population control
luxI/luxR system – the engineered regulatory module
You, Cox, Weiss & Arnold ( 2004 NATURE)
Construction of the population control program
Cells divide
More I More R * More E
Less cells
Less ILess R*Less E
Output module
Regulatory moduleinput
Results : The system reaches a steady state
the cell density in the active programmed cell is 10 fold lower.
Wt cells Programmed cells
Concentration of the killer protein in the active programmed cell is 1000 fold higher
Results : The killer protein concentration
Programmed cellswt cells