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Programmed cells: Interfacing
natural and
engineered gene networks
Noam Vardi
Kobayashi, Kærn, Araki, Chung, Gardner, Cantor & Collins,( PNAS 2004).
You, Cox, Weiss & Arnold ( 2004 NATURE)
outline
•
•
•
•
Biological background
The building blocks of a programmed cell
Examples
summary
The central dogma
Transcription factors control gene expression
• Activators:
B
A
Activator A
RNA pol
ON
Gene B
RNA pol
• Repressors
Repressor A
Gene B
A
B
OFF
Cells need to compute in order to survive
chemo taxis
Sugar
Metabolism
input
Food gradient
output
Direction of
movement
The
composition of
sugars in the
environment
Activation of lac
operon
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
Kobayashi, Kærn, Araki, Chung, Gardner, Cantor & Collins,( PNAS 2004).
input
Sensory
engineered
regulatory
network
output
module
requirments
•the regulatory network can read the input
•The cell can read the output
Example 1 : interfacing the S.O.S pathway with a
genetic switch
The SOS pathway in E.coli
UV
radiation
DNA
damage
SOS genes
RecA
SOS
repressor
A genetic toggle switch
Each promoter is inhibited by the repressor transcribed from the
opposite promoter
B
B promoter
A
A Promoter
All or none reaction – when one promoter is ON , the second one is OFF
Bi-stable system
Phage lambda’s
Phage λ uses a toggle switch to transfer between 2 cycles
Phage lambda toggle switch uses the E.coli SOS
system
UV
radiation
Lytic phase
DNA
damage
SOS
RecA
repressor
Lysogenic
phase
Phage
genes
Phage
genes
ON
OFF
Interfacing the genetic switch with SOS pathway and
an output module
UV
DNA
damage
SS
DNA
RECA
Sensory moduleSOS system
regulatory moduleON
genetic switch
output module - GFP
PL *
GFP
The system is applied using plasmids
Plasmid - an extra-chromosomal DNA molecule which is capable of
replicating
E.Coli cell
GFP
output module
DNA
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
Regulatory
module
input
Cells
divide
Less E
Output
module
More I
More
R*
More E
Less R*
Less I
Less
cells
Results : The system reaches a steady state
Wt cells
Programmed cells
the cell density in the active programmed cell is 10 fold lower.
Results : The killer protein concentration
wt cells
Programmed cells
Concentration of the killer protein in the active programmed cell is
1000 fold higher
summary
•The unity of the genetic code allows us to transfer circuits between
organisms
•The properties of the output is determined by the characteristic of the
network
examples
•DNA damage detecting circuit (example 1)
•Population density control circuit (example 2)
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