Programmed cells: Interfacing natural and engineered gene networks

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Programmed cells Interfacing natural
andengineered gene networks
Noam Vardi

• Kobayashi, Kærn, Araki, Chung, Gardner, Cantor
  Collins,( PNAS 2004).
• You, Cox, Weiss Arnold ( 2004 NATURE)

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outline

• Biological background
• The building blocks of a programmed cell
• Examples
• summary

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The central dogma
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Transcription factors control gene expression

• Activators
• Repressors

RNA pol
ON
Gene B
OFF
Gene B
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Cells need to compute in order to survive
output input
Direction of movement Food gradient chemo taxis
Activation of lac operon The composition of sugars in the environment Sugar Metabolism
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Sugar metabolism genes in E.coli

• The lac genes are transcribed if and only if
• Absence of glucose
• The relevant sugar is present

Expression of alternative sugar genes
AND gate
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A modular programmed cell
Kobayashi, Kærn, Araki, Chung, Gardner, Cantor
Collins,( PNAS 2004).
engineered regulatory network
Sensory module
output
input

• requirments
• the regulatory network can read the input
• The cell can read the output

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Example 1 interfacing the S.O.S pathway with a
genetic switch
The SOS pathway in E.coli
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A genetic toggle switch
Each promoter is inhibited by the repressor
transcribed from the opposite promoter
B promoter
A
B
Promoter A
All or none reaction when one promoter is ON ,
the second one is OFF
Bi-stable system
Phage lambdas
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Phage ? uses a toggle switch to transfer between
2 cycles
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Phage lambda toggle switch uses the E.coli SOS
system
UV radiation
DNA damage
SOS repressor
RecA
Lytic phase
Lysogenic phase
Phage genes OFF
Phage genes ON
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Interfacing the genetic switch with SOS pathway
and an output module
DNA damage
SS DNA
UV
Sensory module- SOS system
RECA
regulatory module- genetic switch
ON
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The system is applied using plasmids
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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
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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.
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Example 2 population control
luxI/luxR system the engineered regulatory
module
You, Cox, Weiss Arnold ( 2004 NATURE)
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Construction of the population control program
Regulatory module
Cells divide
More I
More R
More E
Less cells
Less I
Less R
Less E
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Results The system reaches a steady state
Wt cells
Programmed cells
the cell density in the active programmed cell is
10 fold lower.
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Results The killer protein concentration
Programmed cells
wt cells
Concentration of the killer protein in the active
programmed cell is 1000 fold higher
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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)