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The Programming of a Cell
By L Varin and N Kharma
Biology and Computer Engineering Departments
Concordia University
Motivation
• Cells have advantages over
silicon:
• They have/can have built-in
interfaces, to sense and produce
many biological substances
• They are easy to mass produce,
strore and distribute
• They are generally more robust
than man-made systems
• They are optimizable via (real)
evolution
Artificial Life Group The Programming of a Cell 2
Motivation – precisely
• The aim is to
produce a cell that
implements a
configurable Boolean
logic function in 2
var’s
• Ultimately, we
would like to use
intercellular signalling
to compile larger
circuits using many
smaller ones A mechanical AND gate
Artificial Life Group The Programming of a Cell 3
Outline
• Motivation & Outline
• Biological Background
• Problem Statement
• Alternative Methods
• Biological Realization
• Practical Significance
Artificial Life Group The Programming of a Cell 4
Biological Background:
Flow of genetic information
Gene expression
Transcription Translation
DNA RNA Protein
We can easily manipulate DNA
Artificial Life Group The Programming of a Cell 5
Biological Background:
Gene expression (promoters)
+1
RNA Pol
-35 -10
Box Box RNA
TTGTCA TATAA
Core promoter = Binding site for RNA Polymerase
In this configuration transcription is ON
Artificial Life Group The Programming of a Cell 6
Biological Background:
Gene expression (promoters)
+1
X
R
-35 -10
box box
operator
R = Repressor
In this configuration RNA Polymerase cannot bind
transcription is OFF
Artificial Life Group The Programming of a Cell 7
Biological Background:
Gene expression (synthetic gene)
Modular structure
• Construct a promoter
• Insert an operator
• Select a coding sequence (output)
Output
-35 -10
box box
operator
Artificial Life Group The Programming of a Cell 8
Biological Background:
Biological regulatory network
• The lactose operon of E. coli
lacI X
repressor R
-35 O -10
R Transcription is OFF
Active
repressor
Artificial Life Group The Programming of a Cell 9
Biological Background:
Biological regulatory network
• The lactose operon of E. coli
lacI
repressor RNA Pol
-35 O -10
X
R Transcription is ON
Inactive
repressor
= inducer (lactose)
Artificial Life Group The Programming of a Cell 10
Biological Background:
Artificial regulatory network
• Select an output gene
• Select a promoter
• Select an operator-repressor system
• Assemble the parts together
Artificial Life Group The Programming of a Cell 11
Biological Background:
Artificial regulatory network
- lactose
X OFF
lacI
Repressed by lac repressor Lac promoter l C1 repressor
ON
Repressed by C1 repressor l promoter Green Fluorescent protein
Artificial Life Group The Programming of a Cell 12
Biological Background:
Artificial regulatory network
+ lactose R
X
Repressed by lac repressor Lac promoter l C1 repressor
C1
C1 X
Repressed by C1 repressor l promoter Green Fluorescent protein
OFF
Artificial Life Group The Programming of a Cell 13
Problem Statement ++
• Synthesize a cell that can
be configured to
implement any one of 16
different Boolean
functions in 2 variables
• Such a project will
involve 4 phases:
1 Designing a regulatory
network
2 Constructing a configurable
cell
3 Configuring the cell
4 Using the cell
Artificial Life Group The Programming of a Cell 14
Methodology 1: Using Repressilators
AB
Output
R1
Anti-sense
DNA
R2
Artificial Life Group The Programming of a Cell 15
Methodology 1: Full Picture
AB A B’
Output Output
R1 R3
Anti- Anti-
sense R2 sense R4
DNA DNA
A’ B’ A’ B
Output Output
R5 R7
Anti- Anti-
sense R6 sense R8
DNA DNA
Artificial Life Group The Programming of a Cell 16
Methodology 2: Using Excision
• A Boolean AB Output
function in 2 00 ?
variables has 16 01 ?
possible truth 11 ?
tables 10 ?
• They all involve
1-4 (3) different
terms of 2
variables
Artificial Life Group The Programming of a Cell 17
Methodology 2: Chosen Path
• Design
A regulatory network implementing the 4 terms and allowing
for subsequent excision of any term
• Construct
The regulatory network by embedding 4 gene networks
corresponding to the 4 terms in a real organism (e.g. e.coli)
• Configure
The cell by excising those gene networks corresponding to the
unwanted terms
• Use
The configured cell by adding the inducers (variables) it is
designed to respond to, and monitoring the output
Artificial Life Group The Programming of a Cell 18
Biological Realization
• 2 variables A and B
• A = lactose
• B = arabinose
• 1 promoter
• 4 repressors
• 1 ouput gene (Green Fluorescent Protein)
• 4 terms (A B), (A B), (A B), (A B)
Artificial Life Group The Programming of a Cell 19
Biological Realization
Output (GFP)
(A B)
= Lac operon operator (bound by LacI repressor)
= Arabinose operon operator (bound by AraR repressor)
In the absence of A and B
LacI AraR
X
Output (GFP)
Artificial Life Group The Programming of a Cell 20
Biological Realization
LacI AraR X
Output (GFP)
(A B)
In the presence of A and B ( lactose and arabinose)
LacI AraR
X X
Output (GFP)
Artificial Life Group The Programming of a Cell 21
Biological Realization
Output (GFP)
(A B)
= l Pr operator (bound by C1 repressor)
= Arabinose operon operator (bound by AraR repressor)
LacI X
C1
In the absence of A
AraR
and in presence of B
X
Output (GFP)
Artificial Life Group The Programming of a Cell 22
Biological Realization
Output (GFP)
(A B)
= lactose operon operator (bound by lacI repressor)
= l Prm operator (bound by CRO repressor)
AraR X
CRO
In the presence of A
LacI
and in absence of B
X
Output (GFP)
Artificial Life Group The Programming of a Cell 23
Biological Realization
Output (GFP)
(A B)
= l Pr operator AraR X
(bound by C1 repressor) CRO
= l Prm operator
(bound by CRO repressor)
LacI X
C1
In the absence of A
and in absence of B
Output (GFP)
Artificial Life Group The Programming of a Cell 24
Biological Realization
Output (GFP)
(A B)
Output (GFP)
(A B)
Output (GFP)
(A B)
Output (GFP)
(A B)
Artificial Life Group The Programming of a Cell 25
Practical Significance
Limited
Outputs tied Configurable Inputs tied
to a Decision to a
particular Logic particular
application: application:
GFP etc. lactose,
arabinose
etc.
Artificial Life Group The Programming of a Cell 26
Practical Significance
Application-
Application-
specific
specific
outputs
inputs
Output Extended Input
Interface Decision Logic Interface
Standardized Signals
Artificial Life Group The Programming of a Cell 27
Summary
• A specific Boolean logic function in 5 variables has been recently
realized in living cells, but never a configurable bio-logic device
theoretic value
• We believe we have found a simple means of realizing a
configurable 2-input Boolean function in an e.coli cell simple
methodology
• Both the logic functionality and the practical value of the work
can be considerably enhanced with the use of intercellular
signaling broader vision
• First experiments (for the Method 2) will start in January 2008
and we’ll update you!
Artificial Life Group The Programming of a Cell 28
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