Transcript Turn on Gene 1

Welcome iGEM team 2007
Research at the Interface
Biology
Engineering
Chemistry
Economics
Physics
Computer Science
Programming Cells
Goal:
Can we Program cells in a manner analogous to how we now
program computers?
#include <iostream>
main()
{
int input;
cout << “Please Enter 0 or 1”;
cin >> input;
if (input = = 1)
cout << “Hello iGEM";
else
cout << “Goodbye”;
return 0;
}
Programming Cells
Goal:
Can we Program cells in a manner analogous to how we now
program computers?
Cellular Pseudocode
{
read in input; //light, chemical, etc
if (input is equal to “Chemical A”)
“Turn on Gene 1”;
else
“Gene 1 remains off”;
}
Programming Cells
Goal:
Can we Program cells in a manner analogous to how we now
program computers?
Cellular Pseudocode
Chemical A
Activator
Gene
Promoter
Region
{
read in input; //light, chemical, etc
if (input is equal to “Chemical A”)
“Turn on Gene 1”;
else
“Gene 1 remains off”;
}
Programming Cells
Goal:
Can we Program cells in a manner analogous to how we now
program computers?
Cellular Pseudocode
Chemical A
Activator
Gene
Promoter
Region
{
read in input; //light, chemical, etc
if (input is equal to “Chemical A”)
“Turn on Gene 1”;
else
“Gene 1 remains off”;
}
Programming Cells
Goal:
Can we Program cells in a manner analogous to how we now
program computers?
Cellular Pseudocode
{
read in input; //light, chemical, etc
Chemical A
Activator
Gene
Promoter
Region
if (input is equal to “Chemical A”)
“Turn on Gene 1”;
mRNA
else
“Gene 1 remains off”;
Protein
}
Programming Cells
Goal:
Can we Program cells in a manner analogous to how we now
program computers?
Cellular Pseudocode
Repressor
Promoter
Region
{
read in input; //light, chemical, etc
if (input is equal to “Chemical A”)
“Turn on Gene 1”;
else
“Gene 1 remains off”;
}
Programming Cells
Goal:
Can we Program cells in a manner analogous to how we now
program computers?
Chemical A
Repressor
Promoter
Region
Cellular Pseudocode
{
read in input; //light, chemical, etc
if (input is equal to “Chemical A”)
“Turn on Gene 1”;
else
“Gene 1 remains off”;
}
Programming Cells
Goal:
Can we Program cells in a manner analogous to how we now
program computers?
Cellular Pseudocode
Chemical A
Repressor
Promoter
Region
{
read in input; //light, chemical, etc
if (input is equal to “Chemical A”)
“Turn on Gene 1”;
else
“Gene 1 remains off”;
}
Programming Cells
Goal:
Can we Program cells in a manner analogous to how we now
program computers?
Cellular Pseudocode
Chemical A
{
read in input; //light, chemical, etc
Repressor
Promoter
Region
if (input is equal to “Chemical A”)
“Turn on Gene 1”;
mRNA
else
“Gene 1 remains off”;
Protein
}
Programming Cells
But Really We would like to “write more complex cellular programs”
dozens of lines of code (or even 100s)
Multiple input types
Multiple output types
Crosstalk
Loops
Counters
Perform a Variety of Activities
Engineering Biology
Engineering
-Framework for Design
We would like a toolbox of Modular Genetic Parts
-Standardized Parts (BioBricks)
-Swap components- Put together in new ways to perform new function
-Portability - Transfer into new organisms or strains
-Ability to program
Hierarchy:
Parts
Library of
Parts
http://parts.mit.edu
Devices
Build Devices
With the Parts
Systems
Link Devices
Together
http://parts.mit.edu
BioBrick Parts Assembly Strategy
The Cell is a Complex System
Dynamic System
Although we do know the complete
set of genes for many organisms
We don’t know exactly how
everything works together
(Goal of Systems Biology)
Schematic of an E. coli cell, by D. Goodsell, Scripps
Synthetic Biology
Research at the Interface
What can we do with reprogrammed cells:
1. Harness for production (metabolic engineering)
-Introduce New Pathways
-Malarial Drug (artemisinin)
2. Coordinate Behavior of Cells
Target cells to tissues or other cell types
Respond to disease states or disease cells (biosensor, target cell
death)
2-D Patterns
3. Bacteria to Build or Fabricate Systems
Sensors
Sensors
-respond to external commands
-Can be used to turn genes on and off
-Control motility, etc
1. Cytoplasmic Regulatory Proteins
2. Two-Component Systems
3. Environment Responsive Promoter
4. Regulatory RNAs
Sensors
Cytoplasmic Regulatory Proteins
- Inducers – Usually a small molecule – pass through cell membrane
binds to a cytoplasmic regulatory protein
1. Turn on an activator
2. Turns off a repressor
Maximal Induced State
Graded population induction
(All cells behave similar)
Basal activity
Intermediate Induction Difficult
Dynamic Range of Induction
Sensors
Sensor Domain
NarX
Two Component Systems
Kinase Domain
P tar
-Membrane Bound Sensor with Kinase Domain
-Responds to different stimuli (light, temp, chemicals)
-Phosphorylates a Response Regulator (Triggers Transcription, binds promoter)
Sensors
Sensor Domain
NarX
Environmental Response Promoters
Kinase Domain
P tar
- pH, temp, Oxygen, UV light
-might not know the protein elements involved (but know result)
UV light
Degrade
cI repressor
Promoter
Region
System used in “Tumor Killing Bacteria”
-Anaerobic Inducible Promoter
Sensors
Regulatory RNAs
RNA aptamers – Change Conformation when bound to small molecule,
protein, or peptide
Potentially can be used to regulate any gene
Off conformation
(ligand not bound)
On conformation
(ligand bound)
On Conformation
Binds to target transcript
And inhibits transcription
(Antisense)
Schematic by C. Smolke
Genetic Circuits
Genetic Circuits
Enable Cells to
- Process Input Signals
- Make Logical Decisions
- Cell-Cell Comunication
Switch
-Used to turn on Gene Expression (once input is above a threshold)
Forms:
Transcriptional Activators or Repressors
Pre-transcription
Genetic Circuits
Inverter – a switch that produces a reciprocal response (logic gate)
on
repressor
off
Toggle Switch – can exist in two states
-where one or the other repressor is fully expressed
-switch can be flipped between states
Genetic Circuits
Dynamic Circuits
- Oscillator – Cascade
- 3 Repressors
GFP in a single cell over time (Elowitz and Leibler)
Genetic Circuits
Cell – Cell Communication
Sender Cell
Receiver Cell
Chemical
Signal
acyl-homoserine lactone (AHL)
Figure from Basu … Weiss
Actuators
Actuators-To control the output
Mechanical Device for Moving a System
Invasion of Malignant Cells (hypoxic environment triggers invasion of cells)
Y. pseudotuberculosis
invasin
In Conclusion
We now have the tools to build new and exciting devices within biological cells
Where we can construct new parts, new devices, and new systems
We can build on previous work in Synthetic Biology
Develop novel uses for this technology (Medical applications)
Share with others through iGEM
Thanks!