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Synthetic Biology and iGEM
Cambridge iGEM2007 team
27 July 2007
Synthetic Biology
'...a new and rapidly emerging discipline that aims at the (re-)design and construction of (new) biological systems.' Synthetic Biology 3.0
Simple receiver biobrick
AgrC AgrA
Membrane-bound histidine kinase AIP sensor
Response regulator
Constitutive promoter
P2 (activated by AgrA-P)
PoPS out
'Combines science and engineering in order to design and build novel biological functions and systems.' Wikipedia
+
Synthetic Biology
AN ENGINEERING PERSPECTIVE
Engineers view biology as a technology
Heavy emphasis on developing foundational technologies
International Genetically Engineered Machine competition (iGEM)
Registry of Standard Biological Parts
Synthetic Biology
iGEM
"Can simple biological systems be built from standard, interchangeable parts and operated in living cells? Or is biology just too complicated to be engineered in this way?" Randy Rettberg, Director of the iGEM competition
'Dunno. Let's try to build some devices...'
iGEM – BioBricks
Library of standardized parts (called BioBrick standard biological parts)
Use them
Design your own
Contribute to the registry
B0034
RBS
iGEM – The Registry
iGEM
BROADER GOALS Enable systematic engineering of biology Promote the open and transparent
development of tools for engineering biology
Help construct a society that can productively apply biological technology
Synthetic Biology
ENGINEERED BIOLOGICAL SYSTEMS Maintain and enhance human health and
our environment Fabricate materials and structures Produce energy Provide food Process information
POTENTIAL APPLICATIONS – Health
Synthetic Biology
Sepsis - An overwhelming systemic immune response to toxin-producing bacteria in the bloodstream
Designed feedback loop
Inhibits signaling cascade at MyD88 (a 'weak spot')
26 new BioBricks
Type of artificial immunotolerance
Synthetic Biology
POTENTIAL APPLICATIONS – Materials & Information Processing
Synthetic Biology
POTENTIAL APPLICATIONS – Energy
Carbon sequestration
Bacteria-produced ethanol
Bacteria hydrogen production
Our Team
• A mix of biologists, engineers and physicist.
• Shared enthusiasm of synthetic biology
Front row, from left: Narin Hengrung, Yi Han, David Wyatt Second row, from left: Zhizhen Zhao (Jane), Stefan Milde, Dmitry Malyshev, Xinxuan Soh (Sheila) Third row, from left: Yi Jin Liew, John Crowe, Lovelace Soirez, Stephanie May, Yue Miao Back row, from left: James Brown (PhD student mentor), Jim Haseloff (faculty), Gos Micklem (faculty)
Our Ideas
• Gram Positive bacteria, B. subtilis
• Signalling—two-component peptide signalling system
• Bacterial Amplifier
PoPS outPoPS in Amplifier
B. subtilisGeneral background
Gram-positive soil bacterium Genome ~4100 genes Class I contaminant Often used as a model Gram-Positive
organism Codon usage differs from E. coli
Why use B. subtilis?
Model Gram-positive organism, not yet used in iGEM
Better at secreting substances than Gram-negative bacteria
Easy to transform Adds new biobricks and new capabilities
to Registry
Our aims
Culturing B. subtilis Transformation methods Promoters and shuttle vectors Assembling a system
The agr system of S. aureus
Oligopeptide-based quorum sensing
agrDagrB agrC agrAP2 promoter
AgrB
membrane
AIP
AgrC
AgrAP
Peptide signalling: importance
“Bacterial Maze” Another independent signalling system
for the Registry and a paradigm for more?
Aid to research into S. aureus countermeasures
Peptide signalling: roadmap
Transfer agr system into B. subtilis, then into E. coli
AIP sender device
AIP receiver device
Permeability device
Senders and receivers in
B. subtilis
Senders and
receivers in E. coli
Natural agr
operon
Mutant fepA gene
B. subtilis biobrick chassis
Biological Amplifier
To build a standard amplifier which can be used in any synthetic (biobricked) system
It should take a standard PoPS input and give a standard PoPS output
Biological Amplifier
Amplifier construct
PoPS inPoPS out
RBS activator
Promoter(induced by activator)
Biological Amplifier – Further uses
Repressor Signal divider
Biological Amplifier – Further uses
Logic gates – XOR
PoPS 3
PoPS 1
PoPS 2
Activator 1
Activator 2
Activator 3
Activator 3
Promoter 1
Promoter 2
Promoter 3
Biological Amplifier – Further uses
Logic gates – AND
PoPS 1
PoPS 2
Activator 1
Activator 2
Activator 3
Activator 3
Promoter 1
Promoter 2
Promoter 3
PoPS 3
Biological Amplifier
Overall this system could be widely used within synthetic biology given its
flexibility and the range of possible basic constructs
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