Transcript Synthetic Biology and iGEM

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
Constitutive
promoter
AgrC
AgrA
Membrane-bound histidine Response regulator
kinase AIP sensor
Simple receiver biobrick
P2 (activated by
AgrA-P)
PoPS out
Synthetic Biology
'Combines science and
engineering in order to design
and build novel biological
functions and systems.' Wikipedia
+
Synthetic Biology
AN ENGINEERING PERSPECTIVE
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Engineers view biology as a
technology
Heavy emphasis on developing
foundational technologies
International Genetically
Engineered Machine competition
(iGEM)
Registry of Standard Biological
Parts
iGEM
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"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
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Library of standardized
parts (called BioBrick
standard biological parts)
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Use them
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Design your own
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Contribute to the registry
B0034
RBS
iGEM – The Registry
iGEM
BROADER GOALS
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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
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Maintain and enhance human health and
our environment
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Fabricate materials and structures
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Produce energy
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Provide food
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Process information
Synthetic Biology
POTENTIAL APPLICATIONS – Health
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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
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Carbon sequestration
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Bacteria-produced ethanol
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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—twocomponent peptide
signalling system
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Bacterial Amplifier
PoPS in
Amplifier
PoPS out
B. subtilis
General background
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Gram-positive soil bacterium
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Genome ~4100 genes
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Class I contaminant
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Often used as a model Gram-Positive
organism
Codon usage differs from E. coli
Why use B. subtilis?
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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
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Culturing B. subtilis
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Transformation methods
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Promoters and shuttle vectors
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Assembling a system
The agr system of S. aureus
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Oligopeptide-based quorum sensing
AIP
AgrC
AgrB
membrane
P
AgrA
P2 promoter
agrB
agrD
agrC
agrA
Peptide signalling:
importance
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“Bacterial Maze”
Another independent signalling system
for the Registry
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and a paradigm for more?
Aid to research into S. aureus
countermeasures
Peptide signalling:
roadmap
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Transfer agr system into B. subtilis, then
into E. coli
B. subtilis
biobrick chassis
Natural
agr
operon
AIP sender device
AIP receiver device
Mutant
fepA
gene
Permeability device
Senders and
receivers in
B. subtilis
Senders
and
receivers
in E. coli
Biological Amplifier
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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
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Amplifier construct
RBS
PoPS in
activator
Promoter
(induced by
activator)
PoPS out
Biological Amplifier –
Further uses
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Repressor
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Signal divider
Biological Amplifier –
Further uses
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Logic gates – XOR
Promoter 1
PoPS 1
Activator 1
Activator 3
Promoter 3
PoPS 3
Promoter 2
PoPS 2
Activator 2
Activator 3
Biological Amplifier –
Further uses
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Logic gates – AND
Promoter 1
PoPS 1
Activator 1
Activator 3
Promoter 3
PoPS 3
Promoter 2
PoPS 2
Activator 2
Activator 3
Biological Amplifier
Overall this system could be widely used
within synthetic biology given its
flexibility and the range of possible basic
constructs