Synthetic Biology and iGEM

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Synthetic Biology and iGEM

• Cambridge iGEM2007 team
• 27 July 2007

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Synthetic Biology

• '...a new and rapidly emerging discipline that
  aims at the (re-)design and construction of (new)
  biological systems.' Synthetic Biology 3.0

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Synthetic Biology

• 'Combines science and engineering in order to
  design and build novel biological functions and
  systems.' Wikipedia

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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

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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...'
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iGEM BioBricks

• Library of standardized parts (called BioBrick
  standard biological parts)?
• Use them
• Design your own
• Contribute to the registry

B0034
RBS
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iGEM The Registry
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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

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Synthetic Biology

• ENGINEERED BIOLOGICAL SYSTEMS
• Maintain and enhance human health and our
  environment
• Fabricate materials and structures
• Produce energy
• Provide food
• Process information

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Synthetic Biology

• POTENTIAL APPLICATIONS Health

• 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

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Synthetic Biology

• POTENTIAL APPLICATIONS Materials Information
  Processing

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Synthetic Biology

• POTENTIAL APPLICATIONS Energy
• Carbon sequestration
• Bacteria-produced ethanol
• Bacteria hydrogen production

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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)
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Our Ideas

• Gram Positive bacteria, B. subtilis

• Signallingtwo-component peptide signalling
  system

• Bacterial Amplifier

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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

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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

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Our aims

• Culturing B. subtilis
• Transformation methods
• Promoters and shuttle vectors
• Assembling a system

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The agr system of S. aureus

• Oligopeptide-based quorum sensing

AIP
AgrC
AgrB
membrane
P
AgrA
P2 promoter
agrB
agrA
agrC
agrD
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Peptide signalling importance

• Bacterial Maze
• Another independent signalling system for the
  Registry
• and a paradigm for more?
• Aid to research into S. aureus countermeasures

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Peptide signalling roadmap

• Transfer agr system into B. subtilis, then into
  E. coli

B. subtilis biobrick chassis
Senders and receivers in B. subtilis
Natural agr operon
AIP sender device
AIP receiver device
Senders and receivers in E. coli
Mutant fepA gene
Permeability device
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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

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Biological Amplifier

• Amplifier construct

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Biological Amplifier Further uses

• Repressor
• Signal divider

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Biological Amplifier Further uses

• Logic gates XOR

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Biological Amplifier Further uses

• Logic gates AND

Promoter 1
Activator 1
Activator 3
PoPS 1
Promoter 3
PoPS 3
Promoter 2
Activator 2
Activator 3
PoPS 2
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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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