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

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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

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