Selected Case Studies

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MIT 2006: Engineering bacteria to smell good

BSMTwintergreen

C. breweri S. cerevisia

e

ATF1banana

Slides borrowed from the 2006 MIT Team

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Engineering the scent of bacteria

What is the desired output?

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Components of engineered cell

What is needed to create the desired output?

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Components of engineered cell

What is needed to create the desired output?

Creating devices with BioBricks

Regulatory Part/Promoter

Protein Coding Part

TerminatorRibosome Binding Site

Protein

Components of scent-producing devices

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Components of scent-producing devices

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Components of upstream devices

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How do you regulate when the scents are expressed?

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Goal: Sense the growth state of culture

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Regulating the timing of expression

osmY: active in stationary phase & under high osmotic pressure conditions

osmY

osmY + inverter

Regulating the timing of expression

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Design principles

• What is the desired output? What is needed to create this output?

• What do you want to sense?

• Use of constitutive promoters, inducible promoters, and inverters

Berkeley 2006Bacterial Networks

Need: To transfer DNA messages from one bacterial cell to another

Means: Bacterial Conjugation

Need: To specifically control who can read the DNA message

Means: Riboregulation

Some slides borrowed from the 2006 Berkeley Team

Regulatory Part/Promoter

Terminator

Protein

Protein Coding PartRibosome Binding

Site

Ribosome Binding Site

Protein

DNA

RNARibosome Binding

Site

DNA to RNA to Protein

Protein synthesis from RNA

Protein

RNARibosome Binding

Site

Ribosome

Locked structure prevents ribosome binding

Protein

RNARibosome Binding

Site

Ribosome

RNA “Key” unlocks lock

Protein

RNARibosome Binding

Site

Ribosome

Goal: Create network of cell-cell communication

RNA as a regulatory mechanism

• Can activate some “riboswitches” with small molecules

• Advantage: fast response - transcript is already made

• Alternative method: block translation by adding antisense RNA to RBD