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genetic networks in theory and practice. Mukund Thattai NCBS Bangalore. Ecoli: The best understood living organism. 1 M. 1 M. Ecoli: Complex matter that can be engineered. Network biology. protein. mRNA. DNA. RNAP. gene. Network biology. protein. mRNA. regulator. DNA. RNAP.

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Mukund Thattai NCBS Bangalore

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genetic networks

in theory and practice

Mukund Thattai

NCBS Bangalore


Ecoli: The best understood living organism

1M


1M

Ecoli: Complex matter that can be engineered


Network biology

protein

mRNA

DNA

RNAP

gene


Network biology

protein

mRNA

regulator

DNA

RNAP

gene


A biological wish-list

Embryonic development requires complex regulation

[]Amplification

[ ]Noise reduction

[ ]Memory

[ ]Oscillations

 Alberts et al., 1994


Regulated genes

Activation

Inhibition

(D)

X

[]Amplification

[ ]Noise reduction

[ ]Memory

[ ]Oscillations


Negative feedback

[]Amplification

[]Noise reduction

[ ]Memory

[ ]Oscillations


Positive feedback

[]Amplification

[ ]Noise reduction

[]Memory

[ ]Oscillations


Flip flop

[]Amplification

[ ]Noise reduction

[]Memory

[ ]Oscillations


Hysteretic oscillator

[]Amplification

[ ]Noise reduction

[ ]Memory

[]Oscillations


Ring oscillator

[]Amplification

[ ]Noise reduction

[ ]Memory

[]Oscillations


Emergent network properties

Amplification

Noise reduction

Memory

Oscillations

These predictions have been verified experimentally in engineered genetic networks


Engineering Synthetic Networks

Inducers:

Off-the-shelf chemicals

Reporters:

Fluorescent proteins

Transcriptional regulators:

DNA-binding proteins

The host strain:

Escherichia coli

Promoters:

DNA segments that control gene expression

 parts.mit.edu


Engineering Synthetic Networks

The unity of biology allows us to combine modules in new and powerful ways

 parts.mit.edu


Negative feedback

Noise reduction

X

PLtetO1

tetR*-egfp

PLtetO1

tetR*-egfp

 Becskei & Serrano, 2000

 Figures adapted from Hasty et al, 2002


Positive feedback

Memory

TMG

Plac

lacY

Plac

gfp

 Ozbudak & Thattai et al., 2004


Flip flop

Memory

IPTG

PLs1con

cIts

gfp

Ptrc-2

lacI

Heat

 Gardner et al., 2000

 Figures adapted from Hasty et al, 2002


Ring oscillator

Oscillations

PLtetO1

gfp

PLtetO1

cI

Plac

lacI

tetR

PR

 Elowitz & Leibler, 2000

 Figures adapted from Hasty et al, 2002


Getting your hands dirty...


Elena Budrene

New York Times


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