Transcript SyntheticBioOverview

Synthetic Biology = design and engineering of simple biological systems
that aren’t found in nature
Why would we want to do this?
- Want to understand natural systems. One of the best ways to
understand a system is to change it or make new, related ones
- To fully “understand” a system, we should be able to predict
the outcome when we change the system
- For molecular biology, this means:
- designing new gene circuits and networks
- modeling the designed systems & predicting their properties
- making & testing the designs
- updating our understanding from the model/test agreement
Engineers often look at biological systems & think that the
systems are equivalent to electronic circuits
e.g,
fluorescent proteins
transcription factors
repressors
activators
polymerases
(transcriptional machinery)
light bulbs or LEDs
transistors or logic gates
NOT gates
OR/AND gates
batteries
and so on...
Could they be right?
--> raises the possibility that biological parts (genes, proteins, etc.)
could be combined using the rules established for analog/digital circuits
The Repressilator – an engineered genetic circuit designed
to make bacteria glow in a periodic fashion
= “repressor” + “oscillator”
repressors (genes that turn off other genes)
green fluorescent
protein (glows!)
Elowitz & Leibler, Nature (2000) 403:335-8
The Repressilator – an engineered genetic circuit designed
to make bacteria glow in an oscillatory fashion
Elowitz & Leibler, Nature (2000) 403:335-8
The repressilator in action...
What other kinds of circuits can be built?
First, we need some more parts!
Some of the other parts available include:
- various sensors
- light, dark, heat, cold
- more switches, logic gates
- more repressors, activators
- parts for intracellular communication
- helpful if cells could tell each what condition they’re in
--> quorum sensing
- parts for signaling the output of circuits
- fluorescent & luminescent proteins
Bioluminescence – only occurs when bacteria are present at high density
==> bacteria communicate in order to establish their density
Australian pinecone fish
~1010 Vibrio bacteria / ml fluid
- fish uses to hunt for prey
Hawaiian bobtail squid
~1011 Vibrio bacteria / ml fluid
in light organ in squid mantle
- squid uses for disguise
(light shines downward, looks like moonlight)
Nature Reviews Molecular Cell Biology 3; 685-695 (2002)
Quorum sensing: chemical-based bacterial communication
HSL diffuses
in/out of cells
LuxI
LuxI protein makes HSL
(homoserine lactone)
Bacterial
cell
Neighboring bacteria produce HSL also
- if enough bacteria around, HSL builds up,
activates bioluminescence
LuxR protein
(transcription factor)
binds HSL, becomes active
Light (bioluminescence)
Promoter
for LuxR
An application of quorum sensing
Programming population control into bacteria with a simple designed circuit
HSL =
homoserine
lactone
HSL
makes HSL
HSLdependent
activator
kills cell
You, Cox, Weiss, Arnold, Nature (2004)
& the engineered circuit works ...
circuit off
circuit on
#
of
bacteria
squares = experimental data
lines = predictions from model
Importantly, the behaviour can be predicted with a simple model
cell growth rate
rate of
cell
growth
rate of
killer protein
production
cell death rate
amount of killer
protein
amount of HSL
killer protein
synthesis rate
killer protein
degradation rate
rate of HSL
production
HSL
synthesis rate
HSL
degradation rate
Standardization of parts: MIT’s “BioBricks” project
Standardization of parts: MIT’s “BioBricks” project
A synthetic biology contest
Goal: Construct a bacteria that acts as a finite state machine
Finite state machine:
- essentially a machine that detects an input and
changes its internal state accordingly, choosing
among several (finite) possible states
--> the theoretical basis for computers
Schools: 1st year: MIT, UT, Princeton, Boston University, Cornell
2nd year: 12 schools (the above + UK, Germany, more...)
3rd year: 37 schools,
including Japan/Latin America/Korea/India/more Europe
expected 4th year: >100
UT’s project – build a bacterial edge detector
Projector
Original image
shine image
onto cells
petri dish coated with bacteria
Cells
luminesce
along the
light/dark
boundaries
Adapted from Zack Simpson
How does edge detection work in principle?
A computer might visit each pixel in turn, and check to see if it is
bordered by both black & white pixels. If yes, highlight the pixel.
Is this
pixel part
of an edge?
No
No
Yes
light-dependent gene expression
Anselm Levskaya, Chris Voigt (UCSF)
Jeff Tabor, Aaron Chevalier, et al.
Bacterial photography
Aaron Chevalier, Jeff Tabor, Laura Lavery, et al.
Mask
Cph1/EnvZ
Fiduciary
Mark
Transfer function:
Incident light ->
Color developed
Linear Gradient
Fiduciary
Mark
The first bacterially-based portrait...
Levskaya et al., Nature (2005) 438:441-2
Now for the edge detector...
Dark
Light
HSL
HSL
HSL
HSL
HSL
HSL
HSL
HSL
HSL
HSL
HSL
HSL
HSL
HSL
HSL
HSL
HSL
The edge detector circuit in more detail
Tabor et al., MS in prep
It works!
Projected Mask
Photo strain
Edge detector strain
Tabor et al., MS in prep
Projected Mask
In silico
In vivo
Tabor et al., MS in prep
Escherichia darwinia
Bacterial photography
Anselm Levskaya (UCSF), Aaron Chevalier, Jeff Tabor,
Zack Simpson, Laura Lavery, Matt Levy, Eric Davidson,
Alex Scouras, Andy Ellington, Chris Voigt (UCSF)
More information for the curious-minded:
Biobricks - Registry of standard biological parts
http://parts.mit.edu/
iGEM - the international Genetically Engineered Machine competition
http://parts.mit.edu/wiki/index.php/Main_Page
From their web site:
iGEM addresses the question: Can simple biological systems be built from standard,
interchangeable parts and operated in living cells? Or is biology simply too complicated to be
engineered in this way?
Beyond trying to answer the question above, our broader goals include:
- To enable the systematic engineering of biology
- To promote the open and transparent development of tools for engineering biology
- And to help construct a society that can productively apply biological technology”
Recommended review articles:
Endy, Foundations for engineering biology. Nature (2005) 438:449-53
Sprinzak & Elowitz, Reconstruction of genetic circuits. Nature (2005) 438:443-8
Hasty, McMillen & Collins, Engineered gene circuits. Nature (2002) 420:224-30