gene networks in theory and practice
TRANSCRIPT
Mukund Thattai, NCBS/TIFR
Humboldt Kolleg, January 2011
Gene networks in theory and practice
Synthetic biology:bottom-up engineering of living systems
Complexsystems
Simpleparts
1µM
The Ecoli genome contains about 4000 genes...
... and the human genome contains about 24000 genes
gene
DNA
mRNA
protein
geneRNAP
DNA
mRNA
protein
Genes can be turned on and off so it’s acombinatorial system
geneRNAP
activator
DNA
mRNA
protein
Genes can be turned on and off so it’s acombinatorial system
geneRNAP
inhibitor
DNA
mRNA
protein
Genes can be connected into networks with usefuldynamical properties...
Negative feedback Positive feedback
Flip-flop
Hysteretic oscillator
Ring oscillator
Noise reduction Memory Oscillations
...which we can test by building networks from basic parts
Transcriptional regulators:DNA-binding proteins
Reporters:Fluorescent proteins
Inducers:Off-the-shelf chemicals
The host strain:Escherichia coliPromoters:
DNA segments that controlgene expression
where am I now?(position)
θ
where do I go next?(velocity)
Cartoon: Sudhir P., NCBS
Essential ingredients for oscillations:
Notion of ‘now’ and ‘next' [2 dynamical variables]Tendency to reverse direction [negative feedback]Intertia [reinforcement / delay]
Horikawa et al., Nature, 2006
Drosophila circadian clock Zebrafish segmentation clock
Gallego & Virshup, Nat. Rev. Mol. Cell Biol., 2007
Panda et al., Nature, 2002
[synchronized]
12h dark 12h light
lights outactivity
The “hysteretic oscillator” motif:negative feedback with delay
“limit cycle” oscillations
Synthetic hysteretic oscillators
Atkinson et al., Cell, 2003
Stricker et al., Nature, 2008
Danino et al., Nature, 2010
[synchronized]
pX
LuxI
AHL
LuxR
pR
Output
n-acyl homoserine lactone
Synchronization requires cell-to-cell coupling
sender receiversignal
The Vibrio fischeri quorum sensing systemprovides a coupling mechanism
A synchronized oscillator based onquorum sensing machinery
The synchronization protocol
Inputminimal medium
limiting NH4Cl± AHL
Output:OD600 [cell density]imaging CFP/YFP
Nitrogen-limited chemostat
Control: continuous AHL
Test: Synchronize with 12h AHL measure
measure
measure
Persistent oscillations! ...measure
measure
measure
Herioc experiments by Navneet Rai
YFP
CFP
... but only from a synchronized sub-group of cells
Herioc experiments by Navneet Rai
The onset of synchrony is typically driven by a core group
Strogatz, Physica D, 2000
Kuramoto model of weakly-coupled limit cycle oscillators
steady state phases, for any ωi ≤ Kr
