Anatomy of a Stress Response

1
Anatomy of a Stress Response
Denise M. Wolf1, Chris Voigt2, and Adam P.
Arkin1,2,3 1Physical Biosciences Division,
Lawrence Berkeley National Lab 2Bioengineering
Department, University of California Berkeley,
3Howard Hughes Medical Institute
Synergistic motifs for robustness
Stress ubernetwork
Cascade with feedback structure (a motif nested
motif)
When faced with a harsh environment, B. subtilis
can activate a number of different cellular
programs to aid in its survival. It can become
a hunter-gatherer, either using chemotactic
machinery to swim toward food, or secrete
degradative enzymes that break down
macromolecules in the environment into digestible
nutrients. It can regulate alternative metabolic
processes to enable growth in the absence of
important nutrients. It can also become a
warrior, secreting antibiotics into the
environment to eliminate competitors in the same
ecosystem. In addition to hunter-gatherer and
warrior phenotypes, subtilis can also embark upon
a number of developmental programs, including
sporulation, a process resulting in a heat-, uv-
and chemical- resistant spore, a DNA time
capsule that can remain dormant for years and
then pop back to life should environmental
conditions improve.
Analysis of a mathematical model
revealed that there are a number of regulatory
motifs in the network small networks one sees
again and again across networks and across
species - the signal transduction cascade, a
biphasic amplitude filter, and four
agonist/antagonist operon pairs configured as
switches, a pulse generator/switch hybrid, and
part of a spatial oscillator. These motifs are
arranged in the skeletal structure shown above
a cascade with positive and negative feedback
loops running though a sporulation commitment
signal, Spo0AP.

• At LOW Spo0AP, negative feedback dominates
• If Spo0AP HIGH ENOUGH, positive feedback
  dominates
• If Spo0AP TOO HIGH, negative feedback dominates

Nested motifs shape a robust developmental switch
Ubernetwork-level motif Cross-repression
between sporulation and competence at the
ubernetwork-level contributes to
switching/diversification
Sporulation initiation network
Artificial circuit design
SinI/R switching motif Constructed in E. coli
(Chris Voigt)
If Spo0AP enters ()FB dominant zone,
COMMITMENT
Spo0AP-dependent feedback a
thresholding/bistability mechanism A cascade
alone can either amplify or attenuate a signal,
and can filter out noise. Add feedback loops and
you can get more interesting behaviors, such as a
switchlike sigmoidal response, a multi-stable
switch, or even an oscillator. However, the
particular forms of these competing positive and
negative feedback loops as determined by the
nested regulatory motifs - constrain the behavior
of this network to a three-regime pattern of
feedback dominance. At low Spo0AP, negative
FB dominates positive FB at intermediate
Spo0AP, positive FB dominates negative FB, and
at very high Spo0AP, negative FB dominates
once again. This dominance pattern constitutes a
thresholding/bistability mechanism that can
account for the switching and non-genetic
diversity seen in sporulating cultures.
Regulatory themes

• Nested motifs -gt multistable switch, non-genetic
  diversity
• Robustness through redundancy
• Signal integration/transduction via feedback
  modulation
• Design balances noise control w/noise
  exploitation
• Evolutionary conservation of motif equivalence
  sets
• SinI/R switch motif (6/8), Spo0A biphasic motif
  (4/5), RapA/phrA pulse generator (3/8), Partial
  cascade (7/8)

.
Where is the sporulation initiation switch?
Non-genetic diversity? Sporulation is an
irreversible developmental process. A cell either
sporulates, or it doesnt. That sounds like a
switch of some sort. And a population of cells
with the same exact genome, in the same exact
environmental conditions, have different fates.
Some flip that sporulation switch and some dont.
A natural question is, where is the switch? Is
it within the sporulation subnetwork, or is it a
property of the larger survival ubernetwork, or
both, or neither? How is the switching and
non-genetic diversity seen in sporulating
cultures accomplished by the cell?
Future work

• Mutant data analysis, microarray fluorophore
  analysis (w/ Keasling Lab)
• Comparative dynamics among sporulating species
• In silico ubernetwork dynamics other stress
  responses interconnection