Strategies for analysis of a complex regulatory network in E' coli the acid stress response

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Strategies for analysis of a complex regulatory
network in E. coli - the acid stress response
Neil Burton Matt Johnson Peter Lund
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My definition of the stress response adaptive
response of an entity to any event which
threatens its optimal existence
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What properties should a well-adapted (or
well-engineered) stress response system have?

• It has to be able to
• Detect the stress
• Convert the detection into a signal
• Respond appropriately (i.e., response must
  ameliorate the stress in some way)
• Respond at an appropriate level
• This will include ending the response once the
  stress has ended

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A good understanding of a network implies

• Understanding of its components
• Understanding how the components interact with
  each other (including dynamically)
• Understanding their adaptive value for the
  entity
• Understanding how the network may evolve

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Technical approaches

• omics approaches how do the different omes
  change during stress?
• Analysis of known genes in detail in wt and
  different mutant backgrounds - esp. time series
• Comparisons between related strains that respond
  differently to same stress
• Evolution of novel stress response phenotypes in
  the lab

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Acid resistance (AR) and enteric bacteria

• Important for passage through stomach (pH 1-3)
• E .coli can survive remarkably well in conditions
  of high acidity (ltpH2.5)
• Wide range of genes which protect against acid
  are induced by exposure to mild acid stress (pH
  5.7)

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Mild acid pH 5.7

• Aims
• Describe and understand the dynamics of the
  system
• Identify novel components and their interactions
• Understand the adaptive value of the network and
  its components
• Understand how the network might evolve given new
  selective constraints
• Choice of models
• E. coli K-12 MG1655
• E. coli O157H7 (Sakai)

P
EvgA
EvgS
RpoS
ydeO
gadE
gadBC
Other cytoplasmic and periplasmic components
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Lux plasmid reporter system
Promoter (intergenic region 100-200bp)

• Non-invasive
• Automation for high temporal resolution

Stops, RBS
P. luminescens LuxCDABE Operon
pLUX
Light
Low copy pSC101 replication
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Questions

• Does this system give us usable data?
• Can it be used to explore different mutant
  backgrounds/different strains?
• Can we uncover novel aspects of the network using
  this approach?

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General messages

• Promoter probes using lux/gfp provide
  reproducible, high density time-series data,
  suitable for model fitting
• They can be used to identify potential new links
  in regulatory networks
• However, the outputs dont necessarily map
  directly onto transcriptional outputs
• Lab-based evolution and whole genome resequencing
  has great potential for understanding the nature
  and evolution of stress response systems (and
  other networks) at the whole organism level

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Matt Neil
UoB Nick LomanDov Stekel
George Weinstock, Washington Uni NIH