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Mechanisms of Gene Regulation I

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1 Mechanisms of Gene Regulation I
Virulence: Mechanisms of Gene Regulation I

2 often reside in water at low concentration of organic nutrients
Before ingestion, intestinal pathogens often reside in water at low temperature low ionic strength low concentration of organic nutrients neutral pH

3 higher osmotic strength low pH high pH bile salts
After ingestion, intestinal pathogens must adapt to: higher temperature higher osmotic strength low pH high pH bile salts lack of oxygen and abundant nutrients sequestration of iron by host

4 To survive this journey, the pathogen must rapidly express
a variety of gene products: proteins that help tolerate low pH of stomach flagella and chemotaxis proteins for migration to suitable niche adhesins that permit colonization toxins & invasins to elicit disease iron chelators (siderophores) to scavenge for iron

5 any bacterial property required for
VIRULENCE FACTOR any bacterial property required for entry, growth, or survival in a host examples: capsule - inhibits killing by complement adhesins - permit adherence to host cells acid tolerance factors (ASPs) - adapt pathogen to stomach enzymes - synthesize unavailable nutrients

6 Examples of virulence factors
Chromosome

7 VIRULENCE GENE any gene that encodes a virulence factor
% of Vibrio or Salmonella genes often located on mobile genetic elements (plasmids or phage) or in pathogenicity islands* (large, localized regions of chromosome missing in related non-pathogens) How do cells regulate expression of virulence genes?

8 & THE FLOW OF MOLECULAR INFORMATION
GENE ORGANIZATION & THE FLOW OF MOLECULAR INFORMATION promoter operator gene cistron A cistron B terminator Operon Transcription mRNA Translation Protein

9 Steps of transcription initiation I FORMATION OF CLOSED COMPLEX
promoter operator cistron A cistron B terminator Steps of transcription initiation I FORMATION OF CLOSED COMPLEX closed complex Core RNA polymerase (RNAP) sigma factor (promoter-binding) + = holoenzyme

10 Steps of transcription initiation II FORMATION OF OPEN COMPLEX
closed complex Steps of transcription initiation II FORMATION OF OPEN COMPLEX open complex

11 Steps of transcription initiation III INITIATION & ELONGATION
RNAP elongates sigma factor off mRNA

12 How do cells regulate transcription? lac operon as an example

13 Glucose/cAMP relationship

14 Glucose present / cAMP absent
RNAP 3 REPRESSION Glucose present / cAMP absent lacZ lacY lacA O C P lacR Repression by steric hindrance 2 repressor mRNA 1

15 glucose absent/cAMP present lactose (inducer) present
cAMP-CRP 2 lacZ lacY lacA O C P lacR INDUCTION glucose absent/cAMP present lactose (inducer) present Inducer repressor no DNA binding mRNA 1 lac mRNA 3

16 REPRESSOR binds OPERATOR reducing RNAP binding affinity
RNAP binds PROMOTER REPRESSOR binds OPERATOR reducing RNAP binding affinity (steric hindrance) INDUCER (lactose) binds repressor decreasing REPRESSOR binding affinity ACTIVATOR interacts with RNAP increasing RNAP binding affinity CO-ACTIVATOR (cAMP) binds activator increasing ACTIVATOR binding affinity

17 activators increase stability repressors decrease stability
The probability of transcription initiation increases as the stability of the closed complex increases activators increase stability repressors decrease stability

18 transcription initiation
 &’ CRP dimer -CTD -NTD +1 DNA Flexible linker 5) CRP/alpha-CTD 5 3 3) /alpha-CTD 4) CRP/DNA 4 2 2) DNA/alpha-CTD TTGACA n17 TATAAT 1 1)  /DNA (promoter) Interactions that enhance transcription initiation

19 Regulon: A GENE NETWORK
Stimulus sensor (ex. PhoQ*, ToxS*) signal regulator (ex. PhoP*, ToxR*) + + - operon 1 operon 2 operon 3 regulon proteins response

20 Regulon x - + x Regulator - +

21 Gene regulation is hierarchical
Environmental stimulus

22 A real gene regulatory hierarchy
Published online before print May 23, 2005, /pnas PNAS | May 31, 2005 | vol. 102 | no. 22 | Sean Crosson *, Patrick T. McGrath  , Craig Stephens  , Harley H. McAdams * and Lucy Shapiro  Conserved modular design of an oxygen sensory/signaling network with species-specific output

23 The ToxR Regulon + + Cholera toxin Stimulus tcp toxT acf ctxA ctxB
ToxS toxR toxS ToxR + ToxT acf ctxA ctxB toxT + tcp CtxA Cholera toxin CtxB

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