Gene Network Model and Quorum Sensing in Pseudomonas Aeruginosa

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Gene Network Model and Quorum Sensing in
Pseudomonas Aeruginosa

• ELE 580B- Cellular and Biochemical Computing
• Project Presentation
• Hidekazu OKI Canturk ISCI

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Project Workplan

• Quorum Sensing mechanisms in P.A.
• Gene network for P.A.
• Biochemical Reactions
• Possible Simulation Techniques
• Simulation and results

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Pseudomonas Aeruginosa

• Lethal, opportunistic, Gram negative human
  pathogen
• LasB elastase, LasA Elastase, Alkaline Protease ?
  degrade Elastin (lung blood vessels)
• ExotoxinA ? inhibit protein synthesis
• Uses cell-cell signaling quorum sensing to
  overcome host defense
• Communal behaviour

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Quorum Sensing

• ltDiscovered Vibrio Fischeri ? lux systemgt
• Generic Quorum Sensing Mechanism

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Quorum Sensing

• Signaling Molecules
• Gram - ? HSL ring Fatty acid side chain
• Different side chains ?? Different AIs
• Gram ? Oligo Peptides

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Quorum Sensing in PA

• 2 Hierarchical xxxI-xxxR systems
• 1) las system
• 2) rhl system
• Las System
• lasI ? LasI ? 3-oxo-C12-HSL (PAI1)
• lasR ?LasR
• LasR/3-oxo-C12-HSL ?lasA, lasB, aprA, toxA,
  etc. lasI ?rhlR hierarchy!!

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Quorum Sensing in PA

• Rhl System
• rhlI ? RhlI ? C4-HSL (PAI2)
• rhlR ?RhlR
• RhlR/C4-HSL ?rhlAB operon, lasA, lasB, aprA
  other genes rhlI
• PQS AutoInducer
• Additional link between las-rhl
• LasR ? PQS ? lasB rhlI

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Quorum Sensing in PA

• Informal Description

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PA Gene Network

• Is it important to make a detailed circuit like
  the ? circuit?
• All the promoters, repressors, activators,
  specified explicitly
• We care about i/p-o/p and cause-effect relations
• Our Model
• I/p ? Gene ? O/p Protein (? Secondary o/p)
• Details of i/p strength hidden in affinities of
  chemical reactions

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PA Gene Network

• All mentioned genes
• las system inputs
• additional downstream genes
• LasR/PAI1 ?excitatory on rhlR
• PAI1 ? inhibitory on RhlR

PQS

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PA Gene Network

• All mentioned genes
• additional downstream genes

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PA Biochemical Reactions

• Reactions that describe the core of the quorum
  sensing mechanism
• 1) LasR/PAI1 complex
• R1 Concentration of LasR
• A1 Concentration of PAI1
• C1 Concentration of Lasr/PAI1

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PA Biochemical Reactions

• 2) RhlR/PAI2 complex
• R2 Concentration of RhlR
• A2 Concentration of PAI2
• C2 Concentration of RhlR/PAI2
• 3) RhlR/PAI1 complex
• C3 Concentration of RhlR/PAI1

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PA Biochemical Reactions

• 4) LasR
• bR1 Degradation rate of LasR
• VR1 Maximum production rate of LasR
• KR1 Affinity between C1 and lasR promoter!
• R10 LasR basal production rate

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PA Biochemical Reactions

• 5) RhlR
• bR2 Degradation rate of RhlR
• VR2 Maximum production rate of RhlR
• KR2 Affinity between C1 and rhlR promoter
• R20 RhlR basal production rate

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PA Biochemical Reactions

• 6) RsaL
• S RsaL concentration
• bS Degradation rate of RsaL
• VS Maximum production rate of RsaL
• KS Affinity between C1 and rsaL promoter
• S0 RsaL basal production rate

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PA Biochemical Reactions

• 7) PAI1
• bA1 Degradation rate of PAI1
• VA1 Maximum production rate of PAI1
• KA1 Affinity between C1 and lasI promoter
• KS1 Affinity between RsaL and lasI promoter
• A10 PAI1 basal production rate
• A1ex Extracellular PAI1

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PA Biochemical Reactions

• 8) PAI2
• bA2 Degradation rate of PAI2
• VA2 Maximum production rate of PAI2
• KA2 Affinity between C2 and rhlI promoter
• A20 PAI2 basal production rate
• A2ex Extracellular PAI2

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Simulation Methodology

• Deterministic, Single-Cell model
• Numerical Integration of Ordinary Differential
  Equations.
• C Program simulator.
• Time step 0.01 hours.
• Total simulated time varied from 100 hours to
  10,000 hours.

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Simulation Results (1)

• Low concentration of extra-cellular PAI1 causes
  cell to remain in inactive state.
• LasR/PAI1 complex concentration is low

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Simulation Results (2)

• Increasing extra-cellular concentration of PAI1
  beyond 2.0 causes the system to eventually reach
  active state.

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Simulation Results (3)

• Final Steady-State concentrations vary sharply
  depending on the extra-cellular PAI1
  concentration

(KR1 4, KA1 0.4) (KR1 5.0, KA1
0.6 )
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Index of Terms

• Gram negative cell wall of Gram-negative
  bacteria is a thinner structure with distinct
  layers. There is an outer layer which is more
  like a cytoplasmic membrane in composition with
  the typical trilaminar structure.
• Gram Positive are characterised by having as
  part of their cell wall structure eptidoglycan as
  well as polysaccharides and/or teichoic acids.

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References

• David's Paper (lecture 11) --gt about quorum and
  PA
• http//www.cdc.gov/ncidod/eid/vol4no4/vandelden.ht
  m --gt slides come from this web in the lecture 11
  pres
• M. Miller and B Bassler, Quorum Sensing in
  Bacteria, Annual Review of
• Microbiology, 55 165--199, 2001 --gt Rweiss
  reading list paper
• http//info.bio.cmu.edu/Courses/03441/TermPapers/9
  9TermPapers/Quorum/ --gt WEB page about PA and
  quorum
• L. Passador and B. Iglewski, "Quorum Sensing and
  Virulence Gene Regulation in Pseudomonas
  Aeruginosa", Virulence mechanisms of bacterial
  pathogens, 1995
• lecture 7 slides --gt the lambda cct and the
  determinstic vs stochastic simulation models
• Fagerlind, Magnus. The role of regulators on the
  expression of quorum-sensing signals in
  Pseudomonas aeruginosa A thesis of 20p in
  molecular computational biology for the degree of
  Bachelor of Science at the University of Skovde.
  Oct, 2001
• Albus, Anne M., etal. Vfr Controls Quorum
  Sensing in Pseudomonas Aeruginosa Journal of
  Bacteriology, June 1997, p 3928-3935