Table 2 Biological Description of Selected Simulation Rules and Variables

Dynorphin

Class of opioid peptides, activator of MvfR

OprF

Outer membrane protein, binds INF-γ to enhance virulence

RhlRI

Quorum sensing subsystem composed of RhlI, the C4-HSL (N-butyrylhomoserine lactone) autoinducer synthase and RhlR transcriptional regulator, activates as a consequence of binding INF-γ to OprF

lux box

DNA sequence with dyad symmetry located in the promoter regions of many quorum-sensing-controlled genes including lecA. Functions as binding site for quorum sensing transcriptional regulators RhlR and LasR.

Adenosine-deaminase

Converts adenosine to inosine

Inosine

Activates lecA expression

PstS

Phosphate-binding protein, induced by phosphate limitation

PhoR

Two-component (PhoR/PhoB) sensor kinase, activated during phosphate limitation as a consequence of PstS expression.

PhoB

Two-component (PhoR/PhoB) transcriptional regulator for phosphate regulon genes. Phosphorylation of PhoB by PhoR enhances its binding activity to pho box.

pho box

DNA conserved sequence located in promoter region of phosphate regulon genes, including mvfR.

lecA

Gene encoding PA-I lectin, the expression is regulated by quorum sensing. Exposure of P. aeruginosa to epithelial cell agents adenosine, opioid, and INF-γ induces the expression of lecA.

MvfR

P. aeruginosa LysR-type transcriptional regulator, modulates the expression of multiple quorum sensing (QS)-regulated virulence factors, regulates the biosynthesis of 4-hydroxy-2-alkylquinolines (HAQs) including HQNO and PQS.

mvfR box (corresponds to TNA in Table 1)

DNA consensus palindromic sequence T-[N]₁₁-A with a dyad symmetry located in promoter region of MvfR-regulated genes including pqsABCDE.

pqsABCDE

Operon regulated by MvfR, encodes proteins required for the biosynthesis of HQNO and HHQ, a precursor of PQS. HHQ and PQS potentiate MvfR binding to mvfR box upstream of pqsABCDE forming feedback loop regulation.

HQNO

4-hydroxy-2-heptylquinoline-N-oxide, the P. aeruginosa exoproduct regulated by QS, suppresses the growth of many gram-positive bacteria including Lactobacillus spp., mediates protection of Staphylococcus aureus against aminoglycosides antibiotics.

PQS

2-heptyl-3-hydroxy-4(1 H)-quinolone, the P. aeruginosa exoproduct regulated by QS, plays multifunctional role in quorum sensing including intra-cellular and inter-cellular signaling. Shapes the population structure of Pseudomonas and response to and survival in hostile environmental conditions. Induces apoptosis in mammalian cells.

PA-I lectin

Pseudomonas toxin causes potent epithelial barrier dysfunction