Table 2.
Biological Description of Selected Simulation Rules and Variables
| Compound | Biological Description |
|---|---|
| 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 |
This table presents a more detailed biological description of selected compounds within the ABM (items with an asterisk "*" from Table 1) that are specifically related to gut host-microbial crosstalk and virulence activation. Readers are encouraged to examine Tables 1 and 2 to see how biological descriptions are converted to ABM rules.