Modeling of Cell-to-Cell Communication Processes with Petri Nets Using the Example of Quorum Sensing - Biological Petri Nets - page 192

Fig. 5. Reconstruction of the Aliivibrio salmonicida quorum sensing system in VANESA. Triangles represent the important
elements in the system, which have a fundamental role in the quorum sensing communication processes. Circles/octahedrons
represent the other fundamentals in the system. Squares represent biological processes, such as motility, biofilm formation, and
others. The color is related to pathway activities, which are based on experimental data*.
model into Cell Illustrator the Petri net model in Fig. 6 was devised. However, the modeled system had
to be extended by further elements and simulation techniques to sense the real biological behavior. The
elements and techniques that were added to the system are described in the following.
Those enzymes which synthesize the autoinducer (AI) were connected with a transition to an input
connector to simulate a continuous activation of the AI and enzymes, e.g. LuxS or AinS. Some con-
nections were revised, e.g. the connection between the two AI C-HSL and 3-oxo-C6-HSL. A further
refinement of the model had to be performed, due to the fact that LuxR1 and LuxR2 are only activated
as far as the AI bind to the enzymes. The gene activation was modeled with association connectors to
simulate a continuous activation of biological processes such as biofilm formation, among others.
To model a bacterial state change within the circular transduction, the dynamic quorum sensing
behavior at high and low cell density had to be improved. Several association and inhibitory connectors
were added to the system, e.g. the one from AI-2 to LuxU.
Further more, several transitions can only fire by reaching a certain AI-threshold. Those transitions
were connected with the AI by an association connector. On the other hand, several transitions are not
able to fire at a given threshold level, e.g. the one from AI-2 to LuxU. Those transitions were connected
with the AI by an inhibitory connector.
*A colored version of the figure/chart is available at In Silico Biol. 10 , 0003 < http://www.bioinfo.de/isb/2010/10/0003/ > , 1
February 2010.