• Gillespie
• Halobacterium
• Systems biology

Halobacterium salinarum, an halofile belonging to the Archaea domain, is a microorganism capable of complex responses to light stimuli. The membrane proteins mediating these responses are two rhodopsins called SRI and SRII, both conjugated with a specific transducer that modulates the signal transduction cascade which controls the flagellar motor. The peculiar behaviour of this organism is observed under orange or blue light stimulations. It has been observed that orange light usually generates an attractant response, which means a decrease in the reversals frequency, whereas blue light causes a repellent response, by means of a strong increase in the frequency.
In order to study the molecular mechanisms underlying this behaviour, a systems biology approach has been used. With the information provided by literature and unpublished results, we developed a minimal model which describes SRI's photocycle.
To interpret and simulate it we carried out a simulator based on Gillespie's stochastic simulation algorithm, which allows to describe the temporal evolution of a biochemical system, considering its stochastic behaviour.
A first model, capable of good qualitative responses to simple stimuli, was thus obtained. This work is aimed at improving and extending it to simulate the whole signaling pathway and perform in silico behavioral experiments to be compared with literature and laboratory data.
To do so, an extensive research in the available literature was conducted in order to describe the essential components of the signaling pathway, their concentrations and the reactions they are involved in.
Several different irradiation conditions were then tested on this extended model. We started with simple experiments like absence of stimulations, orange light alone or blue light under an orange background. More complex conditions tested include simultaneous and repetitive stimulations.
The results are in good qualitative agreement with the laboratory data for most of the conditions, with particularly interesting responses to the more complex stimulations.
Current limits and dierences with the in vivo results suggest the lack of components responsible for memory mechanisms, which are essential for the system to correctly simulate the most complex irradiation conditions.