Team:Paris/Transduction modeling

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Summary

• Introduction
• A. The Fec Operon in our system
• B. Deterministic and Stochastic Simulations
• C. Results and discussion

Introduction

As explained in the main, the goal of this part is to answer the following question :

Indeed, our reception system uses the fec operon in order to transmit the signal received on the outer membrane via the vesicules into the cytoplasm to induce a response of the reception cells ; to have a reliable communication system, it is crucial to have a robust reception. Due to a little amount of molecules, stochastic simulations were performed to try and solve this problem.

Fec Operon as used in our system

After receiving a little amount of messengers, we wanted to get a good activation of the receiver cells. As a consequence, the transduction cascade used in our system is based on the over expression of constitutively active molecules that induce a positive retro action.

The Chemical Equations

Transduction of signal is initiated by FecA molecules coming from the vesicules ; these molecules reach the bacteria outer membrane where they are in proper conditions to activate the FeR proteins. This "crossing" from OMV to the outer membrane is explicited as a first reaction :

Then, once in the outer membrane, these FecA molecules are able to activate the FecR proteins constitutively present in the receiver. Here we have two possibilities to describe this step :

• the FecA molecule directly activates FecR, and the phnomenon is described in a single reaction :

• or FecA and FecR form a complex which is then destructed to release an activated FecR protein ; this mechanism is described through the 2 following reactions :

As an hypothesis, we considered that the crossing of the periplasm is the limiting step, we decided to examine these two different approaches in our simulations.

The rest of the mecanism is described through a serie of reactions listed below and shown on scheme. To get more details on this description, please see our ????? page.

Model Hypothesis

For each reaction, we decided to use a mass action law. Each reaction has a kinetic constant k determining the reaction rate given the concentratin of reactants ; the constant names corresponding to each reaction are listed here.

As the number of molecules at stake is very low at the beginning of the reception, we thought that it was more relevant to perform stochastic simulations based on Gillespie algorithm to study the system.

draft

Our reception system uses the fec operon in order to transmit the signal received on the outer membrane via the vesicules into the cytoplasm to induce a response of the reception cells. Once the vesicule has fusioned with the cell, the FecA molecule present on the previous vesicule wall activates the FecR molecule on the inner membrane ; then, the FecI molecule is activated and the pFec promoter is ON and transcription can start.

The plasmid of this reception cell was designed to produce a positive reaction once the signal is received so that, even with a very faint signal (very very few FecA molecules inside the vesicules), the reception population will be activated. To this end, we have placed the of FecR and the FecI coding downstream th epfec promoter. This way, once the first FecR and FecI molecules are produced, they take part in the activation of the pfec promoter thus creating a positive retroaction.

Our modelling study focussed on the description and analysis of this trancriptional cascade in order to caracterize the ability of the system to receive a signal. To this end, we tried to describe the system with elementary chemical equations allowing both deterministic and stochastic simulation runs. To get more information on this study, please visit the following sections :

• The Fec Operon in our system to read more about the chemical equations chosen to describe the system and the kinetics equations associated
• Deterministic and Stochastic Simulations to read more about the different simulations.
• Results and discussion to learn more about the results of this study.