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Bacterium

Asymmetric Cell Division in Caulobacter Crescentus

Summary: 

Caulobacter crescentus is a model organism for the study of asymmetric division and cell type differentiation, as its cell division cycle generates a pair of daughter cells that differ from one another in their morphology and behavior. One of these cells (called stalked) develops a structure that allows it to attach to solid surfaces and is the only one capable of dividing, while the other (called swarmer) develops a flagellum that allows it to move in liquid media and divides only after differentiating into a stalked cell type. Although many genes, proteins, and other molecules involved in the asymmetric division exhibited by C. Crescentus have been discovered and characterized during decades, it remains as a challenging task to understand how cell properties arise from the high number of interactions between these molecular components. This chapter describes a modeling approach based on the Boolean logic framework that provides a means for the integration of knowledge and study of the emergence of asymmetric division. The text illustrates how the simulation of simple logic models gives valuable insight into the dynamic behavior of the regulatory and signaling networks driving the emergence of the phenotypes exhibited by C. crescentus. These models provide useful tools for the characterization and analysis of other complex biological networks.

Curation
Submitter: 
C. Chaouiya

Qualitative modelling of the network controlling Trp biosynthesis

Summary: 

This work is described in [1]. Its central motivation is the definition of a generic approach to obtain an integrated modelling of the regulated Trp biosynthesis pathway. In this context, we refer to Petri net models [2]. First, we present the modelling of the regulatory control of the Trp biosynthesis in E.Coli (download Trp_reg.zginml). The following figure illustrates the simplified logical regulatory graph. Each node of the regulatory graph represents an active component: Trp, the active enzyme (i.e. not associated with Trp), and the active repressor (the dimmeric form of TrpR in association with Trp). The last node (Trpext) accounts for the import of Trp from the external medium (note the permeation process is considered as constitutive here, for sake of simplicity).

All nodes are binary ( i.e. can take the value 0 or 1), except Trp, which is represented by a ternary variable (taking the values 0,1,2). The association of tryptophan (at high levels) with the inactive form of the repressor (aporepressor) gives rise to the active form of the repressor (holorepressor); active repressor inhibits the transcription and thus the production of the enzyme TrpE; this enzyme is needed to produce the aminoacid Trp; the association of Trp (at moderate or high levels) with this enzyme inhibits its activity.

The Petri nets for the biosynthetic pathway and the regulatory control are available below (two PN formats), as well as the model integrating both levels (see additional files and the supporting reference [1]).


References

Curation
Submitter: 
C. Chaouiya
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