Revision as of 17:41, 26 October 2008

Network Design - Part 1

Creating an oscillatory system

Already existing genetic oscillators and their limits

Designing a simple genetic network that presents an oscillatory behavior is one of the first challenge synthetic biology overcame. More or less successfully. We can count more than ten synthetic genetic oscillators that have varied period and mechanisms. Raúl GUANTES and Juan F. POYATOS (2006) studied the most simple oscillators composed of two elements while Michael B. ELOWITZ and Stanislas LEIBLER (2000) designed the more complex "repressilator" (Table 1), to quote only the best known.

Two examples of genetic oscillators. A : a simple oscillator composed of two elements. B : the repressilator. (Legend : Green arrow : Activation. Red blunt arrow : Inhibition)

Both oscillators work : we can observe oscillations but only a limited number of cycles. Actually, they always reach a steady-state because the degradation/dilution rate is often too low : at the end of each cycle, the conditions are not exactly the initial conditions. Experimentally, the longer is the period the more cycles we can observe.

Design of our genetic oscillator : The Feed Forward Loop

We want to design a simple oscillator that oscillates during as many cycles as possible. We propose a system based on an oscillator composed of two elements on which we added a delay at the end of each cycle.

Simple oscillator composed of two elements

Uri ALON described genetic network motifs that generate a delay. Those motifs are the type 1 coherent Feed Forward Loop (C1-FFL).

↓ More on Feed Forward Loop ↑

Definition of a FFL

Fig. 1 : Structure of a type 1 coherent Feed Forward Loop

A Feed-Forward Loop is a genetic network composed of three nodes. This strong network motif is composed of a transcription factor X that regulates a second transcription factor, Y, and both X and Y regulate Z (Figure 1).

The different types of FFL

Depending on the type of regulations between the different nodes, we can define eight types of FFL that can be classified into two groups : coherent and incoherent FFLs. In coherent FFLs, the indirect path has the same overall sign as the direct path. The most abundant FFL is the type-1 coherent FFL (C1-FFL) (Figure 1).

The type 1 coherent Feed Forward Loop with an OR gate introduces a delay after the extinction of the signal

Fig. 2 : The C1-FFL with OR logic in the flagella system of E. coli.

Fig. 3 : Promoter dynamics after an OFF step of X, in the presence of Y. The results are shown for the wild-type bacterium, and for a bacterium in which the gene for Fli1 was deleted from the genome. The FFL generates a delay after an OFF step of X

In addition to the signs of the edges, to understand the dynamics of the FFL, we must also know how the inputs from the two regulators X and Y are integrated at the promoter of the gene Z. Uri ALON considers that there are two biologically reasonable logic functions : "AND" logic, in which both X and Y activities are need to be high in order to turn on Z expression and "OR" logic in which either X or Y is sufficient (Figure 2).

If the input function of the promoter of the gene Z is "OR", Z is expressed when X activity is high. There is no delay following the expression of X. But when X is not expressed anymore, its concentration decreases and reach the activation threshold of Y and Z. Y is not expressed anymore but as the concentration decreases, Z is still expressed. The OR-gate C1-FFL allow the gene Z to be expressed about one more hour after the gene X is OFF. (Figure 3)

Bibliography :

Shen-Orr et al. (2002)

Mangan et al. (2003)

Mangan et al. (2003)

Kalir et al. (2005)

We will use one of those network to increase the run of each period and permit more oscillations.

Our oscillator : a C1-FFL increase the length of each period

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 Uri ALON described genetic network motifs that generate a delay. Those motifs are the type 1 coherent Feed Forward Loop (C1-FFL).
-{{Paris/Toggle|More on Feed Forward Loop|Paris/FFL}}
+<center>{{Paris/Toggle|More on Feed Forward Loop|Paris/FFL}}</center>
 We will use one of those network to increase the run of each period and permit more oscillations.

Team:Paris/Analysis/Design1

From 2008.igem.org