Introduction:
This models, which can predict the gene expression of AimR-AimP systems, is practical for many research. In this model, the genetic circuit describes the biochemical reactions taking place inside the cell (Figure5). The intracellular model describes the fluctuations in concentrations of each substance by modelling each chemical reaction.
Figure 5.the gene expression model of AimR-AimP system[7]
This QS system of AimR-AimP remains to be further studied for potential application. The QS response is quite tightly regulated as expression occurs only once the local bacterial density passes a fixed threshold value, similar unlike a switch. This system is encoded by three phage genes: aimP, which produces the peptide; aimR, the intracellular peptide receptor; and aimX, a negative regulator of lysogeny. In the sender system, aimP produces the peptide and the concentration of peptide changes along with time. While in the receiver system, the peptide binds with aimX which inhibites the target gene expression. The mechanism can briefly described in the following:
The AimR is a transcription factor, which has a helix-turn-helix domain to bind DNA and a TPR domain to bind the signal peptide. The AimP is the propeptide of the mature signal peptide, sequence of the mature signal peptide is SAIRGA. Binding of AimP to the AimR will disrupt the dimer forms of AimR. After that, the AimR can no longer bind to the promoter of AimX, a potential non coding RNA involved in the process of lysis-lysogeny. A superb characteristic of the Aim system is that the AimR only bind to
Modeling:
In this model, we want to quantify the gene expression of the complete AimR-AimP system including the sender and receiver. Let us now consider the complete AimR-AimP system as illustrated in the figure 5. For the rate equation involving [P], we need to add both contributions from the sender and receiver systems and only take a single decay. In the lab,one can "simply" (Biologists clearly agree with this statement) put the sender and receiver to recreate the AimR-AimP system with biobricks. In order to build a reporting system,we replace the aimX into GFP.
The equations of this model read:
Attention:
1. [P] denote the concentration of peptide of AimR-AimP system , [aimR] and [gfp] respectively denote the concentration of aimR and gfp, [CP] denote the peptide of AimR-AimP system and aimR complex. [R+] represents the concentration of the molecular which was formed by the dissociation of the promoter of the AimX gene.
The remaining symbols are defined in Table 2.
Table 3 Definition of symbols used in the recursion equation
Analysis and Results:
As it’s shown, in the early stages of the experiment, extracellular signal molecules increased with time, but soon the signal molecules increased to a bottleneck. Into the late experiment, the signal molecules continue to decrease, and ultimately reach a fairly low level, making the signal molecular curve to form a first increase after the trend.
Figure 6. the gene expression of different type of AimR-AimP systems
The tendency of this curve above matches well with our experimental data. And this crest-like shape of the curve agrees with previously published results[7].
Reference:[7] Erez Z, Steinberger-Levy I, Shamir M, et al. Communication between viruses guides lysis-lysogeny decisions[J]. Nature, 2017, 541(7638):488.