Difference between revisions of "Team:ShanghaiTech/Model Oribosome"
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<p>The construction of increasingly complex genetic networks in engineered bacteria has been particularly susceptible to circuit failure, due to undesirable expressions of proteins involved. Many influencing factors have been identified, including the recombinant plasmid copy number and the competition of translational resources between foreign genes and the bacterial genome. In order to minimize the unpredictable disturbances and stabilize the expression of genetic circuits, a system employing feedforward control and orthogonal ribosomes is devised.</p> | <p>The construction of increasingly complex genetic networks in engineered bacteria has been particularly susceptible to circuit failure, due to undesirable expressions of proteins involved. Many influencing factors have been identified, including the recombinant plasmid copy number and the competition of translational resources between foreign genes and the bacterial genome. In order to minimize the unpredictable disturbances and stabilize the expression of genetic circuits, a system employing feedforward control and orthogonal ribosomes is devised.</p> | ||
| − | <h4>Equations | + | <h4>Equations</h4> |
<p>We used orthogonal ribosome to deal with the interaction between our system and other gene systems in the same cell. First of all, we test the feasibility of adding orthogonal ribosome to our system, to avoid any potential negative impact by using this expression toolkit. We also built a mathematical model for the protein expression regulation on translational layer, and combined it with our NFBL system to assess its fitness to our current system. </p> | <p>We used orthogonal ribosome to deal with the interaction between our system and other gene systems in the same cell. First of all, we test the feasibility of adding orthogonal ribosome to our system, to avoid any potential negative impact by using this expression toolkit. We also built a mathematical model for the protein expression regulation on translational layer, and combined it with our NFBL system to assess its fitness to our current system. </p> | ||
<p>Our orthogonal ribosome comes from the orthogonal 16s RNA. An orthogonal 16s RNA combines with 21s protein and becomes an orthogonal 30s subunit of ribosome. Then, the orthogonal 30s subunit combines with 50s subunit to form the orthogonal ribosome.</p> | <p>Our orthogonal ribosome comes from the orthogonal 16s RNA. An orthogonal 16s RNA combines with 21s protein and becomes an orthogonal 30s subunit of ribosome. Then, the orthogonal 30s subunit combines with 50s subunit to form the orthogonal ribosome.</p> | ||
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<p>Now, the producing rate of protein is in the form of the last equation.</p> | <p>Now, the producing rate of protein is in the form of the last equation.</p> | ||
<p> </p> | <p> </p> | ||
| − | <h4> | + | <h4>Results</strong> </h4> |
<p>Using the above equations, we can describe the whole system with orthogonal ribosome. It is quite exciting to find that the orthogonal ribosome has no negative influence on the NFBL system, and the fidelity is maintained.</p> | <p>Using the above equations, we can describe the whole system with orthogonal ribosome. It is quite exciting to find that the orthogonal ribosome has no negative influence on the NFBL system, and the fidelity is maintained.</p> | ||
<p><a href='file:figures/TLL/oribo-NFBL.png'>oribo-NFBL</a></p> | <p><a href='file:figures/TLL/oribo-NFBL.png'>oribo-NFBL</a></p> | ||
Latest revision as of 12:34, 26 November 2018
Translation Layer
The construction of increasingly complex genetic networks in engineered bacteria has been particularly susceptible to circuit failure, due to undesirable expressions of proteins involved. Many influencing factors have been identified, including the recombinant plasmid copy number and the competition of translational resources between foreign genes and the bacterial genome. In order to minimize the unpredictable disturbances and stabilize the expression of genetic circuits, a system employing feedforward control and orthogonal ribosomes is devised.
Equations
We used orthogonal ribosome to deal with the interaction between our system and other gene systems in the same cell. First of all, we test the feasibility of adding orthogonal ribosome to our system, to avoid any potential negative impact by using this expression toolkit. We also built a mathematical model for the protein expression regulation on translational layer, and combined it with our NFBL system to assess its fitness to our current system.
Our orthogonal ribosome comes from the orthogonal 16s RNA. An orthogonal 16s RNA combines with 21s protein and becomes an orthogonal 30s subunit of ribosome. Then, the orthogonal 30s subunit combines with 50s subunit to form the orthogonal ribosome.
$$ 16S RNA + 21S Protein \rightarrow 30S Subunit$$
$$ K_1[S16]\cdot[Pro21]=K_{1}'[S30] $$
$$ 30S Subunit + 50S Subunit \rightarrow Ribosome $$
$$ K_2[S]\cdot [S50] = K_2'[Ribosome] $$
$$ Ribosome+mRNA \rightarrow Protein $$
$$ \frac{d[Protein]}{dt}=K_3[Ribosome]\cdot [mRNA]-d_{Protein}\cdot Protein $$
This system can be simplified
$$ [Ribosome] = \frac{K_1K_2}{K_1'K_2'}\cdot C_{Protein}\cdot [S16] $$
$$ \frac{d[Protein]}{dt}=K_{S16}\cdot [S16]-d_{Protein}\cdot [Protein] $$
Now, the producing rate of protein is in the form of the last equation.
Results
Using the above equations, we can describe the whole system with orthogonal ribosome. It is quite exciting to find that the orthogonal ribosome has no negative influence on the NFBL system, and the fidelity is maintained.
