Difference between revisions of "Part:BBa K4286100:Design"

Latest revision as of 14:24, 9 October 2022

Effector device in timed suicide switch

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
INCOMPATIBLE WITH RFC[12]
Illegal NheI site found at 481
Illegal NheI site found at 504
21
INCOMPATIBLE WITH RFC[21]
Illegal BamHI site found at 582
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

Design Notes

How to ensure the safety of engineered microorganisms for agricultural applications is a serious issue. In order to prevent the engineered microorganisms from escaping, it is a feasible method to use the conditional triggered suicide switch. However, this is not foolproof, because the triggering conditions in the natural environment are uncertain, and there may still be the possibility of escaping. 2022 SZU-China attaches great importance to the safety of engineered microorganisms and hopes to design a suicide switch activated by endogenous factors.

Based on the classical gene oscillator, we propose a concept of timed suicide switch, hoping to kill the engineered microorganism population at a certain time. Based on the classical model organism Escherichia coli, we have designed and improved the gene circuit. We also explore the properties of the timed suicide switch through a mathematical model.

Source

The effector is designed by 2022 SZU-China.

References

[1]Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000 Jan 20;403(6767):335-8. doi: 10.1038/35002125. PMID: 10659856.

[2]Purcell O, di Bernardo M, Grierson CS, Savery NJ. A multi-functional synthetic gene network: a frequency multiplier, oscillator and switch. PLoS One. 2011 Feb 17;6(2):e16140. doi: 10.1371/journal.pone.0016140. PMID: 21359152; PMCID: PMC3040778.

[3]Potvin-Trottier L, Lord ND, Vinnicombe G, Paulsson J. Synchronous long-term oscillations in a synthetic gene circuit. Nature. 2016 Oct 27;538(7626):514-517. doi: 10.1038/nature19841. Epub 2016 Oct 12. PMID: 27732583; PMCID: PMC5637407.

[4]Hoseini S, Kalani BS, Ghafourian S, Maleki A, Asadollahi P, Badakhsh B, Pakzad I. In Vitro and In Silico Investigation of some Type II TA Genes in H. Pylori. Clin Lab. 2022 Aug 1;68(8). doi: 10.7754/Clin.Lab.2021.211002. PMID: 35975492.

[5]Nigam A, Ziv T, Oron-Gottesman A, Engelberg-Kulka H. Stress-Induced MazF-Mediated Proteins in Escherichia coli. mBio. 2019 Mar 26;10(2):e00340-19. doi: 10.1128/mBio.00340-19. PMID: 30914510; PMCID: PMC6437054.

@@ Line 7: / Line 7: @@
 ===Design Notes===
-First of all, our engineered microorganism will be applied to farmland, in order to prevent possible escape of engineered microorganism, the use of conditional kill switches is not necessarily a good way, because the triggering conditions in the field environment are very uncertain, which greatly increases the possibility of escape of engineered microorganism. Therefore, we conceived this auto-timing kill switch, hoping that the engineered microorganism can commit suicide at a certain time to prevent the escape. However, because Trichoderma atroviride is not a typical model organism, it lacks clearly characterized components, which is also a common problem faced by teams who want to develop new chassis, so we use the classical model organism Escherichia coli as our chassis bacteria. Because of the long experimental period, we plan to use modeling to characterize our auto-timing kill switch.
+How to ensure the safety of engineered microorganisms for agricultural applications is a serious issue. In order to prevent the engineered microorganisms from escaping, it is a feasible method to use the conditional triggered suicide switch. However, this is not foolproof, because the triggering conditions in the natural environment are uncertain, and there may still be the possibility of escaping. 2022 SZU-China attaches great importance to the safety of engineered microorganisms and hopes to design a suicide switch activated by endogenous factors.
+Based on the classical gene oscillator, we propose a concept of timed suicide switch, hoping to kill the engineered microorganism population at a certain time. Based on the classical model organism Escherichia coli, we have designed and improved the gene circuit. We also explore the properties of the timed suicide switch through a mathematical model.
@@ Line 17: / Line 19: @@
 ===References===
 [1]Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000 Jan 20;403(6767):335-8. doi: 10.1038/35002125. PMID: 10659856.
 [2]Purcell O, di Bernardo M, Grierson CS, Savery NJ. A multi-functional synthetic gene network: a frequency multiplier, oscillator and switch. PLoS One. 2011 Feb 17;6(2):e16140. doi: 10.1371/journal.pone.0016140. PMID: 21359152; PMCID: PMC3040778.
 [3]Potvin-Trottier L, Lord ND, Vinnicombe G, Paulsson J. Synchronous long-term oscillations in a synthetic gene circuit. Nature. 2016 Oct 27;538(7626):514-517. doi: 10.1038/nature19841. Epub 2016 Oct 12. PMID: 27732583; PMCID: PMC5637407.
 [4]Hoseini S, Kalani BS, Ghafourian S, Maleki A, Asadollahi P, Badakhsh B, Pakzad I. In Vitro and In Silico Investigation of some Type II TA Genes in H. Pylori. Clin Lab. 2022 Aug 1;68(8). doi: 10.7754/Clin.Lab.2021.211002. PMID: 35975492.
 [5]Nigam A, Ziv T, Oron-Gottesman A, Engelberg-Kulka H. Stress-Induced MazF-Mediated Proteins in Escherichia coli. mBio. 2019 Mar 26;10(2):e00340-19. doi: 10.1128/mBio.00340-19. PMID: 30914510; PMCID: PMC6437054.