Team:Peking S/project/wire

From 2011.igem.org

(Difference between revisions)
(→Reference)
 
(35 intermediate revisions not shown)
Line 15: Line 15:
-
===Harvesting ‘Chemical Wires’ From Nature===
+
===Introduction to ‘Chemical Wire’ toolbox===
<br>
<br>
-
'''Introduction'''
 
-
Multicellular strategy provides us a vista to construct a complex gene network. During gene network constructing, as genetic network scaling up, more cells are involved in compartmentalizing genetic network. Natural quorum sensing and small chemical molecule generator and receiver systems provide a potential platform for multicellular network construction. Unfortunately, naturally existing and well characterized cell-cell communication systems are far from sufficient. Thus， exploiting new systems is significantly important in multicellular network construction using synthetic microbial consortia.
+
Cell-cell communication-based multicellular networks provide an extended vista for synthetic biology. By compartmentalizing complex genetic circuits into separate engineered cells, the difficulty of the construction by layering elementary gates can be dramatically reduced, partly due to the insulation of crosstalk between modules, the suppression of noise by populationally averaging, and the reducing of metabolic burden in host cells. What’s more, cell-cell communication-based multicellular feature enables coordination and synchronization among cells in and between populations and facilitates the generation of reliable non-Boolean dynamics.
-
In exploiting new systems many molecules could serve as candidates of synthetic consortia ‘chemical wire’, but not all of them perform well when applied to microbial chassis. One of the most significant problems is that they are difficult to be synthesized or perceived when chemical molecule generating or receiving mechanism is too complex to engineer. Besides, threshold, response time and coordination of receiver cell performance should also be considered in cell-cell communication system selection. Because only ‘chemical wire’ systems with low threshold, high response speed and coordination response deserve to be converted into signaling-system-compartment.
 
-
According to the selection principles above， in our project two signal generators and receiver systems are selected. One employs autoinducer N-(3-hydroxy-7-cis-tetradecenoyl)-L-homoserine lactone (3OH-C14:1-HSL), as the signal molecule (Figure 1). The other system employs Salicylate (Figure 2).In order to confirm their usability in practical application, we designed experiments covering three aspects of the systems, namely dose response, time dependence and coordination.
 
-
'''Cin system'''
+
However, orthogonal ‘chemical wires’ that allow concurrent communication are far from sufficient, making developing a versatile ‘chemical wire’ toolbox for conducting a complex gene network more necessary. This year we are aiming to develop a ‘chemical wire’ toolbox, applicable for both Boolean and Non-Boolean gene networks.
-
This system derives from Rhizobium leguminosarum which are Gram-negative soil bacteria living in symbiotic association with legumes by forming nodules. In this system, cinI, pcin, cinR are the core elements involved in cin system. CinI is the synthase of 3OH-C14:1-HSL and cinR is the receptor of 3OH-C14:1-HSL. CinI is a typical LuxI-type synthase, and cinR is a LuxR-type transcriptional regulator. Pcin is activated by CinR binding with 3OH-C14:1-HSL.
+
 
 +
As natural quorum sensing systems provide an excellent pool for developing ‘chemical wire’ toolbox, harvesting ‘chemical wires’ from the nature is a fast and affordable way. We selected and evaluated a recently reported quorum sensing system, CinI-CinR system from'' Rhizobium leguminosarum'' as a candidate of our toolbox. An artificial QS system, PchAB-NahR system exploiting salicylate as signaling molecule was also built. Both of them were proved to owe promising performance.
 +
 
 +
<center>[[File:LB2cbbb.png|680px]]
 +
</center>
 +
 
 +
''For more details'', [https://2011.igem.org/Team:Peking_S/project/wire/harvest      ''click here'']
 +
 
 +
 
 +
On the other hand, all of the quorum sensing systems currently exploited in synthetic biology exhibit transcriptional activation, which cannot provide negative feed back loops during cell-cell communication, and the conventional inverter, which was implemented by the repressor-operator pairs, has evident defects. We have developed a ‘from ground up’ approach to synthesize direct, fast and reliable signaling inverters for synthetic microbial consortia, harnessing the conditioned binding of quorum sensing regulators to their cognate DNA boxes to control the accessibility of RNA polymerase.
 +
 
 +
<center>[[File:NN10.png|400px]]</center>
 +
 
 +
''For more details'', [https://2011.igem.org/Team:Peking_S/project/wire/inverter      ''click here'']
 +
 
 +
 
 +
With candidates harvested from nature or re-designed from the natural counterpart, we started to characterize them, specially focusing on their orthogonality, dose response, time dependence (signaling speed) and their ability to coordinate cell population.  
 +
 
 +
<center>[[File:signalingOrthogonal.png|450px]]</center>
 +
 
 +
''For more details'', [https://2011.igem.org/Team:Peking_S/project/wire/matrix    ''click here'']
 +
 
 +
 
 +
== Reference ==
 +
 
 +
 
 +
[1] Li, B. You, L. Synthetic biology: Division of logic labour. Nature 469, 171–172 (2011).
 +
 
 +
[2] Marguet, P. Balagadde F. Tan C. You L. Biology by design: reduction and synthesis of cellular components and behaviour. JR Soc Interface 4, 607–623 (2007).
 +
 
 +
[3] Voigt, C.A. Genetic parts to program bacteria. Curr Opin Biotechnol 17, 548–557 (2006).
 +
 
 +
[4] Clancy, K, Voigt, C.A. Programming cells: towards an automated 'Genetic Compiler'. Curr Opin Biotechnol 21, 572–581 (2010) .
 +
 
 +
 
 +
 
 +
<html>
 +
<a href="#top">Top↑
 +
</div>
 +
 
 +
 
 +
</html>
 +
<br>
 +
<br>

Latest revision as of 03:54, 6 October 2011

Template:Https://2011.igem.org/Team:Peking S/bannerhidden Template:Https://2011.igem.org/Team:Peking S/back2

Template:Https://2011.igem.org/Team:Peking S/bannerhidden

css r corner



Chemical Wire Toolbox


Introduction|Harvesting ‘Chemical Wires’ From Nature|Synthesizing Quorum Sensing Inverters|Orthogonal Activating Matrix


Introduction to ‘Chemical Wire’ toolbox


Cell-cell communication-based multicellular networks provide an extended vista for synthetic biology. By compartmentalizing complex genetic circuits into separate engineered cells, the difficulty of the construction by layering elementary gates can be dramatically reduced, partly due to the insulation of crosstalk between modules, the suppression of noise by populationally averaging, and the reducing of metabolic burden in host cells. What’s more, cell-cell communication-based multicellular feature enables coordination and synchronization among cells in and between populations and facilitates the generation of reliable non-Boolean dynamics.


However, orthogonal ‘chemical wires’ that allow concurrent communication are far from sufficient, making developing a versatile ‘chemical wire’ toolbox for conducting a complex gene network more necessary. This year we are aiming to develop a ‘chemical wire’ toolbox, applicable for both Boolean and Non-Boolean gene networks.


As natural quorum sensing systems provide an excellent pool for developing ‘chemical wire’ toolbox, harvesting ‘chemical wires’ from the nature is a fast and affordable way. We selected and evaluated a recently reported quorum sensing system, CinI-CinR system from Rhizobium leguminosarum as a candidate of our toolbox. An artificial QS system, PchAB-NahR system exploiting salicylate as signaling molecule was also built. Both of them were proved to owe promising performance.

LB2cbbb.png

For more details, click here


On the other hand, all of the quorum sensing systems currently exploited in synthetic biology exhibit transcriptional activation, which cannot provide negative feed back loops during cell-cell communication, and the conventional inverter, which was implemented by the repressor-operator pairs, has evident defects. We have developed a ‘from ground up’ approach to synthesize direct, fast and reliable signaling inverters for synthetic microbial consortia, harnessing the conditioned binding of quorum sensing regulators to their cognate DNA boxes to control the accessibility of RNA polymerase.

NN10.png

For more details, click here


With candidates harvested from nature or re-designed from the natural counterpart, we started to characterize them, specially focusing on their orthogonality, dose response, time dependence (signaling speed) and their ability to coordinate cell population.

SignalingOrthogonal.png

For more details, click here


Reference

[1] Li, B. You, L. Synthetic biology: Division of logic labour. Nature 469, 171–172 (2011).

[2] Marguet, P. Balagadde F. Tan C. You L. Biology by design: reduction and synthesis of cellular components and behaviour. JR Soc Interface 4, 607–623 (2007).

[3] Voigt, C.A. Genetic parts to program bacteria. Curr Opin Biotechnol 17, 548–557 (2006).

[4] Clancy, K, Voigt, C.A. Programming cells: towards an automated 'Genetic Compiler'. Curr Opin Biotechnol 21, 572–581 (2010) .


Top↑



Retrieved from "http://2011.igem.org/Team:Peking_S/project/wire"