Difference between revisions of "Part:BBa K819005"
 
(62 intermediate revisions by 4 users not shown)
Line 2: Line 2:
 
<partinfo>BBa_K819005 short</partinfo>
 
<partinfo>BBa_K819005 short</partinfo>
  
−
a fusion protein consisting of E.coli endogenous SOS system repressor LexA and fungus N.crass photosensor protein VVD with LexA carrying mutation at position 40-42 and VVD carrying mutation N56K, C71V and M135I. This part serves as an ultra sensitive photoreceptor(which can sense light as weak as moonlight) and will induce a light-dependent repression of genes with their promoter containing mutated 408 form of SOS box.
+
Lux operon genes (from [https://parts.igem.org/Part:BBa_K325909:Design BBa_K325909]) and related RBS are placed under T7 promoter (from [https://parts.igem.org/Part:BBa_I712074 BBa_I712074] ). Cells transformed with this part can produce blue luminescence while no exogenous substrate is needed.<br/><br/>
  
−
''Luminesensor'' is designed by following the general principle of optogenetics fusion protein design--attaching a physiologically functional domain to a photoreceptor domain.
+
When introducing synthetic DNA into a cell, it is desirable that the encoded processes be functionally distinct from host processes. Phage polymerases are a means to control orthogonal transcription and are one of the most used tools in genetic engineering. Specifically, T7 RNA polymerase (RNAP) has been shown to function in a variety of hosts, including most bacteria, plant chloroplasts and mammalian cells. One advantage of T7 promoter is low basal expression, for it tightly inactive in the absence of the polymerase.<br/><br/>
  
−
<html><a href="https://static.igem.org/mediawiki/2012/5/55/Peking2012_Design_illustration_of_general_principle_1.png"target="blank"><img src="https://static.igem.org/mediawiki/2012/5/55/Peking2012_Design_illustration_of_general_principle_1.png" width=500  ></a></html>
+
Therefore, T7 promoter separates sensing/circuitry functions from pathways/actuation. It is encoded in genetically distinct regions from other circuits, enabling its driving upon the expression of phage T7 polymerases. Luxbrick under T7 promoter is modular to form a interface between luxbrick and other systems. Also, when transformed into BL21 cells, it can be induced with IPTG to reach a high expression level. It is great improvement regarding time saving and cost efficiency.
  
−
'''FIG.1 The general design of optogenetic fusion protein.'''
 
  
−
In order to circumvent the potential problems of current optogenetic approaches, we concluded that  our ''Luminesensor'' should be highly sensitive, should incorporate no chromophore that cannot be synthesized by bacteria, and should be modular in structure and function. We gladly found that among all these three groups of commonly used light-sensitive domains, phototropins possesses the most distinct modular structure. Phototropins have a structurally conserved light sensor domain, termed LOV (light, oxygen and voltage) domain, which is easily discernable and often precedes, within a single reading frame, a sequence of an enzymatically functional domain, connected by the sequence of a linker domain.
 
−
So far our good phototropin has satisfied two of our requirements: modularity and compatibility. So how about its sensitivity? To date, scientists have, for example, attached Rac1 protein to LOV2 domain from phototropin1 originated from Avena sativa to achieve photoactivatable cell motility, or shuffled the histidine kinase domain of FixL protein, which belongs to a two-component system, to the downstream of the LOV domain of B. subtilis YtvA protein to create a light-regulated histidine kinase, and so on. Among these designs, a particular one that utilizes the photosensor domain of a Vivid (VVD) protein, which originated from Neurospora. Crassa, camptured our attention. The VVD-GAL fusion protein thus designed achieved a rather high light-sensitivity—about 0.04W/m2. This is definitely thrilling news. Moreover, VVD was shown to form a rapidly exchanging homodimer upon blue-light activation, which means, like the Phy-PIF system, the general theme of protein-protein interaction might also be applied to this particular protein. Adding more promise to this VVD protein is its size—the smallest LOV domain containing protein known. This feature makes it easy to engineer and more likely to be stably expressed in bacteria systems.
 
−
 
−
<html><a href="https://static.igem.org/mediawiki/2012/2/27/Peking2012_Design_illustration_of_function_mechanism_of_phototropin_VVD.png"target="blank"><img src="https://static.igem.org/mediawiki/2012/2/27/Peking2012_Design_illustration_of_function_mechanism_of_phototropin_VVD.png" width=350  ></a></html>
 
−
 
−
'''FIG.2 Illustration of function mechanism of phototropin VVD.'''
 
−
 
−
 
−
Based on the discussion above, we have finally chosen the smallest LOV protein (or phototropin) VVD protein’s photosensor domain as our photoreceptor domain. Due to its small size, structural and functional modularity, bacteria compatibility, previous experience of being highly sensitive and its photoswitching mechanism, we reasoned that VVD photosensor domain would be an enabling tool in our coming design of a novel optogenetic module.
 
−
 
−
Our next step is to choose a physiologically functional domain for our new optogenetic module.
 
−
 
−
Based on the function mechanism of phototropin VVD, we can envisage a rough blueprint of our design: the DNA binding domain of a transcription inhibitor shall be fused to the downstream of VVD photosensor domain, and upon blue-light activation, VVD domain will dimerize, helping the DNA binding domain dimerize at the same time to enable its DNA binding activity and inhibition of transcription initiation.
 
−
Based on these criteria, a transcription repressor,LexA, came into our sight. LexA is a transcription repressor of all the genes in the SOS system in E.coli, and its crystal structure has been resolved at high-resolution. LexA protein consists of a N-terminal DNA binding domain and a C-terminal dimerization domain with a short hydrophilic linker linking the two separate domains, making the structure impressively modular. Under normal physiological conditions, two LexA proteins will form a homodimer through the dimerization domain interface and bind to the SOS box target gene sequence in promoters of genes in SOS system and create significant steric hindrance for transcription polymerase binding and thus inhibit transcription initiation.
 
−
<html><a href="https://static.igem.org/mediawiki/2012/0/01/Peking2012_Design_illustration_of_function_mechanism_of_LexA_transcription_repressor.png"target="blank"><img src="https://static.igem.org/mediawiki/2012/0/01/Peking2012_Design_illustration_of_function_mechanism_of_LexA_transcription_repressor.png" width=350  ></a></html>
 
−
 
−
'''FIG.3 Illustration of function mechanism of LexA transcription repressor.'''
 
−
 
−
 
−
<!-- Add more about the biology of this part here
 
 
===Usage and Biology===
 
===Usage and Biology===
−
 
+
To note that the incubating temperature should be no higher than 30<sup>o</sup>C, or the heavy Lux complex can easily aggregate. Optimum incubating conditions provided by Peking iGEM 2012: 250 rpm, 22oC, good ventilation after induction(final concentration of IPTG: round 0.5 mM).
 +
BL21 cells harboring T7-lux operon induced with IPTG at 0.5 mM is shown in the photo<br/><br />
 +
<html>
 +
<img src="https://static.igem.org/mediawiki/parts/0/02/Peking2012_part_T7_lux_operon.png" style="width:200px;"/>
 +
<p></p>
 +
</html>
 +
<br/><br/>
 
<!-- -->
 
<!-- -->
 
<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
−
<partinfo>BBa_K819005 SequenceAndFeatures</partinfo>
+
<partinfo>BBa_K819008 SequenceAndFeatures</partinfo>
  
  
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
 
===Functional Parameters===
 
===Functional Parameters===
−
<partinfo>BBa_K819005 parameters</partinfo>
+
<partinfo>BBa_K819008 parameters</partinfo>
 
<!-- -->
 
<!-- -->

Latest revision as of 14:06, 20 October 2012

Constitutive LuxBrick Generator

Lux operon genes (from BBa_K325909) and related RBS are placed under T7 promoter (from BBa_I712074 ). Cells transformed with this part can produce blue luminescence while no exogenous substrate is needed.

When introducing synthetic DNA into a cell, it is desirable that the encoded processes be functionally distinct from host processes. Phage polymerases are a means to control orthogonal transcription and are one of the most used tools in genetic engineering. Specifically, T7 RNA polymerase (RNAP) has been shown to function in a variety of hosts, including most bacteria, plant chloroplasts and mammalian cells. One advantage of T7 promoter is low basal expression, for it tightly inactive in the absence of the polymerase.

Therefore, T7 promoter separates sensing/circuitry functions from pathways/actuation. It is encoded in genetically distinct regions from other circuits, enabling its driving upon the expression of phage T7 polymerases. Luxbrick under T7 promoter is modular to form a interface between luxbrick and other systems. Also, when transformed into BL21 cells, it can be induced with IPTG to reach a high expression level. It is great improvement regarding time saving and cost efficiency.


Usage and Biology

To note that the incubating temperature should be no higher than 30oC, or the heavy Lux complex can easily aggregate. Optimum incubating conditions provided by Peking iGEM 2012: 250 rpm, 22oC, good ventilation after induction(final concentration of IPTG: round 0.5 mM). BL21 cells harboring T7-lux operon induced with IPTG at 0.5 mM is shown in the photo



Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 3014
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 2012
    Illegal XhoI site found at 2842
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 4401
    Illegal BsaI.rc site found at 1410
    Illegal SapI.rc site found at 4726