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| | <partinfo>BBa_K819005 short</partinfo> | | <partinfo>BBa_K819005 short</partinfo> |
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| − | 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/> |
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| − | ''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/> |
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| − | <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. |
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| − | '''FIG.1 The general design of optogenetic fusion protein.'''
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| − | 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.
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| − | 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.
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| − | <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=500 ></a></html>
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| − | '''FIG.2 Illustration of function mechanism of phototropin VVD.'''
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| − | 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.
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| − | Our next step is to choose a physiologically functional domain for our new optogenetic module.
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| − | 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.
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| − | 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.
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| − | <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=500 ></a></html>
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| − | '''FIG.3 Illustration of function mechanism of LexA transcription repressor.'''
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| − | From these facts, we can conclude that the LexA repressor is the suitable physiological functional domain for our light-sensitive module, as it matches all of our criteria. First of all, a high-resolution crystal structure clearly shows its structural modularity. Beside the apparent structural modularity, various researches have utilized LexA to create versatile gene expression regulating modules that have convincingly demonstrated its functional modularity, further adding to its promise. (For example, a LexA-based genetic system has been devised for monitoring and analyzing protein heterodimerization in Escherichia coli.) Moreover, the DNA binding domain of LexA rigorously requires dimerization to bind efficiently to its targeting site (SOS box), and DNA binding domain itself has no dimerization ability. Last but not least, LexA is bacteria endogenous protein, which means it is likely to be efficiently expressed and function normally in bacteria systems.
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| − | <html><a href="https://static.igem.org/mediawiki/2012/1/1f/Peking2012_Design_illustration_of_function_mechanism_of_our_luminesensor.png"target="blank"><img src="https://static.igem.org/mediawiki/2012/1/1f/Peking2012_Design_illustration_of_function_mechanism_of_our_luminesensor.png" width=500 ></a></html>
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| − | '''FIG.4 Illustration of the function mechanism of our luminesensor.'''
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| − | By choosing the DNA binding domain of a bacteria endogenous transcription repressor, we must use reporter genes that will also be repressed by endogenous LexA protein. If we do not introduce changes into the DNA binding domain of our luminesensor, the only way to rule out the interference of endogenous LexA would be knocking out the genomic sequence of LexA protein. This will indubitably diminish its applicability in the future, since it will not work in any strain with endogenous LexA remaining.
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| − | So we set out to find a solution to this important problem. The most natural way would be creating a mutated form of LexA so that it will only recognize a target sequence different from the sequence the wild-type LexA would recognize. We gladly found that such a thing actually exists. It is called the LexA408 variant, which carries mutations PA40, NS41 and AS42 and has been shown much higher affinity for a symmetrically altered target sequence CCGT (N)8 ACGG, different from the wild type SOS box CTGT (N)8 ACAG, which is specifically recognized by wild-type LexA. Thus by introducing the 408 mutations into the DNA binding domain of our luminesensor, we can insulate our light-sensitive system from the interference from the genetic context of the host strain. This outstanding character that have ensured the orthogonality of our system to the endogenous SOS system will greatly enhance the compatibility of our module to those synthetic modules that have hitherto been designed and thus add to the promise of future application.
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| − | <html><a href="https://static.igem.org/mediawiki/2012/a/a4/Peking2012solution_to_the_orthogonality_problem_correction_2nd.png"target="blank"><img src="https://static.igem.org/mediawiki/2012/a/a4/Peking2012solution_to_the_orthogonality_problem_correction_2nd.png" width=500 ></a></html>
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| − | '''FIG.5 Our solution to the problem of orthogonality.'''
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| − | In order to rationally optimize our Luminesensor’s dynamic range and decay half-life, we need to build a dynamic model in the first place to simulate our Luminesensor system and determine which ones of those parameters in the system would be decisive to the two dynamic features we are interested in.
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| − | We listed all possible states of the molecules involved in our Luminesensor system and transitions between those states and created an ordinary deferential equation system based on law of mass action to describe the dynamic behavior of our system. After in-silico simulation, we singled out 4 critical parameters in our system that would determine the above two aspects of our system’s dynamic performance.
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| − | <html><a href="https://static.igem.org/mediawiki/2012/3/3a/Peking2012_LuminesensorNodes.png"target="blank"><img src="https://static.igem.org/mediawiki/2012/3/3a/Peking2012_LuminesensorNodes.png" width=500 ></a></html>
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| − | '''FIG.6 Kinetic Network of our Luminesensor.'''
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| − | Two of them will affect the background-signal ratio, namely the VVD protein dimerization equilibrium constant and dimerized Luminesensor’s DNA binding equilibrium constant.
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| − | Having singled out these four critical parameters, we set out to search through literature to find mutations that would enhance them. We found that there does not seem to exist mutations that would enhance dimerized Luminesensor’s DNA binding equilibrium constant. Rather, those mutations seem to undermine the DNA binding affinity, which would be detrimental to our system. We further reasoned that any mutation that would facilitate the disassociation of monomer Luminesensors from target DNA sequence is also likely to undermine the DNA binding affinity. So we focused on looking for VVD photosensor domain mutations that would promote VVD dimerization and VVD decay. We eventually localized on two specific mutations of VVD photosensor domain: a M135I mutation that will enhance the VVD dimerization, and a I74V mutation in the vicinity of FAD molecule that will enhance the VVD decay rate.
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| − | Having determined the plausible mutations, when then introduced mutation M135I, I74V and the combination of the two mutations into our 408 form of Luminesensor. By characterizing the dynamic behavior of the mutated Luminesensor along time course, we discovered that mutation M135I indeed improved the signal-background ratio significantly. However, I74V mutation seems to reduce the signal-background ratio dramatically, rendering our Luminesensor useless. So disregarding of the faster decay half-life it may provide, we have to rule I74V out of our design.
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| − | '''Sensitivity'''
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| − | We tested the sensitivity of Luminesensor by examine the light-dependent transcriptional activity of a GFP-ssrA reporter. ssrA is a protein tag that induces fast degradation of protein, which in our case facilitated the observation of transcriptional activity. Based on the consideration of guaranteeing accuracy and precision, our setup (Figure 7):
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| − | <html><a href="https://static.igem.org/mediawiki/2012/a/a4/Peking2012_luminesensor_sen_div.jpg"target="blank"><img src="https://static.igem.org/mediawiki/2012/a/a4/Peking2012_luminesensor_sen_div.jpg" width=350 ></a></html>
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| − | '''FIG.7 The set-up of sensitivity tests.'''
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| − | <!-- Add more about the biology of this part here
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| | ===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> |
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| | <!-- 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> |
| | <!-- --> | | <!-- --> |
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.
