Team:Wageningen UR/Project/CompleteProject1Description

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==Main Project==
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==Synchroscillator==
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===Complete Project Description===
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===Project Description===
====1. Introduction====
====1. Introduction====
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The aim of this project is to design and implement a system exhibiting sustained oscillatory protein expression which should be visible and synchronized on the scale of a physically constrained population of E. coli cells. The principles that govern this type of behaviour have been studied both in theory and in practice, and as such there exists a solid foundation to apply these ideas in the context of the iGEM competition. In essence, this project consists of constructing a plasmid containing genes, the products of which reciprocally affect each other’s expression in a reliable manner. Based on a previously established design, we intend to take advantage of the great variety of standardized, interchangeable and freely available Bio–Bricks to construct modified genetic circuits, aiming at an improved bacterial oscillator. Due to the difficulty in experimentally verifying the phenomena we wish to observe, special considerations regarding the experimental set-up had to be made.
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The aim of this project is to design and implement a system exhibiting sustained oscillatory protein expression which is synchronized across a population of spatially constrained ''E. coli'' cells. The principles that govern this type of behavior have been studied both in theory and in practice, and as such there exists a solid foundation to apply these ideas in the context of the iGEM competition. In essence, this project consists of constructing a plasmid which contains protein encoding genes which reciprocally affect each other’s expression in a reliable manner, and experimentally measuring the expression dynamics to test the predictive value of a mathematical model. Due to the specificity of the required system parameters, and resulting difficulty in experimentally verifying the phenomena we wish to observe, special considerations regarding the experimental set-up had to be made. We hope that this system might be employed as a pace-making device to drive more complex genetic circuits requiring time-dependent gene expression, or as a component in sophisticated metabolic engineering applications.
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The starting point for the genetic circuitry we intend to make is a design recently published in the article “a synchronized quorum of genetic clocks” by Danino & Hasty ([http://www.nature.com/nature/journal/v463/n7279/abs/nature08753.html article “a synchronized quorum of genetic clocks”]). This genetic circuit uses natural elements of bacterial quorum sensing systems to form coupled positive and negative feedback loops which control the expression of a reporter protein: the LuxI enzyme that catalyses the last step of the acyl-homoserine lactone (AHL) biosynthesis, the AHL-responsive transcriptional regulator LuxR, and the reporter Green Fluorescent Protein (GFP) (Figure 1). The AHL molecules can easily diffuse through cell membranes to the extracellular medium. This allows all the cells in a culture to influence each other’s activity in a uniform manner (quorum sensing). The result being that the oscillations arising from the genetic feedback loops are synchronized on the scale of a whole cell culture. All of the parts used in this design exist in the Registry of Standard Biological Parts and are freely available for our use.
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[[File:SOS_2.png]]
[[File:SOS_2.png]]
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'''Fig.1.''' ''What synchronized oscillation of Green Fluorescent Protein in E. coli cells might look like.''
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'''Fig.1.''' ''Artistic rendering of the Synchronized Oscillatory System.''
====2. Mechanism====
====2. Mechanism====
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There are a number of genetic circuit topologies that have the potential to exhibit oscillatory behaviour under certain conditions. One simple design is the Smolen Oscillator which consists of two genes connected through double feedback loops.  The mechanism we intend to construct consists of components of the lux quorum sensing system that are configured in such a way.
 
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There are a number of genetic circuit topologies that have the potential to exhibit oscillatory behavior under the right conditions. However, the requirement that the oscillations should be synchronized posed a constraint on the components that could be used. The starting point for our genetic circuitry was a design recently published in the article “A synchronized quorum of genetic clocks” by Danino et al. This design combines elements of the ''Vibrio fischeri'' quorum sensing system with a quorum quenching enzyme from ''Bacillus subtilis'', resulting in coupled positive and negative feedback loops which regulate the expression of a reporter protein.
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[[File:mainproject01.png]]
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'''Basic Components:'''
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'''Fig.2.''' ''Basic oscillating genetic circuit as published by Danino & Hasty.''
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'''LuxR''' is a transcriptional regulator in the bioluminescent quorum-sensing system of the symbiotic deep sea bacterium ''Vibrio fischeri''. It is induced by binding the auto-inducer molecule N-(3-oxohexanoyl)-homoserine lactone (AHL). The AHL-LuxR complex controls expression of the lux regulon, which contains diverging pRight and pLeft promoter elements. The pRight element has low basal transcription, and is activated by AHL-LuxR; pLeft has higher basal expression, and is repressed by the AHL-LuxR complex. This dual activity makes LuxR a useful element for controlling interconnected genetic feedback loops. The unrestricted diffusion of AHL through the plasma membrane allows spatially proximate populations of cells to experience identical AHL conditions and synchronize AHL-dependent gene expression.
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The main elements that comprise this circuit are the genes LuxI, LuxR, AiiA, GFP, and the promoters that regulate their activity. LuxI encodes the enzyme LuxI which enzymatically produces the molecule acyl-homoserine lactone (AHL). When AHL is bound to the transcription factor LuxR, it becomes active and induces transcription from the LuxI promoter (which normally has very low basal expression). Subsequently, AiiA is expressed and negatively regulates the pRight promoter by catalysing the degradation of AHL. The feedback loop emerging from this configuration results in periodic oscillatory protein expression. AHL is soluble and can freely diffuse through the cell membrane into extracellular medium and into other cells, effectively normalizing the AHL concentration across an entire localized cell culture, which is how synchronization can occur. Placing the gene for a reporter molecule, such as Green Fluorescent Protein or Luciferase, under a copy the LuxI promoter allows the dynamics of protein expression to be monitored.  
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The enzyme '''LuxI''' is an acyl-homoserine-lactone synthase which produces the intercellular signalling molecule N-(3-oxohexanoyl)-homoserine lactone (AHL). Placing LuxI under control of the pRight promoter results in a positive feedback loop: when increases in cell density cause the intracellular AHL concentration to rise above the activation threshold of the pRight promoter, the transcription rate of the LuxI gene is increased which in turn results in the production of more AHL.  
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====3. The designs====
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'''AiiA''' is an enzyme from ''B. subtilis'' which degrades AHL. Its biological function is to interfere with the quorum sensing signals of other bacteria. Placing it under control of the pRight promoter results in negative feedback as a response to increasing AHL concentrations.
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In the original design, Danino & Hasty placed the genes LuxI (from ''V. fischeri''), AiiA (from ''B. Thurigensis'') and yemGFP genes under the control of three identical copies of the natural Lux promoters of ''V. fischerii''. This promoter region actually consists of two promoters regulating transcription in opposite directions. To avoid complications resulting from this, the authors placed a copy of the LuxR gene behind each of the “pLeft” parts of the promoter. Though this in itself should cause (unwanted) oscillations of LuxR levels, the fact that three copies are expressed, and pLeft has intermediate basal expression, results in de facto constitutive expression, and is treated as such in the modelling work.
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[[File:mainproject02.png]]
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The reporter molecule Green Fluorescent Protein ('''GFP''') is also regulated by the pRight promoter and provides a quantitative (albeit delayed) indication of the AHL concentration the cell is exposed to at a given point in time.
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LuxI, AiiA and GFP are all tagged for rapid degradation (LVA-tag). Due to differences in the synthesis and degradation rates of LuxI and AiiA, there exists a space of conditions within which periodic oscillations in AHL concentration, and concomitant oscillatory protein expression can emerge. Under most conditions, the level of AHL within a population of cells will quickly reach a steady state. However, by simulating the system using a quantitative biochemical model, it is possible to predict conditions under which oscillations are likely to occur. See our [https://2011.igem.org/Team:Wageningen_UR/Project/ModelingProj1 modeling page] for details.
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'''Fig.3.''' ''Synchronized Oscillator plasmid designs by Danino & Hasty. LuxRp is the “left” promoter (repressed by AHL-LuxR). LuxIp is the “right” promoter, which is activated by AHL-LuxR. Note that all of the proteins (except for LuxR) have C-terminal degradation tags, as this increases the frequency of the oscillation and reduces noise.''
 
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=====Replica of the construct designed by Danino & Hasty.=====
 
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The first construct we intend to make is an accurate replica of this original design using BioBrick parts from the Registry of Standard Biological Parts.  Given that it has been proven to work, it will be able to serve as a basic starting point for our attempt to observe oscillatory protein expression in ''E. coli''. However, we will also construct modified versions using existing parts which will be more streamlined, and of which, in some cases, might even show enhanced performance.
 
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[[File:System1.png|760px|link=https://static.igem.org/mediawiki/2011/d/d0/System1.png]]
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[[File:mainproject03.png]]
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'''Fig.2.''' ''Genetic circuit of a synchronized oscillator on 2 plasmids''
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'''Fig.4.''' ''Circuit view of the Danino & Hasty design using BioBrick Parts.''
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'''1''': The AHL Synthase LuxI is expressed at a basal level when AHL concentration is low. Relative AHL concentration increases as a function of cell density.
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'''2''': As the concentration of AHL increases, it associates with the constitutively expressed transcription factor LuxR, thereby up-regulating the expression of AiiA, LuxI and GFP. As LuxI accumulates, the concentration of AHL increases rapidly as a result of the LuxR-AHL -> LuxI positive feedback loop.
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=====Streamlined Design=====
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'''3''': The AHL-degrading enzyme AiiA does not accumulate as rapidly as LuxI. However, the degradation of AHL occurs at a faster rate than AHL synthesis, effectively reducing the level of active LuxR (and its transcriptional activity). This delayed negative feedback results in oscillations in AHL concentration.  
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The first modification involves simply replacing the three copies of pLeft-LuxR with a single copy of LuxR behind a constitutive promoter (ptetR, Figure 5). This will significantly reduce the size of the construct (and the complexity of the system) while exhibiting similar behaviour. In addition to this modification, the pRight promoter regulating the expression of LuxI will be replaced by a pRight/lacI hybrid promoter. This should allow the oscillation circuit to remain inactivated until it is induced by adding a pulse of IPTG to the medium. The gene LuxR is under the control of the constituve ptet promoter and should give a steady transcription of the LuXR gene.  
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'''4''': AHL diffuses freely between cells, synchronizing LuxR-AHL dependent transcriptional activity across a population of cells. 
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[[File:mainproject04.png]]
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'''5''': LuxR-AHL dependent GFP expression allows the fluctuations in AHL concentration to be observed in situ. LuxI, AiiA and GFP all have LVA tags and are degraded rapidly (albeit at slightly different rates).  
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'''Fig.5.''' ''Circuit view of the streamlined design with ptetR regulating LuxR, and pRight/LacI (not indicated in circuit) controlling LuxI.''
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[[Team:Wageningen_UR/Project/CompleteProject1Description#Project Description| back to top]]
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[[File:mainproject05.png]]
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====3. Designs====
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'''“Hasty” system:'''
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'''Fig.6.''' ''Streamlined design with ptetR regulating LuxR, and pRight/LacI controlling LuxI. All of the parts shown in the plasmid schematically have been located and verified in the Parts Registry.''
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The first design we implemented was a BioBrick part based on reconstruction of the plasmids used by Danino et al. We intended to make as accurate a replica as possible in order to confirm the previously published results, and to test the viability of our experimental [https://2011.igem.org/Team:Wageningen_UR/Project/Devices platform]. However, there are a few differences between the original Hasty system and “our replica“. While the Hasty system employs the natural lux promoter which contains divergent pLeft and pRight elements (Fig 4), the BioBrick parts we employed have both elements in the same orientation. Both the original and our system contain 3 copies of the luxR gene under control of the pLeft element. Furthermore, a different (high copy) backbone was used during the functional validation of the parts, as opposed to the low copy backbone employed by Hasty.
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=====Differential Feedback Design=====
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[[File:Hasty1.png|x67px|link=http://partsregistry.org/Part:BBa_K546005]]
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The second major modification is the replacement of the inducible promoter pRight controlling expression of LuxI with the repressible pLeft. This will turn the LuxI-AHL positive feedback loop into a negative feedback loop, thus changing the dynamics of the system. Induction will be controlled using the pRight/lacI promoter regulating the AiiA gene. This is an experimental design, and will have to be validated with modelling work.
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'''Fig.4.''' ''BioBrick part K546005 forms the positive feedback loop component of the basic synchonized oscillator.
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[[File:mainproject06.png]]
 
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'''Fig.7.''' ''Genetic circuit of the experimental differential feedback loop.''
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[[File:Hasty2.png|x67px|link=http://partsregistry.org/Part:BBa_K546001]]
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'''Fig.5.''' ''BioBrick part K546001 forms the negative feedback loop component and complements K546005.''
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[[File:mainproject07.png]]
 
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'''Fig.8.''' ''Plasmid diagram of the experimental differential feedback loop.''
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Due to the tendency of interconnected positive and negative feedback loops to reach a steady state rather than sustaining oscillations, the external conditions need to be precisely controlled in order for the system to produce synchronized oscillations. In this system, the only parameters relevant to oscillatory gene expression that can be controlled during operation are the cell density and the external AHL degradation rate (see [https://2011.igem.org/Team:Wageningen_UR/Project/ModelingProj1 model] for details).
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However, maintaining a constant cell density over extended periods of time while independently varying the flow rate (AHL degradation) is difficult to achieve using traditional cultivation and measurement set-ups. In order to control these parameters while keeping the cells microscope-accessible, we developed a custom fluidic platform that can trap cells and allow them to remain viable over the duration of an experiment while maintaining a constant and reproducible cell density (See [https://2011.igem.org/Team:Wageningen_UR/Project/Devices flow chamber page] for details).  
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=====Advanced application: luciferin regeneration=====
 
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If the project advances and the reference design can be constructed and verified without significant delays, it may be possible to implement an advanced application involving luciferin regeneration. This design would involve the replacement of GFP with the Luciferase gene, and the addition of constitutively expressed Luciferin Regenerating Enzyme (LRE), which can regenerate the substrate required for the light-emitting reaction. Though the kinetics need to be considered, this design could theoretically produce regular pulses of visible light as long as cells are provided with sufficient D-cysteine.
 
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'''Double Tunable Synchronized Oscillator'''
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[[File:mainproject08.png]]
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The aforementioned constraints are due to the fact that there are no means by which the expression kinetics of LuxI and AiiA can be externally influenced. In order to gain more control over the expression dynamics, we refactored the system and introduced “tuning knobs” in the form of chemically inducible hybrid promoters (pR/LacI inducible by IPTG and pR/tetR inducible by anhydrotetracycline). The addition of two independent control variables should substantially expand the parameter space (cell density, flow rate) within which oscillations can occur. We also made the design more streamlined by taking advantage of the great diversity of available BioBrick quorum sensing parts in order to remove redundant elements and fit the entire system onto a single plasmid (a 30% reduction in size compared to the original design). Note: in order to take advantage of the tuning capabilities it is necessary to co-transform a plasmid which constitutively expresses LacI or TetR, or both.  
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'''Fig.9.''' ''A circuit for partially self-contained luciferin regeneration coupled to periodic luciferase expression.''
 
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[[File:System2.png|760px|link=https://static.igem.org/mediawiki/2011/a/a8/System2.png]]
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====4. Assembly====
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'''Fig.6.''' ''Genetic circuit of the synchronized oscillating system on a single plasmid.''
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=====Plasmids=====
 
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The plasmids will be constructed in accordance with the BioBrick assembly standard, which is a molecular cloning method with certain constraints. It requires that certain restriction sites be located upstream and downstream of the plasmid insert, but not anywhere else in the sequence. This enables modular assembly of low-level parts into larger composite parts, and the subsequent assembly of the large parts into even larger constructs without the need for special precautions. The exact strategy including each cloning step and the order in which parts are to be constructed is not shown here. The file contains all of the parts and included hyperlinks to the parts registry. Redundant strategies have been conceived of in order to prevent bottlenecks from arising due to certain parts being faulty. The optimal strategy allows all of the plasmids to be assembled completely by ligation of BioBrick parts. “Emergency” BioBrick part replacement strategies involving PCR have also been developed, and the necessary primers have been designed.
 
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=====Strains=====
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[[File:System3.png|760px|link=https://static.igem.org/mediawiki/2011/e/e1/System3.png]]
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For all the cloning steps required in this project we will use high copy plasmids in order to make restriction and purification of the plasmids more efficient. The final constructs will be cloned into a low copy plasmid in order to avoid producing too much of the proteins, which could lead to noise related issues and the risk of inclusion body formation.
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====5. Experimental Design====
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'''Fig.7.''' ''Genetic circuit of a tunable synchronized oscillator.''
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Once the plasmids have been constructed and transformed into their final host system, the oscillation experiment can be performed. Cells should grow in a container with flowing medium until they reach an adequate cell density, and to then activate the oscillation circuit. Over the course of hours, levels of fluorescent light emission should rise and fall in a synchronized manner.
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=====Fluorescence vs. Visible Light=====
 
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Detection of the oscillatory behaviour in the previously described designs relies on the excitation of fluorescent proteins and detection their emissions. Replacing the GFP gene with a gene for Luciferase would allow visible-spectrum light to be emitted via a biochemical reaction if the appropriate substrate were added to the medium. Though they fulfil essentially the same function, which one is more suitable depends on the detection devices available and their compatibility with the platform on which the bacteria are grown. However, having visible light detection is a prerequisite for the implementation our advanced design.
 
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=====Platform=====
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'''1''': The AHL Synthase LuxI is expressed at a basal level when AHL concentration is low. Relative AHL concentration increases as a function of cell density.
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The original Danino & Hasty design is believed to work in part due to the fact that the AiiA gene is longer than LuxI, and therefore the LuxI protein will begin producing the quorum sensing molecule AHL before AiiA is fully expressed. However, once AiiA is present it can degrade AHL faster than it is produced. Achieving oscillatory behaviour via this mechanism does not allow the system many degrees of freedom, and the kinetics involved, both in terms of gene expression and enzyme activity, are crucial. A self-contained system should not have to rely on external manipulation to produce oscillating behaviour. One aspect that can be controlled without compromising the integrity of the system is the rate at which AHL accumulates in the extracellular medium, and by extension, in all of the cells. This control can be provided by growing the cells in container in which they are physically constrained to a small space while a growth medium can flow over them and wash away AHL so that it cannot permanently accumulate, as well as waste and excess cells. It should also allow cell density to reach a stable steady state. The container should also be transparent to allow detection of the reporter molecules.
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====6. Devices====
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'''2''': As the concentration of AHL increases, it associates with the constitutively expressed transcription factor LuxR, thereby up-regulating the expression of AiiA, LuxI and GFP. As LuxI accumulates, the concentration of AHL increases rapidly as a result of the LuxR-AHL -> LuxI positive feedback loop.
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=====Microfluidic devices=====
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The platform best suited for these requirements is a microfluidic device, such as the one used by Danino & Hasty. However, such devices need to be custom designed and are prohibitively expensive. Because the design contains cell traps (ca. 100x50x2μm) the devices are difficult to clean, and it is likely that each device could be used only once. The underlying virtue of using a micro fluidic device is that it is a container that allows high enough cell densities for achieving threshold AHL levels while allowing cell density to remain constant independent of medium flow rate.
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However, there exist a few alternatives that might fulfil the necessary requirements to serve as a platform for detecting oscillations. Some other alternatives besides the one already suggested, could be a standard microfluidic device (as opposed to a custom one) as offered by microliquid, these have a price around 150 euro’s a piece. This device consists of a linear channel which has an inflow and an outflow port. Danino & Hasty employed a similar design in his research of the propagation of the GFP signal. However, the dimensions of standard device are larger than the custom platform the micro-traps. Probably, this means that diffusion of the AHL will increase dramatically, slowing down oscillation periods. On the other hand, this device does not physically trap the cells the same way as the custom device. In this device the cells are trapped between the walls of the device locking them in place. These micro fluidic devices could be reusable.
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=====Small Chemostat=====
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'''3''': The AHL-degrading enzyme AiiA does not accumulate as rapidly as LuxI. However, the degradation of AHL occurs at a faster rate than AHL synthesis, effectively reducing the level of active LuxR (and its transcriptional activity). This delayed negative feedback results in oscillations in AHL concentration.
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A second alternative might be a small chemostat. One of the benefits of using a chemostat is that it is continuously stirred, and thus AHL levels are the same throughout the culture. Therefore the system is not dependent on AHL diffusion. Due to the nature of a chemo-stat there is a continuous out-flow of cells, which might be problematic for reaching sufficient cell densities, and which can produce high enough levels of AHL. One way of solving this could be to use a system in which cells are retained in the system via the means of membranes. Another alternative might be at the molecular level, wildtype LuxR is activated when AHL concentrations reach ~100 nM. In the registry of standard biological parts a mutant LuxR(BBa_I729004) is available, which is activated at a concentration of 10nM. Thus this mutant LuxR can in theory reduce cell densities 10 fold, but still allow a functioning system.
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=====Microsieve=====
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'''4''': AHL diffuses freely between cells, synchronizing LuxR-AHL dependent transcriptional activity across a population of cells.
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However, the most viable alternative to the microfluidic device might be a microsieve. This device also traps cells just like a microfluidic device. However the mechanism of entrapment is different: a microfluidic device traps cells in a physical trap, while microsieves do this by applying an overpressure. Through this overpressure cells are retained on the sieve. By varying the overpressure the thickness of the “cake” of cells can be varied. Furthermore these sieves are chemically inert and can withstand harsh chemical and physical circumstances, meaning that they can be cleaned and reused again.
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The device consists of a microsieve contained in a flow chamber. The microsieve is made of silicon and contains pores as small as 200 nm. Because the sieve is made out of silicon it is chemically inert and can easily be cleaned and reused. The flow chamber has an inflow and two outflow ports. Through the inflow port a liquid enters containing suspended particles. When the liquid passes the micro sieve it will encounters negative pressure whereby particles are trapped by the sieve. As particles accumulated, they eventually form a “cake”. The filtered liquid leaves the device via the outflow port below the sieve, and remaining liquid in the chamber leaves the device via the outflow port 1.
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'''5''': LuxR-AHL dependent GFP expression allows the fluctuations in AHL concentration to be observed in situ. LuxI, AiiA and GFP all have LVA tags and are degraded rapidly (albeit at slightly different rates).
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[[File:mainproject09.png]]
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'''6''': Constitutively expressed RFP allows the distinction between the effects of cell growth and of the true oscillations of GFP expression due to our system.
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'''Fig.10.''' ''Schematic of a micro-filtration device. The microsieve is 5x5mm.''
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'''7''': The repressors LacI and TetR are constitutively expressed. They inhibit the expression of luxI and aiiA respectively. Adding IPTG removes the LacI repressor and aTc removes the TetR repressor.  
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[[File:Dt.png|x67px|link=http://partsregistry.org/Part:BBa_K546546]]
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[[File:mainproject10.png]]
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'''Fig.8.''' ''The complete synchronized oscillator circuit with a single copy of constitutively expressed LuxR.''
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'''Fig.11.''' ''Photograph of cells growing on a microsieve.''
 
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This device is particularly promising for a few reasons. Through the negative pressure a small pore size filter is able to be seeded with micro-organisms that will grow on its surface, as depicted in Figure 11. Once these micro-organisms are trapped and growth medium is supplied as inflow, they will start to divide and form a tight layer on the sieve.
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[[Team:Wageningen_UR/Project/CompleteProject1Description#Project Description| back to top]]
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Furthermore by adjusting the flow rate or filter pore size and porosity the cell layer can be varied of thickness. This could be necessary for reaching the correct balance between AHL production and removal. Another reason why this device is promising is because of its low price. The company Aqua Marijn, which is partly located at the departed of organic chemistry can produce custom versions of the chamber and supply the micro filter for around 50 euros per device. Preliminary discussions with representatives have proven to be promising.
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====4. Experimental verification====
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The individual subcomponents of the oscillatory circuit were tested using a fluorescence spectrophotometer. Changes in GFP expression relative to different AHL concentrations were measured to verify the functionality of the parts (see [https://2011.igem.org/Team:Wageningen_UR/Project/PartsProj1 data page]). However, due to the precise growth conditions required for synchronized oscillations to be sustained, it was necessary to adopt a more sophisticated approach to test the complete system. 
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There were three requirements for the experimental set-up to test the Synchronized Oscillatory System:
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a) ability to grow cells in a physically constrained space to achieve the high cell density necessary for quorum sensing machinery to respond. Ideally, the cell density should remain more or less constant over the course of hours, in addition to being predictable and reproducible.
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b) supplying cells with fresh media to provide nutrients and remove waste (and AHL) without affecting the cell density.
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c) directly observe cells with a fluorescence microscope to perform time-lapse studies aiming at detecting changes in GFP expression over a period of hours.
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Previous studies of oscillatory gene expression have employed microfluidic devices with micron-scale trapping chambers to restrict cells. However, these systems can be prohibitively expensive, require specialized accessories, and are generally not reuseable. We developed a low-cost experimental flow chamber that fulfills all of the aforementioned criteria (for detailed specifications see [https://2011.igem.org/Team:Wageningen_UR/Project/Devices flow chamber page]) .
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[[File:Mainpic.jpg]]
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'''Fig.9.''' ''3D rendering of the flow chamber.''
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To measure the oscillations, the flow chamber was outfitted with a microdish, which is a thin aluminium oxide sheet containing thousands of circular wells. The wells are 180 μm in diameter and 40 μm deep. Small molecules (such as nutrients from growth media) can diffuse through the bottom of the dish and feed cells growing in the wells. For these experiments, the cells were fed through bottom in order to restrict their growth to the wells. This allowed the cells to reach high densities and relative stable populations which could be studied individually (4 wells could be visualized using 100x magnification)
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[[File:Dish.gif]] [[File:Microdish_close.PNG|400px|link=https://static.igem.org/mediawiki/2011/3/3e/Microdish_close.PNG|right]]
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'''Fig.10.''' ''Above: Schematic illustration of the microdish.''
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'''Fig.11.''' ''Right: Microdish installed in flow chamber viewed at 40x magnification, illuminated from the bottom with white light. Growth medium is supplied from the bottom through the 5x5mm socket (rounded corner). Diffusion of nutrients through the aluminium oxide allows cells to grow across the entire dish.
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The cells containing the synchronized oscillator system plasmid were grown overnight in LB medium supplemented with an antibiotic. They were then centrifuged for 10 minutes at 4600 rcf and resuspended in Phosphate Buffered Saline solution before being injected through the top flow port (Fig.12a). Directly after injection, the cells fill the entire chamber volume (Fig.13a). After approximately 5-8 hours the cells situated outside the wells are starved and no longer express detectable levels of GFP (Fig.13b). Cells in the wells continue to grow for approximately 12 hours before reaching a stable cell density (Fig.13c). After the wells were saturated with cells, time-lapse microscopy was initiated. A photograph was taken every 10 minutes using a fluorescence microscope fitted with a GFP filter. Changes in GFP expression over time were subsequently quantified. (Video 1)
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[[File:Bottom_feed_WUR.png‎|380px]] [[File:Zero-flow.PNG|380px]]
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'''Fig.12a.''' ''Schematic view of the bottom fed flow device.'' '''Fig.12b.''' ''Three dimensional impression of cells in the flow device''
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[[File:Fullchamber.PNG|250px]]  [[File:Dish_cells.JPG|250px]]  [[File:4pbs_experiment_incubatenewof17.8_DT_5g_dry.jpg|250px]]
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'''Fig.13a.''' ''Cells in the chamber, directly after injection.'' '''Fig.13b.''' ''Cells in the chamber, a few hours after injection.'' '''Fig.13c.''' ''Cells in the chamber, about twelve hours after injection.''
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====5. Results====
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Per run four wells of the microdish were analyzed, as this is the maximal number of wells that one can focus on with a 10x objective. Pictures were processed with [http://rsbweb.nih.gov/ij/ ImageJ], a program that can measure the different wells separately.
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These time-lapse microscopy studies of cells harboring the Synchroscillator plasmid consistently showed significant periodic changes in GFP expression compared to control experiments with cells constitutively expressing GFP (Fig.15). The observed periodicity is in the range of 60 minutes, and the asymmetry of the peaks is indicative of differences between GFP synthesis and degradation. The oscillations were sustained over multiple periods for a duration of 5 hours after which the expression level of GFP decreased; most likely due to decreases in cell vitality. These findings are consistent with predictions made from mathematical simulations as well as previously published results. It is noteworthy that these dynamics were able to emerge under zero-flow conditions and did not require manipulation the external AHL degradation rate. The synchronization between wells suggests that the diffusion of extracellular AHL through the bottom of the microdish occurred at a rate that allowed spatially separated cell populations to experience similar AHL concentrations.
 +
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[[File:Tunabledata.png|760px]]
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'''Fig.14''' ''Quantitative analysis of GFP expression by the Tunable Oscillator in the microdish. Negative control: ptet-GFP (fluorescent, non-oscillating).
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<html><iframe width="420" height="315" src="http://www.youtube.com/embed/Q6tDQNIaklg" frameborder="0" allowfullscreen></iframe></html>
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'''Fig.15''' ''Time-lapse video of the Tunable Oscillator.''
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====6. Conclusion and Future work====
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Over the course of our experiments we were able to show that quorum sensing genes and regulatory elements composed to form interconnected positive and negative feedback loops can result in sustained synchronized oscillations under appropriate experimental conditions.
 +
 +
These findings highlight the utility of custom designed micro-environments for the study of complex genetic circuits. Our flow chamber outfitted with the microdish proved to be a suitable platform to investigate the temporal dynamics of intercellular communication. The ability to manipulate extracellular conditions without disrupting localized cell populations should prove useful in investigating biological systems in real time.
 +
 +
Future work should focus on defining appropriate wet-lab experiments in order to enhance the quality of the mathematical model by fitting it with the right parameters. Also the stability of the oscillations can be improved by optimizing the supply of nutrients to the bacteria in the wells in order to achieve long term viability of the cell cultures. Additionally, the tunability of the system could enhance the robustness of such synthetic regulatory systems. Modularity BioBrick parts expand functionality without having to redesign the system from the ground up.
 +
 +
===Links and references===
 +
 +
[1][http://www.nature.com/nature/journal/v463/n7279/abs/nature08753.html Danino et al. 2010]
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[2][http://www.nature.com/nature/journal/v463/n7279/suppinfo/nature08753.html Supplementary information]
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[3][https://2007.igem.org/Tokyo/Works Tokyo iGEM 2007]
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[4][http://rsif.royalsocietypublishing.org/content/early/2010/06/28/rsif.2010.0183.short A comparative analysis of synthetic genetic oscillators]
   
   
 +
 +
 +
 +
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[[Team:Wageningen_UR/Project/CompleteProject1Description#Project Description| back to top]]
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}}
}}

Latest revision as of 03:53, 22 September 2011

Building a Synchronized Oscillatory System

Synchroscillator

Project Description

1. Introduction

The aim of this project is to design and implement a system exhibiting sustained oscillatory protein expression which is synchronized across a population of spatially constrained E. coli cells. The principles that govern this type of behavior have been studied both in theory and in practice, and as such there exists a solid foundation to apply these ideas in the context of the iGEM competition. In essence, this project consists of constructing a plasmid which contains protein encoding genes which reciprocally affect each other’s expression in a reliable manner, and experimentally measuring the expression dynamics to test the predictive value of a mathematical model. Due to the specificity of the required system parameters, and resulting difficulty in experimentally verifying the phenomena we wish to observe, special considerations regarding the experimental set-up had to be made. We hope that this system might be employed as a pace-making device to drive more complex genetic circuits requiring time-dependent gene expression, or as a component in sophisticated metabolic engineering applications.


SOS 2.png

Fig.1. Artistic rendering of the Synchronized Oscillatory System.


2. Mechanism

There are a number of genetic circuit topologies that have the potential to exhibit oscillatory behavior under the right conditions. However, the requirement that the oscillations should be synchronized posed a constraint on the components that could be used. The starting point for our genetic circuitry was a design recently published in the article “A synchronized quorum of genetic clocks” by Danino et al. This design combines elements of the Vibrio fischeri quorum sensing system with a quorum quenching enzyme from Bacillus subtilis, resulting in coupled positive and negative feedback loops which regulate the expression of a reporter protein.

Basic Components:

LuxR is a transcriptional regulator in the bioluminescent quorum-sensing system of the symbiotic deep sea bacterium Vibrio fischeri. It is induced by binding the auto-inducer molecule N-(3-oxohexanoyl)-homoserine lactone (AHL). The AHL-LuxR complex controls expression of the lux regulon, which contains diverging pRight and pLeft promoter elements. The pRight element has low basal transcription, and is activated by AHL-LuxR; pLeft has higher basal expression, and is repressed by the AHL-LuxR complex. This dual activity makes LuxR a useful element for controlling interconnected genetic feedback loops. The unrestricted diffusion of AHL through the plasma membrane allows spatially proximate populations of cells to experience identical AHL conditions and synchronize AHL-dependent gene expression.


The enzyme LuxI is an acyl-homoserine-lactone synthase which produces the intercellular signalling molecule N-(3-oxohexanoyl)-homoserine lactone (AHL). Placing LuxI under control of the pRight promoter results in a positive feedback loop: when increases in cell density cause the intracellular AHL concentration to rise above the activation threshold of the pRight promoter, the transcription rate of the LuxI gene is increased which in turn results in the production of more AHL.


AiiA is an enzyme from B. subtilis which degrades AHL. Its biological function is to interfere with the quorum sensing signals of other bacteria. Placing it under control of the pRight promoter results in negative feedback as a response to increasing AHL concentrations.


The reporter molecule Green Fluorescent Protein (GFP) is also regulated by the pRight promoter and provides a quantitative (albeit delayed) indication of the AHL concentration the cell is exposed to at a given point in time. LuxI, AiiA and GFP are all tagged for rapid degradation (LVA-tag). Due to differences in the synthesis and degradation rates of LuxI and AiiA, there exists a space of conditions within which periodic oscillations in AHL concentration, and concomitant oscillatory protein expression can emerge. Under most conditions, the level of AHL within a population of cells will quickly reach a steady state. However, by simulating the system using a quantitative biochemical model, it is possible to predict conditions under which oscillations are likely to occur. See our modeling page for details.



System1.png

Fig.2. Genetic circuit of a synchronized oscillator on 2 plasmids

1: The AHL Synthase LuxI is expressed at a basal level when AHL concentration is low. Relative AHL concentration increases as a function of cell density.

2: As the concentration of AHL increases, it associates with the constitutively expressed transcription factor LuxR, thereby up-regulating the expression of AiiA, LuxI and GFP. As LuxI accumulates, the concentration of AHL increases rapidly as a result of the LuxR-AHL -> LuxI positive feedback loop.

3: The AHL-degrading enzyme AiiA does not accumulate as rapidly as LuxI. However, the degradation of AHL occurs at a faster rate than AHL synthesis, effectively reducing the level of active LuxR (and its transcriptional activity). This delayed negative feedback results in oscillations in AHL concentration.

4: AHL diffuses freely between cells, synchronizing LuxR-AHL dependent transcriptional activity across a population of cells.

5: LuxR-AHL dependent GFP expression allows the fluctuations in AHL concentration to be observed in situ. LuxI, AiiA and GFP all have LVA tags and are degraded rapidly (albeit at slightly different rates).

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3. Designs

“Hasty” system:


The first design we implemented was a BioBrick part based on reconstruction of the plasmids used by Danino et al. We intended to make as accurate a replica as possible in order to confirm the previously published results, and to test the viability of our experimental platform. However, there are a few differences between the original Hasty system and “our replica“. While the Hasty system employs the natural lux promoter which contains divergent pLeft and pRight elements (Fig 4), the BioBrick parts we employed have both elements in the same orientation. Both the original and our system contain 3 copies of the luxR gene under control of the pLeft element. Furthermore, a different (high copy) backbone was used during the functional validation of the parts, as opposed to the low copy backbone employed by Hasty.


Hasty1.png

Fig.4. BioBrick part K546005 forms the positive feedback loop component of the basic synchonized oscillator.


Hasty2.png

Fig.5. BioBrick part K546001 forms the negative feedback loop component and complements K546005.


Due to the tendency of interconnected positive and negative feedback loops to reach a steady state rather than sustaining oscillations, the external conditions need to be precisely controlled in order for the system to produce synchronized oscillations. In this system, the only parameters relevant to oscillatory gene expression that can be controlled during operation are the cell density and the external AHL degradation rate (see model for details). However, maintaining a constant cell density over extended periods of time while independently varying the flow rate (AHL degradation) is difficult to achieve using traditional cultivation and measurement set-ups. In order to control these parameters while keeping the cells microscope-accessible, we developed a custom fluidic platform that can trap cells and allow them to remain viable over the duration of an experiment while maintaining a constant and reproducible cell density (See flow chamber page for details).


Double Tunable Synchronized Oscillator

The aforementioned constraints are due to the fact that there are no means by which the expression kinetics of LuxI and AiiA can be externally influenced. In order to gain more control over the expression dynamics, we refactored the system and introduced “tuning knobs” in the form of chemically inducible hybrid promoters (pR/LacI inducible by IPTG and pR/tetR inducible by anhydrotetracycline). The addition of two independent control variables should substantially expand the parameter space (cell density, flow rate) within which oscillations can occur. We also made the design more streamlined by taking advantage of the great diversity of available BioBrick quorum sensing parts in order to remove redundant elements and fit the entire system onto a single plasmid (a 30% reduction in size compared to the original design). Note: in order to take advantage of the tuning capabilities it is necessary to co-transform a plasmid which constitutively expresses LacI or TetR, or both.


System2.png

Fig.6. Genetic circuit of the synchronized oscillating system on a single plasmid.


System3.png

Fig.7. Genetic circuit of a tunable synchronized oscillator.


1: The AHL Synthase LuxI is expressed at a basal level when AHL concentration is low. Relative AHL concentration increases as a function of cell density.

2: As the concentration of AHL increases, it associates with the constitutively expressed transcription factor LuxR, thereby up-regulating the expression of AiiA, LuxI and GFP. As LuxI accumulates, the concentration of AHL increases rapidly as a result of the LuxR-AHL -> LuxI positive feedback loop.

3: The AHL-degrading enzyme AiiA does not accumulate as rapidly as LuxI. However, the degradation of AHL occurs at a faster rate than AHL synthesis, effectively reducing the level of active LuxR (and its transcriptional activity). This delayed negative feedback results in oscillations in AHL concentration.

4: AHL diffuses freely between cells, synchronizing LuxR-AHL dependent transcriptional activity across a population of cells.

5: LuxR-AHL dependent GFP expression allows the fluctuations in AHL concentration to be observed in situ. LuxI, AiiA and GFP all have LVA tags and are degraded rapidly (albeit at slightly different rates).

6: Constitutively expressed RFP allows the distinction between the effects of cell growth and of the true oscillations of GFP expression due to our system.

7: The repressors LacI and TetR are constitutively expressed. They inhibit the expression of luxI and aiiA respectively. Adding IPTG removes the LacI repressor and aTc removes the TetR repressor.

Dt.png

Fig.8. The complete synchronized oscillator circuit with a single copy of constitutively expressed LuxR.


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4. Experimental verification

The individual subcomponents of the oscillatory circuit were tested using a fluorescence spectrophotometer. Changes in GFP expression relative to different AHL concentrations were measured to verify the functionality of the parts (see data page). However, due to the precise growth conditions required for synchronized oscillations to be sustained, it was necessary to adopt a more sophisticated approach to test the complete system.

There were three requirements for the experimental set-up to test the Synchronized Oscillatory System:

a) ability to grow cells in a physically constrained space to achieve the high cell density necessary for quorum sensing machinery to respond. Ideally, the cell density should remain more or less constant over the course of hours, in addition to being predictable and reproducible.

b) supplying cells with fresh media to provide nutrients and remove waste (and AHL) without affecting the cell density.

c) directly observe cells with a fluorescence microscope to perform time-lapse studies aiming at detecting changes in GFP expression over a period of hours.

Previous studies of oscillatory gene expression have employed microfluidic devices with micron-scale trapping chambers to restrict cells. However, these systems can be prohibitively expensive, require specialized accessories, and are generally not reuseable. We developed a low-cost experimental flow chamber that fulfills all of the aforementioned criteria (for detailed specifications see flow chamber page) .


Mainpic.jpg

Fig.9. 3D rendering of the flow chamber.


To measure the oscillations, the flow chamber was outfitted with a microdish, which is a thin aluminium oxide sheet containing thousands of circular wells. The wells are 180 μm in diameter and 40 μm deep. Small molecules (such as nutrients from growth media) can diffuse through the bottom of the dish and feed cells growing in the wells. For these experiments, the cells were fed through bottom in order to restrict their growth to the wells. This allowed the cells to reach high densities and relative stable populations which could be studied individually (4 wells could be visualized using 100x magnification)


File:Dish.gif
Microdish close.PNG

Fig.10. Above: Schematic illustration of the microdish.



Fig.11. Right: Microdish installed in flow chamber viewed at 40x magnification, illuminated from the bottom with white light. Growth medium is supplied from the bottom through the 5x5mm socket (rounded corner). Diffusion of nutrients through the aluminium oxide allows cells to grow across the entire dish.


The cells containing the synchronized oscillator system plasmid were grown overnight in LB medium supplemented with an antibiotic. They were then centrifuged for 10 minutes at 4600 rcf and resuspended in Phosphate Buffered Saline solution before being injected through the top flow port (Fig.12a). Directly after injection, the cells fill the entire chamber volume (Fig.13a). After approximately 5-8 hours the cells situated outside the wells are starved and no longer express detectable levels of GFP (Fig.13b). Cells in the wells continue to grow for approximately 12 hours before reaching a stable cell density (Fig.13c). After the wells were saturated with cells, time-lapse microscopy was initiated. A photograph was taken every 10 minutes using a fluorescence microscope fitted with a GFP filter. Changes in GFP expression over time were subsequently quantified. (Video 1)


Bottom feed WUR.png Zero-flow.PNG

Fig.12a. Schematic view of the bottom fed flow device. Fig.12b. Three dimensional impression of cells in the flow device


Fullchamber.PNG Dish cells.JPG 4pbs experiment incubatenewof17.8 DT 5g dry.jpg

Fig.13a. Cells in the chamber, directly after injection. Fig.13b. Cells in the chamber, a few hours after injection. Fig.13c. Cells in the chamber, about twelve hours after injection.


5. Results

Per run four wells of the microdish were analyzed, as this is the maximal number of wells that one can focus on with a 10x objective. Pictures were processed with [http://rsbweb.nih.gov/ij/ ImageJ], a program that can measure the different wells separately.

These time-lapse microscopy studies of cells harboring the Synchroscillator plasmid consistently showed significant periodic changes in GFP expression compared to control experiments with cells constitutively expressing GFP (Fig.15). The observed periodicity is in the range of 60 minutes, and the asymmetry of the peaks is indicative of differences between GFP synthesis and degradation. The oscillations were sustained over multiple periods for a duration of 5 hours after which the expression level of GFP decreased; most likely due to decreases in cell vitality. These findings are consistent with predictions made from mathematical simulations as well as previously published results. It is noteworthy that these dynamics were able to emerge under zero-flow conditions and did not require manipulation the external AHL degradation rate. The synchronization between wells suggests that the diffusion of extracellular AHL through the bottom of the microdish occurred at a rate that allowed spatially separated cell populations to experience similar AHL concentrations.


Tunabledata.png

Fig.14 Quantitative analysis of GFP expression by the Tunable Oscillator in the microdish. Negative control: ptet-GFP (fluorescent, non-oscillating).

Fig.15 Time-lapse video of the Tunable Oscillator.

6. Conclusion and Future work

Over the course of our experiments we were able to show that quorum sensing genes and regulatory elements composed to form interconnected positive and negative feedback loops can result in sustained synchronized oscillations under appropriate experimental conditions.

These findings highlight the utility of custom designed micro-environments for the study of complex genetic circuits. Our flow chamber outfitted with the microdish proved to be a suitable platform to investigate the temporal dynamics of intercellular communication. The ability to manipulate extracellular conditions without disrupting localized cell populations should prove useful in investigating biological systems in real time.

Future work should focus on defining appropriate wet-lab experiments in order to enhance the quality of the mathematical model by fitting it with the right parameters. Also the stability of the oscillations can be improved by optimizing the supply of nutrients to the bacteria in the wells in order to achieve long term viability of the cell cultures. Additionally, the tunability of the system could enhance the robustness of such synthetic regulatory systems. Modularity BioBrick parts expand functionality without having to redesign the system from the ground up.

Links and references

[1][http://www.nature.com/nature/journal/v463/n7279/abs/nature08753.html Danino et al. 2010]

[2][http://www.nature.com/nature/journal/v463/n7279/suppinfo/nature08753.html Supplementary information]

[3]Tokyo iGEM 2007

[4][http://rsif.royalsocietypublishing.org/content/early/2010/06/28/rsif.2010.0183.short A comparative analysis of synthetic genetic oscillators]



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