View source for Part:BBa K1123005

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<partinfo>BBa_K1123005 short</partinfo>

This composite part has been built up from a number of separate BioBricks, the most prominent of which the FNR promotor and the EGFP Protein sequence. The FNR promotor sequence enables us to bring the EGFP protein to expression anaerobically. Almost all E.coli strains posses a form of this promotor to induce metabolic processes once the bacteria enters anaerobic regions. The EGFP protein is a frequently used fluorescent protein which we are expressing with the sole purpose of testing the protein expression under the FNR promotor.

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===Usage and Biology===

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===TU-Eindhoven Sequencing Results===
This construct has been submitted to the iGEM registry and has been privately sequenced by the iGEM 2013 TU-Eindhoven. The sequencing results were positive indicating that the sequence and part submitted to the registry are correct. 
''Sequencing was performed by BaseClear Netherlands''

<span class='h3bb'>Sequence and Features</span>
<partinfo>BBa_K1123005 SequenceAndFeatures</partinfo>


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===Functional Parameters===
<partinfo>BBa_K1123005 parameters</partinfo>
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===Characterization===
This part shares general concepts with the Valencia 2012 part: [[Part:BBa_K763002 | BBa_K763002]] 

====Characterization by the TU Eindhoven 2013 iGEM Team====
As part of the iGEM 2013 competition the TU-Eindhoven team attempted to create a promoter which would induce protein expression under anaerobic conditions. This functional promoter could then be used to express CEST proteins (which should enable MRI imaging) upon the bacterium entering tumour regions. To test the functionality of the promoter we decided to express EGFP under anaerobic conditions. EGFP can be easily analysed making it easy for us to characterize the workings of the FNR promoter. This expression of EGFP was performed three times, the first two both at 0% Oxygen whereas the third time we attempted to express at 5% Oxygen. 

If we manage to express EGFP using this FNR promoter: [[Part:BBa_K1123000 | BBa_K1123000]] then we will be able to express other CEST proteins ([[Part:BBa_K1123001 | BBa_K1123001]],[[Part:BBa_K1123002 | BBa_K1123002]],[[Part:BBa_K1123003 | BBa_K1123003]],[[Part:BBa_K1123004 | BBa_K1123004]],[[Part:BBa_K1123006 | BBa_K1123006]],[[Part:BBa_K1123007 | BBa_K1123007]],[[Part:BBa_K1123008 | BBa_K1123008]],[[Part:BBa_K1123009 | BBa_K1123009]]) anaerobically with a high probability of success. 


For the EGFP expression under influence of the FNR promoter we cloned this biobrick into a pBR322 vector. This vector was then transformed into BL21 bacteria. Colonies of this transformation product were grown in (6) 8mL culture tubes and were then injected into a 4L LB solution, found in a bioreactor. After the optical density had reached 0.600 the chamber was constantly flooded with Nitrogen for over 24 hours, having samples taken every few hours during the day. 
After this anaerobic expression was complete the samples were analysed but no EGFP could be observed. A disappointing result. Upon closer investigation of the BL21 E.coli strain, we found that the FNR production, necessary for the proper functioning of the FNR promoter was absent. 

In response to this lack of FNR within the BL21 bacteria it was decided that we attempt expression within a second E.coli strain. For this the XL-1-Blue strain was chosen. Before performing the actual experiments of course some research was performed to ensure that our assumptions were also true. 

Once certain this strain was FNR compatible we transformed this biobrick, once again in the pBR322 vector, into XL-1-Blue E.coli bacteria. These were grown on agar and then picked, placed in 8mL of LB and then brought over into 4L of LB medium. Here they were allowed to grow aerobically until the Optical Density (O.D.) was 0.600 or higher. This protocol was retained for all three expression experiments. 

{|
|[[File:Tu-Eindhoven_Images_GrowthCurve_1.png | thumb | 285px | Anaerobic expression at 0% Oxygen saturation.]]
|[[File:Tu-Eindhoven_Images_GrowthCurve_2.png | thumb | 285px | Anaerobic expression at 0% Oxygen saturation.]]
|[[File:Tu-Eindhoven_Images_GrowthCurve_3.png | thumb | 285px | Anaerobic expression at 5% Oxygen saturation.]]
|}

The graphs above show the growth curves of the bacteria during the course of the experiments. During the first experiment the optical density was measured up until the oxygen was removed from the vessel containing the bacterial culture medium, during the second and third experiments the optical density was measured continually throughout the experiments. In all three experiments, upon reaching an optical density of approximately 0.600 the oxygen inlet was closed and the vessel was flooded with nitrogen until the desired oxygen concentration was reached. The medium was then continually regulated to maintain this desired concentration. For all three experiments you can see that cells are still in their exponential growth phase when the oxygen concentration is reduced. Throughout the rest of each of the experiments, samples of the culture medium were taken at regular intervals so that we could follow the production of EGFP as a result of the anaerobic environment which sets in motion the DNA transcription using FNR promoter.

During the experiments the vessel was left at 37&deg;C for approximately 25 hours before the last samples were taken. At this point all samples taken up until that point were spun down and pelleted so that the bugbuster protocol could be performed. As the samples we had taken whilst performing the expression were no larger than 25mL the volumes we had to work with were relatively small. After performing the bugbuster protocol the solutions were poured into small eppendorf tubes and spun down. The product hereof was a supernatant containing our EGFP protein and a small pellet of waste. 

For the first experiment only a small portion of this supernatant was then taken and loaded onto a 12% SDS gel. 

[[File:TU-Eindhoven_Images_Unpurified_EGFP_Expression.jpg | thumb |750px | Here the time in minutes before each sample was taken is as follows: t1 = 0 minutes, t2 = 39 minutes , t3 = 180 minutes, t4 = 375, t5 = 1190, t6 = 1710.]]

At first we were pleasantly optimistic about the results, as you can see there is an obvious increase of a certain protein in accordance with time increase. However, under scrutiny, it becomes visible that the protein which is being expressed so clearly has a molecular weigh far higher than that of EGFP which we expect at approximately 30kDa. The red boundary shows which bands on the gel we believed could be our EGFP protein.

To improve upon this result, we purified the supernatant. This was also done for the supernatants obtained during the second and third experiments.  We made use of small His-Tag binding spin columns. These would bind only to our EGFP protein, which should be bound to the His-tag we attached.  After purifying the same samples were loaded onto 12% SDS gels which can be viewed below.

{|
|[[File:TU-Eindhoven_Images_Purified_EGFP_Expression.jpg | thumb | 750px | Gel show the same 6 samples as shown in the previous unpurified gel.]]]]
|[[File:TU-Eindhoven_Images_AnaerobicEGFPExpressionPurifiedSDS.png | thumb | 750px | Here the columns marked C- and C+ are respectively a negative and positive control. The negative control consists of a sample taken from a medium which was allowed to grow aerobically for 25 hours. The positive control is a known EGFP samples. Its height can be put down to its binding with a CNA35 protein construct. Futhermore two sets of 6 samples can be seen. The first 6 time samples were taken during experiment 2 (at 0% oxygen concentration) and the second set of 6 were taken during experiment 3 (at 5% oxygen concentration)]]
|}

Due to the purification we did of course dilute the protein concentration somewhat, and the low starting concentration of EGFP as seen on the first gel, it was not entirely unrealistic for us to only see such a slight band on the SDS gel. This is also in accordance with the experiment as we were not over expressing the EGFP protein but expressing it using a standard metabolic promoter. 

One final test performed to check whether or not EGFP was being produced came from a fluorescence measurement. Herein we tested the emission spectra of each of the samples by pipetting a portion of the purified sample into a wells plate. These spectra are shown below, along with a graph showing the maximal emission for each of the samples.

[[File:FluorAnalysis.jpg]]
[[File:FluorAnalysisPeakTime.png]]

In the top graph we see that the intensity of EGFP emission increases in accordance with increasing time steps which is confirmed by viewing the second graph where the maximal emissions are shown for each of the samples. The control is a sample of the elution buffer used to retain our protein after purification. 

With these results we can be quite conclusive in saying that there was EGFP expression, induced by the hypoxic conditions in the medium over the course of time. We do however have to take in to account that the actual expression concentrations were extremely low. On the plus side the promoter does seem to be effective within anaerobic conditions.