Difference between revisions of "Part:BBa K1123005"

Revision as of 10:27, 26 October 2013

EGFP Protein Production Construct

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.

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

Sequence and Features

Characterization

This part shares general concepts with the Valencia 2012 part: 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: BBa_K1123000 then we will be able to express other CEST proteins ( BBa_K1123001, BBa_K1123002, BBa_K1123003, BBa_K1123004, BBa_K1123006, BBa_K1123007, BBa_K1123008, 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.

From this graph we can see that upon having an optical density of 0.600 the cells were still growing in their exponential phase. Upon reaching this level of approximately 0.600 the oxygen inlet was closed and the vessel containing the bacterial growth solution was flooded with Nitrogen. This ensured that an anaerobic environment would ensue. At regular intervals samples were taken so that we could follow the production of EGFP as a result of the anaerobic environment which set in motion the DNA transcription using the FNR promoter.

The vessel was left at 37°C for approximately 25 hours when the last sample was taken. At this point all samples were spun down and pelleted so that the bugbuster protocol could be used. 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 a small eppendorf tube. The product hereof was a supernatant containing our EGFP and a small pellet of waste.

A small portion of this supernatant was then taken and loaded onto a 12% SDS gel.

Here the time in minutes for each sample is given 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 using small His-tag retention 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 again loaded onto a 12% SDS gel which can be viewed below.

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.

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.