Team:MIT/Experiments/EGSH TP901 Experiment
Testing TP901 under the inducible promoter EGSH
System Mechanism
EGSH is an inducible promoter that behaves similarly to the TRE promoter: when its transactivator, the ecdysone receptor (VgEcR) binds to a small molecule called ponasterone A (PonA), it will bind to the EGSH promoter and initiate transcription of the gene downstream from the promoter. In this experiment, that gene is TP901, a serine integrase. Our motivation for using the EGSH/PonA system instead of the TRE/doxycyline system is that as its name suggests, ponasterone A is a hormone, so we expect this system to behave more similarly to our synthetic estrogen and progesterone responsive promoter systems than TRE/doxycycline. To measure the activity of TP901, we used Golden Gate assembly to flank an inverted gene for enhanced yellow fluorescent protein (eYFP) with the attB and attP recognition sites for TP901 and, using gateway cloning, put it under the constitutive mammalian promoter human elongation factor 1-alpha (hEF1a). Thus, the unmodified expression vector does not produce any eYFP, but if TP901 is present and active, it will unidirectionally invert the gene to the correct orientation for the promoter, and the cells will express eYFP.
After successfully cloning our plasmids for the recombinase recognition sites, we transiently transfected them into HEK293 cells and analyzed the data with flow cytometry.
Experiment 1: Characterizing EGSH Promoter
1. Purpose
The purpose of this experiment was to characterize the PonA inducible promoter, pEGSH. pEGSH will be used to test how an inducible promoter can modulate the activity of recombinases, ideally keeping basal expression to a minimum. We wanted to determine the concentration of PonA that gave the highest amount of activation.
2. Set Up
We used a 3:1:1 ratio of EGSH:mKate, transactivator hEF1a:VgEcR, and transfection marker hEF1a:BFP based on our investigation into the ideal DNA ratios for experiments involving EGSH induction. The 2014 MIT iGEM team, which also used EGSH as an inducible promoter, reported seeing the greatest success with this ratio. We induced wells containing these plasmids with 5 varying amounts of PonA. We added a well lacking the trans-activator necessary for EGSH as a control. The purpose of this control is to further characterize any leaky expression of the EGSH promoter.
3. Results
NEED GRAPH! We observed a -- fold increase between induced and uninduced EGSH. There was some basal expression observed with no PonA added. The saturation occurred around 5 uM of PonA.
Experiment 2: Testing the Flipped Gene vs. Transcriptional Stop Signal
1. Purpose
The purpose of this experiment was to make sure that these plasmids did not express the gene of interest, in this case a yellow fluorescent protein. In our final circuit, the fluorescent protein will be replaced with the selected output gene, which will give the diagnosis. We do not want any leaky expression of this gene.
2. Set Up
One well was transfected with a plasmid containing a transcriptional stop signal in front of a fluorescent protein, expressed under a strong constitutive promoter, along with a transfection marker plasmid. Another well contained a plasmid with an upside down fluorescent protein flanked by recombinase recognition sites, expressed under a strong constitutive promoter, along with a transfection marker plasmid.
This transfection marker is a constitutively expressed fluorescent protein, which indicates how many copies of the plasmid a particular cell has. It allows us to analyze data by comparing transfection levels to amount of output.
3. Results
We observed no basal yellow fluorescence of the flipped eYFP gene, and high basal expression of the eYFP gene preceded by the transcriptional stop signal. Thus, we decided to continue our TP901 characterization using the flipped eYFP gene.
Experiment 3: Inducible TP901
1. Purpose
We set out to characterize TP901 under an inducible promoter to determine the basal expression levels in order to determine what further repression systems we would need.
2. Set Up
We cotransfected the EGSH: TP901 and hEF1a: attB-flipped EYFP-attP expression vectors along with EGSH: mKate (to indicate how much TP901 the cells were expressing), hEF1a: VgEcR (the transactivator for EGSH), and hEF1a: BFP (a transfection marker) into HEK293 cells. We induced the cells with six different concentrations of PonA: 0 uM, 0.1 uM, 0.5 uM, 1 uM, 2 uM, and 5 uM.
3. Results
NOT SURE WHY AXIS TITLES GOT SWTICHED BUT NEED TO FIX THIS As shown in the bar graph, we saw approximately a two-fold difference in yellow fluoresence between the uninduced cells and the cells induced with 2 uM or 5 uM (which seemed to be at saturation). We observed a significant amount of basal activity of TP901 even in the absence of PonA, however, so we concluded that an inducible promoter is too leaky to silence the activity of TP901. This issue was our motivation for exploring the L7Ae/k-turn motif as a way to lower the basal expression of TP901, and we hope that this system will allow us to inhibit recombination when the system is uninduced but not when it is activated.
