Team:BostonU/FusionProteins

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Fusion Proteins

Why Fusion Proteins?

As described here, our main goal this summer was to come up with an efficient workflow to design, build and test large genetic devices. To demonstrate the efficacy of our workflow, we started building a priority encoder. Below, we added the fusion proteins to mark where we will need them for the priority encoder. However, when we began we lacked a lot of the internal repressor genes that we wanted to use, so we decided to test well known proteins available in our lab (tetR, lacI, and araC) with a GFP fusion protein.

Priority encoder with fusion GFP shown linked to repressor proteins (CDS1-5)

In order to test the individual transcriptional units and the regulatory arcs associated with them, we needed the output for the individual parts of the device to be fluorescent. One way to do this is by using the bicistronic design shown below that mimics operons seen in natural bacterial systems.

Bicistronic design that could be used as an alternative to fusion proteins

A peculiar effect was observed in relation to this design. When ribosomes bind to the genes sequentially, the ribosome that binds at the 5' end of ene 1 can interrupt the attachment of a ribosome at the 5' end of gene 2block the next ribosome from binding to the mRNA and translating the gene. So, the later genes are expressed less than the genes before.

Figure 4 from Lim et al., 2011. Excerpt from Lim N H et al. (2011): "We found that CFP and YFP expression at the first position in the operons was higher than at the third position for each time point. The protein concentration at each time point was normalized by the final concentration to determine their relative expression (R). R is independent of protein production and depends only on the protein degradation rate and any delay in the induction (SI Materials and Methods). When R was calculated, it was the same for positions 1 and 3 at each time point (Fig. 4 D and E). Therefore, protein degradation and any delay after induction are the same at both positions, indicating the differences in expression must be due to greater protein production in the more proximal position of the operons."

This problem is solved with fused proteins as only one ribosome will then be required to translate the entire sequence, eliminating any possible problems during translation. [1]

Another way to measure function by fluorescence is by using consecutive transcriptional units -

This design drives up the cloning cost as it usually takes more time cloning multiple transcriptional units. Fusion Proteins are fused coding sequences that allow us to measure degradation rate directly. They reduce order effect seen with the bicystronic design and also, should theoretically be much easier to build as compared to cloning multiple TUs.

Assembly

Design strategy for building the fusion proteins. Two PCR products (top lines) with C and I or I and D fusion sites flanking the 5' and 3' ends are cloned into a destination vector to form a cohesive fusion protein containing the repressor protein fused with a green fluorescent protein.

To make fusion proteins, we used the Modular Cloning method that we have used for most digestion-ligation reactions.

First, we added a new MoClo fusion site (I - TCTA) to the genes (at the end of repressors and before the reporter proteins). The fusion site, I (TCTA) was then added to another 2-nucleotide sequence (GA) to make the XbaI site. This was done to allow the two proteins made by the two genes to split up after translation.

Then, we used Phusion Polymerase Chain reaction on the basic MoClo Level 0 parts using primers designed based on the fusion sites. We ended up with repressors with TCTAGA sequence at their ends and reporter proteins with the same sequence at the start. These can be treated as standard Level 0 parts which can then be assembled and tested using MoClo.

Testing

It is important that the fusion proteins made aren’t drastically inferior to the individual action of the repressor or the fusion proteins. In order to test this, the following Level 2 constructs were assembled using MoClo - Gel_8-31

J00-C12m_AE - R10-C40-E40m_EF - R40-E10m_FG

J00-C12m_AE - R10-C40-E30_EF - R40-E10m_FG

J00-C12m_AE - R10-C80-E40m_EF - I13-E10m_FG

J00-C12m_AE - R10-C80-E30_EF - I13-E10m_FG

Gel_8-31

Here onwards, all constructs made were to compare with those above. Simply put, all 6 Level 2s below were used a controls.

J00-C12m_AE - R10-C80_EF - I13-E10m_FG

J00-C12m_AE - R10-E30_EF - I13-E10m_FG

J00-C12m_AE - R10-E40m_EF - I13-E10m_FG

J00-C12m_AE - R10-C40_EF - R40-E10m_FG

J00-C12m_AE - R10-E30_EF - R40-E10m_FG

J00-C12m_AE - R10-E40m_EF - R40-E10m_FG

KEY

J00-C12m_AE = J23100_AB + BCD2_BC + C0012m_CD + B0015_DE
R10-C40-E40m_EF = R0010_EB + BCD2_BC + C0040_CI + E0040m_ID + B0015_DF
R10-C40-E30_EF = R0010_EB + BCD2_BC + C0040_CI + E0030_ID + B0015_DF
R10-C80-E40m_EF = R0010_EB + BCD2_BC + C0080_CI + E0040m_ID + B0015_DF
R10-C80-E30_EF = R0010_EB + BCD2_BC + C0080_CI + E0030_ID + B0015_DF
R10-C80_EF = R0010_EB + BCD2_BC + C0080_CD + B0015_DF
R10-E30_EF = R0010_EB + BCD2_BC + E0030_CD + B0015_DF
R10-E40m_EF = R0010_EB + BCD2_BC + E0040m_CD + B0015_DF
R10-C40_EF = R0010_EB + BCD2_BC + C0040_CD + B0015_DF
R40-E10_FG = R0040_FB + BCD2_BC + E1010m_CD + B0015_DG
I13-E10_FG = I13453_FB + BCD2_BC + E1010m_CD + B0015_DG

Detailed progress on the construction of fusion proteins can be found in the Fusion Proteins notebook.

References

[1] Lim N H et al. (2011) "Fundamental relationship between operon organization and gene expression" , PNAS Vol. 108 No. 26, doi: 10.1073/pnas.1105692108

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 <center><img src="https://static.igem.org/mediawiki/2014/9/9a/BU2014_Fig_4.jpg" width="40%"</center>
-<capt><br><br><center>Figure 4 from Lim et al., 2011.</center></capt></center>
+<capt><br><br><center>Figure 4 from Lim et al., 2011. Excerpt from Lim N H et al. (2011): "We found that CFP and YFP expression at the first position in the operons was higher than at the third position for each time point. The protein concentration at each time point was normalized by the final concentration to determine their relative expression (R). R is independent of protein production and depends only on the protein degradation rate and any delay in the induction (SI Materials and Methods). When R was calculated, it was the same for positions 1 and 3 at each time point (Fig. 4 D and E). Therefore, protein degradation and any delay after induction are the same at both positions, indicating the differences in expression must be due to greater protein production in the more proximal position of the operons."</center></capt></center>
-<br><br>
-Excerpt from Lim N H et al. (2011): "We found that CFP and YFP expression at the first position in the operons was higher than at the third position for each time point. The protein concentration at each time point was normalized by the final concentration to determine their relative expression (R). R is independent of protein production and depends only on the protein degradation rate and any delay in the induction (SI Materials and Methods). When R was calculated, it was the same for positions 1 and 3 at each time point (Fig. 4 D and E). Therefore, protein degradation and any delay after induction are the same at both positions, indicating the differences in expression must be due to greater protein production in the more proximal position of the operons."
 <br><br>This problem is solved with fused proteins as only one ribosome will then be required to translate the entire sequence, eliminating any possible problems during translation. [1]