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T7 promoter based iFFL

Genetic implementation of an incoherent feed forward loop (iFFL) in which a stabilized T7 promoter is controlling GFP expression.

Sequence and Features

The two transcriptional units in this composite part are oriented outwards.

Usage and Biology

A Incoherent feed-forward loop (iFFL) is a unique control systems motif where the output signal is robust to changes in the input signal. This is achieved by the introduction of a repressor.

iFFL can be applied to genetic circuits to achieve expression independent from copy number, transcriptional and translational rates. To implement the iFFL in a genetic circuit, TALE proteins can be used. These proteins consist of repeats where 12th and 13th amino acids can vary, these are called the repeat variable diresidue (RVD). RVDs have been shown to bind to DNA in a simple one-to-one binding code (Segall-Shapiro et al., 2018). The direct correspondence between amino acids allows scientists to engineer these repeat regions to target any sequence they want. In our system, we used the TALE protein as a repressor by engineering promoters to contain the binding site of this specific TALE protein (0.1 T7sp1 promoter, 0.5 T7sp1 promoter and P_BHRsp1 promoter).
In our genetic circuit, a unrepressed promoter controls the expression of TALE protein while the promoters with the TALE binding sites drive expression of GFP.

When transcriptional units are placed in series, due to low effieciency of terminators, leaky expression of the gene in the neighbouring transcriptonal unit can occur. This has been predicted by our model to significantly influences the behavior of the iFFL genetic circuit. Hence, the transcriptional units in the circuit are oriented outward to achieve insulation from influence of the neighboring transcriptional unit.

An interesting application of the iFFL is to achieve controllable gene expression across different bacterial species. Gene expression in different bacterial contexts is influenced by changes in copy number, transcriptional and translational rates. Gene expression independent of transcrioptional rates has been demonstrated below. Stable gene expression can be attained if the ratios of transcriptional rates of GFP and repressor are constant. Transcriptional rates can be tuned using orthogonal T7 promoter and its variants (T7 promoter, 0.5 T7 promoter,0.1 T7 promoter, 0.5 T7sp1 promoter and T7sp1 promoter ).

Strain Construction

The construct was assembled by golden gate assembly based modular cloning system. First, the individual transcriptional units were cloned into level 1 destination vectors pICH47761 and pICH47822 by BpiI based golden gate assembly. The multi-transcriptional unit construct was assembled by a BsaI based golden gate. The assembly was a one-pot restriction-ligation reaction where the individual level 1 constructs were added along with the destination vector pICH48055. The correct clone was distinguished by blue-white screening and the construct was confirmed by sequencing. The cloning protocol can be found in the MoClo section below.

Modular Cloning

Modular Cloning (MoClo) is a system which allows for efficient one pot assembly of multiple DNA fragments. The MoClo system consists of Type IIS restriction enzymes that cleave DNA 4 to 8 base pairs away from the recognition sites. Cleavage outside of the recognition site allows for customization of the overhangs generated. The MoClo system is hierarchical. First, basic parts (promoters, UTRs, CDS and terminators) are assembled in level 0 plasmids in the kit. In a single reaction, the individual parts can be assembled into vectors containing transcriptional units (level 1). Furthermore, MoClo allows for directional assembly of multiple transcriptional units. Successful assembly of constructs using MoClo can be confirmed by visual readouts (blue/white or red/white screening). For the protocol, you can find it here.

Note: The basic parts sequences of the Sci-Phi 29 collection in the registry contain only the part sequence and therefore contain no overhangs or restriction sites. For synthesizing MoClo compatible parts, refer to table 2. The complete sequence of our parts including backbone can be found here.

Table 1: Overview of different level in MoClo

For synthesizing basic parts, the part of interest should be flanked by a BpiI site and its specific type overhang. These parts can then be cloned into the respective level 0 MoClo parts. For level 1, where individual transcriptional units are cloned, the overhangs come from the backbone you choose. The restriction sites for level 1 are BsaI. However, any type IIS restriction enzyme could be used.

Table 2: Type specific overhangs and backbones for MoClo. Green indicates the restriction enzyme recognition site. Blue indicates the specific overhangs for the basic parts

Characterization

According to our model, the genetic implementation of the iFFL loop yields the same gene of interest (GOI) expression levels when the transcription rate of both genes (TALE and GOI) is changed in the same ratio as can be seen in figure 3.

Different transcriptional rates can be achieved by using T7 promoter and its variants (Komura et al., 2018). To demonstrate stable gene expression (GFP), iFFL loops were constructed using two T7 promoter variants and the corresponding promoters with TALEsp1 binding sites. Two circuits were constructed, one where TALE and GFP are expressed with wild-type T7 and T7sp1 promoters (T7 promoter based iFFL) respectively and the other where the two genes are expressed by medium T7 and medium T7sp1 promoters respectively (medium T7 promoter based iFFL).

During initial verification of the iFFL loop, uncontrolled iFFL (i.e GFP was expressed with a promoter not containing the TALEsp1 binding site) was used as control. Unexpectedly, low fluorescence was observed for this control. From flow cytometry results (figure 4) it was seen that the cells containing the uncontrolled iFFL system were smaller in size and had different cell morphology (region R1) compared to E.coli cells without any plasmid (region R0). This suggests that over expression of TALE and GFP could be burdensome to the cells and thus resulting in low fluorescence output. Hence, for further data analysis, GFP expressed from T7_sp1 were used as a control and E.coli BL21 DE (3) were used to correct for background fluorescence.

The scatter plot in figure 5 was used to gate the most dense cell regions of the blank and the same gating was considered to obtain the fluorescence values depicted in figure 6. Cells of similar forward and side scatter were compared.

Gating was performed on the data in the fluorescence histogram (figure 6) to discern between fluorescent and non-fluorescent cells.

The median fluorescence for each sample from figure 6 was plotted for comparison in figure 7.

Figure 7 shows successful implementation of the iFFL system to insulate from transcriptional variations. Despite, changes in transcriptional rates, stable GFP expression is observed.

Therefore, the application of the iFFL system can be extended for stable gene expression across different bacterial species as promoter strengths are dependent on bacterial context. The use of this iFFL system can circumvents the need to characterize promoters per bacterial species.

Figure 6 shows that our T7 based TALE system results in the same expression when both promoters are changed to their medium version. We expected the unrepressed T7 system to have higher expression similarly to the GFP under control of T7 without TALE expressed. However, as shown in figure 6 this is not the case. Although, when comparing the scatter plots of both E. coli TOP10 and the unrepressed T7 system we can see there is a clear difference in forward scatter (FSC) and side scatter (FSC) (figure 9), we believe the overexpression of both proteins significantly affects cell morphology and thus can't be properly compared to the other samples.

References

• Lou, C., Stanton, B., Chen, Y.-J., Munsky, B., & Voigt, C. A. (2012). Ribozyme-based insulator parts buffer synthetic circuits from genetic context. Nature Biotechnology, 30(11), 1137–1142.