Coding

Part:BBa_K4447004

Designed by: Rafael Garcia Gomez   Group: iGEM22_TecMonterrey_GDL   (2022-09-29)


FRET-based system for the detection of erythromycin

FRET-based sensor system for the detection of erythromycin that consists of erythromycin C-12 hydroxylase (BBa_K4447001),an enzyme that catalyzes the oxidation of erythromycin, flanked by two fluorescent proteins: ECFP (BBa_K1159302)as an energy donor and Venus (BBa_K1907000)as an energy acceptor.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal XhoI site found at 1913
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 2562


Usage and Biology

With the rise of synthetic biology, biosensors have gained popularity over the years. Among all of the biosensors available, Förster resonance energy transfer (FRET) biosensors are a powerful approach for dynamically tracking the presence of a particular substrate.

In this composite part, we propose an enzymatic system based on how the Förster resonance energy transfer (FRET) operates: one enzyme capable of recognizing and degrading erythromycin will be flanked by two fluorescent proteins. This part incorporates NcoI and XhoI restriction sites in 5' and 3' ends for protein overexpression in pBAD/Myc-His plasmids, a gly-gly-ser spacer, and a polyhistidine tag before stop codon at the end of Venus for protein purification. Any linker does not separate each protein; for instance, stop codons for ECFP and erythromycin C-12 hydroxylase were removed. Figure 1 displays the three-dimensional structure of this protein system.

Figure 1. Three-dimensional structure of the EryK-FRET system.


TecMonterreyGDL 2023further characterized the FRET-based system in silico and expressed in a biological platform (E. coli BL21). See more details in Results.

Selecting Fluorescent Proteins

Fluorescent proteins are most commonly used as donor and acceptor fluorophores in FRET biosensors, especially since these proteins are genetically encodable and live-cell compatible. For this section, we relied on the articles from Bajar et al. (2016) and Agrawal et al. (2021), where different fluorescent proteins are compared according to the requirements of a particular system. The particularity of fluorescent proteins depends on three main advantages: fluorescent proteins-based biosensors are easily constructed via genetic engineering, they confer high cellular specificity by using specific promoters, and these systems are stable in cells for a long time due to high intracellular stability.

From the pairs suggested by Bajar et al. (2016), enhanced cyan fluorescent protein (ECFP) and mVENUS (YFP) are widely recommended because of a higher quantum yield and better folding at 37 °C. This fact is also confirmed by Agrawal et al. (2021), who successfully developed a functional FRET-based sensor to monitor silver ions using this pair of fluorescent proteins. Agrawal et al. (2021) mention that the emission spectrum was recorded after excitation of the sensor protein at 420 nm, and recording the emission in the range of 450 to 600 nm, reaching a peak in 530 nm.

Sequences from both fluorescent proteins were obtained from the BioBricks catalog provided by iGEM. Finally, we selected these fluorescent proteins: 

•BBa_K1159302: Enhanced Cyan Fluorescent Protein (ECFP). This Biobrick is an improved version of BBa_E0022, 
allowing protein fusion that was not initially possible by assembly criteria.

•BBa_K1907000: Venus. This part is a variant of yellow fluorescent protein, making it more stable and 
improving efficiency maturation.


Characterization

Restriction Enzyme Digestion and Ligation

We performed a restriction enzyme digestion with the synthesized part and the vector defined. Our digestion involved using NcoI and EcoRI restriction enzymes. For both vector and insert, DNA concentration was stated as 4000 nanograms. Table 1 displays the protocol followed for a 50 µL reaction.

Table 1. Restriction digest conditions.
Reactive Quantity
Nuclease-free water To 50 µL
rCutSmart Buffer 5 µL
Template DNA (up to 4000 ng) X µL
NcoI restriction enzyme 1 µL
XhoI restriction enzyme 1 µL
Figure 3. Escherichia coli TOP10 colonies transformed with BBa_K4447004 cloned in pBAD/Myc-HisB. Bacteria were grown in LB medium with carbenicillin.

With the DNA fragments purified from an agarose gel, we performed ligation at a molar ratio of 1:5 for vector and insert, as shown in Figure 3. The total vector concentration was 100 nanograms, whereas the reaction volume was 20 µL. Next, Table 2 displays the protocol followed for the reaction.

Table 2. DNA ligation conditions.
Reactive Quantity
T4 DNA Ligase Buffer (10X) 2 µL
Vector DNA 100 ng
Insert DNA 773.5 ng
Nuclease-free water To 20 µL
T4 DNA Ligase 1.5 µL

Further characterization through protein dynamics simulation (in silico analysis): TecMonterreyGDL_2023

A predicted structure was obtained using ColabFold (Mirdita et al., 2022) (Figure 4). To gain more confidence in the prediction, molecular dynamics (MD) simulations of the obtained model were performed. This helped assess if the predicted structure was maintained after the system was exposed to biophysical potentials.


Figure 4. Predicted structure with the best PAE obtained from ColabFold showing ECFP (blue), EryK (gray), and mVENUS (yellow).

A preliminary simulation was run with GROMACS to assess whether the structure diverges from the predicted configuration of constituent proteins over the 10 ns simulation when biophysical potentials were included. The system was solvated in water, the charges were neutralized with Na+ ions, and the system was energy minimized to avoid problems from disagreement between ColabFold’s predicted structure and the energy minimum of our system according to the AMBER99SB-ILDN forcefield (Lindorff-Larsen et al., 2010).

The most dynamic regions of our system (Figure 5) correspond to the regions that display the greatest conformational change when comparing X-ray structures of the open (PDB ID:3ZKP) and closed (PDB ID: 2JJN) conformations of EryK.

Figure 5. Trajectory (100 ps frame-1) of ECFP–EryK–mVENUS compared to predicted ColabFold (gray) structure.

Cloning of ECFP–EryK–mVENUS into pET28b(+) plasmid: TecMonterreyGDL_2023

The gene sequence for the protein construct was transformed into the pET28b(+) vector. This was done using T4 DNA Ligase (New England Biolabs). Table 3 shows the components used for the ligation reaction. To achieve a 1:5 molar ratio, 11 μL of insert and 6 μL of vector were used.

Table 3. 20 μL ligation of ECFP–EryK–mVENUS insert and pET28b(+) vector
Reagent Quantity
Insert 595 ng
T4 DNA ligase buffer 2 µL
Vector 100 ng
T4 DNA ligase 1 µL


The ligation was then transformed into E. coli BL21 by adding 5 μL of the ligation reaction to 50 μL of competent cells. After incubation, colonies were observed indicating successful transformation (Figure 6A) however a second plate (Figure 6B) was made due to lack of isolated colonies.

Figure 6. Evidence of colony growth after transformation into E. coli BL21 on the A) original plate and B) replating due to poor colony distribution and lack of isolated colonies .

Expression of ECFP_EryK_mVENUS in E. coli BL21: TecMonterreyGDL_2023

Overexpression trials were performed by induction with 0.4 mM isopropyl β-d-1-thiogalactopyranoside (IPTG) to stimulate protein overexpression (Studier, F. W., 2014). After running an SDS-PAGE gel to confirm overexpression, very little protein was obtained (Figure 7). Further purification was unsuccessful and did not yield any protein.


Figure 7. SDS-PAGE gel (8 %) ran to confirm purification of induced colonies for overexpression of ECFP–EryK–mVENUS.

Dosis-response assessment to characterize the effect of erythromycin on ECFP–EryK–mVENUS in vivo: TecMonterreyGDL_2023

To test the efficiency of the FRET system, plates with different non-lethal concentrations of erythromycin were made (Figure 8). It is important to note that the final iteration of the biosensor will use only the purified protein to avoid unwanted mutations and unnecessary environmental risk. While no visible difference was observed in fluorescence levels between the plates, it was not proven whether fluorescence was directly related to erythromycin or if it was basal. This can be done by creating a negative control plate and visually comparing fluorescence.

Figure 8. Transformed BL21 colonies on erythromycin plates at A) 0 μg mL-1, B) 0.02 μg mL-1, C) 2.5 μg mL-1, and D) 10 μg mL-1.

References

[1]. Agrawal, N., Soleja, N., Bano, R., Nazir, R., Siddiqi, T. O., & Mohsin, M. (2021). FRET-Based Genetically Encoded Sensor to Monitor Silver Ions. ACS omega, 6(22), 14164–14173. https://doi.org/10.1021/acsomega.1c00741

[2]. Bajar, B., Lam, A., Badiee, R. et al. (2016). Fluorescent indicators for simultaneous reporting of all four cell cycle phases. Nat Methods 13, 993–996. https://doi.org/10.1038/nmeth.4045

[3]. Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2022). ColabFold: making protein folding accessible to all. Nature methods, 19(6), 679–682. https://doi.org/10.1038/s41592-022-01488-1

[4]. Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O., & Shaw, D. E. (2010). Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins, 78(8), 1950–1958. https://doi.org/10.1002/prot.22711

[5]. Studier F. W. (2014). Stable expression clones and auto-induction for protein production in E. coli. Methods in molecular biology (Clifton, N.J.), 1091, 17–32. https://doi.org/10.1007/978-1-62703-691-7_2
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