Part:BBa_K1583003

CsgA_His

This basic part is contains the csgA gene with a His-tag attached to the C-terminus. It is used in the biobrick BBa_K1583101 and BBa_K1583107, both in combination with the rhamnose inducible promoter (BBa_K914003).

CsgA is a protein monomer which can aggregate to form amyloid nanowires in natural biofilms of E.coli. This protein is transported as an unfolded protein out of the cell. Outside the cell CsgA proteins self-assemble into nanowires after nucleation on the membrane protein CsgB. CsgC prevents CsgA proteins from self-assembling inside the cell and the transport is ensured by the proteins CsgEFG.

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  COMPATIBLE WITH RFC[21]
• 23
  COMPATIBLE WITH RFC[23]
• 25
  COMPATIBLE WITH RFC[25]
• 1000
  COMPATIBLE WITH RFC[1000]

Characterization

This basic part is used in the biobrick BBa_K1583102 and BBa_K1583107. Four different experiments were done to characterise these biobricks:

• Fluorescence assay
• Crystal Violet assay
• Western blot
• Transmission electron microscopy

Fluorescence assay

To be able to ensure that CsgA is expressed, we added a gene encoding for GFPmut3 (BBa_I13504) under induction of the same rhamnose promoter (BBa_K1583112) to check that the promoter works. In this experiment, the fluorescence signal of our csgA construct and csgA-GFP (I13504) constructs was recorded in time after induction with no, 0.2% (w/v) or 0.5% (w/v) rhamnose. Besides the fluorescence, the OD600 was measured in order to normalize the fluorescence signal per cell. All conditions were carried out in triplicates to be able to do a statistical analysis on the data. The different experiments were induced in a 96 well plate. The OD600 and fluorescence signal was recorded in a plate reader during a 18 hour period of induction at 30°C.

In Fig. 1, the fluorescent signal was normalized by the number of cells and plotted as a function of time. The red bars denote the error within each ID.

Fig. 1: Fluorescence signal normalized by the number of cells for 0% (w/v), 0.2% (w/v) and 0.5% (w/v) rhamnose with the csgA and csgA-GFPmut3 construct. The error bars are included for all experiments.

As can be seen from Fig. 1, only the experiments with 0.2% (w/v) and 0.5% (w/v) rhamnose induction with the csgA-GFPmut3 construct gave a clear increase in fluorescence signal in time. All other experiments, gave similar levels of fluorescence, slightly increasing in time. Furthermore, it can be seen that a higher induction level of rhamnose leads to an increase in GFPmut3 and thus fluorescence. Finally, as the fluorescence signal is normalized by the cell density, one can make statements about the activity of the rhamnose promoter. The promoter seems to not be active right after induction, but more after 3 or 4 hours. This is in accordance with data from literature (Wegerer et. al), in which a low amount of fluorescence with a rhamnose promoter was observed after 2 hours of induction.

With this kinetic experiment, we have proven that the rhamnose promoter does indeed induce the expression of the csgA gene.

Crystal violet assay

The assay above showed that the bacteria that we engineered for the project is capable of producing the CsgA proteins after induction with L-rhamnose. However, this did not yet prove that curli are formed. In order to assess whether our bacteria producting CsgA with a His tag can still produce these nanowires, our team adapted the protocol from Zhou et al. (2013) that employs crystal violet (methyl violet 10B) for dying the biofilm-making bacteria that attaches to the surface. In the experiment, our CsgA_His-producing strain of E. coli was induced at a high (0.5% w/v), low (0.2% w/v) and no (0% w/v) concentration of L-rhamnose. Furthermore, csgA deficient bacteria transformed with an empty plasmid (pSB1C3) were used as control. In the end, the wells were diluted with ethanol so all the content can dissolve in the liquid phase. We measured the absorbance at 590 nm of wavelength for all the samples, obtaining the following results (figure 2.).

Fig. 2: Microtiter Plate Assay results for testing biofilm formation. All the measurements were conducted in triplicates. CTRL0, CTRL2 and CTRL5 are E. coli K-12 MG1655 PRO ΔcsgA ompR234 cells with pSB1C3, used as a control. HIST0, HIST2 and HIST5 are E. coli K-12 MG1655 PRO ΔcsgA ompR234 cells expressing a plasmid that contains csgA attached to a 6xHis tag under a rhamnose inducible promoter. The termination "0", "2" and "5" denotes the induction with no rhamnose (0), 0.2% w/v (2) and 0.5% w/v.

The CsgA_His proteins seem to have retained the capability to form curli despite having a peptidic modification on the C-terminus. To confirm that there is a real change between the analysed samples and the empty plasmid control, a significance analysis was performed for α=0.05 (Table 1.).

Table 1: Significance analysis of the samples analysed, with a significance α value of 5%. All the samples display a significant difference when compared to the empty plasmid homologe sample (CTRL).

Sample	p-value	Significant difference (5%)
CTRL2 & HIST2	0.0242	Yes
CTRL5 & HIST5	0.0026	Yes

The significance analysis shows that cells containing the CsgA_His (BBa_K1583101) biobrick can efficiently create a curli, when compared with an empty plasmid control (i.e. without csgA expression).

Western blot

For our modeling, we needed to determine the internal concentration of csgA. Based on the fluorescent assay with GFPmut3, we obtained an internal amount of CsgA in the order of 104 molecules/cell. To validate whether this value was plausible we decided to use Western Bloting. The following strains were used (Table 2.) (ΔcsgA is a csgA deficient strain called E. coli K-12 MG1655 PRO ΔcsgA ompR234).

Table 2: Samples used for the first Western Blot experiment.

Sample #	Description	Time of induction (hours)
1	ΔcsgA - csgA	5
2	ΔcsgA - csgA + Rhamnose	5
3	ΔcsgA - csgA_His	5
4	ΔcsgA - csgA_his + Rhamnose	5
5	ΔcsgA - csgA	Overnight
6	ΔcsgA - csgA + Rhamnose	Overnight
7	ΔcsgA - csgA_his	Overnight
8	ΔcsgA - csgA_his + Rhamnose	Overnight

The procedure of this experiment is described here at Protocols > "Isolation using Ni-column purification assay (QIAGEN kit) for intracellular protein tagged with 6xHis³".

The SDS gel is shown in figure 3. The gel is too condensed to visualize a difference between the non-induced and induced samples, because the gel was overloaded.

Figure 3. Left: SDS page gel, experiment 1 samples as described in Table 2. Rigth: Membrane after blotting, of the samples of experiment 1

We noticed in figure 3 a band in lane 4 and 8, with a size of circa. 17 kDa. The lanes correspond to the rhamnose induced strain E. coli K-12 MG1655 PRO ΔcsgA ompR234 (ΔcsgA) with biobrick BBa_K1583102 (CsgA_His), after 5 hours and 24 hours of induction. The antibodies bind specifically to the his-tag of proteins, which did not bind to the ΔcsgA_csgA samples, lane 1, 2,5 and 6. Therefore it can be concluded that the strain ΔcsgA_csgA_his produced his-tagged CsgA proteins. The effect of rhamnose was visible when compared to the samples with ΔcsgA_csgA_his without rhamnose induction, lane 3 and 7. There are no bands visible, therefore rhamnose induces the production of CsgA_His. We can conclude with experiment 1 that the antibodies bind specifically to CsgA_His proteins. The CsgA_His proteins are only present when induced with 0.5% rhamnose.

We executed a second experiment to quantification the amount of CsgA_His present in the ΔcsgA_csgA strain. We compared this amount by using known concentration of CsgA from a strain called T-SSRA madrid. T-SSRA madrid strain has a set amount of CsgA_His proteins present in the cell.

Table 3: Samples used for the second Western Blot experiment.

Sample #	Description	Time of induction (hours)
1	ΔcsgA - csgA_his + Rhamnose	5
2	ΔcsgA - csgA_his + Rhamnose	Overnight
3	T-SSRA madrid 20µM	/
4	T-SSRA madrid 8µM	/
5	T-SSRA madrid 4µM	/
6	T-SSRA madrid 2µM	/
7	T-SSRA madrid 0.4µM	/
8	T-SSRA madrid 0.2µM	/

The same protocol as in the first western blot experiment (above) was used.

Figure 4. Membrane after western blotting; samples of experiment 2.

As seen in figure 3, the bands of the calibration curve were visible. The bands of the ΔcsgA_csgA_His were not visible. We still wanted to know the correlation between the thickness of the band, and the concentration of internal CsgA_His. We solved this by comparing the band in lane 8 from figure 4 with the bands seen in figure 3, to acquire an approximation of the total concentration. The bands in lane 4, and 5 (right to left) were too saturated to measure with the Typhoon. The band in figure 3 was thinner than the two highest concentrations, therefore we removed the last two points from the calibration line. The trend line of the concentration (in µM) versus intensity has an formula of Intensity = 509067 · concentration + 792496

Figure 5. Calibration curve of CsgA concentration (µM) versus intensity.

We calculated from figure 5 that the average intensity of our samples was 2.3106 Au. We calculated, using the calibration line, that the concentration of the internal CsgA_His proteins was equal to 2.8μM. The amount of sample we loaded on the gel was 10 µl, therefore the amount of CsgA_His protein in the lane 2.75·10^-5µmol.

Because in the beginning we had an OD600 of 10, it means that we had a concentration of 10·8·108 cells/ml. Therefore, the CsgA_His came out of this amount of 8·10⁷ cells in 10µl. By dividing the amount of CsgA_His protein by the amount of cells, we obtained an internal CsgA_His protein amount of2.82·10^-7 µmol/cell, or 2.82·10^-13 mol/cell. With the constant of Avogadro 6·10²³ molecules/mol, we calculated an end internal CsgA_His protein amount is equal to 2.06·10⁵ molecules/cell.

Transmission electron microscopy

Using TEM the formation of curli of the biobrick BBa_K1583100 was visualized (Figure 6). Although this is a different biobrick (no addition His-tag), curli formation can be presumed to be similar for this biobrick.

Fig. 6: TEM images (magnification 7300 x) of cells containing BBa_K1583100. The left picture shows uninduced cells (0% Rhamnose).The picture on the right shows cells incubated with 1% (w/v) rhamnose.

We did not observe formation of curli nanowires in the uninduced cultures of our strain. However, cells from induced cells clearly produced them, as supported by the TEM images.

>Contribution:

Quantum dots binding test

In order to test the effect of binding between CsgA-Histag mutant and inorganic nanoparticles, we apply same amount of suspended QDs solution into M63 medium which has cultured biofilm for 72h. After 30-min incubation, we used PBS to mildly wash the well, and the result was consistent with our anticipation: On the left, CsgA-Histag mutant were induced and thus secreted biofilm, and firmly attached with QDS and thus show bright fluorescence. Therefore, we ensure the stable coordinate bonds between CsgA-Histag mutant and QDs can manage to prevent QDs from being taken away by liquid flow. The picture was snapped by ChemiDoc MP,BioRad, false colored.

Fig. 7：Binding test between CsgA-his and Quantum dots. The image was snaped by ChemiDoc MP,BioRad, false colored.

Comparison test of Quantum dots Binding between CsgA-his and CsgA

In order to prove the effect of binding between CsgA-Histag mutant and inorganic nanoparticles is distinct, we apply same amount of suspended CdSeS/ZnS QDs solution into M63 medium which has cultured biofilm for 72h. After 1h incubation, we used PBS washing 2 times. The picture verify our postulation: On the left, CsgA-Histag mutant were induced and its biofilm bind with QDS. CsgA biofilm cannot bind with QDs thus its red fluorescence is much weaker.

Fig. 8：Comparison test of Quantum dots Binding between CsgA-his and CsgA.

CdS nanorods Templating

As for biofilm characterization, transmission electron microscopy is frequently to be used to visualize the nanofiber network. However, we found it really difficult to find out whether biofilm is well self-assemble extracellularly due to its thin and inconspicuous attributes against the background. Amazingly, after incubation with CdS nanorods , the biofilm areas are densely templated by CdS nanorods and we can easily confirm the expression of biofilm.

Fig. 9：Representative TEM images of biotemplated CdS nanorods on CsgA-His. After applied inducer, CsgA-His mutant constructed and expressed to form biofilm composed by CsgA-His subunits. Incubation with nanorods for 1h, nanomaterials are densely attached to biofilm.

Reference

Wegerer, A., Sun, T. and Altenbuchner and J., 2008. "Optimization of an E. coli L-rhamnose-inducible expression vector: test of various genetic module combinations”, BMC Biotechnology, 8:2

Zhou, Kang, Kangjian Qiao, Steven Edgar, and Gregory Stephanopoulos. 2015. “Distributing a Metabolic Pathway among a Microbial Consortium Enhances Production of Natural Products.” Nature Biotechnology 33(4): 377–83.