Part:BBa_K2201331

NM-domain of Sup35 with an amber codon at position 21 under T7-promoter control

The NM domain of yeast prion Sup35 is responsible for is prion forming ability. This part is the part BBa_K2201231 und control of a T7-promoter.

Usage and Biology

Sup35 is a yeast translation termination factor from Saccharomyces cerevisiae. The prion form of Sup35 is known to form amyloids consisting of beta-sheet rich protein aggregates with beta-strands perpendicular to the long axis of the filament. The domain responsible for the conformational change is the NM region. This region of the protein contains two different sections. The N section (amino acids 1-124) forms the major part of the amyloid core that that directs the protein into the prion form. The M-section (amino acids 124-250) is highly charged and provides the solubility to the native form of Sup35. In the prion form the M region changes its conformation to a beta sheet rich conformation, while the N section stays nearly unchanged in its conformation (Mukhopadhyay et al. 2007,Wickner et al. 2015).

With this protein domain we want to develop a test protein for a prion detection assay. We use the NM-domain as a model prion and incorporate to non canonical amino acids (p-acetophenylalanine at position 121 and propargyllysine at position 21). After the purification of the recombinant produced Sup35 could be labeled with two different fluorophores (Cyanin 3 and Cyanin 5). The emission spectra of the fluorophores depend on their distance between each other. When this test protein gets in contact with prions, the prions conformational changes result in the change of the fluorophores spectra. Therefore, the test prion could be used to detect prions in medical samples. We designed three other variants of the protein. BBa_ K2201233 is the histidine₆ tagged version of this part and K2201231 contains a cysteine codon at position 21 and 121, as a positive control. K2201232 contains only one amber codon and a cysteine codon at position 121 for the incorporation of only one noncanonical amino acid.

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]

Functional Parameters

For our test protein, we decided to order a gene synthesis of the NM-region of sup35. The NM region is 250 amino acids long and responsible for the prion forming function of Sup35. The test protein contains an amber codon at position 21 and one cysteine codon at position 121.
According to our expert Iker Valle Aramburu, the incorporation of two noncanonical amino acids lowers the yield. He recommended us to use only one non-canonical amino acid and one cysteine, which could be labeled in a maleimide coupling reaction. Mukhopadayay 2006 showed that mutants of Sup35 containing no cysteines are still able to form prions. So, we decided to order a gene synthesis of sup35 containing no cysteines.
For our experiments we cloned the gene synthesis of the NM region of Sup35 into pSB1C3 and used site directed mutagenizes to construct the part BBa_K2201231 containing a histag, one amber codon at position 21 and a cysteine codon at position 121. The control BBa_K2201232 contains cysteine codons at positions 21 and 121. In addition, we constructed these three parts also with a T7-promotor and RBS (BBa_K2201331 and BBa_K2201332), for the inducible expression of the Sup35 variants.
The expression plasmid of Sup35 containing one amber stop codon at position 21 (BBa_K2201331) was cotransformed with the evolved PylRS synthetase for the incorporation of PrK (BBa_K2201201). The cells containing both plasmids were cultivated like described in expression of recombinant proteins, without PrK in the media and with 1 mM PrK in the media. Sup35 was purified through NiNTA chromatography. As positive control Sup35 without stop codons was expressed and purified the same way. All three samples were analyzed on the SDS-PAGE shown in figure 1.

Figure 1: SDS-PAGE of the eluates of the three cultivations. The positive control (PC: BBa_K220302) left and BBa_K2201301 without PrK (-PrK) in the media in the middle and with 1 mM PrK (+PrK) in the media on the right side.</p>

The SDS-PAGE confirmed the results from our screening system. The positive control showed a high expression of the recombinant Sup35 and both samples with BBa_K2201301 showed a band on the same height as the positive control. This proved that the PrK-aaRS incorporates endogenous amino acids if PrK is not supplemented in the media. But if PrK is present the expression of Sup35 is stronger. The affinity of PrK-aaRS to PrK seems to be stronger than to the endogenous amino acids, so the test protein is expressed with the non-canonical amino acid as planned.

Labeling of the sup35 test protein The labeling of the test protein was performed in a two-step reaction. The first step was the click chemistry reaction to label the PrK with Cyanin3-azide and the second the maleimide labeling of the cysteine with Cy5 maleimide. The click chemistry reaction of 50 nMol test protein in 100 µL reaction volume was performed in 1x PBS buffer containing 200 µM copper sulfate and 200µM TCEP to prevent Sup35 to aggregate. To start the reaction 100 nMol of Cy3-azide and 200 µM freshly prepared sodium ascorbate were added and after that, the reaction was incubated 2 h at room temperature. After the incubation the Cy3-labeled test protein was washed with maleimide labeling buffer (2x PBS and 8 M guanidine hydrochlorid) and concentrated down to 50 µL by centrifugal filters. To start the maleimide labeling reaction, 100 nMol of Cy5-aleimide were added to the test protein and incubated for 2 h at room temperature. After this step the excess dye should be washed away by centrifugal filters or dialyses and the labeling was confirmed by a fluorescence scan of a SDS-PAGE containing the labeled sample and a negative control. The SDS-PAGE of our test protein before and after the labeling reaction is shown in figure 2. Furthermore, we wanted to detect the labeling efficiency through UV-VIS spectralphotometer, but the results indicate that a high excess of free Cy5 remains in the sample and the background was too high to perform FRET-measurements. To investigate the labeling efficiency and to get a fluorescence signal the labeling reaction and especially the last washing step needs to be improved to generate suitable test protein for the prion detection assay.

Figure 2:SDS-PAGE and fluorescence scan of the SDS-PAGE of the unlabeled and labeled Sup35.</p>

The fluorescence scan proves the successful labeling of Sup35 with Cy3 and Cy5. But in the SDS page a second higher band that seemed to be labeled two. One explanation would be that Sup35 forms aggregates in the labeling reaction. If the test protein is changed to its prionic form it would not be suitable for a prion detection assay. To investigate if Sup35 forms aggregates after the labeling reaction we wanted to check if there are any aggregates through atomic force microscopy (AFM). If there are any prion forming ability, the proteins should form big aggregates like reported by iGEM Kent 2015, who wanted to form nanowires out of Sup35. The AFM images were generated in the Experimental Biophysics & Applied Nanosciences research group from Bielefeld university, Department of Physics with an MultiMode® AFM (Bruker) in tapping mode. The images from the unlabeled and labeled Sup35 are shown in figure 3.

Figure 3:Atomic force microscopy (AFM) images of the unlabeled Sup35 (left) and the labeled Sup35 (right). The AFM images were generated in the Experimental Biophysics & Applied Nanosciences research group from Bielefeld university, Department of Physics with an MultiMode® AFM (Bruker) in tapping mode.</p>

The AFM pictures of Sup35 (figure 3) show no form of aggregated or denaturized proteins, thus our labeling tool is suitable for the specific labeling of protein without changing their conformation. For the further development of the assay, the labeling and washing method need to be improved regarding the remaining free dye in the samples after the labeling reactions to get a FRET signal.