Part:BBa_K1381017

CFY-X6 his

Usage and Biology

CFY, colicin Fy, is a bacteriocin from the colicin family produced by Y. frederiksenii and targets other Yersinia species. Bacteriocins will either attack the cell membrane or a mechanism inside the cell, such as gene expression or protein production.[1] One of colicins Fy main targets is Y. enterocolitica. It kills Y. enterocolitica by creating pores in its cell membrane. Y. enterocolitica is also one among the common pathogens that infects the gut and causes symptoms[2].

Characterization

To be able to characterize colicin Fy we had to couple it to a promoter and an RBS, which we did by creating the construct BBa_K1381023.

SDS page To be able to see that colicin Fy was really produced we needed to run an SDS-Page. Before running the SDS-page we needed to extract colicin Fy from the inside of the cells by sonication and then purify the tests so that we only have our protein colicin Fy. Since the bacteriocin was designed with a histidine tag we could use an IMAC to to do this. After we had done this we could run the SDS-page gel.

[http://2014.igem.org/Team:Uppsala/Project_Killing#ref_point2 link to more results]

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Figure 1: The gel contains the following from the left to the right
Protein ladder
Eluent 1 for lysate produced by colicin Fy producing bacteria
Eluent 3 for lysate produced by colicin Fy producing bacteria
Eluent 2 for lysate produced by colicin Fy producing bacteria
Final eluent test tube 4 for lysate produced by colicin Fy producing bacteria
Final eluent test tube 6 for lysate produced by colicin Fy producing bacteria
Eluent 2 for lysate produced by the negative control
Eluent 3 for lysate produced by the negative control
Final eluent test tube 4 for lysate produced by the negative control
Final eluent test tube 6 for lysate produced by the negative control

The results from the characterization experiments can be seen in figure 1. According to calculations based on the nucleotide sequence, the mass of colicin Fy is about 49,6 kDa. The protein ladder we used is Thermo Scientifics PageRuler Unstained Protein Ladder #26614. The thickest band is 50 kDa so our bands should be at about the same height.

Several IMAC and SDS-pages were run, in all cases eluent 1 was found to be empty. This is not surprising because the eluent volume is so small that the proteins will not come out until eluent 2. Because of this we decided to skip eluent 1 for the negative control in the presented SDS in figure 4. Eluent 2 consists of several proteins, every protein that does not bind to the IMAC should come out in this step. Eluent 3 seems to be when our colicin Fy is eluted, since it shows a band at the correct length, 50kDa. The negative control did not show any band in 50kDa and expression could therefore be confirmed. Since the colicin was eluted at elution 3 no band can be seen at elution 4.

When the SDS-page had been run we knew that we could produce colicin Fy. The next stage is then to see if it actully works. To be able to prove that our system is working we needed to test it on the actual bacteria, Y.enterocolitica. Since Y.enterocolitica is a class two bacteria we had to do it in another lab. We managed to get in contact with Livsmedelsverket (the Swedish authority of food safety) and they allowed us to test our colicin Fy in one of their labs on one of their pathogenic strains of Y.enterocolitica.

To examine the inhibition of colicin Fy an overnight culture of bacteriocin producing bacteria in 200ml LB with no antibiotic was prepared. As negative control, DH5-alpha was grown under the same conditions. No antibiotic was added to ensure that the antibiotics would not affect the results. The cells were then lysed and the supernatant was collected according to protocol [LINK]. The supernatant was added to a final concentration of 1%(v/v) in LB with 10^4 CFU/ml Y.enterocolitica added. The culture was put to grow in 37d C with 100rpm shaking. OD measurements were taken every hour, but due to Y.enterocolitica ability to aggregate the results were inconclusive. Instead 100microL was plated on BHI agar plates after different times. Immediately growth difference could be spotted and after 4 hours the results were very clear as seen in fugure 2.

For more pictures visit results in our [http://2014.igem.org/Team:Uppsala/Project_Killing wiki].

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
  INCOMPATIBLE WITH RFC[25]

  Illegal NgoMIV site found at 4
  
• 1000
  COMPATIBLE WITH RFC[1000]