Part:BBa_K3782000

Flavobacterium frigoris strain PS1 ice-binding protein gene

FfIBP

FfIBP is a protein coding region that codes for an ice binding protein (IBP). IBPs, or more specifically antifreeze proteins (AFP), can bind to ice crystals and thereby prevent further ice growth. They are produced by organisms to survive in extremely cold environments. Activities of AFPs can be characterized by their thermal hysteresis (TH) or by their ice recrystallization inhibition (IRI). TH activity corresponds to the lowering of the freezing point without changing the melting point of a solution. IRI activity inhibits the growth of large ice crystals at the expense of smaller ones. The combination of these activities, which vary depending on the protein structure, prevents the freezing of body fluids and cell damage in organisms that live in environments with extremely cold temperatures.

Profile

Name	FfIBP
Base pairs	744
Number of amino acids	247
Molecular weight	25.35 kDa
Origin	Flavobacterium frigoris strain PS1, synthetic

Usage and Biology

The FfIBP protein coding region was used in the following composite parts (add links). It was expressed in E. coli strain BL21 (DE3) and purified. Various tests and assays were performed to characterize and verify the functionality of this ice-binding protein. FfIBP has moderate TH and IRI activity, and it can bind to ice crystals and inhibit their growth. The aim of our project was to use it on its own or in a mixture of other antifreeze proteins to develop a solution which could be applied on sensitive plant tissues and thereby protect crops from frost damage.

FfIBP is naturally produced by the Gram-negative Antarctic bacterium Flavobacterium frigoris PS1. Its TH activity is around 2.5 K at 50 µM.

!!!ADD Biological context and overall mechanism of the part!!!

Characterization

To reduce frost damage during late spring freeze, we wanted to develop a solution containing antifreeze proteins, which bind to ice crystals and inhibit their growth. FfIBP was therefore chosen as one of three AFPs, cloned and expressed in E. coli BL21 (DE3), and finally purified using a His-tag affinity column and gel filtration.
Two different vectors were used for cloning: pET-17b and pColdI, containing a T7 promoter and a cold-shock protein A (cspA) promoter respectively.

Cloning

Figure 1: (a) FfIBP in the FfIBP-pColdI construct was visualized by a 1% Agarose Gel. Left to right: L - 1 kb DNA Ladder (N3232), 1 – FfIBP colony PCR with pColdI-FPrimer and pColdI-RPrimer. (b) FfIBP in the pET-17b construct was visualized by a 1% Agarose Gel. Left to right: L - 1 kb DNA Ladder (N3232), 2 – FfIBP colony PCR with pET17b-FPrimer and pET17b-RPrimer.

FfIBP was cloned into the pET-17b plasmid using restriction and ligation via HindIII and XhoI and Gibson Assembly. The vector includes an ampicillin resistance gene and a lac operator, which allows for IPTG induced expression. The final construct was checked with a 1% Agarose gel (Fig.1) and via sequencing.

FfIBP was cloned into the pColdI plasmid using restriction and ligation via NdeI and XhoI and Gibson Assembly. The vector includes an ampicillin resistance gene and a lac operator, which allows for IPTG induced expression. The final construct was checked with a 1% Agarose gel (Fig.1) and via sequencing.

Expression and Purification

After we successfully transformed E. coli strain BL21 (DE3) with our pET-17b-FfIBP and pColdI-FfIBP constructs, we inoculated liquid cultures with LB and ampicillin. Before inducing expression in large volumes of liquid cultures, we first did small-scale test purifications to verify if the antifreeze proteins could be correctly purified. Next, we grew 1-liter liquid cultures at 37°C until an OD₆₀₀ of 0.6 was reached. We then placed the culture in a cooling incubator at 15°C for 30 minutes. We added IPTG 1mM and induced expression at 15°C for 24 hours. Afterwards, we removed a small volume of culture to run a total cell SDS-PAGE (15%) of E. coli cultures stained with Coomassie blue and to verify that the antifreeze protein was correctly overexpressed. The remaining culture was centrifuged, and the cell pellet was resuspended in Cold Lysis Buffer. We sonicated the cells and centrifuged the cells once more to collect the supernatant, which we loaded into the His-tag affinity column. We eluted the antifreeze proteins which bound to the column and concentrated the solution to a smaller volume. We performed a gel filtration to further purify the protein and finally stored aliquots at -80°C.

Figure 2: SDS-PAGE electrophoresis before and after FfIBP purification. FfIBP was expressed in E. coli BL21 (DE3) using both pColdI and pET-17b vectors. Left to right: L – PageRuler Plus Prestained Protein Ladder, 10 to 250 kDa (26619), 1 – Bacterial lysate of FfIBP expressed using the pColdI plasmid, 2 – Elution fraction of FfIBP expressed using the pColdI plasmid, 3 – Bacterial lysate of FfIBP expressed using the pET-17b plasmid, 4 – Elution fraction of FfIBP expressed using the pET-17b plasmid.

We induced expression of FfIBP with IPTG and ran a total cell SDS-PAGE (15%) of the E. coli BL21 (DE3) cultures stained with Coomassie blue. We used two different vectors, pET-17b and pColdI, to compare how the promoters influenced expression efficiency. The overexpression was successful for FfIBP. We observed thicker bands that matched the weight of the protein. The pColdI vector worked better than the pET-17b vector, because the band appeared to be stronger for this first plasmid on the gel (Fig.2).

Sequence and Features

Assembly Compatibility:

• 10
  INCOMPATIBLE WITH RFC[10]

  Illegal PstI site found at 269
  Illegal PstI site found at 350
  Illegal PstI site found at 530
  
• 12
  INCOMPATIBLE WITH RFC[12]

  Illegal PstI site found at 269
  Illegal PstI site found at 350
  Illegal PstI site found at 530
  
• 21
  COMPATIBLE WITH RFC[21]
• 23
  INCOMPATIBLE WITH RFC[23]

  Illegal PstI site found at 269
  Illegal PstI site found at 350
  Illegal PstI site found at 530
  
• 25
  INCOMPATIBLE WITH RFC[25]

  Illegal PstI site found at 269
  Illegal PstI site found at 350
  Illegal PstI site found at 530
  
• 1000
  COMPATIBLE WITH RFC[1000]

References

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