Overview of Experiments
1. Production Strains
In order to ensure that the bacteria we are working with are really the ones we want to work with, a 16S rDNA PCR was performed.
As an antibiotic resistance will be used in our later experiments to select transformants, we checked for any native antibiotic resistance against ampicillin, kanamycin, tetracyclin and chloramphenicol in an LB agar plate growth test. It turned out that kanamycin was the only antibiotic, against which none of our strains showed any resistance. For this reason, we decided to use only vectors with kanamycin resistance for our later projects.
After this, we prepared electro competent cells from our strains. All of our strains were grown on LB medium.
2. BioBricks
Our BioBricks were designed using the software SnapGene. The original Genes for our B12 binding proteins, and the torA signal sequence were codon optimized for E. coli.
The DNA containing the Genes were synthesized and friendly provided by IDT Integrated DNA Technologies.
In case of MutB, the length of the gene exceeded the maximum length of 2000 bp from IDT. For this reason, we designed two DNA parts, with a natural occurring HindIII restriction site at both ends. We intended to fuse these both genes by ligation. However, after having diffuculties to fuse the genes by ligation, we decided to fuse them by fusion PCR. In order to multiply the DNA for or cloning experiments, and to equip our genes with restriction sites, PCR was used.
For our purpose, we were searching for a vector with (a) kanamycin resistance and (b) araBAD operon. We thus decided to use the pBAD202 expression system. This vector, however, is equipped with a thioredoxin fusion protein which increases the rate of expression, but prohibits the physiological function of our protein. For this reason, we designed primers for an autarkic synporter protein. In order to test the dependence of the expression system on the B12 export rate, we also decided to use different other vectors.
For vectors ligation, we used a standart ligase reaction, for the pBAD202 expression, which works without ligation but topoisomerase reaction, we followed the manufacturer's protocol.
3. Transformation and Cultivation
For our transformation experiments, we used electroporation for all our self prepared competent cells. For the heat competent E. coli Top10 cells provided with the pBAD202 expression system, we used the manufacturer's heat shock transformation protocol.
For vector multiplication, E. coli cells (Top10 for pBAD202 plasmids, DH5alpha for all other plasmids) were transformed with the constructed plasmids. After the transformation, the cells were cultivated on LB Medium. Transformants were selected, and the respective clones were picked, cultivated in LB medium, and plasmids were extracted.
The Plasmids were then introduced into the production strains: Raoultella planticola ATCC 33531, Shimwellia blattae ATCC 29907, and Salmonella typhimurium TA100.
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