Regulatory

Part:BBa_M36250:Design

Designed by: Evan Masutani and Erica Lieberman   Group: Stanford BIOE44 - S11   (2011-12-09)

PalkB inducible promoter activated by AlkS


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]


Design Notes

When designing this part, efforts were made to extract only the promoter sequence while omitting the surrounding base-pairs as presented by van Beilen, et al., 2001. This may have proven to be a fatal flaw, as it is thought that the original surrounding sequences contribute to the functionality of the part as a whole.

We compared this part to plasmid pSPZ3 employed by Sven Panke successfully and found that their PalkB had about 100 additional bp upstream of our part. Further analysis with m-fold suggests that these additional nucleotides play a large role in PalkB function.

Source

Van Beilen, J.B., S. Panke, S. Lucchini, A.G. Franchini, M. Rothlisberger, and B. Witholt. "Analysis of Pseudomonas Putida Alkane Degradation Gene Clusters and Flanking Insertion Sequences : Evolution and Regulation of the Alk Genes." Microbiology 147 (2001): 1621-630. (alkS sequence optimized for E. coli by EnCor Biotechnology, Inc.'s Codon Optimization Calculator.)

References

Van Beilen, J.B., S. Panke, S. Lucchini, A.G. Franchini, M. Rothlisberger, and B. Witholt. "Analysis of Pseudomonas Putida Alkane Degradation Gene Clusters and flanking Insertion Sequences : Evolution and Regulation of the Alk Genes." Microbiology 147 (2001): 1621-630.

Makart, Stefan, Matthias Heinemann, and Sven Panke. "Characterization of the AlkS/PalkB-expression System as an Efficient Tool for the Production of Recombinant Proteins InEscherichia Coli Fed-batch Fermentations." Biotechnology and Bioengineering 96.2 (2007): 326-36.

Panke, Sven, Andreas Meyer, Caroline Huber, Bernard Witholt, and Marcel Wubbolts. "An Alkane-Responsive Expression System for the Production of Fine Chemicals." Applied Environmental Microbiology 65.6 (1999): 2324-332.

Markham, Nicholas, Andrew Wright, Leslie Zucker, and Michael Zucker. "The UNAFold Web Server." UNAFold | Mfold.rit.albany.edu. University at Albany SUNY, 1995. Web. 10 Dec. 2011. <http://mfold.rna.albany.edu/>.