Regulatory

Part:BBa_M36699:Design

Designed by: Wyatt Woodson   Group: Stanford BIOE44 - S11   (2011-05-06)

PaceBAK


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 207
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

This is an updated version of BBa_M36707. The reason we had to alter the part was because of a missing part of the promoter. In the M36707 version, the -10 region of the promoter was missing, as well as a sequence of what we believe is spacing DNA. When using multiple sources to figure out the sequence we needed, there was a mis-numbering in which the full promoter was included on the one website (biocyc.org) while the numbering on the website we actually copied the sequence from, (genome.jp) had a slightly different numbering system. Without the -10 region of the promoter, and the spacer following it, not only would the polymerase not bind, but without the geographic spacing between the binding site and the start codon, there may not be adequate space for the gene downstream to be synthesized. Thus we concluded that without the -10 region of the promoter, the polymerase will never bind and thus the downstream gene will never made even in the absence of IclR and pyruvate. As for without the spacer, even if the polymerase can bind the DNA, the downstream gene still will not be made because the ribosome does not have adequate space to bind and find the start codon.

Source

Ecocyc.org provided a detailed picture of the region upstream of the promoter to which IclR binds. Specific link: http://tinyurl.com/aceBAK-Depiction

Genomic sequence found at genome.jp (http://tinyurl.com/aceBAK-Sequence). The promoter region is written in black, while the aceBAK coding sequence is written in blue.

References