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Part:BBa_M36998:Design

Designed by: Nick Davis, Rachel RoseFigura   Group: Stanford BIOE44 - S11   (2011-04-28)

Coenzyme B-12 Riboswitch for E. coli (nucleotides 1-240)


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 156
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

We made the decision to include the 5'UTR region following the cobalamin ribowitch (aptamer) sequence. Nucleotides 203-240 represent the 5'UTR upstream of the btuB coding sequence. We chose to include these nucleotides in our part, as it is not completely clear how—if at all—this sequence participates in translational control by the riboswitch, and few studies to date have explored or sufficiently demonstrated the significance of this nucleotide sequence.

For clarification on one of annotations made to our sequence: the B12 box is the localized region/nucleotide sequence where coenzyme B12 (cobalamin) binds to the riboswitch structure; upon binding, vast allosteric changes are made possible.

It should also be noted from supporting literature that, in hybrid fusions of btuB and lacZ, it was demonstrated that there exists a putative terminator sequence that extends from the end of the riboswitch sequence (nucleotides 180-240) into the coding sequence for btuB (through nucleotide +259, as designated relative to start of 5'UTR).

Source

Naturally-occurring, 240-nucleotides upstream of the btuB (B-12 uptake) coding sequence in E. coli. BtuB (the protein coded by the btuB gene) is a B-12 membrane transporter in E. coli bacteria.

References

I. Borovok, et al., "Coenzyme B12 controls transcription of the Steptomyces Class Ia ribonucleotide reductase nrdABS operon via a riboswitch mechanism," Journal of Bacteriology, 2006

M. Mandal and R. Breaker, "Gene regulation by riboswitches," Nature Reviews Molecular Cell Biology, 2004

WC. Winkler and R. Breaker, "Genetic control by metabolite-binding riboswitches," ChemBioChem, 2003

AG. Vitreschak, et al., "Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element," RNA Journal, 2003

A. Nahvi, JE. Barrick, and R. Breaker, "Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes," Nucleic Acids Research, 2003