Constitutive promoter, RBS, IclR gene, terminator, aceBAK promoter, RBS, Gemini, terminator. This is designed so that the IclR gene is synthesized on the same scale as the aceBAK promoter instead of relying on IclR naturally in E. coli.
Deciding how much of the IclR binding sites in the aceBAK promoter was necessary, and determining the IclR gene in its functional state.
Katie Lund and Wyatt Woodson parts obtained from Stanford BIOE44 - S11
IclR binds with pyruvate to form a more stable structure to bind to the inhibitory regulation sites on the aceBAK promoter. By combining the IclR gene and the aceBAK promoter the presence of IclR and pyruvate will inhibit the aceBAK promoter and any genes downstream of it. While there will be some residual transcription in the presence of only IclR, the presence of pyruvate increases the stability of binding with the aceBAK promoter region so inhibitory activities are higher.
Gemini, a Bifunctional Enzymatic and Fluorescent Reporter of Gene Expression. PLOS One. Lance Martin et al.
A medium strength RBS expressing Gemini, ending with a strong terminator.
RBS.3 (medium) -- derivative of BBa_0030
Weak1 RBS based on Ron Weiss thesis. Strength is considered relative to <bb_part>BBa_B0030</bb_part>, <bb_part>BBa_B0031</bb_part>, <bb_part>BBa_B0033</bb_part>.
Varies from -6 to +1 region from original sequence to accomodate BioBricks suffix ("RBS-2" in figure 4-14 of thesis). Contact info for this part: Brian Chow
Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003.
Transcriptional terminator consisting of a 64 bp stem-loop.
Overlap extension of synthetic oligonucleotides
5' Bicistronic UTR (medium), does not include ATG start
Vivek Mutalik et al. c/o BIOFAB Emeryville.
5' UTR based on bicistronic junction architecture. First RBS is strong and drives expression of short leader cistron. Second RBS internal to first cistron control translation of gene of interest. Architecture is optimized so that downstream CDS for gene of interest does not have a chance to form a secondary structure with the 5' UTR. See BIOFAB.org for more information.
Guillaume Cambray et al. c/o BIOFAB Emeryville
E. coli RNA pol transcription terminator designed and tested by Guillaume Cambray at BIOFAB Emeryville. Based on the natural E. coli rnpB T1 terminator.
This coding sequence was obtained from genome.jp
IclR represses the aceBAK promoter in E. coli
IclR inhibits the aceBAK gene in conjunction with pyruvate or glyoxylate by binding these sites on the aceBAK promoter.
amino acids 3-60 from lacZ and amino acids 2-end of GFP (E0043)
This part is a fusion protein between GFP and the alpha fragment of lacZ. It can be measured via fluorescence from GFP or through an assay for beta-galactosidase in a strain containing the omega fragment of lacZ.
The amino acid linker AGGSEGGGSEHHHHHHGSE is between the lacZa and GFP. The 6-his can also facilitate detection on a Western blot, for purification, etc.
Conversion of the iGEM parts registry to SBOL2.1