Team:Queens Canada/Outreach
Our Policy & Practice team this year led various projects and outreach partnerships this summer aimed at educating the Queen's student body and Kingston community about the rising contributions of synthetic biology in scientific advancements and the endless potential of the field itself.
Relating Relative Promoter Units to Transcription Rate
Assumption:
The first major assumption, is declaring "Promoter Activity" , to be a direct model of transcription rate. "Promoter Activity" is the number of RNAP molecules that clear the final base pair of a promoter (with units of [PoPS] = Polymerase per second).
Thus,
Where,
Thus, through simple substitution:
The modelling can further be simplified through a series of assumptions:
1) GFP expressed from test and standard promoters, have equivalent maturation rates, as they mature under the same conditions:
2) Since both the test and standard promoters are carried on the same plasmid backbone, assume they have the same average copy number:
3) Since promoters have been standardized to have identical transcription initiation sites (predicted) and identical sequences downstream of the site, we expect them to produce the same mRNA sequences.
Therefore,
Expect transcribed mRNA to be identical, implying mRNA degradation rates are equivalent:
Thus, we assume translational rates of immature GFP from some mRNA are equal:
4) Assume that immature GFP is stable. Therefore, protein degradation is negligable compared to dilution due to cell growth.
Thus:
Thus,
and if
Then,
Therefore, we assume the difference between growth rates of cells containing the test promoter construct and cells containing the standard promoter construct, is negligible compared to the maturation rate of GFP.
Thus, for the purposes of QGEM's modelling;
Relating Transcription Rate to Proteins Produced
Assumption:
CsgA alone and CsgA-fusions (such as CsgA-AFP8 and CsgA-SpyTag) behave similarly in terms of transcription in the cells.
The transcription rate of the CsgA gene is modeled as follows:
where,
Thus, by the stated assumption, the transcription rate of CsgA-fusions can be modeled with the same equation.
RBS Strength to Translation Rate
Altering the RBS strength of the ribosome binding site in a plasmid, can be completed by altering the genetic makeup of the RBS. This was modeled through the utilization of the RBS Calculator created by Dr. Howard Salis, at Penn State University. Using the forward implementation of the calculator, one input's their protein coding sequence, organism, and target translation initiation rate. The calculator then outputs the RBS sequence required to achieve such a translation initiation rate under the conditions outlined.
Translation Rate to Proteins Produced
