Calculating promoter strengths

The majority of our promoter strengths were calculated as follows.

The paper "Measuring the activity of BioBrick promoters using an in vivo reference standard" published in the Journal of Biological Engineering makes J23101 their reference standard, giving it a strength of 0.03 POPS.

We can directly compare the strengths of all the J series constititive promoters using the standard registry of parts website. From this page we can calculate that if J23101 =0.03 pops then our original LuxI and LuxR promoter J23107 has a strength of ~0.018 POPS and our ammended model LuxR promoter has a strength of ~0.01 POPS. We also find that our constitutive Antiholin promoter has a strength of ~0.0066 POPS

LuxR promoter polymerase per second (PoPS) The following <http><a href="http://partsregistry.org/Part:BBa_F2620">BioBrick F2620</a></http> defines the LuxR responsive promoter. This has been assessed as having 6.6 PoPS promoter activity. I.e. 6..6 RNA polymerisation events per second. However, this seemed unlikely; the most active promoter in E.coli has about 2 polymerisations per second (see my last email on parameters, with the appropriate citation). At the iGEM meeting at the weekend I attended on behalf of the team, I met Barry Canton, the actual experimenter who deduced 6.6 PoPS! The clarification is this; he measured PoPS per cell; the LuxR promoter/GFP construct was on a ‘15 copies per cell’ plasmid, thus there were 15 copies of the LuxR promoter. The actual PoPS = 6.6/15 = 0.44 PoPS i.e. consistent with known E.coli promoters.

This discussion raises important issues about the plamsid backbones on which we mount our final biobricks; bios and theos must inform each other about plasmid copy numbers used, for these kind of reasons.

An estima te for the strength of different E.coli promoters, including lambda P(L)

Journal of Molecular Biology Volume 292, Issue 1, Activities of constitutive promoters in Escherichia coli1

S.-T Liang1, 2, M Bipatnath1, Y.-C Xu1, S.-L Chen2, P Dennis3, Corresponding Author Contact Information, E-mail The Corresponding Author, M Ehrenberg4 and H Bremer1

... comes the following data;

Pspc, 26 polymerase initiations per minute P(L), 17 polymerase initiations per minute Pbla 1.7 polymerase initiations per minute PRNAI, 17 polymerase initiations per minute

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References

[1] Goryachev, A.B., D.J. Toh and T. Lee. “System analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constant.” BioSystems 2006: 83, 178-187.

[2] Alon, Uri. “An Introduction to Systems Biology Design Principles of Biological Circiuts.” London: Chapman & Hall/CRC, 2007.

[3] Kepes, A., 1960, “Etudes cinetiques sur la galactoside-permease D'Escherichia coli. Biochim.” Biophys. Acta 40, 70-84.

[4] Canton, B. and Anna Labno. “Part: BBa_F2620.” BioBrick Registry. 13th August 2009. <http://partsregistry.org/Part:BBa_F2620>

[5] Andersen JB, Sternberg C, Poulsen LK, Bjorn SP, Givskov M, Molin S. “New Unstable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria.” Appl Environ Microbiol. 1998 Jun; 64(6):2240-6.

[6] Elowitz MB, Leibler S.; “A synthetic oscillatory network of transcriptional regulators.” Nature 2000 Jan; 403(6767):335-8.;