Difference between revisions of "Part:BBa K2333434"

Revision as of 23:10, 1 November 2017

pLac0-1 mf-Lon

This is an IPTG-inducible mf-Lon construct containing the pLlac 0-1 promoter. William and Mary 2017 has modified the mf-Lon gene via codon-optimization for iGEM use and added a double terminator.

Usage and Biology

This composite part is a combination circuit with the LacI repressor under the constitutive promoter J23105 and mf-Lon under the control of the PLlac 0-1 promoter. The mf-Lon protease specifically targets different protein degradation tags with varying affinities corresponding to varying degradation rates. This IPTG-inducible mf-Lon construct was used in tandem with aTc-inducible pdt reporter constructs by William and Mary 2017 to obtain gene expression speed measurements.

Characterization

W&M 2017 characterized this mf-Lon containing composite part in combination with aTc-inducible pdt reporter constructs as well as with copper sulfate inducible pdt reporter constructs. The graphs below show this speed data along with the data from the other tags in this series (BBa_K2333413-BBa_K2333419).

Graph 1: Time course measurements were performed according to standard protocol, and fluorescence was normalized to steady state based upon when fluorescence no longer increased. Data is shown for each construct until steady state is reached (this means at least two consecutive subsequent data points do not increase fluorescence). As the no-pdt condition had not reached steady state when time course was ended, it was normalized to the final collected data point, which is likely close to the true steady state. Geometric mean of 10,000 cells each of three biological replicates. Shaded region represents one geometric standard deviation above and below the mean.

Graph 2: Comparison of calculated t1/2 vs degradation rate. Degradation rate was obtained as above, and t1/2 was defined as time at which each biological replicate's regression line reached half of steady state. The blue line represents an optical guide for the eye, and is not fitted. Speed is scaling with degradation rate and following a predicted trend.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
INCOMPATIBLE WITH RFC[12]
Illegal NheI site found at 47
Illegal NheI site found at 70
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal AgeI site found at 3242
Illegal AgeI site found at 3326
Illegal AgeI site found at 3532
Illegal AgeI site found at 3557
1000
COMPATIBLE WITH RFC[1000]

References

[1] Cameron DE, Collins JJ. Tunable protein degradation in bacteria. Nature Biotechnology. 2014;32(12):1276–1281.

[2] Torella JP, Boehm CR, Lienert F, Chen J-H, Way JC, Silver PA. Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic Acids Research. 2013;42(1):681–689.

@@ Line 17: / Line 17: @@
 <html><img src="https://static.igem.org/mediawiki/2017/f/f1/T--William_and_Mary--mScarlet-I_Speed_Normalized_Truncated.png" width="600px"/></html>
-Time course measurements were performed according to standard protocol, and fluorescence was normalized to steady state based upon when fluorescence no longer increased. As the no-Lon condition had not reached steady state when time course was ended, it was normalized to the final collected data point, which is likely close to the true steady state.
+Graph 1: Time course measurements were performed according to standard protocol, and fluorescence was normalized to steady state based upon when fluorescence no longer increased. Data is shown for each construct until steady state is reached (this means at least two consecutive subsequent data points do not increase fluorescence). As the no-pdt condition had not reached steady state when time course was ended, it was normalized to the final collected data point, which is likely close to the true steady state. Geometric mean of 10,000 cells each of three biological replicates. Shaded region represents one geometric standard deviation above and below the mean.
 <html><img src="https://static.igem.org/mediawiki/parts/3/33/T--William_and_Mary--speed_vs_deg_mScarlet.png" width="520px"/></html>
-The graph above shows that speed is scaling with degradation rate and following a predicted trend.
+Graph 2: Comparison of calculated t1/2 vs degradation rate. Degradation rate was obtained as above, and t1/2 was defined as time at which each biological replicate's regression line reached half of steady state. The blue line represents an optical guide for the eye, and is not fitted. Speed is scaling with degradation rate and following a predicted trend.