Team:DTU-Denmark/pBAD SPL
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Revision as of 16:21, 3 October 2013
pBAD SPL
Contents |
pBAD synthetic promoter library
A synthetic promoter library (SPL) is a library of cells each having one promoter sequence that differs between them. This promoter is always the same and is usually upstream a fluorescent protein like GFP/RFP. The term was first coined in 1998 and used in Lactococcus lactis (Jensen, Peter Ruhdal, and Karin Hammer.). The method was adapted by 2010 DTU iGEM team to make a SPL for E.coli that enabled the modulation of constitutive gene expression with great precision. They even made a new standard for this method with the use of biobricks ([http://dspace.mit.edu/handle/1721.1/60080 RFC 63]).
We used the method to build a non-leaky arabinose inducible promoter as a tool for expressing lethal proteins in E. coli. The reason was that many of the proteins we are working with are membrane bound or integral membrane proteins and will be lethal if expressed in to high quantities.
For testing our pathways we needed to grow the transformed cell to a certain concentration and growth with the gene constitutively expressed was not working very well. We needed a inducible system but the standard arabinose inducible system was way too leaky and we got same stood with the same problem as before. Therefore we needed to either build or buy (if an possible) an inducible system with great tightness able to be induced easily. We choose to build such system.
Methods
Experimental procedure
- Random promoter sequences were ordered matching the sequence CTGACGNNNNNNNNNNNNNNNNNNTAWWATNNNNA.
- USER cloning to add RFP downstream of promoter.
- Colonies were plated.
- Plates were induced by spraying them with an aqueous arabinose solution.
- Colonies that were not red prior to induction with arabinose but that did turn red after induction with arabinose were selected and re-innoculated as liquid cultures.
- Biolector: Wells were inoculated from overnight cultures of each of the selected colonies. All wells were run in duplicate.
- All duplicate colonies were run twice -- once with arabinose added at t=0, and again without arabinose.
- The pBAD system [http://parts.igem.org/Part:BBa_K808000 BBa_K808000] was used as a reference.
![](/wiki/images/a/ae/AraSPL_primer.png)
Data analysis
- Data was collected from the Biolector, and analyzed using a series of R scripts written by Chris Workman (unpublished).
- The maturation and degradation times for mCherry were both assumed to be 40 min. TODOref
- The growth rate, mu, was estimated to be 1.28 (from an average of all wells on all plates) since we expect each strain to grow at the same rate.
- A time window representing exponential growth was selected (between 1 and 4.5 hours).
- The RFP measurement for a constitutively expressed strain was used as a standard measure of growth. This is plotted on the x-axis in the detailed plots per colony below.
- Figures were plotted using R.
Results
Summary
Promoter activity when induced (with arabinose added) plotted vs basal activity (without arabinose; ie leakiness of the promoter). The colonies that we selected all show less activity than the the constitutive promoter, and when induced, show higher activity than the constitutive promoter.
Details
Promoter strengths for two trials of each colony with and without arabinose.
Colony Number | With arabinose 1 | With arabinose 2 | Without arabinose 1 | Without arabinose 2 |
---|---|---|---|---|
Col2 | 8.9025 | 7.8699 | 0.727 | 0.9552 |
Col3 | 9.2724 | 12.1142 | 0.5248 | 0.6982 |
Col4 | 9.4571 | 11.4522 | 0.5231 | 0.2508 |
Col12 | 6.3641 | 10.5389 | 0.5897 | 0.6869 |
Col10 | 7.9697 | 9.7949 | 0.3392 | 0.733 |
Col9 | 7.8563 | 20.1094 | 0.6995 | 0.7432 |
Col8 | 12.2318 | 15.4548 | 0.4203 | 0.4538 |
Col13 | 11.0377 | 7.3343 | 0.482 | 0.4641 |
Col15 | 15.6817 | 8.2707 | 0.8169 | 0.1343 |
Col18 | 14.7916 | 15.5736 | 0.6674 | 0.6745 |
Col19 | 14.2126 | 16.4898 | 0.4545 | 0.3566 |
Col29 | 7.1853 | 16.3467 | 0.5445 | 0.5013 |
Col26 | 9.7724 | 9.6269 | 0.7118 | 0.7865 |
Col22 | 8.4168 | 5.5958 | 0.6049 | 0.5645 |
Col33 | 9.1982 | 8.9987 | 0.6508 | 1.374 |
Col34 | 10.6987 | 7.883 | 0.5067 | 0.5031 |
Col35 | 13.8427 | 7.5469 | 0.4363 | 0.6281 |
ConRef | 6.506 | 7.9323 | 8.7811 | 7.9323 |
Example of use
The tight inducible pBAD promoter was used in our "Hello World project" to regulate the expression of GFP SF, which was tagged with a signal peptide to direct it into the periplasm. Production and folding of GFP SF is faster than the transport system of E. coli, which leads to undesired accumulation of GFP SF in the cytoplasm. Only when using a promoter with low leakiness it is possible to translocate a significant fraction of GFP SF after its production has been switched off. Thereby we get a clear signal from the periplasm with low interference from the cytoplasm.
![Alt text](/wiki/images/d/d5/GFP_in_perimplasm_RFP_in_cytoplasm_close_up.png)
See also "Hello World project".
References
- Jensen, Peter Ruhdal, and Karin Hammer. "The sequence of spacers between the consensus sequences modulates the strength of prokaryotic promoters." Applied and environmental microbiology 64.1 (1998): 82-87.