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Team:Cambridge-JIC/Results
From 2014.igem.org
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<p align="center"><img src="https://static.igem.org/mediawiki/2014/0/06/MGFisobig.jpg" width = 600> </img> </p> | <p align="center"><img src="https://static.igem.org/mediawiki/2014/0/06/MGFisobig.jpg" width = 600> </img> </p> | ||
| - | <p>A transformation has not yet been attempted in the growth facility. This growth facility, or a similar custom design is the <b> only </b> non-standard molecular biology equipment needed to carry out Marchantia transformation.</p> | + | <p>A transformation has not yet been attempted in the growth facility. This growth facility, or a similar custom design is the <b> only </b> non-standard molecular biology equipment needed to carry out Marchantia transformation. Its most important function, that of inducing gametophore growth, can be accomplished with any source of far-red light.</p> |
<h3 id="Hammerhead Ribozymes">Hammerhead Ribozymes </h3> | <h3 id="Hammerhead Ribozymes">Hammerhead Ribozymes </h3> | ||
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<p>We had trouble assembling these constructs, which we put down to poor quality competent cells (assembly became considerably more reliable after the creation of a new batch). </p> | <p>We had trouble assembling these constructs, which we put down to poor quality competent cells (assembly became considerably more reliable after the creation of a new batch). </p> | ||
| - | <p>Finally, these constructs were built and sequenced, and Marchantia transformation attempted. However, this failed at the stage of transformation of Agrobacteria, and was eventually abandoned due to time constraints. We leave them as a legacy for future users of Marchantia/Mösbi</p> | + | <p>Finally, these constructs were built and sequenced, and Marchantia transformation attempted. However, this failed at the stage of transformation of Agrobacteria, and was eventually abandoned due to time constraints. We leave them as a legacy for future users of Marchantia/Mösbi.</p> |
<p></p> | <p></p> | ||
Revision as of 13:40, 17 October 2014
Results
Chromoproteins
As an example output plugin we transformed into Marchantia polymorphaa selection of the chromoproteins brought to iGEM by Uppsala 2011. This was to test whether a simple change in colour would work as an easily visible reporter.
Five chromoproteins were selected for expression: eforred (BBa_K592012), tspurple (BBa_K1033906), aspink (BBa_K1033927), aeblue (BBa_K1033929) and amilCP(BBa_K1033930, a deep blue colour). The N7 nuclear localisation tag (BBa_K1484104) was added to tspurple, aspink and amilCP. Each was put into pGreen and transformed first into agrobacterium, then transferred to marchantia.
The transformation procedure yielded a large number of transformants, approximately 100 per construct, which were confirmed via PCR using homogenised plants as a template and chromoprotein-specific primers for each tDNA added.
Left: A PCR of the transformed plants showing successful transformation. Right: A plate of transformants growing happily on hygromycin
For each chromoprotein construct, the transformation yielded approximately 100 transformed sporelings (7-days old plants). The petri dish to the right contains hygromycin as a selective marker. The gel confirms the transformation in three plants each from two other plates. The forward and reverse primers used in the PCR anneal to 35S and N7 respectively, and the template was homogenised plant material.
After approximately four weeks of growth, sparsely distributed bright red cells became apparent under the microscope in the plants transformed with the tsPurple gene. Although similar cells were not found in wild type plants, diffuse red regions were found and are probably due to release of anthocyanins by stressed or aging cells.
The bright red cells seen in Marchantia transformed with the TsPurple construct
It is notable that in the red cells, the vacuole is not visually distinct from the cytoplasm. As GFP, a protein of similar structure, is not accumulated in the vacuole without specific targeting, this implies that either the colour we observe in the bright cells is not due to chromoprotein expression, or perhaps that tsPurple is toxic enough to cause cellular damage and leaky organelles.
Plants transformed with asPink (which is also known as asFP595 due to its fluorescence), nuclear localised with an N7 tag, while not visibly pigmented, did have areas that fluoresced at the literature wavelengths.
Raspberry ketone production
As another example output module, the biosynthetic pathway from coumaroyl-coA to raspberry ketone was assembled, to allow the smell of raspberries to be used as an odour signal that the input module has been activated.
To characterise the enzymes involved, a bacterial constructs was made, and the E. Coli transformed with it we called RaspberrE coli. The construct consisted of an arabinose inducible expression plasmid coding for 4-coumarate coA ligase, benzalacetone synthase, and benzalacetone reductase, and the strain of E. Coli we used had the TnaA indole synthase gene knocked out to somewhat reduce the faecal odour associated with this molecule. (growing in M9 salts with casamino acids and no tryptophan eliminated the faecal odour entirely, as the smell is due entirely to tryptophan derivatives).
The RaspberrE coli were incubated for two and a half days with 3 or 9mM p-coumaric acid and 50mM arabinose to induce expression. The cultures were then shaken with ethyl acetate which was then run on an LCMS setup (which was only possible due to the kind giving of time and expertise by Ben Pilgrim at the Cambridge Department of Chemistry).
As a control, one of the tubes incubated contained a strain of E coli resistant to chloramphenicol but with none of the raspberry ketone producing genes. There was one peak that existed on the RaspberrE coli spectra but not on the control, which when run through the mass spectrometer turned out to be benzalacetone, the precursor to raspberry ketone.
A comparison of E.coli transformed with the benzalacetone generator (BBa_K1484317) against a control strain with none of the relevant enzymes.
None of the E. coli which also contained the benzalacetone reductase gene produced any peaks which gave mass spectrum peaks corresponding to that of raspberry ketone. These results suggest that while the 4-coumarate coA ligase and benzalacetone synthase both worked, the benzalacetone reductase, as shown once already by the Dutch research team who first cloned the enzyme’s gene sequence (led by Jules Beekwilder in Wageninen, The Netherlands), does not actually reduce benzalacetone.
A comparison of bacteria incubated with p-coumaric acid. Top: Transformed with benzalacetone generator (BBa_K1484317) Bottom: Transformed with benzalacetone generator and benzalacetone reductase (BBa_M36705) as a polycistronic operon. No raspberry ketone was detected in either culture.
Enhancer Trap
Marchantia spores have successfully been transformed and are growing at the moment. Screening has just begun and we wait to see some interesting expression pattern as development occurs.
Growth Facility
The Marchantia growth facility was built, and a guide to building one for yourself is available on this wiki.
A transformation has not yet been attempted in the growth facility. This growth facility, or a similar custom design is the only non-standard molecular biology equipment needed to carry out Marchantia transformation. Its most important function, that of inducing gametophore growth, can be accomplished with any source of far-red light.
Hammerhead Ribozymes
We received four hammerhead ribozymes as a kind donation from the Smolke lab. These included 2 versions of theophylline deactivated cleavage, 1 version of theophylline activated cleavage, and 1 always cleaving ribozyme.
Each of these were built into two separate constructs.
The first contained the Cauliflower Mosaic Virus 35S promoter driving expression of eGFP-N7, with the hammerhead ribozymes inserted into the 3' UTR
The second contained the the Cauliflower Mosaic Virus 35S promoter driving expression of the transcription activator HAP1, with the hammerhead ribozymes inserted into the 3' UTR. This then activated the HAP1-UAS, which was driving Venus-YFP-N7.
We had trouble assembling these constructs, which we put down to poor quality competent cells (assembly became considerably faster after the creation of a new batch). Eventually, all four 35S constructs were built using Gibson assembly and sequenced. Two HAP1 constructs were built using LCR, and verified by restriction endonuclease digest, but not sequenced
The Marchantia transformation was hindered at several stages. First, agrobacteria transformation via electroporation was repeatedly unsuccessful. Second, Marchantia transformations were rapidly contaminated, leading to the death of all selected plants (prior to them growing to the stage of being able to assay them). We abandoned transformation knowing that time constraints would prevent us from successfully assaying the results. We left the constructs, being RFC10 incompatible, for further users of Marchantia/Mösbi to try.
Heat Shock Promoter
We received from Jeremy Solly a vector containing a Marchantia heat-shock promoter. 2 constructs were designed, containing this promoter driving Venus-YFP-N7, as well as an input for our system, driving GAL4, which activated the GAL4-UAS driving Venus-YFP-N7.
We had trouble assembling these constructs, which we put down to poor quality competent cells (assembly became considerably more reliable after the creation of a new batch).
Finally, these constructs were built and sequenced, and Marchantia transformation attempted. However, this failed at the stage of transformation of Agrobacteria, and was eventually abandoned due to time constraints. We leave them as a legacy for future users of Marchantia/Mösbi.
