Team:UNAM-Genomics Mexico/Modules/In vivo

Coupling together Biological Chassis

In order to enable the light based communication between bacteria, we have designed a tertiary cycle of different bacteria chassis, assembling each module of reception and emission to construct a light-based feedback loop of red-green-blue light, which will make the proof of concept of communication over distance and proper signal decoding.

Tertiary cycle

Coupling together Biological Chassis through Light communication

First Chassis: inRED-outGREEN

First Chassis: Red Light reception module coupled to Green Light emitter module.

Reception module: Red Light Photosensor cph8

OBJECTIVES

METHODOLOGY

Emission module: LuxAB luciferase from vibrio fischeri plus YFP protein

OBJECTIVES

• The final aim was the construction of the blue light emission bacterial luciferase (LuxAB)from Vibrio fischeri.

The structure of the device was designed as follows:

Because the luciferase coded by luxA and luxB needs a substrate (an aldehyde synthesized by enzymes into the lux operon) and we were not planning the design of a biobrick containing the genes needed for its synthesis we will add the aldehyde to the reaction in an exogenous way.

• Design LuxY biobrick, send to synthesise and transfer the construction from Mr. Gene plasmid to pSB1C3 DNA submission backbone.

• To test that the device works as expected.

METHODOLOGY

The lux operon

Vibrio fischeri’s lux operon is composed of several genes, all of them involved in bioluminescence and its regulation. This is the structure of Vibrio fischeri’s lux operon:

As it is shown in the diagram luxA and luxB genes, those coding for the luciferase, are placed together into the operon so the strategy was amplify them by means of PCR and then ligate PCR product with a strong constitutive promoter; the exogenously aldehyde added to the strain containing luxAB genes would be enough to trigger the luminescence reaction.

In the first place, we decided to purify genomic DNA from Vibrio fischeri strain MJ11 and then make a PCR with the following primers designed to extract luxAB region:

• Forward primer:Standard iGEM prefix+RBS+Coding Region

CGG AAT TCG CGG CCG CTT CTAG AGGA A ACA GCT ATG AAG TTT GGA AAT ATT TGT TTT TCG TAT CAA CC

• Reverse primer: Standard iGEM suffix+Coding Region

CTG CAG CGG CCG CTA CTA GTA TTA TTA GGG TAG ATT CTT TTC AAT TTT TTG GTT CAA C

YFP protein (LuxY)

LuxY is a gene coding for YFP, a protein that shifts the light emission wavelength of Vibrio fischeri’s luciferase from 484nm (blue) to 534nm (green - yellow); because our system needed a green or yellow emission module we looked in the literature for a protein capable of provoke this phenotype.

The sequence was taken from the following article:

Cloning and expression of the luxY gene from Vibrio fischeri strain Y-1 in Escherichia coli and complete amino acid sequence of the yellow fluorescent protein. Thomas O. Baldwin, Mary L. Treat, S. Colette Daubner Biochemistry 1990 29 (23), 5509-5515

And then the sequence was synthesized by Mr.gene.

This is the composition of the synthesized sequence, “Gene” stands only for luxY coding region.

Preffix+ Promoter + RBS + Gene + Double Terminator + Suffix

See [http://partsregistry.org/wiki/index.php?title=Part:BBa_K360100 LuxY -Part:BBa_K360100-] annotation at the registry for more details.

Second Chassis:inGREEN-outBLUE

Second Chassis: Green Light reception module coupled to Blue Light emitter module.

Reception module: Green Light cianobacterial Photosensor CcaS/CcaR

OBJECTIVES

METHODOLOGY

Emission module: LuxAB luciferase from vibrio fischeri plus Lumazine protein

OBJECTIVES

• Obtain LuxAB genes from Vibrio fischeri.

• Design Lumazine biobrick, send to synthesise and transfer the construction from Mr. Gene plasmid to pSB1C3 DNA submission backbone.

• To test that the device works as expected. This characterisation will test if Lumazine protein can also be functional working with the Vibrio fischeri luciferase, instead of its native interacting luciferase from Photobacterium phosphoreum.

METHODOLOGY

Lux operon

The strategy to obtain LuxAB genes from Vibrio fischeri was the aforementioned working with the green light emission.

Lumazine

Lumazine protein of Photobacterium phosphoreum (lumP) is a small protein which shifts the wavelength of light emitted by the P.phosphoreum luciferase LuxAB from 495 nm to about 475 nm, we needed it to tune the blue light emission wavelength towards another one closer to that of LovTap system reception.

A version of the lumazine protein was sent to us by Edinburgh Team, due to this construction hadn't been tested we decided to synthesise it, in order to avoid unexpected results for possible errors in the already assembled biobrick from Edinburgh.

This is the composition of the synthesized sequence, “Gene” stands only for lumazine coding region.

Preffix+ Promoter + RBS + Gene + Double Terminator + Suffix

See [http://partsregistry.org/wiki/index.php?title=Part:BBa_K360122 Lumazine -Part:BBa_K360122-] annotation at the registry for more details.

Third Chassis:inBLUE-outRED

Third Chassis: Blue Light reception module coupled to Red Light emitter module.

Reception module: Blue Light Photosensor LovTAP and blue light inducible promoter

Working in this chassis, we decided to use as blue light receptors: LovTAP photosensor and the native blue light inducible promoter from E.coli.

LOVTAP

OBJECTIVES

• Construct an improved version of the LovTAP photosensor device under the regulation of different constitutive promoters, due to the previous version of LovTAP designed by 2009 Lausanne team didn´t have a differential behavior under the inverting regulator sensitive to LacI and CAP protein, their results showed that the expression levels of LovTAP didn’t show differences to the induction with IPTG. As well, we included a punctual mutation to change the ILE427 by a PHE427, as was proposed by the model results of the team iGEM09_EPF-Lausanne. With this mutation LovTAP should react faster and the conformational change should be more stable (the protein stays in the active form for longer, under light induction).

• Transfer the plasmid with the LovTAP synthesised gene from Mr. Gene Plasmid to pSB1C3 DNA submission backbone and ligate the construction to different weak constitutive promoters.

• Characterize LovTAP reporter systems, both repressor and activator activity.

The structure of the device is designed as follows:

METHODOLOGY

LovTAP design

We decided to synthesize the LovTAP photosensor that in comparison with the Part:BBa_K191003 that is already at the registry, has the following differences:

1. The 2 PstI restriction sites were removed from the coding region of LovTAP.

2. We included a punctual mutation to change the ILE427 by a PHE427, as was proposed by the model results of the team iGEM09_EPF-Lausanne [2]. With this mutation LovTAP should stay in the active form for longer, under light induction.

3. The part does not include a promoter.

4. The RBS was changed from a strong (Part: BBa_B0030) to a medium strength (Part:BBa_B0032).

5. The stop codon tga was changed for two taa.

For more details visit our team [http://partsregistry.org/wiki/index.php?title=Part:BBa_K360121 LovTAP -Part:BBa_K360121-] entry at the registry page.

E.coli Strain Mutant

As the transcriptional response regulated by LovTAP might also be generated by the trpR repressor in E.coli in tryptophan rich conditions , we looked for an Escherichia coli strain mutant in trpR to avoid the cross-talk of the endogenous function of this gene with our system. After a careful look at the literature, we found that Dr. Charles Yanofsky had the mutant, so we sent him an e-mail, asking him to provide us the mutant.

The features of the mutant are:

1.Identification number: CY15001 2.Sex(Hfr,F+,F-,or F'): F-

5 Mutations:

•lamda- (lambda lysogen deletion)

•IN(rrnD-rrnE)1 (Inverts the region between rrnD and rrnE)

•rph-1 (RNase PH )

•tnaA5 (tryptophanase)

•trpR55 (repressor trpR)

LovTAP expression Levels

We got in touch with Dr. Devin Strickland the designer of LovTAP, in order to get some advices. Analyzing some experimental results reported in his dissertation and in the published paper : Light-activated DNA binding in a designed allosteric protein, it seems that at high expression levels of LovTAP, the behavior in the dark versus the light state is the same. So that, the regulation by light becomes not functional, thus we planned to test LovTAP under three different weak constitutive promoters (J23117,J23114 and J23105), expecting that it works well.

trpL promoter

The LovTAP system is composed of two modules, the light-sensitive input module is the LOV2 domain of Avena sativa phototropin 1 (AsLOV2). LOV domains absorb light through a flavin cofactor, photochemically form a covalent bond between the chromophore and a cysteine residue in the protein. The output module is the DNA binding domain of the bacterial transcription factor trp repressor (TrpR). So that, LovTAP activated can bind its operator DNA as a homodimer thus repressing transcription.

The DNA operator region where trp repressor binds was annotated wrongly in the 2009 EPF-Lausanne’s wiki as trpO promoter, but when searching for it in RegulonDB a very well annotated Escherichia coli transcriptional regulation data base, we found that the actually region where trp repressor binds is trpL promoter not trpO.

Knowing that we synthesized only trpLp’s functional elements as an oligonucleotide to introduce by PCR into a selected plasmid as follows:

Primer trpL reverse (5'->3'): NheI site + trpL promoter + XbaI site + EcoRI site:

TTGCTAGCGTGAACTTGCGTACTAGTTAACTAGTTCGATGATTAATTGTCAACAGCCTCTAGAAGCGGCCGCGAATTC

The primer is the reverse complementary of that sequence so we can use it as a reverse primer, which we used along with a suffix forward to introduce the trpL promoter into pSB1C3 plasmid by PCR.

LovTAP Reporter systems

As we are interested in characterize LovTAP activator and repressor activity. We have designed the following constructions.

• LovTAP repressor activity: Reporter system

1.trpL promoter fused to GFP protein:Part:BBa_E0240

2.trpL promoter fused to RFP protein: Part: BBa_E1010

• LovTAP activator activity: Reporter system

trpL promoter fused to lambda Repressor cI: Part:BBa_P0451 + Part:BBa_K098991 regulating GFP protein:Part:BBa_E0240.

Characterising LovTAP

Once LovTAP with the three weak constitutive promoters (J23117,123114 and J23105) and strong promoter (J23102) was correctly obtained in plasmid psb3k3, and the reporter system trpL+RFP was also finished by our team in plasmid psb1c3 , we started the co-transformation procedure in order to have the whole system inside the cells both trpR wild type and trpR mutant. Besides, we also receive the trpL+RFP construction in plasmid pSB1A2 from Lausanne team that was kindly sent it by Edinburgh team, because we didn’t get any response from the members of Lausanne team to provide us with their reporter systems. We are using both our trpL-RFP reporter system and the Lausanne system as a reference, expecting to obtain the similar results. The difference between the reporter systems is that ours doesn’t have the double terminator.

In order to test if LovTAP works correctly we implemented two protocols: the qualitative and the quantitative approach. With the qualitative approach we only want to observe and compare the RFP production in the cells exposed to light vs dark conditions, both in wild type and trpR mutant strains. What we are analyzing is the repressor activity of LovTAP, thus under light condition- when LovTAP repressor activity is activated, we expect to observe a lower level of RFP in comparison to the cells maintained in the dark state.

Considerations to take into account:

• The RFP protein doesn’t include a degradation tag so the time required to observe a clear difference between light and dark states will be long, because although LovTAP starts to repress, the RFP produced previously by the cells will be still present.
• The plasmid in which LovTAP is being express is Psb3k3 with a copy number around 20 to 30, trpL + RFP construction is inside plasmids psb1c3 and pSB1A2 both are high copy number plasmids -100 to 300 per cell-. So there are many trpL binding sites that should be repressed by LovTAP. The ideal condition for this experiment would be to have LovTAP and trpL+RFP constructions inside the same plasmid.
• Using the LovTAP constructions fused to promoters with different strength, we can test at what levels of expression, the LovTAP light regulation is better. We already know that under high expression levels of LovTAP, trpL promoter is repressed even in dark. To test this scenario we used J23102 promoter.

Qualitative experiment

Experimental procedure

1.Co-transform the cells using 5 microliters of each plasmid in the trpR mutant and in the wild type strains. The samples used are:

• Our trpL+RFP reporter system plus:

J23102+LovTAP. J23117+LovTAP. J23114+LovTAP. J23105+LovTAP.

• Lausanne trpL+RFP reporter system plus:

J23117+LovTAP. J23114+LovTAP. J23105+LovTAP.

2.Grow up the transformed cells overnight (~15hrs) in 5ml of LB medium at 37°C with spinning at 250rpm, with the respective antibiotics (Kanamicyn and chloramphenicol/ Kanamicyn and ampicillin ) in dark conditions. 3. Take 1 mL of broth and transfer it into 5 ml of fresh LB medium with antibiotics. 4. Incubate the cells in the two different conditions: the blue light and dark states for ~ 13 hrs.

Blue-Light samples were kept in the incubator covered in aluminium foil with 4 leds inside. The samples in dark conditions were maintained in the non-light devices that were constructed with bottles and newspaper.

5. Spin down the cultures and compare the RFP pellets obtained under blue-light vs. dark condition, and wild type samples vs. mutant samples.

Results

Only one colony of each co-transformation was used along the experiment and was tested under light and dark conditions.

The obtained pellets are showed in the following image.

Samples description is detailed in the next table: