Part:BBa_K1638002:Experience

Team Grenoble-Alpes 2019

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IMPROVE OF THE BACTERIAL ADENYLATE CYCLASE TWO HYBRID

Purpose

The goal here is to prove that an Outer-membrane bacterial two hybrid (mBATCH) can be generated and can be functional by improving two biobricks from the original BACTH system:
BBa_K1638004 : T18 domain of adenylate cyclase from Bordetella pertussis
BBa_K1638002 : T25 domain of adenylate cyclase from Bordetella pertussis

In order to do this, 4 biobricks are created:
K3128017 : OmpX Wild-Type (WT) protein fused with T18 subpart of Bordetella Pertussis AC under constitutive promoter
K3128018 : OmpX WT protein fused with T25 subpart of Bordetella Pertussis AC under constitutive promoter
These two biobricks constitute the negative condition of the mBACTH (free sub-parts condition). OmpX proteins are fused to the adenylate cyclase sub-parts at their C-terminal ends. The fusion protein move freely in the bacterial outer membrane, but they are not forced to get closer by any mean.
The reconstitution of the adenylate cyclase in this condition is only due to random occurrence between both parts.
The signal measured here is considered as background noise.

K3128026 : OmpX WT protein fused with Leucine-zipper (LZ) and T18 sub-part of Bordetella Pertussis AC under constitutive promoter
K3128027 : OmpX WT protein fused with Leucine-zipper and T25 sub-part of Bordetella Pertussis AC under constitutive promoter
These two biobricks constitute the positive condition of the mBACTH (Leucine Zipper condition). OmpX proteins are fused to the AC subparts at their C-terminal ends, and a leucine-zipper sequence is added between the signal peptide of OmpX -to express the recombiant protein in the external membrane- and OmpX gene, in order to force the physical closeness of OmpX proteins.
Leucine zippers are peptides which contain a hydrophobic leucine residue at every seventh position. They are able to dimerize through interactions between their helices.
This is a strategy to force physical closeness. Hence the AC activity will be restored through the interaction of both subparts and will induce the cAMP dependant signalling cascade.

The reporter gene used in the system is the NanoLuciferase enzyme present in the BBa_K3128001 under a cAMP inducible CAP-dependent lactose promoter.
Two major factors affect this promoter :
IPTG, known to have a positive effect on the transcription of the gene by removing the lac repressor from the DNA.
CAP, known to have a positive effect on the transcription when it binds cAMP by helping the fixation of RNA-polymerase on the DNA
To be able to bind the CAP sites on the promoter, the CAP protein has first to interact with a cAMP molecule. As soon as two cAMP-CAP complexes are bound to the CAP sites, the RNA Polymerase initiates the transcription.



ATP is not naturally present in large amount in the periplasm of the bacteria, thereby it has to be added in the bacteria medium to enhance its periplasm diffusion and to be available for the adenylate cyclase catalytic reaction.

Materials and Methods

Bacterial Strain

The assays are made with streptomycin resistant BTH101 E.Coli strain, which are cya- bacteria.
In this strain, the endogenous adenylate cyclase gene has been deleted in order to obtain a bacterium that is unable to produce endogenous cAMP, thus avoiding the presence of potential false positives and making the system more sensitive.

Design of the plasmids

To compare the efficiency of the BACTH system created with the initial BACTH biobricks BBa_K1638004 (containing the T18 subpart) and BBa_K1638002 (containing the T25 subpart), quantification results in BTH101 strain are needed.
pJT18 contains the T18 sub-part ; it has an ampicillin resistant gene and the pMB1 replication origin.
pJT18 contains T18 subpart of Bordetella Pertussis AC under constitutive promoter.
pJT25-Nlc contains the T25 sub-part and the NanoLuciferase gene under the control of the plac promoter. It has a kanamycin resistant gene and the p15A replication origin.
pJT25-Nlc contains NanoLuciferase reporter for BACTH assay and T25 subpart of Bordetella Pertussis AC under constitutive promoter.
Those constructs will constitute the negative condition that will reveal the background noise of the initial BACTH system.

pJT18-ZIP is similar to pJT18-Nlc with the addition of a Leucine Zipper sequence fused at the end of T18.
pJT18-ZIP contains T18 subpart of Bordetella Pertussis AC fused with Leucine-zipper under constitutive promoter.
pJT25-Nlc-ZIP is similar to pJT25-Nlc with the addition of a Leucine Zipper sequence fused at the end of T25.
pJT25-Nlc-ZIP contains NanoLuciferase reporter for BACTH assay and T25 subpart of Bordetella Pertussis AC fused with Leucine-zipper under constitutive promoter.
Those constructs will constitute the positive condition that will reveal how the signal increases when both sub-parts are brought together with the BACTH.

Genetic constructions of pJT18, pJT25-Nlc, pJT18-ZIP and pJT25-Nlc-ZIP plasmids used to test the cytoplasmic BACTH in BTH101 strain.

For the mBACTH, as three biobricks have to be inserted in the bacterium to constitute the entire system, genetic constructions have been made in order to co-transform only two compatible plasmids :
pOT18-Nlc contains OmpX gene fused to the T18 sub-part and the NanoLuciferase gene under the control of the plac promoter; it has an ampicillin resistant gene and the pMB1 replication origin.
pOT18-Nlc contains NanoLuciferase reporter for BACTH assay and OmpX WT protein fused with T18 subpart of Bordetella Pertussis AC under constitutive promoter.
pOT25 contains OmpX gene fused to the T25 subpart. It has a kanamycin resistant gene and the p15A replication origin.
pOT25 contains OmpX WT protein fused with T25 subpart of Bordetella Pertussis AC under constitutive promoter.
Those constructs will constitute the negative condition that will reveal the background noise of the initial mBACTH system.

pOT18-Nlc-ZIP is similar to pOT18-Nlc with the addition of a leucine-zipper sequence between the OmpX signal peptide and the OmpX gene.
pOT18-Nlc-ZIP contains NanoLuciferase reporter for BACTH assay and OmpX WT protein fused with LZ and T18 subpart of Bordetella Pertussis AC under constitutive promoter.
pOT25-ZIP is similar to pOT25 with the addition of a leucine-zipper sequence between the OmpX signal peptide and the OmpX gene.
pOT25-ZIP contains OmpX WT protein fused with LZ and T25 subpart of Bordetella Pertussis AC under constitutive promoter.
Those constructs will constitute the positive condition that will reveal how the signal increases when both sub-parts are brought together with the mBACTH.

Genetic constructions of pOT18-Nlc, pOT25, pOT18-Nlc-ZIP and pOT25-ZIP plasmids used to test the membrane BACTH in BTH101 strain.

Transformation

For the BACTH assay, BTH101 are co-transformed either with
pJT18-Nlc and pJT25 plasmids : Free sub-parts  : negative condition,
or pJT18-Nlc-ZIP and pJT25-ZIP plasmids : Leucine Zipper mediated reconstitution of AC : positive condition.

For the outer-membrane BACTH assays, BTH101 are co-transformed either with
pOT18-Nlc and pOT25 plasmids : AC sub-parts fused to OmpX  : negative condition,
or pOT18-Nlc-ZIP and pOT25-ZIP plasmids : Leucine Zipper mediated reconstitution of AC : positive condition.

Classic cytoplasmic BACTH and mBACTH assay

To test the two different BACTH systems, the bioluminescence intensity produced by the NanoLuciferase enzyme is determined.
Several experimental conditions are tested using decreasing amount of bacterial culture (100µL, 25µL, 5µL and 1µL) at OD600nm = 0.6 : respectively 48E+06 CFU, 12E+06 CFU, 24E+05 CFU and 48E+04 CFU .
In addition, times of induction are tested from 0 to 360 minutes with 30 minutes increments.
Cultures of the different recombinant bacteria are incubated overnight at 18°C under shaking in order to induce an optimal COMPs proteins production [http://2015.igem.org/Team:TU_Eindhoven cf Team Eindhoven 2015].
The low temperature allows a native protein folding and membrane insertion to avoids as much as possible the formation of inclusion bodies.

Then cultures are diluted at OD600nm = 0,4 and let to grow to OD 600nm = 0.6 before induction.
The induction is performed by addition of 0,5 mM IPTG and 2mM of ATP for different periods of time. Bacteria are incubated at 37°C under shaking (180 rpm) to allow an optimal NanoLuciferase production.

After induction, 1, 5, 25 or 100µL of bacteria are distributed in a 96 wells black NUNC plate (ThermoFisher) and the Nano-Glo® Luciferase Assay assay from Promega® is performed (More informations) :
“Prepare the desired amount of reconstituted Nano-Glo® Luciferase Assay Reagent by combining one volume of Nano-Glo® Luciferase Assay Substrate with 50 volumes of Nano-Glo® Luciferase Assay Buffer.For example, if the experiment requires 10 mL of reagent, add 200μl of substrate to 10 mL of buffer.”
Then the amount of bioluminescence is measured using a luminometer by recording Relative Luminescence Units (RLU).

Several measures are made in the same well in order to reduce incertitude induced by the luminometer.
In order to test the reproducibility of our measures the means of 3 differents experiments with 3 measurements per well are calculated.
Data are expressed as the mean +/- standard deviation.

Several controls are performed:
∅ IPTG, ∅ ATP : To check the promoter leakage without any induction.
∅ IPTG, 2 mM ATP :To check if the addition of extracellular ATP helps the production of cAMP and to check if addition of ATP modifies the promoter leakage.
0.5 mM IPTG, ∅ ATP : To check if adding extracellular ATP is needed for protein expression.
0.5 mM IPTG, 2 mM ATP : Is the experimental condition, it correspond to the measure at 360min.

Results

Cytoplasmic BACTH assay

The cytoplasmic BACTH, the following results are obtained with 5µL of bacteria (24E+05 CFU).

Means of measurements obtained through 3 differents experiments with 3 measurements per well for each condition of the BACTH generated with either
pJT18 and pJT25-Nlc : Free AC sub-parts : negative condition,
or pJT18-ZIP and pJT25-Nlc-ZIP : Leucine Zipper mediated reconstitution of AC : positive condition.
Blank was done with 24E+05 CFU of untransformed BTH101 (RLU = 300) and subtracted to the measurements.

With 7.48E+06 RLU of bioluminesce produced in the 0.5 mM IPTG condition compared to 6.02E+06 in the condition without IPTG and 2mM ATP, it seems that IPTG increase slightly the transcription.
Additionally, with the same produced bioluminescence between the without IPTG and 2mM ATP and without IPTG and without ATP conditions, ATP appears to have no effect on transcription.
These two observations were expected because of the large amount of ATP already present in the cytoplasm of the bacteria saturating the adenylate cyclase.
Obviously, those observations do not prove anything but give clues on the way the system operates.


Luminescence production over time of induction for the negative condition strain (yellow curve) and the positive condition strain of the BACTH assay (purple curve).
Area of the significant* difference between both curves is highlighted in yellow.
Blank was done with 24E+05 CFU of untransformed BTH101 (RLU = 300) and subtracted to the measurements.
* A T test was done for the values of time above 90 min and led to a p-value below 0.05.

From 0 to 60 minutes of induction time, the bioluminescence produced by the two strains is similar.
At 60 minutes, the two curves start to split and give rise to a significant difference between the free sub-parts : negative condition and the Leucine Zipper: positive condition from around 90 minutes.

The discrepancy keeps increasing upon time of induction, thus highlighting the efficiency of the amplification signal thanks to the signalling cascade and the strong reporter gene.

These data suggest that the classical cytoplasmic BACTH system is functional in BTH101 strain and can discriminate the presence or absence of the target from a 90 min induction.

Membrane BACTH assay

To make sure that the OmpX-T18 and OmpX-T25 are expressed in the external membrane, OmpX fusion proteins have been muted to be able to integrate an unnatural amino acid in one of their extracellular loops by implementing the amber stop codon TAG. A specific tRNA can then add an azido-modified amino acid to the protein, these modified proteins are called COMPs.
The azido group of the protein reacts with a DIBO group, the reaction allows to click the extracellular DIBO to the functionnalized biosensor (COMP) protein.
COMPs are fused with T18 or T25 subparts and have to be expressed at the external membrane of the bacteria.
To ensure this, microscopy observations have been done with an Dalexia 488 conjugated DIBO group.
Fluorescent microscopy observations of the COMP, COMP-T18 and COMP-T25 clickable proteins show surface labelled bacteria indicating that a the recombinante proteins are expressed at the external membrane of E. coli.

The mBACTH following results are obtained with 5µL of bacteria (24E+05 CFU).

Means of measurements obtained through 3 differents experiments with 3 measurements per well for each condition of the mBACTH generated with either
pOT18-Nlc and pOT25 : AC sub-parts fused to OmpX  : negative condition,
or pOT18-Nlc-ZIP and pOT25-ZIP : Leucine Zipper mediated reconstitution of AC : positive condition.
Blank was done with 24E+05 CFU of untransformed BTH101 (RLU = 300) and subtracted to each the measurements.

Using positive control strain, we measured 1.48E+06 RLU of bioluminescence produced in the 0.5 mM IPTG condition compared to 9.02E+05 in the condition without IPTG and without ATP, indicating that IPTG increase slightly the transcription.
Additionally, with 2.55E+0,6 RLU of bioluminescence produced in the condition without IPTG and 2mM ATP condition compared to 9.02E+05 in the without IPTG and without ATP condition, it seems that ATP have a significant* effect on transcription.
This was expected because of the lack of ATP in the periplasm of the bacteria. Thereby, adding a great amount of ATP in the medium able to diffuse in the periplasm help the cAMP production by the periplasmic adenylate cyclase.
Obviously, those observations do not prove anything but give clues on the way the system operates.
* A T test was done for the values of time above 90 min and led to a p-value below 0.01.


Luminescence production over time of induction for the negative condition strain (red curve) and the positive condition strain of the mBACTH assay (blue curve).
Area of the significant* difference between both curves is highlighted in yellow.
Blank was done with 24E+05 CFU of untransformed BTH101 (RLU = 300) and subtracted to each measurements.
* A T test was done for the values of time above 210 min and led to a p-value below 0.05.

From 0 to 120 minutes of induction time, the bioluminescence produced by the two strains is similar.
At 120 minutes, the two curves start to split and give rise to a significant difference between the two strains from around 210 minutes the negative condition strain compared to the Leucine Zipper_positive condition .

The discrepancy keeps increasing upon induction time, thus highlighting the efficiency of the amplification signal thanks to the signalling cascade and the strong reporter gene.

Comparison of the efficiency of the classic cytoplasmic BACTH and the Outer membrane BACTH of iGEM Grenoble-Alpes team.

Comparison of the efficiency of the classic cytoplasmic BACTH and the external membrane BACTH of iGEM Grenoble-Alpes team.
Blank was done with 24E+05 CFU of untransformed BTH101 (RLU = 300) and subtracted from the measurements.

The results show a higher a quicker bioluminescence with the BACTH than with the mBACTH, this is due to multiple factors :
The proteins diffuse more easily in the cytoplasm than in the outer membrane and so both sub-parts are more likely to encounter each other in the cytoplasm than in the outer membrane. Whereof there is more functional adenylate cyclase in the cytoplasm than in the outer membrane.
With traditional BACTH, cAMP is produced in the cytoplasm making it directly accessible to the proteins that enable transcription (CAP), unlike mBACTH that produce cAMP inside the periplasm. Thereby, to be accessible by the CAP proteins cAMP need to diffuse in the cytoplasm thus increasing the time needed to enable translation and decreasing the quantity of cAMP reaching the CAP protein therefore reducing the amount of NanoLuc produced.

Nevertheless the mBACTH have a lower background noise thus allowing the discrimination of both condition. At the end the mBACTH is operational if the bioluminescence detection and quantification is well optimise for our system.

Conclusion

Biobricks BBa_K1638002 and BBa_K1638004 have been improved in order to allow a functional bacterial two-hybrid system in the bacterium periplasm by being fused with a protein of the outer-membrane.
The data show that COMP protein is expressed at the outer-membrane of bacteria and that there is a significant difference between the negative and the positive condition of the mBACTH assay, suggesting that a bacterial adenylate cyclase two-hybrid can be successfully performed in the periplasm of bacteria which property is required for the sensing and detection of extracellular molecules.

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