Team:Bielefeld-Germany/Project/Theory

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Contents

Introduction

In our iGEM project we tried to create an Escherichia coli cell which is capable to sense capsaicin in a complex sample and report the concentration with a luciferase light signal. We combined a native receptor system of Agrobacterium tumefaciens with the readout system of the firefly luciferase. The native receptor senses the phenolic compound acetosyringone. For this reason we used directed evolution to modify the binding region of the native receptor to generate a new capsaicin receptor because of the chemical similarities of acetosyringone and capsaicin. We established a screening system based on antibiotic concentration gradients to screen the newly generated receptors. In our E. coli acetosyringone sensing system several parts derived from different organisms were assembled. The readout system taken from firefly, luciferase, the receptor sensing system derived from A. tumefaciens and sensitivity tuners consist of phage DNA.


Agrobacterium tumefaciens

Figure 1: Image by Martha Hawe


The model organism A. tumefaciens is a soil bacterium and can be found at nearly every place in the world. Agrobacteria became known as a phyto-pathogen leading to the crown gall disease in dicotyledonous species (DeCleene M and DeLay J, 1976). The infection is caused by a gene transfer system located on an extrachromosomal element, the Ti-plasmid. Furthermore, the infection can be divided into several steps: The first step is the localisation of the hurt plant by the bacteria. Predominantely A. tumefaciens senses phenolic compunds from hurt plants, but also aldose monosaccharides, low pH and low phosphate (Palmer AG. et al.2004; Brencic A and Winans SC, 2005). When A. tumefaciens recognizes phenols with the VirA receptor, a signal transduction cascade is initiated leading to the expression of virulence genes. The next step is a physical interaction with the host plant. A type three secretion system is responsible for the DNA transfer of the Ti-plasmid from the bacterium into the host. The DNA is translocated to the nucleus, leading to the gene expression and the production of opin. A. tumefaciens uses the reprogrammed plant cells for metabolite production and therefore as a nutrient supplier.

For biotechnological purposes the Ti-plasmid was disharmed. Instead of the native transfer region (T-region) and a gene of interest could be easily introduced into the Ti-plasmid. Agrobacterium-mediated DNA transfer is one of the most commonly used techniques of plant transformation (Ziemienowicz A, 2001).


Native receptor

A. tumefaciens needs a precise recognition system for potential hosts to gain an evolutionary advance. The native sensing system is a two-component phospho-relay system in which VirA is a transmembrane-bound sensor while VirG is the intracellular response regulator (Wolanin PM et al., 2002). The two genes for the sensing system are virA and virG (Stachel SE and Nester EW, 1986) which are constitutively expressed at a basal level. VirA is a histidine kinase. An autophosphorylation occurs at the His-474 residue, after sensing the phenol 3,5-dimethoxyacetophenone, acetosyringone (Huang Y et al., 1990 ; Jin SG et al., 1990a). In the next step in the signal transduction cascade, the phosphorylated VirA leads to the transfer of the phosphate to Asp-52 residue of VirG (Jin SG et al., 1990a ; Jin SG et al., 1990b ; Pazour GJ and Das A, 1990). VirG is the response regulator of the two-component system (Brencic A, Winans SC, 2005) and acts as a transcription factor. Hence it binds to the virulence box (vir Box) containing promoters, for example the virB promoter (Jin SG et al., 1990a ; Pazour GJ and Das A, 1990).


VirA receptor structure

The VirA receptor consists of 829 amino acids and is a transmembrane protein in the inner menbrane of A. tumefaciens (Melchers LS, 1989). VirA spans the inner membrane, with two transmembrane domains, a large periplasmic region, and a large C-terminal cytoplasmic domain (Banta LM, 1994). VirA directly senses the phenolic compounds for vir activation (Lee YW et al., 1996). Therefore the linker domain is essential for induction by phenolic compounds (Chang CH and Winans SC., 1992). The linker region is located in the cytosolic site at position 280 to 414 (Lee YW et al., 1996). This region between the amino acids 283 and 304 was highly conserved in four different strains of Agrobacterium, and therefore likely to serve as the receptor region for the phenolic inducers which are common to all four strains (Turk SC et al., 1994).


Figure 2: The structur of virA (Melchers et al., 1989)
Figure 3: The funtional parts of the virA receptor (Lee et al., 1996)


Chang and Winnans (1992) revealed in their studies the parts of the VirA receptor which are essential for the signal transduction (Chang CH and Winans SC., 1992). A structured model for different inducing conditions are shown in figure 4.

Figure 4 : The different binding conditions (Chang and Winans, 1992)

For information about modulation strategy click here


Phenolic Compounds

The ligand receptor interaction between acetosyringone and VirA is based on the interaction of several chemical groups. First of all the hydroxylated aromat is essential. Methoxy groups in the ortho position of the phenol play a crucial role in the signaling as well. It should be mentioned that dimethoxy compounds have a higher activity than monomethoxy compounds. The acetyl and alkyl groups in para position enhance the binding affinity. VirA activating compounds must have two methoxy groups in ortho position and an additional carbonyl group on the R3 chain. The potential capacity of the group para to the phenolic hydroxyl group is associated with higher activities. Moreover the chirality at this carbon center is critical for the inducing activity (Winans SC, 1992). Regarding to the proton transfer model of Hess et al. (1996) the VirA activator transfers a proton to the basic area receptor binding site. The allosteric change leads to the phosphotransfer and the signaltransduction (Hess KM et al., 1991).

Figure 5: Chemical structure of phenol
Figure 6: The proton transfer model according to Hess et al., 1991
Figure 7: Compounds with a structural similarity, which induce virA Winans, 1992

See more possible compounds by clicking here


Inducing enhancers

The sensitivity of this system is highly enhanced when additional aldose monosacchardic suggars occur in the environment of Agrobacterium. The sugar binding protein ChvE interacts with the VirA receptor, leading to a much stronger vir gene expression (Banta LM, et al., 1994).


Subcloning into E. coli and receptor function in new host

In our project we decided to work with E. coli instead of A. tumefaciens. The transcription procedure in E. coli is very similar to A. tumefaciens but not complete homolog. In E. coli the rpoA gene - encoding the α-subunit of RNA polymerase in A. tumefaciens - is not present but essential for the transcription of a virB promoter-driven genes (Lohrke SM et al., 1990) For this reason it was necessary to subclone a modified virG gene that is capable to be trancribed by the E. coli expression system.

Yong-Chul et al. (2004) described VirG mutants that are capable of expressing the virB promoter-driven genes in E. coli without the requirement for the RpoA from A. tumefaciens, suggesting that the virG mutants are able to interact with the transcription system of E. coli (Yong-Chul J et al., 2004). In VirG the amino acid at position 56 is likely to play a key role in the interaction with the RpoA of E. coli. Regarding to Yong-Chul J et al. (2004) we used virG mutants, with amino acid substitutions of G56V and I77V that are capable of activating vir genes in E. coli in response to inducer acetosyringone in a VirA-dependent manner.


Read out system

Firefly Luciferase

We are using luciferase as the read out system. The luciferase was originally extracted from the firefly Photinus pyralis. It is one of the best studied and characterized read out systems. The luciferase enzyme catalyses the chemical reaction from its substrate luceferin to oxyluciferin and light (De Wet et al. 1986). Figure 8 shows the reaction in detail.

We used luciferase as the read out system because it causes only slight negligible noise, hence the signal to noise ration is excellent.

Figure 8: Firefly luciferase reaction (De Wet et al.1986)






Output-signal amplification by Sensitivity Tuner implementation

Using a standard, inducible promoter with reporter system often results in weak reporter expression. So difficulties in quantification can occur. The quantification can be enhanced by an amplification of the transcription rate of the desired reporter genes. Such an amplification can be realized by using a so called sensitivity tuner device. This takes place as promoter induction upregulates a phage activator, which binds to a phage promoter upstream of a reporter gene. As result, a PoPs input (Inducer) generates a PoPs output at a higher signal. PoPs is equivalent to the flow of RNA polymerase molecules along DNA (Julien and Calendar, 1996 ; iGEM Team Cambridge, 2007).

Figure 9: Gene sequence of final test construct including Sensitivity Tuner elements.



Purpose of Sensitivity Tuner application

We presumed weak expression rates of our reporter luciferase indicated by pretesting the native system BBa_K389015. For having a broader range of quantification for our prototype test system, an amplification device was implemented. For amplifying the output signal of luciferase induced by acetosyringone, three sensitivity tuners, distinguished by the amplification factor, were combined with our detection system. To modify the sensitivity tuner for our purpose we took BioBricks with amplification factors from 10 (BBa_I746380) to 35 (BBa_I746390), removed the pBAD/araC promoter (BBa_I0500) and GFP read out (BBa_E0040) and replaced it by the reporter gene luciferase BBa_K389004(Figure 9). This enhanced luciferase BioBrick was assembled to the VirA/G signaling system BioBrick. The benefits of luciferase as reporter gene instead of GFP are a broader range of measurement, higher sensitivity and low half-live making cinetic tests possible (Williams et al.1989).



For test results click Sensitivity Tuner amplified Vir-test system


Receptor modification strategy

The smartest way of receptor-modification is initiated by a silico approach based on a 3D structure of the native receptor. Followed by primer mutagenesis of the computantional gained results a precise adapted peptide emerges. This concept has been proven by Looger et al., 2003.

Because of time limitations within the iGEM competition and a lack of biological data in literature - no x-ray cristalography structure data for VirA linker region available- this strategy was not applicable. Therefore we developed two different stragies in our MARSS project:

The first strategy was an error prone PCR approach by building a mutant data base for selection. The second strategy was a primer mutagenesis based approach.


Random mutagenesis by error-prone PCR (EP-PCR)

In order to detect novel substances (e.g. capsaicin) with the VirA receptor, the first step was to create a mutagenised library of virA variants, which could subsequently be screened for new binding characteristics. Plenty of different strategies for mutagenesis of DNA are known, including the use of nucleotide analogues, bacteria containing mutator genes, the mutagenesis with UV light or chemicals and inaccurate PCR (Cadwell RC and Joyce GF, 1992).

When designing our strategy we rejected the use of bacteria strains with high mutation rates, since the changes in base sequence would occur all over the transformed plasmids. Thereby some mutations would also take place in the backbone of the plasmid, or might even been found in the standardized BioBrick prefix and suffix. We also excluded the possibility of using UV light or mutagenic chemicals, due to reasons of safety and minimizing the exposure of toxic substances.

In our experiment we wanted to alter only the part of the plasmid coding for the VirA receptor, while using a not harmful and thereby safe technique. Thus, our method of choice was inaccurate PCR that allows the exclusive variations of a distinct region of a plasmid, which is defined by the location of the upstream and downstream primers. This mutagenic method of PCR, called error-prone PCR (EP-PCR) has been described and improved a lot in scientific community (McCullum EO et al., 2010).

The basic principle of this technique uses the natural high infidelity of the taq DNA polymerase, which can even be increased by special changes in buffer conditions compared to standard PCR. These alterations may include the unequal distribution of dNTPs (5 mM purines, 25 mM pyrimidines) as well as an increased amount of MgCl2 and the addition of MnCl2. The total rate of base exchange can be adjusted by the number of PCR cycles, since mutations will accumulate during the exponential amplification of the sequence (Wilson DS and Keefe AD, 2000). The experimental conditions of the performed error-prone PCR are described in the section “protocols”.


Directed mutagenesis

After the identification of the 100 amino acids linker region responsible for VirA ligand binding (Compare VirA-Receptor) we compared this region with well characterized capsaicin receptors derived from animal model organisms (TRPV1). The conserved receptor region is shown in the figure beneath.

The species-specific sensitivity of TRPV1 can be ascribed to about eight amino acids in the vicinity of TM3 (Jordt an Julius 2002).

Figure 10: Molecular determinants of species-specific vanilloid sensitivity. Sequence alignment of rat (top), human (middle) and chicken (bottom) VR1 within the TM3-4 region is shown. Conserved residues are indicated by black background. The chimera V3/C contains a minimal segment of rat VR1 that is sufficient to confer vanilloid sensitivity (Jordt and Julius, 2002).

We further aligned the TM3 region of the TRPV1 receptor to the ligand binding region of the native VirA receptor from Agrobacterium by the use of the tool MUltiple Sequence Comparison by Log-Expectation (Muscle).

For detailed approach of directed mutagenesis for VirA_mut1 and VirA_mut2 click here


Screening system

Development of a high-troughput screening

The screening of randomly mutagenised genes for a desired function or application is always a very time-consuming procedure (Beaudry and Joyce, 1992). It requires a huge amount of material and might takes several months or even years to result in a promising new version of a gene (Hanczyc and Dorit, 2000). As we faced the challenge to modify the VirA receptor in only a few weeks we designed a strategy for a fast high-throughput screening by using subsequent steps of different read out systems and a strategy with two different plasmids.

In the first step after mutagenesis of virA it is necessary to separate thousands of transformants with minor or unwanted changes in the virA gene, from few bacteria that included interesting virA variants. Thus, we wanted to construct our system to lead in the expression of a kanamycin resistance after the induction of the VirA receptor, enabling the quick exclusion of all unwanted virA variants.

For that purpose a kanamycin resistance cassette should be set under control of the virB promoter, leading in the expression of aminoglycoside phosphotransferase (APH) that can inactivate kanamycin. The mode of inactivation is the transfer of the y-phosphate from ATP to the hydroxyl group at C3 of the antibiotic (Wright and Thompson, 1999). This phosphorylation results in the loss of binding capacity of the aminoglycoside to the 30S subunit of bacterial ribosomes, which would lead to inhibition of protein synthesis without the presence of the APH (Begg EJ and Barclay ML, 1995).

As indicated by the first results, the reporter genes under control of the virB promoter showed a slight but measureable expression without any induction of VirA with acetosyringone. This basal transcription resulted in the growth of bacteria without induction of VirA at normal working concentrations of kanamycin of 25 to 50 µg mL-1 (Sambrook J and Russell DW, 2001).

Concludingly, prior to the screening experiments it was necessary to adjust the concentration of kanamycin, which inhibits the growth of uninduced bacteria, while allowing bacteria to grow when an appropriate inductor was present and able to activate VirA. This analysis was performed using the method of determination of minimal inhibitory concentrations (MIC) as described below.


Determination of minimal inhibitory concentration (MIC) of kanamycin

There are several ways to investigate the susceptibility of bacteria to inhibiting drugs like antibiotics. Nevertheless, the result of all these tests is the amount of an assayed substance that inhibits visible growth of the bacteria, called the minimal inhibitory concentration (MIC). The most common way of determination is to grow bacteria in liquids with several concentrations of the inhibiting drug. This procedure is chosen mostly, since many different conditions can be measured at the same time by using microtiterplates (Wiegand I et al., 2008).

As we planned not to use the kanamycin in liquid culture but in LB-Agar, we chose to determine the MIC at the same conditions as the desired experiment. Therefore, we planned to construct E. coli inhabiting the native VirA/G signaling system and a kanamycin resistance read out and plated a small volume in different dilutions on LB-Agar without kanamycin. The grown colonies could then be transferred to agar plates with rising concentrations of kanamycin using replica plating. By counting the colonies it should be possible to calculate the percentage of colonies that could withstand each kanamycin concentration. This experiment should be carried out with and without acetosyringone to determine a kanamycin concentration induced E. coli could withstand, while the same population of bacteria dies without the presence of acetosyringone.


Primary selection of virA variants with novel binding properties

After the determination of the MIC the screening for virA variants with new binding properties could be started. The aim of this screening is to find versions of virA that can be induced by one of the tested substances capsaicin, homovanillic acid, dopamine and 3-O methyldopamine.

For that purpose one should transform the mutagenised variants of virA to E. coli and plate the bacteria on LB-agar with the determined kanamycin concentration. At the same time a mixture of all mentioned substances should be present in the agar. All bacteria including a virA variant that is activated by at least one of the substances will grow on the selective agar, since it expresses the kanamycin resistance. With this step it is thereby possible to select thousands of bacteria with unwanted versions of virA from few individuals with wanted binding properties.

At this point it must be mentioned that some grown colonies might still be non-induced and false positive results. As the virA gene has been randomly changed before, it is possible that some variants occur where the receptor is always active. This would lead to a constitutive expression of the reporter gene and thereby a high level of kanamycin resistance. To exclude those false positive clones, the bacteria should be tested whether they are only resistance to the MIC of kanamycin when one of the tested substances is present. Every colony that can withstand the high kanamycin concentration without any inductor includes a constitutive version of virA and should be discarded in further analysis.


Quantitative analysis of virA variants after induction with novel substances

Should we find some bacteria that respond to the presence of the tested substances (capsaicin, homovanillic acid, dopamine and 3-O methyldopamine) by growing on the MIC of kanamycin, it is desirable to quantify the induction. For that purpose it is appropriate to change the read out system from kanamycin resistence to luciferase expression. This complex and time consuming task can easily be achieved without any cloning step, when using the advantage of our two plasmid system.

After primary selection each bacteria includes two plasmids with different origins of replication (oris). The plasmid with the virA is in a common pSB1AT3 backbone with a ColE1 ori. Contrary to that the read out plasmid with KanR has a special ori, named R6K, which can only amplify in E. coli strains that express the gene pir to produce the so called Pir protein. Most of the strains used in laboratory are pir- but few (e.g EC100D) are pir+ (Bowers et al., 2007).

The setup of the different oris was chosen to separate both plamids at this experimental stage. To change the read out system from KanR to luciferase, one just needs to perform two transformations and isolations of plasmids. In the first step plasmids are isolated from colonies with positive binding properties to one of the tested substances. This mixture of plasmids with ColE1 and R6K oris is then transformed to a pir- strain (e.g. TOP10). In the following only the plasmid with ColE1 ori will be amplified during the growth of the transformants, leading to pure plasmids with virA when plasmids are isolated for a second time. In the last step this isolated DNA can be transformed to bacteria including another read out plasmid (e.g. with luciferase).


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