DNA Engineering

A protein array containing different antigens specific for distinct diseases is one of the main parts of the DiaCHIP. To obtain all the DNA constructs requires a lot of cloning, especially because conventional protein expression and expression using a cell-free system are based on different plasmid backbones.
To reduce this ambitious task to a minimum of effort, we elaborated a well-structured cloning strategy including a self-designed multiple cloning site. This site was incorporated into the commercial expression vector pET22b+ resulting in pET_iGEM.
We soon realized that efficient protein expression is a problem many iGEM Teams around the world may be facing during their projects. Therefore, we provide the Registry with pOP, an expression vector suitable for iGEM standard cloning procedures.
To help future iGEM Teams with their decision, which cloning method to use, we compared and contrasted classical cloning and Gibson Assembly in a short review.

Our Cloning Site

Figure 1: Self-designed cloning site. Our cloning site containing the restriction sites Acc65I, BamHI, HindIII and AflII, that are assembled in a way that facilitates exchange of tags without getting a frame-shift.

Design of pET_iGEM

Figure 2: pIG15_001. pSB1C3 backbone containing an altered cloning site in the middle of an expression cassette for improved assembly of protein coding sequences with different tags (N- or C-terminal), which avoids the formation of frameshifts. Important parts for overexpression of proteins in E. coli were added inside the RFC[10].

For protein expression, we designed two vectors based on the submission backbone pSB1C3. pIG15_001 (figure 2) was supposed to be adapted for inducible protein overexpression in E. coli. Therefore, we inserted main features derived from the commercial expression vector pET22b+ between the BioBrick pre- and suffix of pSB1C3. These include a T7 promoter and terminator, a ribosomal binding site, the self-designed cloning site and a lacI expression cassette. Additionally, a pelB signal sequence for periplasmic translocation was added 5’ to the cloning site.

Figure 3: pIG15_104. For cell-free expression the pSB1C3 backbone was altered similarly, but without a pelB secretion signal or lacI coding sequence and with a CMV promoter instead of a T7 promoter.In this case, the coding sequence for TurboYFP is inserted.

The vector for cell-free expression (pIG15_104) was designed analogously, but lacking the lacI expression cassette and the signal sequence. The T7 promoter and terminator were exchanged by a CMV promoter and a WPRE terminator region for secretion into the medium. In figure 3, the vector is shown with an inserted coding sequence for TurboYFP.

Unfortunately, after the first expression experiment in E. coli, we realized that the yields of protein expression are not sufficient for our purposes. Instead of wasting time trying to optimize our own expression vector, we went on using the original vector and modified the cloning site to fit our requirements. The original vector pET22b+ and the modified version pET_iGEM are compared in figure 4.

Using an adapted commercial expression vector finally resulted in sufficiently high protein yields. The advantages of expression vectors like pET22b+ in contrast to cloning vectors like pSB1C3 are discussed in detail on the introduction page for pOP. This is a plasmid backbone we submitted to the iGEM Registry that is optimized for protein overexpression purposes and fully compatible with iGEM idempotent cloning standards of RFC[25].
The backbone for cell-free expression was not changed because a PCR product of the expression cassette serves as a template for the actual expression purpose making the vector it is assembled on irrelevant. Using a high-copy plasmid such as pSB1C3 rather simplifies cloning efforts.

Figure 4: Comparison of pET_iGEM and pET22b+. The two vectors differ in the cloning site that contains only four restriction sites in pET_iGEM (Acc65I, BamHI, HindIII, AflII) compared to the more complex multiple cloning site of the original pET22b+ (BamHI, EcoRI, SacI, SalI, HindIII, NotI, AvaI, XhoI). The 6xHis-Tag from pET22b+ was also removed to enable easy tag-exchanges with our system.

Detailed Cloning Strategy

As mentioned before, we established a cloning strategy that is easy to handle for a team of researchers working together on the same project. It facilitates easy exchange of tags for custom purposes. All our cloning efforts began with either pET_iGEM (the modified version of pET22b+) for E. coli-based protein expression or pIG15_104, where the expression site derived from pET22b+ was inserted into pSB1C3.

The Basic Constructs (Protein Purification Using E. coli)

pET22b+ with our cloning site (pET_iGEM)

To modify the multiple cloning site of pET22b+ for our purposes, we performed a Gibson Assembly with only one fragment. Therefore, we designed primers for the amplification of the whole plasmid, except the MCS. The cloning site we designed ourselves was part of the primer extension.

pET_iGEM with His-tagged Herpes simplex antigen (pET_803)

To insert the very small but commonly used His-tag, we again used Gibson Assembly because classical cloning of such small parts can be a challenging task. The respective primers were designed for amplification of antigen 8 (Herpes Simplex Virus Type 1, glycoprotein G1) to combine the insertion of the tag and an antigen. While the forward primer was a regular Gibson primer, the reverse primer additionally contained the sequence of a 10xHis-tag. After amplification, the part was inserted into the BamHI and AflII digested backbone pET_iGEM resulting in the first antigen with N-terminal His-tag.

pET_iGEM with Spy-tagged Herpes simplex antigen (pET_804)

Another tag we wanted to use for immobilization of the antigens on the surface is the SpyTag. This part of 39 bp length was inserted into pET_iGEM analogous to the 10xHis-tag. The only difference was that the forward primer for amplification of antigen 8 included a standard 6xHis-tag, which enables the purification of the protein. Consistent with our cloning strategy, the amplified part was inserted between Acc65I and AflII as it contains an N-terminal as well as a C-terminal tag. BamHI and HindIII restriction sites were retained flanking the antigen, making it freely exchangeable.

pET_iGEM with Herpes simplex antigen with HaloTag (pET_805)

The only tag we used that was not inserted via Gibson Assembly was the HaloTag. With a length of about 900 bp, classical cloning of this part was no trouble. The HaloTag exists in two variants, one being optimized for C-terminal tagging of the protein, the other for N-terminal tagging. As the tag we had access to was the C-terminal one, the SpyTag in pET_804 was exchanged using the restriction sites HindIII and AflII resulting in pET_805.

Figure 1: Detailed view of our self-designed cloning site. Our cloning site containing the restriction sites Acc65I, BamHI, HindIII and AflII, with initiation site and termination site. Different antigen coding sequences or tags can be easily exchanged. We used this system in our constructs for protein expression in E. coli as well as in constructs we used for cell-free expression.

Tagged Constructs (Protein Purification Using E. coli)

A tag-system minimizes unspecific binding of proteins to the chip surface, therefore we tested many different tag systems.

His-tag

Every antigen was genetically fused to a C-terminal 10xHis-tag, which could be used for its immobilization on the surface as well as for its purification. The basic construct for this purpose was pET_803. The Herpes Simplex Virus derived antigen, which was the very first we finished cloning, had to be excised by restriction with BamHI and HindIII. Thus, all the other antigens digested in the same way could be ligated into this backbone.

SpyTag

Another tag for surface immobilization of the antigen is the SpyTag. To enable protein purification via Ni-NTA columns, proteins fused to the SpyTag were additionally fused to a C-terminal 6xHis-tag. The basic vector for cloning these constructs was pET_804. Excision of the Herpes Simplex Virus derived antigen and insertion of other antigens was performed analogous to the antigen exchange in His-tag constructs.

HaloTag

As a second covalent tag-system for immobilization of the antigens on the surface we used the HaloTag, which specifically binds to a chloroalkane surface. Using our own cloning strategy, the HaloTag could easily be inserted between HindIII and AflII, using pET_803 as basis. Cloning of the HaloTag into pET_803 leads to a new vector, pET_805. This vector is then used to substitute the antigens. As in the SpyTag construct, this new vector contains a C-terminal 6xHis-tag for purification of the antigens.

Cell-Free Backbone

As described above we decided to use the pSB1C3 standard vector as backbone for our cell-free expression constructs. Inserted between the RFC 10 prefix and suffix is our own cloning site, containing the following restriction sites: Acc65I, BamHI, HindIII and AflII. We included a T7 promoter and a ribosomal binding site between the RFC 10 prefix and the Acc65I restriction site. A stop codon cassette and a T7 terminator were inserted between the AflII restriction site and the RFC 10 suffix. These similarities to the expression vector facilitate the easy exchange of fragments between the standard expression vector and the cell-free expression vector. Using our cloning site it is rather simple to exchange different tag-combinations. The advantage of the pSB1C3 backbone is the high copy origin, allowing a rapid multiplication and easy cloning. For the cell-free expression itself the vector backbone is dispensable as only the part amplified via PCR between the prefix and the suffix is mandatory for cell-free expression.

The Basic Constructs (Cell-Free Expression)

Vector for cell-free expression with tYFP with SpyTag (pIG15_104)

For the first basic construct we ordered a gBlock from IDT containing the T7 promoter, ribosomal binding site, our cloning site and the T7 terminator with adjoining stop codon cassette. Between BamHI and HindIII the coding sequence for tYFP and between HindIII and AflII the SpyTag sequence was inserted. This gBlock was then inserted into the pJET1.2 vector. Afterwards, it was digested out of pJET1.2 and classically cloned into the pSB1C3 backbone resulting in the first basic construct for cell-free expression. We inserted tYFP as default fragment into the cell-free expression backbone because we already had some anti-tYFP antibody available. Hence, first measurements for analyzing the binding of anti-tYFP to tYFP could be performed as soon as the basic construct was finished. Besides, tYFP could be used as reporter. Using BamHI and HindIII restriction sites tYFP could be excised and replaced by antigen sequences analogous to the cloning system used for the expression vector.

Vector for cell-free expression with tYFP with HaloTag (pIG15_105)

Using the HindIII and AflII restriction sites, the SpyTag sequence was excised from pIG15_104. For our second covalent tag system we inserted the sequence for the HaloTag via classical cloning and thereby producing our next basic construct for cell-free expression, pIG15_105. This backbone again contains tYFP as default insert, this time with a C-terminal HaloTag.
Using identical cloning strategies as with the first basic construct (pIG15_104) all antigen sequences could be inserted into this vector using BamHI and HindIII.