Serine integrases act to recombine attP and attB sites to integrate DNA and form product sites attL and attR in a highly unidirectional manner; this means that when only the integrase is present, no recombination occurs between attL and attR, and the reaction favours only integration. The reverse reaction (attL recombination with attR) proceeds only in the added presence of the integrase’s RDF. It is thought that RDF proteins bind to integrase subunits to end inhibition of the attL/attR reaction, and this integrase-RDF complex catalyses attL/attR recombination. This reverse recombination reaction usually requires the combination of an integrase and its own RDF. However, it has been suggested that some integrases may be activated by RDFs of other integrases, due to the closely related nature and presence of conserved sequences in these RDFs.
attL/attR substrate to determine to what extent opposite RDFs are able to facilitate this reaction compared to native RDFs. These reactions were first tested in vitro using a recombination assay similar to the one used in the integrase activity assay in Chapter 3 (see Section 3.4.1). Substrate plasmids in this case feature attL and attR sites and are designed for in vitro reactions; pFM52, featuring attL and attR sites for φC31 integrase and pFM139, featuring attL and attR sites for TG1 integrase. These plasmids are detailed in Methods Section 2.5. A diagram describing this in vitro recombination assay is shown in Figure 5.1.
For each integrase, four reactions were set up: 1) no integrase, replaced by buffer IDB as negative blank; 2) integrase only; 3) integrase plus own RDF; 4) integrase plus non-native RDF. Recombination assay reactions were first set up by pre-incubating the integrase and RDF for 15 minutes at room temperature before adding the plasmid substrate (a full protocol is described in Methods Section 2.20). Initial reactions were run for either 30 minutes or 3 hours to determine whether incubation time had an effect on recombination
efficiency. However, when results indicated that there was no discernible difference in result with a longer incubation, 30 minute incubation periods were used for all consequent reactions. Once reactions were completed, NruI was added to create linear products and DNA was run on an agarose gel.
From photos of these agarose gels, relative DNA concentrations of the
products of each reaction were quantified using ImageJ (see Methods Section 2.23). This method gives the relative percentage of the DNA concentration of each band in each lane. Unrecombined DNA is seen as two bands at the top and bottom of each lane, while recombination results in two bands between these unrecombined bands (see Figures 5.1, 5.2 & 5.3 for more detail).
Figures 5.2 and 5.3 show the agarose gels of the above in vitro recombination assays carried out with φC31 integrase and gp3 or gp25 (Figure 5.2), and TG1 integrase with gp25 or gp3 (Figure 5.3), alongside graphs illustrating the recombination levels quantified from each gel lane according to Methods
Figure 5.1: In vitro assay for attL x attR recombination by φC31 integrase (pFM52, top) and TG1 integrase (pFM139, bottom). When incubated with purified integrase and RDF in vitro, attL x attR recombination results in two circular products featuring an attP or attB site, which are both
Figure 5.2: Agarose gel showing DNA from the in vitro attL x attR recombination assay of φC31 integrase with either native RDF gp3 or TG1 RDF gp25. The four lanes of the gel are as follows: 1) substrate pFM52 with IDB buffer as a negative control; 2) pFM52 with φC31 integrase only; 3) pFM52 with φC31 integrase incubated with gp3; 4) pFM52 with φC31 integrase incubated with gp25. Figures below the gel image correspond to the percentage of substrate DNA in the gel that was recombined or unrecombined, calculated with ImageJ (see Methods 2.23). The percentage of substrate DNA recombined in each reaction is represented graphically
Recombined (%) 3.866 6.822 72.888 39.137
Recombined (%) 4.555 9.306 72.359 11.237
Unrecombined (%) 95.445 90.694 27.641 88.763
Figure 5.3: Agarose gel showing DNA from the in vitro attL x attR recombination assay of TG1 integrase with either native RDF gp25 or φC31 RDF gp3. The four lanes of the gel are as follows: 1) substrate pFM139 with IDB buffer as a negative control; 2) pFM139 with TG1 integrase only; 3) pFM139 with TG1 integrase incubated with gp25; 4) pFM139 with TG1 integrase incubated with gp3. Figures below the gel image correspond to the percentage of substrate DNA in the gel that was recombined or unrecombined, calculated with ImageJ (see Methods 2.23). The
It would naturally be expected that only an integrase’s native RDF would be able to activate attL x attR recombination. However, results observed here show that TG1 gp25 is able to significantly activate φC31 integrase attL x attR recombination. The agarose gels of Figure 5.2 show that incubating φC31 integrase with gp25 (Figure 5.2, lane 4) produces a large amount of
recombination product, with 39% of the substrate DNA recombined according to digital quantification of the DNA bands. However, it should be noted that this recombination is less efficient than the natural gp3 activation of φC31 (Figure 5.2, lane 3), which recombined 73% of the substrate DNA.
Interestingly, the reverse does not appear to be true, as φC31 gp3 did not activate TG1 integrase attL x attR recombination at the same level (Figure 5.3, lane 4), with only 11% of the substrate plasmid recombined. This number is very close to the recombination level seen in the reaction containing only TG1 integrase without an RDF (9% recombination; Figure 5.3 lane 2). This demonstrates the low level of attL x attR recombination that TG1 integrase is capable of even in the absence of an RDF.