RecET driven chromosomal gene targeting to generate a RecA deficient Escherichia colistrain for Cre mediated production of minicircle DNA
© Tolmachov et al; licensee BioMed Central Ltd. 2006
Received: 12 July 2005
Accepted: 10 March 2006
Published: 10 March 2006
Minicircle DNA is the non-replicating product of intramolecular site-specific recombination within a bacterial minicircle producer plasmid. Minicircle DNA can be engineered to contain predominantly human sequences which have a low content of CpG dinucleotides and thus reduced immunotoxicity for humans, whilst the immunogenic bacterial origin and antibiotic resistance marker gene sequences are entirely removed by site-specific recombination. This property makes minicircle DNA an excellent vector for non-viral gene therapy. Large-scale production of minicircle DNA requires a bacterial strain expressing tightly controlled site-specific recombinase, such as Cre recombinase. As recombinant plasmids tend to be more stable in RecA-deficient strains, we aimed to construct a recA- bacterial strain for generation of minicircle vector DNA with less chance of unwanted deletions.
We describe here the construction of the RecA-deficient minicircle DNA producer Escherichia coli HB101Cre with a chromosomally located Cre recombinase gene under the tight control of the araC regulon. The Cre gene expression cassette was inserted into the chromosomal lacZ gene by creating transient homologous recombination proficiency in the recA- strain HB101 using plasmid-born recET genes and homology-mediated chromosomal "pop-in, pop-out" of the plasmid pBAD75Cre containing the Cre gene and a temperature sensitive replication origin. Favourably for the Cre gene placement, at the "pop-out" step, the observed frequency of RecET-led recombination between the proximal regions of homology was 10 times higher than between the distal regions. Using the minicircle producing plasmid pFIXluc containing mutant loxP66 and loxP71 sites, we isolated pure minicircle DNA from the obtained recA- producer strain HB101Cre. The minicircle DNA preparation consisted of monomeric and, unexpectedly, also multimeric minicircle DNA forms, all containing the hybrid loxP66/71 site 5'-TACCGTTCGT ATAATGTATG CTATACGAAC GGTA-3', which was previously shown to be an inefficient partner in Cre-mediated recombination.
Using transient RecET-driven recombination we inserted a single copy of the araC controlled Cre gene into the lacZ gene on the chromosome of E. coli recA- strain HB101. The resultant recA- minicircle DNA producer strain HB101Cre was used to obtain pure minicircle DNA, consisting of monomeric and multimeric minicircle forms. The obtained recA- minicircle DNA producer strain is expected to decrease the risk of undesired deletions within minicircle producer plasmids and, therefore, to improve production of the therapeutic minicircle vectors.
Plasmid DNA is recognised as foreign in vertebrate cells because of the abundance and the unmethylated status of CpG dinucleotides in the bacterial sequences. However, bacterially derived non-replicating minicircle DNA, which is created by removal of plasmid backbone DNA through intramolecular site-specific recombination within a minicircle producer plasmid, can be engineered to contain predominantly human sequences with a low incidence of immunostimulatory CpG-containing motifs . Therefore, minicircle DNA is an excellent vector for non-viral gene therapy, where a robust immune response can interfere with gene delivery (reviewed in ). Large-scale production of minicircle DNA requires a bacterial strain containing a tightly controlled gene for site-specific recombinase, which can be expressed for production of the non-replicating minicircle after the bacterial culture harbouring the minicircle producer plasmid reaches the stationary growth phase. Previously we described the generation of a recA+ Escherichia coli strain, MM219Cre, containing the chromosomally located Cre recombinase gene under the tight control of the araC regulon . A single copy of the Cre gene ensures an extremely low leakage level of Cre recombinase expression under repression conditions. Untimely Cre recombinase expression during expansion of bacterial culture can cause maintenance instability of the minicircle producer plasmids and their premature dissociation into the minicircle and the miniplasmid recombination products with the subsequent loss of the non-replicating minicircle .
Low mutation load is of utmost importance in the production of DNA for human gene therapy protocols. RecA-deficient bacterial strains are often advantageous for production of plasmids with eukaryotic DNA sequences because undesirable spontaneous deletion mutations tend to occur with a lower frequency in the RecA-deficient background [5–7]. Therefore, we undertook to construct a RecA-deficient single-copy Cre gene expression system for production of the minicircle vector DNA. To insert the Cre gene into the bacterial chromosome we designed a version of the technique for gene placement, which relies on homology-mediated "pop-in, pop-out" of a plasmid with a temperature sensitive mutation in the pSC101 replication origin . We employed a portable plasmid-born RecET recombination module  to create transient homologous recombination proficiency in the recA- E. coli strain HB101, thus enabling use of "homology arms" to target an insertion of an expression cassette for the araC controlled Cre gene into the chromosomal lacZ gene.
Integration ("pop-in") of plasmid pBAD75Cre into the genome of E. coliHB101
Expression of the recET genes was induced by L-arabinose. Subsequent plating of 2 × 104 HB101 cells harbouring both pBAD75Cre and pGETrec on LB agar containing X-gal, IPTG, Cm and Ap at 44°C enabled us to isolate 10 white LacZ- clones containing an insertion ("pop-in") of the entire pBAD75Cre plasmid in the bacterial lacZ gene (Figure 1B).
To compare the details of our RecET-driven Cre gene placement procedure to a RecA-driven gene placement protocol described by Hamilton et al. , we introduced the targeting plasmid pBAD75Cre into recA+ E. coli strain TB1 harbouring plasmid pUC19. The chromosomal integration target in this case was the lacZΔM15 gene expressing a truncated version of β-galactosidase protein, which attained full enzymatic activity in the presence of pUC19 expressing complementary α-peptide. After plating 1 × 104 cells on X-gal indicator plates at 44°C we isolated 7 white LacZ- "pop-in" clones (see Additional file 1).
Insertions of the oripSC101-plasmids in the bacterial genome often result in poor growth of the bacteria, thus, simplifying subsequent selection of the clones that underwent excision of the plasmid backbone . We duly observed reduction in colony size of the obtained pBAD75Cre insertion derivatives of the recA+ strain E. coli TB1. However, the colony size of the pBAD75Cre insertion derivatives of the recA- strain E. coli HB101 remained unchanged compared to the original strain HB101. Our direct measurements of OD600 of the growing liquid bacterial cultures confirmed lack of significant differences between the growth rates of the HB101-based strains.
Excision ("pop-out") of the pBAD75Cre plasmid backbone
To avoid the potential problem of spurious recombinants, the 10 LacZ- insertion clones were pooled. The pool was passaged 4 times in LB medium supplemented with Ap, Cm, L-arabinose at 30°C to encourage plasmid excision ("pop-out") from the bacterial chromosome. The desired excision of the deletion derivative pBAD75Δ leaves the araC-Cre cassette on the chromosome whilst excision of the entire pBAD75Cre plasmid reconstitutes the intact chromosomal lacZ gene (Figure 1C). To confirm the presence of the LacZ+ class of recombinants that underwent excision of the entire pBAD75Cre plasmid, we plated the passaged cells to produce individual colonies on LB agar supplemented with Cm, Ap, X-gal and IPTG at 30°C. Five LacZ+ blue clones were found among 7511 analysed colonies (6.7 × 10-4).
The obtained Cm-sensitive subclones were checked for their LacZ phenotype on the indicator plates containing LB agar supplemented with IPTG and X-gal, and for the presence of the Cre gene by PCR (Figure 2B). On this occasion we did not find any LacZ+ subclones in which the entire plasmid has been excised and the lacZ gene resealed. All tested Cm-sensitive sublcones were LacZ- suggesting an insertion in the chromosomal lacZ gene. However, according to PCR analysis, 5 partially Cm-sensitive clones produced only Cre-positive subclones, 4 clones produced a mixture of Cre-positive and Cre-negative subclones and 1 clone gave only Cre-negative subclones. In total, among 96 tested subclones the Cre gene was lost in 32 (33%). LacZ- Cre- segregants were probably due to plasmid excisions via illegitimate recombination resulting in deletions.
A similar plasmid "pop-out" strategy was followed with the pBAD75 integration derivatives of the control recA+ E. coli strain TB1 (see Additional file 2). Markedly higher frequencies of excisant recovery were obtained. LacZ+ excisants constituted 2.5 × 10-2 of the passaged cell population (31 out of 1245). Screening at 44°C allowed to find 21 partially Cm sensitive clones out of 500 (4.2 × 10-2), 9 of which were proved to be LacZ+ Cre-negative, 11 clones were LacZ- Cre-positive and 1 clone produced a mixture of LacZ+ Cre-, LacZ- Cre- and LacZ- Cre+ subclones.
The inserted araC-Cre expression cassette and the entire bacterial lacZ::araC-Cre locus were amplified by long-range PCR, thus, proving successful insertion of the araC-Cre cassette into the lacZ gene of the strain HB101 (Figure 3BC). The wild type sequence of the inserted Cre gene was also confirmed (see Additional file 4).
The resultant strain HB101Cre pFIXluc was cured of the pFIXluc plasmid to allow unimpeded introduction of other minicircle producing plasmids. Finally, the RecA- phenotype of the new strain HB101Cre was confirmed by the UV-sensitivity test .
Production and isolation of minicircle DNA in recA-bacterial strain HB101Cre
The minicircle DNA is an attractive "stealth vector" for human gene therapy because it can be engineered to consist virtually entirely of mammalian sequences with low occurrence of CpG motifs that are recognised as a potent signal by the innate immune system. Plasmid DNA for human use is normally produced in recA- bacterial strains  because the rate of deletion mutations in recombinant plasmids in RecA-deficient environment is often lower than in RecA-proficient environment [5, 6]. We describe here an upgrade of our Cre-mediated system for minicircle DNA production  to a recA- status.
The described method of chromosomal gene placement is an adaptation of the method of Hamilton et al.  to the situation where the bacterial strain to be manipulated is RecA-deficient. The major technical difficulty both in the original version of the procedure and its adaptation in our work is negative selection of bacterial clones with resolved plasmid-chromosome co-integrates. Clearly, any selective pressure towards clones with popped-out plasmids simplifies the required screening. Fortuitously for their experiments, Hamilton et al observed, "this method works because the presence of the pSC101 replication origin in the E. coli chromosome dramatically reduced the growth rate of the cell; pSC101 co-integrates grew very poorly at 30°C on L-agar containing chloramphenicol". In our experiments we confirmed this crucial growth retardation phenomenon for the control recA+ strain E. coli TB1 and pSC101-based plasmid pBAD75Cre. In this case we were able to obtain plasmid pop-out clones with a comfortable frequency of 4.2 × 10-2. However, we did not detect any growth retardation for the bacterial clones harbouring co-integrates of the recA- E. coli HB101 chromosome and pBAD75Cre. Still we were able to recover plasmid pop-out clones, although with a lower frequency of 7.4 × 10-3.
Our intention to generate a bacterial strain for production of therapeutic minicircle DNA limited the scope of available strategies to achieve the desired combination of a chromosomally located Cre gene and the recA mutation. For example, the required Cre-expressing recA- strain could have been created by the exchange of the recA+ allele for a recA- allele in the previously constructed Cre-expressing strain MM219Cre  through generalised transduction by the bacteriophages P1 or T4GT7 from a srl::Tn10 recA strain . However, the presence of Tn10 in the minicircle DNA producer strain is undesirable since some human therapeutic genes contain potential mutational hotspots for this element (5'-GCTNAGC-3' ). Thus, cDNA for the human CFTR gene, the therapeutic gene for cystic fibrosis, has one hotspot consensus sequence and cDNA for the human dystrophin gene, the therapeutic gene for DMD, has three such potential hotspots. Similarly, we wished to avoid methods of chromosomal gene placement that directly employ insertions by transposons, bacteriophage Mu or IS-elements . The remaining options for construction of the new recA- strain included hijacking of the site-specific chromosomal integration systems of the bacteriophages λ, φ80 and P2, and also homology-mediated gene targeting enabled by introduction of RecA , RecET or Redαβ-expressing plasmids.
Here we describe the construction of the recA- minicircle DNA producer E. coli HB101Cre using transient homologous recombination proficiency created by the plasmid-born recET genes and homology-mediated chromosomal "pop-in, pop-out" of a plasmid with a temperature sensitive replication origin, pBAD75Cre.
It is not clear why the observed frequency of recombination leading to the excision of the entire pBAD75Cre plasmid from the lacZ gene (5 LacZ+ excisants out of 7511 colonies, 6.7 × 10-4) was 10 times lower than the frequency of recombination leading to the excision of the plasmid backbone pBAD75Δ, which left the araC-Cre expression cassette in the bacterial chromosome (9 LacZ- Cre-positive individual excisants out of 1355 colonies, 6.6 × 10-3). Using homologous recombination driven by the plasmid-expressed RecA protein, some authors observed a strong bias towards one or the other type of "pop-out" recombination among individual plasmid insertions but did not notice any common predisposition among all the plasmid insertions . We did not observe any significant disproportion between recombination classes in RecA-driven plasmid pop-out in the control strain TB1. Screening of 500 colonies yielded 11 LacZ+ Cre- (2.2 × 10-2) and 9 LacZ- Cre+ clones (1.8 × 10-2). Therefore, we hypothesise that predominant recombination between two proximal regions of homology (compared to recombination between two distal regions of homology) can be a feature of RecET-driven recombination. If this is indeed so, this property of RecET recombination is extremely advantageous for the selection of insertions into the bacterial chromosome or large plasmids after the "pop-out" step of the "pop-in, pop-out" scheme of recombinogenic engineering (, reviewed in ).
Using the new recA- strain HB101Cre we obtained a yield of 248 ± 25 μg of pure minicircle DNA per half a litre of bacterial culture and observed formation of minicircle multimers.
The recA13 mutation in the HB101Cre strain inhibits homologous recombination. At the same time, the hybrid loxP66/71 site, which is present on the minicircle mFIXluc, contains 10 nucleotide substitutions in the 34 bp sequence of the wild type loxP site and is known to be a poor substrate for Cre recombination . Therefore, formation of the minicircle multimers in the HB101Cre bacteria, containing the wild type Cre gene, does not fit well both the homologous recombination mechanism of multimerisation and the Cre-mediated recombination mechanism of multimerisation .
Formation of the loxP66/71 minicircle multimers in a recA- strain can be attributed to induction of the resident chromosomal recET genes  or induction of an additional recA-independent pathway, such as discovered recently . Recombinant plasmids are known to change host gene expression patterns in E. coli  and so, the minicirlcle producer plasmid pFIXluc might have been the trigger for induction of the endogenous recombination genes in our bacterial strain HB101Cre.
There are no data to suggest that the multimeric minicircle forms are inferior to the minicircle monomer in terms of gene delivery to mammalian cells. In fact, the multimeric minicircle forms might be of some benefit for higher levels of transient transgene expression [23, 24].
In summary, we inserted the araC-Cre gene expression cassette into the chromosomal lacZ gene of E. coli recA- strain HB101 by creating transient homologous recombination proficiency using the plasmid-born recET genes and employing homology-mediated chromosomal "pop-in, pop-out" of a Cre plasmid pBAD75Cre with a temperature sensitive replication origin. Favourably for the Cre gene placement, at the "pop-out" step, the observed frequency of RecET-led recombination between the proximal homology regions was 10 times higher than that between the distal homology regions. We isolated pure minicircle DNA, which was generated in RecA-deficient background, and showed the presence of the multimeric minicircle forms containing mutant loxP66/71 site 5'-TACCGTTCGT ATAATGTATG CTATACGAAC GGTA-3', known to be a poor substrate for Cre-recombinase. Therefore, we question the view that Cre-mediated recombination is the dominant mechanism for formation of minicircle multimers. The obtained recA- minicircle DNA producer strain is expected to decrease the risk of undesired deletions within minicircle producer plasmids and, therefore, to improve production of the therapeutic minicircle vectors.
E. colistrains and bacterial culture conditions
The following E. coli strains were used:
HB101 F- Δ(gpt-proA)62 leuB6 glnV44 ara-14 galK2 lacY1 Δ(mcrC-mrr) rpsL20(Str R ) xyl-5 mtl-1 recA13 (Promega);
HB101Cre F- Δ(gpt-proA)62 leuB6 glnV44 ara-14 galK2 lacZ::(araC Cre) lacY1 Δ(mcrC-mrr) rpsL20(Str R ) xyl-5 mtl-1 recA13 (this work);
MM219Cre F- endA1 hsdR17(r K -m K +) glnV44 thi-1 relA1? rfbD1? spoT1? lacZ::(araC Cre) ;
TB1 F- ara Δ(lac-proAB) [φ 80dlac:: Δ(lacZ)M15] rpsL(Str R ) thi hsdR (New England Biolabs),
TB1Cre F- ara Δ(lac-proAB) [φ 80dlac::(araC-Cre) Δ(lacZ)M15] rpsL(Str R ) thi hsdR (this work).
The bacteria were cultured as described before . A lacY mutation in the strain E. coli HB101 results in a poor transport of the chromogenic substrate X-gal into the cells. Thus, for reliable identification of the LacZ+ phenotype of the bacterial colonies, the sparsely seeded LB-agar indicator plates supplemented with X-gal and IPTG were incubated overnight at 37°C and then for additional 2–3 days at room temperature for the blue colour of the colonies to mature.
Plasmids, oligonucleotides, long distance PCR and sequencing
Minicircle producer plasmid pFIXluc and the Cre gene containing plasmid pBAD75Cre were described previously . Plasmid pGETrec  contains a truncated recE gene, the recT gene and the bacteriophage λ Redγ gene under control of the araC regulon.
Oligonucleotides CRF 5'-TGCCACGACCAAGTGACAGC AATG-3' and CRR 5'-CTCTACACCTGCGGTGCTAACCAGCG-3' were used to screen bacterial colonies for the presence of the Cre gene by PCR. Primers AR1F 5'-TTCCCAGCGG TCGGTCGATA AAAAAATCGA-3' and RE2R 5'-CAAGTACCCG GCAGTGGAAA GCAGTTCCTA-3' were used to amplify the 680 bp segment from the plasmid pGETrec containing pBAD promoter and a portion of the recE gene. The PCR in this case was led by Taq polymerase starting with 2 min at 93°C, followed with 30 cycles of 30 s at 93°C, 1 min at 58°C, 1 min at 72°C; and concluding with 7 min at 72°C.
The "Expand Long Template PCR" kit (Roche) and primers LACZ-FA 5'-CATGGTCAGGTCATGGATGAGCAGACG-3' and LACZ2 5'-GCGCCACCATCCAGTGCAGGAGCTCG-3' homologous to the lacZ gene were used to amplify the 3094 bp fragment with the araC-Cre insert in the lacZ gene of the HB101Cre and TB1Cre strains. The Cre gene within the amplified 3094 bp fragment was sequenced from both strands using primers ARAC-SEQ 5'-GATGGGCATT AAACGAGTAT CCCGGCAG-3', OPP-CRE 5'-GGGCACACAC TACTTGAAGC ACTC-3', CRF and CRR (Advanced Biotechnology Centre, Imperial College London). The same long distance PCR kit and primers LACZ-START 5'-ATGACCATGA TTACGGATTC ACTGGCCGTC GTTTT-3' and LACZ-END 5'-TTATTTTTGA CACCAGACCA ACTGGTAATG GTAGC-3' were used to amplify the entire 5219 bp lacZ::(araC Cre) genome segment of the HB101Cre strain. Long distance PCR algorithm was: 2 min at 93°C; 10 cycles of 10 s at 93°C, 30 s at 65°C and 4 min at 68°C; then 20 cycles at 10 s at 93°C, 30 s at 65°C, 4 min at 68°C with 20 s extension of the last (elongation) step in each new cycle; then 7 min at 68°C.
Primers SEQ-CMV 5'-ACATGGCGGT CATATTGGAC ATGAG-3' and SEQ-D 5'-CAATAAACAA GTTAACAACA ACAAT-3' were employed for the automated sequencing of both strands of the hybrid loxP66/71 site and its flanking regions in the minicircle mFIXluc.
Minicircle DNA production
Induction of the Cre gene using L-arabinose, extraction of supercoiled DNA and minicircle DNA purification were performed essentially according to the previously described "Technique 2"  with two protocol changes. Firstly, expansion of the bacterial culture, which was destined for Cre induction, was performed at 32°C instead of 37°C, because this lower temperature was shown to support more consistent minicircle DNA yields (Thorsten Trimbuch, personal communication). Secondly, to improve resolution of the minicircle producer plasmid by the induced Cre recombinase in HB101Cre cells, incubation of bacteria with L-arabinose was performed for 18 hrs instead of 4–6 hrs (at 37°C, as described previously). Closed circular DNA was extracted by the alkaline method and digested with PvuII to fragment all non-minicircle products of Cre recombination. Finally, the supercoiled minicircle DNA was isolated using fractionation in CsCl-propidium iodide density gradient .
List of abbreviations
cystic fibrosis transmembrane conductance regulator
Duchenne muscular dystrophy
optical density measured at 600 nm
polymerase chain reaction
polymerase chain reaction
We are grateful to Dr. Panos Ioannou for the plasmid pGETrec. We thank Thorsten Trimbuch for sharing his fortuitous observation on the optimal temperature regimen for the minicircle DNA production. This work was supported by a grant from the UK Medical Research Council.
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