Homologous recombination in a mammalian plasmid

A DNA recombination-based approach to eliminate papillomavirus infection

At present, no treatments exist that effectively target and eliminate papillomaviruses (PVs) from infected cells or prevent its replication. We are employing a strategy to prevent virus replication in PV-infected cells through the conditional expression of the herpes simplex virus type 1 thymidine kinase (TK) gene. Expression of TK in this system is expected to be triggered by a homologous recombination event between the endogenous PV genome and a nonexpressing TK gene cassette. Recombination between these two DNAs is expected to change the nonexpressing cassette into a form that expresses TK. Various constructs were generated to express the TK in the above manner. Transfection of cell lines with a TK nonexpressing plasmid did not result in TK production due to alternative splicing and polyadenylation site selection. However, cotransfection of cell lines with PV plasmids along with the above TK construct containing short segments of PV sequences resulted in a recombination event that led to TK expression as shown by Northern and Western blot analyses. We also developed a TK expression cassette utilizing an adeno-associated virus (AAV) vector. Delivery of the cassette by AAV to PV-infected cells resulted in TK expression, and ganciclovir treatment resulted in efficient killing of these cells.

Long CTG.CAG repeat sequences markedly stimulate intramolecular recombination

Previous studies have shown that homologous recombination is a powerful mechanism for generation of massive instabilities of the myotonic dystrophy CTG.CAG sequences. However, the frequency of recombination between the CTG.CAG tracts has not been studied. Here we performed a systematic study on the frequency of recombination between these sequences using a genetic assay based on an intramolecular plasmid system in Escherichia coli. The rate of intramolecular recombination between long CTG.CAG tracts oriented as direct repeats was extraordinarily high; recombinants were found with a frequency exceeding 12%. Recombination occurred in both RecA(+) and RecA(-) cells but was approximately 2-11 times higher in the recombination proficient strain. Long CTG.CAG tracts recombined approximately 10 times more efficiently than non-repeating control sequences of similar length. The recombination frequency was 60-fold higher for a pair of (CTG.CAG)(165) tracts compared with a pair of (CTG.CAG)(17) sequences. The CTG.CAG sequences in orientation II (CTG repeats present on a lagging strand template) recombine approximately 2-4 times more efficiently than tracts of identical length in the opposite orientation relative to the origin of replication. This orientation effect implies the involvement of DNA replication in the intramolecular recombination between CTG.CAG sequences. Thus, long CTG.CAG tracts are hot spots for genetic recombination.

Gene targeting with a replication-defective adenovirus vector

Wide application of the gene-targeting technique has been hampered by its low level of efficiency. A replication-defective adenovirus vector was used for efficient delivery of donor DNA in order to bypass this problem. Homologous recombination was selected between a donor neo gene inserted in the adenovirus vector and a target mutant neo gene on a nuclear papillomavirus plasmid. These recombinant adenoviruses allowed gene transfer to 100% of the treated cells without impairing their viability. Homologous recombinants were obtained at a level of frequency much higher than that obtained by electroporation or a calcium phosphate procedure. The structure of the recombinants was analyzed in detail after recovery in an Escherichia coli strain. All of the recombinants examined had experienced a precise correction of the mutant neo gene. Some of them had a nonhomologous rearrangement of their sequences as well. One type of nonhomologous recombination took place at the end of the donor-target homology. The vector adenovirus DNA was inserted into some of the products obtained at a high multiplicity of infection. The insertion was at the end of the donor-target homology with a concomitant insertion of a 10-bp-long filler sequence in one of the recombinants. The possible relationship between these rearrangements and the homologous recombination is discussed. These results demonstrate the applicability of adenovirus-mediated gene delivery in gene targeting and gene therapy.

Homology-associated nonhomologous recombination in mammalian gene targeting

Nonhomologous (illegitimate) recombination of DNA underlies many changes in the genome. It involves no or little homology between recombining DNAs and has been considered unrelated with homologous recombination, which requires long homology. In mouse cells, however, we found recombination products whose sequences suggest that homologous interaction between DNAs caused nonhomologous recombination with another DNA. The intermediates of homologous recombination were apparently trapped at various stages and shunted to nonhomologous recombination. In one product, the nonhomologous recombination disrupted gene conversion. In another, it took place exactly at the end of long homology shared between two DNAs. This finding explains why gene targeting needs long uninterrupted homology and why mammalian homologous recombination is often nonconservative. We discuss possible consequences and roles of this type of homology-driven gene destruction mechanism.

Gene conversion in the Escherichia coli RecF pathway: a successive half crossing-over model

Gene conversion--apparently non-reciprocal transfer of sequence information between homologous DNA sequences--has been reported in various organisms. Frequent association of gene conversion with reciprocal exchange (crossing-over) of the flanking sequences in meiosis has formed the basis of the current view that gene conversion reflects events at the site of interaction during homologous recombination. In order to analyze mechanisms of gene conversion and homologous recombination in an Escherichia coli strain with an active RecF pathway (recBC sbcBC), we first established in cells of this strain a plasmid carrying two mutant neo genes, each deleted for a different gene segment, in inverted orientation. We then selected kanamycin-resistant plasmids that had reconstituted an intact neo+ gene by homologous recombination. We found that all the neo+ plasmids from these clones belonged to the gene-conversion type in the sense that they carried one neo+ gene and retained one of the mutant neo genes. This apparent gene conversion was, however, only very rarely accompanied by apparent crossing-over of the flanking sequences. This is in contrast to the case in a rec+ strain or in a strain with an active RecE pathway (recBC sbcA). Our further analyses, especially comparisons with apparent gene conversion in the rec+ strain, led us to propose a mechanism for this biased gene conversion. This "successive half crossing-over model" proposes that the elementary recombinational process is half crossing-over in the sense that it generates only one recombinant DNA duplex molecule, and leaves one or two free end(s), out of two parental DNA duplexes. The resulting free end is, the model assumes, recombinogenic and frequently engages in a second round of half crossing-over with the recombinant duplex. The products resulting from such interaction involving two molecules of the plasmid would be classified as belonging to the gene-conversion type without crossing-over. We constructed a dimeric molecule that mimics the intermediate form hypothesized in this model and introduced it into cells. Biased gene conversion products were obtained in this reconstruction experiment. The half crossing-over mechanism can also explain formation of huge linear multimers of bacterial plasmids, the nature of transcribable recombination products in bacterial conjugation, chromosomal gene conversion not accompanied by flanking exchange (like that in yeast mating-type switching), and antigenic variation in microorganisms.

Reconstitution of an episomal mouse aprt gene as a consequence of recombination

When a functional murine adenine phosphoribosyltransferase (aprt) gene linked to bovine papilloma virus (BPV) DNA is transfected into Aprt- L cells, the cells are rendered Aprt+ and the aprt gene persists as an episome. Cotransfection with two BPV vectors, one containing the 5' half of the aprt gene and the other the 3' half of the gene, that share about 300 bp of common sequence in intron 2, produces Aprt+ cells with functional aprt as an episome. Southern blot analysis of low molecular weight DNA derived from Hirt extracts revealed the regeneration of a diagnostic SmaI fragment, consistent with establishment of an episome with functional aprt that was reconstituted as a consequence of recombination. To establish cells with an episomal target for recombination, BPV vectors containing a G418 resistance marker and either the 5' half or 3' half of aprt were transfected into Aprt- L cells. Stably transfected cells, selected by their growth in G418, were in turn transfected with DNA containing the other half of the aprt gene. Following selection of Aprt+ cells, Southern blot and polymerase chain reaction (PCR) analysis of low molecular weight DNA confirmed the presence of a complete episomal aprt gene. The region of DNA shared by the episomal aprt fragment and the transfected aprt half was sequenced after PCR amplification of the reconstituted, episomal gene and was found to be wild type. The region of overlap that serves as the substrate for recombination lies entirely within an intron and can, therefore, tolerate nucleotide substitutions and deletions. The absence of such errors in the sequences examined is consistent with recombination events that are not error prone.

Single-stranded DNA as a recombination substrate in plants as assessed by stable and transient recombination assays

Two separate assays, one that requires stable integration of recombination products and one that does not, were employed to elucidate the role of single-stranded DNA in extrachromosomal homologous recombination in Nicotiana tabacum. Both assays revealed that single-stranded DNA in linear and in circular forms was an efficient substrate for recombination, provided that the cotransformed recombination substrates were of complementary sequence, so that direct annealing was possible. Recombination was inefficient when both single-stranded recombination partners contained homologous regions of identical sequence and generation of a double-stranded DNA was required prior to heteroduplex formation. These results indicate that direct annealing of single strands is an important initial step for intermolecular recombination in tobacco cells. Annealed cotransformed single-stranded molecules yielded intermediates that could be further processed by either continuous or discontinuous second-strand synthesis. The type of intermediate had no influence on the recombination efficiency. Double-stranded circles were unable to recombine efficiently either with each other or with single-stranded DNA. Our results suggest that a helicase activity is involved in the initial steps of double-stranded DNA recombination which unwinds duplex molecules at the site of double-strand breaks.

Test of the double-strand-break repair model of recombination in Xenopus laevis oocytes

A direct test was made of predictions of the double-strand-break repair (DSBR) model of recombination in Xenopus laevis oocytes. The DNA substrate injected into oocytes had two directly repeated copies of a 1.25-kb sequence and was cleaved within one of them. Different products were expected to result from concerted, conservative events, as predicted by the DSBR model, and from nonconservative events. Only very low levels of recombination products, both conservative and nonconservative, were observed. When individual, apparent DSBR products were cloned and characterized, it emerged that the majority of them had arisen by nonconservative recombination through short, terminal homologies and not from the gene conversion events predicted for DSBR. Two cloned products among 44 tested corresponded to the predications of the DSBR model, but these could also have been generated by other processes. The most efficient recombination events in oocytes are nonconservative and are based on long, terminal homologous overlaps; when these are not available, short, imperfect overlaps support a lower level of nonconservative recombination; genuine, conservative DSBR events occur rarely, if at all.

Single-stranded DNA as a recombination substrate in plants as assessed by stable and transient recombination assays

Two separate assays, one that requires stable integration of recombination products and one that does not, were employed to elucidate the role of single-stranded DNA in extrachromosomal homologous recombination in Nicotiana tabacum. Both assays revealed that single-stranded DNA in linear and in circular forms was an efficient substrate for recombination, provided that the cotransformed recombination substrates were of complementary sequence, so that direct annealing was possible. Recombination was inefficient when both single-stranded recombination partners contained homologous regions of identical sequence and generation of a double-stranded DNA was required prior to heteroduplex formation. These results indicate that direct annealing of single strands is an important initial step for intermolecular recombination in tobacco cells. Annealed cotransformed single-stranded molecules yielded intermediates that could be further processed by either continuous or discontinuous second-strand synthesis. The type of intermediate had no influence on the recombination efficiency. Double-stranded circles were unable to recombine efficiently either with each other or with single-stranded DNA. Our results suggest that a helicase activity is involved in the initial steps of double-stranded DNA recombination which unwinds duplex molecules at the site of double-strand breaks.

Test of the double-strand-break repair model of recombination in Xenopus laevis oocytes

A direct test was made of predictions of the double-strand-break repair (DSBR) model of recombination in Xenopus laevis oocytes. The DNA substrate injected into oocytes had two directly repeated copies of a 1.25-kb sequence and was cleaved within one of them. Different products were expected to result from concerted, conservative events, as predicted by the DSBR model, and from nonconservative events. Only very low levels of recombination products, both conservative and nonconservative, were observed. When individual, apparent DSBR products were cloned and characterized, it emerged that the majority of them had arisen by nonconservative recombination through short, terminal homologies and not from the gene conversion events predicted for DSBR. Two cloned products among 44 tested corresponded to the predications of the DSBR model, but these could also have been generated by other processes. The most efficient recombination events in oocytes are nonconservative and are based on long, terminal homologous overlaps; when these are not available, short, imperfect overlaps support a lower level of nonconservative recombination; genuine, conservative DSBR events occur rarely, if at all.

Homologous recombination between plasmid DNA molecules in maize protoplasts

The requirements for homologous recombination between plasmid DNA molecules have been studied using the PEG (polyethylene glycol)-mediated transformation system of maize (Zea mays L.) protoplasts coupled with the transient expression assay for beta-glucuronidase (GUS). Two plasmids were introduced into maize protoplasts; one plasmid (pB x 26) contained a genomic clone of the Adh1 maize gene; the other plasmid (piGUS) was a promoterless construction containing part of intron A of the Adh1 gene fused to the gusA coding sequence. Thus, the two vectors shared an effective homologous region consisting of a 459 bp (HindIII-PvuII) fragment of the Adh1 intron A sequence. An active gusA fusion gene would result upon homologous recombination between the plasmids within the intron A sequence, and indeed GUS activity was observed in extracts following co-transformation of maize protoplasts with the two plasmids. The presence of recombinant DNA molecules in protoplast DNA isolated 1 day after co-transformation was verified using polymerase chain reactions (PCR) and Southern blots. For efficient homologous recombination, both plasmids had to be linearized. The recombination reaction was induced by restriction of the plasmid molecules either inside the effective homologous region or at the borders of the intron sequence. However, the presence of even small, terminal, nonhomologous sequences at the 3' end of the pB x 26 fragment inhibited the recombination reaction. Also, both ends of the linearized piGUS DNA molecules were involved in the recombination reaction. The results revealed some features of homologous recombination reactions occurring in plant cells which cannot be accommodated by mechanisms postulated for similar reactions in animal system and in lower eukaryotes.

Illegitimate recombination in a bovine papillomavirus shuttle vector: a high level of site specificity

Recombination in a bovine papillomavirus shuttle vector carrying direct repeats of Moloney murine leukemia virus LTR sequence was examined. Differently from similar vectors carrying direct repeats of SV40 polyA addition signal or neomycin resistance gene, the vector exhibited no homologous recombination between the repeats. Instead, illegitimate recombination took place. There were two major types of recombination products from the restriction cleavage pattern. The plasmids in independent cellular clones belonging to the same recombination type shared the identical crossover point. Thus, in this plasmid, illegitimate recombination occurred at preferential sites involving exactly the same sequences.

Homologous recombination in bovine papillomavirus shuttlevecter; effect of relative orientation of substrate sequences

Relative orientation of recombination substrates, neo gene, strongly influenced homologous recombination events in a bovine papillomavirus shuttle vector. Between direct repeats, recombination occurred at a high frequency while between inverted repeats, it was rare. Double strand break near the mutation site increased the recombination frequency between inverted repeats but not between direct repeats. Formation of long heteroduplex as a recombination intermediate may explain this apparently paradoxical phenomenon.