Homologous recombination between transfected DNAs

Formation and loss of large, unstable tandem arrays of the piggyBac transposable element in the yellow fever mosquito, Aedes aegypti

The Class II transposable element, piggyBac, was used to transform the yellow fever mosquito, Aedes aegypti. In two transformed lines only 15-30% of progeny inherited the transgene, with these individuals displaying mosaic expression of the EGFP marker gene. Southern analyses, gene amplification of genomic DNA, and plasmid rescue experiments provided evidence that these lines contained a high copy number of piggyBac transformation constructs and that much of this DNA consisted of both donor and helper plasmids. A detailed analysis of one line showed that the majority of piggyBac sequences were unit-length donor or helper plasmids arranged in a large tandem array that could be lost en masse in a single generation. Despite the presence of a transposase source and many intact donor elements, no conservative (cut and paste) transposition of piggyBac was observed in these lines. These results reveal one possible outcome of uncontrolled and/or unexpected recombination in this mosquito, and support the conclusion that further investigation is necessary before transposable elements such as piggyBac can be used as genetic drive mechanisms to move pathogen-resistance genes into mosquito populations.

Agrobacterium proteins VirD2 and VirE2 mediate precise integration of synthetic T-DNA complexes in mammalian cells

Agrobacterium tumefaciens-mediated plant transformation, a unique example of interkingdom gene transfer, has been widely adopted for the generation of transgenic plants. In vitro synthesized transferred DNA (T-DNA) complexes comprising single-stranded DNA and Agrobacterium virulence proteins VirD2 and VirE2, essential for plant transformation, were used to stably transfect HeLa cells. Both proteins positively influenced efficiency and precision of transgene integration by increasing overall transformation rates and by promoting full-length single-copy integration events. These findings demonstrate that the virulence proteins are sufficient for the integration of a T-DNA into a eukaryotic genome in the absence of other bacterial or plant factors. Synthetic T-DNA complexes are therefore unique protein:DNA delivery vectors with potential applications in the field of mammalian transgenesis.

Reexpression of a cluster of silenced transgenes is associated with their rearrangement

Irreversible inactivation or silencing of tumor suppressor genes occurs frequently in the development of cancer. A similar process of silencing can occur after the integration of transfected or microinjected genes into the genomes of recipient cells. The inactivation of transfected genes seems particularly efficient in cells with stem cell characteristics. We have been studying the inactivation of genes transfected into cultured P19 embryonal carcinoma cells and found that the CpG-rich sequence comprising the coding region of the lacZ reporter gene becomes extensively methylated after integration into the genome. 5-Aza-2'-deoxycytidine (5AdC), an inhibitor of DNA methylation, induced the reexpression of silent transgenes in one clone of P19 cells studied in detail. However, the reexpressed genes remained heavily methylated over the lacZ coding sequence. We used pulsed-field gel electrophoresis to analyze the structure of the transgenic locus in the parental and in 5AdC-treated cells and found that, in each of the cells reexpressing the transgene, the cluster of transgenes had been rearranged. Each clone had undergone a different rearrangement that appeared to involve recombination within the tandemly repeated copies of the transgene. Our data seem consistent with the idea that 5AdC induces efficient DNA recombination between tandemly repeated genes and that the reexpression of silenced genes induced by 5AdC might be triggered by the chromatin reorganization at the site of DNA recombination.

Cointegration of transforming DNAs in Aspergillus nidulans: a model using autonomously-replicating plasmids

Transforming DNAs form cointegrates in Aspergillus nidulans by homologous and non-homologous recombination as well as by end-to-end ligation of linear fragments. This process has been studied by means of a model in which the linkage of a marker gene to the origin of autonomous replication AMA1 was selected for. Recombinant plasmids were rescued into Escherichia coli and subjected to restriction mapping and sequence analysis. It was shown that circular DNA molecules recombined predominantly within homologous fragments. Linear DNA fragments integrated into circular plasmids by invasion of their ends into random non-homologous sites, but exhibited some bias in choice of a target sequence. Cointegrates of multiple plasmid copies were often observed. In some of the plasmids analysed, short duplications of the target sequence flanking an inserted linear DNA fragment have been revealed.

An 'instant gene bank' method for gene cloning by mutant complementation

We describe a new method of gene cloning by complementation of mutant alleles which obviates the need for construction of a gene library in a plasmid vector in vitro and its amplification in Escherichia coli. The method involves simultaneous transformation of mutant strains of the fungus Aspergillus nidulans with (i) fragmented chromosomal DNA from a donor species and (ii) DNA of a plasmid without a selectable marker gene, but with a fungal origin of DNA replication ('helper plasmid'). Transformant colonies appear as the result of the joining of chromosomal DNA fragments carrying the wild-type copies of the mutant allele with the helper plasmid. Joining may occur either by ligation (if the helper plasmid is in linear form) or recombination (if it is cccDNA). This event occurs with high efficiency in vivo, and generates an autonomously replicating plasmid cointegrate. Transformants containing Penicillium chrysogenum genomic DNA complementing A. nidulans niaD, nirA and argB mutations have been obtained. While some of these cointegrates were evidently rearranged or consisted only of unaltered replicating plasmid, in other cases plasmids could be recovered into E. coli and were subsequently shown to contain the selected gene. The utility of this "instant gene bank" technique is demonstrated here by the molecular cloning of the P. canescens trpC gene.

Co-transformation with autonomously-replicating helper plasmids facilitates gene cloning from an Aspergillus nidulans gene library

Autonomously-replicating, marker-less "helper" plasmids were added to transformations of Aspergillus nidulans with plasmids which normally transform by chromosomal integration. This resulted in as much as a 200-fold increase in transformation efficiency. Recovery of autonomously-replicating plasmid co-integrates indicated that co-transformation involves recombination between integrating and helper plasmids, which occurs at a high frequency. Increasing DNA sequence-homology between pairs of plasmids used in simultaneous transformations enhanced co-transformation efficiency. Using helper plasmids and an A. nidulans gene library in a normally-integrating vector, the genes adC and adD were cloned as part of such a co-integrate. In effect, the addition of helper plasmid converts an integrating into an autonomously-replicating gene library in vivo.

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.

Gene expression from heterologous promoters in a replication-defective avian retrovirus vector in quail cells

Avian retrovirus vectors, with potential for use in avian transformation, were constructed to evaluate the relative efficiency of promoters placed internal to the viral long terminal repeats (LTR). The vectors are replication-defective reticuloendotheliosis plasmids that contain the neomycin phosphotransferase gene under control of the 5' LTR and an internal promoter that directs expression of the chloramphenicol acetyltransferase gene. The internal promoters were the SV40 early, the mouse metallothionein I, and the human cytomegalovirus immediate early (HCMV-IE) promoters. Under transient conditions in QT6 cells, the HCMV-IE promoter construct was by far the strongest. However, expression dropped greatly from the HCMV-IE promoter after integration into the quail cell genome. Evidence suggests that the HCMV-IE promoter is selectively suppressed by methylation after stable transfection but not after infection.

Molecular characterization of HIV-1 isolated from a serum collected in 1976: nucleotide sequence comparison to recent isolates and generation of hybrid HIV

Human immunodeficiency virus type 1 (Z321 designate, HIV-1Z321), the oldest known HIV, was isolated from a serum sample collected in Zaire in 1976 and was molecularly cloned. Restriction enzyme analysis of unintegrated viral DNA revealed the presence of conserved restriction enzyme cleavage sites in the long terminal repeat sequences. Nucleotide sequence analysis of the 3' end of the viral DNA revealed a pattern similar to other HIV-1 isolates described. However, some of the common restriction sites present in other isolates were absent in HIV-1Z321. The extent of differences between HIV-1Z321 and recent isolates from North America and Zaire was 17.86-18.36% on the nucleotide sequence level and 26.5-33.2% difference in the predicted amino acid sequence in the envelope gene. Differences were also noted in 3'-orf (nef: according to HIV gene nomenclature; see Ref. 42) gene and U3 region of the long terminal repeat sequences of HIV-1Z321 and other isolates. Nucleotide sequence of a HIV-1 isolate, 12 years apart from the present isolates, will provide an important time calibration point for the evolutionary divergence of HIV isolates. Hybrid HIV was also generated by transfecting HIV-1Z321 and HIV-1HTLV-III viral DNAs into cells.

Expression of porcine pro-opiomelanocortin cDNA in an established fibroblastic cell line: constitutive secretion of the precursor without proteolytic processing

Pro-opiomelanocortin (POMC) is the common precursor of several pituitary hormones including alpha-melanotropic hormone, adrenocorticotropic hormone, beta-lipotropin and beta-endorphin. The porcine POMC cDNA was inserted downstream from the late promoter of an SV40-derived expression vector and co-transfected in NIH 3T3 cells with a marker plasmid carrying the neomycin resistance gene. Colonies resistant to the neomycin analog G418 were selected and analyzed for the production of POMC-related peptides by radioimmunoassay. Three clones were found to produce from 350 to 1750 pg of POMC-related peptides per 10(6) cells in 16 h and selected for further analysis. The number of POMC cDNA copies integrated in the host cell genome was determined and the levels of transcription were compared. POMC-related material released in the culture medium by the best producing clone (NJP 4-4) was further analyzed by gel filtration and reversed-phase high-pressure liquid chromatography combined with radioimmunoassays. POMC was found to be synthesized and secreted without further processing or degradation. Negligible amounts of POMC-immunoreactive species were found in cellular extracts indicating that the prohormone is secreted from the NIH 3T3 cells without storage, presumably through a constitutive pathway. Our results suggest that NIH 3T3 fibroblasts do not contain the enzymatic machinery to process complex precursors such as POMC.

Analysis of homologous recombination in cultured mammalian cells in transient expression and stable transformation assays

Recombination between plasmid molecules, each containing a nonoverlapping deletion mutation in the hamster adenine phosphoribosyltransferase gene, was measured after coinjection into rat cells. Using these two plasmids, as linear or circular molecules, the recombination efficiency was measured soon after injection in a transient expression assay or after selection for stable transformants. The transient assay revealed that linear molecules were a better substrate for recombination, with double strand breaks within the region of homology stimulating recombination more than breaks outside the region of homology. A 20 to 70-fold increase in the efficiency of recombination was observed when two linear molecules were coinjected as compared to two circular molecules. Linear molecules were found to not only stimulate recombination but also to facilitate stable integration of the recombinant molecule into the host genome.

Shuttling of integrated vectors from mammalian cells to E. coli is mediated by head-to-tail multimeric inserts

With the aim of producing nonviral shuttle vectors for mammalian cells, we have constructed mouse mitochondrial DNA derivatives comprising the xanthine-guanine phosphoribosyltransferase gene as a selectable marker. Complete or subcomplete mitochondrial genomes were inserted into the plasmid pBB3 and transferred into hepatoma cells in order to generate, in vivo, new recombinant molecules. A second- and a third-generation vector, p12.2b and p delta respectively, were thus isolated for their ability to shuttle from mammalian cells to recA+ E. coli. Transfection of rodent fibroblasts and hepatoma cells showed that, contrary to our expectations, p12.2b and p delta are not self-replicating episomes; their shuttling from mammalian cells to recA+ E. coli is mediated by tandem integrated copies. The relevant property of p12.2b and p delta is a ubiquitous propensity to form head-to-tail multimeric structures when they integrate into mammalian host chromosomes. This ability is missing in pBB3 and appears only following the insertion of various mitochondrial or nuclear DNA fragments into the plasmid. These data are discussed in terms of homologous recombination and shuttling of integrated vectors.

Homologous recombination of polyoma virus DNA in mouse cells

We have produced nonviable deletion mutants of polyoma virus in order to study homologous recombination after DNA transfection into mouse cells. The frequency of recombination was determined by the formation of infectious virus. It was dependent on the amount of DNA transfected and the size of the region of homology between the mutations. Recombination frequencies were highest when both mutated genomes were transfected in closed circular form rather than after linearization of one or both of the recombination partners. The system described may be useful for a more detailed analysis of physiological and genetic conditions influencing the frequency of homologous recombination in mouse cells as well as to study enzymes involved and intermediates produced in this process.

Effect of concentration on the subsequent fate of plasmid DNA in human fibroblasts

The physical fate of plasmid DNA after entry into human fibroblasts was studied using Southern hybridisation and electron microscopy. Exposure of the cells (5 X 10(5) per well) to pC194 DNA-CaPi, containing 50 micrograms plasmid DNA, resulted in the occasional formation of interlocked molecules. Exposure to a co-precipitate containing 100 micrograms pC194 plasmid DNA per well resulted in an increase of interlocked molecules by a factor of 10-20 relative to the number of monomers. In addition, new classes of molecules were observed. After prolonged incubation of the cells exposed to the higher DNA concentration, the plasmid DNA was partly contained in structures with a very low electrophoretic mobility. Upon restriction endonuclease digestion of the re-extracted DNA, a pattern of bands was observed, suggesting the involvement of illegitimate recombination between non-random plasmid DNA sequences in the formation of the new classes of molecules.

Effect of cell cycle position on transformation by microinjection

We have investigated the effect of cell cycle position on the efficiency of transformation by microinjection. Linear recombinant plasmids transform synchronized cells with similar frequencies following injections at all cell cycle stages, whereas supercoiled molecules show a decreased ability to generate transformants in early S phase. This inhibition is not due to an inability to transiently express a transferred gene, since cells at all stages of the cycle efficiently expressed a hamster adenine phosphoribosyltransferase gene introduced on a supercoiled plasmid. Southern transfer analyses of the cell cycle specific transformants revealed that tandem arrays of plasmids, integrated into the host chromosomes, could be generated at all cell cycle stages.

Tumorigenic activity of polyoma virus and SV40 DNAs in newborn rodents

A procedure has been developed whereby the oncogenicity of the DNA from polyoma (Py) virus and Simian virus 40 (SV40) can be tested directly by injecting recombinant DNA into newborn rodents. Injection of 0.2-2.0 micrograms of linear DNA induced the development of subcutaneous liposarcomas and fibrosarcomas at the site of inoculation. Coinjection of high-molecular-weight rat DNA as carrier had little or no effect on tumor formation but plasmids pBR322, pAT153 , and pML2 behaved as strong inhibitors. Tumor induction by injecting DNA into newborn rodents provides an in vivo equivalent to a transformation assay but appears to be a more stringent and rigorous criterion of oncogenic transformation. The oncogenic potential of Py virus in newborn hamsters could be expressed by a recombinant encoding only the middle T protein, although with average tumor latencies 5-10 times longer than those observed with wild-type Py DNA. Py middle T required the cooperation from small T to induce tumors in newborn rats. SV40 DNA was tumorigenic only in newborn hamsters. delta 2005 DNA which is unable to produce the SV40 small T antigen was much less active and required a latent period about twice that of wild-type SV40 DNA. However, its tumorigenic potential was restored by addition of the Py small T antigen gene. This indicates that Py and SV40 small T antigens are interchangeable and that they probably play an identical role in malignant transformation. Finally, evidence was provided that intermolecular recombination or recombination between DNA fragments can occur in vivo.

Inhibition of thymidine kinase gene expression by anti-sense RNA: a molecular approach to genetic analysis

As an alternative approach to classical genetic analysis, we are investigating the potential of anti-sense (nonsense) DNA strand transcription to inhibit gene activity. A promoter will direct transcription of the complementary nonsense DNA strand when the protein coding sequence of a cloned gene is excised and then reinserted in reverse orientation. When such flipped gene constructions of the HSV thymidine kinase (TK) gene are coinjected with the wild-type gene at a 100:1 ratio, there is a reduction of transient TK expression in TK- mouse L cells. The proportion of viable cells with demonstrable TK activity drops 4-fold as compared with neighboring cells coinjected with TK and an excess of control plasmid. Furthermore, autoradiography of the cells still expressing TK shows that 3H-thymidine incorporation is reduced. Cells contransformed with flipped TK gene constructions have a reduced capacity to express subsequently microinjected TK genes, suggesting that the anti-message phenomenon is due to a trans-inhibition of TK and is probably not an artifact of rearrangements following microinjection.

Do we understand the genetic mechanisms of oncogenesis? Keynote address for Honey Harbor meeting on cellular and molecular biology of neoplasia, October 2-6, 1983

Different experiments with viruses and transfection now support the classical view that cancer is the result of a multistep process. This analysis further indicates that some of these steps involve mutations affecting the qualitative and quantitative expression of dominant transforming genes or oncogenes. These mutations are spontaneous or induced and of various kinds, including base pair changes, deletions, translocations, and amplifications. The actions of the active transforming genes or oncogenes lead to the properties of the tumor cell. However, these activities are effective only in the appropriate cell with targets for the products of the oncogenes and without inhibitors. Because there will be multiple genetic changes in tumor cells, it is difficult to determine which changes are significant for the oncogenesis. Retrovirus vectors may be useful in this determination. In addition, our present methods of analysis may be missing certain of the multiple steps in oncogenesis, in particular, those involved with tissue-, organ-, and organism-specific controls.