Characterization of an ATP-dependent DNA strand transferase from human cells

DNA Interaction and Dimerization of Eukaryotic SMC Hinge Domains

The eukaryotic SMC1/SMC3 heterodimer is essential for sister chromatid cohesion and acts in DNA repair and recombination. Dimerization depends on the central hinge domain present in all SMC proteins, which is flanked at each side by extended coiled-coil regions that terminate in specific globular domains. Here we report on DNA interactions of the eukaryotic, heterodimeric SMC1/SMC3 hinge regions, using the two known isoforms, SMC1alpha/SMC3 and the meiotic SMC1beta/SMC3. Both dimers bind DNA with a preference for double-stranded DNA and DNA rich in potential secondary structures. Both dimers form large protein-DNA networks and promote reannealing of complementary DNA strands. DNA binding but not dimerization depends on approximately 20 amino acids of transitional sequence into the coiled-coil region. Replacement of three highly conserved glycine residues, thought to be required for dimerization, in one of the two hinge domains still allows formation of a stable dimer, but if two hinge domains are mutated dimerization fails. Single-mutant dimers bind DNA, but hinge monomers do not. Together, we show that eukaryotic hinge dimerization does not require conserved glycines in both hinge domains, that only the transition into the coiled-coil region rather than the entire coiled-coil region is necessary for DNA binding, and that dimerization is required but not sufficient for DNA binding of the eukaryotic hinge heterodimer.

Anti-(U1)snRNP autoantibodies inhibit homologous pairing activity of the human recombination complex

The co-purification of the U1snRNP particle with a high-molecular-weight human homologous pairing activity has been observed consistently. Using human autoimmune sera directed against various snRNPs, it has been found that autoantibody binding to antigenic determinants specifically associated with the U1snRNP particle inhibits the formation of paired DNA molecules by the human homologous pairing activity. Immunoprecipitation of U1snRNP with anti-(U1)RNP autoantibodies significantly reduced the homologous pairing activity in these fractions. NaDodSO4-PAGE analysis of immunoprecipitated samples has revealed their content to be mostly composed of anti-(U1)RNP precipitable material. Taken together, these results suggest that some biochemical reactions in the process of homologous pairing promoted by high-molecular-weight complex are dependent upon U1snRNP components. It is postulated that the U1snRNP may be associated with the recombination complex in human cells.

Mammalian mitochondria possess homologous DNA recombination activity

Mitochondrial protein extracts from normal and immortalized mammalian somatic cells catalyze homologous recombination of plasmid DNA substrates. Mitochondrial homologous recombination activity required exogenous adenosine triphosphate, although substantial activity remained when non-hydrolyzable analogs were used instead. There was no requirement for added nucleoside triphosphates, and the reaction was not inhibited by dideoxyadenosine triphosphate or aphidicolin. The majority of recombinant plasmid molecules result from a conservative process, indicating that nuclease-mediated strand-annealing is not responsible for the mitochondrial homologous recombination activity. Affinity-purified anti-recA antibodies inhibited the reaction, suggesting that activity is dependent on a mammalian mitochondrial homolog of the bacterial strand-transferase protein. The presence of homologous recombination activity within mammalian mitochondrial extracts suggests that this process is involved in mitochondrial DNA repair.

Isolation of multiple activities from mouse FM3A cells which promote homologous pairing of DNA molecules

We describe the detection and partial purification of three homologous pairing activities from extracts of mouse mammary carcinoma FM3A cells. These activities, designated MHP1a, 1b, and 1c, form joint molecules between circular single-stranded DNA and homologous linear duplex DNA and are distinguished from one another by their chromatographic behaviors or isoelectric properties. The reactions promoted by these activities require homologous substrates but not ATP. All the reactions also show Mg2+ dependence in the absence of exogenous ATP. Analysis of the reaction products has revealed that strand exchange proceeds for lengths of up to at least 271 bp during the homologous pairing reaction. The finding of multiple types of homologous pairing and strand exchange activity in mouse cells may facilitate the elucidation of the mechanism of homologous recombination in somatic mammalian cells.

The RecA protein as a recombinational repair system

The Escherichia coli RecA protein plays a central role in homologous genetic recombination, recombinational repair, and several other processes in bacteria. In vitro, an extended filament involving thousands of RecA monomers promotes a reaction in which individual DNA strands switch pairing partners (DNA strand exchange). This reaction has been extensively studied as a paradigm for the central steps in recombination. Because the strand-exchange reaction is relatively simple and isoenergetic, the complexity of the RecA system that carries it out has led to controversy about the functional significance of many fundamental properties of RecA. Filamentous protein structures involving thousands of RecA monomers, which hydrolyse 100 ATPs per base pair of heteroduplex DNA formed, are hard to rationalize in the context of recombination between two homologous DNAs. The thermodynamic barriers to strand exchange are much too small. These molecular features of the system can be easily rationalized, however, by shifting the focus to DNA repair.

An overview of homologous pairing and DNA strand exchange proteins

Processes fundamental to all models of genetic recombination include the homologous pairing and subsequent exchange of DNA strands. Biochemical analysis of these events has been conducted primarily on the recA protein of Escherichia coli, although proteins which can promote such reactions have been purified from many sources, both prokaryotic and eukaryotic. The activities of these homologous pairing and DNA strand exchange proteins are either ATP-dependent, as predicted based on the recA protein paradigm, or, more unexpectedly, ATP-independent. This review examines the reactions promoted by both classes of proteins and highlights their similarities and differences. The mechanistic implications of the apparent existence of 2 classes of strand exchange protein are discussed.

Saccharomyces cerevisiae proteins involved in hybrid DNA formation in vitro

RecA-like activities that can form hybrid DNA in vitro have been identified in a wide variety of organisms. We have previously described the strand exchange protein 1 (SEP1) from the yeast Saccharomyces cerevisiae that can form hybrid DNA in vitro. Purified as an Mr 132,000 polypeptide, recent molecular and immunological studies have now shown that the native form is an Mr 175,000 polypeptide containing strand exchange activity. The gene encoding SEP1 has been cloned and sequenced. The primary sequence failed to reveal any significant sequence homology to other sequences in data base searches. In vivo SEP1 was found to be essential for normal meiosis as cells containing a homozygous insertion mutation in the SEP1 gene failed to sporulate. In order to identify additional factors that are involved in hybrid DNA formation in S cerevisiae, we used an in vitro stimulation assay to identify proteins that reconstitute strand exchange activity in reactions containing limiting amounts of SEP1. We have identified two proteins that functionally interact with SEP1. First, an Mr 34,000 single-stranded DNA binding protein stimulated the reaction by lowering the requirement for SEP1 about 3-4 fold. This protein is a fragment of the large subunit of a hetero-trimeric complex called yRP-A (yRF-A) which is thought to be the functional eukaryotic equivalent of single-stranded DNA binding proteins in prokaryotes. The gene encoding this protein (RPA1) is essential for growth. Second, an Mr 33,000 polypeptide, termed Stimulatory Factor 1 (SF1), dramatically stimulated the SEP1 catalyzed reaction by lowering the requirement for SEP1 about 300 fold.(ABSTRACT TRUNCATED AT 250 WORDS)

Relative frequencies of homologous recombination between plasmids introduced into DNA repair-deficient and other mammalian somatic cell lines

Twelve mammalian somatic cell lines, some of them DNA damage-sensitive mutants paired with their respective wild-type parental lines, were assayed for their ability to catalyze extrachromosomal, intermolecular homologous recombination between pSV2neo plasmid recombination substrates. All of the somatic cell lines analyzed are capable of catalyzing homologous recombination; however, there is a wide range of efficiencies with which they do so. Five human cell lines display a fourfold range of recombination frequencies, and six hamster cell lines vary almost 20-fold. Linearizing one of the recombination substrates stimulates recombination in all but one of the cell lines. Two of the three paired mutant cell lines display a threefold reduction in their ability to catalyze homologous recombination when compared to their respective parental cell lines, indicating that the mutations that render them sensitive to DNA damaging agents might also play a role in homologous recombination.

ATP-independent strand transfer protein from murine spermatocytes, spermatids, and spermatozoa

A protein-catalyzing D-loop formation is present in murine spermatocytes, spermatids, and spermatozoa, but is not found in somatic tissue or in premeiotic cells of the germline. Unlike the Escherichia coli RecA protein and the meiotic rec protein (m-rec) previously described, D-loop formation by this protein (referred to as "mAi-rec") does not require ATP. The meiotic profile of mAi-rec activity is only partly similar to that of m-rec. Like m-rec, it rises steeply during early prophase and reaches a peak at pachytene. Unlike m-rec, its activity remains high during the postmeiotic phase of spermatid development and is prominent in immunochemically stained spermatozoa. A polyclonal antibody to E. coli RecA reacts with mAi-rec and inhibits its activity. No such reaction occurs with m-rec protein. The extent of sequence homology between E. coli RecA and murine mAi-rec is highly limited; none of the several monoclonal antibodies tested reacted with mAi-rec.

Intrachromosomal homologous recombination in human cells which differ in nucleotide excision-repair capacity

To examine the mechanism of recombination and the role of DNA repair in this process, we transfected a plasmid carrying duplicated copies of the Herpes simplex virus I thymidine kinase (Htk) gene, each containing an 8 bp XhoI site inserted in a unique site and with the neo coding for geneticin resistance located between them, into tk-deficient human cell lines which differ in their ability to carry out nucleotide excision repair. One parental cell line has a normal level of repair activity; the second has an intermediate level, and the third has virtually no repair activity. Several geneticin-resistant transfectant cell strains from each parental line were isolated and assayed for the ability to undergo productive recombination giving rise to tk+ cells. Approximately 25% of them could do so. Southern blot analysis of these transfectants indicated that the majority contained a single copy, or at most, two copies of the plasmid integrated into the chromosome. Fluctuation analysis tests to determine the rate of spontaneous recombination (events per 10(6) cells per cell generation) in the various cell strains showed that the rates ranged from 0.15 to 4.1. The mean rate for the cell strains derived from the repair-deficient cell line was 3.6; for those derived from the cells with an intermediate rate, it was 0.8; and for those with a normal rate of excision repair, it was 0.9. Southern blot analysis of tk+ recombinants showed that in all cases, one of the Htk genes had become wild-type, i.e., XhoI-resistant. 90% of the recombinants retained the Htk gene duplication, consistent with non-reciprocal transfer of genetic information, i.e., gene conversion. The rest contained a single, wild-type Htk gene, consistent with a single reciprocal exchange within a chromatid or a single unequal exchange between sister chromatids. These cell strains will be useful for investigating the role of DNA damage and repair in homologous recombination.

Hypervariable minisatellite DNA is a hotspot for homologous recombination in human cells

Hypervariable minisatellite DNA sequences are short tandemly repeated sequences that are present throughout the human genome and are implicated to enhance recombination. We have constructed a consensus hypervariable minisatellite sequence and analyzed its effect on homologous recombination in human cells in culture. The consensus sequence d(AGAGGTGGGCAGGTGG)6.5 is shown to stimulate homologous recombination up to 13.5-fold. The stimulation occurs at a distance and in both directions but does show a quantitative directionality. Stimulation occurs in a codominant manner, and the sequence is inherited equally in the products. Enhancement is maintained, but at a reduced level, when double-strand breaks are introduced into the substrates. Multiple unselected recombination events are promoted, and preferential stimulation of reciprocal exchange events is demonstrated.

A recombination hotspot in the LTR of a mouse retrotransposon identified in an in vitro system

The recombinational frequency between two long terminal repeat elements (LTR-IS) of a mouse retrotransposon was about 13 times higher, compared with that of two control DNA sequences in extracts from mouse testes, but not in extracts from ascites cells. Deletion of a 37 bp region from the LTR-IS element strongly suppresses its recombinational activity. This 37 bp region encompasses an area of potentially single-stranded DNA and interacts with at least two nuclear proteins. One of them binds sequence-specifically to single-stranded DNA and is present in both types of extracts. Another protein(s) binds to dsDNA at the motif TGGAAATCCCC and is absent in extracts from testes. Our results suggest that a cis-acting DNA sequence within the 504 bp LTR-IS element is responsible for its high recombinational activity in vitro, and they further support the previous suggestion that the LTR-IS elements are meiotic recombinational hotspots in vivo.

Analysis of recombination in mammalian cells using SV40 and SV40-derived vectors

Viruses and viral vectors have played a crucial role in our understanding of the pathways of homologous and non-homologous recombination in mitotically dividing mammalian cells. In particular, they have allowed the confirmation of the preponderance of non-homologous over homologous recombination events and led to schemes for the selection and isolation of homologous recombination products. These studies have allowed an examination of the properties of reciprocal and non-reciprocal homologous recombination events extrachromosomally, in the chromosome and between plasmids and chromosomes. They suggest that it is feasible now to direct DNA segments to predetermined chromosomal locations by homologous recombination.

Molecular analysis of homologous recombination catalysed by human nuclear extract: fidelity and DNase protection

We present a molecular analysis of DNA's resulting from homologous recombination, between two duplex molecules, and catalysed by human nuclear extracts. Sequence analysis of 20 recombined clones (400 nucleotides per clone), in a genetically silent sequence surrounding the recombination initiation or termination site, shows no modification compared to the parental sequence. Transient protection of the DNA's against DNase treatment was brought about by the nuclear extract. This protection was found to be strickly confined to the homologous sequences potentially implicated in recombination.

Human placental endonuclease cleaves Holliday junctions

A partially purified endonuclease from human placenta cleaves cruciform structures. The placental enzyme is active both on extruded cruciform structures from negatively supercoiled covalently closed circular plasmid DNA and on synthetic X-junctions formed by reannealing short oligonucleotides. Plasmids containing natural or cloned palindromes such as pBR322 and pHD101-3 were used as substrates. The synthetic X-junction tetramer DNA formed by reannealing short oligonucleotides, was converted into dimer form by the enzyme. This is the first report of an enzyme activity involved in resolution of recombination intermediates in higher eukaryotes and second report of a cellular enzyme.