A recombinase from Drosophila melanogaster embryos

Improved bacterial recombineering by parallelized protein discovery

Exploiting bacteriophage-derived homologous recombination processes has enabled precise, multiplex editing of microbial genomes and the construction of billions of customized genetic variants in a single day. The techniques that enable this, multiplex automated genome engineering (MAGE) and directed evolution with random genomic mutations (DIvERGE), are however, currently limited to a handful of microorganisms for which single-stranded DNA-annealing proteins (SSAPs) that promote efficient recombineering have been identified. Thus, to enable genome-scale engineering in new hosts, efficient SSAPs must first be found. Here we introduce a high-throughput method for SSAP discovery that we call "serial enrichment for efficient recombineering" (SEER). By performing SEER in Escherichia coli to screen hundreds of putative SSAPs, we identify highly active variants PapRecT and CspRecT. CspRecT increases the efficiency of single-locus editing to as high as 50% and improves multiplex editing by 5- to 10-fold in E. coli, while PapRecT enables efficient recombineering in Pseudomonas aeruginosa, a concerning human pathogen. CspRecT and PapRecT are also active in other, clinically and biotechnologically relevant enterobacteria. We envision that the deployment of SEER in new species will pave the way toward pooled interrogation of genotype-to-phenotype relationships in previously intractable bacteria.

RecA-like strand-transfer activity at the meiotic prophase in Bombyx mori

An ATP-independent strand-transfer activity has been identified in nuclear extracts prepared from Drosophila tissue culture cells and isolated nuclei from Bombyx testes. Extraction of the activity from testes at larval stages where the majority of the cells were in meiotic prophase was only possible when the chromosome scaffold/synaptonemal complex was dissolved by addition of high concentrations of DTT (80 mM). No cross reaction was detected when partly purified extracts were assayed with antibodies against E. coli RecA protein.

Direct and rapid modification of a porcine xenoantigen gene (GGTA1)

The ability to modify animal genomes rapidly at a specific locus would be valuable both for research purposes and in the development of animals suitable for xenotransplantation. In a proof-of-concept study, we used a unique, homology-dependent strand transferase protein called drosophila recombination-associated protein (DRAP) and DNA oligonucleotides to modify the porcine gene encoding alpha 1,3 galactosyl transferase (GGTA1). This gene is responsible for generating xenotransplantation antigens resulting in hyperacute rejection. Pronuclear injection of DRAP and mutant oligonucleotides yielded piglets with heritable, modified alleles of GGTA1 in a direct, rapid and efficient manner. Cells derived from these piglets had markedly reduced alpha 1,3 galactosyl sugar epitopes. The simplicity of this method should permit rapid sequential or simultaneous modification of the various genes encoding or producing antigens that impose limits on xenotransplantation as they are discovered.

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.

Characterization of two nuclear mammalian homologous DNA-pairing activities that do not require associated exonuclease activity

We have developed an assay to study homologous DNA-pairing activities in mammalian nuclear extracts. This assay is derived from the POM blot assay, described earlier, which was specific for RecA activity in bacterial crude extracts. In the present work, proteins from mammalian nuclear extracts were resolved by electrophoresis on SDS/polyacrylamide gels and then electrotransferred onto a nitrocellulose membrane coated with circular single-stranded DNA (ssDNA). The blot obtained was incubated with a labeled homologous double-stranded DNA (dsDNA). Homologous pairing between the ssDNA and the labeled dsDNA was detected by autoradiography as a radioactive spot on the membrane. In nuclear extracts from mammalian cells, we found two major polypeptides of 100 and 75 kDa, able to promote the formation of stable plectonemic joints. Joint molecule formation required at least one homologous end on the dsDNA, but either end of the dsDNA could be recruited to initiate the reaction. For each polypeptide, the reaction required divalent cations such as Mg2+, Ca2+, or Mn2+. Although ATP was not necessary, ADP was inhibitory in each case. Unlike most of the known eukaryotic DNA-pairing proteins, both activities identified here were able to promote the formation of joint molecules without requiring an associated exonuclease activity. In addition, these two proteins were detected in cell lines from different tissues and from different mammalian species (human, mouse, and hamster).

ATP-independent DNA renaturation catalyzed by a protein from Ustilago maydis

A protein that catalyzes the renaturation of complementary strands of DNA has been purified from mitotic cells of the lower eukaryote Ustilago maydis. The most highly purified fraction contains a polypeptide with a molecular mass of 20 kDa as determined by SDS/PAGE and glycerol gradient sedimentation. DNA reannealing is enhanced by the presence of a divalent cation but does not require ATP nor any other nucleotide triphosphate. Reassociation proceeds with fast kinetics as more than 60% of the DNA is reannealed within 4 min at a 30:1 nucleotide/protein monomer ratio, results which suggest that the protein acts in a stoichiometric fashion. Amino acid analysis revealed that the protein contained an elevated level of basic residues and low levels of tryptophan and tyrosine. The protein binds to an oligonucleotide of ten residues but not to one having only five. As judged by agarose gel assays, the protein does not catalyze strand-transfer reactions but does promote the annealing of a 58-residue polynucleotide onto single-stranded circles and gapped linear duplexes. These latter reactions are dependent on the presence of DNA sequence similarity between the pairing partners.

ATP-dependent DNA renaturation and DNA-dependent ATPase reactions catalyzed by the Ustilago maydis homologous pairing protein

Purification of the ATP-dependent homologous pairing activity from Ustilago maydis yields a protein preparation that is enriched for a 70-kDa polypeptide as determined by SDS-gel electrophoresis. The protein responsible for the ATP-dependent pairing activity, using renaturation of complementary single strands of DNA as an assay, has a Stokes radius of 3.6 nm and a sedimentation coefficient of 4.3 S consistent with the interpretation that the activity arises from a monomeric globular protein of 70 kDa. Including heparin-agarose and FPLC gel filtration chromatography steps in the previously published protocol improves the purification of the protein. ATP and Mg2+ are necessary cofactors for optimal DNA renaturation activity. ADP inhibits the reaction. Analysis of the ATP-dependent renaturation kinetics indicates the reaction proceeds through a first-order mechanism. The protein has an associated DNA-dependent ATPase as indicated by co-chromatography with the purified ATP-dependent renaturation activity through an FPLC gel-filtration column. Single-stranded DNA and Mg2+ are required for optimal ATP hydrolytic activity, although a number of other polynucleotides and divalent cations can substitute to varying degrees. Hydrolysis of ATP is activated in a sigmoidal manner with increasing amounts of the protein. At ATP concentrations below 0.1 mM the ATPase activity exhibits positive cooperativity as indicated from the Hill coefficient of 1.8 determined by steady-state kinetic analysis of the reaction. ADP and adenosine 5'-[beta,gamma-imido]triphosphate are inhibitors of the ATPase activity although they appear to exert their inhibitory effects through different modes. These results are interpreted as evidence for protein-protein interactions.

DNA strand exchange catalyzed by proteins from vaccinia virus-infected cells

Vaccinia virus infection induces expression of a protein which can catalyze joint molecule formation between a single-stranded circular DNA and a homologous linear duplex. The kinetics of appearance of the enzyme parallels that of vaccinia virus DNA polymerase and suggests it is an early viral gene product. Extracts were prepared from vaccinia virus-infected HeLa cells, and the strand exchange assay was used to follow purification of this activity through five chromatographic steps. The most highly purified fraction contained three major polypeptides of 110 +/- 10, 52 +/- 5, and 32 +/- 3 kDa. The purified protein requires Mg2+ for activity, and this requirement cannot be satisfied by Mn2+ or Ca2+. One end of the linear duplex substrate must share homology with the single-stranded circle, although this homology requirement is not very high, as 10% base substitutions had no effect on the overall efficiency of pairing. As with many other eukaryotic strand exchange proteins, there was no requirement for ATP, and ATP analogs were not inhibitors. Electron microscopy was used to show that the joint molecules formed in these reactions were composed of a partially duplex circle of DNA bearing a displaced single-strand and a duplex linear tail. The recovery of these structures shows that the enzyme catalyzes true strand exchange. There is also a unique polarity to the strand exchange reaction. The enzyme pairs the 3' end of the duplex minus strand with the plus-stranded homolog, thus extending hybrid DNA in a 3'-to-5' direction with respect to the minus strand. Which viral gene (if any) encodes the enzyme is not yet known, but analysis of temperature-sensitive mutants shows that activity does not require the D5R gene product. Curiously, v-SEP appears to copurify with vaccinia virus DNA polymerase, although the activities can be partially resolved on phosphocellulose columns.

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.

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.

Cloning and characterization of Rrp1, the gene encoding Drosophila strand transferase: carboxy-terminal homology to DNA repair endo/exonucleases

We previously reported the purification of a protein from Drosophila embryo extracts that carries out the strand transfer step in homologous recombination (Lowenhaupt, K., Sander, M., Hauser, C. and A. Rich, 1989, J. Biol. Chem. 264, 20568). We report here the isolation of the gene encoding this protein. Partial amino acid sequence from a tryptic digest of gel purified strand transfer protein was used to design a pair of degenerate oligonucleotide primers which amplified a 635 bp region of Drosophila genomic DNA. Recombinant bacteriophage were isolated from genomic and embryo cDNA libraries by screening with the amplified DNA fragment. These bacteriophage clones identify a single copy gene that expresses a single mRNA transcript in early embryos and in embryo-derived tissue culture cells. The cDNA nucleotide sequence contains an open reading frame of 679 amino acids within which are found 5 tryptic peptides from the strand transfer protein. Expression of this cDNA in E. coli produces a polypeptide with the same electrophoretic mobility as the purified protein. The deduced protein sequence has two distinct regions. The first 427 residues are basic, rich in glutamic acid and lysine residues and unrelated to known proteins. The carboxy-terminal 252 residues are average in amino acid composition and are homologous to the DNA repair proteins, Escherichia coli exonuclease III and Streptococcus pneumoniae exonuclease A. This protein, which we name Rrp1 (Recombination Repair Protein 1), may facilitate recombinational repair of DNA damage.

Drosophila Rrp1 protein: an apurinic endonuclease with homologous recombination activities

A protein previously purified from Drosophila embryo extracts by a DNA strand transfer assay, Rrp1 (recombination repair protein 1), has an N-terminal 427-amino acid region unrelated to known proteins, and a 252-amino acid C-terminal region with sequence homology to two DNA repair nucleases, Escherichia coli exonuclease III and Streptococcus pneumoniae exonuclease A, which are known to be active as apurinic endonucleases and as double-stranded DNA 3' exonucleases. We demonstrate here that purified Rrp1 has apurinic endonuclease and double-stranded DNA 3' exonuclease, activities and carries out single-stranded DNA renaturation in a Mg(2+)-dependent manner. Strand transfer, 3' exonuclease, and single-stranded DNA renaturation activities comigrate during column chromatography. The properties of Rrp1 suggest that it could promote homologous recombination at sites of DNA damage.

rar mutations which increase artificial chromosome stability in Saccharomyces cerevisiae identify transcription and recombination proteins

In an attempt to identify trans-acting factors involved in replication origin function, we have characterized the RAR3 and RAR5 genes, identified by mutations which increase the mitotic stability of artificial chromosomes whose replication is dependent on the activity of weak ARS elements. Sequence analysis has shown that the RAR3 gene is identical to GAL11/SPT13, which encodes a putative transcription factor involved in the expression of a wide range of genes. Change-of-function mutations that truncate the RAR3 protein appear to be required to enhance chromosome stability. In contrast, loss of the RAR5 protein results in enhanced chromosome stability, as if the protein is an inhibitor of ARS function. The RAR5 gene encodes the 175 kDa DNA strand transfer protein beta, an activity that can promote the transfer of a strand from a double-stranded DNA molecule to a complementary single strand. This observation implies that a presumed recombination activity can affect eukaryotic chromosomal replication.

Repair of deletions and double-strand gaps by homologous recombination in a mammalian in vitro system

We have designed an in vitro system using mammalian nuclear extracts, or fractions derived from them, that can restore the sequences missing at double-strand breaks (gaps) or in deletions. The recombination substrates consist of (i) recipient DNA, pSV2neo with gaps or deletions ranging from 70 to 390 bp in the neo sequence, and (ii) donor DNAs with either complete homology to the recipient (pSV2neo) or plasmids whose homology with pSV2neo is limited to a 1.0- to 1.3-kbp neo segment spanning the gaps or deletions. Incubation of these substrates with various enzyme fractions results in repair of the recipient DNA's disrupted neo gene. The recombinational repair was monitored by transforming recA Escherichia coli to kanamycin resistance and by a new assay which measures the extent of DNA strand transfer from the donor substrate to the recipient DNA. Thus, either streptavidin- or antidigoxigenin-tagged beads are used to separate the biotinylated or digoxigeninylated recipient DNA, respectively, after incubation with the isotopically labeled donor DNA. In contrast to the transfection assay, the DNA strand transfer measurements are direct, quantitative, rapid, and easy, and they provide starting material for the characterization of the recombination products and intermediates. Accordingly, DNA bound to beads serves as a suitable template for the polymerase chain reaction. With appropriate pairs of oligonucleotide primers, we have confirmed that both gaps and deletions are fully repaired, that deletions can be transferred from the recipient DNA to the donor's intact neo sequence, and that cointegrant molecules containing donor and recipient DNA sequences are formed.

Different mechanisms inferred from sequences of human mitochondrial DNA deletions in ocular myopathies

We have sequenced the deletion borders of the muscle mitochondrial DNA from 24 patients with heteroplasmic deletions. The length of these deletions varies from 2.310 bp to 8.476 bp and spans from position 5.786 to 15.925 of the human mitochondrial genome preserving the heavy chain and light chain origins of replication. 12 cases are common deletions identical to the mutation already described by other workers and characterized by 13 bp repeats at the deletion boundaries, one of these repeats being retained during the deletion process. The other cases (10 out of 12) have shown deletions which have not been previously described. All these deletions are located in the H strand DNA region which is potentially single stranded during mitochondrial DNA replication. In two cases, the retained Adenosine from repeat closed to the heavy strand origin of replication would indicate slippage mispairing. Furthermore in one patient two mt DNA molecules have been cloned and their sequences showed the difference of four nucleotides in the breakpoint of the deletion, possibly dued to slippage mispairing. Taken together our results suggest that deletions occur either by slippage mispairing or by internal recombination at the direct repeat level. They also suggest that different mechanisms account for the deletions since similarly located deletions may display different motives at the boundaries including the absence of any direct repeat.

Repair of deletions and double-strand gaps by homologous recombination in a mammalian in vitro system

We have designed an in vitro system using mammalian nuclear extracts, or fractions derived from them, that can restore the sequences missing at double-strand breaks (gaps) or in deletions. The recombination substrates consist of (i) recipient DNA, pSV2neo with gaps or deletions ranging from 70 to 390 bp in the neo sequence, and (ii) donor DNAs with either complete homology to the recipient (pSV2neo) or plasmids whose homology with pSV2neo is limited to a 1.0- to 1.3-kbp neo segment spanning the gaps or deletions. Incubation of these substrates with various enzyme fractions results in repair of the recipient DNA's disrupted neo gene. The recombinational repair was monitored by transforming recA Escherichia coli to kanamycin resistance and by a new assay which measures the extent of DNA strand transfer from the donor substrate to the recipient DNA. Thus, either streptavidin- or antidigoxigenin-tagged beads are used to separate the biotinylated or digoxigeninylated recipient DNA, respectively, after incubation with the isotopically labeled donor DNA. In contrast to the transfection assay, the DNA strand transfer measurements are direct, quantitative, rapid, and easy, and they provide starting material for the characterization of the recombination products and intermediates. Accordingly, DNA bound to beads serves as a suitable template for the polymerase chain reaction. With appropriate pairs of oligonucleotide primers, we have confirmed that both gaps and deletions are fully repaired, that deletions can be transferred from the recipient DNA to the donor's intact neo sequence, and that cointegrant molecules containing donor and recipient DNA sequences are formed.

Pairing of homologous DNA sequences by proteins: evidence for three-stranded DNA

We show that recombinases form joint molecules over very short regions of homology. When these molecules are deproteinized the three strands are in a structure that is surprisingly resistant to dissociation by branch migration, even at elevated temperatures. The joint molecules dissociate at temperatures comparable to those required to melt DNA duplexes of the same length and sequence. We also show that nonenzymatically formed structures of the same length and sequence, which have a free third strand ready to branch migrate, dissociate at much lower temperatures. These results provide compelling evidence that the three DNA strands in the region of pairing are hydrogen bonded to each other. Our observations suggest that such a novel three-stranded DNA molecule, or a structure very similar to it, may be the intermediate in general recombination that is used in the recognition of sequence homology. We discuss some of the structural features implicit in this molecule containing any base sequence and compare them with those manifest in true DNA triple helices containing special sequence motifs.