Ho Endonuclease Cleaves MAT DNA in Vitro by an Inefficient Stoichiometric Reaction Mechanism*

(Received for publication, April 5, 1996, and in revised form, December 17, 1996)

Yongjie Jin Dagger , Gloria Binkowski Dagger , Lee D. Simon Dagger and David Norris Dagger §

From the Dagger  Waksman Institute and the § Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08855-0759

ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
FOOTNOTES
Acknowledgments
REFERENCES


ABSTRACT

Mating type switching in Saccharomyces cerevisiae initiates when Ho endonuclease makes a double-stranded DNA break at the yeast MAT locus. In this report, we characterize the fundamental biochemical properties of Ho. Using an assay that monitors cleavage of a MAT plasmid, we define an optimal in vitro reaction, showing in particular that the enzyme has a stringent requirement for zinc ions. This suggests that zinc finger motifs present in Ho are important for cleavage. The most unexpected feature of Ho, however, is its extreme inefficiency. Maximal cleavage occurs when Ho is present at a concentration of 1 molecule/3 base pairs of substrate DNA. Even under these conditions, complete digestion requires >2 h. This inefficiency results from two characteristics of Ho. First, Ho recycles slowly from cleaved product to new substrate, in part because the enzyme has an affinity for one end of its double strand break product. Second, high levels of cleavage in the in vitro reaction correlate with the appearance of large protein-DNA aggregates. At optimal Ho concentrations, these latter aggregates, referred to as "florettes," have an ordered structure consisting of a densely staining central region and loops of radiating DNA. These unusual properties may indicate that Ho plays a role in other aspects of mating type switching subsequent to double strand break formation.


INTRODUCTION

Genetic recombination is the intracellular process that moves DNA sequence information from one genomic location to another. A plethora of genetic and biochemical experiments, conducted primarily in prokaryotic and fungal systems, has led to a detailed understanding of the DNA intermediates that arise during this process. Examples of such intermediates include broken duplexes, heteroduplex DNA joints, and Holliday junctions. The first of these intermediates (broken duplexes or double-stranded breaks (DSBs)1) are thought to initiate recombination. Thus, in the yeast Saccharomyces cerevisiae, an organism in which DSB formation has been intensively analyzed, the following lines of evidence indicate that DSBs initiate meiotic recombination. First, DSBs are repaired using gene products required for meiotic recombination (reviewed in Ref. 1). Second, certain meiotic segregation patterns of yeast genes are consistent with molecular models of recombination that posit a DSB initiation event (2). Third, DSBs occur at regions of the genome defined genetically as initiators of recombination (3-11). Fourth, DSBs introduced into DNA during meiosis stimulate nearby meiotic recombination (12). Finally, meiotic DSBs precede and are independent of pairing between homologs, implying that DSBs initiate chromosomal pairing (13, 14). However, despite the intensive analysis of DSB formation in yeast, the endonuclease(s) that generates DSBs during meiotic recombination remains unidentified.

DSBs have also been shown to initiate yeast mating type switching, a mitotic recombination reaction (for a review of yeast mating type, see Ref. 15). Haploid yeast cells come in two mating types, designated a and alpha . These mating types are determined by a master regulatory locus on chromosome III called MAT. MAT contains five sequence blocks: W, X, Y (Ya or Yalpha ), Z1, and Z2 (Fig. 1A). The W, X, Z1, and Z2 blocks are identical in a and alpha  cells, but each mating type contains a unique MAT Y sequence: Ya in a cells and Yalpha in alpha  cells. Roughly once per cell generation, new Ya or Yalpha information transposes into MAT from two unlinked and transcriptionally inactive loci known as HMLalpha and HMRa, thereby switching the cell's mating type.


Fig. 1. Mating type switching in S. cerevisiae. A, during mating type switching, Y information from HMLalpha (black boxes) or from HMRa (stippled boxes) is transposed into the expressed MAT locus. Switching initiates when Ho endonuclease makes a double-stranded break at the MAT YZ border as shown. B, shown is a close-up of the MAT locus near the Ho recognition sequence. Ho makes a staggered double-stranded break that centers on Z5-Z6 (base pairs are numbered going away from the YZ border). The bar marked Recognition sequence in vitro indicates the sequence required for in vitro cleavage by Ho; the black boxes indicate base pairs that are thought to contact Ho (19, 20). The bars marked Active in vivo and Inactive in vivo indicate sequences that function or fail to function, respectively, in an in vivo cleavage assay (see text).
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Mating type switching initiates when an endogenous, site-specific endonuclease known as Ho makes a DSB at the MAT YZ border (16-18). The cleavage products and recognition sequence for Ho have been analyzed in detail by Heffron and co-workers (16, 17, 19, 20). Ho cleaves in Z1 between Z3 and Z4 on one strand and between Z7 and Z8 on the other to produce 3'-overhangs that are four nucleotides long (base pairs are numbered going away from the YZ junction) (Fig. 1B). A 16-bp region spanning the YZ border (Y6-Z10) can be cleaved in vitro by purified Ho endonuclease (Fig. 1B). Eight noncontiguous base pairs located within this region are necessary for cleavage. One located in Y (Y4) is an AT base pair conserved in both Ya and Yalpha . The other seven are located in Z1 (Z1-Z4, Z6, Z7, and Z9). Surprisingly, however, the 16-bp region sufficient for in vitro cleavage (Y6-Z10) and a larger, inclusive 20-bp region (Y8-Z12) are insufficient for in vivo cleavage (19, 20). Instead, a 24-bp fragment (Y11-Z13) is required for cleavage inside cells (Fig. 1B).

An analysis of Ho site recognition distinguishes Ho endonuclease from typical prokaryotic type II restriction endonucleases (19, 20). Heffron and co-workers (16, 17, 19, 20) showed that gross changes outside the recognition sequence affect Ho cleavage, while some changes inside of it are tolerated by the enzyme. These properties indicate that the Ho recognition site should not be thought of as a highly defined "restriction" site. In this respect, Ho would bind to DNA in a manner similar to transcription factors, an intriguing idea given that Ho contains several putative zinc fingers, structural motifs common to certain classes of transcription factors (21).

While its recognition sequence has been analyzed in great detail, Ho endonuclease itself has been the subject of little biochemical analysis. In this report, we characterize the fundamental biochemical parameters of the enzyme. This study has two purposes. The first is to increase our understanding of the mechanism by which Ho generates a DSB at MAT. Given the similar genetic requirements for mating type switching and "standard" meiotic recombination, this information should increase our understanding of DSB formation in other types of recombination reactions. The second purpose is to identify biochemical parameters of Ho that can be used as base lines in future experiments on accessory factors that may be required for in vivo cleavage. Our results indicate that Ho is not merely the yeast version of a bacterial restriction enzyme. In fact, Ho has some very unusual characteristics that may indicate that the enzyme has other roles in mating type switching subsequent to DSB formation.


MATERIALS AND METHODS

Strains and DNA

Plasmid pRK128 is a bacteriophage lambda -derived vector containing the gene for the thermolabile repressor cI857 and the PR promoter driving the complete coding sequence of Ho endonuclease (17). Plasmid pDC283 is a pBR322-based plasmid carrying the entire MATa locus and flanking DNA sequences (17). Both pRK128 and pDC283 were kindly supplied by Richard Kostriken. Plasmid pAV115, kindly supplied by Andrew Vershon, is a pBR322-based plasmid carrying the entire MATalpha locus and flanking DNA sequences (22). Plasmid pRW17 is a YCp50-based plasmid containing MATalpha DNA from Y22 to Z22 cloned between the HindIII and BamHI sites. Oligonucleotide RHo has the following sequence: GTA AAA TTT TAT AAA CTT TAT AAA ATT TTA CTG TT. Oligonucleotide LHo has the following sequence: GCG GAA AGC TGA ACT TCA GCT TTC CGC AAC A. The Escherichia coli strain used in this study was DH5alpha F' (F'/endA, hsdR17 (rK-mK-), supE44, thi-1, recA1, gyrA (Nalr), relA1, Delta (lacZYA-argF)U169, deoR (phi 80dlacDelta (lacZ)M15)).

Chemicals and Enzymes

Sepharose CL-4B, DEAE-Sephacel, and Sephadex G-200 were from Pharmacia Biotech Inc. Bio-Rex 70 and Chelex 100 were from Bio-Rad. Phosphocellulose P-11 was from Whatman and was prepared by the manufacturer's instructions. Dithiothreitol (DTT), benzamidine hydrochloride, phenylmethylsulfonyl fluoride (PMSF), N-ethylmaleimide, and 1,10-phenanthroline were from Sigma. Ethylene glycol was from J. T. Baker Co. Low molecular weight protein standards were from Bio-Rad. High and low molecular weight calibration standards for gel filtration were from Pharmacia.

Assay for Ho Endonuclease

The standard reaction mixture (25 µl) contained 20 mM Tris-HCl, pH 7.5, 80 mM NaCl, 8 mM MgSO4, 4 mM DTT, 2 mM benzamidine, 0.45 nmol of EcoRI-cleaved pDC283 (expressed in molar concentration of nucleotides), and Ho endonuclease. Reactions were incubated at 30 °C for 60 min and then terminated by the addition of 5 µl of stop solution (100 mM EDTA, 1% (w/v) SDS, 1 mg/ml proteinase K, 0.25% (w/v) bromphenol blue, and 50% glycerol), followed by a 30-min incubation at 65 °C. Terminated reactions were loaded on a 0.8% (w/v) agarose gel made up in 0.04 M Tris acetate and 1 mM EDTA and electrophoresed at 7 V/cm for 2 h. Gels were stained in 0.5 µg/ml ethidium bromide, and digitized pictures were generated on a GDS 7500 gel documentation system (UVP). Quantitation of digitized pictures was carried out using the IP Lab gel software package (Signal Analytics Corp.). One unit of activity is defined as the amount that cleaves 1 µg of EcoRI-linearized pDC283 in 1 h at 30 °C.

To test the effects of pH on Ho activity, the Tris-HCl in the standard reaction was replaced with 20 mM KH2PO4/K2HPO4 for the pH range from 6.4 to 8.1 or with 40 mM Tris maleate/NaOH for the pH range from 8.6 to 9.2. All other reaction components were the same.

Cell Growth

The HO bacterial strain was grown at 30 °C in 3.6 liters of LB medium supplemented with 50 µg/ml ampicillin. When the culture reached an absorbance at 600 nm of 0.8, 2.4 liters of the same medium pre-equilibrated to 65 °C were added to bring the temperature of the culture immediately to 42 °C. The cells were then grown for an additional hour at 42 °C and harvested by centrifugation. The resulting cell pellet was washed one time in ice-cold 50 mM Tris-HCl, pH 7.5, and pelleted again by centrifugation. The washed pellet was quick-frozen in liquid nitrogen and stored at -80 °C. For a typical preparation, the above procedure was repeated four times to yield ~30 g of wet cell pellet.

Purification of Ho Endonuclease

Purification of Ho was carried out as described by Kostriken and Heffron (17)2 with minor modifications. All procedures were performed on ice or at 4 °C. Quantitation of the purification is given in Table I.

Table I.

Purification of Ho endonuclease


Fraction Step Protein Activitya Specific activity Yield Purification

mg units units/mg % -fold
I Crude extract 4200 10,800 2.6 100 1
II (NH4)2SO4 cut 610 6600 11 61 4.2
III Phosphocellulose 70 2100 110 19 42
IV Phenyl-Sepharose 4.8 900 190 8.3 73
V DEAE-Sephacel 3.9 900 230 8.3 88
VI Bio-Rex 70 0.04 14 350 0.13 135

a One unit is defined as the amount of Ho that cleaves 1 µg of pDC283 in 1 h at 30 °C.

The frozen cell pellet (30 g) was resuspended in 20 ml of Buffer A (100 mM Tris-HCl, pH 7.5, 5 mM EDTA, 5 mM DTT, 2 mM benzamidine HCl, 0.2 mM PMSF, and 50% glycerol). Lysozyme was added to a final concentration of 2 mg/ml, and the resulting solution was incubated for 20 min on ice. After adding 140 ml of Buffer B (100 mM Tris-HCl, pH 7.5, 500 mM (NH4)2SO4, 10 mM MgSO4, 5 mM DTT, 0.2% Triton X-100, 2 mM benzamidine HCl, and 0.2 mM PMSF), incubation was continued for another 30 min. The cell lysate was centrifuged in a Beckman Ti-45 rotor (21,000 rpm, 1 h, 4 °C), and the supernatant was collected (Fraction I; 26.25 mg/ml, 160 ml). Fraction I was brought to 30% saturation with solid ammonium sulfate, gently stirred for 30 min, and centrifuged in a Beckman Ti-45 rotor (21,000 rpm, 20 min, 4 °C). The supernatant was collected, brought to 45% saturation with solid ammonium sulfate, gently stirred for 30 min, and centrifuged in a Beckman Ti-45 rotor (30,000 rpm, 20 min, 4 °C). The pellet was redissolved in 60 ml Buffer C (100 mM KPO4, pH 7.5, 10 mM MgSO4, 5 mM DTT, 10% glycerol, 2 mM benzamidine HCl, and 0.2 mM PMSF). The resulting solution was centrifuged to remove precipitated MgNH4PO4, and the supernatant was collected (Fraction II; 10.17 mg/ml, 60 ml). Fraction II was applied at 25 ml/h to a phosphocellulose column (2.0 cm2 × 6.0 cm) equilibrated with Buffer C. The column was washed with 10 ml of Buffer C, and proteins were eluted with a 240-ml linear gradient of 0-1 M NaCl in Buffer C. Fractions containing Ho endonuclease activity were pooled (Fraction III; 0.29 mg/ml, 69 ml). Fraction III was brought to 1 M NaCl with a 5 M NaCl solution and loaded at 6 ml/h on a phenyl-Sepharose CL-4B column (0.64 cm2 × 3.8 cm) equilibrated with Buffer D (20 mM Tris-HCl, pH 7.5, M NaCl, 10 mM MgSO4, 5 mM DTT, 10% glycerol, 2 mM benzamidine HCl, and 0.2 mM PMSF). After washing with 4 ml of Buffer D, the column was eluted at 6 ml/h with a 10-ml linear gradient of 10-50% ethylene glycol in Buffer E (20 mM Tris-HCl, pH 7.5, 1 M NaCl, 10 mM MgSO4, 5 mM DTT, 2 mM benzamidine HCl, and 0.2 mM PMSF), followed by a 5-ml wash with 50% ethylene glycol and 2% Triton X-100 in Buffer E. Fractions containing Ho endonuclease were pooled to generate Fraction IV (0.8 mg/ml, 6 ml). Fraction IV was diluted with 18 ml of Buffer F (20 mM Tris-HCl, pH 7.5, 10 mM MgSO4, 5 mM DTT, 2 mM benzamidine HCl, and 0.2 mM PMSF) and loaded at 6 ml/h on a DEAE-Sephacel column (0.64 cm2 × 0.5 cm) equilibrated with Buffer G (20 mM Tris-HCl, pH 7.5, 10 mM MgSO4, 5 mM DTT, 10% glycerol, 2 mM benzamidine HCl, and 0.2 mM PMSF). The flow-through fraction was collected (Fraction V; 0.22 mg/ml, 18 ml). Fraction V was loaded at 6 ml/h on a Bio-Rex 70 column (0.64 cm2 × 1 cm) equilibrated with Buffer G. The column was washed with Buffer G until the ultraviolet absorption of the effluent was 0 and then eluted with a 10-ml linear gradient of 0-1 M NaCl in Buffer G. Fractions containing Ho endonuclease activity and showing only one band by SDS-polyacrylamide gel electrophoresis were pooled (Fraction VI; 0.1 mg/ml, 0.4 ml). Fraction VI was concentrated to 50 µl in a Microcon-10 concentrator (Amicon, Inc.), made 50% (v/v) glycerol, and stored at -20 °C.

High-resolution Gel-filtration Chromatography

The Stokes radius of Ho was determined by gel filtration according to the method of Laurent and Killander (23). Typically, 50 µl of Fraction III were loaded at 0.2 ml/min on a Sephadex 200 HR 5/20 column (Pharmacia) equilibrated with Buffer C. Eluted fractions (0.027 ml) were collected and analyzed for Ho by the standard cleavage assay. A calibration curve was generated using ribonuclease A, chymotrypsinogen A, ovalbumin, albumin, aldolase, catalase, and ferritin, with Stokes radii of 16.4, 20.9, 30.5, 35.5, 48.1, 52.2, and 61.0 Å, respectively. Blue dextran 2000 (Pharmacia) was used to mark the void volume.

Zinc Ion Dialysis

All dialysis and reaction buffers were pretreated with Chelex 100 chelating resin to remove zinc ions. Zinc ions were subsequently removed from Ho fractions by dialysis against buffer containing the Zn2+-specific chelator 1,10-phenanthroline. Typically, 100 µl of Fraction III were dialyzed at 4 °C for 2 h against 100 ml of Buffer C containing 2 mM 1,10-phenanthroline. This procedure was repeated two more times using fresh dialysate. In control experiments, 100 µl of Fraction III were dialyzed under the same conditions, with the exception that the 1,10-phenanthroline was omitted from the dialysate.

Other Procedures

SDS-polyacrylamide gel electrophoresis of purified fractions was performed on 10% gels (24). Proteins were visualized by staining with Coomassie Brilliant Blue R-250. Protein concentrations were determined by the method of Bradford (25) using bovine serum albumin as the standard. Electron microscopy of Ho-DNA complexes was carried out according to the method of Inman and Schnös (26) with the following modifications. After adsorption of DNA and protein-DNA complexes, the grids were positively stained by brief immersion in 95% ethanol containing 3% uranyl acetate. A thin film of platinum-palladium was subsequently evaporated at low angle onto the grid to make the DNA and protein-DNA complexes clearly visible.


RESULTS

Purification of Ho Endonuclease

To isolate biochemically homogeneous Ho endonuclease, we used the bacterial overexpression system of Kostriken and Heffron (17). This system utilizes a plasmid containing the yeast HO gene driven by the PR promoter of bacteriophage lambda . Also carried on the plasmid is the gene for the thermolabile repressor cI857, which represses the PR promoter at low but not high temperatures. Ho endonuclease was induced by heat shock, and the enzyme was purified by the method of Kostriken and Heffron (17) with slight modifications (see "Materials and Methods"). The assay for Ho monitored the cleavage of a linear DNA molecule that contained the MATa locus and flanking sequences; 1 unit of activity is defined as the amount of enzyme that cleaves 1 µg of substrate in 1 h at 30 °C (see "Materials and Methods"). The results of a typical purification are summarized in Table I and Fig. 2. The purified protein migrated as a single band of Mr = 65,000 on an SDS gel, in close agreement with the predicted molecular weight of the Ho polypeptide (Mr = 65,940). The final fraction retained >85% of its activity after 12 months of storage at -20 °C.


Fig. 2. Purification of Ho from a bacterial overexpression system. Ho was purified as described under "Experimental Procedures." Aliquots from Fractions I-VI (see Table I) were electrophoresed on a 12% polyacrylamide gel and stained with Coomassie Blue. Lane M contains electrophoretic standards (Bio-Rad) with the indicated molecular weights.
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Fundamental Biochemical Characteristics of Ho Endonuclease

We used the homogeneous protein to characterize the fundamental biochemical properties of Ho. The first step in this process was to determine the optimal in vitro conditions for the enzyme. Cleavage reactions were carried out under varying conditions, and the activity of Ho under these conditions was determined by the standard agarose gel assay. Several conclusions were drawn from these data. First, Mg2+ ions were absolutely required for Ho activity, as no cleavage was observable in the absence of the ion (Fig. 3A). The optimal concentration of MgCl2 was 5-30 mM (Fig. 3A). Second, NaCl was not required for activity, as reasonable cleavage was seen in its absence (Fig. 3B). Cleavage, however, was stimulated 2.5-fold when NaCl was present at concentrations between 50 and 100 mM (Fig. 3B). Third, the activity of Ho exhibited a relatively broad pH range, with optimal cleavage occurring between pH 7.5 and 9.0 (Fig. 3C). Fourth, a reduced sulfhydryl group(s) on the enzyme may be involved in Ho activity, as the addition of N-ethylmaleimide to the cleavage reaction at a concentration of 50 mM eliminated product formation (data not shown). Finally, the enzyme appeared relatively stable, as the addition of protein stabilizers had no effect on cleavage (data not shown). These parameters are similar to those of standard type II restriction endonucleases.


Fig. 3. Optimization of the in vitro Ho cleavage reaction. In vitro cleavage assays were carried out at different MgCl2 concentrations (A), at different NaCl concentrations (B), and at different pH values (C). Cleavage was quantitated by the standard agarose gel assay.
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Effect of Zinc Ions on Ho Endonuclease Activity

One interesting feature of the amino acid sequence of Ho is that the carboxyl-terminal 100 amino acids contain five putative zinc finger motifs (21). Recently, a mutation in the HO gene product that eliminates activity was mapped to one of these potential zinc fingers, providing genetic evidence for the importance of these motifs (27). To provide further biochemical evidence that these fingers are important for Ho activity, we asked whether zinc ions were required in the in vitro cleavage reaction. This was determined by carrying out two experiments (see "Materials and Methods"). In the first, an aliquot of Fraction III was dialyzed for 6 h against a buffer containing 1,10-phenanthroline, a Zn2+-specific chelating agent. In the second, an identical aliquot was dialyzed for the same time against a buffer lacking 1,10-phenanthroline. The two samples were then added back to reaction mixtures containing Mg2+ ions, but no Zn2+ ions, and the activities of the dialyzed proteins were determined by the standard agarose gel assay. The results showed that the aliquot dialyzed against 1,10-phenanthroline retained only 0.4% of its activity, as predicted for a protein that requires zinc. By comparison, the aliquot dialyzed against buffer lacking 1,10-phenanthroline retained 95.5% of its activity, indicating that dialysis per se was not responsible for the inactivation of the first aliquot.

These results argue that the removal of zinc ions from the Ho preparation inactivates the enzyme. However, another interpretation is that the 1,10-phenanthroline inactivated the protein through some other nonspecific mechanism. To rule out this possibility, the enzyme that had been dialyzed against 1,10-phenanthroline was added to a standard reaction supplemented with 10-5 M ZnCl2. Under these conditions, cleavage was stimulated 40-fold, i.e. the inactivated aliquot went from 0.4 to 16% wild-type activity. Thus, a large part of the inactivation was directly attributable to the loss of zinc ions. Further experiments showed that optimal activity required a final Zn2+ concentration between 10-6 and 10-4 M. Even under optimal conditions, the reconstituted activity was 6-fold lower than the original wild-type activity. The reason for this partial reactivation remains unclear. However, it is possible that refolding a zinc finger after removal of the Zn2+ ion is a kinetically unfavorable reaction. Alternatively, the 1,10-phenanthroline might have inactivated a fraction of Ho by other nonspecific means.

Ho Is a Monomer in Solution

We next determined whether Ho existed in solution as a monomer or some higher order multimer. (Given the asymmetry of the Ho recognition sequence, there was no a priori reason to expect that the enzyme would exist as a dimer like many type II restriction endonucleases.) Purified Ho was subjected to high-resolution gel-filtration chromatography (see "Materials and Methods"), and the elution of Ho activity was compared with the elution of known molecular weight standards. From these data, the apparent molecular weight of Ho was calculated using the method of Laurent and Killander (23). Ho endonuclease activity eluted as a symmetrical peak that corresponded to a native molecular weight of 81,000 (Fig. 4). Ho therefore appears to be a slightly elongated monomer in solution.


Fig. 4. Ho is a monomer in solution. The Stokes radius of Ho was determined by gel filtration according to the method of Laurent and Killander (23). Typically, 50 µl of Fraction III were loaded at 0.2 ml/min on a Sephadex 200 HR 5/20 column equilibrated with Buffer C. Eluted fractions (0.027 ml) were collected and analyzed for Ho by the standard cleavage assay. A calibration curve was generated using ribonuclease A (16.4 Å), chymotrypsinogen A (20.9 Å), ovalbumin (30.5 Å), albumin (35.5 Å), aldolase (48.1 Å), catalase (52.2 Å), and ferritin (61.0 Å). Blue dextran 2000 was used to mark the void volume.
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In Vitro Cleavage by Ho Is Inefficient

We defined 1 unit of activity for Ho as the amount of enzyme necessary to cleave 1 µg of MAT vector in 1 h. According to this definition, Fraction VI, which appeared to be electrophoretically pure, had a specific activity of 350 units/mg of protein. By comparison, using 1 unit defined in an analogous fashion, a purified fraction of EcoRI had a specific activity of ~1.5 × 106 units/mg of protein (28). Thus, the specific activity of our purified Ho fraction was >4000-fold lower than that of a typical EcoRI preparation. We also observed that many of our in vitro reactions never went to completion at lower enzyme concentrations, even when the digestion period extended over several hours (data not shown). These data indicated that Ho was extremely inefficient in the in vitro reaction.

To better understand this property, we further characterized the stoichiometry requirements of Ho. Different amounts of enzyme were incubated with a fixed amount of DNA; aliquots were removed at various times; and the extent of cleavage was determined by the standard agarose gel assay (Fig. 5). Full cleavage occurred in the reaction when Ho was present at 3.45 µM (2 units/25 µl), i.e. 1 Ho molecule/2.6 bp of substrate DNA. For the 8100-bp MAT vector, this translated into ~3000 Ho molecules/recognition sequence. When Ho was present at a concentration of 1 molecule/6.5 bp (0.8 units/25 µl), ~10% of the molecules remained uncleaved. Moreover, product formation plateaued after 2-3 h of incubation in all the reactions, indicating that Ho cleavage was exceedingly slow even at high concentrations of enzyme.


Fig. 5. Ho acts in a stoichiometric fashion. Cleavage reactions containing Ho at 2 units/25 µl (triangles), 0.8 units/25 µl (circles), or 0.4 units/25 µl (squares) were incubated at 30 °C. At the indicated times, aliquots were removed; the reaction was terminated; and cleavage was quantitated by the standard gel assay.
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One way to account for this inefficiency is to hypothesize a gross inactivation of the enzyme during the extensive purification. Four observations, however, argue against this interpretation. First, the use of earlier chromatographic fractions led to similar kinetic parameters (data not shown). Second, as described above (see "Purification of Ho Endonuclease"), purified Ho remained stable after long periods of storage, which argued against any inherent instability of the enzyme. Third, as described above (see "Effect of Zinc Ions on Ho Endonuclease Activity"), purified Ho could be dialyzed for up to 6 h at 4 °C and still retain full activity, again indicating that the activity was stable. Finally, endonucleases that are structurally and functionally homologous to Ho, such as I-SceI, I-SceII, I-SceIII, I-SceIV, and PI-SceI, are also much less active than standard restriction enzymes in in vitro cleavage reactions, arguing that the inefficiency seen in the Ho reaction is common to all members of this class of endonucleases (29-38).

Ho Forms Large Aggregates with DNA

What then accounts for the inefficiency of Ho in the in vitro reaction? One possibility is that the majority of Ho is shunted down a cleavage-deficient pathway. Our first evidence in support of this possibility came during a band shift analysis. We observed that the addition of Ho to short double-stranded oligonucleotides carrying the Ho recognition sequence resulted in protein-DNA complexes that were too large to migrate into the gel (data not shown). This suggested to us that Ho, which is a monomer in solution, might bind as a multimer to DNA. If true, then at least some of the Ho molecules bound to substrate might not participate in cleavage.

We used electron microscopy to further analyze the formation of complexes between Ho and DNA. Two sets of reactions were conducted. In the first set, the substrate DNA was linearized pRW17, a YCp50-based vector carrying the Ho recognition sequence (see "Materials and Methods"). Ho was added at concentrations of 0.2 molecules/bp (Reaction R1), 0.02 molecules/bp (Reaction R2), and 0 molecules/bp (Reaction R3). In the second set, the substrate DNA was linearized pSF21, a YCp50-based vector carrying non-MAT DNA. Ho was added again at concentrations of 0.2 molecules/bp (Reaction R4), 0.02 molecules/bp (Reaction R5), and 0 molecules/bp (Reaction R6). All six reactions were incubated at 30 °C for 30-45 min, and the resulting protein-DNA complexes were spread on collodion grids according to the protocol of Inman and Schnös (26). Electrophoretic examination indicated that 70% of the substrate DNA was cleaved in Reaction R1 and <5% in Reaction R2. No cleavage occurred in the other reactions.

These experiments confirmed that Ho forms aggregates with DNA (Table II). In Reaction R1, which contained 1 Ho molecule/5 bp, DNA molecules in the solution aggregated into structures referred to here as "florettes" (Fig. 6C). A florette is defined as a large complex containing a densely staining central region and surrounding loops of DNA. The sizes of the florettes were somewhat variable, although most contained ~15-20 loops. The formation of florettes in Reaction R1 was very efficient, as they comprised 66% of the visible structures in the solution; the other 30% constituted mainly of discrete molecules, defined as unaggregated single molecules of DNA (Fig. 6 and Table II). It is important to state, however, that since the florettes likely contain multiple molecules of DNA (see "Discussion"), significantly >66% of the total DNA molecules may be present within florettes.

Table II.

Electron microscopic analysis of Ho-DNA complexes


Reaction Substrate Ho Discrete molecules Tangled aggregates Florettes Total

mol Ho/bp
1 pRW17 0.2 62 7 136 205
(30.2%) (3.4%) (66.3%)
2 pRW17 0.02 51 183 2 236
(21.6%) (77.5%) (0.8%)
3 pRW17 0 219 4 0 223
(98.2%) (1.8%) (0%)
4 pSF21 0.2 124 10 145 279
(44.4%) (3.6%) (52.0%)
5 pSF21 0.02 60 180 1 241
(24.9%) (74.7%) (0.4%)
6 pSF21 0 196 6 0 202
(97.0%) (3.0%) (0%)


Fig. 6. Visualization of Ho-DNA complexes by electron microscopy. Shown is the electron microscopic visualization of discrete molecules (A), tangled aggregates (B), and florettes (C). The vector was pRW17 (see "Materials and Methods"), and all molecules were viewed at the same magnification. Bar = 1 µm.
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The Ho recognition sequence was not necessary for florette formation. As seen in Table II, florettes formed as efficiently on linearized pSF21 as on pRW17. Moreover, electron microscopic examination of the florettes revealed no significant differences between the two substrates (data not shown). This lack of specificity indicated that florette formation depended upon some other feature of the DNA, possibly the ends of the linear substrate molecules. As seen in Fig. 6C, florettes contain loops of DNA. Even though the original substrate was linear, relatively few DNA ends were visible in florettes, suggesting that they were sequestered within the densely staining core region. If the formation of florettes was primarily dependent upon ends, it might be expected that they would form efficiently on any linear substrate, even those lacking an Ho recognition sequence. Further evidence for the binding of Ho to ends is described below (see "The Y-proximal End of the Break Competes Efficiently in the Ho Cleavage Reaction").

The amount of protein required to form florettes correlated with the amount of protein required for cleavage. Thus, when the protein/DNA ratio was decreased 10-fold to 1 Ho molecule/50 bp, cleavage and florette formation dropped to <5% (Table II). Aggregation of substrate still occurred under these conditions, but the aggregates were much more unstructured, forming what is referred to as "tangled aggregates" (Fig. 6B). Again, the frequency of tangled aggregate formation was very high, and an Ho recognition sequence was not required. The amount of DNA in tangled aggregates appeared more variable. These results suggest that florettes, rather than aggregation per se, are required for optimal cleavage in vitro.

Ho Cleavage Occurs by a Stoichiometric Reaction Mechanism

The kinetic analysis shown in Fig. 5 also indicates that Ho recycles inefficiently from product DNA to new substrate. At subsaturating amounts of Ho, product formation reached a series of plateaus below full cleavage. This characteristic is the hallmark of a stoichiometric mechanism, defined as a reaction mechanism in which a protein catalyst carries out one round of product formation and then fails to recycle to a new substrate. By comparison, if Ho recycled, as is true of most enzymes, full cleavage would occur at subsaturating amounts, although the slope of product formation with time would decrease with decreasing amounts of enzyme. We hypothesize that Ho fails to recycle because of its sequestration within florettes (see "Discussion").

The Y-proximal End of the Break Competes Efficiently in the Ho Cleavage Reaction

Ho is a member of a class of endonucleases with similar protein sequences. One well studied member of this class is I-SceI, a Group I intron-encoded endonuclease present in yeast mitochondria. The studies described above indicate that Ho and I-SceI share not only structural homology, but also functional homology. A detailed kinetic analysis showed that I-SceI, like Ho, recycles inefficiently from cleaved product DNA to new substrate (39). Another interesting characteristic of I-SceI is that it has an affinity for one of the ends of its double strand break product (39). Given the similarities between the two enzymes, we wondered whether the same might be true for Ho.

To test this, we carried out standard cleavage reactions in the presence of oligonucleotide LHo or RHo, two self-complementary competitor oligonucleotides that mimicked the Y-proximal and Z-proximal ends, respectively, of the double-stranded break. Renaturation of LHo generated a "snap-back," double-stranded molecule consisting of the 16 bp normally Y-proximal of the cleavage site. The competitor was also designed to maintain the appropriate 3'-overhang generated after Ho cleavage. Renaturation of RHo produced a similar double-stranded molecule, with the exception that the 16 bp were from the Z side of the break. The Y-proximal oligonucleotide strongly inhibited cleavage in the in vitro reaction, regardless of whether the substrate was a MATa or MATalpha vector (Fig. 7). The Z-proximal oligonucleotide, however, had a much smaller effect (Fig. 7). We conclude that Ho, like I-SceI, has a higher affinity for one end of its double strand break product, in this case, the Y-proximal end. As described under "Discussion," this preferential binding is consistent with molecular studies of mating type switching in yeast.


Fig. 7. The Y-proximal side of the break is a stronger competitor than the Z-proximal side. Standard cleavage reactions were carried out in the presence of oligonucleotides LHo (squares) and RHo (circles). Substrate DNA contained the MATalpha locus (closed symbols) or the MATa locus (open symbols).
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DISCUSSION

Mating type switching in yeast is an ideal model system for analyzing genetic recombination (15). The reaction is relatively simple, highly efficient, and controllable (40-42). Moreover, the mechanism of mating type switching shares the following important similarities with meiotic recombination. First, DNA intermediates that arise during mating type switching (heteroduplex DNA joints, Holliday junctions, etc.) are extremely similar to those that arise during meiotic recombination (42). Second, gene products required for optimal mating type switching are also required for meiotic recombination, such as the products of the RAD51, RAD52, RAD54, RAD55, RAD57, and XRS2 genes (41, 43-45). Finally, mating type switching, like meiotic recombination, initiates with a DSB (16-18). Regarding this last point, the mating type system is particularly attractive in that Ho endonuclease, the enzyme responsible for generating the DSB, has been identified (16, 17).

This laboratory is using the mating type system to analyze molecular mechanisms that regulate the formation of DSBs at MAT. To understand these mechanisms, it is crucial to understand the biochemical characteristics of Ho endonuclease. As a result of the studies of Heffron and co-workers (16, 17, 19, 20), DNA sequences required for cleavage within the Ho recognition sequence have been identified and characterized (Fig. 1B). In the studies described here, we have characterized several fundamental biochemical parameters of the enzyme itself.

Perhaps the most salient feature of Ho is its extreme inefficiency in an in vitro cleavage reaction. We observed that maximal cutting occurred when Ho was present at a concentration of 1 Ho molecule/3 bp of DNA, which for our substrate translated into ~3000 Ho molecules/recognition sequence. Moreover, even when present at optimal concentrations, complete digestion in the in vitro reaction required >2 h. Given the affinity of Ho for the Y-proximal end of the break (Fig. 7), we wondered whether the ends of our linear substrates might nonspecifically titrate out the enzyme, thereby leading to the apparent low activity in the cleavage assays. Three results, however, argue against this interpretation. First, the right end of the break competed very inefficiently (Fig. 7). Second, linearized pBluescript DNA was not an efficient competitor in the in vitro cleavage reactions (data not shown). Finally, cleavage of relaxed circular DNA, i.e. DNA that lacks ends, did not cleave significantly more efficiently than linear substrates (data not shown). We suggest instead that Ho requires other proteins to cleave MAT DNA efficiently. Recently, we identified a protein called YZ-binding protein that acts as a positive activator of Ho cleavage inside cells (46). Other proteins may also be required.

An unusual characteristic of the in vitro cleavage reaction was the formation of large protein-DNA aggregates, referred to as florettes, which are defined as structures containing a densely staining core region and radiating loops of DNA. When reactions containing the optimal concentration of Ho were spread for electron microscopic analysis, the number of separate DNA molecules/grid was significantly lower than the number seen in the control reactions containing no Ho. This suggests to us that the florettes contain multiple DNA molecules. In support of this, Ho at suboptimal levels generated tangled aggregates that clearly contained multiple molecules. It is difficult to ascertain whether florettes result from an artifactual aggregation process. However, all of the florettes within a sample (and in fact between samples) were strikingly similar in their morphology, relative lack of free DNA ends, and number of loops. This morphological consistency might not be expected to result from a random aggregation process. Moreover, other proteins known to aggregate DNA do not generate the type of structure observed here (47-49). We therefore suggest that the ability to aggregate multiple DNA molecules may be intrinsic to Ho.

Florette formation may partially explain the unusual kinetics of the in vitro reaction. Ho cleavage occurred by a stoichiometric mechanism, in which the protein recycled poorly from product to new substrate. To account for this, we hypothesize that florettes, once formed, are relatively stable, i.e. their dissociation and reassembly on new molecules are slow. Inherent to this model is the assumption that florettes are required for cleavage. In support of this, florettes failed to form at lower concentrations of Ho (300 Ho molecules/recognition sequence), and this failure correlated with a low level of cleavage. It is important to state that an unstructured aggregate still formed under these latter conditions, indicating that aggregation per se was not required for cleavage. If we also hypothesize that florette formation is relatively slow, which seems reasonable given its complex structure, this might explain why cleavage, even in the presence of optimal amounts of Ho, is also slow.

Ho belongs to a family of nucleases that share a common dodecapeptide motif first identified in mitochondrial endonucleases. This family of enzymes includes intron-homing endonucleases, such as I-SceI, I-SceII, I-SceIII, I-SceIV, and Endo.SceI from yeast (29, 30, 33-38). Also included in this group are endonucleases encoded by inteins (<UNL>in</UNL>ternal pro<UNL>tein</UNL> sequences that are cleaved from larger primary translation products), such as PI-SceI (31, 32). These proteins share many biochemical characteristics with Ho. For instance, all recognize large, non-palindromic sequences, and several have specific activities significantly lower than those of type II restriction endonucleases. In the case of I-SceI, this lower activity has been studied in depth by careful kinetic analysis of the in vitro cleavage reaction (39). The I-SceI cleavage reaction was found to separate into two kinetically distinct phases, an early and rapid cleavage phase and a later and slower turnover phase.

Given the similarities between Ho and I-SceI, we wondered whether the functional homology between the enzymes might extend to other characteristics. One interesting characteristic of I-SceI is that one end of its DNA break was a more efficient competitor than the other end in an in vitro cleavage reaction (39). Based on this observation and the enzyme's slow turnover, Perrin et al. (39) hypothesized that I-SceI remains bound to one side of the break after cleavage. This may occur so that the protein can participate in later steps of the mitochondrial recombination reaction; alternatively, it may occur so that the protein can help regulate the RNA splicing reaction responsible for I-SceI production (39). Our experiments also show that the Y-proximal side of the Ho break is a better competitor than the Z-proximal side, further extending the similarities between these two proteins.

During mating type switching in vivo, the DSB formed by Ho is acted upon by an unknown exonuclease(s) that exposes single-stranded DNA for subsequent invasion into the silent loci (42). It is intriguing to note, however, that exonucleolytic degradation into Y is blocked after Ho cleavage, while degradation into Z occurs normally (42). Degradation into Y does occur, however, in strains lacking the silent loci. This latter observation makes two points regarding the asymmetric degradation. First, it is not intrinsic to the exonuclease that attacks the break; and second, it is dependent upon an interaction between MAT and the silent loci (42). One simple model to account for these phenomena hypothesizes that a protein complex remains bound to the Y side of the break, thereby blocking entrance of the exonuclease. If true, then formation of the complex depends upon an interaction between MAT and one of the silent loci. The properties of Ho defined in this study suggest that it might participate in such a complex. As required by the model, 1) Ho does not recycle efficiently from cleaved DNA; 2) it forms aggregates containing multiple DNA molecules; and 3) it binds more tightly to the Y-proximal side of the break than to the Z-proximal side. We therefore hypothesize that Ho remains bound to the Y-proximal side of break and participates in the formation of a synaptic complex between MAT and the silent loci.

The conclusion that Ho remains bound to the Y-proximal side of the break, however, must be tempered by another set of studies carried out by Sugawara and Haber (40). These authors showed that both ends of the break were susceptible to exonucleolytic degradation in vivo when the Ho recognition sequence was integrated into non-MAT DNA in the yeast genome. Thus, with respect to nuclease sensitivity, cleavage in this latter system is similar to cleavage at MAT in the absence of the silent loci (42). Therefore, Ho may remain stably bound in vivo to the Y-proximal side of the break only in the context of other factors specific to the mating loci.

Finally, the primary structure of Ho, predicted from the sequence of the HO gene, indicated several potential zinc finger motifs (21). Recently, Raveh and co-workers (27) have shown that a single mutation that maps to the first of these zinc fingers eliminates Ho cleavage activity in vivo. These latter results, in combination with our observation that zinc ions are required for Ho activity, strongly argue that Ho endonuclease contains a zinc finger(s) that is necessary for activity.


FOOTNOTES

*   This work was supported by Grant 3978 from the Council for Tobacco Research, U. S. A. and Grant GM52192-01A1 from the National Institutes of Health.The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
   To whom correspondence should be addressed: Dept. of Molecular Biology and Biochemistry, Rutgers, State University of New Jersey, P. O. Box 759, Piscataway, NJ 08855-0759. Tel.: 908-445-0731; Fax: 908-445-5735.
1   The abbreviations used are: DSBs, double-stranded breaks; bp, base pair(s); DTT, dithiothreitol; PMSF, phenylmethylsulfonyl fluoride.
2   R. Kostriken, personal communication.

Acknowledgments

We thank Richard Kostriken for providing reagents and invaluable advice throughout all aspects of this work. We also thank Andrew Vershon for careful reading of this manuscript.


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