Origin Function in Saccharomyces cerevisiae - Europe PMC

MOLECULAR AND CELLULAR BIOLOGY, Oct. 1992, p. 4305-4313 0270-7306/92/104305-09$02.00/0 Copyright © 1992, American Society for Microbiology

Vol. 12, No. 10

The ARS Consensus Sequence Is Required for Chromosomal Origin Function in Saccharomyces cerevisiae ATUL M. DESHPANDE AND CAROL S. NEWLON* Department of Microbiology and Molecular Genetics, University of Medicine and Dentistry of New JerseyNew Jersey Medical School, 185 South Orange Avenue, Newark, New Jersey 07103-2174 Received 20 May 1992/Returned for modification 22 June 1992/Accepted 9 July 1992

Replication origins have been mapped to positions that coincide, within experimental error (several hundred base pairs), with ARS elements. To determine whether the DNA sequences required for ARS function on plasmids are required for chromosomal origin function, the chromosomal copy of ARS306 was deleted and the chromosomal copy of ARS307 was replaced with mutant derivatives of ARS307 containing single point mutations in domain A within the ARS core consensus sequence. The chromosomal origin function of these derivatives was assayed by two-dimensional agarose gel electrophoresis. Deletion of ARS306 deleted the associated replication origin. The effects on chromosomal origin function of mutations in domain A paralleled their effects on ARS function, as measured by plasmid stability. These results demonstrate that chromosomal origin function is a property of the ARS element itself. The autonomously replicating sequence (ARS) elements of the yeast Saccharomyces cerevisiae allow colinear DNA molecules to replicate extrachromosomally (reviewed in reference 7). ARS elements are detected by a plasmid transformation assay, and the efficiency of ARS elements is determined by plasmid stability assays (reviewed in reference 7). By using two-dimensional (2-D) agarose gel electrophoresis techniques for replicon mapping (6, 15), it has been shown that replication origins map to positions that coincide with ARS elements, not only in plasmids but also in chromosomes (reviewed in reference 11). The methods used to map origins place them within several hundred base pairs of ARS elements. This lack of precision and the observation that some ARS elements appear not to function as chromosomal replication origins (10) have led us to investigate the role of specific DNA sequences required forARS function in chromosomal origin function. Mutational analysis of several ARS elements has shown that DNA sequences that are essential for ARS function on plasmids include an 11-bp consensus sequence [5'-(AIT)TT TAT(A/G)TlIT(A/T)-3'] and a region of variable length 3' to the T-rich strand of the consensus sequence, called domain B (reviewed in reference 7). The 11-bp consensus sequence is part of a 14- to 15-bp domain A sequence (19, 23). Quantitative analyses of the effects of point mutations in ARS307 (39) and of newly created ARS elements in M13 vector sequences (20) have defined the specific base pairs within the consensus sequence that are required for ARS function on plasmids. These studies have shown that mutations that reduce or abolish ARS activity occur at every position within the 11-bp sequence. The high conservation and stringent sequence requirements of domain A suggest that it is likely a protein-binding site. A protein binding specifically to the T-rich strand of the core consensus sequence has been isolated in three different laboratories (14, 21, 32). In addition, Bell and Stillman (3a) have recently reported the isolation of a multiprotein complex, the origin recognition complex, which recognizes the double-stranded form of the ARS consensus sequence. While binding of both *

the single-strand-binding protein and the origin recognition complex to mutantARS sequences correlates well with ARS function, it is not yet known whether either of these proteins binds to domain A in vivo or plays an essential role in DNA replication. The function(s) of domain B and the role of specific DNA sequences in mediating its function(s) are not well understood. Binding sites for ARS binding factor 1 (ABF1 or OBF1) serve as enhancers of ARS function and are active when present in domain B or on the other side of the consensus sequence in domain C (23, 40). In addition to an ABF1 binding site, domain B of ARSI has been shown to contain two other short sequence elements that enhance ARS function, as measured by plasmid stability. These two functionally distinct short sequence elements, one of which is a near match to the ARS consensus sequence, may function as protein-binding sites (29), a DNA-unwinding element (26), or nuclear scaffold attachment sites (1). When coupled with domain A, any two of the three domain B elements can provide ARS function (23). To provide a rigorous test of the equivalence of ARS elements and chromosomal origins of replication, we have examined the effects on chromosomal origin function of deleting ARS306 and replacing ARS307 with mutant derivatives whose activities in plasmids had been analyzed previously (39). In this report, we demonstrate that deletion of a 220-bp fragment containing ARS306 abolishes a chromosomal origin of replication and that the effects on chromosomal origin function of point mutations in domain A of ARS307 correlate with their effects on ARS function.

MATERIALS AND METHODS Strains and media. S. cerevisiae YNN216 (MA Ta/MATat ura3-52Iura3-52 lys2-801/lys2-801 ade2-101/ade2-101) was used for the construction of the ARS306 deletion (34). Strain YNN214 (AL4Ta ura3-52 lys2-801 ade2-101) was used for the analysis of ARS307 point mutations (34). Escherichia coli JA226 was used for amplification of plasmid DNA (9). E. coli transformants were grown in Luria broth supplemented with 50 ,ug of ampicillin per ml (22). Yeast transformants were

Corresponding author. 4305

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TABLE 1. ARS307 derivatives CEN3 CEN 3

B

P RI

ARS307 ARS308 ARS309

ARS306

ARS305

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ARS307

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FIG. 1. Maps of regions of chromosome III. (A) Physical map of a 90-kb region showing the positions of five ARS elements and the centromere. ARS305 is approximately 40 kb from the left telomere. (B) The 5.3-kb PstI fragment containing ARS306. (C) The 4.5-kb BamHI-EcoRV fragment containing ARS307. (D) The 5.1-kb PstI fragment containing the ARS306 deletion. (E) The 522-bp EcoRIClaI fragment containing the pseudo-wild-type ARS307. The SphI and Sall sites marked by asterisks flank domain A and are not present in the wild-type ARS element. Solid rectangles show the regions with ARS activity. The solid triangle shows the position of the deletion of the HindIII-BglII fragment. The lines labeled probe indicate the fragments used for probing 2-D gels. Bg, BglII; C, ClaI; H, HindIII; P, PstI; RI, EcoRI; RV, EcoRV; Sa, SalI; Sp, SphI.

selected on plates lacking uracil (39). For DNA preparations, yeast strains were grown in liquid YEPD medium (33).

Plasmid construction. The ARS306 deletion plasmid was constructed by Ann Dershowitz and carries a deletion of the 220-bp HindIII-BglII fragment containing ARS306 (28). For the replacement of the chromosomal copy of wildtype ARS307 with mutant derivatives containing single point mutations (Fig. 1), plasmids containing the mutant derivatives flanked by wild-type chromosomal sequences were constructed. The plasmid used for this purpose, pRS306, contains URA3 as a selectable marker (34). The 2.3-kb BamHI-EcoRI fragment flanking the left side of ARS307 (Fig. 1C) was cloned into the multiple cloning site of pRS306 to create plasmid pAC21. The 1.75-kb ClaI fragment flanking the right side of ARS307 (Fig. 1C) was modified by converting the right ClaI site to anXXhoI site by filling in the ClaI site and adding an XhoI linker. This ClaI-XhoI fragment was cloned into the multiple cloning site of pAC21 to create pAC22. The 522-bp EcoRI-ClaI fragment containing wildtype ARS307 was cloned into M13mpl8, and a SalI site was created at position 196 by oligonucleotide-directed mutagenesis. This construct was called M13mpl8:500. The 196-bp wild-type EcoRI-SalI fragment from M13mpl8:500 was then replaced with EcoRI-SalI fragments containing point mutations isolated from plasmids pVH402, pVH410, pVH412, pVH418, pVH420, pVH421, and pVH428 (38, 39) to create M13mpl8:502, M13mpl8:510, M13mpl8:512, M13mpl8:518, M13mpl8:520, M13mpl8:521, and M13mpl8:528, respectively. After the presence of the desired point mutations was confirmed by DNA sequencing, the 522-bp EcoRI-ClaI fragments from the double-stranded M13 replicative forms were cloned into pAC22 to create the seven plasmids listed in Table 1. Transformations. E. coli transformations were carried out by the method of Dagert and Erlich (8). Yeast transformations were done by the lithium acetate method (17) or by electroporation (3). ARS phenotype determination. YNN214 was transformed with the ARS307 plasmids (Table 1) by electroporation.

Plasmid

ARS phenotype

Sequence domain A'of

Yeast construct strain carrying

pAC502b pAC510 pAC512 pAC518 pAC520 pAC521 pAC528 pAC528

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YP502 YP510 YP512 YP518 YP520 YP521 YP528 YP628C

a Lowercase letters identify single-base-pair mutations in the wild-type ARS307 sequence.

Pseudo-wild-type ARS307 construct (39; this work). c The wild-type popout obtained from the same transformant which yielded the YP528 mutant popout. b

Plasmids were considered Ars+ if the initial Ura+ transformants continued to grow through two sequential restreakings on plates lacking uracil. All others were scored as Ars-. Construction of ARS deletion and replacements. Plasmids carrying the desired ARS306 deletion and ARS307 derivatives (Table 1) were used to transform the appropriate yeast strains; integrants were selected, and then strains from which the plasmid had been spontaneously excised by homologous recombination between duplicated flanking sequences were selected on 5-fluoroorotic acid-containing medium (5). Excision of the plasmid either regenerates the wild-type chromosome (wild-type "popout") or removes the wild-type sequence and replaces it with the mutant construct

(mutant popout). For the ARS306 deletion (Fig. 1D), a diploid strain (YNN216) was transformed and a strain carrying the mutant popout was identified by the presence of the expected 5.1-kb PstI fragment carrying theARS306 deletion. The diploid was sporulated, and the sizes of theARS306 PstI fragments in the four spores from one tetrad were determined. As expected, two spores carried the ARS306 deletion and two spores carried wild-type ARS306 (8a). One of the wild-type spores (strain YP306A) and one of the ARS306 deletion-containing spores (strain YP306D) were used for further analysis. For the ARS307 substitutions, plasmids carrying the desired ARS307 constructs were linearized by digestion with ClaI to direct integration into chromosome III. Popouts were screened by Southern analysis, and mutant popouts were identified by the presence of SphI and SalI restriction sites not present in wild-type ARS307 (Fig. 1E). Preparation of DNA. Small-scale E. coli plasmid preparations were carried out by the alkaline lysis method of Birnboim and Doly (4). Large-scale plasmid preparations were performed by the alkaline lysis method (22). Plasmid DNA was purified on cesium chloride-ethidium bromide step gradients (12). For isolation of yeast genomic DNA, cultures in the late log phase (4 x 107 cells per ml) were mixed with an equal volume of toluene stop solution (95% ethanol, 3% toluene, 20 mM Tris [pH 7.4]); 0.25 M EDTA was added immediately to a final concentration of 10 mM (18). Cells were harvested either by filtration onto a nylon membrane (1.2-,um pore size) or by centrifugation and washed three times with ice-cold sterile water. Genomic DNA was isolated by the procedure of Huberman et al. (15). 2-D agarose gel electrophoresis. The neutral-neutral 2-D agarose gel electrophoresis technique of Brewer and Fangman (6) was used for the analysis of replication intermediates. Approximately 10 to 20 ,ug of genomic DNA was

VOL. 12, 1992

digested with appropriate restriction endonucleases (New England Biolabs), using the buffers supplied with the enzymes or the buffer described by Mirkovitch et al. (25). The direction of replication fork movement was determined by a modification of the standard 2-D gel technique (reviewed in reference 11). Briefly, DNA was digested and run in the first dimension as usual, and then DNA in the gel lane was digested with a second restriction endonuclease before electrophoresis in the second dimension. The in-gel restriction digestion was accomplished by first incubating the gel slice for 30 min in 10 mM Tris (pH 8.0)-0.1 mM EDTA at room temperature. It was then equilibrated for 1 h at room temperature with 500 ml of the restriction endonuclease buffer recommended by the supplier. The equilibrated gel slice was overlaid with 800 U of restriction endonuclease in 600 ,ul of 1 x restriction buffer and incubated for 4 to 5 h at 37°C. An additional 800 U of restriction enzyme in 600 ,ul of 1 x restriction buffer was added, and the gel slice was incubated overnight at 37°C. After this gel slice was washed in 500 ml of 10 mM Tris (pH 8.0)-1.0 mM EDTA for 30 min, it was placed in a second-dimension gel and run under the usual conditions for 16 to 20 h (6). Transfer of DNA to membranes. DNA was transferred from agarose gels to nitrocellulose or Nytran membranes by the method of Smith and Summers (36). Hybridization. Hybridizations were carried out at 65°C in 5x SSC (lx SSC is 0.15 M NaCl plus 0.015 M sodium citrate)-50 mM sodium PP,-5x Denhardt's solution (lx is 0.02% each bovine serum albumin, polyvinylpyrrolidone, and Ficoll)-0.5% sodium dodecyl sulfate (SDS)-100 ,g of calf thymus DNA per ml. The Multiprime random primer labeling kit (Amersham Corp.) was used to prepare 32p_ labeled probes with [a-32P]dCTP, purchased from Amersham Corp. The DNA probes used are shown in the figures and are described in the figure legends. Quantitative analysis of efficiency of origin usage. Efficiency of origin usage was determined by densitometric analysis of autoradiograms with a Molecular Dynamics computing densitometer (model 300B). RESULTS Deletion of 220-bp fragment containing ARS306 abolishes a chromosomal replication origin. As a first approach to determining whether the DNA sequences required for chromosomal replication origin function are the same as those required for ARS function, the 220-bp HindIII-BglII fragment previously shown to contain ARS306 (28) was deleted from chromosome III. Figure 2A shows the 2-D agarose gel pattern obtained after analysis of the 5.3-kb PstI fragment containing ARS306 (Fig. 1B). The transition from a bubble arc to a Y arc shown is the pattern expected if an active origin coincides with ARS306. Analysis of overlapping restriction fragments (data not shown) confirmed that the replication origin maps to ARS306, in agreement with the results of Zhu et al. (41). Deletion of the 220-bp ARS306containing fragment also deletes the replication origin, as shown by the disappearance of the bubble arc in the 2-D gel pattern obtained with the ARS306 deletion strain (Fig. 2B). This pattern demonstrates that the PstI fragment carrying the ARS306 deletion (Fig. 1D) is replicated for its entire length as a Y-shaped replication intermediate. To show that the failure to detect a replication bubble arc in the ARS306 deletion fragment was not due to loss of replication bubbles from the DNA preparation, the 3.2-kb EcoRV fragment containing ARS307 was analyzed. A chro-

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FIG. 2. Deletion of ARS306 removes a replication origin. In this and subsequent figures, electrophoresis in the first dimension was from left to right and electrophoresis in the second dimension was from top to bottom. (A) Pattern obtained from analysis of the 5.3-kb PstI fragment containing ARS306. (B) Pattern obtained with the 5.1-kb PstI fragment containing the ARS306 deletion. In panels A and B, the 4.7-kb HindIII-PstI fragment (Fig. 1B) was used as a probe, and the length of exposure was 12 days. The spots along the line of linear fragments (marked by arrows) are partial restriction digest products. (C) Diagram of the pattern shown in panel A. (D) Diagram of the pattern shown in panel B. In panels C and D, the arcs are labeled to identify the replication intermediates that migrate in them. Bubble, bubble-shaped intermediates; Y, Y-shaped intermediates; X, X-shaped intermediates. The dashed line shows the position of migration of the linear molecules. The dark spot in the lower right corner from which the replication arcs arise is the position at which the monomer-length, nonreplicating molecules detected by the probe migrate.

mosomal origin of replication has been mapped to ARS307 (Fig. 1A), and deletion of the 522-bp EcoRI-ClaI fragment containing ARS307 abolishes its origin activity (13). As expected, a replication bubble arc was readily detected at ARS307 (data not shown). These results demonstrate that DNA sequences required for chromosomal replication origin function are contained within the same DNA fragments as ARS elements and encouraged us to examine the effects on origin function of point mutations within the consensus sequence of ARS307. In addition to the arcs of replication intermediates described above, the autoradiogram in Fig. 2A and diagram in Fig. 2C contain an arc that has been ascribed to X-shaped recombination intermediates (6a). We have seen this arc regularly in association with bubble arcs but never in association with simple Y arcs (see also Fig. 3). In this case, several lines of evidence suggest that it is unlikely that this arc actually contains simple recombination intermediates. First, if it resulted from recombination intermediates, then

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FIG. 3. Effect on origin function of point mutations in domain A of ARS307. In all panels except F, the 3.2-kb EcoRV fragment containing ARS307 (Fig. 1D) was analyzed. The 1.75-kb ClaI fragment (Fig. 1D) was used as a probe in panels B, E, and G. The 522-bp EcoRI-ClaI fragment (Fig. 1D) was used as a probe in panels A, C, D, H, I, and J. The pattern shown in panel F was obtained by stripping the blot shown in panel C and reprobing it with the 1.2-kb BamHI-ClaI fragment from plasmid A6C (28). Strains: (A) YNN214; (B) YP502; (C) YP528; (D) YP510; (E) YP521; (F) ARS305 in YP528; (G) wild-type popout in YP628; (H) YP520; (I) YP518; (J) YP512. The length of exposure varied from 7 to 15 days. Partial restriction digestion products are marked by arrows. The streak which goes up from some of the monomer spots and the line which goes leftward from the monomer may be the result of overloading of DNA. Hybridization along the line of linear molecules between partial digestion products in panels D and H resulted from degradation of DNA during isolation.

the X arc should be present when the chromosomal DNA is cut at the origin, releasing Y-shaped replication intermediates. We have been unable to detect the arc in this situation. Second, the arc is apparent in both haploid (Fig. 2 and 3) and diploid strains. Therefore, it must result from sister chromatid exchange if it is the result of recombination. Finally, the abundance of the structure makes it unlikely that it is a recombination intermediate, although little is actually known about rates of sister chromatid exchange in S. cerevisiae. It is possible that this arc results from daughter strand extrusion from replication bubbles, as proposed by Dijkwel et al. (9a) to explain the occurrence of complex branched molecules in their DNA preparations. Effect on origin activity of point mutations in domain A of ARS307. To replace the chromosomal copy of wild-type ARS307, plasmids were constructed carrying mutant derivatives of ARS307 containing single point mutations in domain A (see Materials and Methods). In the previous analysis of these ARS307 mutants (39), 196-bp EcoRI-SalI fragments containing ARS307 were analyzed in a different vector and within a different DNA sequence context than were used here. Since DNA sequence context effects on ARS function have been described (reviewed in reference 27), it was necessary to determine the ARS phenotypes of the plasmids constructed to replace the chromosomal copy of ARS307. Table 1 shows that the phenotypes determined correlate well with published results, demonstrating that flanking chromosomal sequences and the vector context do not have any significant influence on the phenotypes of the point mutants. After replacement of the chromosomal copy of ARS307 with each of these constructs, their chromosomal origin

function was assessed by 2-D gel analysis of the 3.2-kb EcoRV fragment shown in Fig. 1C. At least two DNA preparations of each of the yeast strains listed in Table 1 were analyzed. Figure 3A shows the pattern obtained with DNA prepared from the haploid strain used for subsequent studies, YNN214. The transition from bubble to Y arc shows that, as expected, there is an active chromosomal origin of replication at or nearARS307. The construct used to replace the chromosomal copy of ARS307, called the pseudo-wildtype (Table 1), differs from the wild type by having SphI and SalI sites flanking domain A (Fig. 1E) and by the elimination of a near match (10 of 11) that overlaps the exact match to the ARS consensus sequence in domain A (39). In order to confirm that these changes did not affect origin function, we replaced the chromosomal copy of ARS307 with the pseudowild-type construct (strain YP502). Figure 3B shows that this construct maintains origin activity indistinguishable from that of the wild type. The effects on origin function of three single base mutations in domain A ofARS307 which abolishARS activity (39) were examined. The mutations analyzed included a T to G transversion at position 9 of the consensus sequence (strain YP528, Fig. 3C), a T to G transversion at position 3 (strain YP510, Fig. 3D), and a G to T transversion at position 7 (strain YP521, Fig. 3E). In each case, only a simple Y arc was detected when the EcoRV fragments containing these mutations were analyzed by 2-D gel electrophoresis, suggesting that all three point mutations abolish origin function. No bubble arcs were detected on these blots even after 20 days of exposure, which is three times longer than the exposures shown. With the background on these filters taken

VOL. 12, 1992


into account, origin function of 10 to 15% of wild-type origin function would have been detected. To show that the failure to detect a bubble arc is due to the mutation in ARS307 and is not an artifact of DNA preparation, the blots shown in Fig. 3C, D, and E were stripped and reprobed with a probe specific for ARS305, which was shown previously to be an active origin of replication (16). The pattern shown in Fig. 3F, which was obtained from the blot shown in Fig. 3C, is representative of the results obtained with the blots shown in Fig. 3D and E. The strong transition from bubble arc to Y arc indicates that bubble arcs can be detected readily on these filters. To show that the plasmid integration and excision process used to construct the chromosomal ARS307 mutations did not alter origin function, origin function at ARS307 was analyzed in a wild-type popout obtained from the same transformant which yielded the YP528 mutant popout. As expected, origin function was retained in this wild-type popout (Fig. 3G). Taken together, these results demonstrate that single point mutations within domain A of ARS307 reduce chromosomal replication origin function to less than 10 to 15% of the normal level. In addition to point mutations that abolish ARS function, the effects on origin function of point mutations that either do not affect or reduce ARS function were examined. Of particular interest was a T to C transition at position 6 of domain A. This mutation results in wild-type ARS function on plasmids (39), but the original ARS consensus sequence does not allow a C at position 6. The bubble arc in Fig. 3H shows that this mutant derivative indeed has chromosomal origin function. Fork direction analysis (see below) corroborates the conclusion that this point mutant retains full origin function. Other single base mutations in the ARS307 consensus sequence, e.g., a T to A transversion at position 6 and a T to A transversion at position 4, reduce ARS efficiency on plasmids (39). Figures 3I and J show the results obtained when the wild-type ARS307 was replaced by mutant derivatives carrying these single base changes. In each case, the patterns show predominantly simple Y arcs, but faint bubble arcs can also be seen. These results suggest that these mutations reduce origin activity as well as ARS function. Efficiency of origin usage. If a replication origin is active in only a fraction of the population, then an origin-containing fragment should replicate as a bubble-containing intermediate when the origin is active and as a Y-shaped intermediate when the origin is inactive. In principle, it should be possible to estimate the efficiency of origin usage from the ratio of bubble-shaped molecules to Y-shaped molecules in the patterns shown in Fig. 3. However, as discussed by Fangman and Brewer (11), quantitating the relative signal is difficult because of the different shapes of the arcs and because bubble-containing intermediates have half the life span of Y-shaped intermediates. In addition, breakage of bubblecontaining intermediates at one of the replication forks can convert them to Y-shaped intermediates. A more accurate estimate of the efficiency of origin use can be obtained by determining the direction of replication fork movement in the regions flanking the origin. If the origin is active in every cell cycle, then only forks moving away from the origin are expected. However, if the origin is inactive in a fraction of the population, then forks moving toward the origin in one flanking region or the other should be seen. In the case of ARS307, the nearest active replication origins are at ARS306, 34 kb to the left (41; this study), and ARS308 and ARS309, 6 and 24 kb, respectively, to the right

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FIG. 4. Patterns expected from fork direction analysis. (A) Physical map of the 13.8-kb region around ARS307, showing the 4.1-kb PstI-BamHI fragment immediately to the left and the 3.4-kb EcoRI fragment extending to the right of ARS307. It also shows the positions of CEN3 and ARS308. Thick lines show the fragments released after in-gel restriction digestion at sites marked by asterisks. The solid square shows the position of ARS307 in the EcoRI fragment. The lines labeled probe indicate the fragments used for probing fork direction gels. (B) Diagram of intermediates obtained after in-gel restriction digestion of replicating DNA when a replication fork emanating fromARS307 replicates the EcoRI fragment. (C) Diagram of replication intermediates expected after in-gel restriction digestion of replicating DNA when replication forks from either ARS308 or ARS309 replicate the fragment containing ARS307. In panels B and C, early replication intermediates are shown on the right-hand side and late intermediates are shown on the left-hand side, paralleling their migration during first-dimension electrophoresis. (D and E) 2-D gel patterns expected following in-gel digestion between first- and second-dimension electrophoresis. Panel D shows the pattern expected from the situation diagrammed in panel B, and panel E is the pattern expected from panel C. In panels D and E, the arcs marked with an arrow show the pattern expected without in-gel digestion. H, HindIII; P, PstI; RI, EcoRI; RV, EcoRV; B, BamHI.

(13). Replication initiates at ARS308 only 10 to 20% of the time (13). If replication initiates at these origins at similar times and the forks move at constant rates, then it is expected that the ARS307-containing fragment would be replicated by a fork emanating from ARS308 or ARS309. A modification of the neutral-neutral 2-D gel technique in which replication intermediates are cleaved with a restriction endonuclease between the first- and second-dimension electrophoretic separations can be used to determine fork direction (reviewed in reference 11). Figure 4 shows a map of the chromosomal region surrounding ARS307 and summarizes the 2-D gel patterns expected for the flanking regions. To determine fork direction in the right flanking region, chromosomal DNA was cut with EcoRI prior to electrophoresis in the first dimension. It was then cut in the gel with EcoRV prior to electrophoresis in the second dimension, and the blot was probed to detect the larger (2.2-kb) EcoRIEcoRV fragment. If the 3.4-kb EcoRI fragment containing the right flanking

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FIG. 5. Fork direction analysis. (A, B, C, and D) Patterns obtained from fork direction analysis of the PstI-BamHI fragments (Fig. 4A) to the left of ARS307 in strains YP502, YP528, YP518, and YP520, respectively. (E, F, G, and H) Patterns obtained from fork direction analysis of the EcoRI fragments containingARS307 (Fig. 4A) in strains YP502, YP528, YP518, and YP520, respectively. The fragments used to probe the filters are shown in Fig. 4A. The partial restriction digestion products are marked by arrows. The sparks seen in panels E and G are due to static electricity released when the films were removed from the blots prior to developing. The line which runs leftward from the completely and incompletely digested monomer spots probably results from overloading of DNA. This line of hybridization obscures the spots resulting from the release of linear fragments from Y-shaped replication intermediates.

region of ARS307 is replicated by forks emanating from ARS307 (Fig. 4B), then the large EcoRI-EcoRV fragments released by in-gel cleavage of early replication intermediates are Y-shaped but smaller in mass than those from an undigested sample. The Y arc will originate from the 2.2-kb EcoRI- plus EcoRV-digested (shifted) monomer spot but will end abruptly when the replication fork passes the EcoRV site used for in-gel cleavage, because linear fragments are released from late Y-shaped intermediates. These cleaved late intermediates are seen as a dark spot with an electrophoretic mobility the same as that of the shifted monomer spot (Fig. 4D). On the other hand, if this region is replicated by a fork moving toward ARS307 from an active origin to the right of ARS307 (Fig. 4C), then the large EcoRI-EcoRV fragments released from the earliest replication intermediates will be linear and of the same mass as the shifted monomer spot. These linear molecules released from early replication intermediates are detected as a line extending leftward from the shifted monomer spot (Fig. 4E). After the replication fork has passed the in-gel restriction site, the Y-shaped intermediates detected by the probe are released. These intermediates are seen as Y arcs arising some distance to the left of the shifted monomer spot. Because the separation of DNA in the first dimension is proportional to the logarithm of the molecular weight, the distribution of molecules replicated to a greater extent is compressed relative to that of less-replicated molecules. This causes the horizontal signal from linear fragments released by in-gel digestion of replicating molecules to be shorter in Fig. 4D than in Fig. 4E and the "hook" on the Y arc in Fig. 4E to be more nearly vertical than that in Fig. 4D.

Similar reasoning applies to the analysis of the 4.1-kb PstI-BamHI fragment to the left of ARS307. The direction of fork movement was analyzed in the regions flanking ARS307 in the pseudo-wild-type construct, strain YP502; an Ars- mutant, strain YP528; a reducedefficiency mutant, strain YP518; and the mutant carrying the change at position 6 that results in wild-type ARS function, strain YPS20 (Fig. 5). The patterns obtained from the analysis of the regions flankingARS307 in the pseudo-wild-type strain show that the forks move away in both directions. In Fig. 5A, which shows the left flanking region, it can be seen that the in-gel digestion with HindIII releases early replication intermediates that are Y-shaped and are seen in an arc emanating from the shifted monomer spot. The in-gel digestion was incomplete, so a second pattern containing uncleaved monomer-length molecules and uncleaved replication intermediates can also be seen. Similarly, Fig. 5E shows that in-gel cleavage with EcoRV releases the early Y-shaped intermediates expected if forks move to the right, away from ARS307. The absence from both of these patterns of the arcs predicted for forks moving toward ARS307 suggests that ARS307 is active as a chromosomal origin of bidirectional DNA replication in every cell cycle. From densitometric analysis of the film shown in Fig. SE and other exposures of the same blot, it was estimated that forks moving toward ARS307 20% of the time would have been detected. Analysis of the direction of fork movement in the Arspoint mutant (Fig. SB and F) revealed that, as expected for this strain, the ARS307-containing fragment is replicated by a fork that approaches ARS307 from the right. The fork direction pattern for the left flanking region (Fig. SB) is the

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same as that for the pseudo-wild type (Fig. 5A). The pattern for the right flanking region (Fig. 5F) was the opposite of that found for the pseudo-wild type, as in-gel digestion with EcoRV released an arc of Y-shaped replication intermediates that arose well to the left of the monomer spot. This pattern is expected if replication forks move through the right flanking region toward ARS307. These results confirm that the Ars- point mutant lacks detectable chromosomal origin function. With the reduced-efficiency mutant (Fig. SC and G), it can be seen that replication forks traverse the right flanking region in both directions. Two arcs of Y-shaped molecules are released by in-gel digestion with EcoRV, one arising from the cut monomer spot and the second arising well to the left. In conjunction with the analysis of the left flanking region, which reveals only forks moving away fromARS307, this result demonstrates that the mutation that reduces ARS efficiency also reduces the frequency of initiation of chromosomal DNA replication at ARS307. From densitometric analysis of the Y arcs in Fig. 5G at several places along their length, it was estimated that replication initiates at ARS307 in about 40% of the population. Finally, the analysis of the point mutation that results in wild-type ARS function (Fig. 5D and H) demonstrates that replication initiates at ARS307 with wild-type efficiency in this strain. Only forks moving away from ARS307 can be seen in both flanking regions. While the patterns in Fig. 5F and G clearly show largesubfragment Y arcs ascending from a point well to the left of the large-subfragment monomer spot, the shape of the Y arc differs somewhat from what was expected (Fig. 4E). In the autoradiograms shown, the hook on the Y arc apparently descends from a region of intense hybridization at the apex of the Y arc and appears to extend somewhat to the left of the intact-fragment Y arc. We have been unable to account satisfactorily for the intense hybridization or for the unexpected extension of the hook. DISCUSSION The results presented in this article show directly that the DNA sequences required for ARS function on plasmids are also required for chromosomal origin function. Deletion of a 220-bp fragment containingARS306 (this study) and a 522-bp fragment containingARS307 (13) removes replication origins from chromosome III. Moreover, point mutations in domain A of ARS307 which abolished ARS function (39) also abolished detectable chromosomal origin function. These results confirm and extend the recent observations of Rivier and Rine (31), who showed that replacing domain A of a synthetic HMR silencer with random DNA sequence abolished the ability of that silencer to function as a weak chromo-

somal origin. The results of the analysis of the effects of mutations in ARS307 on chromosomal origin function presented here correlate very well both qualitatively and quantitatively with those of previous analyses of their effects onARS function in plasmids (39). First, three different mutations (present in strains YP510, YP521, and YP528) that destroyed the ability of ARS307-containing plasmids to transform cells at high efficiency also abolished detectable origin function, as measured both by standard neutral-neutral 2-D gel analysis and by fork direction analysis. Second, two point mutations (in YP512 and YP518) that reduced ARS efficiency also reduced chromosomal origin function. Third, changes that had no effects on plasmid stability, including removal of an overlap-


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ping match to the consensus sequence and the introduction of restriction sites flanking domain A (pseudo-wild type) and a point mutation at position 6 (strain YP520), had no effect on origin function. Quantitation of replication intermediates on 2-D gels is difficult for the reasons discussed above. The most accurate quantitation can be obtained from fork direction analysis. From this analysis of the constructs with wild-type plasmid stabilities, it was estimated that the ARS307 origin is active in at least 80% of the population, a number in good agreement with estimated plasmid loss rates (the percentage of cell divisions per generation in which a plasmid-containing and a plasmid-free cell are produced) of 23% (39). OtherARS elements, e.g., ARS1, show higher plasmid stabilities than ARS307 (39). More-sensitive origin function measurements will be necessary to determine whether the chromosomal origin associated with ARS307 is less efficient than the one associated with ARS1. The initiation frequency of about 40% measured in the reduced-efficiency mutant YP518 is also in excellent agreement with the measured plasmid loss rate of 72%. Finally, by conservative estimate, it would have been possible to detect an arc arising from forks moving rightward through the ARS307 flanking region if replication initiated 20% of the time in the Ars- derivative. Neither the transformation assay for ARS function (reviewed in reference 27) nor the 2-D gel assay for origin function is able to detect low-level function. The possibility that the T to G mutation at position 9 of domain A may drastically reduce rather than abolish origin function was suggested by the finding of a very weak bubble arc in a single DNA preparation from strain YP528. Analysis of two independent DNA preparations from Ars- strains YP510 and YP521 and four other independent DNA preparations from the Ars- strain YP528 revealed only Y arcs. While we cannot eliminate the possibility that a revertant arose in the culture from which the bubble-containing DNA preparation was made, these results point out the difficulty in definitively establishing that either ARS function or origin function is abolished. It was particularly interesting that the mutant carrying the T to C mutation at position 6 of domain A demonstrates wild-type chromosomal origin function. This was the only point mutation analyzed that produced a domain A that differed from the ARS consensus sequence but did not cause reduced plasmid stability (39). The finding that this mutant also has wild-type origin function demonstrates that the consensus sequence should include an alternative C at position 6. Allowing a C at position 6 produces a perfect match to the consensus sequence in several S. cerevisiae ARS elements previously thought to lack one, including ARS310 (30), the rDNA ARS (35), and several other heterologous ARS elements as well, e.g., the Drosophila mitochondrial fragment HHa 240 (24), the Chlamydomonas chloroplast fragment 01 (37), and the M13 mutant fragment D10 (20). Another example of a near match with a C at position 6 that has been shown to play a role in ARS activity is in the pSRI plasmid, which also has two perfect matches to the ARS core consensus sequence (2). The effects of point mutations in domain A on origin function indicate that domain A plays an important role in either initiation or the very early stages of replication. Because very little is known about the early events taking place at yeast origins of replication, we can only speculate that the abolition of origin activity may be due to the

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alteration of a recognition site to which a protein required for the initiation of replication binds. ACKNOWLEDGMENTS We thank Sarah Taylor and Virginia Van Houten for reconstructing the EcoRI-ClaI fragments carrying the ARS307 point mutations, Ann Dershowitz for constructing theARS306 deletion, Jim Theis for comments on the manuscript, and members of the Newlon laboratory for helpful discussions. This work was supported by Public Health Service grant GM35679 from the National Institutes of Health. A.M.D. was partially supported by a graduate stipend from the UMDNJ Foundation. REFERENCES 1. Amati, B. B., and S. M. Gasser. 1988. Chromosomal ARS and CEN elements bind specifically to the yeast nuclear scaffold. Cell 54:967-978. 2. Araki, H., and Y. Oshima. 1989. An autonomously replicating sequence of pSR1 plasmid is effective in two yeast species, Zygosaccharomyces rouxii and Saccharomyces cerevisiae. J. Mol. Biol. 207:757-769. 3. Becker, D. M., and L. Guarente. 1991. High-efficiency transformation of yeast by electroporation. Methods Enzymol. 194:182187. 3a.Bell, S. P., and B. Stillman. 1992. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature (London) 357:128-134. 4. Birnboim, H. C., and J. Doly. 1979. A rapid alkaline extraction procedure for screening recombinant DNA. Nucleic Acids Res. 7:1513-1523. 5. Boeke, J. D., J. Trueheart, G. Natsoulis, and G. R. Fink. 1987. 5-Fluoro-orotic acid as a selective agent in yeast molecular genetics. Methods Enzymol. 154:164-175. 6. Brewer, B. J., and W. L. Fangman. 1987. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51:463-471. 6a.Brewer, B. J., E. Sena, and W. L. Fangman. 1988. Analysis of replication intermediates by two-dimensional agarose gel electrophoresis. Cancer Cells 6:229-234. 7. Campbell, J. L., and C. S. Newlon. 1991. Chromosomal DNA replication, p. 41-146. In J. R. Broach, J. R. Pringle, and E. W. Jones (ed.), The molecular and cellular biology of the yeast Saccharomyces: genome dynamics, protein synthesis, and energetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. 8. Dagert, M., and S. D. Erlich. 1979. Prolonged incubation in calcium chloride imuproves the competence of Escherichia coli cells. Gene 6:23-28. 8a.Dershowitz, A., and C. S. Newlon. Unpublished data. 9. Devenish, R. J., and C. S. Newlon. 1982. Isolation and characterization of a yeast ring chromosome III by a method applicable to other circular DNAs. Gene 8:277-288. 9a.Dikwel, P. A., J. P. Vaughn, and J. L. Hamlin. 1991. Mapping of replication initiation sites in mammalian genomes by twodimensional gel analysis: stabilization and enrichment of replication intermediates by isolation on the nuclear matrix. Mol. Cell. Biol. 11:3850-3859. 10. Dubey, D. D., L. R. Davis, S. A. Greenfeder, L. Y. Ong, J. Zhu, J. R. Broach, C. S. Newlon, and J. A. Huberman. 1991. Evidence suggesting that the ARS elements associated with silencers of the yeast mating-type locus HML do not function as chromosomal DNA replication origins. Mol. Cell. Biol. 11:

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