(Received for publication, August 23, 1995)
From the
Calf 5` to 3` exo/endonuclease, the counterpart of the human FEN-1 and yeast RTH-1 nucleases, performs structure-specific cleavage of both RNA and DNA and is implicated in Okazaki fragment processing and DNA repair. The substrate for endonuclease activity is a primer annealed to a template but with a 5` unannealed tail. The results presented here demonstrate that the nuclease must enter the 5` end of the unannealed tail and then slide to the region of hybridization where the cleavage occurs. The presence of bound protein or a primer at any point on the single-stranded tail prevents cleavage. However, biotinylation of a nucleotide at the 5` end or internal to the tail does not prevent cleavage. The sliding process is bidirectional. If the nuclease slides onto the tail, later binding of a primer to the tail traps the nuclease between the primer binding site and the cleavage site, preventing the nuclease from departing from the 5` end. A model for 5` entry, sliding, and cleavage is presented. The possible role of this unusual mechanism in Okazaki fragment processing, DNA repair, and protection of the replication fork from inappropriate endonucleolytic cleavage is presented.
A 5` to 3` exonuclease purified from calf has been shown to
cooperate functionally with calf DNA polymerase to perform nick
translation (Siegal et al., 1992). In this reaction,
exonucleolytic activity on a downstream primer required synthesis from
an upstream primer. The exonuclease was later found to be much more
active on a nicked compared with a gapped double-stranded DNA substrate
(Murante et al., 1994). This suggests that stimulation of
nuclease activity by DNA synthesis resulted from continuous generation
of the favored substrate.
The calf 5` to 3` exonuclease has been implicated in processing of Okazaki fragments (Turchi et al., 1994). A DNA template, primed with an oligoribonucleotide that had been extended at the 3` end with DNA, was used as a model Okazaki fragment. Calf RNase H1 removed the initiator RNA with a single cut at the 5` side of the ribonucleotide at the RNA-DNA junction. The 5` to 3` exonuclease then could remove the remaining ribonucleotide, creating a 5` DNA. Extension of an upstream primer by polymerization in the presence of DNA ligase I allowed the two primers to be joined, as expected on the lagging replication fork strand in vivo.
In addition to the above activities, the 5` to 3` exonuclease could also cleave endonucleolytically (Murante et al., 1994). The substrate for this reaction was a DNA primer-template, having a downstream primer with a noncomplementary, unannealed region at the 5` end. Additionally, an upstream primer was annealed directly adjacent to the first annealed nucleotide of the downstream primer. Endonucleolytic cleavage removed the unannealed region as an intact segment. Cleavage occurred either at the point of annealing to make a nicked substrate or one nucleotide downstream to make a 1-nucleotide gap. The 5` to 3` exonuclease domains of Escherichia coli DNA polymerase I and Thermus aquaticus (Taq) DNA polymerase (Lyamichev et al., 1993) are functionally homologous to the calf nuclease. The homologous nuclease has also been purified from murine cells and designated cca nuclease (Goulian et al., 1990) and flap endonuclease (FEN-1) (Harrington and Lieber, 1994). The corresponding HeLa cell nuclease has been purified (Ishimi et al., 1988; Waga et al., 1994; Robins et al., 1994; Murray et al., 1994), and called maturation factor I (Waga et al., 1994) and DNase IV (Robins et al., 1994). The homolog of this mammalian protein has been identified in Saccharomyces cerevisiae and named the RTH-1 nuclease (Sommers et al., 1995; Johnson et al., 1995). Knockout mutants are temperature-sensitive for DNA replication and repair of methylmethane sulfonate lesions (Sommers et al., 1995). RTH-1 nuclease was also found to be necessary for the stability of DNA repeats in yeast, suggesting that mutation of the human counterpart could impair the mismatch repair pathway that protects from colorectal cancer (Johnson et al., 1995).
In this report, we explore the substrate structure requirements for endonuclease activity of the calf nuclease. We show that the nuclease must slide over the 5` end of the unannealed tail of the primer and then along the single-stranded tail to the point of cleavage. The sliding action is bidirectional. The presence of a primer or protein on the tail prevents entry of the nuclease or traps a nuclease that is already on the tail. Cleavage is observed on tails with covalent adducts on nucleotides either at the 5` end or within the tail. A model is proposed that has implications for the biological role of this unusual nuclease.
Figure 3:
Preincubation of nuclease with substrate
prior to annealing of a blocking primer permits endonucleolytic
cleavage by trapping the enzyme on the 5` tail. A,
endonucleolytic activity was assessed on the D4:U2:T2 substrate having
one of three different blocking primers, B2, B3, or B4, hybridized
respectively at distances leaving a gap of 53, 31, or 0 nucleotides
from the first annealed nucleotide on the downstream primer beyond the
73-nucleotide tail. In the even numbered lanes, enzyme was preincubated
with the substrate in the absence of a blocking primer (lanes
4, 6, and 8) or the presence of dT,
a noncomplementary primer (NC in lane 2) as described
under ``Experimental Procedures.'' No prebinding (odd
lanes) indicates that the enzyme was added after the addition and
annealing of the blocking primers. Products were resolved on a
denaturing 10% polyacrylamide gel and visualized by autoradiography. B, native 7.5% polyacrylamide gel analysis was used to detect
enzyme-substrate complexes. Preincubation and primers are indicated as
in A. In lane 2, migration of substrate in the
absence of enzyme (-E) and blocking primer is indicated
by I. Preincubation with enzyme results in a mobility shift of
substrate without blocking primer to position II. Substrate
with blocking primer migrates to III and is shifted to IV when bound by enzyme.
Gel shifts with calf 5` to 3` exo/endonuclease were also employed.
For these experiments, the initial reaction mixtures lacked
Mg, and the amount of substrate and total volume were
doubled to 10 fmol and 50 µl, respectively. Each of the four
different substrates in Fig. 3were incubated with enzyme either
before or after addition of primers D2, D3, or D4 or a noncomplementary
primer. The nuclease was bound at 4 °C for 5 min. The blocking
primers, added in a 100-fold molar excess, were annealed by placing the
reaction at 37 °C for 2 min and then at room temperature for 10
min. Half of the reaction solution was mixed with 5
loading
buffer (50% glycerol with bromphenol blue and xylene cyanole markers).
These samples were analyzed by separation on a 7.5% native gel followed
by autoradiography. To the remaining sample, MgCl
was added
to 5 mM, and endonuclease activity was assayed as described
above.
Figure 1:
Measurement of rates for exonucleolytic
and endonucleolytic degradation of either 5` phosphorylated or
nonphosphorylated downstream primers. Rates of exonucleolytic and
endonucleolytic activity were determined using substrates pictured in
the graph inset. The exonuclease substrate (I)
consisted of primers U2 and D1 annealed directly adjacent to each other
on template T1. See Table 1for the key to oligonucleotide
sequences in this and subsequent figures. The endonuclease substrate (II) had an unannealed 5` tail of 12 nucleotides that formed
when primer D2 was annealed downstream of U2 on T1. Downstream primers
D1 and D2 were 3` end P-labeled. Assays were performed as
described under ``Experimental Procedures'' with 5 fmol of
substrate and 2.25 units of calf 5` to 3` nuclease per reaction. In the
graph, plots of exonucleolytic activity (circles) were derived
from calculations of percent substrate degraded by a single nucleotide;
endonucleolytic activities (triangles) were based on the
amount of substrate cleaved to products 18 or 19 nucleotides long from
release of the tail as a 12- or 13-nucleotide fragment. These products
were resolved in a denaturing 12% polyacrylamide gel and quantitated
using a Molecular Dynamics PhosphorImager(TM) and ImageQuant(TM)
software. Closed symbols indicate activity on substrates
having a 5` phosphorylated downstream primer; open symbols represent values for nonphosphorylated substrates. The 5`
phosphate was unlabeled and introduced by polynucleotide kinase. Each
time point represents the mean of three experiments; the error bars are
S.E.
Figure 2: Blocking of endonucleolytic cleavage with primers that hybridize to the single-stranded 5` tail. Assays measuring cleavage of an endonuclease substrate (D3:U2:T1) with a 25-nucleotide 5` tail are depicted in A. Blocking primer B1 anneals to the 5` end of D3 and leaves a single-stranded gap of 8 nucleotides between itself and the point at which the tail anneals to the template. A time course with substrate lacking a blocking primer is shown in lanes 1-6; substrate with the blocking primer is in lanes 7-12. B shows endonuclease activity on a substrate with a 73-nucleotide tail (D4:U2:T2). Primer B2 hybridizes to the 5` tail at a position that generates a single-stranded gap of 53 nucleotides. Lanes 1-6 show a time course with substrate lacking a blocking primer; lanes 7-12 have substrate with the blocking primer. Substrate structures and oligonucleotide composition are shown above the appropriate lanes. Downstream primers D3 and D4 were 5` radiolabeled, and reaction conditions were as described under ``Experimental Procedures.'' Size markers at the left indicate product length in nucleotides.
To determine whether the calf nuclease slides along the 5` tail, we employed a substrate with a 73-nucleotide tail. The longer single-stranded region allowed us to position primers at three distinct locations along the tail: primer B2 was annealed at the 5` end, primer B3 was annealed in the middle, and primer B4 was juxtaposed to the site of cleavage. Fig. 2B shows a time course experiment in which the nuclease was able to cleave off the 73-nucleotide tail in the absence of a blocking primer (lanes 1-6). When the 5` end of the tail was blocked with Primer B2, essentially no cleavage was observed (Fig. 2B, lanes 7-12). In this case, the single-stranded region of the tail between the 3` end of the blocking primer and the site of cleavage was 53 nucleotides compared with only 8 nucleotides with the first substrate tested. It would seem that the nuclease cannot enter in the middle of the tail, even if a long single-stranded region is available. Primer B2 forms a duplex up to the very 5` end of the tail. Its blocking capability implies that either the nuclease must enter at the 5` end of the single-stranded region of the tail or must recognize the 5` end of the tail before it can enter at another location.
Figure 8: Models of nuclease binding to tailed substrates. A, looping model. The enzyme binds at the cleavage site but must also interact with the 5` terminus of the single-stranded tail for cleavage to occur. B, threading model. The enzyme must bind and enter at the 5` terminus of the single-stranded tail (I). Movement of the enzyme on the tail is bidirectional (II). Cleavage can occur when the enzyme slides down to the point at which the tail is annealed to a template (III).
A portion of each of the above reactions was
taken prior to addition of Mg and fractionated on a
native polyacrylamide gel (Fig. 3B). The migration
position of the labeled substrate is shown in lane 2 of Fig. 3B. Addition of the nuclease shifts the mobility
of the substrate in the absence of a blocking primer (Fig. 3B, lane 3) or in the presence of the
noncomplementary primer (Fig. 3B, lane 1).
When primer B2, B3, or B4 was annealed prior to addition of the
nuclease, no gel shift was observed. Gel shifts were observed, however,
when the nuclease was preincubated with substrate before annealing
primers B2 and B3. In fact, under these conditions, more substrate is
shifted than that observed without any blocking primer. We interpret
this result as a trapping of the nuclease on the substrate, with it
caught on the single-stranded region between the blocking primer and
the cleavage site. This result also indicates that movement of the
nuclease on the tail is bidirectional, with nuclease molecules
continuously sliding onto and off of the 5` end of the tail.
Primer B4 is not able to trap the nuclease, possibly because it does not leave any single-stranded space for the enzyme to occupy. This interpretation implies that the binding of primer B4 forces bound nucleases to move in the direction of the 5` end of the tail, where they fall off. Alternatively, the primer induces direct dissociation of the nuclease from the region of the tail that is complementary to primer B4. Interestingly, a 53-nucleotide region of the tail between the 5` end and the primer remained available to bind the nuclease after primer B4 was annealed, but no shift was observed. This suggests that the nuclease has greater affinity for the cleavage site than for various positions along the tail.
Figure 4: Effect of single-stranded binding protein on endonucleolytic cleavage. A, analysis of endonucleolytic activity for reactions performed in the presence (even lanes) or absence (odd lanes) of 1.5 µg of E. coli DNA SSB is shown. Preincubation of substrate before the addition of nuclease is detailed under ``Experimental Procedures.'' In lanes 1 and 2, the substrate had a short 12-nucleotide 5` tail (D2:U2:T1), whereas substrate in lanes 3 and 4 (D3:U2:T1) had a longer 25-nucleotide tail. Separation and detection of cleavage products was performed as described in the legend to Fig. 2. Indicators for nucleotide lengths are given on both sides of the autoradiograph. B, reaction mixtures in A were sampled before the addition of enzyme and treated as described under ``Experimental Procedures.'' The substrate in lanes 1, 2, and 3 was D2:U2:T1 with a 12-nucleotide tail; the substrate with the 25-nucleotide tail (D3:U2:T1) was in lanes 4, 5, and 6. Samples incubated without SSB were run in lanes 1 and 4. In lanes 2 and 5, substrates were incubated with SSB. Lanes 3 and 6 are aliquots from SSB-incubated substrates treated with proteinase K and excess unlabeled downstream primer. Numerals II and II` indicate mobilities of intact substrates D2:U2:T1 and D3:U2:T1, respectively. DNA-SSB complexes are labeled III and III`. Unannealed D2 and D3 downstream primers have mobilities I and I`, respectively.
SSB can unwind duplexed DNA through cooperative binding of additional SSB molecules. In our experiment, it was possible that SSB displaced the oligomer with the 25-nucleotide tail from the substrate, disrupting the recognition site for cleavage. We therefore sampled each of the reactions before the addition of nuclease and performed gel shift analysis on a native gel. As seen in lanes 2 and 5 of Fig. 4B, the mobility of the different substrates was shifted by SSB. When samples containing SSB were treated with proteinase K, along with a 1000-fold excess of unlabeled primer strand, the SSB was digested away, and any displaced labeled strands were unable to reanneal. Lane 3 of Fig. 4B shows that almost all of the short tailed substrate was still present as an annealed primer-template after proteinase K treatment, but less than half of the longer tailed substrate could be recovered as primer-template in lane 6 of Fig. 4B. The displacement of the tailed strand from the second substrate would decrease the concentration of substrate in the primer-template configuration and result in a smaller amount of cleavage product. Nevertheless, inhibition of cleavage was very effective and could not be accounted for solely by this strand displacement phenomenon.
Because all of the longer tailed substrate was shifted by SSB and yet some cleavage product could still be detected (Fig. 4A, lane 4), the nuclease may either have some capacity to act on tails bound by protein or be able to displace SSB even when it is bound to the longer substrate. With the shorter tailed substrate, although a majority of the substrate was bound by SSB, we were unable to obtain a complete shift. A time course experiment measuring cleavage in both the presence and absence SSB revealed very similar rates; this also supports the conclusion that the nuclease can cleave a substrate when SSB is bound to or equilibrating with the tail.
Figure 5:
Effects of biotin adducts and streptavidin
binding on endonucleolytic activity. Time course experiments on
substrates that were preincubated with or without streptavidin are
shown. Substrate structure, nucleotide position of biotin
substitutions, and complexes formed with streptavidin are depicted above the autoradiograph. Biotin (b) was covalently
bound to the 1st and 7th nucleotides from the 5` end of the downstream
primer. Streptavidin, in a 25-fold molar excess, was preincubated with
5 fmol of substrate for 5 min at 37 °C in 1 binding buffer
(12% glycerol, 12 mM HEPES-NaOH, pH 7.9, 4 mM Tris-Cl, pH 7.9, 60 mM KCl, 1 mM EDTA, and 1
mM dithiothreitol) (lanes 5-8, 13-16, and 21-24). Endonuclease reactions
were then initiated by the addition of purified calf 5` to 3`
exonuclease according to ``Experimental Procedures.'' Lanes 1-8, nonbiotinylated downstream primer; lanes
9-16, biotin-substituted primer at position 1; lanes
17-24, biotin-substituted primer at position
7.
When streptavidin was allowed to bind to the biotinylated substrates prior to addition of the nuclease, no cleavage was observed with substrates that were biotinylated at either of the two downstream primer sites (Fig. 5, lanes 13-16 and 21-24). Cleavage still occurred on the substrate with a biotinylated upstream primer (data not shown). These results indicate that although an adduct larger than the base can be passed, when the adduct is protein sized, the sliding mechanism is thwarted.
Figure 6: Role of the upstream primer 3` hydroxyl group in endonucleolytic cleavage. Substrates were prepared with both a 5` end-radiolabeled downstream primer (D2) and an upstream primer (either U1 or U2). Primer U1 was extended with a single dideoxycytosine triphosphate to generate a 3` end that terminated in a hydrogen instead of a hydroxyl group. In the presence of 100 mM dNTPs, Sequenase(TM) could not further extend U1 on T1 (lane 15). Synthesis occurred to the end of the template when U2 was the upstream primer (lane 16). Lanes 1-7 show the time course of endonuclease activity on substrate having a 3` hydrogen on the upstream primer. In lanes 8-14, time course reactions contained substrate with U2 that had the 3` hydroxyl group.
Because the 3` hydroxyl was not responsible for stimulation dependent on nicked structure, we next examined the importance of base pairing of the upstream primer near the cleavage site. In Fig. 7,the left panel shows the structure and sequence of the substrates tested. The right panel illustrates the cleavage products generated after digestion with the calf nuclease for 20 min at 37 °C. In the absence of upstream primer (Fig. 7, right, lane 2), little activity was observed. The major and minor products obtained from the substrate with a fully annealed upstream primer correspond to the positions described earlier. When the terminal 3` nucleotide of the upstream primer formed a 1-nucleotide 3` mismatched tail, the cut was primarily before the first annealed nucleotide (Fig. 7, right, lane 4). Unlike previous results, the 1-nucleotide gap between the annealed portions of the upstream and downstream primer formed by this 3` mismatch caused more rather than less cleavage. If the annealed regions of the upstream and downstream primers were directly adjacent but an extra mismatched nucleotide formed a 3` tail on the upstream primer, the downstream primer was cleaved after its first annealed nucleotide (Fig. 7, right, lane 5). Finally, an upstream primer with a 3` nucleotide tail and a 1-nucleotide gap before the downstream primer generated the longest cleavage product. Though this primer was only a single nucleotide longer than the primer used in lane 5 (Fig. 7, right), the cut was positioned 2 nucleotides downstream.
Figure 7: Effects of upstream primers with various 3` structures on endonucleolytic cleavage site specificity. The left panel illustrates the structures of the substrates assayed in the right panel. For all substrates, downstream primer D5 was 5` radiolabeled and formed a 10-nucleotide 5` tail when annealed to template T2. Upstream primers annealed either directly adjacent to the annealed region of the downstream primer (U2 and U4) or one nucleotide away (U3 an U5). Additional structural features are as follows: -U, no upstream primer; U2, fully annealed primer; U3 and U4, 1-nucleotide 3` tail; U5, 3-nucleotide 3` tail. The right panel is an autoradiograph of reactions with the various substrates assayed for endonuclease activity and resolved on a denaturing 12% polyacrylamide gel. Reaction time was 20 min at 37 °C. Lanes 1 and 3 show reactions with substrate U2. Lane 1 contained no enzyme as a control. Substrates with -U, U3, U4, and U5 were assayed in lanes 2, 4, 5, and 6, respectively. In lanes 2-6, reactions were carried out with 2.25 units of enzyme.
The calf 5` to 3` exo/endonuclease is a member of the RTH-1 class of eukaryotic nucleases that perform structure-specific cleavage of DNA and have important roles in DNA replication and repair. The substrate for endonuclease activity is a primer-template in which the primer has a noncomplementary, unannealed 5` end region. Here we show that in order to catalyze cleavage, the nuclease must slide over the 5` end of the unannealed tail, move down the length of the tail to the point of annealing with the template, and then carry out cleavage. The sliding process is bidirectional, such that nucleases can also slide off of the tail at the 5` end. Evidence is also presented that the nuclease binds with highest stability to the point of cleavage. The presence of biotin adducts on the tail do not affect either recognition of the 5` end or the sliding process. However, protein bound to the tail, either SSB or streptavidin, has an inhibitory effect on cleavage, presumably by blocking the movement of the nuclease to the site of cleavage. The steps taken by the nuclease to carry out this process are depicted in Fig. 8.
Biochemical and genetic evidence suggests
that nucleases of this class are components of the DNA replication
machinery. Studies of simian virus 40 DNA replication in vitro indicated the requirement of the human 5` to 3` exo/endonuclease
in the removal of the RNA primer before joining of viral lagging strand
DNA segments (Ishimi et al., 1988; Waga et al.,
1994). The mouse nuclease was able to partially remove RNA from
initiator RNA primers made and elongated with DNA by DNA polymerase
in vitro (Goulian et al., 1990). Using a model
Okazaki fragment substrate consisting of an initiator RNA elongated by
DNA and annealed to a template, we showed that two nucleases can effect
complete RNA removal (Turchi et al., 1994). Mammalian RNase HI
cleaves off the initiator RNA as an intact segment, leaving only a
single ribonucleotide at the RNA-DNA junction (Turchi et al.,
1994; Huang et al., 1994). The 5` to 3` exo/endonuclease can
then remove the last ribonucleotide. Null mutants of the counterpart
nuclease in S. cerevisiae, the RTH-1 nuclease, are
temperature-sensitive for DNA replication (Sommers et al.,
1995). The appearance of dumbbell-shaped cells with a nucleus at the
isthmus as the terminal phenotype is characteristic of mutations in DNA
polymerases
and
(reviewed in Bambara and Huang(1995)). The
RTH-1 mutation causes hyper-recombination, symptomatic of the presence
of long-lived breaks in the chromosome (Sommers et al., 1995).
These would be expected if joining of Okazaki fragments was delayed by
the mutation.
The sensitivity of the RTH-1 mutants to damage by the agent methylmethane sulfonate (Sommers et al., 1995), which adducts to bases, suggests that the RTH-1 class of nucleases participate in repair of base damage. The demonstration that null mutants in RTH-1 increase the instability of simple repetitive DNA indicates a role for this nuclease in the mismatch repair pathway (Johnson et al., 1995). Our results show that biotinylation of nucleotides on a tail do not inhibit the movement of the nuclease to its site of cleavage. This suggests that in vivo the nuclease can traverse an unannealed, damaged segment of DNA and cut it away from the chromosome. Because the nuclease does not have to cut at the damaged nucleotide to accomplish this process, it should be able to remove even modified nucleotides that would not be substrates for cleavage attempted at the modified site.
Our results show that the nuclease cannot enter the tail strand except at the 5` end. Because the RTH-1 class nucleases are expected to be present at the replication fork, this property would be expected to protect the lagging strand template from unintentional cleavage. There is a risk of such cleavage because the extension of the leading strand primer continuously generates a structure with most of the characteristics of the substrate for RTH-1 endonuclease activity, at the point where the parental strands separate. In this structure, the lagging strand template would be the equivalent of the single-stranded tail in our model substrates, except that the lagging strand template does not have a nearby 5` end. The absence of this single feature prevents endonucleolytic cleavage.
Properties of the calf 5` to 3` exo/endonuclease suggest another
means by which it can participate in the removal of the initiator RNA
segments of Okazaki fragments. It could remove this RNA by
endonucleolytic cleavage of the Okazaki fragment in the region of DNA
just downstream of the initiator RNA. DNA polymerase has been
proposed to be responsible for completion of the extension of Okazaki
fragments in vivo (reviewed in Bambara and Huang(1995)). This
polymerase partially copurifies with DNA helicase E (Siegal et
al., 1992). The Ku autoantigen is also a helicase that copurifies
with human DNA polymerase
(Hwang et al., 1995),
suggesting that helicase E is the calf Ku protein. Helicase E moves in
a 3` to 5` direction on the template and so can displace primers ahead
of the advancing polymerase. It is possible that the polymerase,
helicase, and RTH-1 class nuclease collaborate in a pathway for removal
of initiator RNAs of Okazaki fragments.
In summary, the calf 5` to 3` exo/endonuclease can cleave off the 5` unannealed tail of a primer annealed to a template by cutting near the point of complementarity and releasing the tail as an intact segment. Here we show that to catalyze this reaction, the nuclease must enter the tail at the 5` end and slide to the point of cleavage. This unique mechanism of action is consistent with a proposed role for the nuclease in removal of the initiator primers from Okazaki fragments during DNA replication and in cleaving off segments of damaged DNA during DNA repair. The yeast counterpart nuclease RTH-1 has been shown to be necessary to maintain stability of repetitive DNA and apparently is involved in the MSH2-MLH1-PMS1 mismatch repair pathway (Johnson et al., 1995). Mutations in the mammalian mismatch repair pathway are associated with colorectal cancers (Reenan and Kolodner, 1992; Prolla et al., 1994). This suggests that the human RTH-1 counterpart applies its unique cleavage specificity for repair surveillance that prevents colorectal cancer.