From the Department of Biochemistry and ¶ Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina 27710
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ABSTRACT |
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MutS, MutL, and DNA helicase II are required for the mismatch-provoked excision step that occurs during Escherichia coli methyl-directed mismatch repair. In this study MutL is shown to enhance the unwinding activity of DNA helicase II more than 10-fold on a conventional helicase substrate in which a 35-residue oligonucleotide is annealed to a M13 circular single-stranded phage DNA under conditions where the two proteins are present at approximately molar stoichiometry with respect to the substrate. MutS- and MutL-dependent activation of DNA helicase II has also been demonstrated with a model substrate in which a 138-residue oligonucleotide was hybridized to a 138-nucleotide gap in an otherwise duplex 7,100-base pair circular DNA. Displacement of the oligonucleotide requires MutS, MutL, DNA helicase II, and ATP and is dependent on the presence of a mismatch within the hybrid region. Although DNA helicase II and Rep helicase share substantial sequence homology and features of mechanism, Rep helicase is inactive in this reaction.
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INTRODUCTION |
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Escherichia coli methyl-directed mismatch repair
initiates via the mismatch-provoked incision of the unmethylated strand
at a hemimethylated d(GATC) sequence in a reaction that involves the
MutS- and MutL-dependent activation of the MutH d(GATC)
endonuclease activity (1). The single-strand break thus produced may
occur either 3' or 5' to the mismatch on the unmethylated strand and directs the exonucleolytic excision of that portion of the unmodified strand spanning the incised d(GATC) sequence and the mispair (2, 3).
Excision requires MutS, MutL, DNA helicase II, and an appropriate exonuclease. When the strand break that directs repair occurs 5' to the
mismatch, excision requires RecJ exonuclease or exonuclease VII (3, 4),
both of which support 5' 3' hydrolysis (5, 6). For repair directed
by a strand break 3' to the mismatch, the 3'
5' hydrolytic activity
of exonuclease I (7) is sufficient to meet the exonuclease requirement
(2).1
Since helicase II is required for excision from either side of the mismatch and because each of these exonucleases is specific for single-stranded DNA (5-7), the action of helicase II presumably serves to unwind the incised strand so as to render it exonuclease sensitive. According to this interpretation, the exonuclease functions in excision are secondary to those of DNA helicase II. We have therefore sought partial reactions in which MutS, MutL, and a mismatch might enhance the activity of helicase II. We show here that MutL stimulates helicase II activity on a conventional substrate and that helicase activity on incised duplex DNA is enhanced by MutS and MutL in a mismatch-dependent manner. The accompanying paper (8) demonstrates that MutS, MutL, and mismatch-dependent entry of helicase II into an incised heteroduplex occurs at the strand break with helicase entry biased so that translocation occurs toward the mispair.
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EXPERIMENTAL PROCEDURES |
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Proteins, DNA, and Nucleotides--
MutS (9) and DNA helicase II
(10) were purified as described. Rep helicase (11) was kindly provided
by Timothy Lohman (Washington University, St. Louis, MO). Exonuclease was from Life Technologies, Inc., restriction enzymes and
VENT polymerase from New England BioLabs, and T4 polynucleotide kinase
from Amersham Pharmacia Biotech. E. coli MutL was purified
by a modification of the method described previously (12) after
subcloning the mutL gene from pAL51 (13) into a pET3a
expression vector that had been cleaved with NdeI and
BamHI to yield L1-pET3a. Briefly, a 180-liter culture of
E. coli BL21(DE3)/pLysS/L1-pET3a was grown at 37 °C in L
broth supplemented with thymine (4 µg/ml), thiamine (10 µg/ml),
glucose (10 mg/ml), and 10 mM KPO4, pH 7.4. The
culture was induced at A590 = 1.0 by addition of
isopropyl-1-thio-
-galactopyranoside (Amersham) to 0.4 mM. The culture was chilled to 10 °C 2.75 h after
induction and harvested by centrifugation. Cell paste (780 g) was
stored at
70 °C. MutL was purified from 175 g of cell paste
as described (12), except that the Bio-Rex 70 column was increased in
size to 20-cm × 30-cm2, and the concentration step
and the Sephadex G-150 column were eliminated. Fractions from the
Bio-Rex 70 column were pooled and dialyzed against 0.05 M
KPO4 (pH 7.4), 0.05 M KCl, 0.1 mM
EDTA, 0.5 mM dithiothreitol
(DTT),2 1 mM
phenylmethylsulfonyl fluoride, frozen in small aliquots in liquid
N2, and stored at
70 °C. The concentration of the MutL preparation used in this work, which was about 98% pure as judged by
Coomassie-stained sodium dodecyl sulfate gels, was determined by
Bradford assay (14). MutL preparations isolated by the previous procedure contain low levels of a DNA-dependent ATPase
(12), which immunological analysis has shown to be DNA helicase II (not shown). MutL isolated as described above also contains helicase II, but
the trace levels of the activity present had no effect on the
experiments described here. When cited in molar terms, protein
concentrations are expressed as monomer equivalents assuming 100%
activity.
Conventional Helicase Assays--
The 35-residue oligonucleotide
d(ATCGTCGCTATTAATTAATTTTCCCTTAGAATCCT) was 5'-end-labeled using T4
polynucleotide kinase and [-32P]ATP (3000 Ci/mmol).
After phenol extraction, phenol-chloroform-isoamyl alcohol extraction,
and chloroform-isoamyl alcohol extraction, the labeled oligonucleotide
was ethanol precipitated, resuspended in 25 µl of 10 mM
Tris-HCl, pH 7.6, 1 mM EDTA, and residual ATP was removed
by filtration through a 1-ml Sephadex G-50 column (Amersham Pharmacia
Biotech, 7.5-cm × 0.196-cm2) equilibrated in 10 mM Tris-HCl (pH 7.6), 150 mM NaCl, 1 mM EDTA (TNE). A 10-fold molar excess of oligomer was
hybridized to 1.75 pmol M13mp2 viral strand in 20 mM
Tris-HCl, pH 7.6, 10 mM MgCl2, 100 mM NaCl, 1 mM DTT in a 175-µl reaction (16).
Incubation was at 95 °C for 1 min, 65 °C for 3 min, followed by
slow cooling to room temperature. Excess oligomer was removed by
filtration through a 1-ml Sepharose-4B column (Amersham Pharmacia
Biotech, 7.5-cm × 0.196-cm2) equilibrated with
TNE.
Duplex Helicase Assays-- Wild type M13mp2 RF DNA (500 µg) was cleaved with FspI and EcoRI. Reactions were deproteinized as described above and the 7059- and 138-bp products separated by filtration through a 30-ml Sephacryl 400 column (Amersham Pharmacia Biotech, 25-cm × 0.785-cm2) equilibrated with TNE. A gapped circle was prepared by mixing a 10-fold molar excess of the wild-type M13mp2 viral strands with 100 µg purified 7059-bp fragment, followed by alkaline denaturation, neutralization, and annealing (17). The gapped product was separated from excess viral strands by hydroxylapatite chromatography (17), dialyzed against 10 mM Tris-HCl (pH 7.6), 1 mM EDTA, concentrated 10-fold by butanol extraction, and filtered through Sephadex G-50 (7-cm × 0.19-cm2) as described above.
A 138-residue single-strand oligomer was prepared for hybridization to the gapped circular duplex by PCR amplification of a segment of M13mp2 wild type RF DNA or C103 M13mp2 RF DNA using 5'-P-d(CACTGGCCGTCGTTTTACAACGTC) and 5'-OH-d(GCAACTGTTGGGAAGGGCGATCGG) as primers. Reactions (0.1 ml) contained 375-ng template DNA (wild-type or C103 M13mp2 RF DNA depending on whether no mismatch or a G-T mismatch was to be generated in the final substrate), 100 pmol of each primer, and 4 units of Vent DNA polymerase, which was used according to the recommendations of the manufacturer. Amplification used a Perkin Elmer Gene Amp 9600 with an initial incubation at 94 °C for 2 min, followed by 12 cycles of 30 s at 94 °C, 30 s at 70 °C, and 30 s at 72 °C. Protein was extracted as described above and excess primers, dNTPs, and templates were removed by filtration through Sephacryl-400 (Amersham Pharmacia Biotech, 25-cm × 0.785-cm2) equilibrated with TNE. Pooled fractions containing the 138-bp PCR product were concentrated by ethanol precipitation, and the washed pellet was dissolved in 200 µl of 67 mM glycine-NaOH (pH 9.4), 2.5 mM MgCl2, 50 µg/ml bovine serum albumin. The 5'-phosphorylated viral strand component of the PCR product was hydrolyzed by digestion with 5 units of ![]() |
RESULTS |
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MutL Stimulates DNA Helicase II-- During initial attempts to identify a partial reaction dependent on MutS, MutL, and DNA helicase II, we found that near homogeneous preparations of MutL markedly stimulated helicase activity on a conventional substrate constructed by hybridization of a 35-residue oligonucleotide to M13mp2 viral strand DNA (see "Experimental Procedures"). Under conditions where helicase II was present at one monomer equivalent per mol of substrate (as molecules), the addition of two monomer equivalents of MutL enhanced the initial rate of oligonucleotide displacement 11-fold (Fig. 1, upper panel). MutS and/or the presence of a G-T mismatch within the hybrid region had no effect on the rate of oligonucleotide displacement in the presence or absence of MutL (not shown).
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MutS and MutL Enhance Helicase Unwinding at a Strand Break in a Mismatch-dependent Manner-- The failure to observe MutS or mismatch effects with the conventional helicase substrate might be due to the presence of mismatches within the secondary structure assumed by the 7 kilobases of single-stranded DNA in the molecule. To circumvent this potential problem, we constructed a duplex helicase substrate similar to that described by Washburn and Kushner (21) by hybridizing a 138-residue oligonucleotide to M13mp2 circular duplex DNA that contained a 138-nucleotide gap (Fig. 2). The 138-residue oligonucleotide was produced by PCR amplification using two different templates so that duplex helicase substrates could be constructed with or without a G-T mismatch between the two strand breaks (see "Experimental Procedures").
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Activation of Unwinding by MutS and MutL Is Specific for DNA Helicase II-- In contrast to mutU (uvrD) mutations that inactivate helicase II function in mismatch repair (17, 26), rep mutants are not mutators (27), and despite the significant MutL stimulation of Rep in conventional helicase assays (Fig. 1), the protein has no known function in mismatch repair. As shown in Fig. 5, activation of unwinding of the nicked duplex G-T substrate by MutS and MutL is specific for helicase II. Rep activity with this DNA was limited, and the presence of MutS and MutL had no significant effect on unwinding even at Rep concentrations 50 times that of the highest helicase II level tested.
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DISCUSSION |
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Previous work has demonstrated that in addition to their roles in the initiation stage of methyl-directed repair, MutS and MutL are required for one or more subsequent steps (2), including the excision stage of the reaction (3). The experiments described here provide further support for involvement of these two proteins in the excision stage of the reaction. Results obtained with duplex substrates of the type shown in Fig. 2 indicate that the two proteins activate unwinding by helicase II in a mismatch-dependent manner. We have not directly addressed the mechanism of this effect, but it is possible that activation may involve several steps in the unwinding reaction.
The accompanying paper (8) demonstrates that mismatch-dependent unwinding by MutS- and MutL-activated helicase II initiates at a strand break. Whereas helicase II is capable of unwinding from a nick (28), this reaction requires very high helicase II concentrations with initiation being rate-limiting (29). Nevertheless, the finding that a genetically altered form of helicase II is selectively defective in unwinding from a nick suggests that this reaction may be biologically significant (30). In view of these findings, our observations with the duplex helicase substrate indicate that MutS and MutL act in mis-match-dependent manner to enhance the rate of helicase II initiation at a strand break. As noted above, this effect is specific for helicase II and does not occur with 40% homologous Rep helicase, consistent with known requirements for helicase II in mismatch repair (17, 26).
In contrast to our failure to observe significant unwinding of a 138-residue oligonucleotide in the duplex substrate at low helicase II concentrations (Figs. 2-4), a 12-residue oligonucleotide in this type of molecule was previously shown to be efficiently displaced at low concentrations of the protein (21). We think it likely that these disparate results are due to the smaller size of the oligonucleotide in the latter substrate. Since helicase II binds at nicks (29), it is possible that proximity of the two strand breaks in the latter DNA results in a concerted effect on initiation of unwinding by the enzyme. Differences due to chain length effects may also reflect the relatively modest processive behavior of helicase II (31), and it has been shown that the number of base pairs unwound by the activity depends on the amount of the protein (32).
In addition to the MutS- and MutL-dependent activation of
helicase II at a strand break, we have also found that MutL markedly enhances the activity of helicase II, and to a lesser extent the Rep
enzyme, on conventional substrates. This effect is evident at very low
protein concentrations (in the case of helicase II, about one monomer
equivalent and 2 MutL monomer equivalents per 7-kb DNA molecule),
indicating high specificity. In fact, preliminary experiments indicate
that MutL and helicase II interact in the absence of DNA as judged by
native electrophoretic analysis (33). Thus, in addition to its role
with MutS in activating helicase II initiation at a nick, it is likely
that MutL also functions as a helicase activator subsequent to
initiation of unwinding. This activation could occur by increasing the
processive behavior of the helicase by a direct interaction as is the
case for X174 gene-A protein and Rep helicase (34). The differential
effects observed with the Rep helicase in the two assays are also
consistent with the idea that MutS and/or MutL modulate helicase action
at several levels of the unwinding reaction. MutL stimulation of both
Rep and helicase II in conventional assays can be understood in terms
of the 40% sequence homology shared by the two helicases (19).
However, the failure of MutS and MutL to activate Rep unwinding at a
single-strand break must be due to amino acid sequence elements that
distinguish Rep from helicase II.
Although MutL is required for several steps in methyl-directed mismatch repair, precise molecular roles for the protein in the reaction have not been assigned. MutL binds to MutS-heteroduplex complexes (12), is required along with MutS and a mismatch for activation of the latent d(GATC) endonuclease of MutH (1), and stimulates the ATP-dependent MutS-catalyzed formation of heteroduplex DNA loops (35). Such observations have led to the suggestion that MutL serves to interface mismatch recognition by MutS to other components of the repair system (36, 37). The observations that MutL physically interacts with and activates helicase II are consistent with this view (33). Coupled with the finding that MutL is also required for the mismatch, MutS, and helicase II-dependent unwinding observed with nicked circular heteroduplex substrate, we think it likely that the protein has an important role in the mismatch-dependent loading of helicase II into the nicked heteroduplex, an event that is shown in the accompanying paper (8) to occur at the strand break.
A single hemimodified d(GATC) sequence is sufficient to provide strand
specificity to heteroduplex repair by the E. coli
methyl-directed pathway (4, 38), and mismatch-provoked incision of the
unmethylated strand of this d(GATC) site by activated MutH (1) provides a strand break that is thought to serve as the initiation site for
exonucleolytic removal of that portion of the new strand spanning the
nick and the mispair (3). The latter conclusion is based on the finding
that excision on a single d(GATC) site heteroduplex depends not only on
MutS, MutL, and DNA helicase II (2, 3), but also requires an
appropriate 3' 5' or 5'
3' single-strand exonuclease, depending
on whether the MutH strand break is produced 3' or 5' to the mispair
(4). By contrast, we have shown here that MutS, MutL, and helicase II
are sufficient to displace a mismatched oligonucleotide from a
heteroduplex in which a strand break is present on either side of the
mismatch, raising questions concerning the biological significance of
this exonuclease-independent reaction. Unfortunately, it is
difficult to compare results obtained with the two types of
heteroduplex. In the single d(GATC) site substrates examined
previously, the distance between the MutH-produced strand break and the
mispair is 1,000 bp (39), whereas nicks in the heteroduplex described
here were located 45- and 92-bp to either side of the mismatch. Since
activated helicase II can clearly unwind the latter substrate,
concurrent exonucleolytic hydrolysis of the displaced strand product
may be necessary for continued unwinding of the 1000 base pairs that
separate the mismatch and the strand break in the former
heteroduplexes. The distinct properties of these two types of
substrates may be clarified by study of two d(GATC) site molecules and
by examination of doubly incised heteroduplexes as a function of strand
break-mismatch separation distance.
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ACKNOWLEDGEMENTS |
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We thank Dwayne Allen, Keith Bjornson, and Gregory Runyon for comments on the manuscript.
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Note Added in Proof |
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Using two-hybrid analysis and protein affinity chromatography, Steve Matson and colleagues (Hall, M. C., Jordon, J. R., and Matson, S. W. (1998) EMBO J. 17, 1535-1541) have also demonstrated a physical interaction between MutL and DNA helicase II.
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FOOTNOTES |
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* Supported in part by Grant GM23719 from the National Institute of General Medical Sciences.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.
Present address: Dept. Microbiology, University of Buffalo School
of Medicine and Biomedical Sciences, 3435 Main St., Buffalo, NY
14214.
§ Present address: Access Pharmaceuticals, 2600 Stemmons Freeway, Dallas, TX 75207.
To whom correspondence should be addressed. Tel.:
919-684-2775; Fax: 919-681-7874; E-mail:
modrich{at}biochem.duke.edu.
1 E. coli extracts deficient in functional exonuclease I contain a second unidentified activity that supports mismatch repair directed by a 3' strand signal (4).
2 The abbreviations used are: DTT, dithiothreitol; RF, replicative form; bp, base pair(s); PCR, polymerase chain reaction.
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REFERENCES |
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