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J. Biol. Chem., Vol. 281, Issue 41, 30305-30309, October 13, 2006
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From the Department of Biochemistry and Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina 27710
| INTRODUCTION |
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| Mismatch Repair in Eukaryotic Cell Extracts |
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Available information on the mechanism of eukaryotic mismatch repair is largely derived from analysis of the nick-directed repair of circular heteroduplexes in mammalian cell extracts. As shown in Fig. 1, the strand break that directs repair may reside either 3' or 5' to the mispair as viewed along the shorter path linking the two sites in the circular substrate, and processing of such molecules in extracts is largely restricted to this region. Examination of intermediates produced in HeLa nuclear extracts when repair DNA synthesis is blocked has demonstrated that mismatch-provoked excision removes that portion of the incised strand spanning the shorter path between the nick and the mismatch (Fig. 1) with excision tracts extending from the strand break to a number of sites within a region
90170 nucleotides beyond the mispair (7, 8). Radiolabeling of repair DNA synthesis tracts is also consistent with this view (9). The mammalian repair system thus displays a bidirectional capability in the sense that it responds to both 3'- and 5'-heteroduplex orientations, and functionality is retained at nick mismatch separation distances as large as 1000 bp (7).
The nicks that direct the E. coli mismatch repair also serve as sites for initiation of excision (2), and function of the strand break in the eukaryotic reaction has generally been interpreted in a similar manner (13). However, a distinct mechanism for mismatch-provoked excision has been proposed based on radiolabeling of repair DNA synthesis tracts in Xenopus egg extracts. In contrast to results obtained with the human system (9), radiolabeling of repair products in Xenopus extracts was significantly higher near the mismatch than the strand break (10). Based on this analysis, Varlet et al. (10) suggested that the nick that directs repair does not correspond to the site of excision initiation. Rather, a mismatch-activated strand-specific endonuclease is postulated to introduce a second nick near the mispair, with this nick serving as an entry site for the excision system. As described below, recent experiments suggest that the mammalian repair system supports both of these modes of excision.
| Mammalian MutS and MutL Activities |
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(MSH2·MSH6 heterodimer) and MutS
(MSH2·MSH3 heterodimer). MutS
, which represents 8090% of the cellular MSH2, preferentially recognizes base-base mismatches and insertion/deletion (ID)2 mispairs in which one strand contains 1 or 2 unpaired nucleotides but is also capable of recognition of larger ID heterologies with reduced affinity (1113, 15). MutS
recognizes ID mismatches of 2 to about 10 nucleotides, weakly recognizes single-nucleotide ID mispairs, and is essentially inert on base-base mismatches (12, 15). MSH2 and MSH6 defects have been implicated in tumor development, but the cancer predisposition conferred by MSH6 inactivation is less severe (4, 16). The association of MSH3 defects with tumor development appears to be limited (4, 5, 16).
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, a heterodimer of MLH1 and PMS2, is the primary MutL activity in human mitotic cells and supports repair initiated by either MutS
or MutS
(17). MutL
accounts for
90% of the MLH1 in human cells (18, 19), but two low abundance complexes involving MLH1 have also been identified. A human MLH1·PMS1 heterodimer (MutL
) has been isolated, but involvement in mismatch repair has not been demonstrated (18). However, the MutL
MLH1·MLH3 complex has been reported to support modest levels of base-base and single-nucleotide ID mismatch repair in vitro, events that are presumably initiated by MutS
(19). Genetic inactivation of MLH1 or PMS2 confers cancer predisposition, but mutations in PMS1 do not (4, 16). Involvement of MLH3 defects in tumor development is uncertain (4, 5). | Other Activities in Mammalian Mismatch Repair |
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Exo1/ mice display modest cancer predisposition, and Exo1 deficiency is associated with a 30-fold elevation of hypoxanthine-guanine phosphoribosyltransferase mutability, substantially less than the 150-fold increase observed with Msh2/ cells (23). Although extracts of Exo1/ mouse cells are virtually devoid of repair activity on base-base mismatches, they retain significant activity on one- or two-nucleotide ID mispairs (23). These findings imply the existence of one or more alternate excision activities, and several possibilities have been suggested. Involvement of the 3' to 5' editing exonuclease functions of DNA polymerases
and
in mismatch repair has been proposed on genetic and biochemical grounds (2628), but this idea has been questioned (29, 30). Using a small interfering RNA knockdown approach, Vo et al. (31) have suggested that the Mre11 3' to 5'-exonuclease participates in 3'-directed mismatch repair. Mre11 depletion was shown to reduce the efficiency of 3'-directed repair by
40%, and repair was restored to normal levels by the addition of partially purified Mre11. However, the involvement of other activities in repair restoration was not excluded because the Mre11 fraction tested was relatively crude. This is of concern because down-regulation of Mre11 also leads to relatively rapid chromosome breakage and can interfere with cell proliferation (32).
Experiments in human cell extracts and partially purified fractions have also indicated involvement of several DNA binding proteins in eukaryotic mismatch repair. The extract reaction is abolished by antibody against the single-stranded DNA binding protein RPA (33), which stimulates excision, stabilizes the ensuing gap against endonuclease attack, and promotes repair DNA synthesis (34). The non-histone chromatin protein HMGB1, which interacts with MutS
, may also play an important role in the initiation of mismatch-provoked excision in nuclear extracts (35).
The PCNA replication clamp and DNA polymerase
have also been implicated in mismatch repair in human cell extracts (3639). PCNA, which confers processivity on polymerase
(40), plays multiple roles in mismatch repair. As might be expected, PCNA is necessary for repair DNA synthesis (38, 39), but it is also required for mismatch-provoked excision (36). The most compelling evidence for PCNA involvement in the excision step of mismatch repair has been provided by p21 inhibition studies. By forming a stable complex with DNA-bound PCNA, p21 interferes with downstream PCNA-dependent events (41). Although p21 abolishes 3'-directed mismatch-provoked excision in HeLa cell extracts, only 4050% of 5'-directed excision events are subject to p21 inhibition, implying occurrence of at least two hydrolytic modes on 5'-heteroduplexes (36, 39, 42).
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| Mismatch-provoked Excision in Purified Systems |
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, MutL
, Exo1, RPA, and ATP (39), and similar results have been obtained in a system that also contains HMGB1 (43). As illustrated in Fig. 2, 5'-directed excision in this system is mismatch-provoked and terminates upon mismatch removal. Analysis of this reaction has revealed several features of the hydrolytic mechanism. MutS
activates Exo1 hydrolysis on a 5'-heteroduplex in a mismatch- and ATP-dependent manner. In the absence of other proteins, 5' to 3' hydrolysis by Exo1 occurs by a distributive mechanism, but MutS
renders the enzyme highly processive, resulting in removal of
2,000 nucleotides prior to dissociation (39), an effect attributed to formation of a MutS
·Exo1 complex. Hydrolysis by the MutS
·Exo1 complex is controlled in part by RPA, which reduces processivity of the MutS
·Exo1 complex to
250 nucleotides, and by binding to gaps, RPA controls access of Exo1 to 5' termini in excision intermediates/products (39). Although an RPA-filled gap is a very poor substrate for Exo1, MutS
promotes Exo1 loading at such sites provided that the gapped molecule contains a mismatched base pair. The ramifications of these RPA effects are 2-fold. Excision on 5'-heteroduplexes proceeds via a set of pseudo-discrete hydrolytic intermediates, which differ in size by about 250 nucleotides, an effect attributed to multiple reloading of MutS
and Exo1 (39, 43). Second, hydrolysis is dramatically attenuated upon mismatch removal because MutS
can no longer promote Exo1 loading at the RPA-filled gap in the excision product. RPA thus has both negative and positive regulatory effects on this reaction; by suppressing processive behavior of the MutS
·Exo1 complex and by restricting hydrolytic activity on excision products, it promotes turnover of the system after mismatch removal, allowing other heteroduplex molecules to participate in the reaction.
MutL
is not required for mismatch- and MutS
-dependent activation of Exo1, but it does play a significant role in excision. By acting in concert with MutS
to suppress Exo1 hydrolysis on DNA that lacks a mispair, MutL
enhances the mismatch dependence of the reaction (39, 44). MutL
also participates in excision termination in this system, but two different mechanisms have been proposed to account for its function in this regard. Genschel et al. (39) have attributed MutL
involvement in termination to its role in suppressing Exo1 activity on mismatch-free DNA. In this mechanism MutL
simply stabilizes excision products against nonspecific hydrolysis by Exo1. By contrast, Zhang et al. (43) have concluded that MutL
, acting in concert with RPA, plays an active role in excision termination upon mismatch removal. This issue has not been resolved.
MutS
, MutL
, Exo1, and RPA also support mismatch-provoked excision on a 3'-heteroduplex. As in the case of a 5'-substrate, hydrolysis on a 3'-heteroduplex proceeds 5' to 3' from the strand break (Fig. 2), which is the wrong polarity for mismatch removal (22, 45). The 5' to 3' directionality of this system has been referred to as a default polarity (2). Although PCNA has no significant effect on the restricted directionality of this system, supplementation with both PCNA and RFC (RFC loads PCNA onto the helix (40)) yields a system that supports mismatch removal from both 5' and 3'-heteroduplexes (45). Excision products obtained from a 5'-heteroduplex in this six-component system are similar to those produced by MutS
, MutL
, Exo1, and RPA. However, when the nick is located 3' to the mismatch, Exo1 5' to 3' hydrolysis initiating at the nick is largely repressed by RFC, and excision occurs with apparent 3' to 5' polarity resulting in mismatch removal. Although excision in this six-component system displays similarities to the bidirectional reaction that has been studied in nuclear extracts, the distribution of excision products in the purified system is more disperse than that observed in extracts. This purified system therefore lacks one or more activities that play significant roles in mismatch repair (45).
Because an Exo1 active site mutant failed to support both 5'- and 3'-directed excision in this system, mismatch removal in both cases was attributed to this exonuclease (45). It was suggested that a cryptic Exo1 3' to 5' hydrolytic function is responsible for 3'-directed excision. However, the necessity for a 3' to 5'-exonuclease in this purified system was rendered moot by the demonstration that MutS
, RFC, and PCNA activate a latent MutL
endonuclease in an ATP- and mismatch-dependent manner (46). As shown in Fig. 3 incision by activated MutL
endonuclease occurs on both 3'- and 5'-heteroduplexes and is strongly biased to the nicked heteroduplex strand. For heteroduplexes with a nick mismatch separation distance of
100 bp, incision tends to occur on the distal side of the mismatch relative to the strand break but at larger separation distances readily occurs between the two DNA sites.3 In the case of a 3'-heteroduplex, incision distal to the mismatch provides an initiation site for mismatch removal by the 5' to 3' action of MutS
-activated Exo1 (Fig. 3). Inasmuch as PCNA-dependent and independent modes of 5'-directed excision have been invoked in nuclear extracts (39, 42), it is noteworthy that this PCNA-dependent endonucleolytic system also incises 5'-heteroduplexes (46).
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The probable active site of the MutL
endonuclease has been localized to a divalent metal binding site within the PMS2 subunit that is defined by a DQHA(X)2E(X)4E motif (46). Amino acid substitution mutations within this motif abolish MutL
endonuclease activity as well as the ability of the protein to support mismatch repair in nuclear extracts. This motif is conserved in homologs of eukaryotic PMS2 and in archaeal and eubacterial MutL proteins but is conspicuously absent in MutL proteins from bacteria like E. coli that rely on d(GATC) methylation to direct mismatch repair. The presence or absence of this MutL motif may therefore define two distinct classes of mismatch repair systems.
| Mismatch Repair in Purified Systems |
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, MutL
, Exo1, RPA, HMGB1, and DNA polymerase
are sufficient to support repair of 5'-heteroduplexes containing a G-T mismatch or a 3-nucleotide ID mispair and that covalently closed repair products are obtained upon supplementation of these proteins with DNA ligase I. As observed for 5'-directed excision (39), MutL
is not required for repair in this system (43). The functions of RPA and HMGB1 in this reconstituted reaction appear to be largely redundant because either protein is sufficient to support reconstituted repair, and excision in the presence of RPA is only modestly enhanced by the addition of HMGB1. Interestingly, substitution of MutS
for MutS
yields a system that supports 5'-directed excision and repair of a 3-nucleotide ID mismatch, implying that like MutS
, MutS
can activate Exo1. One surprising feature of this reconstituted system is that repair is independent of RFC and PCNA. This is unexpected because the DNA synthesis step of 5'-heteroduplex repair in nuclear extracts is PCNA-dependent (38, 39). Furthermore, in contrast to its activity on a 5'-heteroduplex, this purified system does not support 3'-directed excision or repair when supplemented with RFC and PCNA (43).
A reconstituted repair system with somewhat different properties has been described by Constantin et al. (30). In contrast to the 5'-directed repair system described above (43), this system supports bidirectional mismatch repair dependent on MutS
, MutL
, Exo1, RPA, DNA polymerase
, RFC, and PCNA (30). MutL
is dispensable for 5' repair in this system but required for 3'-heteroduplex repair. The RFC and PCNA requirement for 5'-directed correction is because of their involvement in the repair DNA synthesis step, whereas both proteins are also required for excision on a 3'-heteroduplex.
The different results obtained by Zhang et al. as compared with those of Constantin et al. (30) and Dzantiev et al. (45) have been attributed to activity differences between the RFC preparations used (43, 46). Whereas Zhang et al. (43) employed recombinant human RFC, Constantin et al. (30) used native human RFC. Dzantiev et al. (45) obtained similar results using either native human or recombinant yeast RFC.
| Some Unanswered Questions |
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endonuclease and control 3'-directed excision have also been invoked (45, 46), but these have not been characterized.
The defining feature of the replication error correction reaction is its strand-specific character, an effect that depends on the interaction of a mismatch and strand break that can be separated by hundreds of base pairs. Several models, which attempt to explain the molecular nature of this interaction, have been thoroughly debated in the literature (13), but the mechanism responsible for communication between the two DNA sites has not been established. However, the recent finding that mismatch-dependent incision by activated MutL
endonuclease is strongly biased to the nicked heteroduplex strand (46) suggests that interaction of the mismatch and strand break may involve keeping track of a DNA strand.
The sequence of events during the course of nick-directed mismatch repair is presumably dictated by the temporal course of protein-protein interactions that occur on the heteroduplex. A number of protein-protein interactions have been documented in this system, including MutS
-MutL
, MutS
-PCNA, MutS
-PCNA, MutL
-PCNA, MutS
-Exo1, MutL
-Exo1, Exo1-PCNA, and PCNA-polymerase
(13, 40). With the exception of interactions between MutS
and Exo1 and between PCNA and polymerase
, the significance of these protein-protein interactions in nick-directed mismatch repair has not been established.
| FOOTNOTES |
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1 To whom correspondence should be addressed: Dept. of Biochemistry and HHMI, Box 3711, Duke University Medical Center, Durham, NC 27710. Tel.: 919-684-2775; Fax: 919-681-7874; E-mail: modrich{at}biochem.duke.edu.
2 The abbreviations used are: ID, insertion/deletion; PCNA, proliferating cell nuclear antigen; RPA, replication protein A; RFC, replication factor C. ![]()
3 F. Kadyrov and P. Modrich, unpublished data. ![]()
| ACKNOWLEDGMENTS |
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| REFERENCES |
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