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Logo of hhmipaAbout Author manuscriptsSubmit a manuscriptHHMI Howard Hughes Medical Institute; Author Manuscript; Accepted for publication in peer reviewed journal
 
J Biol Chem. Author manuscript; available in PMC 2008 February 8.
Published in final edited form as:
PMCID: PMC2234602
HHMIMSID: HHMIMS38439
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MECHANISMS IN EUKARYOTIC MISMATCH REPAIR*
Paul Modrich
Paul Modrich, Department of Biochemistry & Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina 27710;
Address correspondence to: Paul Modrich, Department of Biochemistry & 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
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Inactivation of the human mismatch repair system confers a large increase in spontaneous mutability and a strong predisposition to tumor development. Mismatch repair provides several genetic stabilization functions: it corrects DNA biosynthetic errors, ensures the fidelity of genetic recombination, and participates in the earliest steps of checkpoint and apoptotic responses to several classes of DNA damage (see refs. 1-3 for recent reviews). Defects in this pathway are the cause of typical and atypical hereditary nonpolyposis colon cancer (4), but may also play a role in the development of 15 to 25% of sporadic tumors that occur in a number of tissues (5). The system is also of biomedical interest because mismatch repair-deficient tumor cells are resistant to certain cytotoxic chemotherapeutic drugs (2,3), a manifestation of its involvement in the DNA damage response. Of the several mutation avoidance functions of mismatch repair, the reaction responsible for replication error correction has been the most thoroughly studied, and the discussion that follows is restricted to this pathway.
Correction of DNA biosynthetic errors requires targeting of mismatch repair to the newly synthesized strand at the replication fork. In contrast to E. coli, where mismatch repair is directed by the transient absence of adenine methylation at d(GATC) sites within newly synthesized DNA, the strand signals that direct replication error correction in eukaryotes have not been identified. However, the function of the hemimethylated d(GATC) strand signal in E. coli mismatch repair is provision of a nick on the unmethylated strand, which serves as the actual signal that directs the reaction (2). Similarly, a strand-specific nick or gap is sufficient to direct mismatch repair in extracts of mammalian and Drosophila cells, as well as Xenopus egg extracts (1-3). These findings, coupled with the observation that mismatch repair is more efficient on the lagging strand at the replication fork (6), suggest that DNA termini that occur as natural intermediates during replication (3’-terminus on the leading strand; 3’ and 5’ termini on the lagging strand) may suffice as strand signals to direct the correction of DNA biosynthetic errors in eukaryotic cells.
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 ≈ 90 to 170 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 1,000 base pairs (bp) (7).
Fig. 1
Fig. 1
Substrates and requirements for in vitro mismatch repair
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 (1-3). 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.
The activities responsible for initiation of E. coli mismatch repair are MutS and MutL, which function as homo-oligomers (2). MutS is responsible for mismatch recognition and MutL serves to interface mismatch recognition by MutS to activation of downstream activities. Mammalian cells possess two MutS activities that function as heterodimers and share MSH2 as a common subunit (11-14): MutSα (MSH2•MSH6 heterodimer) and MutSβ (MSH2•MSH3 heterodimer). MutSα, which represents 80 - 90% of the cellular MSH2, preferentially recognizes base-base mismatches and insertion/deletion (ID) mispairs in which one strand contains 1 or 2 unpaired nucleotides, but is also capable of recognition of larger ID heterologies with reduced affinity (11-13,15). MutSβ 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).
Three eukaryotic MutL activities have been identified, and like eukaryotic MutS activities function as heterodimeric complexes, with MLH1 serving as a common subunit. MutLα, a heterodimer of MLH1 and PMS2, is the primary MutL activity in human mitotic cells and supports repair initiated by either MutSα or MutSβ (17). MutLα 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 (MutLβ) has been isolated, but involvement in mismatch repair has not been demonstrated (18). However, the MutLγ 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 MutSα (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).
Yeast genetic studies and analysis of the mammalian extract reaction have implicated six additional activities in eukaryotic mismatch repair. The key finding that culminated in the reconstitution studies described below was the demonstration that exonuclease I (Exo1) participates in the reaction. Genetic evidence for Exo1 involvement in yeast mismatch repair (20,21) led to the subsequent demonstration that Exo1 is required for repair of base-base and single-nucleotide ID mismatches in mammalian cell extracts (22,23). Because Exo1 hydrolyzes duplex DNA with 5’ to 3’ polarity (24,25), the surprising feature of this requirement is that the enzyme is necessary for excision and repair directed by strand break located either 5’ or 3’ to the mismatch. This paradoxical requirement led to the suggestion that Exo1 might play a positive regulatory role in 3’ excision or that the reaction may be mediated by a cryptic Exo1 3’ to 5’ hydrolytic activity (22). As discussed below, this issue has been recently resolved, and it is not necessary to invoke either of these possibilities.
Exo1−/− mice display modest cancer predisposition, and Exo1-deficiency is associated with a 30-fold elevation of HPRT mutability, substantially less than the 150-fold increase observed with Msh2−/− cells (23). While 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 δ and ε in mismatch repair has been proposed on genetic and biochemical grounds (26-28), but this idea has been questioned (29,30). Using an siRNA 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 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 MutSα, may also play an important role in the initiation of mismatch-provoked excision in nuclear extracts (35).
The PCNA replication clamp and DNA polymerase δ have also been implicated in mismatch repair in human cell extracts (36-39). PCNA, which confers processivity on polymerase δ (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). While p21 abolishes 3’-directed mismatch–provoked excision in HeLa cell extracts, only 40 - 50% of 5’-directed excision events are subject to p21 inhibition, implying occurrence of at least two hydrolytic modes on 5’-heteroduplexes (36,39,42).
These findings have led to several reconstituted systems that rely on near-homogeneous proteins and support mismatch-provoked excision and repair. The simplest excision system depends on MutSα, MutLα, 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. MutSα 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 MutSα renders the enzyme highly processive, resulting in removal of ≈ 2,000 nucleotides prior to dissociation (39), an effect attributed to formation of a MutSα•Exo1 complex. Hydrolysis by the MutSα•Exo1 complex is controlled in part by RPA, which reduces processivity of the MutSα•Exo1 complex to ≈ 250 nucleotides, and by binding to gaps, controls access of Exo1 to 5’-termini in excision intermediates/products (39). Although an RPA-filled gap is a very poor substrate for Exo1, MutSα promotes Exo1 loading at such sites provided that gapped molecule contains a mismatched base pair. The ramifications of these RPA effects are two-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 MutSα and Exo1 (39,43). Secondly, hydrolysis is dramatically attenuated upon mismatch removal because MutSα 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 MutSα•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.
Fig. 2
Fig. 2
5’ to 3’ default hydrolytic system
MutLα is not required for mismatch- and MutSα-dependent activation of Exo1, but it does play a significant role in excision. By acting in concert with MutSα to suppress Exo1 hydrolysis on DNA that lacks a mispair, MutLα enhances the mismatch dependence of the reaction (39,44). MutLα 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 MutLα involvement in termination to its role in suppressing Exo1 activity on mismatch-free DNA. In this mechanism MutLα simply stabilizes excision products against nonspecific hydrolysis by Exo1. By contrast, Zhang et al. (43) have concluded that MutLα, acting in concert with RPA, plays an active role in excision termination upon mismatch removal. This issue has not been resolved.
MutSα, MutLα, 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 MutSα, MutLα, 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. While 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 MutSα, RFC, and PCNA activate a latent MutLα endonuclease in an ATP- and mismatch-dependent manner (46). As shown in Fig. 3 incision by activated MutLα 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 (F. Kadyrov and P. Modrich, unpublished). 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 MutSα-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).
Fig. 3
Fig. 3
MutLα endonuclease in mismatch-provoked excision
The endonucleolytic mode of action of this system is reminiscent of the mechanism for mismatch repair in Xenopus egg extracts proposed by Varlet et al (10). As discussed above, this model posits that the nick that directs repair serves as a strand signal, but not as a site for excision initiation, which actually occurs at a strand break produced by a mismatch-activated endonuclease. This mode of excision is fundamentally different than used by the E. coli methyl-directed pathway, where hydrolysis initiates at a 3’ or 5’ strand break that directs repair (2).
The probable active site of the MutLα 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 MutLα endonuclease activity, as well as 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.
Several defined systems that support mismatch correction have also been described, but these differ in several respects. Zhang et al. (43) have shown that MutSα, MutLα, Exo1, RPA, HMGB1, and DNA polymerase δ 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), MutLα 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 addition of HMGB1. Interestingly, substitution of MutSβ for MutSα yields a system that supports 5’-directed excision and repair of a 3-nucleotide ID mismatch, implying that like MutSα, MutSβ 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 MutSα, MutLα, Exo1, RPA, DNA polymerase δ, RFC and PCNA (30). MutLα is dispensable for 5’-repair in this system, but required for 3’-heteroduplex repair. The RFC and PCNA requirement for 5’-directed correction is due to 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 to 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.
The recent establishment of defined systems that support mismatch-provoked excision and repair reactions should facilitate study of this elaborate reaction. However, because the reconstituted reactions described to date are minimal systems, it is premature to assume that they can account for mismatch repair as it occurs in the eukaryotic cell. There is excellent evidence for participation of hydrolytic activities in addition to Exo1 (23), but these have not been convincingly identified. Activities that regulate the action of MutLα 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 (1-3), 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 MutLα 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 MutSα-MutLα, MutSα-PCNA, MutSβ-PCNA, MutLα-PCNA, MutSα-Exo1, MutLα-Exo1, Exo1-PCNA, and PCNA-polymerase δ (1-3,40). With the exception of interactions between MutSα and Exo1 and between PCNA and polymerase δ, the significance of these protein-protein interactions in nick-directed mismatch repair has not been established.
Footnotes
*Work in my laboratory was supported by NIH grants R01 GM45190 and P01 CA92584, and funds from the Howard Hughes Medical Institute. I thank Vickers Burdett, Leo Dzantiev, Jochen Genschel, Ravi Iyer, and Anna Pluciennik for valuable comments and suggestions.
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