MINIREVIEW

DNA mismatch repair system

Classical and fresh roles
Sung-Hoon Jun, Tae Gyun Kim and Changill Ban
Department of Chemistry and Division of Molecular & Life Science, Pohang University of Science and Technology, Korea

Key words The molecular mechanisms of the DNA mismatch repair (MMR) system
antibody diversification; DNA damage have been uncovered over the last decade, especially in prokaryotes. The
response; DNA mismatch repair; MutL;
results obtained for prokaryotic MMR proteins have provided a frame-
MutS
work for the study of the MMR system in eukaryotic organisms, such as
Correspondence yeast, mouse and human, because the functions of MMR proteins have
C. Ban, Department of Chemistry, Pohang been conserved during evolution from bacteria to humans. However, muta-
University of Science and Technology, tions in eukaryotic MMR genes result in pleiotropic phenotypes in addition
Pohang 790–784, Korea to MMR defects, suggesting that eukaryotic MMR proteins have evolved
Fax: +82 54 2793399 to gain more diverse and specific roles in multicellular organisms. Here, we
Tel: +82 54 2792127
summarize recent advances in the understanding of both prokaryotic and
E-mail: ciban@postech.ac.kr
eukaryotic MMR systems and describe various new functions of MMR
(Received 12 December 2005, accepted proteins that have been intensively researched during the last few years,
10 February 2006) including DNA damage surveillance and diversification of antibodies.

doi:10.1111/j.1742-4658.2006.05190.x

The mismatch repair (MMR) system is essential to all

organisms because it maintains the stability of the gen-
ome during repeated duplication. It is composed of a
few well-conserved proteins whose functions in the
postreplicative repair of mismatched DNA have been
characterized by co-ordinated genetic, biochemical and
structural approaches. Various functions, in addition
to mismatch repair during replication, have been
reported for MMR proteins such as antirecombination
activity between divergent sequences, promotion of
meiotic crossover, DNA damage surveillance and
diversification of immunoglobulins (Fig. 1). Recent
research has provided a great deal of information
about how MMR proteins are involved in these
diverse processes.
Prokaryotic mismatch repair
Essential components of the MMR system – MutS,
MutL, MutH and Uvr – were identified in Escherichia
coli through the genetic studies of mutants that showed
elevated mutation levels [1,2]. MMR reactions have
also been reconstituted with purified components in
E. coli [3], which drove extensive studies on prokaryotic
MMR systems.
MutS detects mismatches in DNA duplexes and initi-
ates the MMR machinery. A microscopic study sugges-
ted a possible mechanism for how MutS discriminates
between heteroduplex and homoduplex DNA [4].
According to this proposal, nonspecifically bound MutS
bends DNA to search for a mismatch. If it recognizes a

Abbreviations
AID, activation-induced cytidine deaminase; ATM, ataxia telangiectasia mutated; ATR, ATM and Rad3-related; Chk1, checkpoint kinase 1;
Chk2, checkpoint kinase 2; CSR, class switch recombination; LC20, MutL C-terminal 20 kDa; LN40, MutL N-terminal 40 kDa; MLH, MutL
homolog; MMR, mismatch repair; MSH, MutS homolog; PCNA, proliferating cell nuclear antigen; PMS, postmeiotic segregation; RPA,
replication protein A; RFC, replication factor C; S, switch; SHM, somatic hypermutation; V, variable.

FEBS Journal 273 (2006) 1609–1619 ª 2006 The Authors Journal compilation ª 2006 FEBS 1609
Various functions of mismatch repair proteins
specific mismatch, MutS undergoes a conformational
change and unbends the bent DNA. Crystallographic
studies of Thermus aquaticus and E. coli MutS
complexed with mismatched DNA provided the molecu-
lar details of mismatch recognition [5–7], suggesting that
a homodimer of MutS binds asymmetrically to hetero-
duplex DNA (Fig. 2A). MutS has two functional
domains (a DNA-binding domain and an ATPase ⁄
dimerization domain) and the asymmetry in the
ATPase ⁄ dimerization domain was also reported to be
essential in the MMR process in vivo [8]. These two
domains are widely separated from each other, but
affect each other by conformational changes that are
induced by the binding of DNA or ATP [9]. This inter-
action is a key molecular mechanism for modulating the
function of the MutS protein in the MMR process. Only
two residues, both in the same subunit of MutS, take
part in the sequence-specific interaction with a mis-
matched base. One, a conserved glutamate (Glu41 in
T. aquaticus MutS and Glu38 in E. coli MutS), forms a
hydrogen bond with the mismatched base. Recently, this
hydrogen bond was suggested to induce an inhibition
of the ATPase activity of MutS, helping to form a stable
MutS–ATP–DNA intermediate of the downstream
repair process [10]. The other specific interaction is
between an aromatic ring stack of a conserved phenyl-
alanine (Phe39 in T. aquaticus MutS and Phe36 in
E. coli MutS) and the mismatched base. In contrast to
these sequence–specific interactions, van der Waals
1610 FEBS Journal 273 (2006) 1609–1619 ª 2006 The Authors Journal compilation ª 2006 FEBS
S.-H. Jun et al.
Fig. 1. Various functions of mismatch repair
(MMR) proteins. MMR proteins are involved
in diverse genetic pathways through interac-
tions with different proteins. MMR proteins
increase replication fidelity by repairing
errors generated during replication. Prolifer-
ating cell nuclear antigen (PCNA) and replica-
tion factor C (RFC) work with MMR proteins
during mismatch repair in replication. Various
kinds of DNA damage trigger MMR protein-
dependent DNA damage responses that are
implemented through the activation of
ataxia telangiectasia mutated and Rad3-relat-
ed (ATR) and p53. Antibody diversification is
formed by mutations in immunoglobulin
genes that are introduced by MMR proteins
in conjunction with activation-induced cyti-
dine deaminase (AID) and DNA polymerase
g. In addition, MMR proteins regulate recom-
bination and promote meiotic crossover.
The functions of MMR proteins in green
boxes are discussed in this article, whereas
those in red boxes are not.
interactions and hydrogen bonds between the DNA
backbone and side chains of MutS are sequence inde-
pendent [5,6]. After the recognition of mismatched
DNA, MutS initiates the MMR system through direct
or indirect interactions with other proteins, including
MutL, MutH and UvrD. Although an exact answer to
this puzzle is yet to be found, a few groups have sugges-
ted various models for detailed molecular events during
MMR reactions (Fig. 3) [11].
The function of MutL in the MMR system is to
make a connection between the recognition of a mis-
match and the excision of the mismatch from the
strand within which it is contained [12]. To do this, a
MutL homodimer interacts with MutS [13] and stimu-
lates the endonuclease activity of MutH [14]. MutL
also loads UvrD onto the DNA. UvrD is a DNA
helicase II that unwinds the DNA duplex from the
nick generated by MutH [15,16]. MutL is a member of
the GHKL superfamily of ATPases, which includes gy-
rase, a type II topoisomerase, Hsp90, histidine kinase
and MutL [17]. A biochemical study demonstrated that
MutL has ATPase activity [17,18]. Crystallographic
studies have demonstrated that ATP binding drives
dimerization of the N-terminal domain of the protein
(Fig. 2B) [18], and the accompanying structural chan-
ges may play key roles in co-ordinating the initial steps
of mismatch recognition with downstream processing
steps. A model for the intact MutL protein, which
includes a large central cavity, was suggested based on
S.-H. Jun et al. Various functions of mismatch repair proteins

Fig. 2. Structures of MutS, MutL and MutH. (A) Crystal structure of the Thermus aquaticus MutS heteroduplex DNA complex (PDB acces-
sion code: 1EWQ). The MutS homodimer is formed by asymmetric subunits that are represented by ribbon diagrams in green and purple.
The heteroduplex DNA is a space-filling model. Two adjacent large channels with dimensions of  30 · 20 Å and  40 · 20 Å penetrate the
disk-like protein structure, and the latter is occupied by the heteroduplex DNA. The DNA is kinked sharply towards the major groove by
 60
at the unpaired base. Only one subunit (in purple) interacts with the unpaired base, thereby breaking the molecular twofold symmetry
of the homodimer. (B) Crystal structure of the N-terminal 40 kDa fragment (LN40) of Escherichia coli MutL complexed with ADPnP (PDB
accession code: 1B63). The structure of LN40 is homologous to that of an ATPase-containing fragment of DNA gyrase. ADPnP drives the
dimerization of LN40, and the dimer interface is well ordered and made entirely of the segments that were disordered in the apoprotein. (C)
A crystal structure of MutH (PDB accession code: 1AZO). The structure resembles a clamp, with a large cleft dividing the molecule into two
halves. Each half forms a subdomain that contains similar structural elements. The two subdomains share a hydrophobic interface and are
connected by three polypeptide linkers. The active site is located at an interface between two subdomains, and DNA binds in the cleft that
is 15–18 Å wide and 12–14 Å deep.

the structures of the N-terminal domain (LN40) and
the C-terminal domain (LC20), which were reported
separately [17–19]. A biochemical assay, using various
mutant MutL proteins, suggested that LC20 is involved
in the DNA-binding activity of MutL. An increase in
the DNA-binding activity of MutL also resulted in
higher UvrD helicase activity [19].
MutH is a member of the type II family of res-
triction endonucleases and cleaves at hemimethyl-
ated GATC sites for excision of mismatch-containing
strands [20]. The nicking activity of MutH is stimula-
ted in a mismatch-dependent manner by MutS, MutL
and ATP [20]. A structural study suggested that the
C-terminal helix of MutH might act as a molecular
lever through which MutS and MutL communicate
and activate MutH (Fig. 2C) [21]. The nick generated
by MutH serves as a point of entry for single-stranded
DNA-binding protein and UvrD ⁄ helicase II, whose
loading at the nick is facilitated via protein–protein
interactions with MutL [15,16]. Excision of the newly
synthesized strand between the nick and the mismatch
is carried out by four redundant single-strand DNA-
specific exonucleases: the 3¢ fi 5¢ exonucleases ExoI
and ExoX and the 5¢ fi 3¢ exonucleases RecJ and
ExoVII [22]. DNA polymerase III, single-stranded
DNA-binding protein and DNA ligase carry out repair
synthesis [3].
Eukaryotic mismatch repair
All eukaryotic organisms, including yeast, mouse and
human, have MutS homologs (MSHs) and MutL
homologs (MLHs). The eukaryotic MMR system has
been well conserved during the evolutionary process
[3,23]. However, in contrast to MutS and MutL in
bacteria, which function as homodimers, in eukaryotes
MSHs and MLHs form heterodimers with multiple
proteins. Five highly conserved MSHs (MSH2 to
MSH6) are present in both yeast and mammals.
MSH1, which is present in mitochondria, exists only in

FEBS Journal 273 (2006) 1609–1619 ª 2006 The Authors Journal compilation ª 2006 FEBS 1611
Various functions of mismatch repair proteins
Fig. 3. Models for the assembly of the DNA mismatch repair
complex in a schematic drawing. A mismatch base is detected
by MutS, and ATP-bound MutS recruits MutL. In model I, the
MutS–MutL complex stays at the mismatch site and activates
MutH at some distance. MutS leaves the mismatch site, after bind-
ing ATP, in both model II and model III. ATP is used as an energy
source for translocation of MutS in model II (translocation model)
but it acts as a molecular switch of MutS in model III, like GTP of
G-proteins (molecular switch model).
yeast [24]. MSH4 and MSH5 show reproductive tis-
sue-specific expression, and null mutations of these
genes do not confer mutator phenotypes because they
are involved in meiotic recombination but not postrep-
lication repair [25]. Genetic and biochemical studies
have indicated that MSH2 is required for all mismatch
correction in nuclear DNA, whereas MSH3 and
MSH6 are required for the repair of some distinct and
overlapping types of mismatched DNA during replica-
tion [26]. These three MutS homologs make two
heterodimers: MutSa (MSH2 ⁄ MSH6) and MutSb
(MSH2 ⁄ MSH3). The former plays the major role in
recognition of mismatched DNA in eukaryotic MMR.
That is, MutSa functions in the repair of base–base
mispairs as well as a range of insertion ⁄ deletion loop
mispairs, whereas MutSb primarily functions in the
repair of insertion ⁄ deletion loop mispairs [27,28].
MutL homologs in eukaryotic organisms were iden-
tified as genes whose amino acid sequences showed
high similarity with prokaryotic MutL proteins, or
whose mutation phenotypes were increased levels of
postmeiotic segregation (PMS) that resulted from a
failure to repair mismatches in meiotic recombination
intermediates [29]. There are four homologs of MutL
in both yeast and mammals. In a genetic analysis,
defects in MLH1 and PMS1 in yeast resulted in more
severe mutator phenotypes, reminiscent of those of
1612 FEBS Journal 273 (2006) 1609–1619 ª 2006 The Authors Journal compilation ª 2006 FEBS
S.-H. Jun et al.
MSH2 and MSH6, than defects in the two other MutL
homologs [30]. Also, MLH1 interacted with the other
three MutL homologs in a yeast two-hybrid analysis
[31]. Overall, yeast MLH1 ⁄ PMS1 and mammalian
MLH1 ⁄ PMS2 heterodimers (each known as MutLa)
play a major role in mutation avoidance, and the other
two heterodimers of MutL homologs take part in the
repair of specific classes of mismatches [32]. The bio-
chemical activities and structure of MutL homologs
are closely related to those of prokaryotic MutL pro-
teins, especially in the N-terminal domain. The X-ray
crystallographic structure of the conserved N-terminal
40-kDa fragment of human PMS2 resembles that of
the ATPase fragment of E. coli MutL [33].
Extensive genetic studies in yeast have failed to find
orthologs of MutH and UvrD in the MMR system,
and there may be no homolog of these two proteins in
the eukaryotic genome [34]. Therefore, some diver-
gence in the MMR system from strand discrimination
and the nicking process might occur between prokary-
otes and eukaryotes. A recent increase in our know-
ledge of the eukaryotic MMR system provides some
understanding of this divergence.
In mammalian cell extracts, mismatches provoke ini-
tiation of excision at pre-existing nicks in exogenous
DNA substrates with high efficiency and specificity
[35,36]. The molecular nature of eukaryotic MMR
could be assessed using cell extract assays in vitro, and
components of the eukaryotic MMR system have been
identified with depletion and complementation assays
using cell extracts. One protein, identified in this way,
is proliferating cell nuclear antigen (PCNA). PCNA is
known to function as a processivity factor for replica-
tive polymerase, but some mutations in the PCNA
gene result in mutator phenotypes [37], and its interac-
tions with MSH2 and MLH1 [38], and with MSH6
[39], suggest that it functions in MMR. PCNA has
biochemical activity that increases the binding of
MutSa to mismatched DNA; the interactions between
PCNA and MSH6 are essential for this biochemical
activity, which suggests that PCNA might play a role
in MMR at the mispair recognition stage [39]. PCNA
has been proposed to function in the mismatch recog-
nition stage of MMR by helping MutSa search for
mismatched DNA [40] or increasing the mismatch-
binding specificity of MutSa [39]. One intriguing point
about the role of PCNA in eukaryotic MMR is that
the requirement for PCNA depends on the direction of
the nick in the in vitro MMR assay. Although PCNA
is required for mismatch-provoked excision directed
by a 3¢ strand break in HeLa nuclear extracts, it
is not essential for excision directed by a 5¢ nick
[41,42]. Moreover, whereas 3¢ nick-directed excision is
S.-H. Jun et al.
completely abolished by the inhibition of PCNA, 5¢
nick-directed excision is affected only minimally [42].
Finally, a mismatch-provoked 5¢ fi 3¢excision reaction
can be reconstituted in a purified system that compri-
ses only MutSa, MutLa, ExoI and replication protein
A (RPA), without PCNA, and the process is similar
to that observed in nuclear extracts [41]. RPA, the
eukaryotic single-stranded DNA-binding protein, has
been shown to enhance excision and stabilize excision
intermediates in crude fractions [43,44]. The activities
of ExoI are described below.
Genetic studies in yeast, and biochemical studies of
MMR activity in cell extracts, indicate that eukaryotes
use a mechanism similar to prokaryotes, with both
3¢ fi 5¢ and 5¢ fi 3¢ exonuclease activities for mis-
match correction [45]. ExoI, a 5¢ fi 3¢ exonuclease,
was found to play a role in mutation avoidance and
mismatch repair in yeast [46], and its physical inter-
action with MSH2 and MLH1 also support a role in
MMR [47]. Intriguingly, the mammalian ExoI was
reported to be involved in both 5¢- and 3¢ nick-directed
excision in extracts of mammalian cells [48], but how
ExoI can have a 3¢ fi 5¢ exonuclease activity was
unclear. Recent research by the Modrich group pro-
vides a plausible answer to this question [49]. They
reconstituted mismatch-provoked excision, directed by
a strand break located either 3¢ or 5¢ to the mispair, in
a defined human system using purified human proteins.
In the presence of the eukaryotic clamp loader replica-
tion factor C (RFC) and PCNA, 3¢ fi 5¢ excision was
supported by MutSa, MutLa, ExoI and RPA. More-
over, RFC and PCNA act to suppress 5¢ fi 3¢ excision
when the strand break that directs hydrolysis is located
3¢ to the mismatch, which suggests that the polarity of
mismatch-provoked excision by ExoI is regulated by
PCNA and RFC. Once the strand is excised beyond
the mismatch, DNA resynthesis occurs by the activity
of polymerase d [50] in the presence of PCNA [51] and
RPA [43,44]. The remaining nick is then sealed by
an as-yet-unidentified ligase, completing the repair
process.
MMR proteins in the DNA damage
response
The involvement of MMR proteins in the DNA dam-
age response first became apparent when it was discov-
ered that MMR-defective bacterial and mammalian
cells are resistant to cell death caused by alkylating
agents [52]. MMR-deficient cells are also resistant to
other DNA-damaging agents, including methylation
agents, cisplatin and UV radiation [53]. Subsequent
studies on the roles of MMR proteins in response to
FEBS Journal 273 (2006) 1609–1619 ª 2006 The Authors Journal compilation ª 2006 FEBS
Various functions of mismatch repair proteins
DNA damage in normal cells showed that N-methyl-
N¢-nitro-N-nitrosoguanidine, an alkylating agent, trig-
gers MMR-dependent G2 ⁄ M arrest [54], which is
followed by the induction of MMR-dependent apopto-
sis [55].
The role of MMR proteins in response to DNA
damage can be inferred from the interactions of MMR
proteins with the tumor suppressor protein, p53, and
p53-related proteins. p53 acts as a major point in a
complex network that responds to diverse cellular
stresses, including DNA damage [56]. Once stabilized
and activated by genotoxic stress, p53 can either acti-
vate or repress a wide array of different gene targets
by binding to their promoter regions, which in turn
can regulate cell cycle, cell death and other outcomes
[57]. The p53 homologs p63 and p73 induce p53-inde-
pendent apoptosis as well as affect trans-activation
of certain target genes by p53 [58,59]. Treatment of
human cells with methylating agents results in phos-
phorylation of p53 and induction of apoptosis, a
response that depends on the presence of functional
hMutSa and hMutLa [60]. UVB-induced apoptosis is
significantly reduced in MSH2-deficient cells, and it
correlates with decreased activation of p53, which sug-
gests that MSH2 may act upstream of p53 to induce
post-UVB apoptosis [61]. Cisplatin-caused DNA dam-
age increases the stability of p73, which induces apop-
tosis that is dependent on functional hMLH1 protein
[62]. Moreover, cisplatin stimulates the interaction
between PMS2 and p73, which is required for the acti-
vation of p73 and subsequent induction of apoptosis
[63]. PMS2 and p73 can also interact with each other,
independently of MLH1, suggesting that MMR pro-
teins have specific roles in the DNA damage response.
Taken together, these reports indicate that MMR pro-
teins may play roles in multiple steps of the DNA
damage response, as damage sensors and adaptors of
the pathways (Fig. 4).
The roles of MMR proteins in the response to DNA
damage are further supported by the failure of MMR
mutants to trigger G2 ⁄ M arrest in response to the
methylator N-methyl-N¢-nitro-N-nitrosoguanidine and
similar alkylators [64]. The G2 ⁄ M checkpoint prevents
cells from initiating mitosis when they experience
DNA damage during G2, or when they progress into
G2 with unrepaired damage incurred during the previ-
ous S or G1 phases [65]. A study with a cell line lack-
ing hMLH1 expression and an inducible hMLH1
expression system showed that methylation-induced
G2 ⁄ M arrest requires a full complement of hMLH1
(expression level similar to that of the wild type),
whereas MMR proficiency was restored, even at low
hMLH1 concentrations ( 10% of wild-type expres-
1613
Various functions of mismatch repair proteins
Fig. 4. A simplified model of DNA damage response pathways
that are dependent on mismatch repair (MMR) proteins. MMR
proteins bind to damaged DNA and recruit various signal-transducing
kinases, including ataxia telangiectasia mutated (ATM), ATM and
Rad3-related (ATR), and checkpoint kinase 1 ⁄ checkpoint kinase 2
(Chk1 ⁄ Chk2). They in turn stabilize and activate p53, a key compo-
nent in DNA damage responses, such as cell cycle checkpoint
activation and programmed cell death (apoptosis). p73, a p53
homolog, is also a transducer of the MMR protein-dependent DNA
damage response, and postmeiotic segregation 2 (PMS2) is known
to bind and stabilize p73. The p38 mitogen-activated protein (MAP)
kinase pathway connects MMR proteins and p53 ⁄ p73 in this
pathway. c-Abl is a tyrosine kinase that acts upstream of p73 and
stabilizes it [59].
sion) [66], suggesting that these two responses are
carried out by different genetic pathways. The compo-
nents that transduce the G2 ⁄ M checkpoint signal
pathway, such as ataxia telangiectasia mutated (ATM),
ATM and Rad3-related (ATR), checkpoint kinase 1
(Chk1) and checkpoint kinase 2 (Chk2), are activated
in the MMR system-dependent G2 ⁄ M arrest induced
by DNA methylation [67,68]. ATR and Chk1 path-
ways are essential for this response [67]. The mitogen-
activated protein (MAP) kinase, p38a, is activated in
MMR-proficient cells exposed to the methylating
agent, temozolomide, but not in MLH1 knockdown
cells [69], suggesting that the p38 MAP kinase pathway
links the MMR system to the G2 ⁄ M checkpoint. The
1614 FEBS Journal 273 (2006) 1609–1619 ª 2006 The Authors Journal compilation ª 2006 FEBS
S.-H. Jun et al.
interaction between MMR proteins and checkpoint
proteins also suggests direct roles for MMR proteins
in the DNA damage response. Both in vitro and in vivo
approaches show that MSH2 binds to Chk1 and Chk2
[68], that MLH1 associates with ATM [70] and that
these interactions are enhanced after treatment with a
methylating agent [68]. MSH2 protein physically inter-
acts with ATR in the damage response to DNA
methylation, and their interaction is required for the
phosphorylation of Chk1 [71]. ATR also serves as a
haploinsufficient tumor suppressor in MMR-deficient
cells, suggesting the genetic interaction of these pro-
teins [72]. Taken together, these findings suggest that
MMR proteins function early in the pathway that
leads from DNA methylating agents to G2 ⁄ M arrest
(Fig. 4).
The molecular mechanism of the involvement of
MMR proteins in various DNA damage responses
is unclear. Given the original function of the MMR
system in detecting and repairing errors that occur
during replication, the MMR protein complex could
serve as a sensor for DNA damage [71]. A large com-
plex, named BRCA1-associated genome surveillance
complex, which includes tumor suppressors and the
MMR ⁄ DNA damage-repair proteins MSH2, MSH6,
MLH1, ATM, Bloom’s syndrome, and RAD50–
MRE11–NBS1, has also been suggested to be a poss-
ible sensor for DNA damage [73]. The roles of MMR
proteins in the DNA damage response may not be
simple from the viewpoint of their various relation-
ships with other regulators of the DNA damage
response, especially with ATM and p53. For instance,
hMLH1 and hPMS2 were identified as direct target
genes of p53 [74]. Cisplatin induces the accumulation
of hPMS1, hPMS2 and hMLH1 through ATM-medi-
ated protein stabilization, and the induced level of
these MMR proteins is important for the phosphorylat-
ion of p53 by ATM in the response to DNA damage
[75]. MMR proteins and p53 therefore may act as a
kind of positive feedback regulation for the DNA
damage response, or a more complicated network may
regulate their activity and expression.
MMR proteins in antibody
diversification
In addition to the initial generation of antibody diver-
sity by gene rearrangement during B-cell development
[76], specific antigen recognition triggers a second wave
of antibody diversification through somatic hypermu-
tation (SHM) and class switch recombination (CSR).
SHM introduces multiple single-nucleotide substitut-
ions into variable (V) regions of immunoglobulin
S.-H. Jun et al. Various functions of mismatch repair proteins

genes and CSR is a region-specific intrachromosomal to deaminate dC to dU subsequently in ssDNA

recombination that replaces the Cl form of the immu-
noglobulin (Ig) heavy chain constant region (CH) gene
with other CH genes, resulting in a switch of the Ig iso-
type from IgM to IgG, IgE, or IgA [77]. The mole-
cular processes of SHM and CSR, and the proteins
involved in these processes, have been investigated in
detail over the last few years. Advances in gene target-
ing techniques have led to the availability of mice with
loss-of-function mutations in MMR genes, and recent
studies using these mice have suggested that MMR
proteins are directly involved in antibody diversifica-
tion. MSH2-deficient mice accumulated fivefold fewer
mutations in the V region of antibody genes [78].
MSH6 deficiency caused similar effects, but MSH3
deficiency did not [79], suggesting that MutSa plays an
essential role in SHM. Similarly, mice with loss-
of-function mutations in MSH2 or MSH6 have a
decreased frequency of CSR, but those with MSH3
do not [80]. Mice carrying a mutation in the MSH2
ATPase domain are deficient in SHM and CSR, sug-
gesting that the ATPase activity of MSH2 is essential
for antibody diversification [81]. It will be interesting
to understand how MMR proteins are involved in the
processes of SHM and CSR, which require the induc-
tion of mutations.
Both SHM and CSR start with the activity of acti-
vation-induced cytidine deaminase (AID), which is a
homolog of the RNA editing enzyme, but is known
[82,83]. Transcription of the Ig gene in the V and
switch (S) regions is required for SHM and CSR,
respectively [84], because AID deaminates cytidine
residues in single-stranded DNA located in the tran-
scription bubble of the V and S regions [85,86],
(Fig. 5). AID-induced mutations of cytidine explain
some SHM and mutations in CSR, but up to half of
the mutations of the V and S regions are independent
of AID. Phenotypic analyses of MSH2- and MSH6-
defective mice showed that the spectra of SHM were
different in these mice than in wild-type mice [78,79],
indicating that MSH2 and MSH6 are required for
mutations at AT base pairs during SHM and CSR
[78,79]. These results suggested that mutations in
SHM and CSR are achieved in two steps: in the first
step, AID generates mutations in GC base pairs, and
in the second step, the MMR system is recruited to
the mismatched DNA and resynthesizes the DNA
strand with the help of an error-prone polymerase,
such as pol g (Fig. 5) [87]. This model is supported
by a report that MSHa not only binds to a U:G
mispair, but also physically interacts with DNA poly-
merase g and functionally stimulates its catalytic
activity [88]. Moreover, the phenotypes of mice
mutant for ExoI are similar to those of MSH2– ⁄ –
mice, with reduced SHM and CSR, and ExoI and
MLH1 physically interact with mutating variable
regions [89].

Fig. 5. A model of somatic hypermutation that is dependent on the mismatch repair (MMR) protein. (A) During transcription of the immuno-
globulin gene in the variable (V) region, activation-induced cytidine deaminase (AID) deaminates cytidine residues in single-stranded DNA to
produce UG mismatches. (B) MutSa and MutLa are recruited to the mismatched DNA, and activate ExoI. (C) The gaps generated by the
activity of ExoI are refilled by error-prone DNA polymerase g, resulting in mutations in AT base pairs. (D) The diversity of the V regions of
antibody genes is thus accomplished by the formation of mutations by a mechanism that depends on MMR proteins.

FEBS Journal 273 (2006) 1609–1619 ª 2006 The Authors Journal compilation ª 2006 FEBS 1615
Various functions of mismatch repair proteins
Conclusion
The MMR system was originally discovered as a
mechanism that maintains the integrity of the genome
during replication. Increasingly, however, components
of the system are being found to participate in diverse
cellular processes, including the repair of DNA dam-
age and antibody diversification. How MMR proteins
are regulated to perform these various functions will
be an important question for the co-ordinated under-
standing of MMR proteins. Searching for the unidenti-
fied components of the MMR system will also provide
further information in the growing body of research
on the mechanism of the MMR system. Finally,
understanding the MMR system will provide insights
into cancer development related to the defects in
MMR genes and the treatment of tumors, both hered-
itary and sporadic, with defective MMR.
Acknowledgements
This work was supported by the Center for Integrated
Molecular Systems through KOSEF, the POSRIP res-
earch grant (1RC0402301), and the Center for Innova-
tive Bio-Physio Technology at BNU (grant number:
02-PJ3-PG6-EV05-0001).
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