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INTRODUCTION |
Reactive oxygen species attack many reactive moieties of DNA. When
DNA is subjected to oxidative damages, cellular dysfunction, mutagenesis, and carcinogenesis follow (1-3). Among the oxidative damages of DNA, 8-oxoguanine (8-oxo-7,8-dihydroguanine,
8-oxoG),1 an oxidized form of
guanine, is a major causative lesion for mutagenesis by oxygen
radicals, because it can pair with adenine and cytosine during DNA
replication with almost equal efficiency (4, 5). Thus, 8-oxoG would
cause A:T to C:G and G:C to T:A transversion mutations (6, 7).
In Escherichia coli, two DNA glycosylases encoded by
mutM and mutY genes function to repair 8-oxoG.
MutM removes 8-oxoG paired with cytosine (8), and MutY removes adenine
paired with 8-oxoG in DNA (9, 10). The oxidized form of guanine is also
formed in a nucleotide pool of cells and can be eliminated by a
mutT gene product. MutT hydrolyzes 8-oxo-dGTP to 8-oxo-dGMP,
thereby preventing misincorporation of 8-oxo-dGMP into DNA (4, 11). Human homologues of the three genes (MTH1, OGG1,
and MYH for mutT, mutM, and
mutY, respectively) are cloned (12-14). Human MTH1 (15) and
OGG1 (16) also exist in mitochondria. The endogenous activities of
8-oxo-dGTPase (15) and 8-oxoG DNA glycosylase (16, 17) are actually
detected in mitochondria. Although endogenous activity of adenine DNA
glycosylase is not detected in human mitochondria so far, the
transfection of cDNA of Human MYH indicates that human MYH can
be localized in mitochondria (18). Thus, the similar error avoidance
system against oxidative damage of guanine may work in mitochondria.
Mitochondria are power plants that are responsible for more than 80%
of energy in eukariotic cells. Mitochondria have extranuclear genes,
which is common for all vertebrates. One cell contains 103
to 104 molecules of mitochondrial DNA (mtDNA). mtDNA codes
for 13 subunits of the mitochondrial respiratory chain, 22 tRNAs, and 2 rRNAs, all of which are essential for proper function of the
respiratory chain. Maintaining the integrity of mtDNA is, therefore,
essential for aerobic ATP synthesis (19).
More than 1% of the oxygen consumed by cells is converted to reactive
oxygen species under physiological conditions (20). Mitochondrial
respiration accounts for about 90% of cellular oxygen consumption, and
thus the respiratory chain in mitochondria is principally responsible
for the production of reactive oxygen species. Accordingly, mtDNA may
suffer from more oxidative damage than nuclear DNA. In fact, there are
a number of reports that mtDNA contains much more 8-oxoG than does
nuclear DNA (see Ref. 21 for review). The amount of 8-oxoG in mtDNA is
reported to further increase with age (2, 22). Recently, the
mitochondrial dysfunction caused by the oxidative damage of mtDNA has
been implicated in aging, neurodegenerative diseases, and
cardiovascular disorders.
Despite such a high amount of 8-oxoG in mtDNA, mtDNA is barely cleaved
with MutM protein (23, 24). This discrepancy between the insensitivity
of mtDNA to MutM protein and the high amount of 8-oxoG in mtDNA has
remained to be resolved. At present, little is known about actually
pairing partners with 8-oxoG in mtDNA in vivo. We report
here that human mtDNA is cleaved at A:T sites on the mtDNA sequence by
another 8-oxoG-recognizing enzyme MutY protein, suggesting that 8-oxoG
accumulates as an A:8-oxoG pair but not as a C:8-oxoG pair.
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EXPERIMENTAL PROCEDURES |
Materials--
Restriction enzymes EcoRI,
BamHI, and PvuII were purchased from Takara
(Seta, Japan). Phosphocellulose P11 was from Whatman. DNAzol reagent
was from Life Technologies, Inc. Mono S column (1 ml) was from Amersham
Pharmacia Biotech. Other reagents were of analytical grade.
Plasmid Construction--
The DNA fragment corresponding to MutY
protein was amplified by polymerase chain reaction using
gene-specific primers Y1 (5'-GTCGCTGTGCTGCAATCTTG-3') and Y2
(5'-GACGGATCCTCTTTATCGACTCACG-3'), which contains a
BamHI site at its 5'-end. The
EcoRI-BamHI fragment of the polymerase chain
reaction product was subcloned into a vector, pUC8, and designated
pU85Y. The plasmid for MutM protein, pFPG50, was from Dr. J. Laval,
Centre Nationale de la Recherche Scientifique, France (25, 26).
Purification of MutM and MutY Proteins--
MutM and MutY
proteins were overproduced in E. coli strains MK603 (25)
harboring pFPG50 and SURE® (Stratagene, La Jolla, CA)
harboring pU85Y, respectively.
MutY was purified to homogeneity essentially according to the methods
of Lu and co-workers (27). Briefly, the cells overproducing MutY (5 g)
were suspended in 15 ml of Buffer T (50 mM Tris-HCl, pH
7.6, 0.1 mM EDTA, 0.5 mM dithiothreitol, and
0.1 mM phenylmethylsulfonyl fluoride) and sonicated. The
cell debris was removed by centrifugation, and 16 ml of the supernatant
was treated with 4 ml of 25% streptomycin sulfate. After stirring for
45 min on ice, the solution was centrifuged, and 18 ml of the
supernatant was collected. Ammonium sulfate (3.6 g) was added to the
supernatant, and the proteins were precipitated for 1 h on ice.
After centrifugation, the protein pellets were resuspended in 3 ml of
Buffer T and dialyzed against 500 ml of Buffer T at 4 °C for 3 h. The dialyzed sample (5 ml) was diluted 4-fold with Buffer A (20 mM potassium phosphate, pH 7.4, 0.5 mM dithiothreitol, 0.1 mM EDTA, and 0.1 mM
phenylmethylsulfonyl fluoride) containing 50 mM KCl and
applied to a 2-ml phosphocellulose column equilibrated with Buffer A
containing 50 mM KCl. After washing with 20 ml of
equilibration buffer at 0.2 ml/min, proteins were eluted with a linear
gradient of KCl (50-500 mM) at 0.2 ml/min for 300 min.
Fractions containing the A:G-specific nicking activity were pooled. The
pool fractions (20 ml) were dialyzed two times against 1 liter of
Buffer A containing 50 mM KCl and 10% glycerol at 4 °C
for 1 h. The dialyzed sample was applied to a 1-ml Mono S column
equilibrated with Buffer S (50 mM potassium phosphate, pH
7.5, 0.5 mM dithiothreitol, 0.1 mM EDTA, 0.1 mM phenylmethylsulfonyl fluoride, and 10% glycerol)
containing 100 mM NaCl. After washing with 10 ml of
equilibration buffer at 1.0 ml/min, proteins were eluted with a linear
gradient of NaCl (100-500 mM) for 20 min in Buffer S. The
fractions containing the activity were pooled and stored at
80 °C.
All chromatography was performed with an Amersham Pharmacia Biotech
FPLC System. MutM was purified to homogeneity essentially the same as
described above except for omitting streptomycin sulfate precipitation.
Cleavage Reaction by MutM or MutY--
The cells in a
half-confluent state were harvested, and the total DNA was extracted
with DNAzol reagent according to the manufacturer's instructions. The
extracted DNA was digested with RNase A and BamHI (or
PvuII), phenol-extracted, ethanol-precipitated, and solubilized in 0.1× TE (1 mM Tris-HCl, pH 7.5, and 0.1 mM EDTA). The concentration of DNA was determined by
measuring absorbance at 260 nm.
The standard reaction was performed in 10 µl of the mixture
containing 25 mM HEPES-NaOH, pH 7.6, 0.5 mM
EDTA, 10 mM NaCl, 0.5 mM dithiothreitol, 50 µg/ml bovine serum albumin, 30 ng of MutM or 300 ng of MutY, and 0.5 µg of the total DNA at 37 °C for 3 h. In some cases, the
reaction was performed in the presence of the 35-mer oligonucleotide
substrates listed in Table I.
For detection of the fluorescein isothiocyanate-labeled
oligonucleotides, DNA was denatured in 80% formamide by boiling,
resolved on a 15% polyacrylamide/6 M urea gel, and
analyzed with a FluorImager 595 (Molecular Dynamics). The mtDNA was
analyzed by Southern blotting as described below.
Southern Blotting and Ligation-mediated Polymerase Chain
Reaction--
Southern blotting of mtDNA and the nuclearly encoded 18 S rRNA gene was performed as described previously (28). Total DNA (0.5 µg) was treated with the purified MutM or MutY protein. After glyoxal-dimethylsulfate denaturation (29), the DNA was electrophoresed on a 0.6% agarose gel in 10 mM sodium phosphate, pH 7.0, and transferred onto a nylon membrane (Hybond-N+, Amersham
Pharmacia Biotech). mtDNA (16 kbp) was probed with a 1.9-kbp fragment
of mtDNA (nt 2573-4431) for the BamHI-digested DNA. For the
PvuII-digested DNA, mtDNA (~16 kbp) and the 18 S rRNA gene
(~12 kbp) were probed with a 0.8-kbp XbaI fragment of mtDNA (nt 7441-8286) and a 1.5-kbp XbaI fragment of the 18 S rRNA gene (nt 435-1951), respectively. Each probe was labeled with [
-32P]dCTP using a Megaprime DNA labeling kit
(Amersham Pharmacia Biotech) or alkaline phosphatase using an Alkphos
Direct labeling kit (Amersham Pharmacia Biotech). In the former case,
the signals were detected and quantified with a radio image scanner,
STORM (Molecular Dynamics). In the latter case, the signals were
visualized using CDP-Star chemiluminescent reagent (Amersham
Pharmacia Biotect) and quantified with LAS1000 (Fuji Film, Tokyo,
Japan). The MutM- or MutY-cleaved strands of mtDNA were amplified by
ligation-mediated polymerase chain reaction (LMPCR) using the primer
sets D6, D7, and D8 as described previously (30).
Quantification of 8-Oxo-2'-deoxyguanosine(8-oxo-dG)--
Mitochondria were prepared by differential
centrifugation from approximately 1 × 109 cells of
HeLa MRV11. mtDNA was purified as supercoiled DNA from the
mitochondrial fraction by using a Qiagen plasmid mini kit (Hilden,
Germany) according to the manufacturer's instructions. The amount of
8-oxo-dG in mtDNA was measured by an electrochemical method as
described previously (25).
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RESULTS |
Cleavage of Oligonucleotides Containing C:8-oxoG or A:G Pair
by Recombinant MutM and MutY--
As shown in Fig.
1A, recombinant MutM and MutY
proteins were highly purified to homogeneity. 30 ng of MutM and 300 ng
of MutY proteins cleaved almost all of 400 fmol of oligonucleotides FM and FY (Table I), respectively, in the
presence of 0.5 µg of total DNA (Fig. 1B). The amount of
8-oxoG in total DNA is reported to be, at most, 1/105 G or
roughly 4 fmol of 8-oxoG in 0.5 µg of DNA (21, 31). Therefore, the
MutM or MutY is sufficient for digesting the endogenous 8-oxoG sites in
the following experiments.

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Fig. 1.
Cleavage of oligonucleotides containing
C:8-oxoG or A:G pair by recombinant MutM and MutY proteins.
A, recombinant MutM (left panel) and MutY
(right panel) were purified. Proteins were separated on 10%
SDS-polyacrylamide gels and visualized by silver staining.
B, the 5'-fluorescein isothiocyanate-labeled
oligonucleotide substrates, FM and FY (Table I), were cleaved in the
presence of 0.5 µg of the total DNA of U937 cells by 30 ng of MutM
(shown as M) and 300 ng of MutY (shown as Y),
respectively. The DNA was denatured, resolved on 15% polyacrylamide/6
M urea gels, and analyzed with FluorImager 595.
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Table I
Oligonucleotide substrates used in this study
8-Oxoguanine is shown in bold character. The clevage site is marked by
an underline. FITC, fluorescein isothiocyanate.
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DNA Digestion by MutM and MutY--
After treatment of total DNA
with the purified MutM or MutY protein, the amount of uncleaved mtDNA
was quantified by Southern blot analysis. As reported by other groups
(23, 24), mtDNA remained uncleaved by the MutM protein both in the
nondenaturing and denaturing conditions (Fig.
2A, lanes 2 and
5). In contrast, the amount of uncleaved mtDNA was decreased
to approximately one-half by the MutY protein in the glyoxal denaturing
conditions (Fig. 2A, lane 4). The MutY-treated
mtDNA was apparently uncleaved in the nondenaturing conditions (Fig.
2A, lane 1), indicating that single-strand
cleavage occurs by the MutY protein treatment, which is consistent with
the nature of adenine DNA glycosylase. In Fig. 2B, changes
in the amount of 16-kbp mtDNA on the denaturing gels are shown. The
amount of full-length mtDNA of HeLa MRV11 cells was barely decreased by
the MutM protein (91.9 ± 26.9, n = 12, mean ± S.D.), whereas the amount was decreased to nearly one-half that of
the control by the MutY protein (46.2 ± 11.0, n = 12). In the case of HeLa MR51 cells that over-produce human MTH1
approximately 100-fold (15), the amounts of full-length mtDNA after
treatment of the MutM and MutY proteins were 99.6 ± 26.2 and
59.1 ± 17.3 that of the control (mean ± S.D.,
n = 6), respectively (Fig. 2B).

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Fig. 2.
Southern blotting of mtDNA cleaved with MutM
or MutY. A, the total DNA was extracted from HeLa MRV11
cells and digested with BamHI. The BamHI-digested
DNA was treated with 30 ng of MutM or 300 ng of MutY. After the native
(left panel) or denatured (right panel) DNA was
electrophoresed, mtDNA was probed with the 32P-labeled
1.9-kbp fragment of mtDNA (nt 2573-4431) and quantified. C,
control; M, MutM; Y, MutY. B, the
amount of mtDNA was quantified and is shown as a percent of the
control. The values represent means of twelve and six independent
experiments (HeLa MRV11 and MR51 cells, respectively) with standard
deviations.
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Identification of the Cleavage Sites by MutY--
To determine the
cleavage sites, we amplified the cleaved strands by LMPCR. Consistent
with the results in the Southern blot experiments, there were few
signals detected in the control and MutM protein-treated DNAs (Fig.
3, lanes 5 and 6),
whereas signals were observed in the MutY protein-treated DNA (Fig. 3,
lane 7). The same pattern was also observed in other regions
of mtDNA when using other primer sets, D6 and D7 (results not shown).
Essentially all of the MutY cleavage sites were mapped to adenine sites
without sequence specificity around the adenines. This cleavage pattern is completely compatible with an adenine DNA glycosylase activity of
MutY protein. All adenine sites were not evenly cleaved by the MutY
protein (Fig. 3, lane 7). The cleavage was preferentially observed at sites where an A:T pair runs consecutively.

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Fig. 3.
Determination of cleavage sites. After
the treatment with MutM or MutY as in Fig. 2, the cleaved strands of
mtDNA were amplified by LMPCR using the primer set D8 (30).
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Cleavage of mtDNA and Nuclear DNA--
To examine whether the
MutY-sensitive sites accumulate in mtDNA more than in nuclear DNA, we
detected the cleavage of nuclear DNA and mtDNA simultaneously. The
cleavage of a nuclear 18 S rRNA gene (about 12 kbp) was marginal
compared with that of mtDNA (Fig. 4A), suggesting that mtDNA
contains more MutY-sensitive sites than does the nuclear 18 S rRNA
gene. It is known that damage-specific glycosylases can attack normal
nucleotide pairs as a part of the damage-scanning process (32). mtDNA
was cleaved by the MutY in a saturable manner (Fig. 4A). If
A:T were a target of the MutY, the cleavage would proceed with
increasing doses of the MutY. The 18 S rRNA gene should also have been
cleaved similarly. Thus, A:T may not occupy a major part of the
MutY-sensitive sites in this assay system.

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Fig. 4.
Cleavage of nuclear DNA and mtDNA with the
MutY. A, the PvuII-digested total DNA was
used. The total DNA (1 µg) of HeLa MRV11 cells was treated with
various amounts of MutY. mtDNA (16 kbp) and an 18 S rRNA gene (12 kbp)
were simultaneously detected and quantified by Southern blotting using
alkaline phosphatase-labeled probes for mtDNA and the 18 S rRNA gene as
described under "Experimental Procedures." B, the
PvuII-digested total DNA of U937 cells was treated with MutM
or MutY. mtDNA was first probed. After deprobing, the 18 S rRNA gene
was reprobed. The detection and quantification were performed as in
A.
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To see whether this MutY cleavage of mtDNA is restricted in HeLa MRV11
cells, we examined a human monocytic cell line, U937. The ratio of the
18 S rRNA gene to mtDNA in the MutY protein-treated sample is reduced
to approximately 50% of that in the control (Fig. 4B). The
18 S rRNA gene was barely cleaved by either the MutM or MutY protein.
Similar results were also obtained when using Jurkat cells (results not shown).
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DISCUSSION |
Preparation of mtDNA from purified mitochondria raises a
possibility that intact mtDNA is preferentially collected from intact mitochondria. This is considered to be one of the reasons why mtDNA is
resistant to MutM (21, 33). Although we used total cellular DNA to
avoid any possible bias resulting from the mtDNA preparation, we could
hardly detect MutM-dependent cleavage of mtDNA by Southern
blot analysis. The collective number of MutM-cleavable lesions such as
C:8-oxoG, C:formamidepyrimidine (Fapy), and an abasic site is below 1 per 10 molecules of mtDNA as long as we observe the amount of 16-kbp
mtDNA. It has been recently reported that the oxidized bases exist
predominantly in fragmented mtDNA (33). We, however, did not observe
such fragmented bands of mtDNA by Southern blot analysis (Fig.
2A).
In contrast, approximately one-half of mtDNA molecules were sensitive
to the MutY protein, i.e. there is one MutY-sensitive site
per two mtDNA molecules. The cleavage of mtDNA is not due to
nuclease(s) remaining in the purified MutY sample for the following reasons: 1) the MutY protein was highly purified (Fig. 1A);
2) the cleavage was a single-strand break in nature (Fig. 2); 3) essentially all of the cleavage sites were mapped to adenines (Fig. 3);
4) a nuclearly encoded 18 S rRNA gene was barely cleaved (Fig. 4); and
5) the oligonucleotide FY was specifically cleaved at an A:G site (Fig.
1B). Accordingly, we conclude that mtDNA is cleaved by an
adenine DNA glycosylase activity of the MutY.
MutY removes adenine residues from A:G and A:8-oxoG pairs with similar
efficiency and also removes the residue from an A:C pair, but with
20-fold lower efficiency (27). In general, MutY-sensitive sites are
generated the following three ways: misincorporation of normal
nucleotides (A:G and A:C pairs); misincorporation of dAMP opposite
8-oxo-dG in DNA (A:8-oxoG pair); and misincorporation of 8-oxo-dGMP
opposite template adenine (A:8-oxoG pair). The MutY cleavage sites in
mtDNA were adenines of A:T on the mtDNA sequence (Fig. 3), suggesting
that dGMP, dCMP, or 8-oxo-GMP is misincorporated opposite template
adenine. Chick embryo DNA polymerase
exhibits a fidelity of less
than one error for every 260,000 bases polymerized when normal dNTPs
are used as substrates (34). It is therefore unlikely that human DNA
polymerase
misincorporates dGMP or dCMP opposite template adenine
as frequently as observed here. On the other hand, an A:T to C:G
transversion rate for the chick embryo DNA polymerase
is increased
more than 1000-fold for synthesis in the presence of 8-oxo-dGTP at a
concentration equal to that of normal dGTP (35). We electrochemically
measured 8-oxo-dG in mtDNA that is prepared from mitochondria by an
alkaline SDS method for extraction of closed circular DNA. The amount
of 8-oxo-dG was approximately 2.2/104 G. There are about
3,500 G per single strand of mtDNA. One MutY-sensitive site per two
mtDNA molecules means that human mtDNA contains approximately one
MutY-sensitive site per 7,000 G or 1.4 per 104 G, roughly
corresponding to electrochemically measured 8-oxo-dG of
2.2/104G. Taken together, although the nature of the
MutY-sensitive sites is not completely understood at present, it is
plausible that a certain part of the MutY-sensitive sites are A:8-oxoG.
The over-expression of human MTH1, however, did not much reduce the
MutY-sensitive sites (Fig. 2B). Km of
human MTH1 for 8-oxo-dGTP is 12.5 µM (36), the value of
which is level with intracellular concentration of normal dGTP (~30
µM) (37). The inability of human MTH1 in reducing the
MutY-sensitive sites might rather suggest that additional factor(s) may
be required to eliminate 8-oxo-dGTP.
8-Oxo-dGMP is incorporated opposite C and A with essentially the same
efficiency (4). Given that a certain part of the MutY-sensitive sites
are A:8-oxoG, the fewer MutM-sensitive sites than the MutY-sensitive
sites suggest that C:8-oxoG is more efficiently repaired in
mitochondria than is A:8-oxoG that is formed by misincorporation of
8-oxo-dGMP opposite adenine. C and A are incorporated opposite 8-oxoG
with almost the same efficiency after removal of A from A:8-oxoG,
whereas G is predominantly incorporated opposite C after removal of
8-oxoG from C:8-oxoG. Thus a MutY-like activity is intrinsically less
efficient in eliminating A:8-oxoG than is a MutM-like activity in
eliminating C:8-oxoG. In addition, a MutY-like activity itself might be
insufficient for repair of A:8-oxoG in mitochondria. The activity of
8-oxoG DNA glycosylase is actually detected in human mitochondria (16).
On the other hand, the activity of adenine DNA glycosylase has not been
detected in human mitochondria to date, although recombinant human MYH
is targeted into mitochondria (18). This might reflect the fact that
the human MYH activity is low relative to the human OGG1 activity in
mitochondria. Another possibility is that human MYH might be less
effective in repair of A:8-oxoG formed by misincorporation of
8-oxo-dGMP than that formed by misincorporation of dAMP. Although hydrolysis of 8-oxo-dGTP is proposed for prevention of 8-oxo-dGMP misincorporation in the current MutM, Y, and T systems (6, 7), the
repair of A:8-oxoG once formed by 8-oxo-dGMP misincorporation is not
well elucidated. In the case that 8-oxo-dGMP is misincorporated opposite adenine, a strong MutY-like activity would enhance A:T to C:G
transversion (6, 7). In this light, it is conceivable that human MYH is
regulated in mitochondria to act mainly on A:8-oxoG formed by
misincorporation of dAMP. If so, A:8-oxoG formed by misincorporation of
8-oxo-dGMP might be repaired at later stages by other unknown
mechanism(s), e.g. in a transcription-coupled way. We might
also need to consider mechanism(s) other than base excision repair,
such as selective degradation of mtDNA containing 8-oxoG.
Despite presumed strong oxidative damage of mtDNA, A:T to C:G or C:G to
A:T transversion does not frequently occur as is evident from reported
mutations (38). It is yet unclear to what extent 8-oxoG contributes to
oxidative damage-induced mutations in mitochondria. The mutual roles of
MutT-, MutM-, and MutY-like activities are not completely understood in
mitochondria, either. Examination of pairing partners with 8-oxoG in a
steady state is important both for understanding of mutagenesis by
8-oxoG and for estimation of relative activities among the three repair
enzymes in vivo. To this purpose, the combination of DNA
cleavage by DNA glycosylases and LMPCR, as used here, appears to be useful.