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73:39 85
doi: 10.1146/annurev.biochem.73.011303.073723
Copyright 2004 by Annual Reviews. All rights reserved
First published online as a Review in Advance on January 20, 2004
Key Words damage recognition, excision repair, PIKK family, Rad17-RFC/9-11 complex, signal transduction
f Abstract DNA damage is a relatively common event in the life of a cell and
may lead to mutation, cancer, and cellular or organismic death. Damage to DNA
induces several cellular responses that enable the cell either to eliminate or cope with
the damage or to activate a programmed cell death process, presumably to eliminate
cells with potentially catastrophic mutations. These DNA damage response reactions
include: (a) removal of DNA damage and restoration of the continuity of the DNA
duplex; (b) activation of a DNA damage checkpoint, which arrests cell cycle
progression so as to allow for repair and prevention of the transmission of damaged
or incompletely replicated chromosomes; (c) transcriptional response, which causes
changes in the transcription profile that may be beneficial to the cell; and (d)
apoptosis, which eliminates heavily damaged or seriously deregulated cells. DNA
repair mechanisms include direct repair, base excision repair, nucleotide excision
repair, double-strand break repair, and cross-link repair. The DNA damage checkpoints employ damage sensor proteins, such as ATM, ATR, the Rad17-RFC complex, and the 9-1-1 complex, to detect DNA damage and to initiate signal
transduction cascades that employ Chk1 and Chk2 Ser/Thr kinases and Cdc25
phosphatases. The signal transducers activate p53 and inactivate cyclin-dependent
kinases to inhibit cell cycle progression from G1 to S (the G1/S checkpoint), DNA
replication (the intra-S checkpoint), or G2 to mitosis (the G2/M checkpoint). In this
review the molecular mechanisms of DNA repair and the DNA damage checkpoints
in mammalian cells are analyzed.
0066-4154/04/0707-0039$14.00
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CONTENTS
INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
SUBSTRATES AND SIGNALS FOR DNA REPAIR AND DNA DAMAGE
CHECKPOINTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Replication, Recombination, and Repair Intermediates . . . . . . . . . . . . . . . .
DNA Base Damages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
DNA Backbone Damages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Cross-links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
DNA DAMAGE RECOGNITION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Direct Damage Recognition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Multistep Damage Recognition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Recognition by Proxy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Recognition of DNA Repair Intermediates. . . . . . . . . . . . . . . . . . . . . . . .
DNA REPAIR MECHANISMS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Direct Repair . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Base Excision Repair . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Nucleotide Excision Repair . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Double-Strand Break Repair and Recombinational Repair . . . . . . . . . . . . . .
Cross-link Repair . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
DNA DAMAGE CHECKPOINTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
What Are the DNA Damage Checkpoints? . . . . . . . . . . . . . . . . . . . . . . .
Molecular Components of the DNA Damage Checkpoints . . . . . . . . . . . . . .
The G1/S Checkpoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
The Intra-S-Phase Checkpoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
The G2/M Checkpoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
The Replication Checkpoint (S/M Checkpoint) . . . . . . . . . . . . . . . . . . . . .
CONCLUSIONS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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INTRODUCTION
The primary structure of DNA is constantly subjected to alteration by cellular
metabolites and exogenous DNA-damaging agents. These alterations may cause
simple base changes or they may cause more complex changes including
deletions, fusions, translocations, or aneuploidy. Such alterations may ultimately
lead to cellular death of unicellular organisms or degenerative changes and aging
of multicellular organisms.
DNA damages can perturb the cellular steady-state quasi-equilibrium and
activate or amplify certain biochemical pathways that regulate cell growth and
division and pathways that help to coordinate DNA replication with damage
removal. The four types of pathways elicited by DNA damage known, or
presumed, to ameliorate harmful damage effects are DNA repair, DNA damage
checkpoints, transcriptional response, and apoptosis (1) (Figure 1). Defects in
any of these pathways may cause genomic instability (2). This review focuses
upon the mechanisms of DNA repair and the DNA damage checkpoints.
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Figure 1 DNA damage response reactions in mammalian cells. The four responses
(DNA repair, transcriptional response, DNA damage checkpoints, and apoptosis)
may function independently, but frequently a protein primarily involved in one
response may participate in other responses.
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Cross-links
Bifunctional agents such as cisplatin, nitrogen mustard, mitomycin D, and
psoralen form interstrand cross-links and DNA-protein cross-links. DNA-protein
cross-links may also be produced by reaction of the aldehyde form of abasic sites
with proteins (7). Although noncovalent, but tight, DNA-protein complexes are
not considered damage in the strict sense, some extremely tight complexes may
elicit the same cellular responses as covalent lesions by constituting roadblocks
to transcription or replication.
Figure 2 DNA lesions and structures that elicit DNA response reactions. Some of the base backbone lesions and noncanonical DNA
structures that elicit DNA response reactions are shown. O6 MeGua indicates O6-methyldeoxyguanosine, TT indicates a
cyclobutane thymine dimer, and the cross-link shown is cisplatin G-G interstrand cross-link.
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Several strategies are utilized for damage recognition to initiate DNA damage
responses: direct recognition (bimolecular), multistep recognition (molecular
matchmakers and combinatorial), recognition by proxy, and recognition of DNA
repair intermediates.
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tively. RFC loads PCNA onto DNA and then dissociates, allowing PCNA to act
as a DNA polymerase clamp and confer high processivity upon the polymerase.
UvrA recognizes DNA damage and loads UvrB onto the damage site, and in the
process, a conformational change in both UvrB and DNA takes place such that
a very stable UvrB-DNA complex is formed. UvrA must then dissociate from
this complex to allow the formation of the UvrB-UvrC-DNA complex in which
the dual incisions are made.
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COMBINATORIAL RECOGNITION
Recognition by Proxy
Proteins that carry out functions not directly related to DNA repair can become
part of the recognition process, as exemplified by transcription-coupled repair in
E. coli. When RNA polymerase encounters a lesion in the transcribed strand, it
arrests at the damage site and, in so doing, creates a target for proteins with
affinity for RNA polymerase in the elongation mode (19, 20). One such protein
is the bacterial transcription-repair coupling factor (TRCF) that binds to the
stalled RNA polymerase and recruits the damage-recognition complex,
UvrA2UvrB1, to the damage site (21). TRCF also facilitates the dissociation of
UvrA2 from the UvrA2UvrB1-DNA complex, accelerating the rate of formation
of the rate-limiting UvrB1-DNA complex. Consequently, lesions in the transcribed strand are marked by RNA polymerase and are excised more rapidly than
lesions in the nontranscribed strand (or nontranscribed regions of the genome)
(22, 23). Because the RNA polymerase does not actively recognize damage but
simply arrests at the damage site and thus helps recruit the repair machinery, it
is not a matchmaker that actively searches for the target; instead it provides a
proxy mechanism of recognition. Transcription-coupled repair occurs in mammalian cells as well (22). However, the molecular details of the mechanism are
not known.
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Direct Repair
There are two direct repair mechanisms in the majority of organisms: the
photoreversal of UV-induced pyrimidine dimers by DNA photolyase and the
removal of the O6-methyl group from O6-methylguanine (O6MeGua) in DNA by
methylguanine DNA methyltransferase. Photolyase is not present in many
species, including humans, whereas methylguanine DNA methyltransferase has
nearly universal distribution in nature.
PHOTOLYASE
Many species from each of the three kingdoms of life and even
some viruses have photolyase, whereas many species in all three kingdoms do
not (11). Photolyase repairs UV-induced cyclobutane pyrimidine dimers and
(6-4) photoproducts using blue-light photons as an energy source (Figure 3).
Photolyase is a monomeric protein of 55 65 kDa with two chromophore
cofactors, a pterin in the form of methenyltetrapydrofolate and a flavin in the
form of FADH. There are two types of photolyases, one that repairs cyclobutane pyrimidine dimers (photolyase) and the other that repairs (6-4) photoproducts (6-4 photolyase) (8, 10, 11, 26). The structures and reaction mechanisms of
the two types are similar, and the reaction mechanism of E. coli photolyase will
be used for illustration (Figure 3). The folate, which is located at the surface of
the enzyme and functions as a photo-antenna, absorbs a violet/blue-light photon
(350 450 nm) and transfers the excitation energy to the flavin cofactor. The
excited FADH transfers an electron to the cyclobutane pyrimidine dimer to
generate a dimer radical anion that splits into two canonical pyrimidines concomitant with back electron transfer to restore the flavin to its catalytically
competent form. Placental mammals lack photolyase but contain two proteins
with high sequence and structural similarities to photolyase, but no repair
function. These proteins, named cryptochromes, function as photoreceptors for
setting the circadian clock (11, 27).
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METHYLGUANINE DNA METHYLTRANSFERASE
This is a small protein of 20 kDa
that does not contain a cofactor and is ubiquitous in nature. Like photolyase, it
is presumed to recognize damage by three-dimensional diffusion, and after
forming a low-stability complex with the DNA backbone at the damage site, it
is thought to flip-out the O6MeGua base into the active site cavity (28), wherein
the methyl group is transferred to an active site cysteine (29). The protein then
dissociates from the repaired DNA, but the C-S bond of methylcysteine is stable,
and therefore, after one catalytic event the enzyme becomes inactivated and is
accordingly referred to as a suicide enzyme. Mice lacking O6MeGua methyltransferase are highly susceptible to tumorigenesis by alkylating agents (30).
Some human tumors or cell lines resistant to drugs that alkylate DNA are
defective in mismatch repair. O6MeGua has a high frequency of pairing to T, and
the O6MeGuaT base pair activates the mismatch repair system, which leads to
futile excision and resynthesis of the T residue, eventually initiating an apoptotic
response. Inactivation of the mismatch repair system by either mutation or
promoter silencing prevents the futile cycle and the ensuing apoptosis, resulting
in resistance to alkylating drugs (31).
In addition to these relatively ubiquitous direct repair enzymes, there are two
other direct repair enzymes with more limited phylogenetic distribution: spore
photoproduct lyase of spore-forming bacteria, which repairs UV-induced spore
photoproducts that form in DNA-A (32), and oxidative methyl transferase in
bacteria (AlkB) and humans (hABH13), which repairs 1-methyladenine and
3-methylcytosine (3336). This latter enzyme uses DNA or RNA as a substrate,
requires Fe2 and 2-oxoglutarate, and releases the hydroxylated methyl group as
formaldehyde.
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around the phosphodiester bond axis, flipping the base out into the active site
cavity of the enzyme, wherein the glycosylic bond is finally attacked by the
active site residues. Hence, glycosylases also employ multiple proofreading
mechanisms to achieve specificity. Despite these safeguards, however, some
glycosylases such as methylpurine glycosylases from E. coli, yeast, and humans
release guanine in addition to N3-methyladenine and, in fact, E. coli 3-mAde
DNA glycosylase II releases all four normal bases at low, but physiologically
significant levels (47). Thus attacking normal DNA is a price that has to be paid
by glycosylases with relatively wide substrate ranges.
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Activity
Role in repair
XPA
XPA/p31 (Rad14)
DNA binding
Damage recognition
RPA
p70
DNA binding
Damage recognition
p32
Replication factor
p11
XPC
XPC/p106 (Rad4)
DNA binding
HR23B/p58 (Rad23)
Damage recognition
Molecular matchmaker
DNA-dependent
ATPase
Helicase
General transcription
factor
XPG/ERCC5/p135 (Rad2)
Nuclease
3-incision
Nuclease
5-incision
TFIIH
XPB/ERCC3/p89 (Rad25)
XPD/ERCC2/p80 (Rad3)
p62 (Tfb1)
p52 (Tfb2)
p44 (Ssl1)
p34 (Tfb4)
XPG
ERCC1/p33 (Rad10)
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The damage recognition factors for the human excision nuclease are RPA,
XPA, and XPC (5759). Each of these is a DNA-binding protein with some
preference for damaged DNA (59 63). However, the discrimination between
undamaged and damaged nucleotides afforded by the individual factors is of
insufficient magnitude to confer the necessary in vivo specificity (57, 64). The
specificity problem in mammalian nucleotide excision repair has been solved by
combining two fundamental mechanisms utilized in high-specificity macromolecular interactions: (a) cooperative binding and (b) kinetic proofreading. In
cooperative binding, specificity is achieved by binding of two or more interacting
proteins to adjacent or overlapping sites on DNA (or any macromolecular lattice)
such that occupancy of one site by a protein facilitates the occupancy of the
adjacent sites by the other proteins by increasing the local concentration of the
other proteins by protein-protein interaction (65). Thus, considering the relative
abundance of the repair factors (RPA is the most abundant), their DNA affinities
(XPC has the highest specific and nonspecific binding constants), and their
affinities for each other [RPA to XPA (60) and XPA and XPC to TFIIH (66, 67)],
the unique properties of each of the three damage recognition factors are likely
utilized in a cooperative manner to assemble the excision nuclease regardless of
the order of binding (recognition by random rather than by ordered assembly).
The moderate specificity provided by cooperative binding is amplified by the
kinetic proofreading function of TFIIH. This is a six-subunit transcription/repair
factor (68) with 3 to 5 and 5 to 3 helicase activities imparted by the XPB and
XPD subunits, respectively. In kinetic proofreading, one or more high-energy
intermediates are placed in the reaction pathway such that nonspecific (incorrect)
products can be aborted at any step along the reaction pathway in a manner that
slows down the reaction rate somewhat without seriously compromising the rate
of the specific reaction to a physiologically unacceptable level (69). In excision
repair, once TFIIH is recruited by the three damage recognition factors to form
PIC1 (preincision complex 1), the DNA is unwound by about 20 bp at the
assembly site. If the assembly is at a nondamage site, ATP hydrolysis by TFIIH
leads to the disassembly of the complex (kinetic proofreading). In contrast, PIC1
formed at a damage site is more stable, and the unwound DNA constitutes a
high-affinity binding site for XPG. The XPG protein has higher affinity to
unwound DNA than a duplex (70), and therefore binding of XPG, concurrent
with dissociation of XPC from the complex, leads to formation of PIC2, which,
by virtue of XPG entry and XPC exit, provides an additional layer of specificity.
At this step the 3 incision may take place. However, as a nick can be easily
ligated, PIC2 formation is not necessarily irreversible and kinetic proofreading
may take place at this step as well. Finally, the entry of XPFERCC1 into the
complex to form PIC3 results in the irreversible dual incisions and release of the
excised oligomer.
To summarize, damage recognition by human excision nuclease utilizes
cooperative binding and kinetic proofreading to provide a physiologically relevant degree of specificity at a biologically acceptable rate. However, it must be
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noted that despite all of these thermodynamic and kinetic safeguards aimed at
ensuring excision of only damaged nucleotides, the discrimination of human
excision nuclease between damaged and undamaged DNA is not absolute, and
the enzyme excises oligomers from undamaged DNA (gratuitous repair) at a
significant and potentially mutagenic rate (71).
As noted above, in both prokaryotes and eukaryotes, transcribing DNA is
repaired at a faster rate than nontranscribing DNA (22, 23, 72). This transcription-coupled repair requires the CSA and CSB gene products (mutated in
Cockaynes syndrome) in humans (20, 73, 74) and the Mfd protein in E. coli
(75). In vivo data indicate that in humans, but not in yeast, XPC is dispensable
for transcription-coupled repair (76). This repair mode is well understood in E.
coli but has not been reconstituted in vitro with eukaryotic proteins, and therefore
its precise mechanism in humans remains to be elucidated. In addition to
transcription, excision repair is also affected by chromatin structure, which exerts
a strong inhibitory effect (77 80). Chromatin remodeling factors (81 83) and
histone modification (84) partially alleviate the inhibitory effect of nucleosomes.
Finally, the role of an enigmatic protein called DDB (Damaged DNA Binding
protein) in nucleotide excision repair deserves some comment. Of all the human
damaged DNA-binding proteins identified to date, DDB has the highest affinity
for damaged DNA (85, 86) as exemplified by a KD 5 1010 for (6-4)
photoproducts (87). Ironically, DDB is not required for repair (48 51), and it is
uncertain whether DDB plays a direct role in excision repair or in any other repair
reaction. DDB is a heterodimer of p127, the product of the DDB1 gene, and p48,
the product of the DDB2 gene (88). Mutations in DDB2 give rise to xeroderma
pigmentosum group E (XP-E) (89), a mild form of the disease. There are
contradictory findings on the direct involvement of DDB in excision repair (74,
90 92). However, it appears that, both in vivo (93) and in vitro (64, 94), DDB
has no or only a minor role in the excision nuclease function. DDB interacts with
several cellular and viral proteins involved in transcriptional regulation and other
cellular processes (95). Current evidence suggests that DDB might be involved
in a general cellular response to DNA damage rather than a specific repair
pathway. Two recent studies support such a model. In one study, it was found
that nontransformed fibroblasts from XP-E patients had greatly reduced basal and
damage-inducible p53 levels and the levels of p53-regulated proteins (96). These
cells are deficient in caspase 3 activation and apoptosis, and as a consequence,
more resistant than normal cells to killing by UV irradiation. Another study
found that a complex consisting of DDB1, DDB2, Cul4A, and Roc1 exhibited a
robust ubiquitin ligase activity and that this core complex was associated with the
8-subunit COP9 signalosome (CSN) in which the ubiquitin ligase activity of the
core complex was inhibited (97). Interestingly, this study also identified an
essentially identical complex in which the DDB2 subunit was replaced with the
CSA protein. An interesting model was proposed for how these two complexes
may regulate global repair and transcription-coupled repair by stimulating ubiq-
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uitin ligase activity or suppressing it in the DDB2/CSN and CSA/CSN complexes, respectively.
Finally, in addition to the well-characterized nucleotide excision and base
excision repair pathways, in a number of organisms, including Schizosaccharomyces pombe, there exists an alternative excision repair pathway in which an
enzyme called UV dimer endonuclease incises DNA immediately 5 to the
damage, and then the damage is removed by a 5 to 3 exonuclease (98, 99).
Similarly, AP endonucleases such as the Nfo of E. coli and the APE1 in humans
can incise immediately 5 to many nonbulky oxidatively damaged bases to
initiate their removal by 5 to 3 exonucleases (100).
SINGLE-STRAND ANNEALING
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loss due to the exonuclease action. In addition to the M/R/N complex, Rad52 and
RPA are also likely to participate in the SSA pathway.
NONHOMOLOGOUS END-JOINING (NHEJ)
In this form of repair in eukaryotes, the
Ku heterodimer binds to the two ends of a double-strand break and recruits
DNA-PKcs (115) and the ligase4-XRCC4 heterodimer, which then ligates the
two duplex termini regardless of whether the two ends come from the same
chromosome (116, 117). The M/R/N complex may also participate in NHEJ,
particularly when this pathway is utilized for V(D)J recombination.
Genetic data indicate that HR is important for the recovery of collapsed
replication forks. In contrast, NHEJ is essential for V(D)J recombination and is
thought to be the major pathway for repair of double-strand breaks induced by
ionizing radiation and radiomimetic agents. The relative contribution of SSA to
the repair of double-strand breaks is unknown.
Cross-link Repair
Many chemotherapeutic drugs and bifunctional DNA-damaging agents induce
interstrand DNA cross-links. In E. coli and in Saccharomyces cerevisiae, nucleotide excision repair and homologous recombination systems work coordinately
or in tandem to remove the cross-link (118, 119). In humans, it is unknown
whether nucleotide excision repair plays a significant role in repairing crosslinks. In CHO cells, mutations in XPF (ERCC4) and ERCC1 render cells
extremely sensitive to cross-linking agents, whereas mutations in other excision
repair genes have a less drastic effect (120). This has been taken as evidence that
the structure-specific XPFERCC1 nuclease plays a special role in cross-link
repair aside from its function in nucleotide excision repair.
When cross-linked DNA is used as a substrate for the human excision
nuclease in vitro, two activities are detected. One requires all six excision
nuclease factors and results in dual incisions, both of which occur 5 to the lesion
and excise a fragment free of damage that is 2228 nt in length from either strand
of the duplex (121, 122). This gap might initiate a recombination reaction that
may ultimately remove the cross-link or might initiate a futile repair synthesis
reaction in which the cell excises an oligonucleotide, fills in the gap, and then
re-excises the oligonucleotide. The second activity involves XPFERCC1, which,
in an RPA-dependent reaction, digests the DNA in a 3 to 5 direction past the
cross-link and thus converts the interstrand cross-link to a single-strand diadduct
(122).
Cross-links induce double-strand breaks during replication both in vivo and in
vitro (123, 124), presumably due to replication fork collapse and consequent
nuclease attack. The following is a working model for cross-link repair in
mammalian cells (Figure 7). Starting at the double-strand break induced by
replication, the XPFERCC1 nuclease degrades one of the cross-linked strands in
a 3 to 5 direction past the cross-link and thus converts the interstrand cross-link
into an intrastrand dinucleotide adduct adjacent to a double-strand break (122).
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checkpoint responses becomes better defined, it also becomes clear that they are
not cellular counterparts of international border checkpoints, but instead analogous to constant surveillance and response systems in that they continuously
monitor the integrity of the genome and control cell-cycle progression accordingly (131).
All eukaryotic cells have four phases within the cell cycle, G1, S, G2, and M,
and one outside, G0. In some unicellular organisms, G1 or G2 are extremely short
and difficult to observe, but in mammalian somatic cells, the phases are
well-defined and represent stages in the life of a cell in which distinct biochemical reactions take place. In an unperturbed cell cycle, the transition points G1/S
and G2/M, as well as S-phase progression, are tightly controlled, and available
evidence indicates that the same proteins involved in regulating the orderly
progression through the cell cycle are also involved in the checkpoint responses.
Thus, the DNA damage checkpoints are not unique pathways activated by DNA
damage, but rather are biochemical pathways operative under normal growth
conditions that are amplified upon an increase in DNA damage. Whether there
are thresholds for the level of damage necessary to elicit the checkpoint
responses is not known.
Although the checkpoint pathways are operational during the entire cell cycle
and hence may slow down the cell cycle at any point during the four phases, the
slowing or arrest of progression from one phase to another represents qualitative
changes in the cellular state as opposed to quantitative changes that may occur
within states. The term checkpoint is defined based upon the interstate transition
that is being inhibited by DNA damage as the G1/S, intra-S, and G2/M
checkpoints.
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Figure 7 Cross-link (X-link) repair. (A) In the error-free mechanism, a replication fork
induces a double-strand break upon encountering a cross-link. XPFERCC1, aided by RPA,
then digests the duplex 3 to 5 past the cross-link. The resulting intermediate is annealed
to a homologous duplex and is converted to a duplex with a dinucleotide cross-link by a
recombination reaction. Prior to or following the resolution of the Holliday intermediate, the
dinucleotide cross-link is eventually eliminated by nucleotide excision repair. Note that in
this mode of repair, only one of the six excision repair factors, XPFERCC1, is required for
the initial conversion of the interstrand cross-link into a single-strand lesion. (B) In the
error-prone pathway, the 6-factor excision nuclease makes dual incisions 5 to the cross-link
in one or the other strand to produce a 26-nucleotide gap 5 to the cross-link. An error-prone
polymerase (such as Pol) fills in the gap and may synthesize past the cross-link to generate
a triple-stranded intermediate that may constitute a substrate for the excision nuclease
system. Following damage removal by excision repair, the gap is filled in and ligated.
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Mammals
S. pombe
S. cerevisiae
Rad17
Rad17
Rad24
Sensors
RFC-like
PCNA-like
PI3-Kinases (PIKK)
PIKK binding partner
Rad9
Rad9
Ddc1
Rad1
Rad1
Rad17
Hus1
Hus1
Mec3
ATM
Tel1
Tel1
ATR
Rad3
Mec1
ATRIP
Rad26
Ddc2/Lcd1/Pie1
Cut5
Dpb11
Claspin
Mrc1
Mrc1
BRCA1
Crb2/Rph9
Rad9
Chk1
Chk1
Chk1
Chk2
Cds1
Rad53
Mediators
MDC1
53BP1
TopBP1
Transducers
Kinase
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Figure 8 Components of the DNA damage checkpoints in human cells. The damage is
detected by sensors that, with the aid of mediators, transduce the signal to transducers. The
transducers, in turn, activate or inactivate other proteins (effectors) that directly participate
in inhibiting the G1/S transition, S-phase progression, or the G2/M transition.
varying degrees (1, 132). The effector components (proteins that inhibit phase
transition) of the checkpoints are, naturally, what gives the checkpoints their
unique identities. However, various sensors, mediators, and signal transducers
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may play more prominent roles in one checkpoint than in others (133, 134), as
is apparent when the checkpoints are analyzed separately, below.
As in DNA repair, DNA damage checkpoints require the recognition
of DNA damage to initiate subsequent events. Although it is commonly believed
that the sensors for repair and for the checkpoint response are distinct, future
research will likely reveal considerable overlap at the damage detection step.
Clearly, RPA is an important damage sensor for both nucleotide excision repair
(48, 50) and the DNA damage checkpoints (135). Nevertheless, two groups of
proteins have been identified as checkpoint-specific damage sensors: the two
phosphoinositide 3-kinase-like kinase (PIKK) family members, ATM and ATR
(136), and the RFC/PCNA (clamp loader/polymerase clamp)-related Rad17RFC/9-1-1 complex (137).
SENSORS
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light rather than by ionizing radiation, and it is the main PIKK family member
that initiates signal transduction following UV irradiation (132).
The relative specificity of ATR for UV irradiation raised the possibility that
the enzyme might directly recognize specific damages formed by this agent.
Assays for electrophoretic mobility shift, DNA pulldown with immobilized
ATR, ATR pulldown with immobilized DNA, and UV-induced DNA-protein
cross-linking showed that ATR binds directly to DNA (154). The enzyme binds
to a 50-bp duplex containing a (6-4) photoproduct with about twofold higher
affinity than undamaged duplex. Analysis of ATR-DNA interactions by electron
microscopy further showed that binding to DNA increases with increasing UV
irradiation. Furthermore, when linear DNA was used, ATR was rarely seen at the
DNA termini, indicating that, in contrast to ATM, ATR does not recognize
double-strand breaks. When phosphorylation of p53 by ATR was measured, it
was found that undamaged DNA stimulates the kinase activity (155, 156) and
that UV-irradiated DNA increased the rate of phosphorylation moderately and in
a dose-dependent manner (154). Thus, at present it appears that ATM is a sensor
and transducer responding to double-strand breaks, and ATR serves an analogous
role for base damages, at least from UV irradiation.
The prototype of the PIKK family, DNA-PK, is a heterotrimer of a 450-kDa
catalytic subunit (DNA-PKcs) and a dimer of Ku70 and Ku80. The Ku70/Ku80
dimer binds to DNA ends and recruits DNA-PKcs, which then becomes activated
as a DNA-dependent protein kinase (115). It has been suggested that ATM and
ATR are recruited to DNA through the intermediacy of a similar DNA-binding
partner. Indeed, in both S. cerevisiae and S. pombe, the ATR homologs (scMec1
and spRad3, respectively) were shown to be in a complex with scDdc2 and
spRad3. Although the existence of an ATM-associated partner has not yet been
reported in mammalian cells, ATR interacts with an 86-kDa protein, ATRIP
(ATR Interacting Protein), that has very limited homology to scDdc2 and
spRad26 (157). Although DNA recruitment studies in S. cerevisiae showed that
the scMec1-scDdc2 complex functions in a manner analogous to DNA-PKcs/
Ku70/Ku80 (i.e., scMec1 requires scDdc2 for DNA binding), this is not the case
for ATR (135, 154). ATRIP is not required for the binding of ATR to naked or
RPA-covered single-strand DNA or double-strand DNA (135, 154). However,
ATRIP may confer some specificity for the binding of the ATR-ATRIP complex
to RPA coated DNA rather than naked DNA (135).
Rad17-RFC and the 9-1-1 complex The Rad17-RFC complex is a checkpointspecific structural homolog of the replication factor, RFC. The replicative form
of RFC is a heteropentamer composed of p140, p40, p38, p37, and p36. In
Rad17-RFC, the p140 subunit is replaced by the 75-kDa Rad17 protein (158
161). Electron microscopy has revealed that the two complexes have similar
structures: a globular shape with a deep groove running down the length of the
complex (162, 163).
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inhibits its nuclear export and degradation, thus resulting in increased levels of
p53 (211). p53 activates its target genes, including p21WAF-1/Cip1, which binds to
and inhibits the S-phase-promoting Cdk2-CyclinE complex, thereby maintaining
the G1/S arrest. p21WAF-1/Cip1 also binds to the Cdk4-CyclinD complex and
prevents it from phosphorylating Rb (212). The phosphorylation of Rb results in
its release of the E2F transcription factor, which is required for the transcription
of S-phase genes in order for S phase to proceed (204, 213).
An important issue in studies on the G1/S checkpoint is the identity of the
initiating signal. Several studies in budding yeast suggest that processing of the
damage by excision repair may be necessary to initiate the checkpoint response
(214 217). When G1-arrested yeast cells are UV-irradiated, entry into S phase is
delayed when the cells are released from the arrest. This checkpoint response is
dependent on a functional excision repair system and on the yeast homologs of
ATR, Rad17-RFC, and the 9-1-1 complex. When excision repair deficient cells
are subjected to the same treatment, they progress into S phase with no delay.
Once they enter the S phase, however, the checkpoint is activated, presumably
via replication blocks at UV photoproducts. These data have been interpreted to
mean that single-strand gaps generated by excision repair were the necessary
intermediates for activating the G1/S checkpoint by UV irradiation. Experiments
with Xenopus egg extracts have generally supported this model (190, 218 220).
There is less evidence for a role of excision repair in checkpoint activation in
mammalian cells. At low doses of UV irradiation, however, p53 accumulation
during G1 is defective in XPA (-/-) cells, which cannot make UV-induced nicks
or gaps (221). At high doses of UV, by contrast, p53 does accumulate during G1
even in excision repair-defective cells. Indeed, a recent report shows that in
budding yeast, activation of the G1/S checkpoint at moderately high UV doses is
independent of excision repair (222). It is possible that cyclobutane pyrimidine
dimers, which predominate at low doses of UV, do not constitute a significant
signal for checkpoint activation, but that (6-4) photoproducts, which become a
substantial fraction of the damage at high UV doses, can be recognized by the
damage sensors for checkpoint activation.
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in subunits of the M/R/N complex (232, 237, 238) and in FANCD2 (239).
However, RDS is not necessarily associated with increased sensitivity to ionizing
radiation. Thus, although BRCA1 mutants exhibit RDS, they are only mildly
sensitive to ionizing radiation; and NBS1 and FANCD2 mutants, which also have
the RDS phenotype, are only marginally sensitive to ionizing radiation, but very
sensitive to cross-linking agents. Perhaps ATM, the loss of which results in RDS
and extreme sensitivity to ionizing radiation, possesses a nonredundant function
in the S-phase checkpoint, which encompasses both checkpoint and repair/
recovery reactions, so that its loss results in a more severe radiation-sensitivity
phenotype.
In contrast to ATM as a sensor for double-strand breaks, when DNA is
damaged by UV or chemicals that make bulky base lesions, the main PIKK
family damage sensor is the ATR protein, or more precisely, the ATR-ATRIP
heterodimer (132, 157). ATR binds to chromatin (240) and can bind directly to
UV-induced lesions (154), or to RPA-coated single-stranded DNA (135) generated from the repair or replication of these lesions, and becomes activated.
Activated ATR phosphorylates Chk1, which in turn phosphorylates and downregulates Cdc25A, and thus inhibits firing of replication origins (229) (Figure
11). Recent evidence from Xenopus egg extracts suggests that the presence of
single-stranded DNA during S phase induces an ATR-dependent checkpoint that
inhibits origin firing by downregulating Cdc7-Dbf4 protein kinase activity, which
is required for Cdc45 binding to chromatin (241). Therefore, the downregulation
of either Cdk2/Cyclin E (CDK complex) or Cdc7/Dbf4 (DDK complex) may
result in the inhibition of late replication origins during the intra-S checkpoint. As
for the ATM-initiated checkpoint, ATR-initiated signaling also results in the
phosphorylation of BRCA1 (242, 243), NBS1, and other targets, promoting the
recovery of stalled/regressed/collapsed replication forks and thereby coordinating the inhibition of replication initiation with the recovery of active replication
forks by homologous recombination and related processes.
Genetic analyses of yeast have demonstrated that DNA Polymerase (Pol)
may play a role in sensing DNA damage during S phase (244, 245). Pol is
required for coordinated and efficient chromosomal DNA replication in
eukaryotes (246 249) and has also been implicated in nucleotide excision (250,
251), base excision (252), and recombinational repair (253). The catalytic subunit
4
Figure 10 The ATM-regulated intra-S-phase checkpoint. In response to double-strand
breaks induced by ionizing radiation, ATM triggers two cooperating parallel cascades to
inhibit replicative DNA synthesis. ATM, through the intermediacy of MDC1, H2AX, and
53BP1, phosphorylates Chk2 on Thr68 to induce ubiquitin-mediated degradation of
Cdc25A phosphatase. The degradation locks the S phasepromoting Cyclin E/Cdk2 in its
inactive, phosphorylated form and prevents the loading of Cdc45 on the replication origin.
ATM also initiates a second pathway by phosphorylating NBS1 of the M/R/N complex, as
well as SMC1, BRCA1, and FANCD2.
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not the N-terminal polymerase domain, is essential for viability (245, 255, 256),
indicating that the checkpoint sensor function of Pol is more important for
cellular physiology than its polymerase functions. Mutations in the essential
C-terminal domain abolish the inducibility of the RNR3 subunit of ribonucleotide reductase in response to DNA damage or hydroxyurea (244). In mammalian
cells, the C terminus of Pol interacts with Mdm2, perhaps as part of a DNA
damage response (257, 258).
Studies with S. cerevisiae and S. pombe have shown that lesions in replicating
DNA cause replication fork arrest, and that recombination proteins, such as
Rad51, the M/R/N complex, and the MUS81MMS4 resolvase (259), and the
replication proteins, such as the error-prone Pol (260), aid in the recovery of the
stalled replication fork (231). S-phase checkpoint mutants lack a coordinated
replication fork arrest and retrieval/recombinational process. As a consequence,
intermediates with long single-stranded regions accumulate following DNA
damage in these mutants (261) and eventually lead to potentially lethal doublestrand breaks (226, 262). Although these double-strand breaks are expected to
occur in a stochastic manner, evidence indicates that in both S. cerevisiae Mec1
mutants (263) and in human ATR mutants (264), the breaks preferentially occur
during G2 in specific regions of chromosomes that under physiological conditions replicate slower than the rest of the genome [called replication slow zones
(RSZ) in yeast and Fragile sites (FRA) in humans]. These breaks are thought to
occur in unreplicated chromosomal regions from stalled forks that escape the
scMec1/ATR-mediated intra-S checkpoint and are, in part, the source of chromosome rearrangements often seen in tumor cells (264).
SANCAR et al.
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Figure 12 The G2/M checkpoint. The ionizing radiation- (ATM) and UV damageresponsive sensor proteins (ATR-ATRIP, Rad17-RFC, and 9-1-1) are recruited to the
damage site. The mediator proteins such as MDC1, BRCA1 and/or 53BP1 communicate the DNA damage signal to Chk1 and/or Chk2, thereby regulating the Cdc2/
CyclinB, Wee1, and Cdc25A proteins that are crucial for the G2/M transition by
changing their expression, phosphorylation, and cellular localization.
77
CONCLUSIONS
DNA damage activates several distinct biochemical pathways. First, DNA repair
enzymes of varying complexities recognize and eliminate the damage. Second,
DNA damage activates DNA damage checkpoints, which arrest cell cycle
progression. Under most circumstances, checkpoints aid in cellular survival.
Third, DNA damage activates transcription of certain genes (transcriptional
response). The role of the transcriptional response in cell survival is unknown.
Finally, apoptosis in metazoans is the programmed cell death that is activated by
either cell death ligands or DNA damage, and serves to eliminate superfluous or
deregulated and dangerous cells.
The four DNA damage response pathways described above can and do
function independently under certain circumstances. However, under most con-
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LITERATURE CITED
1. Zhou BB, Elledge SJ. 2000. Nature 408:
43339
2. Kolodner RD, Putnam CD, Myung K.
2002. Science 297:55257
3. Modrich P, Lahue R. 1996. Annu. Rev.
Biochem. 65:10133
4. Kolodner RD, Marsischky GT. 1999.
Curr. Opin. Genet. Dev. 9:89 96
5. Cox MM, Goodman MF, Kreuzer KN,
Sherratt DJ, Sandler SJ, Marians KJ.
2000. Nature 404:37 41
6. Cox MM. 2002. Mutat. Res. 510:10720
7. Minko IG, Zou Y, Lloyd RS. 2002. Proc.
Natl. Acad. Sci. USA 99:19059
8. Sancar A. 1994. Biochemistry 33:29
9. Deisenhofer J. 2000. Mutat. Res. 460:
143 49
10. Todo T. 1999. Mutat. Res. 434:89 97
11. Sancar A. 2003. Chem. Rev. 103:220338
12. Park H, Zhang KJ, Ren YJ, Nadji S,
Sinha N, et al. 2002. Proc. Natl. Acad.
Sci. USA 99:1596570
13. Orren DK, Selby CP, Hearst JE, Sancar
A. 1992. J. Biol. Chem. 267:780 88
14. Sancar A, Hearst JE. 1993. Science 259:
141520
79
80
SANCAR et al.
81
82
153.
154.
155.
156.
157.
158.
159.
160.
161.
162.
163.
164.
165.
166.
167.
168.
169.
170.
171.
SANCAR et al.
hoeven Y, Smit B, et al. 2000. Curr.
Biol. 10:479 82
ODriscoll M, Ruiz-Perez VL, Woods
CG, Jeggo PA, Goodship JA. 2003. Nat.
Genet. 33:497501
nsal-Kac maz K, Makhov AM, Griffith
U
JD, Sancar A. 2002. Proc. Natl. Acad.
Sci. USA 99:667378
Hall-Jackson CA, Cross DA, Morrice N,
Smythe C. 1999. Oncogene 18:670713
Lakin ND, Hann BC, Jackson SP. 1999.
Oncogene 18:3989 95
Cortez D, Guntuku S, Qin J, Elledge SJ.
2001. Science 294:171316
Griffiths DJ, Barbet NC, McCready S,
Lehmann AR, Carr AM. 1995. EMBO J.
14:581223
Kondo T, Matsumoto K, Sugimoto K.
1999. Mol. Cell. Biol. 19:1136 43
Green CM, Erdjument-Bromage H,
Tempst P, Lowndes NF. 2000. Curr.
Biol. 10:39 42
Lindsey-Boltz LA, Bermudez VP, Hurwitz J, Sancar A. 2001. Proc. Natl. Acad.
Sci. USA 98:11236 41
Griffith JD, Lindsey-Boltz LA, Sancar
A. 2002. J. Biol. Chem. 277:1523336
Shiomi Y, Shinozaki A, Nakada D, Sugimoto K, Usukura J, et al. 2002. Genes
Cells 7:861 68
Venclovas C, Thelen MP. 2000. Nucleic
Acids Res. 28:248193
St Onge RP, Udell CM, Casselman R,
Davey S. 1999. Mol. Biol. Cell 10:
198595
Volkmer E, Karnitz LM. 1999. J. Biol.
Chem. 274:56770
Burtelow MA, Kaufmann SH, Karnitz
LM. 2000. J. Biol. Chem. 275:26343 48
Burtelow MA, Roos-Mattjus PM, Rauen
M, Babendure JR, Karnitz LM. 2001.
J. Biol. Chem. 276:259039
Yuzhakov A, Kelman Z, Hurwitz J,
ODonnell M. 1999. EMBO J. 18:
6189 99
Paulovich AG, Armour CD, Hartwell
LH. 1998. Genetics 150:7593
Longhese MP, Foiani M, Muzi-Falconi
172.
173.
174.
175.
176.
177.
178.
179.
180.
181.
182.
183.
184.
185.
186.
187.
188.
189.
83
84
SANCAR et al.
248.
249.
250.
251.
252.
253.
254.
255.
256.
257.
258.
259.
260.
261.
262.
263.
264.
265.
266.
85
CONTENTS
39
87
107
147
177
209
241
269
293
321
355
383
417
437
467
491
539
559
589
617
657
705
749
791
837
861
891
925
953
991
1019
1051