DNA repair
0
Department of Genetics, Institute of Molecular Biology, University of Copenhagen
,
ster Farimagsgade 2A, DK-1353 Copenhagen K
,
Denmark
Organisms are permanently exposed to endogenous and exogenous agents that damage DNA. If not repaired, such damage can result in mutations, diseases and cell death. The cellular responses to DNA damage include processes that deal with its consequences (e.g. tolerance and apoptosis) as well as direct correction of the damage by DNA repair mechanisms, which may require activation of checkpoint pathways. There are various forms of DNA damage, such as base modifications, strand breaks, crosslinks and mismatches. There are also numerous DNA repair pathways. Each repair pathway is directed to specific types of damage, and a given type of damage can be targeted by several pathways. Major DNA repair pathways are mismatch repair (MMR), nucleotide excision repair (NER), base excision repair (BER), homologous recombinational repair (HR), and non-homologous end joining (NHEJ). These MMSLHHG21MPSHM6S2 Stranddiscrimination Mediatedby PCNA? 3-5exonuclease? Exo1? Alkylation Oxidation Deamination Crosslinking Ionizing agents radiation G T<>T G T A A C MismatchesLoops dPiymriemrsidinBCeruolksyslaindkdsucts C APendo Pol Phosphodiesterase C Pol LigaseII XRCC1 C APendo PCNA RFC G C LigaseI C G Pol dRPase C G LigaseII XRCC1
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Exo1 Pol d , Pole
PCNA RFC,RPA LigaseI
Homologous recombinational repair (HR)
pathways each require a number of
proteins. By contrast, O-alkylated bases,
such as O6-methylguanine can be
repaired by the action of a single protein,
O6-methylguanine-DNA
methyltransferase (MGMT). MGMT
removes the alkyl group in a suicide
reaction by transfer to one of its cysteine
residues. Photolyases are able to split
covalent bonds of pyrimidine dimers
produced by UV radiation. They bind to
a UV lesion in a light-independent
process, but require light (350-450 nm)
as an energy source for repair. Another
NER-independent pathway that can
remove UV-induced damage, UVER, is
present in only a few organisms, such
as the yeast Schizosaccharomyces
pombe. A key factor in UVER is the
endonuclease Uve1/UVDE, which cuts
5 of various types of damage. Recent
work has uncovered novel pathways,
such as transcription-coupled BER,
break-induced replication, and
nucleotide incision repair as well as
interconnections between known
pathways. For simplicity, we do not
consider these here. Although most
repair proteins are usually homologous
between organisms, their designations
are often different. Here we generally
use the names of human proteins.
Mismatch repair
The main task of MMR is to remove
base mismatches and small insertion/
deletion loops (IDLs) introduced during
replication. In Escherichia coli, the
main players in MMR are MutS, MutL
and MutH. MutH nicks the
nonmethylated strand and thereby enables
discrimination between the newly
synthesized strand and the template.
MMR is bidirectional, i.e. nicking and
degradation can occur from either the 5
or 3 side of the mismatch. In eukaryotes,
several MutS and MutL homologues are
involved in MMR; MutH homologues
appear to be absent. Inactivation of
human MMR causes hereditary
nonpolyposis colorectal cancer
(HNPCC) and some types of sporadic
tumor. In the course of human MMR,
base mismatches are bound by the
MutS-homologous heterodimer
MSH2MSH6, while small IDLs can be bound
by MSH2-MSH6 and MSH2-MSH3.
Subsequently, the MutL-homologous
heterodimer MLH1-PMS2 is recruited.
Oliver Fleck and Olaf Nielsen
AA
AA
XPB TFIH RPA XPD
PCNA RFC,RPA LigaseI
G =O
C
Non-homologous end joining (NHEJ)
Pol
Pold /e
Base excision repair (BER)
G APendo
G Pol
In some eukaryotes additional MutL
homologues exist. These form
heterodimers with MLH1 and may play
a minor role in MMR. It is not yet
understood how eukaryotes distinguish
between the new and the old strand.
Strand discrimination may be either
mediated by the replication accessory
factor PCNA or could be simply
achieved by recognition of nicks, gaps or
free 3 ends that are present in the
nascent strand during replication. In a
downstream step, the newly synthesized
strand is degraded, which removes the
mismatch. MMR patches are ~100 to
>1000 nucleotides in length. EXO1 is
involved in 5 to 3 excision. It is not yet
clear which factors participate in 3 to 5
excision, but DNA Pol d and e and
EXO1 may be involved. MMR is
completed after DNA synthesis by the
replication machinery and ligation of the
remaining nick.
Nucleotide excision repair
NER removes a variety of forms of DNA
damage, including photoproducts
induced by UV and other bulky lesions.
NER consists of two subpathways:
global genome repair (GGR), which
removes damage in the genome overall
and transcription-coupled repair (TCR),
which specifically repairs the transcribed
strand of active genes. The main
difference between GGR and TCR is the
requirement for different factors during
the initial recognition steps. UV-DDB,
consisting of DDB1 and DDB2, and
XP (...truncated)