Biology Reference
In-Depth Information
stress.
16
In such cases, the oxidized 5
0
dRP is displaced during gap-filling
synthesis together with 2-8 additional nucleotides (nts) as an ssDNA flap,
which is then removed by flap endonuclease I (FEN-1). FEN-1 is an
essential enzyme normally involved in the removal of Okazaki fragment
primers during lagging strand DNA replication.
17
A second flap endonu-
clease, DNA2, that acts in concert with FEN-1 in processing long flap
structures has recently been discovered in both nuclei and mitochondria of
human cells.
18,19
Several other end-processing enzymes are also involved in
processing various blocked termini at SSBs directly generated in mamma-
lian genomes; these are discussed in Section I.
C
.
(iii)
Gap-filling after lesion excision
. Lesion excision and termini processing
usually leave a 1-nt gap at the damaged base site, which is filled in with the
template strand-guided nucleotide by a DNA polymerase. Depending on
the repair patch size, two types of BER have been characterized: single nt
incorporation repair (SN-BER) involving replacement of only the base
lesion with the parent base, and long-patch repair (LP-BER) involving
repair patch size of 2-8 nt upstream of the lesion site. As already mentioned,
LP-BER requires FEN-1 (and possibly DNA2) to remove the displaced
DNA flap. Mammalian cells express multiple DNA polymerases that func-
tion in BER/SSBR pathways. Pol
b
, ubiquitous in mammalian tissues, is the
primary BER polymerase and carries out SN-BER in nondividing cells,
although Pol
b
may also participate in LP-BER in coordination with
FEN-1.
20,21
However, LP-BER generally utilizes DNA replication machin-
ery including replicative DNA pols, Pol
d
/
e
, the sliding clamp PCNA, clamp
loader replication factor-C (RF-C), DNA ligase I (LigI), and FEN-1.
16,22,23
The complex issue of choice between SN-BER and LP-BER is yet to be
completely understood although initial studies suggested that the nature of
the 5
0
-phosphoribose terminus (normal vs. oxidized) would be a deciding
factor.
24
However, involvement of DNA replication proteins with LP-BER
strongly suggests that LP-BER could be the preferred pathway during DNA
replication, irrespective of the 5
0
terminal group.
(iv)
Nick sealing by DNA ligases
. The sealing of the nick with 3
0
OH and 5
0
P
termini by a DNA ligase to restore genomic integrity is the final step in
BER/SSBR. DNA ligase III
a
(LigIII
a
) and Lig I are the major DNA ligases
(in addition to Ligase IV, which is involved in DSB repair) in human cells;
the former is generally associated with SN-BER and the latter with
LP-BER although the distinction may not be absolute.
25
B. DG: The BER-initiating Enzyme
BER is unique among excision repair pathways in that the damaged bases
are recognized by distinct damaged base-specific DGs. DGs are relatively small
(
30-50 kDa) monomeric proteins that do not require cofactors for their
