Biology Reference
In-Depth Information
A. BER of Oxidized Bases and AP sites in
Mammalian Genomes
The major process for restoring genomic integrity by repairing oxidative as
well as spontaneous alkylation base damage, and AP sites and abnormal bases
such as U generated by spontaneous deamination of C is the base excision
repair (BER) pathway. BER proteins are involved in the repair of SSBs as well,
as discussed in Section I.
C
. While evolutionarily conserved organisms range
from bacteria to mammals, BER is a versatile DNA repair process that handles
many types of damage including base damage, AP sites and their oxidation
products, and DNA SSBs. BER is initiated with lesion base excision by a mono-
or bifunctional DNA glycosylase (DG), and consists of the following basic
steps, as also outlined in
Fig. 1
.
(i)
Base lesion recognition, excision, and cleavage of AP site
. Monofunctional
DGs including uracil-DNA glycosylase (UDG) and methylpurine-DNA gly-
cosylase (MPG, alsonamed alkyladenine-DNAglycosylase or AAG) recognize
and excise uracil and alkylated bases, respectively, via
N
-glycosyl bond cleav-
age to generate AP sites. In contrast, all oxidized bases are excised by bifunc-
tional DGs with intrinsic AP lyase activity.
8,9
These, in a concerted action,
excise substrate bases and cleave the resulting AP sites via
b
or
bd
elimination
reaction.
8,10,11
Five oxidized base-specific DGs have so far been discovered
in mammalian cells, which belong to two families named after the prototypes
in
Escherichia coli
: OGG1 andNTH1 in theNth family possess
b
lyase activity
and generate SSBs with 3
0
phospho
ab
unsaturated aldehyde (3
0
PUA) and 5
0
P
termini. In contrast, NEIL1 andNEIL2 in the Nei family possess
bd
AP lyase
activity generating anSSBwith3
0
Pand5
0
Ptermini.
11
NEIL3, another paralog
in the Nei family, was identified at about the same time as NEIL1 andNEIL2,
based on sequence homology, and it has recently been characterized as having
predominantly
b
lyase (and weak
bd
lyase) activity.
12,13
Another evolutionarily
conserved DG, MYH (ortholog of
E. coli
MutY), excises the normal base A
from an 8-oxoG
ApairinDNA.
14
AP sites generated directly by ROS or by
monofunctional DG are hydrolyzed by AP endonuclease 1 (APE1) in mam-
malian cells to generate an SSB with 3
0
OH and 5
0
deoxyribose phosphate
(dRP) ends. Thus, the SSB products of DGs or APE1 have a 3
0
or 5
0
terminus
that prevents subsequent gap-fillingDNA synthesis or ligation. These blocked
termini are removed in the second step of BER.
(ii)
End-processing of SSB termini to generate 3
0
OH/5
0
P
. SSB end-
processing is an essential step in BER/SSBR, utilizing diverse enzymes to
process various blocked termini. The two major 3
0
end-processing enzymes
involved in mammalian BER/SSBR are APE1 and polynucleotide kinase 3
0
phosphatase (PNKP), which remove 3
0
dRP (
b
elimination product) and 3
0
P
