base excision repair (BER)

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DESCRIPTION:

Base excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair initiated by lesion-specific DNA glycosylases and completed by either of the two sub-pathways: short-patch BER where only one nucleotide is replaced and long-patch BER where 2-13 nucleotides are replaced. Each sub-pathway of BER relies on the formation of protein complexes that assemble at the site of the DNA lesion and facilitate repair in a coordinated fashion. This process of complex formation appears to provide an increase in specificity and efficiency to the BER pathway, thereby facilitating the maintenance of genome integrity by preventing the accumulation of highly toxic repair intermediates.

Base excision repair (BER) is an evolutionarily conserved process for maintaining genomic integrity by eliminating several dozen damaged or inappropriate (oxidatived, methylated, alkylated, hydrated, and some type of mismatched) bases that are generated endogenously or induced by genotoxicants, predominantly, reactive oxygen species (ROS).

EXTERNAL DATABASES:
KEGG database - BER - Homo sapiens (human)
REACTOME database - BER - Homo sapiens (human) 
KEGG database - BER - Mus musculus (mouse)
REACTOME database - BER - Mus musculus (mouse)
KEGG database - BER - Caenorhabditis elegans (nematode)
REACTOME database - BER - Caenorhabditis elegans (nematode)
KEGG database - BER - Drosophila melanogaster (fruit fly)
REACTOME database - BER - Drosophila melanogaster (fruit fly)
KEGG database - BER - Saccharomyces cerevisiae (budding yeast) 
REACTOME database - BER - Saccharomyces cerevisiae (budding yeast)
KEGG database - BER - Schizosaccharomyces pombe (fission yeast)
REACTOME database - BER - Schizosaccharomyces pombe (fission yeast)
KEGG database - BER - Escherichia coli K-12 MG1655
REACTOME database BER - Escherichia coli K-12 MG1655
KEGG database - BER - Arabidopsis thaliana (thale cress)
REACTOME database - BER - Arabidopsis thaliana (thale cress )


ABBREVIATIONS:
BER


RELATED DISEASES:


DAMAGES RECOGNIZED AND REMOVED:

1,N2-etheno-G (1,2εG) in dsDNA
N2,3-etheno-G (N2,3-εG)
1,N6-etheno-A (1εA)
3,N4-etheno-C (εC) in dsDNA
N1-OH-ethyl A (1heA)
N1-methyl A (1meA)
1,N6-ethano A (EA)
1-methyl G (1meG)
3,N4-hydroxypropyl-C (HPC)
3,N4-alpha-HPC
3,N4-alpha-OH-gamma-methyl-propano-C (mHPC)
3-methyl C (3meC)
3-methyl A (3meA)
N3-methyl G (3meG)
7-methyl A (7meA)
N7-methyl G (7meG)
8-methyl G (8meG)
O2-methyl T (O2meT)
deoxyuridine
O2-methyl C (O2meC)
5-hydroxy-U (5-OH-U)
5-hydroxymethyl U (5-OH-me-U)
5-hydroxy C (5-OH-C)
5-formyl dU (5-foU)
thymine glycol (Tg)
uracil glycol (Ug)
cytosine glycol (Cg)
FapyA
FapyG
5,6-dihydroxy C (5,6-diOH-C)
5,6-dihydroxy U (5,6-diOH-U)
5-fluoro-dU
aflatoxin-FapyG
imidazole ring-opened N-2-aminofluorene-C8-guanine
dU in dsDNA
dU in ssDNA
3-methyl A (3-meA) in ssDNA
8-oxoG
Fapy-7meG
2-oxoA
A from A:8-oxoG
A from A:G
A from A:C
2-oxoA from 2-oxoA:G
dU from U:A
dU from U:G
T from T:G
Tg from Tg:A
Tg from Tg:G
8-oxoG from 8-oxoG:C
8-oxoG from 8-oxoG:A
8-oxoG from 8-oxoG:G
8-oxoG from 8-oxoG:T
FapyG from FapyG:C
Fapy-7meG from Fapy-7meG:C
5-OH-meU from 5-OH-meU:G
5-OH-meU from 5-OH-meU:A
5-formyl dU from 5-formylU:G
5-fluoroU from 5-fluoroU:G
5-fluoroU from 5-fluoroU:A
ethenoC from ethenoC:G
open ring forms of ethenoA
T from T:C
T from T:T
T from T:O6-meG
5-OH-meU in ssDNA
U or T from U/TpG:5meCpG
U or T from U/T:G
FapyG:A
FapyG from FapyG:G
FapyG from FapyG:T
AP-site
3'-OH end
3'-P
3'-PUA termini
3'-TOP1 termini
5'-P end
5'-dRP termini
5-bromoU
3,N4-ethano-C (EC)
8-(hydroxymethyl)-εC
1,N6-etheno-A in (1εA) dsDNA
8-oxoA
2-hydroxy-A (2-OH-A)
5-hydroxy-6-hydro-U (5-OH-6-H-U)
5,6-dihydro U (5,6-diH-U)
5-hydroxy-6-hydro-T (5-OH-6-H-T)
5,6-dihydro T (5,6-diH-T)
5-hydroxy-6-hydro-C (5-OH-6-H-C)
8-hydroxyA (8-OH-A)
DNA-psoralen

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ORTHOLOGY CLASS Homo sapiens L. (human) [HSA] Mus musculus L. (mouse) [MMU] Caenorhabditis elegans Maupas (nematode) [CEL] Drosophila melanogaster Meigen (fruit fly) [DME] Saccharomyces cerevisiae Meyen ex E.C. Hansen (budding yeast) [SCE] Schizo-saccharomyces pombe Lindner (fission yeast) [SPO] Escherichia coli Migula (bacterium) K-12 MG1655 [ECO] Arabidopsis thaliana (L.) Heynh. (mouse-ear cress) [ATH]
ko:K10862 (tyrosyl-DNA phosphodiesterase 1 [EC:3.1.4.-]) TDP1 Tdp1 Tdp1 Dmel_Tdp1 Tdp1p Tdp1 Ath_TDP1
ko:K10803 (DNA-repair protein XRCC1) XRCC1 Xrcc1 XRCC1 ATXRCC1
ko:K10802 (high mobility group protein B1) HMGB1 Hmgb1 Dsp1 HMGB1
ko:K10801 (methyl-CpG-binding domain protein 4 [EC:3.2.2.-]) MBD4 (MED1) Mbd4 ATMBD4
ko:K10800 (single-strand selective monofunctional uracil DNA glycosylase [EC:3.2.2.-]) SMUG1 Smug1 CG5285
ko:K10798 (poly [ADP-ribose] polymerase [EC:2.4.2.30]) PARP3
PARP1
PARP2
PARP4
Parp3
Parp1
Parp4
Parp2
pme-2
pme-1
Parp PARP2
APP
ko:K10776 (DNA ligase 3 [EC:6.5.1.1]) LIG3 Lig3 lig3
ko:K10773 (endonuclease III [EC:4.2.99.18]) NTHL1 Nthl1 nth-1 Dmel_CG9272 NTG1
NTG2
nth1 Nth (endo III) NTH2 (AtEndo III)
ATNTH1
ko:K10772 (AP endonuclease 2 [EC:4.2.99.18]) APEX2 Apex2 APN2 apn2 AtEndo 2
ko:K10771 (AP endonuclease 1 [EC:4.2.99.18]) APEX1 Apex1 apn-1
exo-3
Rrp1 APN1 apn1
ko:K10747 (DNA ligase 1 [EC:6.5.1.1]) LIG1 Lig1 lig-1 DmDNA Lig I CDC9 adl1
cdc17
At1g49250
ATLIG1
ko:K10569 (endonuclease VIII-like 3) NEIL3 Neil3 Neil3-like
ko:K10568 (endonuclease VIII-like 2 [EC:3.2.2.- 4.2.99.18]) NEIL2 Neil2
ko:K10567 (endonuclease VIII-like 1 [EC:3.2.2.- 4.2.99.18]) NEIL1 Neil1
ko:K10563 (formamidopyrimidine-DNA glycosylase [EC:3.2.2.23 4.2.99.18]) Fpg (MutM) AtMMH-1
ko:K07462 (single-stranded-DNA-specific exonuclease [EC:3.1.-.-]) RecJ
ko:K05522 (endonuclease VIII [EC:3.2.2.- 4.2.99.18]) Nei (endo VIII)
ko:K04802 (proliferating cell nuclear antigen) PCNA Pcna pcn-1 Mus209 (Pcna)
Pcna2
POL30 pcn1 PCNA1
PCNA2
ko:K04799 (flap endonuclease-1 [EC:3.-.-.-]) FEN1 (DNase IV) Fen1 crn-1 Fen1 RAD27 rad2 AT5G26680
ko:K03660 (N-glycosylase/DNA lyase [EC:3.2.2.- 4.2.99.18]) hOGG1 Ogg1 Ogg1 OGG1 OGG1
ko:K03652 (DNA-3-methyladenine glycosylase [EC:3.2.2.21]) ANPG (MPG) Mpg gi:15229928
ko:K03649 (TDG/mug DNA glycosylase family protein [EC:3.2.2.-]) TDG Gm5806 (TDG/Mug-like)
Tdg
Thd1 thp1 Mug
ko:K03648 (uracil-DNA glycosylase [EC:3.2.2.27]) UNG Ung ung-1 UNG1 ung1 Ung UNG
ko:K03575 (A/G-specific adenine glycosylase [EC:3.2.2.-]) MUTYH Mutyh myh1 MutY gi:42566730
ko:K03512 (DNA polymerase lambda subunit [EC:2.7.7.7 4.2.99.-]) POLλ (POLL) mPolλ (mPOLL) DNA Pol lambda
ko:K03506 (DNA polymerase epsilon subunit 4 [EC:2.7.7.7]) POLE4 Pole4 DNA Pol epsilon sub 4 Mes4 DPB3 SPCC16C4.22
ko:K03505 (DNA polymerase delta subunit 4) POLD4 Pold4 cdm1 POLD4
ko:K03504 (DNA polymerase delta subunit 3) POLD3 Pold3 PolD3 CG3975
Dmel_CG3975
POL32 cdc27 POLD3
ko:K02335 (DNA polymerase I [EC:2.7.7.7]) DNA Pol I POLGAMMA2
POLGAMMA1
ko:K02330 (DNA polymerase beta subunit [EC:2.7.7.7 4.2.99.-]) POLβ (POLB) mPolβ (mPolB)
ko:K02328 (DNA polymerase delta subunit 2) POLD2 Pold2 DNA Pol delta sub 2 DNA pol delta small sub POL31 cdc1 POLD2
ko:K02327 (DNA polymerase delta subunit 1 [EC:2.7.7.7]) POLδ (POLD) mPolδ (mPolD) DNA Pol delta DNApol-delta POL3
POL3
cdc6 POLD1
ko:K02326 (DNA polymerase epsilon subunit 3 [EC:2.7.7.7]) POLE3 Pole3 Chrac-14 DPB4 dpb4
ko:K02325 (DNA polymerase epsilon subunit 2 [EC:2.7.7.7]) POLE2 Pole2 DNA Pole-2 Pole2 DPB2 dpb2 ATDPB2
ko:K02324 (DNA polymerase epsilon subunit 1 [EC:2.7.7.7]) POLε (POLE) mPolε (mPolE) DNA Pol epsilon sub 1 (hypothetical protein) DNApol-epsilon POL2 cdc20 TIL1
TIL2
ko:K01972 (DNA ligase (NAD+) [EC:6.5.1.2]) DNA ligase I
DNA ligase B
ko:K01247 (DNA-3-methyladenine glycosylase II [EC:3.2.2.21]) MAG1 mag1
gi:19112661
AlkA gi:15230333
gi:145323948
gi:18410802
ko:K01246 (DNA-3-methyladenine glycosylase I [EC:3.2.2.20]) Tag gi:42571455
gi:15241554
gi:15218379
gi:79331243
gi:18399721
gi:18410766
ko:K01151 (deoxyribonuclease IV [EC:3.1.21.2]) Nfo (endo IV)
ko:K01142 (exodeoxyribonuclease III [EC:3.1.11.2]) XthA (exo III) ARP

References:

  • Early-onset ataxia with ocular motor apraxia and hypoalbuminemia/ataxia with oculomotor apraxia 1.

    , , : [PUBMED]
  • Short-patch single-strand break repair in ataxia oculomotor apraxia-1.

    , , : [PUBMED]
  • Aprataxin, poly-ADP ribose polymerase 1 (PARP-1) and apurinic endonuclease 1 (APE1) function together to protect the genome against oxidative damage.

    , , : [PUBMED]
  • Oxidative DNA damage repair in mammalian cells: a new perspective.

    , , : [PUBMED]
  • The intricate structural chemistry of base excision repair machinery: implications for DNA damage recognition, removal, and repair.

    , , : [PUBMED]
  • Base damage and single-strand break repair: mechanisms and functional significance of short- and long-patch repair subpathways.

    , , : [PUBMED]
  • Bacterial DNA repair genes and their eukaryotic homologues: 1. Mutations in genes involved in base excision repair (BER) and DNA-end processors and their implication in mutagenesis and human disease.

    , , : [PUBMED]
  • DNA repair in mammalian cells: Base excision repair: the long and short of it.

    , , : [PUBMED]
  • Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells.

    , , : [PUBMED]
  • Base excision repair and lesion-dependent subpathways for repair of oxidative DNA damage.

    , , : [PUBMED]
  • A review of recent experiments on step-to-step "hand-off" of the DNA intermediates in mammalian base excision repair pathways.

    , , : [PUBMED]

Last modification date: Oct. 11, 2011