ENTRY       sly03410                    Pathway
NAME        Base excision repair - Solanum lycopersicum (tomato)
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.
CLASS       Genetic Information Processing; Replication and repair
PATHWAY_MAP sly03410  Base excision repair
DBLINKS     GO: 0006284 0006285 0006286 0006287 0006288
ORGANISM    Solanum lycopersicum (tomato) [GN:sly]
GENE        101258844  formamidopyrimidine-DNA glycosylase isoform X1 [KO:K10563] [EC:3.2.2.23 4.2.99.18]
            101268340  N-glycosylase/DNA lyase OGG1 [KO:K03660] [EC:3.2.2.- 4.2.99.18]
            101257755  putative DNA glycosylase At3g47830 [KO:K10773] [EC:4.2.99.18]
            101262253  endonuclease III homolog 1, chloroplastic-like isoform X1 [KO:K10773] [EC:4.2.99.18]
            101248783  endonuclease III homolog 1, chloroplastic [KO:K10773] [EC:4.2.99.18]
            101266297  probable DNA-3-methyladenine glycosylase 2 [KO:K01247] [EC:3.2.2.21]
            101265434  DNA-3-methyladenine glycosylase 1 isoform X1 [KO:K01247] [EC:3.2.2.21]
            101246304  uncharacterized protein LOC101246304 [KO:K01246] [EC:3.2.2.20]
            101245051  uncharacterized protein LOC101245051 [KO:K01246] [EC:3.2.2.20]
            101247118  uncharacterized protein LOC101247118 [KO:K01246] [EC:3.2.2.20]
            101257468  uncharacterized protein LOC101257468 [KO:K01246] [EC:3.2.2.20]
            101250399  uncharacterized protein LOC101250399 [KO:K01246] [EC:3.2.2.20]
            101258999  uncharacterized protein LOC101258999 [KO:K01246] [EC:3.2.2.20]
            101267869  uncharacterized protein LOC101267869 isoform X1 [KO:K01246] [EC:3.2.2.20]
            101255344  uracil-DNA glycosylase, mitochondrial isoform X2 [KO:K03648] [EC:3.2.2.27]
            101262147  adenine DNA glycosylase isoform X2 [KO:K03575] [EC:3.2.2.31]
            101264772  DNA-3-methyladenine glycosylase isoform X1 [KO:K03652] [EC:3.2.2.21]
            101255935  methyl-CpG-binding domain protein 4-like protein isoform X1 [KO:K10801] [EC:3.2.2.-]
            101255875  DNA-(apurinic or apyrimidinic site) lyase, chloroplastic isoform X1 [KO:K01142] [EC:3.1.11.2]
            101246406  DNA-(apurinic or apyrimidinic site) lyase 2 isoform X1 [KO:K10772] [EC:4.2.99.18]
            101252794  DNA polymerase I B, chloroplastic/mitochondrial isoform X2 [KO:K02335] [EC:2.7.7.7]
            101264323  DNA polymerase lambda [KO:K03512] [EC:2.7.7.7 4.2.99.-]
            101246064  DNA-repair protein XRCC1 [KO:K10803]
            544248  pcna; proliferating cell nuclear antigen [KO:K04802]
            101256637  DNA polymerase delta catalytic subunit [KO:K02327] [EC:2.7.7.7]
            101243681  DNA polymerase delta small subunit [KO:K02328]
            101258997  muscle M-line assembly protein unc-89 [KO:K03504]
            101262116  uncharacterized protein LOC101262116 [KO:K03505]
            101255630  uncharacterized protein LOC101255630 [KO:K03505]
            101253967  DNA polymerase epsilon catalytic subunit A-like isoform X1 [KO:K02324] [EC:2.7.7.7]
            101254462  DNA polymerase epsilon subunit B [KO:K02325] [EC:2.7.7.7]
            101260506  DNA polymerase epsilon subunit 3 [KO:K02326] [EC:2.7.7.7]
            101262281  DNA ligase 1 [KO:K10747] [EC:6.5.1.1 6.5.1.6 6.5.1.7]
            101247901  poly [ADP-ribose] polymerase 1 isoform X3 [KO:K24070] [EC:2.4.2.30]
            101267967  poly [ADP-ribose] polymerase 3 [KO:K10798] [EC:2.4.2.30]
            101246372  poly [ADP-ribose] polymerase 3-like isoform X1 [KO:K10798] [EC:2.4.2.30]
            101251710  poly [ADP-ribose] polymerase 2-like [KO:K10798] [EC:2.4.2.30]
            101252016  poly [ADP-ribose] polymerase 2 isoform X1 [KO:K10798] [EC:2.4.2.30]
            101268807  flap endonuclease 1 isoform X2 [KO:K04799] [EC:3.1.-.-]
REFERENCE   PMID:17893748
  AUTHORS   Krwawicz J, Arczewska KD, Speina E, Maciejewska A, Grzesiuk E.
  TITLE     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.
  JOURNAL   Acta Biochim Pol 54:413-34 (2007)
REFERENCE   PMID:17337257
  AUTHORS   Almeida KH, Sobol RW.
  TITLE     A unified view of base excision repair: lesion-dependent protein complexes regulated by post-translational modification.
  JOURNAL   DNA Repair (Amst) 6:695-711 (2007)
            DOI:10.1016/j.dnarep.2007.01.009
REFERENCE   PMID:21665970
  AUTHORS   Moen MN, Knaevelsrud I, Haugland GT, Grosvik K, Birkeland NK, Klungland A, Bjelland S
  TITLE     Uracil-DNA glycosylase of Thermoplasma acidophilum directs long-patch base excision repair, which is promoted by deoxynucleoside triphosphates and ATP/ADP, into short-patch repair.
  JOURNAL   J Bacteriol 193:4495-508 (2011)
            DOI:10.1128/JB.00233-11
REFERENCE   PMID:11436317
  AUTHORS   Ikeda S, Seki S.
  TITLE     [Base excision repair: DNA glycosylase and AP endonuclease]
  JOURNAL   Tanpakushitsu Kakusan Koso 46:916-23 (2001)
KO_PATHWAY  ko03410
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