Table 6

DNA repair genes and pathways encoded by D. radiodurans.

PathwayPredicted biochemical activities and comments
Genes in D. radiodurans
Nucleotide excision repair
UvrABCDCorresponds to UV endonuclease α; uvrA = mtcAB, uvrD = irrB(31)
Transcription repair coupling
MFD Experiments suggest that this process may not be present (34)
UV excision repair
UVDECorresponds to UV endonuclease β (uvsCDE)
Base excision repair
AlkA 3-methyl-guanine glycosylase
MPG-3MG 3-methyl-guanine glycosylase
Ung Uracil DNA glycosylase
Mug G:U mismatch glycosylase
Ung2Uracil DNA glycosylase? (35)
MutM-Fpg FAPY and 8-oxo-guanine DNA glycosylase
MutY-Nth-1 Likely a G:A glycosylase because most similar to MutYs
MutY-Nth-2 Thymine glycol glycosylase from (36)?
MutY-Nth-3 Second FAPY glycosylase from (36)?
MutY-Nth-4 Unknown
AP endonuclease
Xth May also be an exonuclease
Mismatch excision repair
MutLS Absence of MutH suggests different strand recognition system than E. coli
Recombinational repair
Initiation
RecFJNRQ Nearly complete RecF pathway (RecO missing)
RecD Absence of RecB and RecC orthologs suggests that this gene functions differently than in E. coli
SbcCD Homology to Rad50/MRE11 suggests a role in DSB repair (37)
Recombination
RecARecombinase; may also regulate transcription of other genes
Resolution
RuvABC Likely redundant to the RecG pathway (38)
RecG Likely redundant to RuvABC pathway (38)
DNA polymerases
PolA Repair replication polymerase (39)
PolC Chromosomal replication polymerase
PolX DNA polymerase of unknown function (PolX family)
Ligation
DnlJ Ligation activity is required for all excision and recombinational repair pathways
dNTP pools, cleanup
MutT and Nudix family dNTP cleanup; more copies than any other prokaryote
NrdEFI Ribonucleotide reductase
NrdX Ribonucleotide reductase
Induction
LexA Transcription repressor, possibly for SOS response
Other
RadA/SMS DNA damage response?
HepA Likely role in transcription or DNA repair (or both); member of SNF2 family (24)
MutS2 Possible role in recognizing mismatches but not likely involved in mismatch repair (24)
XseA Exonuclease VII subunit (but XseB is absent)
UvrA2 Export of damaged DNA?
Extracellular nucleases Degradation of exported DNA?
SSBSingle-strand DNA binding protein
CinA May recruit RecA to cell membrane
XerD Site-specific recombinase