Table 2.
DNA repair genes and pathways encoded by D. radiodurans.
|
Pathway Genes in D. radiodurans |
Predicted Biochemical Activities and Comments |
|---|---|
| Nucleotide Excision Repair | |
| UvrABCD | Corresponds to UV endonuclease α; uvrA=mtcAB, uvrD =irrB (31). |
| Transcription Repair Coupling | |
| MFD | Experiments suggest this process may not be present (33). |
| UV Excision Repair | |
| UVDE | Corresponds 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. |
| 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 (34)? |
| MutY-Nth-3 | Second FAPY glycosylase from (34)? |
| 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 this gene functions differently than in E. coli. |
| SbcCD | Homology to Rad50/MRE11 suggests a role in DSB repair (35). |
| Recombination | |
| RecA | Recombinase. May also regulate transcription of other genes. |
| Resolution | |
| RuvABC | Likely redundant to the RecG pathway (36). |
| RecG | Likely redundant to RuvABC pathway (36). |
| DNA polymerases | |
| PolA | Repair replication polymerase (37). |
| PolC | Chromosomal replication polymerase. |
| PolX | DNA polymerase of unknown function (PolX family). |
| Pol | DNA polymerase of unknown function (similar to spo1 phage). |
| 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 and/or DNA repair. 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? |
| SSB | Single strand DNA binding protein. |
| CinA | May recruit RecA to cell membrane. |
| XerD | Site-specific recombinase. |