Review Article
Understanding DNA Repair in Hyperthermophilic Archaea: Persistent Gaps and Other Reasons to Focus on the Fork
Table 1
Gene-deletion studies in hyperthermophilic archaea.
| Gene | ORF ID | Organism | Predicted function | Phenotype | Reference |
| Group I (relevant phenotype) | udg2 | SiRe_0084 | S. islandicus | Uracil DNA glycosylase | Impaired growth | [10] | udg4 | SiRe_1884 | S. islandicus | Uracil DNA glycosylase | Impaired growth | [10] | hef/xpf | TK1021 | Tc. kodakarensis | Structure-specific endonuclease | General damage sensitivity | [34] | hjm/hel308 | TK1332 | Tc. kodakarensis | DNA helicase | Sensitive to mitomycin C | [34] | phr | Saci_1227 | S. acidocaldarius | DNA photolyase | Loss of photoreactivation | [59] | dbh | Saci_0554 | S. acidocaldarius | Y-family DNA polymerase | Increased G:C to T:A | [11] | radC1 | SiRe_0240 | S. islandicus | RadA paralog | Increased damage sensitivity | [60] | phrB | SiRe_0261 | S. islandicus | DNA photolyase | Photorepair deficiency | [10] |
| Group I′ (possible phenotype) | xpf | SiRe_1280 | S. islandicus | 3′-flap endonuclease | Slow DNA replication? | [10] | dpo4 | | S. solfataricus | Y-family DNA polymerase | Possible sensitivity to cisplatin | [61] | xpb | TK0928 | Tc. kodakarensis | NER-related helicase | Marginal damage sensitivity | [36] | xpd | TK0784 | Tc. kodakarensis | NER-related helicase | Marginal damage sensitivity | [36] |
| Group II (no observed impact) | xpd | SiRe_1685 | S. islandicus | NER-related helicase | None observed | [10] | xpb1 | SiRe_1128 | S. islandicus | NER-related helicase | None observed | [10] | xpb2 | SiRe_1526 | S. islandicus | NER-related helicase | None observed | [10] | bax1 | SiRe_1524 | S. islandicus | Nuclease | None observed | [10] | uvde | Saci_1096 | S. acidocaldarius | Putative UV endonuclease | No effect on UV survival | [59] | hjc | TK1175 | Tc. kodakarensis | Holliday-junction resolvase | None observed | [36] | hjc | SiRe_1431 | S. islandicus | Holliday-junction resolvase | None observed | [10] | hje | SiRe_930 | S. islandicus | Holliday-junction resolvase | None observed | [10] |
| Group II′ (synthetic lethality) | hje + hjc | SiRe_930 & 1431 | S. islandicus | Holliday-junction resolvases | Double mutant is lethal | [62] |
| Group III (presumed lethal) | radA | TK1899 | Tc. kodakarensis | Recombinase | Lethal (not recovered) | [36] | rad50 | TK2211 | Tc. kodakarensis | DSB end-processing | Lethal (not recovered) | [36] | mre11 | TK2212 | Tc. kodakarensis | DSB end-processing | Lethal (not recovered) | [36] | herA | TK2213 | Tc. kodakarensis | DSB end-processing | Lethal (not recovered) | [36] | nurA | TK2210 | Tc. kodakarensis | DSB end-processing | Lethal (not recovered) | [36] | xpg/fen1 | TK1281 | Tc. kodakarensis | 5′-flap endonuclease | Lethal (not recovered) | [36] | radA | SiRe_1747 | S. islandicus | Recombinase | Lethal | [10] | herA | SiRe_0064 | S. islandicus | Bipolar helicase | Confirmed lethal | [62, 63] | xpg/fen1 | SiRe_1830 | S. islandicus | 5′-flap endonuclease | Lethal | [10] | nurA | SiRe_0061 | S. islandicus | DSB end-processing | Confirmed lethal | [10, 62] | rad50 | SiRe_0062 | S. islandicus | DSB end-processing | Confirmed lethal | [10, 62] | mre11 | SiRe_0063 | S. islandicus | DSB end-processing | Confirmed lethal | [10, 62] | hjm | SiRe_0250 | S. islandicus | DSB end-processing | Lethal | [62, 64] |
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