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]