Table 1.
DNA repair protein-coding genes from reconstructed and minimal genomes.
| Structural Superfamily | Process | E. coli | Human | Function a |
|---|---|---|---|---|
| LUCA genome reconstruction: Mirkin et al. [89] b | ||||
| O6-methylguanine-DNA–protein-cysteine methyltransferase | DR | Ada, Ogt, Atl1 | MGMT | exocyclic O-alkyltransferases |
| NUDIX hydrolases | nucleotide pool sanitization | MutT | MTH1 | oxidized NTP/dNTP hydrolysis |
| Uracil–DNA glycosylase | BER | Ung, Mug | UNG, TDG, SMUG1 | uracil–DNA glycosylase |
| Helix–hairpin–helix | BER | Nth, MutY, AlkA | NTHL1, OGG1, MUTYH, MBD4 | DNA glycosylases for various lesions |
| TIM barrel | BER | Nfo | – | AP endonuclease |
| 5′ → 3′ exonucleases | various | PolA, Exo | FEN1 | normal and damaged DNA degradation; flap endonucleases |
| Family A DNA polymerases; DnaQ-like 3′ → 5′ exonucleases |
repair DNA synthesis, proofreading | PolA | POLN, POLQ | DNA polymerases; proofreading activity may or may not be present |
| DEAD-box helicases | NER, recombination repair | UvrD, RecB | PARPBP1 | monomeric DNA helicases involved in recombination, replication, and repair |
| ATP-binding cassette transporters | MMR | MutS | MSH2–MSH6 | mismatch detection |
| S5-like fold;histidine kinase-, DNA gyrase B-, and HSP90-like ATPase | MMR | MutL | MLH1, MLH3, PMS1, PMS2 | mismatch signal transduction |
| P-loop NTPases | recombination repair; non-homologous end joining | SbcC | SMC3, RAD50 | DSB recognition and/or processing |
| Calcineurin-like phosphoesterases | recombination repair; non-homologous end joining | SbcD | MRE11 | DSB recognition and/or processing |
| Haloacid dehalogenases | recombination repair | RecJ | – | 5′ → 3′ exonucleases |
| P-loop NTPases | recombination repair | RecA | RAD51, DMC1 | strand exchange |
| LUCA genome reconstruction: Weiss et al. [12] | ||||
| PDDEXK nucleases | specialized mismatch repair | Vsr | – | T:G mismatch cleavage |
| PDDEXK nucleases | specialized mismatch repair | – | – | archaeal mismatch endonucleases (NucS/ EndoMS) |
| RNase H-like | AER | Nfi | ENDOV | deoxyinosine 3′-endonuclease |
| P-loop NTPases | recombination repair | RuvB | WRNIP1 | hexameric DNA helicases driving branch migration during recombination |
| Family Y DNA polymerases | translesion synthesis | DinB, UmuC | POLH, POLI, POLK, REV1 | DNA polymerases capable of translesion synthesis |
| DEAD-box helicases | various | RecQ | BLM, WRN | monomeric DNA helicases involved in recombination, replication, and repair |
| DEAD-box helicases | unknown, DNA damage-induced | Lhr | ASCC3 | DNA damage-inducible DNA:RNA helicase |
| DEAD-box helicases | NER | RadD (YejH) | ERCC3 | DNA helicase that functions in transcription and NER |
| DNA topoisomerases, subtype IA | possibly break repair and chromatin remodeling/maintenance | – | – | archaeal reverse gyrase; introduces positive supercoils into DNA |
| Radical_SAM | ? | – | – | putative DNA modification/repair FeS-containing radical SAM protein |
| Minimal genome: Glass et al. [87] c | ||||
| Uracil–DNA glycosylase | BER | Ung | UNG | uracil–DNA glycosylase |
| TIM barrel | BER | Nfo | – | AP endonuclease |
| ATP-binding cassette transporters | NER | UvrA | – | NER lesion search |
| ATP-binding cassette transporters | NER | UvrB | – | NER lesion search |
| RNase H-like | NER | UvrC | – | NER nuclease |
| Minimal genome: Venetz et al. [88] d | ||||
| dUTPases | nucleotide pool sanitization | Dut | DUT | trimeric dUTP diphosphatase |
| Uracil–DNA glycosylase | BER | Ung | UNG | uracil–DNA glycosylase |
| Haloacid dehalogenases | recombination repair | RecJ | – | 5′ → 3′ exonucleases |
a Genes with an essential function in replication are not included except DNA polymerase I (PolA); b LUCA1.0 from [89]; c Minimal genome reconstruction based on combined data from [82,83,84,85,87]. The experimental gene essentiality data were from Mycoplasma genitalium, M. pneumoniae and Bacillus subtilis genomes; d Minimized Caulobacter crescentus genome.