Table 1.
Distribution of DNA repair genes. ∗1Related human diseases are listed by referencing the following databases: KEGG disease (http://www.genome.jp/kegg/disease/), GeneCards (http://www.genecards.org/), and Online Mendelian Inheritance in Man (http://www.ncbi.nlm.nih.gov/omim). ∗2Descriptions in the parentheses indicate the subunit organizations of holoenzymes.
| Repair pathways | Molecular functions | T. thermophilus | E. coli | S. cerevisiae | A. thaliana | M. musculus | H. sapiens | Related disease∗1 |
|---|---|---|---|---|---|---|---|---|
| Direct reversal | ||||||||
| Photoreactivation | Photoreactivation | Phr (TTHB102) | PhrA | PHR1 | PhrB | |||
|
| ||||||||
| Alkyltransfer | Alkyltransfer or recognition | ATL (TTHA1564) | Ada, AGT, ATL | MGT1 | MGMT | MGMT | ||
| alkyltransfer | AlkB | AlkBH1 | ALKBH2, ALKBH3 | |||||
|
| ||||||||
|
| ||||||||
| Base excision repair | ||||||||
| Base excision | Remove ring-saturated or fragmented pyrimidines | EndoIII (TTHA0112) | Nth (EndoIII) | Ntg1p, Ntg2p | AT1G05900 | Nthl1 | NTHL1 | |
| remove 3-meA, ethenoA, hypoxanthine | AlkA (TTHA0329) | AlkA, TagA | Mag1p | AT3G12040 (MAG) | Mpg | MPG, (MAG, AAG) | ||
| Remove U | UDGA (TTHA0718) | Ung | Ung1p | AT3G18630 uracil DNA glycosylase family protein | Ung | Ung | Hyper IgM syndromes, autosomal recessive type | |
| UDGB (TTHA1149) | ||||||||
| Remove U, hydroxymethyl U | Smug1 | SMUG1 | ||||||
| Remove U or T opposite G at CpG sequences | Mbd4 | MBD4 (MED1) | ||||||
| Remove U, T, or ethenoC opposite G | Mug | Tdg | TDG | |||||
| Remove 8-oxoG opposite C | MutM (TTHA1806) | Fpg (MutM) | Ogg1p | OGG1 | Ogg1 | OGG1 | Lung cancer | |
| Remove A opposite 8-oxoG | MutY (TTHA1898) | MutY | AT4G12740 (MYH-related) | MUTYH | MUTYH | |||
| Remove thymine glycol | Nei (EndoVIII) | Neil1 | NEIL1 | |||||
| Remove oxidative products of C, U | NEIL2 | |||||||
| Not known | NEIL3 | |||||||
| Alternative strand incision | Incision 3′ of hypoxanthine and uracil | EndoV (TTHA1347) | Nfi (EndoV) | EndoV | EndoV | EndoV | ||
|
| ||||||||
| AP site processing and resynthesis | AP endonuclease | EndoIV (Nfo) (TTHA0834) | Nfo (EndoIV) | Apn1p | ||||
| AP endonuclease | XthA (ExoIII) | Apn2p (Eyh1) | ARP | Apex1 | APEX1 (APE1, APEX, HAP1, REF1), | |||
| AP endonuclease | AT4G36050 | Apex2 | APEX2 | |||||
| gap-filling DNA polymerase | PolX (TTHA1150) | Polβ | Polβ | |||||
| DNA polymerase, 5′ flap endonuclease | PolI (TTHA1054) | PolI | ||||||
| replication and BER in mitochondrial DNA | Mip1p | Polγ | Polγ | |||||
| NAD-dependent DNA ligase | LigA (TTHA1097) | LigA | ||||||
| ATP-dependent DNA ligase | AT1G66730 (ATP-dependent) | Lig3 (ATP-dependent) | LIG3 (ATP-dependent) | |||||
| accessory factor for LIG3 and BER | AT1G80420 (putative XRCC1) | Xrcc1 | XRCC1 | |||||
| poly (ADP-ribose) polymerase | PARP2 | Parp1 | PARP1 (ADPRT) | |||||
| ADPRT-like enzyme | APP (Arabidopsis poly(ADP-ribose) polymerase) | Parp2 | PARP2 (ADPRTL2) | |||||
|
| ||||||||
|
| ||||||||
| Nucleotide excision repair | ||||||||
| DNA binding | Bind damaged DNA in complex with UvrB | UvrA (TTHA1440) | UvrA | |||||
| Catalyze unwinding in preincision complex | UvrB (TTHA1892) | UvrB | ||||||
| Bind disordered DNA as complex | RAD4 | RAD4 | Xpc | XPC | Xeroderma pigmentosum (XP) | |||
| Bind disordered DNA as complex | RAD23 | RAD23 | Rad23b (Hr23b) | RAD23B (HR23B) | ||||
| RAD23B paralog | Rad23a (Hr23a) | RAD23A (HHR23A) | ||||||
| Bind DNA and proteins in preincision complex | RAD14 | Xpa | XPA | XP, | ||||
|
| ||||||||
| TFIIH subunits | 3′-5′ DNA helicase TFIIH subunit | SSL2 (RAD25) | XPB2 | Xpb (Ercc3) | XPB (ERCC3) | XP, Cockayne syndrome (CS), Trichothiodystrophy (TTD) | ||
| 5′-3′ DNA helicase TFIIH subunit | RAD3 | UVH6 | Xpd (Ercc2) | ERCC2 | XP, CS, TTD | |||
| TFIIH subunit p62 | TFB1 | AT1G55750 | Gtf2h1 | GTF2H1 | ||||
| TFIIH subunit p44 | SSL1 | GTF2H2 | Gtf2h2 | GTF2H2 | ||||
| TFIIH subunit p34 | TFB4 | AT1G18340 | Gtf2h3 | GTF2H3 | ||||
| TFIIH subunit p52 | TFB2 | AT4G17020 | Gtf2h4 | GTF2H4 | ||||
| TFIIH subunit p8 | TFB5 | AT1G12400 | Gtf2h5 | GTF2H5 (TTDA) | TTD | |||
| Kinase subunits of TFIIH | KIN28 | CDKD1;3 | Cdk7 | CDK7 | ||||
| Kinase subunits of TFIIH | CCL1 | CYCH;1 | Ccnh | CCNH | ||||
| THIIH subunit | TFB3 | AT4G30820 | Mnat1 (Mat1) | MNAT1 (MAT1) | ||||
|
| ||||||||
| Strand incision and excision | 3′ and 5′ incision nuclease | UvrC (TTHA1548) | UvrC | |||||
| 3′ incision nuclease | Cho | |||||||
| 3′ incision nuclease | RAD2 | UVH3 | Xpg (Ercc5) | ERCC5 | XP, CS | |||
| 5′ incision nuclease subunits | RAD10 | ERCC1 | Ercc1 | ERCC1 | XP | |||
| 5′ incision nuclease subunits | RAD1 | UVH1 | Xpf (Ercc4) | ERCC4 | XP | |||
|
| ||||||||
| Separating two annealed strands | DNA helicase | UvrD (TTHA1427) | UvrD | |||||
| Other factors | Transcription- repair coupling factor | Mfd (TTHA0889) | Mfd | |||||
| Cockayne syndrome, needed for TC-NER | ERCC6 | Csb (Ercc6) | CSB (ERCC6) | CS, UV-sensitive syndrome (UVS) | ||||
| Cockayne syndrome, needed for TC-NER | AT1G19750 | Csa (Ckn1, Ercc8) | CSA (ERCC8) | CS | ||||
| P127 subunit of DDB | DDB1 | Ddb1 | DDB1 (XPE) | |||||
| P48 subunit of DDB, defective in XP-E | DDB2 | Ddb2 (Xpe) | DDB2 (XPE) | XP | ||||
| transcription and NER | AT5G48120 | Mms19 | MMS19 | |||||
|
| ||||||||
|
| ||||||||
| Mismatch repair | ||||||||
| Mismatch recognition | DNA-binding ATPase | MutS (TTHA1324) | MutS | MutSα
(MSH2/MSH6) MutSβ (MSH2/MSH3) |
MutSα
(MSH2/MSH6) MutSβ (MSH2/MSH3) |
MutSα
(MSH2/MSH6) MutSβ (MSH2/MSH3) |
MutSα
(MSH2/MSH6) MutSβ (MSH2/MSH3) |
Colorectal cancer, Ovarian cancer |
|
| ||||||||
| Strand incision | Activation of MutL homologue | DNA polymerase III, β subunit (TTHA0001) | — | PCNA | PCNA | PCNA | PCNA | |
| Activation of MutL homologue | DNA polymerase III, δ, δ′, γ, τ subunits (TTHA0788, 1860, 1952) | RFC (RFC1-5)∗2 | RFC (RFC1-5)∗2 | RFC (RFC1-5)∗2 | RFC (RFC1-5)∗2 | |||
| Endonuclease ATPase | MutL (TTHA1323) | — | MutLα (MLH1/PMS1) MutLβ (MLH1/MLH2) MutLγ (MLH1/MLH3) | MutLα (MLH1/PMS1) MutLγ (MLH1/MLH3) | MutLα (MLH1/PMS2) MutLβ (MLH1/PMS1) MutLγ (MLH1/MLH3) | MutLα (MLH1/PMS2) MutLβ (MLH1/PMS1) MutLγ (MLH1/MLH3) | Colorectal cancer, Endometrial cancer, Ovarian cancer | |
|
| ||||||||
| Match making | ATPase | — | MutL | — | — | — | — | |
| Strand excision | 5′-3′ exonuclease | RecJ (TTHA1167) | RecJ | |||||
| 3′-5′ exonuclease | ExoI (TTHB178) | ExoI | ||||||
| 5′-3′ exonuclease | ExoVII | |||||||
| 3′-5′ exonuclease | ExoX | |||||||
| 5′-3′ exonuclease | EXO1 | AT1G29630 | Exo1 | EXO1 | ||||
| Single-stranded DNA binding protein | SSB (TTHA0244) | SSB | ||||||
| Single-stranded DNA binding protein complex | RFA (RFA1-3)∗2 | RPA (RPA1-3)∗2 | Rpa (Rpa1-3)∗2 | RPA (RPA1-3)∗2 | ||||
| DNA helicase | UvrD (TTHA1427) | UvrD | ||||||
| Recombination repair | ||||||||
|
| ||||||||
| End resection and recombinase loading | 5′-3′ exonuclease | RecJ (TTHA1167) | RecJ | |||||
| 5′-3′ exonuclease | EXO1 | AT1G29630 | Exo1 | EXO1 | ||||
| 5′-flap endonuclease | DNA2 | AT1G08840 | Dna2 | DNA2 | ||||
| RECQ family DNA helicase | RecQ | SGS1 | AT1G10930 (RECQ4A) | Blm | BLM | Bloom syndrome | ||
| Endonuclease, interact with MRN complex | SAE2 | AT3G52115 (ATGR1) | CtIP (Rbbp8) | CTIP (RBBP8) | ||||
| SMC-like ATPase, complex with SbcD (Mre11) | SbcC (TTHA1288) | SbcC | RAD50 | AT2G31970 (RAD50) | Rad50 | RAD50 | Nijmegen breakage syndrome-like disorder | |
| 3′-5′ exonuclease, endonuclease, complex with SbcC (Rad50) | SbcD (TTHA1289) | SbcD | MRE11 | AT5G54260 (MRE11) | Mre11a | MRE11A | Ataxia telangiectasia -like disorder | |
| Accessory protein for MR complex | XRS2 | AT3G02680 (NBS1) | Nbn (Nbs1) | NBN (NBS1) | Nijmegen breakage syndrome | |||
| SMC-like ATPase | RecN (TTHA1525) | RecN | ||||||
| Helicase/nuclease complex | RecB | |||||||
| Helicase/nuclease complex | RecC | |||||||
| Helicase/nuclease complex | RecD | |||||||
| 5′-3′ exonuclease | RecE | |||||||
| ssDNA annealing | RecT | |||||||
| Single-stranded DNA binding protein | SSB (TTHA0244) | Ssb | ||||||
| Single-stranded DNA binding protein complex | RFA (RFA1-3) | RPA (RPA1-3) | Rpa (Rpa1-3) | RPA (RPA1-3) | ||||
| ATPase, complex with RecR | RecF (TTHA0264) | RecF | ||||||
| Recombinase mediator, ssDNA annealing | RecO (TTHA0623) | RecO | ||||||
| DNA binding, complex with RecF and RecO | RecR (TTHA1600) | RecR | ||||||
| Recombinase mediator, ssDNA annealing | Rad52-like (TTHA0081) | RAD52 | Rad52 | RAD52 | ||||
| Recombinase mediator | AT5G01630 (BRCA2B) | Brca2 | BRCA2 | Pancreatic cancer, Ovarian cancer, Breast cancer, Fanconi anemia | ||||
| RAD54 family DNA translocase, recombinase mediator | RAD54 | AT3G19210 (ATRad54) | Rad54l | RAD54L | Adenocarcinoma, Non-Hodgkin lymphoma | |||
| RAD54 family DNA translocase, recombinase mediator | RDH54 | Rad54b | RAD54B | Colon cancer, Non-Hodgkin lymphoma | ||||
| RAD51-like, recombinase mediator | AT5G64520 (XRCC2) | Xrcc2 | XRCC2 | Breast cancer | ||||
| RAD51-like, recombinase mediator | AT5G57450 (XRCC3) | Xrcc3 | XRCC3 | Breast cancer, Melanoma | ||||
| RAD51-like, recombinase mediator | RAD57 | AT2G28560 (RAD51B) | Rad51l1 | RAD51L1 | Uterine leiomyoma | |||
| RAD51-like, recombinase mediator | AT2G45280 (RAD51C) | Rad51c | RAD51C | Fanconi anemia-like disorder, Breast-Ovarian cancer | ||||
| RAD51-like, recombinase mediator | RAD55 | AT1G07745 (RAD51D) | Rad51l3 | RAD51L3 | ||||
|
| ||||||||
| Strand exchange | Recombinase | RecA (TTHA1818) | RecA | AT2G19490 (recA) | ||||
| Recombinase | RAD51 | AT5G20850 (ATRAD51) | Rad51 | RAD51 | ||||
|
| ||||||||
| Branch migration | Branch migration complex | RuvA (TTHA0291) | RuvA | |||||
| Branch migration complex | RuvB (TTHA0406) | RuvB | ||||||
| DNA helicase | RecG (TTHA1266) | RecG | AT2G01440 (RecG) | |||||
| RecA-like ATPase | RadA/Sms (TTHA0541) | RadA/Sms | AT5G50340 | |||||
| RAD54 family DNA translocase, recombinase mediator | RAD54 | AT3G19210 (ATRad54) | Rad54l | RAD54L | Adenocarcinoma, Non-Hodgkin lymphoma | |||
| RAD54 family DNA translocase, recombinase mediator | RDH54 | Rad54b | RAD54B | Colon cancer, Non-Hodgkin lymphoma | ||||
| RECQ family DNA helicase | RecQ | SGS1 | AT1G10930 (RECQ4A) | Blm | BLM | Bloom syndrome | ||
| RECQ family DNA helicase | Wrn | WRN | Werner syndrome | |||||
| RECQ family DNA helicase | AT1G31360 (RECQL2) | Recql | RECQL | |||||
| RECQ family DNA helicase | MPH1 | AT1G35530 | Fancm | FANCM | Fanconi anemia | |||
|
| ||||||||
| Holliday junction resolution | HJ resolvase | RuvC (TTHA1090) | RuvC | |||||
| HJ resolvase | RusA | |||||||
| HJ resolvase | YEN1 | AT1G01880 | Gen1 | GEN1 | ||||
| Structure-specific endonuclease | MUS81 | AT4G30870 (MUS81) | Mus81 | MUS81 | ||||
| complex with MUS81 | MMS4 | AT2G22140 (ATEME1B) | Eme1 | EME1 | ||||
| Structure-specific endonuclease | RAD1 | AT5G41150 (UVH1) | Ercc4 | ERCC4 | Xeroderma pigmentosum | |||
| complex with ERCC4 (RAD1) | RAD10 | AT3G05210 (ERCC1) | Ercc1 | ERCC1 | Cerebro-oculo-facio-skeletal syndrome | |||
| HJ resolvase | SLX1 | AT2G30350 | Slx1 (Giyd2) | SLX1 (GIYD2) | ||||
| Accessory protein for structure-specific nucleases | SLX4 | Slx4 (Btbd12) | SLX4 (BTBD12) | |||||
|
| ||||||||
| Anti-recombination | Recombinase inhibitor | RecX (TTHA0848) | RecX | AT3G13226 (RecX) | ||||
| DNA helicase | UvrD (TTHA1427) | UvrD | SRS2 | AT4G25120 | ||||
| Structure-specific endonuclease | MutS2 (TTHA1645) | AT1G65070 (MutS2) | ||||||