Journal of Nucleic Acids / 2010 / Article / Tab 1

Review Article

Molecular Mechanisms of the Whole DNA Repair System: A Comparison of Bacterial and Eukaryotic Systems

Table 1

Distribution of DNA repair genes. βˆ— 1 Related human diseases are listed by referencing the following databases: KEGG disease (, GeneCards (, and Online Mendelian Inheritance in Man ( βˆ— 2 Descriptions in the parentheses indicate the subunit organizations of holoenzymes.

Repair pathwaysMolecular functionsT. thermophilusE. coliS. cerevisiaeA. thalianaM. musculusH. sapiensRelated disease βˆ— 1

Direct reversal
PhotoreactivationPhotoreactivationPhr (TTHB102)PhrAPHR1PhrB

AlkyltransferAlkyltransfer or recognitionATL (TTHA1564)Ada, AGT, ATLMGT1MGMTMGMT
alkyltransferAlkBAlkBH1ALKBH2, ALKBH3

Base excision repair
Base excisionRemove ring-saturated or fragmented pyrimidinesEndoIII (TTHA0112)Nth (EndoIII)Ntg1p, Ntg2pAT1G05900Nthl1NTHL1
remove 3-meA, ethenoA, hypoxanthineAlkA (TTHA0329)AlkA, TagAMag1pAT3G12040 (MAG)MpgMPG, (MAG, AAG)
Remove UUDGA (TTHA0718)UngUng1pAT3G18630 uracil DNA glycosylase family proteinUngUngHyper IgM syndromes, autosomal recessive type
Remove U, hydroxymethyl USmug1SMUG1
Remove U or T opposite G at CpG sequencesMbd4MBD4 (MED1)
Remove U, T, or ethenoC opposite GMugTdgTDG
Remove 8-oxoG opposite CMutM (TTHA1806)Fpg (MutM)Ogg1pOGG1Ogg1OGG1Lung cancer
Remove A opposite 8-oxoGMutY (TTHA1898)MutYAT4G12740 (MYH-related)MUTYHMUTYH
Remove thymine glycolNei (EndoVIII)Neil1NEIL1
Remove oxidative products of C, UNEIL2
Not knownNEIL3
Alternative strand incisionIncision 3 ξ…ž of hypoxanthine and uracilEndoV (TTHA1347)Nfi (EndoV)EndoVEndoVEndoV

AP site processing and resynthesisAP endonucleaseEndoIV (Nfo) (TTHA0834)Nfo (EndoIV)Apn1p
AP endonucleaseXthA (ExoIII)Apn2p (Eyh1)ARPApex1APEX1 (APE1, APEX, HAP1, REF1),
AP endonucleaseAT4G36050Apex2APEX2
gap-filling DNA polymerasePolX (TTHA1150)Pol 𝛽 Pol 𝛽
DNA polymerase, 5 ξ…ž flap endonucleasePolI (TTHA1054)PolI
replication and BER in mitochondrial DNAMip1pPol 𝛾 Pol 𝛾
NAD-dependent DNA ligaseLigA (TTHA1097)LigA
ATP-dependent DNA ligaseAT1G66730 (ATP-dependent)Lig3 (ATP-dependent)LIG3 (ATP-dependent)
accessory factor for LIG3 and BERAT1G80420 (putative XRCC1)Xrcc1XRCC1
poly (ADP-ribose) polymerasePARP2Parp1PARP1 (ADPRT)
ADPRT-like enzymeAPP (Arabidopsis poly(ADP-ribose) polymerase)Parp2PARP2 (ADPRTL2)

Nucleotide excision repair
DNA bindingBind damaged DNA in complex with UvrBUvrA (TTHA1440)UvrA
Catalyze unwinding in preincision complexUvrB (TTHA1892)UvrB
Bind disordered DNA as complexRAD4RAD4XpcXPCXeroderma pigmentosum (XP)
Bind disordered DNA as complexRAD23RAD23Rad23b (Hr23b)RAD23B (HR23B)
RAD23B paralogRad23a (Hr23a)RAD23A (HHR23A)
Bind DNA and proteins in preincision complexRAD14XpaXPAXP,

TFIIH subunits 3 ξ…ž - 5 ξ…ž DNA helicase TFIIH subunitSSL2 (RAD25)XPB2Xpb (Ercc3)XPB (ERCC3)XP, Cockayne syndrome (CS), Trichothiodystrophy (TTD)
5 ξ…ž - 3 ξ…ž DNA helicase TFIIH subunitRAD3UVH6Xpd (Ercc2)ERCC2XP, CS, TTD
TFIIH subunit p62TFB1AT1G55750Gtf2h1GTF2H1
TFIIH subunit p44SSL1GTF2H2Gtf2h2GTF2H2
TFIIH subunit p34TFB4AT1G18340Gtf2h3GTF2H3
TFIIH subunit p52TFB2AT4G17020Gtf2h4GTF2H4
TFIIH subunit p8TFB5AT1G12400Gtf2h5GTF2H5 (TTDA)TTD
Kinase subunits of TFIIHKIN28CDKD1;3Cdk7CDK7
Kinase subunits of TFIIHCCL1CYCH;1CcnhCCNH
THIIH subunitTFB3AT4G30820Mnat1 (Mat1)MNAT1 (MAT1)

Strand incision and excision 3 ξ…ž and 5 ξ…ž incision nucleaseUvrC (TTHA1548)UvrC
3 ξ…ž incision nucleaseCho
3 ξ…ž incision nucleaseRAD2UVH3Xpg (Ercc5)ERCC5XP, CS
5 ξ…ž incision nuclease subunitsRAD10ERCC1Ercc1ERCC1XP
5 ξ…ž incision nuclease subunitsRAD1UVH1Xpf (Ercc4)ERCC4XP

Separating two annealed strandsDNA helicaseUvrD (TTHA1427)UvrD
Other factorsTranscription- repair coupling factorMfd (TTHA0889)Mfd
Cockayne syndrome, needed for TC-NERERCC6Csb (Ercc6)CSB (ERCC6)CS, UV-sensitive syndrome (UVS)
Cockayne syndrome, needed for TC-NERAT1G19750Csa (Ckn1, Ercc8)CSA (ERCC8)CS
P127 subunit of DDBDDB1Ddb1DDB1 (XPE)
P48 subunit of DDB, defective in XP-EDDB2Ddb2 (Xpe)DDB2 (XPE)XP
transcription and NERAT5G48120Mms19MMS19

Mismatch repair
Mismatch recognitionDNA-binding ATPaseMutS (TTHA1324)MutSMutS 𝛼
MutS 𝛽
MutS 𝛼
MutS 𝛽
MutS 𝛼
MutS 𝛽
MutS 𝛼
MutS 𝛽
Colorectal cancer, Ovarian cancer

Strand incisionActivation of MutL homologueDNA polymerase III, 𝛽 subunit (TTHA0001)β€”PCNAPCNAPCNAPCNA
Activation of MutL homologueDNA polymerase III, 𝛿 , 𝛿 ξ…ž , 𝛾 , 𝜏 subunits (TTHA0788, 1860, 1952)RFC (RFC1-5) βˆ— 2 RFC (RFC1-5) βˆ— 2 RFC (RFC1-5) βˆ— 2 RFC (RFC1-5) βˆ— 2
Endonuclease ATPaseMutL (TTHA1323)β€”MutL 𝛼 (MLH1/PMS1) MutL 𝛽 (MLH1/MLH2) MutL 𝛾 (MLH1/MLH3)MutL 𝛼 (MLH1/PMS1) MutL 𝛾 (MLH1/MLH3)MutL 𝛼 (MLH1/PMS2) MutL 𝛽 (MLH1/PMS1) MutL 𝛾 (MLH1/MLH3)MutL 𝛼 (MLH1/PMS2) MutL 𝛽 (MLH1/PMS1) MutL 𝛾 (MLH1/MLH3)Colorectal cancer, Endometrial cancer, Ovarian cancer

Match makingATPaseβ€”MutLβ€”β€”β€”β€”
Strand excision 5 ξ…ž - 3 ξ…ž exonucleaseRecJ (TTHA1167)RecJ
3 ξ…ž - 5 ξ…ž exonucleaseExoI (TTHB178)ExoI
5 ξ…ž - 3 ξ…ž exonucleaseExoVII
3 ξ…ž - 5 ξ…ž exonucleaseExoX
5 ξ…ž - 3 ξ…ž exonucleaseEXO1AT1G29630Exo1EXO1
Single-stranded DNA binding proteinSSB (TTHA0244)SSB
Single-stranded DNA binding protein complexRFA (RFA1-3) βˆ— 2 RPA (RPA1-3) βˆ— 2 Rpa (Rpa1-3) βˆ— 2 RPA (RPA1-3) βˆ— 2
DNA helicaseUvrD (TTHA1427)UvrD
Recombination repair

End resection and recombinase loading 5 ξ…ž - 3 ξ…ž exonucleaseRecJ (TTHA1167)RecJ
5 ξ…ž - 3 ξ…ž exonucleaseEXO1AT1G29630Exo1EXO1
5 ξ…ž -flap endonucleaseDNA2AT1G08840Dna2DNA2
RECQ family DNA helicaseRecQSGS1AT1G10930 (RECQ4A)BlmBLMBloom syndrome
Endonuclease, interact with MRN complexSAE2AT3G52115 (ATGR1)CtIP (Rbbp8)CTIP (RBBP8)
SMC-like ATPase, complex with SbcD (Mre11)SbcC (TTHA1288)SbcCRAD50AT2G31970 (RAD50)Rad50RAD50Nijmegen breakage syndrome-like disorder
3 ξ…ž - 5 ξ…ž exonuclease, endonuclease, complex with SbcC (Rad50)SbcD (TTHA1289)SbcDMRE11AT5G54260 (MRE11)Mre11aMRE11AAtaxia telangiectasia -like disorder
Accessory protein for MR complexXRS2AT3G02680 (NBS1)Nbn (Nbs1)NBN (NBS1)Nijmegen breakage syndrome
SMC-like ATPaseRecN (TTHA1525)RecN
Helicase/nuclease complexRecB
Helicase/nuclease complexRecC
Helicase/nuclease complexRecD
5 ξ…ž - 3 ξ…ž exonucleaseRecE
ssDNA annealingRecT
Single-stranded DNA binding proteinSSB (TTHA0244)Ssb
Single-stranded DNA binding protein complexRFA (RFA1-3)RPA (RPA1-3)Rpa (Rpa1-3)RPA (RPA1-3)
ATPase, complex with RecRRecF (TTHA0264)RecF
Recombinase mediator, ssDNA annealingRecO (TTHA0623)RecO
DNA binding, complex with RecF and RecORecR (TTHA1600)RecR
Recombinase mediator, ssDNA annealingRad52-like (TTHA0081)RAD52Rad52RAD52
Recombinase mediatorAT5G01630 (BRCA2B)Brca2BRCA2Pancreatic cancer, Ovarian cancer, Breast cancer, Fanconi anemia
RAD54 family DNA translocase, recombinase mediatorRAD54AT3G19210 (ATRad54)Rad54lRAD54LAdenocarcinoma, Non-Hodgkin lymphoma
RAD54 family DNA translocase, recombinase mediatorRDH54Rad54bRAD54BColon cancer, Non-Hodgkin lymphoma
RAD51-like, recombinase mediatorAT5G64520 (XRCC2)Xrcc2XRCC2Breast cancer
RAD51-like, recombinase mediatorAT5G57450 (XRCC3)Xrcc3XRCC3Breast cancer, Melanoma
RAD51-like, recombinase mediatorRAD57AT2G28560 (RAD51B)Rad51l1RAD51L1Uterine leiomyoma
RAD51-like, recombinase mediatorAT2G45280 (RAD51C)Rad51cRAD51CFanconi anemia-like disorder, Breast-Ovarian cancer
RAD51-like, recombinase mediatorRAD55AT1G07745 (RAD51D)Rad51l3RAD51L3

Strand exchangeRecombinaseRecA (TTHA1818)RecAAT2G19490 (recA)
RecombinaseRAD51AT5G20850 (ATRAD51)Rad51RAD51

Branch migrationBranch migration complexRuvA (TTHA0291)RuvA
Branch migration complexRuvB (TTHA0406)RuvB
DNA helicaseRecG (TTHA1266)RecGAT2G01440 (RecG)
RecA-like ATPaseRadA/Sms (TTHA0541)RadA/SmsAT5G50340
RAD54 family DNA translocase, recombinase mediatorRAD54AT3G19210 (ATRad54)Rad54lRAD54LAdenocarcinoma, Non-Hodgkin lymphoma
RAD54 family DNA translocase, recombinase mediatorRDH54Rad54bRAD54BColon cancer, Non-Hodgkin lymphoma
RECQ family DNA helicaseRecQSGS1AT1G10930 (RECQ4A)BlmBLMBloom syndrome
RECQ family DNA helicaseWrnWRNWerner syndrome
RECQ family DNA helicaseAT1G31360 (RECQL2)RecqlRECQL
RECQ family DNA helicaseMPH1AT1G35530FancmFANCMFanconi anemia

Holliday junction resolutionHJ resolvaseRuvC (TTHA1090)RuvC
HJ resolvaseRusA
HJ resolvaseYEN1AT1G01880Gen1GEN1
Structure-specific endonucleaseMUS81AT4G30870 (MUS81)Mus81MUS81
complex with MUS81MMS4AT2G22140 (ATEME1B)Eme1EME1
Structure-specific endonucleaseRAD1AT5G41150 (UVH1)Ercc4ERCC4Xeroderma pigmentosum
complex with ERCC4 (RAD1)RAD10AT3G05210 (ERCC1)Ercc1ERCC1Cerebro-oculo-facio-skeletal syndrome
HJ resolvaseSLX1AT2G30350Slx1 (Giyd2)SLX1 (GIYD2)
Accessory protein for structure-specific nucleasesSLX4Slx4 (Btbd12)SLX4 (BTBD12)

Anti-recombinationRecombinase inhibitorRecX (TTHA0848)RecXAT3G13226 (RecX)
DNA helicaseUvrD (TTHA1427)UvrDSRS2AT4G25120
Structure-specific endonucleaseMutS2 (TTHA1645)AT1G65070 (MutS2)

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