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Table 1 Major Conserved Metazoan DDR Genes

From: Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers

Gene

Gene Description

KO

#

Cel

Dme

Hsa

Direct Reversal (DR)

 PHRB

deoxyribodipyrimidine photo lyase

K01669

4

 

X

 

 ALKBH1

alkylated DNA repair protein

K10765

1

X

X

X

 MGMT

alkylated DNA repair protein

K00567

1

X

X

X

Base Excision Repair (BER)

 FPG

formamidopyrimidine-DNA glycosylase

K10563

2

   

 NEIL1/2/3

endonuclease VIII like 1,2, or 3

K10567/8/9

0

  

X

 MPG

DNA-3-methyladenine glycosylase

K03652

0

  

X

 OGG1

8-oxoguanine DNA glycosylase

K03660

3

 

X

X

 AlkD

DNA alkylation repair enzyme

K00000

2

   

 MUTYH

mutY homolog

K03575

2

  

X

 SMUG1

ss-selective monofunctional uracil DNA glycosylase

K10800

0

  

X

 MBD4

methyl-CpG-binding domain protein 4

K10801

0

  

X

 NTHL1

nth endonuclease III-like 1

K10773

1

X

X

X

 TDG/MUG

TDG/ MUG DNA glycosylase family protein

K20813

4

 

X

X

 UNG1

mitochondrial uracil DNA glycosylase

K03648

2

X

 

X

 UNG2

nuclear uracil DNA glycosylase

K03648

4

X

 

X

 APEX1

AP endonuclease 1

K10771

4

X

X

X

 APEX2

AP endonuclease 2

K10772

2

  

X

 PARP1

poly (ADP-ribose) polymerase family, member 1

K10798

4

X

X

X

 XRCC1

X-ray repair complementing defective repair in Chinese hamster cells 1

K10803

2

 

X

X

 TDP1

tyrosyl-DNA phosphodiesterase 1

K10862

2

 

X

X

 FEN1

flap endonuclease-1

K04799

3

X

X

X

 POLB

DNA polymerase beta

K02330

2

  

X

 LIG3

DNA ligase 3

K10776

2

  

X

Nucleotide Excision Repair (NER)

 RBX1

RING-box protein 1

K03868

4

X

X

X

 CUL4

cullin 4

K10609

4

X

X

X

 DDB1, XPE

xeroderma pigmentosum group E-complementing protein

K10610

3

X

X

X

 DDB2

DNA damage binding protein 2

K10140

2

  

X

 CSA, ERCC8

excision repair cross-complementing rodent repair deficiency, complementation group 8

K10570

2

X

X

X

 XPC

xeroderma pigmentosum group C-complementing protein

K10838

2

X

X

X

 RAD23

UV excision repair protein RAD23

K10839

4

X

X

X

 CETN2

centrin-2

K10840

4

  

X

 XPA

xeroderma pigmentosum group A-complementing protein

K10847

2

X

X

X

 ERCC1

excision repair cross-complementing rodent repair deficiency, complementation group 1

K10849

2

X

X

X

 ERCC2, XPD

xeroderma pigmentosum group D-complementing protein

K10844

2

X

X

X

 ERCC3, XPB

xeroderma pigmentosum group B-complementing protein

K10843

3

X

X

X

 ERCC4, XPF

xeroderma pigmentosum group F-complementing protein

K10848

2

X

X

X

 ERCC5, XPG

xeroderma pigmentosum group G-complementing protein

K10846

2

X

X

X

 ERCC6, CSB

excision repair cross-complementing rodent repair deficiency, complementation group 6

K10841

2

X

 

X

 TFIIH1

transcription initiation factor TFIIH subunit 1

K03141

1

X

X

X

 TFIIH2

transcription initiation factor TFIIH subunit 2

K03142

2

X

X

X

 TFIIH3

transcription initiation factor TFIIH subunit 3

K03143

1

X

X

X

 TFIIH4

transcription initiation factor TFIIH subunit 4

K03144

1

X

X

X

 MMS19

DNA repair/transcription protein MET18/MMS19

K15075

1

X

X

X

 RPB1

DNA-directed RNA polymerase II subunit RPB1

K03006

4

X

X

X

 RPB2

DNA-directed RNA polymerase II subunit RPB2

K03010

2

X

X

X

 RPB3

DNA-directed RNA polymerase II subunit RPB3

K03011

1

X

X

X

 RPB4

DNA-directed RNA polymerase II subunit RPB4

K03012

2

X

X

X

 RPB5

DNA-directed RNA polymerases I, II, and III subunit RPABC1

K03013

4

X

X

X

 RPB6

DNA-directed RNA polymerases I, II, and III subunit RPABC2

K03014

4

X

X

X

 RPB7

DNA-directed RNA polymerase II subunit RPB7

K03015

2

X

X

X

 RPB8

DNA-directed RNA polymerases I, II, and III subunit RPABC3

K03016

2

X

X

X

 RPB11

DNA-directed RNA polymerase II subunit RPB11

K03008

2

X

X

X

 RPB12

DNA-directed RNA polymerases I, II, and III subunit RPABC4

K03009

2

X

X

X

Alternative Excision Repair (AER)

 UVDE

UV DNA damage endonuclease

K13281

2

   

 SMC6

structural maintenance of chromosomes 6

K22804

4

 

X

X

 RAD51

DNA repair protein RAD51

K04482

4

X

X

X

 RAD54

DNA repair and recombination protein RAD54 and RAD54-like protein

K10875

2

X

X

X

 RAD54L2

RAD54-like protein 2

K10876

3

X

X

X

 EXO1

exonuclease 1

K10746

2

X

X

X

 FEN1

flap endonuclease-1

K04799

3

X

X

X

Cross Pathway

 LIG1

DNA ligase 1

K10747

2

X

X

X

 LIGK

DNA ligase (ATP)

K00000

4

   

 PCNA

proliferating cell nuclear antigen

K04802

4

X

X

X

 PNKP

bifunctional polynucleotide phosphatase/kinase

K08073

4

X

X

X

 HMGB1

high mobility group protein B1

K10802

2

 

X

X

 RFC1

replication factor C subunit 1

K10754

4

X

X

X

 RFC2

replication factor C subunit 2 of RFC2_4

K10755

4

X

X

X

 RFC4

replication factor C subunit 4 of RFC2_4

K10755

2

X

X

X

 RFC3_5

replication factor C subunit 3_5

K10756

2

X

X

X

 RPA1

replication protein A1

K07466

4

X

X

X

 RPA2

replication protein A2

K10739

3

X

X

X

 RPA3

replication protein A3

K10740

2

 

X

X

Mismatch Repair (MMR)

 MSH2

DNA mismatch repair protein MSH2

K08735

1

X

X

X

 MSH3

DNA mismatch repair protein MSH3

K08736

0

  

X

 MSH6

DNA mismatch repair protein MSH6

K08737

2

X

X

X

 MSH4

DNA mismatch repair protein MSH4, canonically meiotic

K08740

2

X

X

X

 MSH5

DNA mismatch repair protein MSH5, canonically meiotic

K08741

2

X

X

X

 PMS2

DNA mismatch repair protein PMS2

K10858

2

X

X

X

 MLH1

DNA mismatch repair protein MLH1

K08734

2

X

X

X

 MLH3

DNA mismatch repair protein MLH3

K08739

0

  

X

 EXO1

exonuclease 1

K10746

2

X

X

X

Homologous Recombination (HR)

 RAD50

DNA repair protein RAD50

K10866

4

X

X

X

 MRE11

double-strand break repair protein MRE11

K10865

2

X

X

X

 NBS1

nibrin

K10867

0

 

X

X

 ATM

ataxia telangectasia mutated family protein

K04728

2

X

X

X

 RAD51

DNA repair protein RAD51

K04482

4

X

X

X

 RAD51L1

RAD51-like protein 1

K10869

2

  

X

 RAD51L2

RAD51-like protein 2

K10870

2

 

X

X

 RAD52

DNA repair protein RAD52

K10873

0

  

X

 BRCA2

breast cancer 2 susceptibility protein

K08775

0

  

X

 RAD54

DNA repair and recombination protein RAD54 and RAD54-like protein

K10875

2

X

X

X

 RAD54L2

RAD54-like protein 2

K10876

3

X

X

X

 EME1

crossover junction endonuclease EME1

K10882

1

 

X

X

 MUS81

crossover junction endonuclease MUS81

K08991

2

X

X

X

 RECQ1

ATP-dependent DNA helicase Q1

K10899

4

X

 

X

 BLM

Bloom’s syndrome DNA helicase

K10901

5

X

X

X

 RECQL5

ATP-dependent DNA helicase Q5

K10902

2

X

X

X

 RMI1

RecQ-mediated genome instability protein 1

K10990

1

X

 

X

 TOP3A

DNA topoisomerase 3 alpha

K03165

2

X

X

X

 TOP3B

DNA topoisomerase 3 beta

K03165

2

X

X

X

 SLX1

structure specific endonuclease subunit SLX1

K15078

2

X

X

X

 SLX4

structure-specific endonuclease subunit SLX4

K10484

2

  

X

 GEN1

Gen homolog 1, endonuclease

K15338

2

X

X

X

Non-Homologous End Joining (NHEJ)

 KU70

ATP-dependent DNA helicase 2 subunit 1

K10884

4

X

X

X

 KU80

ATP-dependent DNA helicase 2 subunit 2

K10885

4

X

X

X

 DNAPKcs

DNA-dependent protein kinase catalytic subunit

K06642

3

  

X

 ARTEMIS

DNA cross-link repair 1C protein

K10887

4

  

X

 APTX

aprataxin

K10863

2

 

X

X

 APLF

aprataxin and PNK-like factor

K13295

8

 

X

X

 POLL

DNA polymerase lambda

K03512

6

  

X

 XLF

non-homologous end-joining factor 1

K10980

2

  

X

 XRCC4

DNA-repair protein XRCC4

K10886

3

  

X

 LIG4

DNA ligase 4

K10777

1

  

X

Replicative Polymerases (Pol)

 POLA1

DNA polymerase alpha subunit A

K02320

2

X

X

X

 POLA2

DNA polymerase alpha subunit B

K02321

2

X

X

X

 POLD1

DNA polymerase delta subunit 1

K02327

2

X

X

X

 POLD2

DNA polymerase delta subunit 2

K02328

2

X

X

X

 POLE1

DNA polymerase epsilon subunit 1

K02324

2

X

X

X

 POLE2

DNA polymerase epsilon subunit 2

K02325

2

X

X

X

 POLG1

DNA polymerase gamma 1

K02332

2

X

X

X

 POLG2

DNA polymerase gamma 2

K02333

2

 

X

X

Translesion Synthesis (TLS) Polymerases (Pol)

 POLH

DNA polymerase eta

K03509

2

X

X

X

 POLK

DNA polymerase kappa

K03511

2

X

 

X

 POLQ

DNA polymerase theta

K02349

1

X

X

X

 REV1

DNA polymerase zeta, Rev1 subunit

K03515

2

X

X

X

 REV7

DNA polymerase zeta, Rev7 subunit

K03508

2

  

X

 REV3L

DNA polymerase zeta, Rev3-like subunit

K02350

2

X

X

X

  1. Genes are classified into the ten categories shown in Fig. 1; some genes appear in more than one category. See Additional file 1 for specific A. vaga locus identifiers and other details. KO: KEGG Ontology accession; #: copy number in A. vaga; Cel: C. elegans; Dme: D. melanogaster; Hsa: H. sapiens. An “X” indicates an ortholog is present in the KEGG Orthology Database for the indicated species