Table of genes encoded by the Arabidopsis thaliana complete nuclear genome that have been predicted and/or experimentally shown to be involved in DNA repair.

 

Pathway

Protein Name(s)

Conserved Biochemical Activity(s).

Gene Ids

Chromosome#_Gene ID

Derived from Plastid Lineage

Derived from Mitochondrial

Lineage

 

A. thaliana Mutants and/or Gene Name

A. thaliana specific Comments

 

 

 

Direct Repair

 

 

 

 

 

 

 

 

 

 

 

 

 

Photoreactivation

 

 

 

 

 

 

Photolyase ClassI Family

Photolyase (CPDs or 6-4s) or blue-light receptor

4_hy4

-

-

CRY1/HY4

a blue light photoreceptor [1]

"

"

3_MSJ11.2

-

-

6-4 PHR

6-4 photolyase [2].  Related to human CRY

"

"

1_F19P19.14

+

-

CRY2/PHH1

Blue-light photoreceptor [3]

"

"

5_F6A4.60

+

-

-

Closely related to cyanobacterial Phr homologs.

"

"

2_T30B22.11

+

-

PHR2

Closely related to cyanobacterial Phr homologs.

Photolyase ClassII Family

Photolyase (CPDs or 6-4s)

1_F5O11.5

-

-

PHR1/ UVR2

CPD photolyase [4]

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Base Excision Repair

 

 

 

 

 

 

 

 

 

 

 

 

 

Ung

Glycosylase (Uracil)

3_K24M9.12

?

?

 

 

Ogg

Glycosylase (8-oxoG)

1_F8K7.14

-

-

 

 

MutY-Nth family

Glycosylase (many)

2_T28P16.6

-

-

 

Most like Nth1

"

"

1_T20M3.15

-

-

 

Most like Nth2

"

"

4_T20K18_90

-

-

 

Most like MutY

Fpg/MutM

Glycosylase (8-oxoG, FAPY)

1_F6D8.38

+

 

 

Derived from cyanobacterial lineage [5]

MPG (3MG, AAG)

Glycosylase (3-MeA)

3_T21B14.14

3_MEC18.15

-

-

-

-

 

2 entries may be the same gene. Also see [6]

TagI, 3MG1

Glycosylase (3-MeA)

5_K23L20_1

-

+

 

Large expansion in plants – all appear to be derived from a-proteobacteria.

"

"

3_MBK21.7

-

+

 

"

"

"

1_T24D18.7

-

+

 

"

"

"

1_F9E10.6

-

+

 

"

"

"

5_MTI20_23

-

+

 

"

"

"

1_F23A5.15

-

+

 

"

AlkA (3MG2/TagII/MAG)

Glycosylase (3-MeA, many others)

1_F22H5.5

-

-

 

Expansion since divergence from rice.

"

"

3_F18B3_160

-

-

 

"

 

 

 

 

 

 

 

AP Endonucleases

 

 

 

 

 

 

Xth (APE1,ExoA)

5’ AP endonuclease

2_T26J13.5

?

?

ARP

Also see Babiychuk et al 1994.

"

"

3_T29H11_60

-

-

 

Also contains CbbY domain

"

"

4_T19K4_180

-

-

 

Most like APE2/APN2

Nfo (APN1)

5’ AP endonuclease

-

 

 

 

 

 

 

 

 

 

 

 

Mismatch Excision Repair

 

 

 

 

 

 

 

 

 

 

 

 

 

Mismatch Recognition

 



 

 

 

 

MutS family

Binds mismatches and loops

 

 

 

 

 

  MSH1

Mitochondrial mismatch repair

-

 

 

 

 

  MSH2

 

3_MYF24.24 3_K24M9.1

-

-

-

-

 

May be two halves of same gene. Also see [7, 8].

  MSH3

Repair of mismatches in nucleus

4_M7J2_90

-

-

 

Also see [7, 9].

  MSH6

Repair of loops in nucleus

4_T10M13_8

-

-

 

Also see [Ade, 1999 #2693; [9].

  MSH7

????

???

-

-

 

Gene not yet present in genome data. see [9].

  MutS1

Repair of loops and mismatches

-

-

-

 

 

  MSH4

Meiotic chromosome segregation

4_dl4725w?

 

 

 

 

  MSH5

Meiotic chromosome segregation

3_MQC12.24

-

-

 

 

  MutS2

Unknown

1_F16G16.7

5_MJP23_7

+

+

-

-

 

Both closely related to cyanobacterial MutS2

 Unclassified MutS

 

3_K7M2.7

-

-

 

Most similar to MSH6

MutL family

Binds MutS

 

 

 

 

 

 

 

  MLH1

 

4_F23J3_170

-

-

 

See [10].

  PMS1/hPMS2

 

4_T14P8_6

-

-

 

 

  hMLH3/scYPL164c

 

4_F8D20_30

-

-

 

 

Vsr

T:G mismatch endonuclease

-

 

 

 

 

 

 

 

 

 

 

 

Exonucleases[i]

 

 

 

 

 

 

DHS1(ExoI)/Din7 family

Exonuclease

1_F15D2.37

-

-

 

 

"

"

1_T10F20.6

-

-

 

 

FEN1

Exonuclease

5_F21E10.3

-

-

 

 

 

 

 

 

 

 

 

Exision Helicase

 

 

 

 

 

 

UvrD/Helicase II

Excision helicase

4_F13M23_260

-

-

 

More similar to Rep subfamily

 

 

 

 

 

 

 

Nucleotide Excision Repair

 

 

 

 

 

 

 

 

 

 

 

 

 

Bacterial NER

 

 

 

 

 

 

UvrD

Excision helicase

4_F13M23_260

-

-

 

More similar to Rep subfamily

MFD

Transcription repair coupling

3_F1C9.16

+

-

 

Most closely related to cyanobacterial MFDs.

 

 

 

 

 

 

 

Eukaryotic NER

 

 

 

 

 

 

 

 

 

 

 

 

 

Recognition

 

 

 

 

 

 

Rad14 (XPA)

Binds damaged DNA

-

 

 

 

 

RFA1/RPA1

ssDNA binding w/ RFA2,3

4_T18B16_100

5_MFC19_7

2_T12H3.6

5_MSL3_120

5_F13G24_220

-

-

-

-

-

-

-

-

-

-

 

Many additional RFA1 like proteins in genome.

RFA2/RPA2

ssDNA binding w/ RFA1,3

2_T28I24.22

3_F13E7.13

-

-

-

-

 

 

RFA3/RPA3-human

ssDNA binding w/ RFA1,2

-

 

 

 

 

RFA3/RPA3-yeast

ssDNA binding w/ RFA1,2

-

 

 

 

 

 

 

 

 

 

 

 

Initiation

 

 

 

 

 

 

Rad3 (XPD) (ERCC2)

TFIIH – helicase

1_F15K9.19

-

-

 

 

Rad25 (XPB) (ERCC3)

TFIIH – helicase

5_MYC6_8 5_MYC6_7

-

-

-

-

 

Recent duplication. Also see [11]

SSL1 (p44)

TFIIH -

1_T7A14.8

-

-

 

 

TFB1 (p62)

TFIIH -

1_F20N2.8

1_F20N2.10

3_F2A19_20

-

-

-

-

-

-

 

Recent duplication.

TFB2 (p52)

TFIIH -

-

 

 

 

 

TFB3 (MAT1) (p35)

TFIIH - CDK activating kinase

-

 

 

 

 

TFB4 (p34)

TFIIH -

-

 

 

 

 

CCL1 (CyclinH)

TFIIH - cyclin

-

 

 

 

 

Kin28 (CDK7)

TFIIH - protein kinase

-

 

 

 

 

 

 

 

 

 

 

 

Incision

 

 

 

 

 

 

Rad2 (XPG) (ERCC5)

3' incision (flap endonuclease)

3_MMG15.4

-

-

 

 

Rad10 (ERCC1)

5' incision endonuclease w/ Rad1

3_T12H1.18

-

-

 

 

Rad1 (XPF) (ERCC4)

5' incision endonuclease w/ Rad10

5_MEE6_22

-

-

urh1

[12-14]

 

 

 

 

 

 

 

Specificity

 

 

 

 

 

 

Rad4 (XPC)

Repair of inactive DNA

5_MTG13_7

-

-

 

 

Rad23 (HHRAD23)

Repair of inactive DNA

1_F20B17.8

3_F16B3.17

1_T24D18.27

F3O9.1

-

-

-

-

-

-

-

-

 

 

Rad7

Repair of inactive DNA

-

 

 

 

 

Rad16

Repair of inactive DNA

1_T14P4.33 ±

-

-

 

 

Rad26 (CSB) (ERCC6)

Transcription-repair coupling

2_MSF3.14

-

-

 

 

CSA (ERCC8)

Transcription-repair coupling

1_F6F9.31

1_F14P1.30 ±

-

-

-

-

 

 

Recombinational Repair

 

 

 

 

 

 

 

 

 

 

 

 

 

Initiation

 

 

 

 

 

 

 

 

 

 

 

 

 

RecF pathway

 

 

 

 

 

 

RecQ family

3'-5' DNA helicase, other functions

1_T19D16.15

-

-

 

Bloom’s like

"

"

1_T7P1.7

-

-

 

Bloom’s like

"

"

3_F10A16.2

-

-

 

Bloom’s like

"

"

5_T1G16_10

-

-

 

Werner’s like

"

"

1_T19E23.9

-

-

 

RecQ1 like

"

"

4_F8D20_250

-

-

 

RecQ5 like

 

 

 

 

 

 

 

Rad52 pathway

 

 

 

 

 

 

Rad52, Rad59

n/a

-

 

 

 

 

Mre11/Rad32

Nuclease w/ Rad50

5_MDK4_8

-

-

 

 

Rad50

Nuclease w/ Mre11

2_F22D22.28

-

-

 

 

 

 

 

 

 

 

 

Recombinase

 

 

 

 

 

 

 

 

 

 

 

 

 

Rad51

DNA binding, strand exchange

5_F22D1.20

-

-

Rad51

 

DMC1

DNA binding, strand exchange

3_F5N5.5

-

-

DMC1

 

RecA

DNA binding, strand exchange

2_F3P11.

?

?

 

 

"

"

1_YUP8H12R.18

+

-

 

Plastid derived and targeted. Also see [15, 16].

"

"

3_T22K18.3

?

?

 

 

"

"

3_T7B9.15

?

?

 

 

Rad51B

n/a

2_T17D12.12

-

-

 

 

Rad51C

n/a

2_F4L23.21

-

-

 

 

XRCC1

n/a

1_T21F11.25

-

-

 

 

XRCC2

n/a

5_MUB3_4

-

-

 

May not be a true ortholog of XRCC2.

XRCC3

n/a

5_MUA2_3

-

-

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Branch migration/resolution

 

 

 

 

 

 

 

 

 

 

 

 

 

Branch migration/resolution

 

 

 

 

 

 

RecG

Resolvase, 3'-5' junction helicase

2_F2I9.6

+

-

 

Most closely related to cyanobacterial RecGs.

CCE1

Junction endonuclease

-

 

 

 

 

 

 

 

 

 

 

 

Other recombination proteins

 

 

 

 

 

 

Rad54

n/a

3_MVI11.12

-

-

 

 

Rad55

n/a

-

 

 

 

 

Rad57

n/a

-

 

 

 

 

Xrs2

Assists Rad50/MRE11?

-

 

 

 

 

ATM

 

?????

 

 

 

[17]

 

 

 

 

 

 

 

Non-homologous end joining

 

 

 

 

 

 

Ku70

Subunit of DNA-PK

1_F6I1.9

-

-

 

Also matches to 1_F21D18.21, 1_T2J15.4 (probably the same gene)

Ku86

Subunit of DNA-PK

 

 

 

 

 

DNA-PKcs

Catalytic subunit of DNA-PK

 

 

 

 

 

XRCC4

Recruits ligase?

3_MXC7.14

-

-

 

see [18]

 

 

 

 

 

 

 

DNA Ligases

 

 

 

 

 

 

LigII family – Ligase I

ATP-dependent DNA ligase

1_T6D22.10

-

-

 

A different splicing of the cDNA described in [19].  Most like eukaryotiic DNA liagse I.

"

"

1_F13F21.31

-

-

 

Most like eukaryotiic DNA liagse I.

"

"

1_T23G18.1

-

-

 

A different splicing of the cDNA described in [19] Most like eukaryotiic DNA liagse I.

"

"

1_F4N21.14

-

-

 

Most like eukaryotiic DNA liagse I.

LigII family – Liagse IV

"

5_MUL3_11

-

-

 

Most like eukaryotiic DNA liagse IV. Also see [18]

 

 

 

 

 

 

 

Nucleotide pools

 

 

 

 

 

 

NUDIX family

Some memebrs of family repairs 8-oxy-dGTP, GTP.

1_T2H7.9

-

-

 

Closely related to MutT but may not have MutT activity.

Dut

Keeps dUTP pool low

3_T6H20_30

-

-

 

 

 

 

 

 

 

 

 

Replication

 

 

 

 

 

 

PolA family (Pols A,g)

DNA polymerase

3_K10D20.7

-

-

 

Most like Pol A

"

"

1_F8A12.8

-

+

 

Most like Pol g. Probably mitochnodrially derived.

"

"

4_F4D11_100

-

-

 

Most like Pol theta

PolB family (PolsB, a, d, z)

DNA polymerase

5_MBM17_6, 1_F27J15.5

-

-

-

-

 

Most like Pol d

"

"

1_T1F5.3
1_F12B7.5

-

-

 

Most like DPOX

"

"

5_K21H1_6

-

-

 

Most like Pol a

PolC family (DnaE)

DNA polymerase

-

 

 

 

 

UmuC family

SOS mutagenesis, DNA polymerase

1_F2J10.13

-

-

 

Most like DinB1

"

"

5_K23L20_8

-

-

 

Most like pol-eta.  Also see [20].

PCNA

Sliding clamp

2_F16P2.5

 

-

-

 

Recent duplication in plants

"

"

1_F22G5.23

-

-

 

Recent duplication in plants

 

 

 

 

 

 

 

Other Repair Proteins

 

 

 

 

 

 

SMS, RadA

Unknown

5_MXI22_5

+

-

 

Most closely related to cyanobacterial genes.

SSB

Binds ssDNA

3_K24M9.7

 

-

+

 

Probably mitochnodrially derived.

"

"

4_T22B4_40

-

+

 

Probably mitochnodrially derived.

Lon

Protease

5_MQD22_18

-

+

 

Probably mitochnodrially derived.

"

"

5_F2P16_120

-

+

 

Probably mitochnodrially derived.

"

"

3_F10A16.8

-

+

 

Probably mitochnodrially derived.

"

"

3_F10A16.7

-

+

 

Probably mitochnodrially derived.

RAD24/spRad17/hRad17

cell cycle checkpoint

5_K2A18_21

-

-

 

 

AlkB

 

3_MAG2.11

1_F25C20.6

5_T20L15_50
3_MAG2.9

-
-

-

-

?

-

?

?

 

Many may be mitochondrially derived.

Spombe Rad21

DSBR

5_T21H19_190

-

-

 

 

 

 

 

 

 

 

 

 

1.   Ahmad M, Jarillo JA, Smirnova O, and Cashmore AR: Cryptochrome blue-light photoreceptors of Arabidopsis implicated in phototropism. Nature 1998, 392: 720-3.

2.   Nakajima S, Sugiyama M, Iwai S, Hitomi K, Otoshi E, Kim ST, Jiang CZ, Todo T, Britt AB, and Yamamoto K: Cloning and characterization of a gene (UVR3) required for photorepair of 6-4 photoproducts in Arabidopsis thaliana. Nucleic Acids Res 1998, 26: 638-44.

3.   Lin C, Yang H, Guo H, Mockler T, Chen J, and Cashmore AR: Enhancement of blue-light sensitivity of Arabidopsis seedlings by a blue light receptor cryptochrome 2. Proc Natl Acad Sci U S A 1998, 95: 2686-90.

4.   Jiang CZ, Yee J, Mitchell DL, and Britt AB: Photorepair mutants of Arabidopsis. Proc Natl Acad Sci U S A 1997, 94: 7441-5.

5.   Ohtsubo T, Matsuda O, Iba K, Terashima I, Sekiguchi M, and Nakabeppu Y: Molecular cloning of AtMMH, an Arabidopsis thaliana ortholog of the Escherichia coli mutM gene, and analysis of functional domains of its product. Mol Gen Genet 1998, 259: 577-90.

6.   Santerre A and Britt AB: Cloning of a 3-methyladenine-DNA glycosylase from Arabidopsis thaliana. Proc Natl Acad Sci U S A 1994, 91: 2240-4.

7.   Ade J, Belzile F, Philippe H, and Doutriaux MP: Four mismatch repair paralogues coexist in Arabidopsis thaliana: AtMSH2, AtMSH3, AtMSH6-1 and AtMSH6-2. Mol Gen Genet 1999, 262: 239-49.

8.   Culligan KM and Hays JB: DNA mismatch repair in plants. An Arabidopsis thaliana gene that predicts a protein belonging to the MSH2 subfamily of eukaryotic MutS homologs. Plant Physiol 1997, 115: 833-9.

9.   Culligan KM and Hays JB: Arabidopsis MutS homologs-AtMSH2, AtMSH3, AtMSH6, and a novel AtMSH7- form three distinct protein heterodimers with different specificities for mismatched DNA. Plant Cell 2000, 12: 991-1002.

10. Jean M, Pelletier J, Hilpert M, Belzile F, and Kunze R: Isolation and characterization of AtMLH1, a MutL homologue from Arabidopsis thaliana. Mol Gen Genet 1999, 262: 633-42.

11. Ribeiro DT, Machado CR, Costa RM, Praekelt UM, Van Sluys MA, and Menck CF: Cloning of a cDNA from Arabidopsis thaliana homologous to the human XPB gene. Gene 1998, 208: 207-13.

12. Liu Z, Hossain GS, Islas-Osuna MA, Mitchell DL, and Mount DW: Repair of UV damage in plants by nucleotide excision repair: Arabidopsis UVH1 DNA repair gene is a homolog of Saccharomyces cerevisiae Rad1. Plant J 2000, 21: 519-28.

13. Gallego F, Fleck O, Li A, Wyrzykowska J, and Tinland B: AtRAD1, a plant homologue of human and yeast nucleotide excision repair endonucleases, is involved in dark repair of UV damages and recombination. Plant J 2000, 21: 507-18.

14. Fidantsef AL, Mitchell DL, and Britt AB: The Arabidopsis UVH1 gene is a homolog of the yeast repair endonuclease RAD1. Plant Physiol 2000, 124: 579-86.

15. Cerutti H, Osman M, Grandoni P, and Jagendorf AT: A homolog of Escherichia coli RecA protein in plastids of higher plants. Proc Natl Acad Sci U S A 1992, 89: 8068-72.

16. Cao J, Combs C, and Jagendorf AT: The chloroplast-located homolog of bacterial DNA recombinase. Plant Cell Physiol 1997, 38: 1319-25.

17. Garcia V, Salanoubat M, Choisne N, and Tissier A: An ATM homologue from Arabidopsis thaliana: complete genomic organisation and expression analysis. Nucleic Acids Res 2000, 28: 1692-9.

18. West CE, Waterworth WM, Jiang Q, and Bray CM: Arabidopsis DNA ligase IV is induced by gamma-irradiation and interacts with an Arabidopsis homologue of the double strand break repair protein XRCC4. Plant J 2000, 24: 67-78.

19. Taylor RM, Hamer MJ, Rosamond J, and Bray CM: Molecular cloning and functional analysis of the Arabidopsis thaliana DNA ligase I homologue. Plant J 1998, 14: 75-81.

20. McDonald JP, Rapic-Otrin V, Epstein JA, Broughton BC, Wang X, Lehmann AR, Wolgemuth DJ, and Woodgate R: Novel human and mouse homologs of Saccharomyces cerevisiae DNA polymerase eta. Genomics 1999, 60: 20-30.


Table generated by Jonathan A. Eisen and Anne B. Britt. For more information contact Jonathan A. Eisen (jeisen@tigr.org).

Last modified on: January 20, 2001