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Table 1 S. cerevisiae DNA polymerases and proteins that participate in the five primary DNA repair pathways.

From: Stripped-down DNA repair in a highly reduced parasite

Base Excision Repair (BER)

Nucleotide Excision Repair (NER)

Gene Name

Present in E. cuniculi

S. cerevisiae Protein ID

E. cuniculi Protein ID

Gene Name

Present in E. cuniculi

S. cerevisiae Protein ID

E. cuniculi Protein ID

Apn1

Y

CAA81954

CAD26065

Rad1 (XPF)

Y

P06777

CAD26381

Apn2

Y

NP_009534

NP_585892

Rad2 (XPG)

Y

CAA97287

CAD27314/XP_955715

Mag1

Y

NP_011069

CAD25924/CAD26679

Rad3 (Ercc2/XPD)

Y

CAA46255

NP_585776

Mus81

Y

NP_010674

NP_584664

Rad4 (XPC)

Y

CAA39375

CAD24914

Ntg1

Y

NP_009387

CAD26394

Rad10 (Ercc1)

Y

CAA86642

CAD25852/NP_586248

Ogg1

Y

NP_013651

CAD26383

Rad14 (XPA)

Y

P28519

NP_586232

PCNA

Y

AAS56041

NP_597446

Rad25 (Ssl2/XPB)

Y

Q00578

CAD24977

Rad1 (XPF)

Y

P06777

CAD26381

Rad26 (Ercc6/CSB)

Y

CAA57290

CAD27013/XP_955594

Rad10 (Ercc1)

Y

CAA86642

CAD25852/NP_586248

Rpa1

Y

NP_009404

CAD25779

Rad27 (Fen1)

Y

CAA81953

CAD26252

Rpa2

Y

NP_014087

CAD25396

Ung1

Y

CAA86634

CAD26772

Ssl1

Y

CAA97527

CAD25215

* Xrcc1 (Cut5)

Y

P32372

NP_584657

Tfb2

Y

AAB40628

CAD24937

Cdc9 (DNA lig I)

N

CAA48158

-

Tfb3

Y

AAB64899

CAD25932

Ddc1 (Rad9)

N

NP_015130

-

Tfb4

Y

NP_015381

CAD25620

Mec3 (Hus1)

N

NP_013391

-

Rad7

?

CAA85071

-

Mms4

N

NP_009656

-

Rad16

?

CAA89580

-

Rad17 (Rad1)

N

CAA99699

-

Rad23 (HR23B)

N

AAB28441

-

    

Tfb1

N

AAB64747

-

Methyltransferase Repair

DNA Polymerases

Gene Name

Present in E. cuniculi

S. cerevisiae Protein ID

E. cuniculi Protein ID

Gene Name

Present in E. cuniculi

S. cerevisiae Protein ID

E. cuniculi Protein ID

Mgt1

N

CAA42920

-

α Pol1

Y

AAZ22505

CAD26619

    

α Pol12

Y

NP_009518

CAD25827

Mismatch Repair (MMR)

α Pri1

Y

AAT92878

CAD26368

Gene Name

Present in E. cuniculi

S. cerevisiae Protein ID

E. cuniculi Protein ID

α Pri2

Y

NP_012879

CAD26641

    

δ Pol3

Y

CAA43922

CAD27015

Exo1

Y

NP_014676

CAD25986

δ Hys2

Y

NP_012539

CAD27050

Mlh1

Y

NP_013890

NP_597370

ε Dpb2

Y

NP_015501

NP_597373

Msh2

Y

CAA99102

CAD26200/NP_597565

ε Pol2

Y

NP_014137

CAD25840

Msh6

Y

NP_010382

NP_586186

β Pol4

N

NP_009940

-

PCNA

Y

AAS56041

NP_597446

γ Mip1

N

NP_014975

-

Pms1

Y

P14242

NP_586432

η Rad30

N

NP_010707

-

Msh3

N

CAA42247

-

ζ Rev3

N

NP_015158

-

    

ζ Rev7

N

AAA98667

-

    

Rev1

N

CAA99674

-

Homologous Recombination (HRR)

Non-Homologous End Joining (NHEJ)

Gene Name

Present in E. cuniculi

S. cerevisiae Protein ID

E. cuniculi Protein ID

Gene Name

Present in E. cuniculi

S. cerevisiae Protein ID

E. cuniculi Protein ID

Mre11 (Rad32)

Y

BAA02017

CAD26648/NP_597471

Mre11 (Rad32)

Y

BAA02017

CAD26648/NP_597471

Rad50

Y

CAA65494

CAD25593/NP_585989

Rad27 (Fen1)

Y

CAA81953

CAD26252

Rad51

Y

CAA45563

CAD25992/NP_586388

Rad50

Y

CAA65494

CAD25593/NP_585989

Rad52

Y

CAA86623

XP_955647

Lif1 (Xrcc4)

?

NP_011425

-

Rpa1

Y

NP_009404

CAD25779

*Xrs2 (Nbs1)

?

BAC80248

-

Rpa2

Y

NP_014087

CAD25396

Ddc1 (Rad9)

N

NP_015130

-

Sgs1

Y

NP_013915

CAD25646

Dnl4

N

CAA99193

-

Rad55 (Rad51C)

?

BAA01284

-

Mec3 (Hus1)

N

NP_013391

-

Rad57 (Xrcc3)

?

NP_010287

-

Ku70

N

NP_014011

-

*Xrs2 (Nbs1)

?

BAC80248

-

Ku80

N

NP_013824

-

Ddc1 (Rad9)

N

NP_015130

-

Rad17 (Rad1)

N

CAA99699

-

Hpr5 (Srs2)

N

CAA89385

-

    

Mec3 (Hus1)

N

NP_013391

-

    

Rad17 (Rad1)

N

CAA99699

-

    

Rad24 (Rad17)

N

P32641

-

    

Rad54

N

CAA88534

-

    

Rdh54 (Rad54B)

N

CAA85017

-

    
  1. Presence or absence in E. cuniculi is indicated (as defined in Methods), along with the genbank accession numbers for both S. cerevisiae and E. cuniculi proteins. Absent proteins are presented in bold type. Italicized accession numbers indicate that the presence or absence of these proteins in E. cuniculi was unclear. (See results for more information.) When S. pombe proteins appeared to be more conserved among eukaryotes than S. cerevisiae homologues (or where S. cerevisiae homologues do not exist), they were used to conduct the BLAST and PSI-BLAST searches. These proteins are marked with asterixes. S. cerevisiae nomenclature is used, with S. pombe or animal homologues given in brackets. Pathway components were largely compiled from the following sources: MMR from Marti et al. [22], BER from Boiteux and Guillet [12], NER from Prakash and Prakash [17], NHEJ from Daley et al. [57], HRR from Aylon and Kupiec [24], DNA polymerases from Burgers [58] and Hubscher et al., [4].
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BMC Molecular Biology

ISSN: 1471-2199

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