TABLE 24.

Genes involved in DSB initiation and processinga

S. cerevisiae genebNeurospora homologueE valueBest match to protein in SP + TrEMBLE value (BLASTP)
Before the DSB
    CLB5NCU02758.1 hyp protein3e-51A. nidulans G2/mitosis-specific cyclin B2.1e-161
    CLB65e-59S. pombe G2/mitosis-specific cyclin cdc133.6e-129
    sds (Arabidopsis)2e-11S. cerevisiae G2/mitosis-specific cyclin 21.0e-106
Human G2/mitosis-specific cyclin B27.9e-75
DSB generation
    HOP2NoneS. pombe MEI138e-08
P. falciparum hyp. protein8e-04
Human BRCA1-associated protein9e-04
    MEI4NoneNone
    MEK1/MRE4NCU02814.12e-36S. cerevisiae DUN11e-72
Human CHK24e-72
S. cerevisiae MEK11.5e-27
    MER1NoneNone
    MER2/REC107NoneSimilarity only to myosin heavy-chain genes
    MER3NCU09793.1 hyp. proteine-148S. cerevisiae HFM1/MER37.4e-170
A. thaliana genomic DNA7.1e-93
D. melanogaster GH18520 full-length cDNA1.3e-65
Human mRNA for putative RNA helicase, 3′ end1.0e-52
    MRE2/NAM8NCU00768.18e-55A. thaliana at5g549003e-67
Nicotiana tabacum putative RNA binding protein4e-65
S. cerevisiae NAM82e-58
Human hyp. protein flj205035e-37
    REC102NoneNone
    REC103/SK18NCU03517.1 hyp. protein2.00e-17S. pombe rec141.0e-71
Human REC141.2e-25
    REC104NoneNone
    REC114NoneSome homology to S. pombe Rec7
    RED1NoneKluyveromyces lactis red12e-70
Human KIAA0874 protein4e-06
    SPO11NCU01120.1 S. pombe rec12-related protein2e-10Coprinus cinereus spo113e-29
S. pombe rec122e-28
Human SPO113e-25
S. cerevisiae SPO111e-08
Removal of Spo11 protein from DNA
    MRE11NCU08730.1 mus-23 (AB002530)e-123Magnaporthe grisea (NK73)e-178
A. nidulans meiotic recombination proteine-158
S. cerevisiae MRE11e-118
Human MRE11e-103
    RAD50NCU00901.1 uvs-6 (AB055069)e-175S. cerevisiae RAD50e-175
Mouse RAD50e-159
Human RAD50e-159
    SAE2/COM1NoneNone
Resection of ends
    XRS2NoneP. falciparum e1-e2 putative ATPase/hydrolase8e-06
Human neurofilament, heavy polypeptide4e-05
    Human NBS1NCU04329.13e-05A. fumigatus hyp. proteine-116
S. cerevisiae LP193e-15
Strand invasion
    DMC1NoneWidely conserved, including mammals
    RAD51NCU02741.1 mei-3e-123A. nidulans uvsCe-178
Penicillium paxilli pp rad51e-174
Human RAD51e-135
S. cerevisiae RAD51e-131
    RAD52NCU04275.1 mus-115e-46M. grisea NK724e-95
A. nidulans radC2e-67
S. cerevisiae RAD526e-28
Human RAD522e-22
    RAD54NCU02348.1 (AB032901) mus-250.0M. grisea NK740.0
S. pombe RAD540.0
S. cerevisiae RAD540.0
Human RAD540.0
    RAD55NCU08806.17e-05Methanopyrus kandleri rada7e-04
S. pombe rhp550.001
S. cerevisiae RAD550.003
    RAD57NCU01771.1 RAD57 homologue2e-23S. pombe RHP572e-32
S. cerevisiae RAD571e-16
Human XRCC36e-12
    RDH54/TID1NCU02348.1 RAD54 homologuee-107
NCU07837.11e-57S. pombe RHP260.0
S. cerevisiae RAD260.0
Human ercc-6e-156
S. cerevisiae RDH546.8e-51
    RFA1NCU03606.1e-115S. pombe RFA1e-170
Human RFA1e-119
S. cerevisiae RFA1e-114
    RFA2NCU07717.12e-23A. fumigatus possible Rfa2e-34
S. pombe RFA21e-28
Human RFA22e-16
S. cerevisiae RFA27e-13
    RFA3NoneNone
    SAE3NoneNone
Synapsis and synaptonemal complex formation
    HOP1NoneK. lactis HOP11e-93
Poorer matches (6e-14 to e-07) to proteins involved in synapsis in plants and animals
    MND1Human GAJ. Also mouse, A. thaliana, and S. pombe1e-17 to 1e-08
    ZIP1NCU00658.18e-24Rat Golgi complex-associated protein2e-75
Human centromeric protein3e-69
S. cerevisiae ZIP12e-21
    ZIP2NoneNone
Regulation of crossover frequency
    MEI5NoneHuman ninein (GSK3B-interacting protein)2e-04
    MLH1NCU08309.1e-159S. cerevisiae MLH1e-168
    Human MLH1e-167
    MLH3NCU08309.1 mlh-15e-23
NCU08020.1 pms-19e-18
NCU09373.1 mlh-25e-10
NCU05385.12e-09S. cerevisiae MLH33.4e-13
A. thaliana PMS12e-09
Mouse PMS23e-08
Human PMS22e-07
    MSH4NCU02230.1 msh-21e-40
NCU08115.1 msh-38e-32
NCU08135.1 msh-68e-27
NCU09384.1 msh-53e-22
NCU07407.1 msh-16e-18
Contig 3.27 (scaffold 2)2e-36 (TBLASTN)Mouse MSH44e-39
Thermotoga maritima MutS4e-39
S. cerevisiae MSH42e-35
Human MSH43e-34
    MSH5NCU09384.11e-58S. cerevisiae MSH51e-55
Human MSH54e-42
    TAM1/NDJ1NoneNone
    Drosophila mei-9NCU07440.1 mus-38e-119S. pombe chromosome III cosmid2e-270
Mouse DNA repair endonuclease XPF5.3e-199
Human excision repair2.2e-197
S. cerevisiae RAD15.9e-170
A. thaliana 5′ repair endonuclease1.5e-139
    Drosophila mei-218NoneNone
Mismatch repair
    MLH2NCU08020.1 pms-16e-19
NCU08309.1 mlh-16e-16
NCU09373.1 mlh-24e-15Human PMS14e-24
Phaeosphaeria nodorum hyp. protein5e-24
S. cerevisiae MLH25.0e-15
    MSH2NCU02230.1 msh-20.0S. cerevisiae MSH20.0
Human MSH20.0
    MSH3NCU08115.1 msh-3e-115Human MSH3e-168
Mouse MSH3e-164
S. cerevisiae MSH3e-105
    MSH6NCU08135.1 msh-60.0S. pombe MSH60.0
S. cerevisiae MSH60.0
Human MSH6e-157
    PMS1NCU08020.1 pms-18e-82S. pombe PMS15e-83
S. cerevisiae PMS18e-81
Human PMS24e-80
Resolution of recombination intermediates
    MMS4/SLX2NCU04047.12e-04Xenopus laevis nucleolar phosphoprotein5e-04
Human nucleolar phosphoprotein0.002
    SLX1NCU01236.12e-26S. cerevisiae SLX12e-23
S. pombe hyp. protein5e-17
Human hyp. protein MGC51787e-12
    SLX3/MUS81NCU07457.12e-52S. cerevisiae MUS818.2e-50
S. pombe hyp. protein5e-76
Human MUS812e-36
    SLX4NoneHuman SMC42e-05
    SLX8NCU03872.12e-07S. pombe zinc finger protein1e-69
S. cerevisiae Chr XII sequence7e-39
Human RNF106e-17
S. cerevisiae SLX84e-05
    HEX3/SLX5NoneNone
    TOP1/MAK1/MAK17NCU09118.10.0A. nidulans TOP10.0
S. pombe TOP10.0
S. cerevisiae TOP10.0
Human TOP1e-114
    TOP2/TOR3/TRF3NCU06338.10.0A. niger TOP20.0
Penicillium chrysogenum TOP20.0
S. cerevisiae TOP20.0
Human TOP20.0
    TOP3/EDR1NCU00081.1e-114S. pombe topoisomerase 3e-115
C. elegans topoisomerase Ie-105
Human topoisomerase IIIe-104
S. cerevisiae TOP3e-101
Nonhomologous end joining
    LIF1NoneHuman hyaluronan-mediated motility receptor (RHAMM) isoform A4e-05
    LIG4NCU06264.17e-97S. pombe DNA ligase 4e-143
C. albicans LIG41e-94
Human ligase IV3e-89
S. cerevisiae LIG41e-88
    YKU70/HDF1/NES24NCU08290.11e-27S. pombe putative DNA helicase3e-91
Gallus gallus ku701e-58
Human ku706e-51
S. cerevisiae YKU704e-25
    YKU80/HDF2NCU00077.12e-14S. pombe putative DNA helicase3e-73
Mouse Ku802e-26
Human DNA helicase9e-26
S. cerevisiae HDF28e-12
  • a Searches of the literature and of the Saccharomyces database (http://genome-www4.stanford.edu/cgi-bin/SGD/SAGE/querySAGE) were used to identify candidate genes. The resulting amino acid sequences were used to find orthologues in the Neurospora predicted protein database. Where this approach yielded nothing, a TBLASTN search of the whole Neurospora genome sequence was performed, thus allowing us to locate msh-4. The amino acid sequence of the best match for each gene was used to search the Swiss Prot + TrEMBL nonredundant protein databases. For msh-4, the Neurospora nucleotide sequence was used in a BLASTS search against Swiss Prot + TrEMBL. S. cerevisiae genes with no Neurospora orthologue were used to search Swiss Prot + TrEMBL or the human genome protein database (http://www.ncbi.nih.gov/genome/seq/HsBlast.html).

  • b Unless otherwise specified.