Table 3.
R. taiwanensis MD1149 homologs of genes that are known from other fungi to be involved in DNA repair, oxidative stress, Mn homeostasis, resistance to heavy metals, and selected hydrolase genes.
| Representative KEGG genes | Function | Nr. of homologs in MD1149 | Homologs numbers (BMF94_) | |
|---|---|---|---|---|
| HOMOLOGOUS DNA RECOMBINATION | ||||
| RAD50 | DNA repair protein RAD50 | 1 | 4958 | |
| MRE11 | Double-strand break repair protein MRE11 | 1 | 1623 | |
| RAD57 | DNA repair protein RAD57 | 1, low similarity | 1476 | |
| RFA1 | Replication factor A1 | 1 | 6843 | |
| RAD51 | DNA repair protein RAD51 | 1 | 4285 | |
| RAD52 | DNA repair and recombination protein RAD52 | 1 | 1177 | |
| BRCA2 | Breast cancer 2 susceptibility protein | 1 | 4266 | |
| RAD54 | DNA repair and recombination protein RAD54 | 2 | 1178 | 0432 |
| POLD1 | DNA polymerase delta subunit 1 | 1 | 4972 | |
| BLM | Bloom syndrome protein, ATP dependent DNA helicase | 4 | 4946 | 4947 |
| low similarity | 6361 | 3460 | ||
| TOP3 | DNA topoisomerase III | 1 | 1732 | |
| MUS81 | Crossover junction endonuclease MUS81 | 1 | 5222 | |
| EME1 | Crossover junction endonuclease EME1 | 0 | 4418 | |
| NON-HOMOLOGOUS END-JOINING | ||||
| KU70 | ATP-dependent DNA helicase 2 subunit 1 | 1 | 5927 | |
| KU80 | ATP-dependent DNA helicase 2 subunit 2 | 1 | 4455 | |
| RAD50 | DNA repair protein RAD50 | 1 | 4958 | |
| MRE11 | Double-strand break repair protein MRE11 | 1 | 1623 | |
| POLL | DNA polymerase lambda | 1 | 4374 | |
| RAD2 | Flap endonuclease-1 | 1 | 1460 | |
| DNL4 | DNA ligase 4 | 1 | 5514 | |
| OXIDATIVE STRESS | ||||
| SOD2 (S. cerevisiae) | Fe-Mn family superoxide dismutase | 1 | 4448 | |
| CTA1, CTT1 (S. cerevisiae) | Catalase | 2 | 3212 | 0981 |
| CTT1 (S. cerevisiae) | Cytosolic catalase T | 2 | 3212 | 0981 |
| TSA1, TSA2 (S. cerevisiae) | Peroxiredoxin, thioredoxin peroxidase | 1 | 1596 | |
| TSA2 (S. cerevisiae) | Stress inducible cytoplasmic thioredoxin peroxidase | 1 | 1596 | |
| PRX1 (S. cerevisiae) | Mitochondrial peroxiredoxin, thioredoxin peroxidase | 1 | 1823 | |
| DOT5 (S. cerevisiae) | Nuclear thiol peroxidase | 1, low similarity to peroxiredoxins | 1737 | |
| GPX1, GPX2, GPX3 (S. cerevisiae) | Glutathione peroxidase | 1 | 0010 | |
| HYR1 (S. cerevisiae) | GPX3 Thiol peroxidase | 1 | 0010 | |
| GTT1 (S. cerevisiae) | ER associated glutathione S-transferase | 1 | 4445 | |
| GTO1, ECM4, GTO3 (S. cerevisiae) | Omega-class glutathione S-transferase | 1 | 2093 | |
| GRX1, GRX2 (S. cerevisiae) | Dithiol glutaredoxin | 1 | 4981 | |
| GRX3, GRX4, GRX5 (S. cerevisiae) | Monothiol glutaredoxin | 2 | 1659 | 3737 |
| GLR1 (S. cerevisiae) | Cytosolic and mitochondrial glutathione oxidoreductase | 1 | 0249 | |
| TRX1, TRX2, TRX3 (S. cerevisiae) | Thioredoxin | 5 | 6822 | 6320 |
| 0478 | 4390 | |||
| 7059 | ||||
| TRR2 (S. cerevisiae) | Mitochondrial thioredoxin reductase | 5997 | ||
| NCU05770 (N. crassa) | Cytochrome c peroxidase | 2 | 5958 | 4954 |
| NCU07386 (N. crassa) | Fe-Mn family superoxide dismutase | 1 | 2434 | |
| NCU05780 (N. crassa) | Theta-class glutathione S-transferase | 2 | 3517 | 1660 |
| NCU01320 (N. crassa) | Microsomal glutathione S-transferase | 1 | 2590 | |
| NCU03339 (N. crassa) | Glutathione-disulfide reductase | 1 | 249 | |
| Mn HOMEOSTASIS | ||||
| SMF2 (S. cerevisiae) | Divalent metal ion transporter involved in manganese homeostasis has broad specificity for di-valent and tri-valent metals | 0853 | ||
| PHO84 (S. cerevisiae) | Inorganic phosphate (Pi) transporter, also low-affinity manganese transporter | 2 | 2399 | 0582 |
| PMR1 (S. cerevisiae) | CaMn P-type ATPase transporter | 2 | 5512 | 2539 |
| BSD2 (S. cerevisiae) | Heavy metal ion homeostasis protein | 1 | 5777 | |
| CCC1 (S. cerevisiae) | Similar to putative vacuolar FeMn transporter | 1 | 3438 | |
| RESISTANCE TO HEAVY METALS | ||||
| PCA1 | Copper or cadmium transporting P-type ATPase | 1 | 6825 | |
| YCF1 | Proteins with high similarity to the yeast vacuolar glutathione S-conjugate transporter with a known role in detoxifying Cd, Hg and As | at least 3 | 6201 | 3559 |
| 3360 | ||||
| COT1, ZRC1 | Transporter of heavy metals | 1 | 0535 | |
| HYDROLASE FAMILIES | ||||
| GNAT family acetyltransferases | 23 | 5507 | 6265 | |
| 5757 | 2541 | |||
| 5786 | 7019 | |||
| 4676 | 7020 | |||
| 1320 | 0152 | |||
| 1591 | 0305 | |||
| 4302 | 0442 | |||
| 1061 | 0435 | |||
| 1055 | 1739 | |||
| 1059 | 3511 | |||
| 1060 | 1915 | |||
| 6163 | ||||
| NUDIX hydrolases | 15 | 5675 | 1605 | |
| 5713 | 3374 | |||
| 5980 | 0416 | |||
| 5976 | 4813 | |||
| 1054 | 1893 | |||
| 0871 | 6385 | |||
| 6480 | 5468 | |||
| 4228 | ||||
| A/B superfamily hydrolases | 25 | 5552 | 3298 | |
| 1350 | 3063 | |||
| 5239 | 3669 | |||
| 1589 | 2387 | |||
| 6322 | 4897 | |||
| 5970 | 4890 | |||
| 0382 | 0636 | |||
| 0738 | 0676 | |||
| 7045 | 1717 | |||
| 6437 | 3427 | |||
| 6642 | 3439 | |||
| 0295 | 1961 | |||
| 3113 | ||||