Table 1.
Classification of putative transcription factors of Medicago into families and sub-families
| TF Family |
No. of Genes |
Characteristic Domain (InterPro No.) |
Domain Function |
Domain Description |
| MYB/HD-like | 76 | IPR001005, IPR009057 | D | Myb, DNA-binding; homeodomain like |
| MYB | 58 | IPR001005 | D | Myb, DNA-binding |
| C2H2 (Zn) | 64 | IPR007087 | NA | Zn-finger, C2H2 type |
| AP2/EREBP | 55 | IPR001471 | D | Pathogenesis-related transcriptional factor and ethylene response factor |
| BHLH | 49 | IPR001092 | D | Basic helix-loop-helix dimerisation region bHLH |
| HD-like | 50 | IPR009057 | D | Homeodomain like |
| HD family | IPR001356 | D | Homeobox | |
| HD | 25 | |||
| HD-ZIP | 5 | IPR006712 | P | HD-ZIP protein, N terminus |
| HD-PHD finger | 2 | IPR001965 | P | Zn-finger like, PHD-finger |
| MADS | 48 | IPR002100 | D | TF, MADS-box |
| BZIP | 41 | IPR004827 | D | Basic Leu zipper (bZIP) TF |
| PHD | 34 | IPR001965 | P | Zn-finger like, PHD-finger |
| WRKY family | IPR003657 | D | DNA-binding WRKY | |
| WRKY | 29 | |||
| LLR WRKY | 1 | IPR001611 | Leu-rich repeat | |
| ABI3/VP1 | 29 | IPR003340 | D | TF B3 |
| NAC | 29 | IPR003441 | D | No apical meristem (NAM) protein |
| C3H-type1(Zn) | 27 | IPR000571 | D | Zn-finger, C-x8-C-x5-C-x3-H type |
| ARF | 23 | IPR003340, IPR010525, IPR011525 | D | |
| JUMONJI | 20 | IPR003347 | D | TF jumonji, jmjC |
| GRAS | 19 | IPR005202 | P | GRAS TF |
| HMG | 15 | IPR000637 | D | HMG-I and HMG-Y, DNA binding |
| AS2 | 14 | IPR004883 | P | Lateral organ boundaries |
| C2C2 (Zn) | ||||
| Dof | 13 | IPR003851 | D | Zn-finger, Dof type |
| GATA | 7 | IPR000679 | D | Zn-finger, GATA type |
| CO-like | 6 | IPR000315 | D | Zn-finger, B-box |
| YABBY | 5 | IPR006780 | D | YABBY protein |
| CCAAT-HAP3 type | 12 | IPR003958 | D | TF CBF/NF-Y/archaeal histone |
| GRF | 8 | IPR010666 | D | Zn-finger, GRF type |
| SBP | 8 | IPR004333 | D | SBP |
| EIL | 7 | IPR006957 | D | Ethylene insensitive 3 |
| LIM | 7 | IPR001781 | P | Zn-binding protein, LIM |
| SNF2 | 6 | IPR000330 | D | SNF2 family N-terminal domain |
| E2F/DP | 5 | IPR003316 | D | TF E2F/dimerisation partner (TDP) |
| TCP | 5 | IPR005333 | D | TCP TF |
| FHA | 5 | IPR000253 | D | Forkhead-associated |
| ARID | 4 | IPR001606 | D | AT-rich interaction region |
| HSF | 4 | IPR000232 | D | Heat shock factor (HSF)-type, DNA binding |
| AUX/IAA | 3 | IPR003311 | D | AUX/IAA protein |
| SRS | 3 | IPR006510 | D | Zn-finger, LRP1 type |
| TUB | 3 | IPR000007 | D | Tubby |
| ZIM | 3 | IPR010399 | D | ZIM |
| DDT | 3 | IPR004022 | D | DDT |
| ZF-HD | 2 | IPR006455 | D | Homeobox domain, ZF-HD class |
| MBF1 | 2 | IPR001387 | D | Helix-turn-helix type 3 |
| S1Fa-like | 2 | IPR006779 | D | DNA binding protein S1FA |
| CAMTA | 2 | IPR005559 | D | CG-1 |
| LFY | 1 | IPR002910 | D | Floricaula/leafy protein |
| Nin-like | 1 | IPR003035 | D | Plant regulator RWP-RK |
| TAZ | 1 | IPR000197 | P | Zn-finger, TAZ-type |
| Potentially novel plant TFs and transcriptional regulators | ||||
| CCHC (Zn) | 112 | IPR001878 | NA | Zn-finger, CCHC-type |
| RR | 16 | IPR001789, IPR011006 | RD | Response regulator receiver |
| DHHC (Zn) | 14 | IPR001594 | D or P | Zn-finger, DHHC-type |
| HTH | ||||
| FIS | 11 | IPR002197 | D | Helix-turn-helix, Fis-type |
| AraC | 2 | IPR000005 | D | Helix-turn-helix, AraC type |
| BTB/POZ | 7 | IPR000210 | P | BTB |
| TTF-type (Zn) | 6 | IPR006580 | D | Zn-finger, TTF-type |
| BD | 6 | IPR001487 | P | Bromodomain |
| Lambda-DB | 3 | IPR010982 | D | Lambda_DNA_bd |
| TrpR | 3 | IPR010921 | D | Trp repressor/replication initiator |
| TPR | 3 | IPR001440 | P | Tetratricopeptide TPR_1 |
| KRAB-box | 2 | IPR001909 | P | KRAB box |
| NRs | 2 | IPR008946 | LBD | Steroid nuclear receptor, ligand binding |
| R3H | 2 | IPR001374 | NA | Single-stranded nucleic acid binding R3H |
| YEATS | 2 | IPR005033 | TA | YEATS |
| U1-type (Zn) | 2 | IPR003604 | NA | Zn-finger, U1-type |
| A20-like | 2 | IPR002653 | P | Zn-finger, A20-type |
| Euk_TF | 1 | IPR008917 | D | Euk_TF, DNA binding |
| NGN | 1 | IPR006645 | D | NGN |
| p53-like | 1 | IPR008967 | D | p53-like TF, DNA binding |
| SSB protein | 1 | IPR011344 | D | Single-strand binding protein |
| ssDB TR | 1 | IPR009044 | D | Single-strand DNA binding transcriptional regulator |
| TCoAp15 | 1 | IPR003173 | D | Transcriptional coactivator p15 |
| BED-type (Zn) | 1 | IPR003656 | D | Zn-finger, BED-type predicted |
| TCoA | 1 | IPR009255 | TA | Transcriptional coactivation |
| Tc/PD | 1 | IPR001533 | TA | Transcriptional coactivator |
IMGAG (International Medicago Gene Annotation Group)-proteins were classified as putative TFs if they contained characteristic DNA-binding or other characteristic TF domains and if annotations of matching proteins obtained by BLAST searches were consistent with such a classification. TF families previously identified in plants are presented in the first part of the table while potentially novel plant TF families, which were identified by the presence of domains associated with TFs and other transcriptional regulators outside the plant kingdom, are presented in the latter part of the table. D = DNA binding domain; P = protein-protein interaction domain; NA = nucleic acid (DNA and RNA) binding domain; RD = receiver domain; LBD = ligand binding; transcriptional co-activator. Plant-specific TF families and sub-families are indicated in bold (according to [12])