Introduction
Transcription factors (TFs) interact with the basal transcription apparatus at target gene promoters to activate or repress the target gene function. They are essential for the regulation of gene expression, response to development, and intercellular signals. The portion of TF genes in Arabidopsis genome and diversity of DNA-binding specificity are higher than that of D. melanogaster and C. elegans. These suggest that Arabidopsis TFs play more important roles in plant than animals. Despite of its extreme importance, the functions of most TFs currently are poorly understood.
Transcription factors (TFs) play important roles in plants. However, there is no systematic study of their structures and functions of most TFs in plants. Here, we performed template-based structure prediction for all TFs in Arabidopsis thaliana, with their full-length sequences as well as C-terminal and N-terminal regions. A total of 2918 model structures were obtained with a high confidence score. We found that TF families employ only a smaller number of templates for DNA-binding domains (DBD) but a diverse number of templates for transcription regulatory domains (TRD). Although TF families are classified according to DBD, their sizes have a significant correlation with the number of unique non-DNA-binding templates employed in the family (Pearson correlation coefficient of 0.74). That is, the size of TF family is related to its functional diversity. Network analysis reveals new connections between TF families based on shared TRD or DBD templates; 81% TF families share DBD and 67% share TRD templates. Two large fully connected family clusters in this network are observed along with 69 island families. In addition, 25 genes wih unknown functions are found to be DNA-binding and/or TF factors according to predicted structures. This work provides a global view of the classification of TFs based on their DBD or TRD templates, and hence, a deeper understanding of DNA-binding and regulatory functions from structural perspective.
Transcription Factor Families:
| ABI3VP1 (57) | Alfin-like (9) | AP2-EREBP (153) | ARF (24) | ARID (11) |
| ARR-B (17) | AUX/IAA (27) | BBR/BPC (16) | BES1 (14) | bHLH (150) |
| BSD (12) | bZIP (87) | C2C2-CO-like (17) | C2C2-Dof (36) | C2C2-GATA (32) |
| C2C2-YABBY (6) | C2H2 (106) | C3H (83) | CAMTA (9) | CCAAT (44) |
| Coactivator (7) | CPP (8) | CSD (4) | DBP (5) | DDT (5) |
| E2F-DP (10) | EIL (6) | FAR1 (24) | FHA (19) | G2-like (51) |
| GeBP (20) | GNAT (41) | GRAS (33) | GRF (9) | HB (92) |
| HMG (19) | HRT (2) | HSF (23) | IWS1 (2) | Jumonji (18) |
| LFY (1) | LIM (10) | LOB (49) | LUG (7) | MADS (117) |
| MBF1 (3) | MED6 (1) | MED7 (3) | mTERF (36) | MYB (157) |
| MYB-related (92) | NAC (115) | NOZZLE (1) | OFP (18) | Orphans (96) |
| PBF-2-like (4) | PHD (59) | PLATZ (14) | Pseudo (5) | RB (1) |
| Rcd1-like (3) | RWP-RK (13) | S1Fa-like (3) | SAP (1) | SBP (16) |
| SET (46) | Sigma70-like (6) | SNF2 (45) | SOH1 (1) | SRS (13) |
| SWI/SNF-BAF60b (17) | SWI/SNF-SWI3 (5) | TAZ (8) | TCP (25) | Tify (26) |
| TRAF (29) | Trihelix (27) | TUB (10) | ULT (2) | VOZ (3) |
| WRKY (74) | zf-HD (18) |
Predicted DNA-binding Proteins:
| Non-TFs (245) | TFs / Putative TFs (25) |