TOBFAC: The database of tobacco transcription factors
Family: Homeodomain
Minimum number of tobacco Homeodomain genes: 129
Count of tobacco Homeodomain sequences: 142
Pfam accession: Homeobox KNOX1 KNOX2
SHOULD possess Homeobox KNOX1 KNOX2 domains and COULD possess ELK HALZ HD-ZIP_N PHD domains
Homeodomain proteins were initially discovered during the study of homeotic mutants in Drosophila and have since been shown to play important roles in the developmental regulation of all eukaryotic lineages. The homeodomain is a 60 amino acid domain that consists of three helices and an N-terminal arm . The third helix lies in the major groove of the DNA, and along with the N-terminal arm, is responsible for DNA recognition. The first homeobox gene found in plants was knotted1 (kn1) that was isolated from maize plants carrying a dominant mutation that alters leaf development . Subsequently, other plant homeodomain proteins were found and these include hooded in barley that gives rise to modified flowers, glabra2 that results in a failure to develop trichomes and Bell1 that is involved in ovule development. Additionally, the homeodomain proteins WUSCHEL (WUS) and SHOOTMERISTEM-LESS (STM) have positive functions in regulating stem cell fate in the shoot apical meristem . Plants also contain homeodomain leucine zipper proteins (HDZip) where the homeodomain is associated with a leucine zipper. These are found exclusively in the plant kingdom and appear to be regulators that response to environmental factors .
Bharathan, G; Janssen, BJ; Kellogg, EA; Sinha, N. Did homeodomain proteins duplicate before the origin of angiosperms, fungi, and metazoa? Proc. Natl. Acad. Sci. U.S.A. 1997. 94(25):13749-53 PMID: 9391098
Chan, RL; Gago, GM; Palena, CM; Gonzalez, DH. Homeoboxes in plant development. Biochim. Biophys. Acta 1998. 1442(1):1-19 PMID: 9767075
Scott, MP; Tamkun, JW; Hartzell, GW. The structure and function of the homeodomain. Biochim. Biophys. Acta 1989. 989(1):25-48 PMID: 2568852
Sessa G, Morelli G, Ruberti I. DNA-binding specificity of the homeodomain-leucine zipper domain. J Mol Biol. 1997 Dec 5;274(3):303-9. PMID: 9405140
Homeodomain genes were isolated from the tobacco GSSs by searches with the homeodomain from at least one member of each of the major subgroups of plant homeodomain protein (Chan et al., 1998). This approach was crucial to success as, unlike the other transcription factor families, searches with a homeodomain from one family often only resulted in isolation of genes from that family and not the complete homeodomain family. The different groups of tobacco homeodomain genes are quite dissimilar. To illustrate this, searches with the homeodomain from glabra2 resulted in 74 hits whereas searches with knotted1 only yielded 15 hits and none of these were present in those obtained with glabra2. The combined results from all searches revealed a minimum of 128 homeodomain genes in the tobacco genome.
Number of N terminal – 19
Number of C terminal – 29
Number of full – 88
Number of genes with middle part of domain – 6
Total – 117
There are 13 published homeodomain genes that were not present in GSSs search (except knotted1) and they were added manually to the data set.
Total minimum number – 129
| Family | Genbank ID | Name |
| Homeodomain | AF544054 | knotted 3 |
| Homeodomain | AF544053 | knotted 2 |
| Homeodomain | AF544052 | knotted 1 |
| Homeodomain | AY169493 | H1 |
| Homeodomain | AY101610 | Hfi22 |
| Homeodomain | AB025715 | homeobox 22 |
| Homeodomain | AB025714 | homeobox 20 |
| Homeodomain | AB025713 | homeobox 9 |
| Homeodomain | AJ006180 | NTHD2 |
| Homeodomain | AJ006179 | HD1 |
| Homeodomain | AB025573 | NTH1 |
| Homeodomain | AB004797 | NTH23 |
| Homeodomain | AB004785 | NTH15 |
Paul J Rushton
Marta T. Bokowiec
Xianfeng (Jeff) Chen
Thomas (Tom) W Laudeman
Jennifer F. Brannock
Michael P. Timko
