CCAAT-HAP3 Genomic sequences

Minimum number of tobacco CCAAT-HAP3 genes: 15

Count of tobacco CCAAT-HAP3 sequences: 18

Pfam accession: NF-YB

SHOULD possess NF-YB domain and COULD   possess CBFD_NFYB_HMF domain but SHOULD NOT possess CCAAT-Dr1 domain

Proteins that bind to the CCAAT motif were first characterized in the yeast Saccharomyces cerevisiae through analysis of mutants with reduced levels of expression of the CYC1 gene (encoding iso-1-Cyt c) (Guarente et al., 1984; Hahn et al., 1988). The CYC1 promoter comprises two UAS, one of which (UAS2) contains an inverted CCAAT motif that is required for UAS2-directed transcription. Activation of transcription from UAS2 requires HAP2, HAP3, and HAP5 (Pinkham and Guarente, 1985; Pinkham et al., 1987; Hahn et al., 1988; McNabb et al., 1995), which form a heterotrimeric CCAAT-box-binding complex. The yeast HAP complex recruits a fourth polypeptide, HAP4 (Forsburg and Guarente, 1989), which does not bind to DNA but associates with the HAP2,3,5 complex and activates transcription through an acidic domain. The HAP complex appears to control expression of genes important for mitochondrial biogenesis (de Winde and Grivell, 1993), demonstrated by the fact that yeast hap mutants show identical pleiotropic phenotypes, with a general reduction in cytochromes and reduced growth on nonfermentable carbon sources.

CCAAT-box-related motifs have also been identified in the promoters of a variety of vertebrate genes. A range of transcription factors has been shown to bind to different CCAAT boxes, with varying levels of specificity (Dorn et al., 1987; Raymondjean et al., 1988), and each is thought to play a distinct role in gene expression or DNA replication (Santoro et al., 1988). Direct homologs of the yeast HAP complex (called NF-Y, CP1, or CBF) have been identified in vertebrates (Maity et al., 1990; Becker et al., 1991; Li et al., 1992; Sinha et al., 1995). The individual vertebrate HAP subunits showed a remarkable similarity to the yeast homologs over short domains (Maity et al., 1990; Vuorio et al., 1990), which is sufficient to enable formation of a functional heterologous complex between the human HAP2 homolog and yeast HAP3 and HAP5 (Becker et al., 1991). However, outside of the highly conserved core protein motifs associated with DNA binding and subunit interactions, there is considerable divergence. Furthermore, there is no HAP4 homolog. Instead, the vertebrate HAP complex probably interacts with other classes of transcription factors to influence the level of transcription (Bellorini et al., 1997).

Based on their presence in other eukaryotes and sequence conservation between related plant gene promoters, putative CCAAT-box motifs have been identified for several plant genes (Rieping and Sch?ffl, 1992; Kehoe et al., 1994; Ito et al., 1995). As with vertebrates, there is no unifying expression pattern for plant genes containing putative CCAAT-promoter elements, indicating that they may play a complex role in regulating plant gene transcription, with greater similarity to the vertebrate model than to the yeast system. A homolog with sequence similarity to HAP3 has been isolated from maize (Li et al., 1992), and recently, a HAP2 homolog was characterized from Brassica napus (Albani and Robert, 1995).

Papers

Lotan, T; Ohto, M; Yee, KM; West, MA; Lo, R; Kwong, RW; Yamagishi, K; Fischer, RL; Goldberg, RB; Harada, JJ. Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryo development in vegetative cells. Cell 1998.93(7):1195-205 PMID: 9657152

Gusmaroli, G; Tonelli, C; Mantovani, R. Regulation of novel members of the Arabidopsis thaliana CCAAT-binding nuclear factor Y subunits. Gene 2002.283(1-2):41-8 PMID: 11867211

Edwards D, Murray JA, Smith AG Multiple genes encoding the conserved CCAAT-box transcription factor complex are expressed in Arabidopsis. Plant Physiol. 1998 Jul;117(3):1015-22. PMID: 9662544



Number of contigs: 18

Number of singlets: 6

First half of the domain – 1

Last 20 aa – 1

Second half of the domain – 1

3 prime end of first half (FISFIT) – 1

First 30 aa – 1

Number of full – 13

Total minimum number – 15




Search sequences and info


Transcription factor sequences
Locus
Description
NCBI
CCAAT-HAP3_2 [comment=Full] ET048854
ET050525
CCAAT-HAP3_3 [comment=full] ET043736
ET049050
CCAAT-HAP3_4 [comment=first half (to FISFIT)] ET043386
ET046872
ET042468
CCAAT-HAP3_5 [comment=full] ET049530
ET048328
ET045801
CCAAT-HAP3_7 [comment=full] ET049366
ET044154
ET044155
ET049076
CCAAT-HAP3_8 [comment=full] ET048327
ET042491
ET042100
ET050116
CCAAT-HAP3_9 [comment=full] ET042593
ET046944
ET042594
ET043826
CCAAT-HAP3_11 [comment=full] ET048169
ET042203
ET043095
ET049584
ET049583
CCAAT-HAP3_13 [comment=full] ET041677
ET046720
ET048578
ET046116
ET046721
ET048921
CCAAT-HAP3_14 [comment=full] ET042172
ET045138
ET046660
ET046995
ET042171
ET046659
CCAAT-HAP3_15 [comment=full] ET044285
ET049534
ET048575
ET044284
ET042316
ET048833
ET044283
CCAAT-HAP3_16 [comment=full] ET045302
ET049848
ET043458
ET045301
ET044413
ET041811
ET041812
CCAAT-HAP3_17 [comment=full] ET042726
ET049618
ET047998
ET047350
ET042725
ET046402
ET047115
ET051637
CCAAT-HAP3_18 [comment=full] ET042617
ET049378
ET047352
ET045157
ET047690
ET049379
ET047351
ET047691
CCAAT-HAP3_19 [comment=last 20 amino acids] ET043197
CCAAT-HAP3_20 [comment=second half] ET045381
CCAAT-HAP3_22 [comment=short. 3 prime end of first half (FISFIT)] ET044517
CCAAT-HAP3_23 [comment=short first 30 amino acids] ET043196


Tobacco published genes related to transcription factor family CCAAT-HAP3
Family Genbank ID Name
Authors of this site:

Paul J Rushton
Marta T. Bokowiec
Xianfeng (Jeff) Chen
Thomas (Tom) W Laudeman
Jennifer F. Brannock
Michael P. Timko

Contact:

pr8y@virginia.edu