CCAAT-Dr1 Genomic sequences

Minimum number of tobacco CCAAT-Dr1 genes: 3

Count of tobacco CCAAT-Dr1 sequences: 6

Pfam accession: CCAAT-Dr1

SHOULD possess CCAAT-Dr1 domain and COULD   possess CBFD_NFYB_HMF NF-YB domains

The CCAAT-Dr1 domain is characteristic of the CCAAT-Dr1 transcription factor family. There are two sequences belonging to this family in Arabidopsis thaliana, a multiple alignment of the full length of both proteins was used to build an hmm, to find more members of this family.

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 Schuffl, 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).


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: 2

Number of singlets: 3

First 55 aa – 1

18 aa – 48 aa – 2

48 aa – end – 1

First 18 aa – 2

3 x 18-48 or 1-18

Total minimum number – 3

Search sequences and info

Transcription factor sequences
CCAAT-Dr1_9 [comment=first 55 amino acids] ET044671
CCAAT-Dr1_13 [comment=18-48 amino acids] ET046285
CCAAT-Dr1_15 [comment=48 amino acids to end] ET045288
CCAAT-Dr1_16 [comment=first 18 amino acids] ET046183
CCAAT-Dr1_17 [comment=18-48 amino acids] ET045289
CCAAT-Dr1_18 [comment=first 18 amino acids] ET048192

Tobacco published genes related to transcription factor family CCAAT-Dr1
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