Nucleotide sequence of a novel diverged human homeobox gene encodes a DNA binding protein

Homeobox genes encode sequence specific DNA-binding proteins which have been implicated in the control of gene expression both in developing as well as in adult tissues (1). The carboxy terminus of the homeodomain exhibits similarity to the helix-turnhelix motif of DNA-binding regulatory proteins of prokaryotes and yeast, which suggested that the homeobox performed a similar function (2). Indeed, homeodomain containing proteins have been shown to be sequence specific DNA binding proteins (3). We report here the identification of a previously unknown human homeobox gene, HB9, which is 38-58% identical to the major classes of mammalian and Drosophila homeodomain. The HB9 cDNA clone (1204 nt) from a human activated B lymphocyte cDNA library and overlapping genomic clones (3.5 kb) were sequenced and an open reading frame was found which when translated encoded a homeobox. The predicted HB9 protein has a molecular weight of 54 kd and is enriched for alanine (16%), proline (16%), and glycine (21 %) at the carboxy terminus (aa 346-427). HB9 is a basic protein with an extremely basic region which immediately follows the carboxy terminus of the homeodomain (aa 265 -275). A strongly acidic region (aa 314-327) is also present with a net negative charge of -12. In addition, a number of phosphorylation sites are predicted to exist including a cAMP/cGMP dependent site, a casein kinase H site, and 6 protein kinase C sites. The homeobox region of HB9 is highly homologous to a consensus sequence for homeobox containing proteins (19/21 aa). The most conserved portion of the homeobox spans the second helix in the helix-turn-helix motif and has been implicated in DNA binding (2, 3), amino acid residues 42-50 in this homeodomain. When the homeodomain from HB9 was compared to known mammalian homeodomains it was found to be only moderately conserved intermediate between the prototypic HOX families and the highly diverged POU domain contain proteins such as Oct-2, suggesting the existence of other diverged homeobox genes (Table 1). Furthermore, the HB9 homeodomain is only 38-58% identical to the maor classes of mammalian and Drosophila homeodomains. HB9 lacks the conserved pentapeptide IYPWM found in front of the homeodomain of many homeobox genes (4). Outside the homeodomain region, HB9 does not share any significant homology with other homeodomain proteins with the exception of some similarity to the murine HOX 2.6 protein (5). By our studies of expression, HB9 is likely to have an important role in regulating gene transcription in activated lymphocytes as well as in a limited number of developing tissues.