THE PEM HOMEOBOX GENE - RAPID EVOLUTION OF THE HOMEODOMAIN, X-CHROMOSOMAL LOCALIZATION, AND EXPRESSION IN REPRODUCTIVE TISSUE

A hallmark of homeobox genes is their high degree of sequence conserva tion in distantly related species. Here, we report the chromosomal loc alization, sequence, and expression pattern of an orphan homeobox gene , Pen, that encodes a homeodomain (HD) that has undergone a surprising ly high rate of evolutionary change. The N-terminal portion of the Pen HD, which includes the first two alpha-helices, exhibits only 44% seq uence identity between rat Pen (r.Pem) and mouse Pen (m.Pem). This N-t erminal subdomain exhibited an extremely high frequency of nonsynonymo us substitutions, severalfold higher than other regions of the Pen pro tein. In contrast, the third helix, which is known to confer most of t he base-specific contacts of HDs with DNA, was almost identical in r.P em and m.Pem. Several lines of evidence suggested that the rat and mou se genes that we identified as Pen genes are true homologues: (1) the r.Pem and m.Pem genes both reside on the X chromosome; (2) they posses s identical exon/intron splice junctions; (3) they both encode a disti nctive motif upstream of the HD that is unique to Pen; and (4) the onl y m.Pem-like gene we were able to identify in the rat genome other tha n r.Pem was a pseudogene, r.Pem-ps, whose sequence and chromosomal loc alization indicated that it was derived by reverse transcription and r einsertion into the genome. The functional r.Pem gene is selectively e xpressed in placenta, testis, epididymis, and ovary. This expression p attern is of interest since other genes transcribed in reproductive ti ssue have also been shown to undergo high rates of sequence divergence . The high rate of amino acid substitutions in the N-terminal region o f the Pen HD suggests the possibility of species-specific directional selection. (C) 1996 Academic Press, Inc.