Molecular evolution of the human pgk-2 retroposon

The human phosphoglycerate kinase (Pgk) gene family includes the functional, Intronless Pgk-2 gene and the intronless ψhPgk-1 pseudogene, both of which are retroposons of the intron-containing Pgk-i gene. The divergence of the Pgk-2 retroposon from Pgk-1 is compared with that of the ψhPgk-1 retroposon from Pgk-1 to reveal nucleotide characteristics diagnostic of functional genes. A comparison of the human and mouse Pgk genes indicates that Pgk-2 has evolved more rapidly than Pgk-1 since the two genes diverged early in mammalian evolution, but that the lack of introns in Pgk-2 may have diminished inter-exon variation. The hypothesis that codon bias is related to expressIon level is shown not to hold for the Pgk genes; however, the idea that a deficiency of TA and CG dinucleotides and an excess of TG and CT dinucleotides contributes to codon bias is supported. Finally, the hypothesis that the Pgk-2 retroposon initially included a copy of the Pgk-1 housekeeping' promoter and subsequently evolved a tissue-specific promoter is examined and supported. It is concluded that this process involved the loss of the 5' CpG island present in the Pgk-1 gene, and that selection for cell type-specific expression of Pgk-2 at high levels has driven the divergence of this retroposon from its progenitor, Pgk-1.