Structural organization and complete sequence of the human α- N-acetylgalactosaminidase gene: Homology with the α-galactosidase A gene provides evidence for evolution from a common ancestral gene

Abstract

Human α- N-acetylgalactosaminidase (α-GalNAc; EC 3.2.1.49), the lysosomal glycohydrolase that cleaves α- N-acetylgalactosaminyl moieties in glycoconjugates, is encoded by a gene localized to chromosome 22q13→qter. The deficient activity of this enzyme results in Schindler disease, an autosomal recessive disorder characterized by the increased urinary excretion of glycopeptides and oligosaccharides containing α- N-acetylgalactosaminyl moieties. Recently, the 3.6-kb full-length α-GalNAc cDNA sequence was isolated and found to have remarkable nucleotide and predicted amino acid homology (55.8 and 46.9%, respectively) with the human α-galactosidase A (α-Gal A) cDNA. To investigate the possible evolutionary relatedness of the two glycosidases, the α-GalNAc chromosomal gene was isolated and characterized. Screening of a human genomic DNA cosmid library resulted in the identification of a clone, gAGB-1, with an ∼ 35-kb insert that contained the entire α-GalNAc gene. A single ∼ 15-kb EcoRI fragment of gAGB-1, which contained the complete 3.6-kb cDNA sequence, was digested and the subcloned fragments were sequenced in both orientations. The 13,709-bp α-GalNAc gene had nine exons ranging from 95 to 2028 bp and intronic sequences of 304 to 2684 bp. All exon/intron junctions conformed to the GT AG consensus rule. Analysis of 1.4 kb of 5′ flanking sequence revealed three Sp1 and two CAAT-like promoter elements. This region was GC-rich (56%), but no HTF island was identified. The gene contained six Alu-repetitive elements, all in the reverse orientation. Comparison of the structural organization of the α-GalNAc and the α-Gal A genes revealed that all six α-GalA introns were identically positioned in the homologous α-GalNAc exonic sequence. Two additional introns, 1 and 8, were identified in the α-GalNAc gene. The predicted amino acid sequences of α-GalNAc exons 2 through 7 and those of corresponding α-Gal A exons 1 through 6 were 46.2 to 62.7% identical. In contrast, there was little, if any, similarity between the deduced amino acid sequences of α-Gal A exon 7 and α-GalNAc exons 8 and 9. The remarkable amino acid identity and the identical exonic interruption by six introns of the α-GalNAc and α-Gal A genes suggest that this region in both genes is evolutionarily related and arose through duplication and divergence from a common ancestral gene.