Identification of three additional genes contiguous to the glucocerebrosidase locus on chromosome 1q21: implications for Gaucher disease

Abstract

Gaucher disease results from the deficiency of the lysosomal enzyme glucocerebrosidase (EC 3.2.1.45). Although the functional gene for glucocerebrosidase (GBA) and its pseudogene (psGBA), located in close proximity on chromosome 1q21, have been studied extensively, the flanking sequence has not been well characterized. The recent identification of human metaxin (MTX) immediately downstream of psGBA prompted a closer analysis of the sequence of the entire region surrounding the GBA gene. We now report the genomic DNA sequence and organization of a 75-kb region around GBA, including the duplicated region containing GBA and MTX. The origin and endpoints of the duplication leading to the pseudogenes for GBA and MTX are now clearly established. We also have identified three new genes within the 32 kb of sequence upstream to GBA, all of which are transcribed in the same direction as GBA. Of these three genes, the gene most distal to GBA is a protein kinase (clk2). The second gene, propin1, has a 1.5-kb cDNA and shares homology to a rat secretory carrier membrane protein 37 (SCAMP37). Finally, cote1, a gene of unknown function lies most proximal to GBA. The possible contributions of these closely arrayed genes to the more atypical presentations of Gaucher disease is now under investigation.

Figure 1

Map of clones and subclones on chromosome 1q21. (A) The YAC clone MNG1 was subcloned to cosmid YC11 or YAC MNG4. The λ subclones were derived from MNG4. The sequences of cosmid and λ subclones were compared to the sequences of genes in the GenBank database. The shaded boxes represent the genes at this locus. Genes shown above the line are transcribed left to right; MTX is transcribed in the opposite direction. (psMTX is not transcribed.) (B) Expanded map of λ clones, showing the EcoRI plasmid subclones used for sequencing.

Figure 2

Schematic representation of the 75 kb of sequence surrounding the GBA gene. (A) Order of the seven genes and two pseudogenes at the locus. (B) Intron/exon organization of clk2, propin1, and cote1. Genes shown in boxes above the line are transcribed left to right. MTX is transcribed right to left.

Figure 3

Human multitissue Northern blot hybridized to clk2 cDNA (A), propin1 cDNA (B), cote1 cDNA (C), and β-actin cDNA (D). Lanes 1–8 are heart, brain, placenta, lung, liver, skeletal muscle, kidney, and pancreas, respectively.

Figure 4

Schematic illustration of the alignment of 5′ flanking regions of GBA and psGBA. Arrows represent Alu sequences. A large insert of 6113 bp contains eight complete Alu sequences and several partial Alu sequences. The remaining sequence has been aligned with 88% identity.