BACE Maps to Chromosome 11 and a BACE Homolog, BACE2 , Reside in the Obligate Down Syndrome Region of Chromosome 21

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Abstract
Abundant deposition of amyloid-β (in senile plaques) is a key neuropathological hallmark of Alzheimer's disease (AD). The major component of plaques is the 39– to 43–amino acid amyloid-β peptide. Amyloid-β is generated via proteolytic processing of the amyloid precursor protein (APP) by two proteases, β- and γ-secretase, that cleave at the amino- and carboxyl-terminal ends of the amyloid-β domain, respectively. Candidates for these enzymes have recently been reported. Presenilin 1 has been proposed to be either the γ-secretase or at least necessary for the enzyme's activity ([1][1]). The β-site APP cleaving enzyme (BACE) is a newly identified transmembrane aspartyl protease possessing β-secretase activity ([2][2]). Our computer-based search for genomically mapped DNA sequences homologous to BACE led to the identification of a BACE homologue that we have termed BACE2 . We initially set out to determine the chromosomal localization of BACE by identifying mapped ESTs (expressed sequence tags) encoding identical amino acid sequences. For this purpose, the complete amino acid sequence of BACE was used to screen various GenBank databases in the National Center for Biotechnology Information (NCBI) website ([www.ncbi.nlm.nih.gov][3]). Specifically, BACE was first screened against the “human ests” database using the program “tblastn”. ESTs with identical coding sequences included [AI290317][4],[R55398][5], [AF150387][6], [H60273][7], [AA293614][8], and [AA298516][9], among others. The largest of these was [AF150387][6] (1114 nucleotides). The previous chromosomal mapping of several of these ESTs permitted the chromosomal localization of BACE to the long arm of chromosome 11. Among these, R55298 had been previously mapped to 11q23.2-11q23.3 (see accompanying Technical Response by Fan et al .). A similar screen of the “dbest” database identified the exact match EST, [H60581][10]. This EST had been previously localized to centimorgan position 121.037 on the summary map for chromosome 11, which can be accessed in “The Genetic Location Database” at web address ([cedar.genetics.soton.ac.uk/pub/chrom11/map.htm][11]). Additional screening with the BACE amino acid sequence led to the retrieval of two full-length cDNAs ([AF050171][12], [AF117892][13]) from the “nr” database. Both of these cDNAs encode a novel transmembrane aspartyl protease (BACE2) that is highly homologous to BACE. One of the BACE2 cDNAs, [AF050171][12], was previously localized to the long arm of chromosome 21 at 21q22.3. Further screening of the “htgs” database led to the retrieval of a phase 2 ordered cosmid contig ([AJ011929][14]; HSMX1). By comparing the nucleotide sequence of [AF050171][12] with that of the cosmid contig, we determined that the contig contains a portion of the genomic sequence of BACE2 starting at nucleotide 418 and ending at nucleotide 1863. The cosmid contig containing the BACE2 gene is derived from chromosome 21, specifically between the loci D21S349 and MX1. The map position of these loci is consistent with the cytogenetic localization of BACE2 to chromosome 21q22.2-21q22.3. This portion of chromosome 21 contains the obligate Down syndrome (DS; trisomy 21) region, a minimal region of chromosome 21 that must be inherited in a trisomic state for expression of the constellation of features and symptoms characteristic of DS. BACE and BACE2 exhibit 52% amino acid sequence identity and 68% similarity. BACE2 contains two aspartyl protease active sites at virtually identical positions to the two active sites in BACE ([Fig. 1][15]). The amino acid sequences of BACE and BACE2 are divergent only at the COOH-terminal 30 amino acids and the NH2-terminal 80 amino acids. The divergent COOH-terminal regions in BACE and BACE2 both contain predicted single membrane-spanning domains ([Fig. 1][15]). The significant sequence similarity and predicted topology of BACE and BACE2 suggest that both proteins are transmembrane aspartyl proteases and that both are candidates for the β-secretase involved in AD. ![Figure 1][16] Figure 1 Amino acid sequence comparison of BACE and BACE-2. Bold amino acids indicate conserved aspartyl protease active sites. A line above or below the sequence indicates the putative single transmembrane domain. It is interesting that BACE2 maps to the obligatory DS region of chromosome 21. This implies that in addition to the contribution of a third copy of the APP gene ([3][17]), a third copy of BACE2 may also significantly contribute to enhanced amyloid-β deposition inevitably observed in the brains of middle-aged DS patients. Based on these data, DS patients would be expected to not only express more substrate for amyloid-β production (APP) but also more of a protease (BACE2) that would be predicted to cleave at the β-secretase site of APP, thereby exacerbating the release of amyloid-β. The identification of BACE and BACE2 as strong candidates for β-secretase provides novel molecular targets for mechanistic (protein-based) high-throughput drug screening for specific protease inhibitors. Identification of such inhibitors could afford a potentially powerful new generation of AD and DS therapeutics. Furthermore, the precise chromosomal mapping of BACE and BACE2 to the long arms of chromosomes 11 and 21, respectively, should greatly facilitate attempts to test these genes for genetic linkage to AD. 1. [↵][18]1. B. De Strooper 2. et al. , Nature 391, 387 (1998); [OpenUrl][19][CrossRef][20][PubMed][21] 1. M. S. Wolfe 2. et al. , Nature 398, 513 (1999). [OpenUrl][22][CrossRef][23][PubMed][24] 2. [↵][25]1. R. Vassar 2. et al. , Science 286, 735 (1999). [OpenUrl][26][Abstract/FREE Full Text][27] 3. [↵][28]1. R. E. Tanzi 2. et al. , Science 235, 880 (1987). [OpenUrl][29][Abstract/FREE Full Text][30] # BACE Maps to Chromosome 11 and a BACE...