The gamma-secretase complex comprises presenilin (PS), nicastrin (NCO, anterior pharynx-defective 1 (Aph1), and presenilin enhancer 2 (Pen2). PS has two homologues, PS1 and PS2. Aph1 has two isoforms, Aph1 a and Aph1b, with the former existing as two splice variants Aph1aL and Aph1aS. Each complex consists of one subunit each, resulting in six different gamma-secretases. To better understand the functional differences among the gamma-secretases, we reconstituted them using a yeast system and compared Notch1-cleavage and amyloid precursor protein (APP)-cleavage activities. Intriguingly, PS2/Aph1b had a clear substrate specificity: APP-Gal4, but not Notch-Gal4, was cleaved. In HEK cell lines expressing defined gamma-secretase subunits, we showed that PS1/Aph1b, PS2/Aph1aL, PS2/Aph1aS and PS2/Aph1b gamma-secretase produced amyloid beta peptide (A beta) with a higher A beta 42+A beta 43-to-A beta 40 (A beta 42(43)/A beta 40) ratio than the other gamma-secretases. In addition, PS2/Aph1aS gamma-secretase produced less Notch intracellular domain (NICD) than did the other 5 gamma-secretases. Considering that the A beta 42(43)/A beta 40 ratio is relevant in the pathogenesis of Alzheimer's disease (AD), and that inhibition of Notch cleavage causes severe side effect, these results suggest that the PS2/Aph1aS gamma-secretase complex is a potential therapeutic target in AD. (C) 2016 The Authors. Published by Elsevier Inc.