Ubiquilin was originally identified as a presenilin-interacting protein. We previously reported that ubiquilin interacts with both the loop and carboxyl terminus of presenilin proteins and that the ubiquitin-associated (UBA) domain of ubiquilin, which binds poly ubiquitin chains, is important for mediating this interaction. In the present study, we examined whether ubiquitination of presenilin-2 (PS2) is required for interaction with ubiquilin-1 by mutating lysine residues that may be targets for ubiquitination in the presenilin loop and carboxyl terminus regions. Mutation of two lysine residues in the PS2-loop region suggested that ubiquitination is not required for interaction with ubiquilin-1 and may, in fact, even negatively regulate the interaction. Similarly, we found that ubiquitination of the PS2 carboxyl terminus (PS2-C-terminus) is not required for interaction with ubiquilin-1, although our results suggest that it could play some role. Instead, we found that the mutation of either one of the two lysine residues in the carboxyl terminus of PS2 or the proline residues in the highly conserved PALP motif in this region results in destabilization of the mutant PS2 polypeptides because of increased degradation by the proteasome. Furthermore, by GST-pull-down assays we found that the mutant polypeptides were unable to bind ubiquilin, suggesting that loss of ubiquilin interaction leads to destabilization of presenilin polypeptides. Paradoxically, however, knockdown of ubiquilin expression by RNA interference did not alter the rate of turnover of PS2 proteins in cells. Instead, we found that PS2 synthesis was reduced, and PS2 fragment production was increased, suggesting that ubiquilin expression modulates biogenesis and endoproteolysis of presenilin proteins.