1.A.54 The Presenilin ER Ca²⁺ Leak Channel (Presenilin) Family

Alzheimer's disease (AD) is a progressive and irreversible neurodegenerative disorder that affects ~2% of the population in industrialized countries. Mutations in presenilins 1 and 2 (PS1 and PS2) account for ~40% of familial AD cases (Tandon and Fraser, 2002). Familial AD mutations and genetic deletions of presenilins have been associated with calcium (Ca²⁺) signaling abnormalities. Presenilins regulate capacitative calcium entry independently of gamma-secretase activity. Tu et al. (2006) have demonstrated that wild-type presenilins, but not PS1-M146V and PS2-N141I familial AD mutants, can form low-conductance divalent-cation-permeable ion channels in planar lipid bilayers. In experiments with PS1/2 double knockout mouse embryonic fibroblasts, they found that presenilins account for 80% of passive Ca²⁺ leak from the endoplasmic reticulum. Deficient Ca²⁺ signaling in double knockout fibroblasts can be rescued by expression of wild-type PS1 or PS2 but not by expression of PS1-M146V or PS2-N141I mutants. The ER Ca²⁺ leak function of presenilins is independent of their γ-secretase activity. The data of Tu et al. (2006) suggest a Ca²⁺ signaling function for presenilins and provide support for the 'Ca²⁺ hypothesis of AD.' The presenilin 1 calcium leak conductance pore involves TMSs 7 and 9, but not 6, as well as a hydrophilic catalytic cavity (Nelson et al., 2011).  Presenilins play a role in calcium-mediated lysosomal fusion (Bezprozvanny 2012; Coen et al. 2012).  Individual presenilin TMSs play roles in the cleavage of C99 and the generation of Abeta peptides (Schmidt et al. 2023).

Familial Alzheimer's disease (FAD) mutant presenilin 1 (PS1) (M146L) and PS2 (N141I) interact with the inositol 1,4,5-trisphosphate receptor (InsP3R) Ca²⁺ release channel and exert profound stimulatory effects on its gating activity in response to saturating and suboptimal levels of InsP3. These interactions result in exaggerated cellular Ca²⁺ signaling in response to agonist stimulation as well as enhanced low-level Ca²⁺ signaling in unstimulated cells. Parallel studies in InsP3R-expressing and -deficient cells revealed that enhanced Ca²⁺ release from the endoplasmic reticulum as a result of the specific interaction of PS1-M146L with the InsP3R stimulates amyloid beta processing, an important feature of AD pathology. These observations provide molecular insights into the 'Ca²⁺ dysregulation' hypothesis of AD pathogenesis and suggest novel targets for therapeutic intervention (Cheung et al., 2008).

Most cases of AD are idiopathic and are characterized by late onset (>60 years of age). A small fraction of AD cases (familial AD) are characterized by an earlier onset and genetic inheritance. Presenilins are 50 kDa proteins that contain nine transmembrane domains (Laudon et al., 2005) and reside in the endoplasmic reticulum (ER) membrane. They maintain a 9 TMS topology throughout the secretory pathway (Spasic et al., 2006). The complex of presenilins with nicastrin (NCT), APH-1 and PEN-2 subunits functions as γ-secretase, which cleaves the amyloid precursor protein (APP) and releases the amyloid β-peptide (Aβ), the principal constituent of the amyloid plaques in the brains of AD patients. Consistent with the role of presenilins as catalytic subunits of γ-secretase, familial AD mutations in presenilins affect APP processing. These familial AD mutations also result in deranged calcium (Ca²⁺) signaling (reviewed in Smith et al., 2005). Tu et al. (2006) established that presenilins function as passive ER Ca²⁺ leak channels and that the familial AD mutations of presenilins affect their ability to conduct Ca²⁺ ions. These results provide new insight into the normal physiological function of presenilins and strengthen the emerging connection between deranged neuronal Ca²⁺ signaling and AD.

Presenilin-1 (γ-secretase) is a multisubunit aspartate protease requiring the coordinated action of presenilins (PSs) (Wolfe and Kopan, 2004), nicastrin (NCT), PEN-2 and APH-1 and is crucial for the intramembrane proteolysis of type I membrane proteins such as the amyloid precursor protein (APP) and Notch. The catalytic component, PS1, is a polytopic membrane protein that undergoes endoproteolysis resulting in stable PS1 NH_2^- and COOH-terminal fragments (PS1-NTF and -CTF). PS1 has 9 TMSs (Spasic et al., 2006).

Presenilin-associated rhomboid-like (PARL) is an inner mitochondrial membrane rhomboid, belonging to a family of evolutionarily conserved integral membrane proteases that participate in signaling. The yeast orthologue is involved in mitochondrial fusion. PARL associates with presenilins 1 and 2 and cleaves type 1 transmembrane proteins. Parl^-/- mice undergo progressive atrophy leading to death, due to increased apoptosis. Parl^-/- cells are not protected against intrinsic apoptotic death stimuli by the dynamin-related mitochondrial protein OPA1 (Cipolat et al., 2006).

The hydrophilic 'catalytic pore' structure of γ-secretase is formed by TMSs 6, 7 and 9 of presenilin 1 (PS1), the catalytic subunit of γ-secretase in the membrane. The first hydrophobic region, putative TMS1 of PS1, is located in proximity to the catalytic GxGD and PAL motifs within the C-terminal fragment of PS1, facing directly the catalytic pore (Takagi et al., 2010).

Presenilins show a region of similarity (residues 217-305 in PS-2) with the 'Bacteroides development protein' (TC #9.A.18.1.2) BacA (residues 53-149 in this 420 aa protein) of Rhizobium meliloti (e-value of 0.001). Most homologues are from eukaryotes (both plants and animals), but a distant homologue is found in the halobacterial archaeon, Haloquadratum walsbyi (TC #1.A.54.2.1). Many other archaea encode homologues in their genomes, but they do not appear to be present in bacteria.

Kuo et al. 2015 examined two archaeal GxGD proteases (PSH and FlaK), with known three-dimensional structures. Both are in the same GxGD family as presenilin, a protein mutated in Alzheimer's Disease. They demonstrated that PSH and FlaK form cation channels in lipid bilayers. A mutation that affected the enzymatic activity of FlaK rendered the channel catalytically inactive and altered the ion selectivity, indicating that the ion channel and the catalytic activities are linked. Thus, PSH and FlaK, are true 'chanzymes' with interdependent ion channel and protease activity conferred by a single structural domain embedded in the membrane, supporting the proposal that higher-order proteases, including presenilin, have channel function.

Intramembrane proteolysis involves the cleavage of substrate proteins within their hydrophobic TMSs. Several families of intramembrane proteases have been identified including the aspartyl proteases Signal peptide peptidase (SPP) and its homologues, the SPP-like (SPPL) proteases SPPL2a, SPPL2b, SPPL2c and SPPL3 (see TC subfamily 1.A.54.3). As presenilin homologues, they employ a similar catalytic mechanism as the well-studied gamma-secretase. However, SPP/SPPL proteases cleave transmembrane proteins with a type II topology. Mentrup et al. 2020 summarized how phenotypes  are linked to the molecular function of the enzymes. At the cellular level, SPP/SPPL-mediated cleavage events provide specific regulatory switches. Then many pathways are influenced including signal transduction, membrane trafficking and protein glycosylation.

The transport reactions catalyzed by presenilins is:

Ca²⁺ and other cations (out) → Ca²⁺ and other cations (in)

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