Abstract
γ-Secretase is a four subunit, 19-pass transmembrane enzyme that cleaves amyloid precursor protein (APP), catalyzing the formation of amyloid beta (Aβ) peptides that form amyloid plaques, which contribute to Alzheimer’s disease (AD) pathogenesis. γ-Secretase also cleaves Notch, among many other type I transmembrane substrates. Despite its seemingly promiscuous enzymatic capacity, γ-secretase activity is tightly regulated. This regulation is a function of many cellular entities, including but not limited to the essential γ-secretase subunits, nonessential (modulatory) subunits, and γ-secretase substrates. Regulation is also accomplished by an array of cellular events, such as presenilin (active subunit of γ-secretase) endoproteolysis and hypoxia. In this review we discuss how γ-secretase is regulated with the hope that an advanced understanding of these mechanisms will aid in the development of effective therapeutics for γ-secretase-associated diseases like AD and Notch-addicted cancer.
Introduction
γ-Secretase is an intramembrane aspartyl protease that cleaves an array of type 1 transmembrane substrates, of which amyloid precursor protein (APP) and Notch are the most widely studied. APP undergoes sequential proteolytic processing by β-secretase (BACE1) and γ-secretase to generate amyloid beta (Aβ) peptides, which are 37–43 amino acids long. Notch, a protein that resides on the surface of signal-receiving cells as a heterodimeric receptor, is also subject to a series of proteolytic cleavages (Figure 1). The scientific scrutiny sustained by both APP and Notch results from their role in disease: aberrant γ-secretase cleavage of APP and Notch can lead to Alzheimer’s disease (AD) and cancer, respectively. γ-Secretase is an important potential drug target for both diseases and γ-secretase inhibitors (GSIs) and modulators (GSMs) are currently in clinical trials.
Figure 1
Biochemical studies indicated that γ-secretase activity is catalyzed by the presenilin (PS)-containing macromolecular complex (Li et al.,
Figure 2

γ-Secretase complex formation and regulatory roles of individual essential subunits. The γ-Secretase complex is formed by the sequential assembly of Aph1, nicastrin, presenilin, and Pen-2. First, Aph-1 and nicastrin come together to form the scaffold. Next, full length presenilin is incorporated. Last, Pen-2 is recruited and full length presenilin is endoproteolysed into presenilin-NTF/CTF, activating the enzyme. Nicastrin, a heavily glycosylated single-pass transmembrane protein, plays a role in scaffolding, enzyme stabilization, substrate recognition, and trafficking. Nicastrin’s amino acids 312–340 are important for substrate recognition and deletion of these residues reduces γ-secretase activity and nicastrin’s interaction with APP and Notch. Furthermore, mutation of nicastrin’s C213 and C230 leads to different impact on processing of APP and Notch, underscoring nicastrin’s role in substrate selectivity. Aph-1, a 7-pass transmembrane protein with 3 human isoforms, is crucial for scaffolding and stability, and may have an additional role in determining length of Aβ species produced depending on which isoform is incorporated into the γ-secretase complex. The GXXXG motif in Aph-1 is critical for γ-secretase complex assembly. Presenilin, a 9-pass transmembrane protein with 2 isoforms, is the catalytic subunit of γ-secretase, and full length presenilin is a zymogen that must be endoproteolysed into NTF/CTF to be enzymatically active. Mutations in presenilin1 and presenilin2-encoding genes account for the majority of genetic mutations leading to Familial Alzheimer’s disease. Pen-2, a 2-pass transmembrane protein, is required for presenilin endoproteolysis and γ-secretase activation, but also may play an endoproteolysis-independent role in γ-secretase regulation. Active γ-secretase constitutes a small percentage of total γ-secretase and resides primarily in the plasma membrane.
γ-Secretase processing of its substrates produces distinct amino and carboxy termini with variable functions; some products of γ-secretase cleavage function as transcriptional regulators while others are thought to play roles in signaling, cell adhesion, and cytoskeletal dynamics. As the list of putative γ-secretase substrates continues to grow, now reaching over 90 reported proteins (Haapasalo and Kovacs,
γ-Secretase activity is regulated by the assembly of its four essential subunits as well as at the level of the entire complex. Extensive investigation of the former revealed that each of the four essential γ-secretase subunits is tightly and independently controlled. More recently, the importance of regulation of the entire complex has emerged, suggesting additional levels of modulation in γ-secretase function. CD147, phospholipase D1, TMP21, GPR3, γ-secretase activating protein (GSAP), syntaxin-1, Arc, voltage-dependent anion channel 1 (VDAC1), contactin-associated protein 1 (CNTNAP1), TPPP, NDUFS7, Erlin-2, β-arrestin-1, β-arrestin-2, Hif-1α and Nexin 27 have all been implicated as nonessential γ-secretase interacting partners that modulate γ-secretase activity (Zhou et al., 2005; Cai et al.,
We begin by discussing the four essential subunits of γ-secretase, their physiological roles, and, where known, the way in which they regulate γ-secretase activity. Next we move to γ-secretase modulation by nonessential γ-secretase interacting partners, in particular GSAP and Hif-1α, which have been convincingly shown to specifically engage with the active γ-secretase complex. Last we comment on γ-secretase’s regulation by its substrate, APP.
γ-Secretase is regulated by its four essential subunits
γ-Secretase’s enzymatic promiscuity may on first glance suggest a kind of rampant cleavage activity that indiscriminately chops up anything in its way. Actually, the opposite is true. γ-Secretase may be flexible in its choice of substrate and cleavage site, but its activity is controlled in the cell by a variety of mechanisms, not the least of which is regulation of active complex formation. Perhaps the most basic evidence for this is the finding that γ-secretase activity cannot be increased through the overexpression of PS alone (Levitan et al.,
The issue is further complicated by the fact that active complexes fall into a wide range of activities with respect to both catalytic efficiency and substrate specificity. Despite the deceptive language used here to describe γ-secretase as “active” and “inactive,” γ-secretase activity is far from a simple on/off switch. Let’s look at the statistics: assuming γ-secretase complexes have a 1:1:1:1 ratio of all essential subunits (Sato et al.,
The inherent complexity of γ-secretase can be put into perspective by comparing it to signal peptide peptidase (SPP), the only other family of intramembrane aspartyl proteases. Unlike γ-secretase, SPP appears to function alone without the participation of other protein co-factors (Weihofen et al., 2002), although it does form higher order oligomers (Nyborg et al.,
Presenilin
PS1 and and its less abundant isoform PS2, are ~50 kDa multipass transmembrane proteins that contain the catalytic core of the γ-secretase complex. These proteins were implicated in γ-secretase function when knock-out of PS1 resulted in severely reduced γ-secretase activity (De Strooper et al.,
PS is synthesized as a full length (FL) protein but PS-FL is unstable and is quickly either endoproteolysed or degraded (Ratovitski et al.,
As mentioned previously, the formation of an active complex is only the first hurdle in regulating γ-secretase activity in the cell. An added layer of regulation resides in the choice to form PS1 vs. PS2-containing complexes. Different PS variants play different, albeit overlapping, roles as evidenced by genetic knock out studies (De Strooper et al.,
PS1 is not only the more active of the two isoforms, but also may be the more amyloidogenic. A reconstitution study in which four γ-secretase isoforms (PS1–aph-1a, PS1–aph-1b, PS2–aph-1a, PS2–aph-1b) were analyzed showed that PS1 complexes form more aggregation-prone Aβ42 (relative to Aβ40) compared to PS2 complexes (Lee et al.,
Pen-2
Pen-2, a ~10 kDa protein with two TMDs (Crystal et al.,
The roles of Pen-2 in PS endoproteolysis and γ-secretase activity raised the question—is Pen-2 necessary for γ-secretase activity per se, or is Pen-2-inspired endoproteolysis of PS the only requirement for activity? To answer this question the catalytically active PS1ΔE9 endoproteolysis deficient mutant was expressed in Pen-2−/– MEFs and found to have no activity, suggesting that Pen-2 is required for γ-secretase activity per se, and not just for endoproteolysis of PS (Bammens et al.,
Nicastrin
In the search for cofactors required for γ-secretase activity, Nct, a type I transmembrane glycoprotein, was the first to be discovered through coimmunoprecipitation with PS1-directed antibody (Yu et al., 2000). A 1.95 Å-resolution crystal structure of Nct from an amoeboid eukaryote Dictyostelium purpureum has been solved (Xie et al., 2014). Four hydrophilic residues in the proximal one third of the N-terminal portion of the Nct TMD are critical for interaction between Nct and the rest of the γ-secretase complex (Capell et al.,
While Nct’s role as the substrate-binding subunit of γ-secretase may be controversial, its importance in γ-secretase regulation is uncontested: mutation of two conserved cysteine residues to serine (C213S and C230S) in Nct’s ectodomain resulted in differential γ-secretase processing of APP and Notch in MEF cells lacking endogenous Nct. In particular, APP processing was reduced compared to Notch, suggesting that Nct plays a role in substrate selectivity, although the exact mechanism was not identified (Pamrén et al.,
Aph-1
Aph-1, a ~29 kDa protein with seven TMDs, was discovered in the same genetic screen as Pen-2 (Francis et al.,
Humans have two Aph-1 genes that give rise to three versions of the Aph-1 protein (Aph-1aS, Aph-1aL, Aph-1b) due to alternative splicing of the Aph-1a gene (Shirotani et al.,
γ-Secretase is regulated by modulatory proteins
γ-Secretase is regulated not only by its four essential subunits, but also by other pathways and proteins, many of which have been identified through LCMS analysis (Teranishi et al.,
GSAP
GSAP is a ~98 kDa holoprotein whose ~16 kDa processed fragment was identified as a γ-secretase-interacting partner. The story began when GSAP was implicated in the mechanism by which imatinib (Gleevec) selectively lowers Aβ without affecting Notch cleavage: a photoactivatable form of imatinib specifically labeled GSAP and not any of the γ-secretase subunits. Further investigation revealed that GSAP may form a complex with γ-secretase and APP-CTF, thereby imparting γ-secretase with substrate specificity for APP over Notch. GSAP RNAi mice crossed with double transgenic APPswe and PS1ΔE9 AD model mice presented a reduced Aβ burden (He et al.,
Hif-1α
Hif-1α, a ~93 kDa protein, is a master regulator of cellular response to hypoxia. While Hif-1α’s properties as a transcription factor and role in Notch signaling are well documented (Gustafsson et al.,
Figure 3

Modulatory-protein-based regulation of γ-secretase. Hif-1α, a master regulator of cellular response to hypoxia, is a γ-secretase interacting partner. In the presence of sufficient oxygen, no Hif-1α is produced. However, in oxygen-deficient conditions, Hif-1α is upregulated. Hif-1α binding to γ-secretase enhances γ-secretase activity by increasing the ratio of active:inactive γ-secretase complexes in the cell, thereby increasing γ-secretase cleavage of its substrates, such as APP and Notch. The implication is twofold: first, inactive γ-secretase complexes are physiologically important, and second, γ-secretase can be temporally regulated.
γ-Secretase is regulated via its substrate, APP
APP proteolysis falls into one of two pathways: either APP is cleaved sequentially by α and γ-secretase in the nonamyloidogenic pathway, or it is cleaved by β and γ-secretase in the amyloidogenic pathway. α-Secretase cleavage of APP occurs in the Aβ region, which precludes Aβ production, so the choice to preferentially undergo more α cleavage can mean the difference between healthy and disease states. What factors determine the decision to participate in one pathway over the other? It has been suggested that α-secretase competes with β-secretase for the APP substrate, thereby lowering Aβ formation (Lammich et al.,
Figure 4

Substrate-based regulation of γ-Secretase. α or β-secretase cleave amyloid precursor protein to generate αCTF or βCTF, respectively. αCTF and βCTF, which are γ-secretase substrates, can then interact with γ-secretase to form a substrate-enzyme complex. The substrate inhibitory domain (ASID) in αCTF and βCTF interacts with γ-secretase in a location distinct from both the active site and the substrate binding site of the enzyme. Binding of αCTF to γ-secretase results in a low-productivity complex: the ASID in αCTF inhibits γ-secretase activity for Aβ production. ASID in βCTF is a less potent inhibitor of γ-secretase. The implication is that α-secretase cleavage potentiates γ-secretase inhibition by at least two mechanisms: first, α-secretase cleaves APP in the middle of the Aβ region, precluding Aβ formation, and second, α-secretase cleavage results in formation of αCTF, which inhibits γ-secretase activity through its ASID. γ-Secretase cleavage of αCTF produces p3 and cleavage of βCTF produces the amyloidogenic Aβ.
Conclusion
γ-Secretase is regulated at many levels, including but not limited to regulation by “essential” subunits, complex formation, “nonessential” subunits, substrates, and lipid composition (Holmes et al.,
Currently, GSMs are being developed as a promising treatment for AD (Crump et al.,
Statements
Acknowledgments
We thank David B. Iaea for critically reading the manuscript. This work is supported by NIH grant R01AG026660 (Yue-Ming Li), R01NS076117 (Yue-Ming Li), Alzheimer Association IIRG-12-242137 (Yue-Ming Li), the MetLife Foundation (Yue-Ming Li), the JPB Foundation (Yue-Ming Li), training grant NIH T32 CA062948 (Danica Chiu), Mr. William H. Goodwin and Mrs. Alice Goodwin and the Commonwealth Foundation for Cancer Research, the Experimental Therapeutics Center of MSKCC, and the William Randolph Hearst Fund in Experimental Therapeutics.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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Summary
Keywords
γ-Secretase, Alzheimer’s disease, presenilin, β-amyloid, Notch, APP, Hif-1α
Citation
Gertsik N, Chiu D and Li Y-M (2015) Complex regulation of γ-secretase: from obligatory to modulatory subunits. Front. Aging Neurosci. 6:342. doi: 10.3389/fnagi.2014.00342
Received
25 November 2014
Accepted
09 December 2014
Published
06 January 2015
Volume
6 - 2014
Edited by
Xiongwei Zhu, Case Western Reserve University, USA
Reviewed by
Huaxi Xu, Sanford Burnham Medical Research Institute, USA; Guojun Bu, Mayo Clinic, USA
Copyright
© 2015 Gertsik, Chiu and Li.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution and reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Yue-Ming Li, Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, 10065 NY, USA e-mail: liy2@mskcc.org
This article was submitted to the journal Frontiers in Aging Neuroscience.
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