12
Pen2 and Presenilin-1 Modulate the Dynamic Equilibrium of Presenilin-1 and Presenilin-2 -Secretase Complexes * S Received for publication, September 19, 2008, and in revised form, November 24, 2008 Published, JBC Papers in Press, November 25, 2008, DOI 10.1074/jbc.M807269200 Lisa Placanica ‡§1,2 , Leonid Tarassishin ‡1 , Guangli Yang , Erica Peethumnongsin , Seong-Hun Kim 3 , Hui Zheng , Sangram S. Sisodia , and Yue-Ming Li ‡§4 From the Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, the § Department of Pharmacology, Weill Graduate School of Medical Science of Cornell University, New York, New York 10065, the Huffington Center on Aging, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, and The Center for Molecular Neurobiology, The University of Chicago, Chicago, Illinois 60637 -Secretase is known to play a pivotal role in the pathogenesis of Alzheimer disease through production of amyloidogenic A42 peptides. Early onset familial Alzheimer disease muta- tions in presenilin (PS), the catalytic core of -secretase, invari- ably increase the A42:A40 ratio. However, the mechanism by which these mutations affect -secretase complex formation and cleavage specificity is poorly understood. We show that our in vitro assay system recapitulates the effect of PS1 mutations on the A42:A40 ratio observed in cell and animal models. We have developed a series of small molecule affinity probes that allow us to characterize active -secretase complexes. Further- more we reveal that the equilibrium of PS1- and PS2-containing active complexes is dynamic and altered by overexpression of Pen2 or PS1 mutants and that formation of PS2 complexes is positively correlated with increased A42:A40 ratios. These data suggest that perturbations to -secretase complex equilib- rium can have a profound effect on enzyme activity and that increased PS2 complexes along with mutated PS1 complexes contribute to an increased A42:A40 ratio. -Amyloid (A) 5 peptides are believed to play a causative role in Alzheimer disease (AD). A peptides are generated from the processing of the amyloid precursor protein (APP) by two proteases, -secretase and -secretase. Although -secretase generates heterogenous A peptides ranging from 37 to 46 amino acids in length, significant work has focused mainly on the A40 and A42 peptides that are the major constituents of amyloid plaques. -Secretase is a multisubunit membrane aspartyl protease comprised of at least four known subunits: presenilin (PS), nicastrin (Nct), anterior pharynx-defective (Aph), and presenilin enhancer 2 (Pen2). Presenilin is thought to contain the catalytic core of the complex (1– 4), whereas Aph and Nct play critical roles in the assembly, trafficking, and sta- bility of -secretase as well as substrate recognition (5, 6). Lastly Pen2 facilitates the endoproteolysis of PS into its N-terminal (NTF) and C-terminal (CTF) fragments thereby yielding a cat- alytically competent enzyme (5, 7–10). All four proteins (PS, Nct, Aph1, and Pen2) are obligatory for -secretase activity in cell and animal models (11, 12). There are two homologs of PS, PS1 and PS2, and three isoforms of Aph1, Aph1aS, Aph1aL, and Aph1b. At least six active -secretase complexes have been reported (two presenilins three Aph1s) (13, 14). The sum of apparent molecular masses of the four proteins (PS1-NTF/ CTF 53 kDa, Nct 120 kDa, Aph1 30 kDa, and Pen2 10kDa) is 200 kDa. However, active -secretase complexes of varying sizes, ranging from 250 to 2000 kDa, have been reported (15–19). Recently a study suggested that the -secretase com- plex contains only one of each subunit (20). Collectively these studies suggest that a four-protein complex around 200 –250 kDa may be the minimal functional -secretase unit with addi- tional cofactors and/or varying stoichiometry of subunits exist- ing in the high molecular weight -secretase complexes. CD147 and TMP21 have been found to be associated with the -secre- tase complex (21, 22); however, their role in the regulation of -secretase has been controversial (23, 24). Mutations of PS1 or PS2 are associated with familial early onset AD (FAD), although it is debatable whether these familial PS mutations act as “gain or loss of function” alterations in regard to -secretase activity (25–27). Regardless the overall outcome of these mutations is an increased ratio of A42:A40. Clearly these mutations differentially affect -secretase activity for the production of A40 and A42. Despite intensive studies of A peptides and -secretase, the molecular mechanism con- * This work was supported, in whole or in part, by National Institutes of Health Grants R01-AG026660 (to Y. M. L.) and R01-AG20670 (to H. Z.), Institutional Training Grant T32 GM073546-01A1 (to L. P.), and Ruth L. Kirschstein National Research Service Award T32 CA062948-11A1 (to L. P.). This work was also supported by William H. and Alice Goodwin and the Common- wealth Foundation for Cancer Research, the Experimental Therapeutics Center of Memorial Sloan Kettering Cancer Center, the William Randolph Hearst Fund in Experimental Therapeutics, and the American Health Assistance Foundation (to Y. M. L.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. S The on-line version of this article (available at http://www.jbc.org) contains supplemental Table S1 and Figs. 1 and 2. 1 Both authors contributed equally to this work. 2 Present address: Albert Einstein College of Medicine, Bronx, NY 10461. 3 Present address: Dept. of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610. 4 To whom correspondence should be addressed: Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave., New York, NY 10065. E-mail: [email protected]. 5 The abbreviations used are: A, -amyloid; AD, Alzheimer disease; APP, amyloid precursor protein; CTF, C-terminal fragment; FAD, familial early onset AD; NTF, N-terminal fragment; PS, presenilin; Nct, nicastrin; Aph, anterior pharynx-defective; Pen2, presenilin enhancer 2; WT, wild type; MES, 4-morpholineethanesulfonic acid; CHAPSO, 3-[(3-cholamidopropyl)- dimethylammonio]-2-hydroxy-1-propanesulfonic acid; PIPES, 1,4-pipera- zinediethanesulfonic acid; L458, L-685,458; L646, L-852,646. THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 284, NO. 5, pp. 2967–2977, January 30, 2009 © 2009 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in the U.S.A. JANUARY 30, 2009 • VOLUME 284 • NUMBER 5 JOURNAL OF BIOLOGICAL CHEMISTRY 2967 by guest on December 7, 2020 http://www.jbc.org/ Downloaded from

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Pen2 and Presenilin-1 Modulate the Dynamic Equilibrium ofPresenilin-1 and Presenilin-2 �-Secretase Complexes*□S

Received for publication, September 19, 2008, and in revised form, November 24, 2008 Published, JBC Papers in Press, November 25, 2008, DOI 10.1074/jbc.M807269200

Lisa Placanica‡§1,2, Leonid Tarassishin‡1, Guangli Yang‡, Erica Peethumnongsin¶, Seong-Hun Kim�3, Hui Zheng¶,Sangram S. Sisodia�, and Yue-Ming Li‡§4

From the ‡Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065,the §Department of Pharmacology, Weill Graduate School of Medical Science of Cornell University, New York, New York 10065, the¶Huffington Center on Aging, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030,and �The Center for Molecular Neurobiology, The University of Chicago, Chicago, Illinois 60637

�-Secretase is known to play a pivotal role in the pathogenesisof Alzheimer disease through production of amyloidogenicA�42 peptides. Early onset familial Alzheimer disease muta-tions in presenilin (PS), the catalytic core of �-secretase, invari-ably increase the A�42:A�40 ratio. However, themechanism bywhich these mutations affect �-secretase complex formationand cleavage specificity is poorly understood.We show that ourin vitro assay system recapitulates the effect of PS1mutations onthe A�42:A�40 ratio observed in cell and animal models. Wehave developed a series of small molecule affinity probes thatallow us to characterize active �-secretase complexes. Further-morewe reveal that the equilibriumof PS1- and PS2-containingactive complexes is dynamic and altered by overexpression ofPen2 or PS1 mutants and that formation of PS2 complexes ispositively correlated with increased A�42:A�40 ratios. Thesedata suggest that perturbations to �-secretase complex equilib-rium can have a profound effect on enzyme activity and thatincreased PS2 complexes along with mutated PS1 complexescontribute to an increased A�42:A�40 ratio.

�-Amyloid (A�)5 peptides are believed to play a causativerole inAlzheimer disease (AD). A� peptides are generated from

the processing of the amyloid precursor protein (APP) by twoproteases, �-secretase and �-secretase. Although �-secretasegenerates heterogenous A� peptides ranging from 37 to 46amino acids in length, significant work has focused mainly onthe A�40 and A�42 peptides that are the major constituents ofamyloid plaques. �-Secretase is a multisubunit membraneaspartyl protease comprised of at least four known subunits:presenilin (PS), nicastrin (Nct), anterior pharynx-defective(Aph), and presenilin enhancer 2 (Pen2). Presenilin is thoughtto contain the catalytic core of the complex (1–4), whereas Aphand Nct play critical roles in the assembly, trafficking, and sta-bility of �-secretase as well as substrate recognition (5, 6). LastlyPen2 facilitates the endoproteolysis of PS into its N-terminal(NTF) and C-terminal (CTF) fragments thereby yielding a cat-alytically competent enzyme (5, 7–10). All four proteins (PS,Nct, Aph1, and Pen2) are obligatory for �-secretase activity incell and animal models (11, 12). There are two homologs of PS,PS1 andPS2, and three isoforms ofAph1,Aph1aS, Aph1aL, andAph1b. At least six active �-secretase complexes have beenreported (two presenilins � three Aph1s) (13, 14). The sum ofapparent molecular masses of the four proteins (PS1-NTF/CTF � 53 kDa, Nct � 120 kDa, Aph1 � 30 kDa, and Pen2 �10kDa) is �200 kDa. However, active �-secretase complexes ofvarying sizes, ranging from250 to 2000 kDa, have been reported(15–19). Recently a study suggested that the �-secretase com-plex contains only one of each subunit (20). Collectively thesestudies suggest that a four-protein complex around 200–250kDa may be the minimal functional �-secretase unit with addi-tional cofactors and/or varying stoichiometry of subunits exist-ing in the highmolecularweight�-secretase complexes. CD147and TMP21 have been found to be associated with the �-secre-tase complex (21, 22); however, their role in the regulation of�-secretase has been controversial (23, 24).

Mutations of PS1 or PS2 are associated with familial earlyonset AD (FAD), although it is debatable whether these familialPS mutations act as “gain or loss of function” alterations inregard to �-secretase activity (25–27). Regardless the overalloutcomeof thesemutations is an increased ratio ofA�42:A�40.Clearly these mutations differentially affect �-secretase activityfor the production of A�40 andA�42. Despite intensive studiesof A� peptides and �-secretase, themolecular mechanism con-

* This work was supported, in whole or in part, by National Institutes of HealthGrants R01-AG026660 (to Y. M. L.) and R01-AG20670 (to H. Z.), InstitutionalTraining Grant T32 GM073546-01A1 (to L. P.), and Ruth L. KirschsteinNational Research Service Award T32 CA062948-11A1 (to L. P.). This workwas also supported by William H. and Alice Goodwin and the Common-wealth Foundation for Cancer Research, the Experimental TherapeuticsCenter of Memorial Sloan Kettering Cancer Center, the William RandolphHearst Fund in Experimental Therapeutics, and the American HealthAssistance Foundation (to Y. M. L.). The costs of publication of this articlewere defrayed in part by the payment of page charges. This article musttherefore be hereby marked “advertisement” in accordance with 18 U.S.C.Section 1734 solely to indicate this fact.

□S The on-line version of this article (available at http://www.jbc.org) containssupplemental Table S1 and Figs. 1 and 2.

1 Both authors contributed equally to this work.2 Present address: Albert Einstein College of Medicine, Bronx, NY 10461.3 Present address: Dept. of Pharmacology and Therapeutics, University of

Florida, Gainesville, FL 32610.4 To whom correspondence should be addressed: Molecular Pharmacology

and Chemistry Program, Memorial Sloan Kettering Cancer Center, 1275York Ave., New York, NY 10065. E-mail: [email protected].

5 The abbreviations used are: A�, �-amyloid; AD, Alzheimer disease; APP,amyloid precursor protein; CTF, C-terminal fragment; FAD, familial earlyonset AD; NTF, N-terminal fragment; PS, presenilin; Nct, nicastrin; Aph,anterior pharynx-defective; Pen2, presenilin enhancer 2; WT, wild type;MES, 4-morpholineethanesulfonic acid; CHAPSO, 3-[(3-cholamidopropyl)-

dimethylammonio]-2-hydroxy-1-propanesulfonic acid; PIPES, 1,4-pipera-zinediethanesulfonic acid; L458, L-685,458; L646, L-852,646.

THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 284, NO. 5, pp. 2967–2977, January 30, 2009© 2009 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in the U.S.A.

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trolling the specificity of �-secretase activity for A�40 andA�42 production has not been resolved. It has been found thatPS1 mutations affect the formation of �-secretase complexes(28). However, the precisemechanism bywhich individual sub-units alter the dynamics of �-secretase complex formation andactivity is largely unresolved. A bettermechanistic understand-ing of �-secretase activity associated with FAD mutations hasbeen hindered by the lack of suitable assays and probes that arenecessary to recapitulate the effect of these mutations seen incell models and to characterize the active �-secretase complex.In our present studies, we have determined the overall effect

of Pen2 and PS1 expression on the dynamics of PS1- and PS2-containing complexes and their association with �-secretaseactivity. Using newly developed biotinylated small molecularprobes and activity assays, we revealed that expression of Pen2or PS1 FAD mutants markedly shifts the equilibrium of PS1-containing active complexes to that of PS2-containing com-plexes and results in an overall increase in the A�42:A�40 ratioin both stable cell lines and animalmodels. Our studies indicatethat perturbations to the equilibriumof active�-secretase com-plexes by an individual subunit can greatly affect the activity ofthe enzyme.Moreover they serve as further evidence that thereare multiple and distinct �-secretase complexes that can existwithin the same cells and that their equilibrium is dynamic.Additionally the affinity probes developed here will facilitatefurther study of the expression and composition of endogenousactive �-secretase from a variety of model systems.

EXPERIMENTAL PROCEDURES

Affinity Probes andAntibodies—L-685,458 (L458), L-852,646(L646), and compounds 2 and 4 were prepared as describedpreviously (1, 29). Synthesis of compounds 1 and 3, newly devel-oped �-secretase inhibitors, will be published elsewhere (30).Themonoclonal 9E10 antibody againstMycwas obtained fromthe Memorial Sloan Kettering Cancer Center core facility.Antibodies against PS1-NTF and Pen2 were kindly provided byDr. Min-tain Lai (Merck Research Laboratories) and Dr. JanNaslund (Karolinska Institutet). Antibodies against PS2-CTF(PC235) and PS1-CTF (MAB5232) andAph1aL (38-3600) werepurchased fromCalbiochem, Chemicon, and Zymed Laborato-ries Inc., respectively. Antibodies against APP and Nct weregenerated by our laboratories.Cell Lines—N2A cell lines that stably express human wild

type (WT) PS1 and FAD mutants were cultured as describedpreviously (31). The HEK293-APP stable cell line (a gift fromDr. Elizabeth Chen, Merck Research Laboratories) was trans-fected with Myc-tagged Pen2 expressed from the pcDNA 4.1vector and selected with Zeocin (Invitrogen) at 0.4–0.8mg/ml. Cultures were maintained in Dulbecco’s modifiedEagle’s medium high glucose containing 10% fetal calf serumand antibiotics.Membrane Preparation and in Vitro �-Secretase Assay—

Membrane fractions were isolated from HeLa-S3 cells(National Cell Culture Center). Briefly 1-liter equivalents wereresuspended in Buffer A (50 mM MES, pH 6.0, 150 mM KCl, 5mM CaCl2, 5 mM MgCl2, and protease inhibitors) and lysed bypassage through a French press. Nuclear debris were pelleted,and the resulting supernatant was ultracentrifuged 100,000� g

for 1 h. The resulting pellet represented the total membranefraction. Total membrane fractions were solubilized with 1%CHAPSO in Buffer A for 1 h 4 °C. Non-solubilizedmaterial wasremoved by ultracentrifugation at 100,000 � g for 1 h, and theresulting supernatant represented the CHAPSO-solubilizedfraction. Protein concentration was determined with the DCProtein Assay kit (Bio-Rad) according to the manufacturer’sinstructions. �-Secretase activity was measured by electro-chemiluminescence as described previously (18, 33). CHAPSO-solubilizedmembranewas incubated in Buffer B (50mMPIPES,pH 7.0, 150 mM KCl, 5 mM CaCl2, 5 mM MgCl2, and proteaseinhibitors) with 0.25% (v/v) CHAPSO, 1�M substrate, and 0.1%bovine serum albumin (v/v) in the presence or absence of�-secretase inhibitors for 2.5 h 37 °C. The reactionmixture wasincubated with biotinylated 4G8 and ruthenylated G2-10 orG2-11 in Buffer C (1� phosphate-buffered saline, 0.5% (w/v)bovine serum albumin, and 0.5% (v/v) Tween 20) for 2 h at25 °C, and immunocomplexes were captured with magneticstreptavidin beads (Dynal). A�40 and A�42 production wasmeasured by electrochemiluminescence on an Analyzer (Bio-Veris) and expressed as relative light units.Affinity Capture of Endogenous �-Secretase and Western

Blotting—CHAPSO-solubilized membrane was incubated inthe presence or absence of 2 �M L458 in Buffer B for 0.5 h at37 °C. A biotinylated affinity probe at 20 nM was added for anadditional 1.5 h at 37 °C. Streptavidin-agarose (Pierce) wasadded to the reaction and incubated overnight 4 °C. Capturedcomplexes were washed in Tris-buffered saline with 0.1% (v/v)Tween 20 and eluted with 2� Laemmli sample buffer. Sampleswere resolved by SDS-PAGE and transferred to a polyvinyli-dene difluoridemembrane. The following antibodies were usedfor Western blotting: PS1-NTF (1:1000), PS1-CTF (1:1000),Aph1aL (1:250), Nct (1:1000), Pen2 (1:500), and PS2-CTF(1:1000). Anti-mouse or anti-rabbit horseradish peroxidase-conjugated (Amersham Biosciences) secondary antibodieswere used in conjunction with standard electrochemilumines-cence detection methods. In all cases, blots shown are repre-sentative of three or more experiments.Photolabeling of �-Secretase—Solubilized membrane was

incubated in the presence or absence of 2 �M L458 in Buffer Bfor 0.5 h at 37 °C. 20 nM biotinylated affinity probe was addedfor an additional 1 h at 37 °C. Samples were then irradiated at350 nm on ice for 0.75 h. The reaction was either denatured byaddition of RIPAbuffer (50mMTris, pH8.0, 150mMNaCl, 0.1%(w/v) SDS, 1% (v/v) Nonidet P-40, and 0.5% (w/v) deoxycholicacid) or left in the native condition for 1 h at 25 °C. Streptavidin-agarose was added to the reaction mixture and incubated over-night at 4 °C. Captured complexes were washed with RIPAbuffer and eluted with 2� Laemmli sample buffer. Sampleswere Western blotted as described above. In all cases, blotsshown are representative of three or more experiments.

RESULTS

Pen2 Overexpression Causes an Increase in the A�42:A�40Ratio in Cells and in Vitro—Pen2 is essential for �-secretaseactivity and is thought to stabilize the complex as well as pro-mote endoproteolysis of PS (9, 10). To further investigate thefunction of Pen2 on �-secretase activity and complex forma-

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tion, we generated two stable cell lines: HEK293 that overex-press APP (referred to as APP) and HEK293 that co-expressAPP and C-terminal Myc-tagged Pen2 (referred to as Pen2).Expression of Pen2 was confirmed by Western blotting withboth anti-Myc and anti-Pen2 antibodies and showed consider-able overexpression of Pen2 (Fig. 1a). Endogenous and taggedPen2 was unresolved under our current SDS-PAGE condition.Furthermore tagged Pen2 co-immunoprecipitated with Nct(Fig. 1b), suggesting that Pen2 is incorporated into the �-secre-tase complex as Pen2 incorporation is proposed as a final step inthe formation of active �-secretase complexes (9). However,overexpression of Pen2 caused a reduction in the expression ofthe known components of �-secretase (Fig. 1c). This is consist-entwith earlier reports that showed that theC terminus of Pen2is critical for complex formation (34) and that expression of aC-terminally tagged Pen2 (Pen2-Myc-His6) resulted in destabi-lization of the PS1 heterodimer and mature Nct (8). There was

no effect on the expression level of APP in the Pen2 cell linecompared with the parental cell line (Fig. 1c).We next determined the effect of Pen2-Myc expression on

�-secretase activity for the 40 and 42 site cleavage of APP. Totalmembrane fractions isolated from the Pen2 and APP cell lineswere incubated with the APP transmembrane substrate, andA�40 and A�42 cleavage products were measured (33). Pro-duction of A�40 was greatly reduced in the Pen2 cell line, butthere was no effect on the production of A�42 (Fig. 2, leftpanel). This resulted in an overall increase in the A�42:A�40ratio in the Pen2 line (0.25) compared with the APP line (0.15)(Fig. 2, right panel). To verify the in vitro results, we examinedthe secretion of A�40 and A�42 peptides from both cell lines(Fig. 2, middle panel). Consistent with the in vitro data, wefound that there was a marked reduction in A�40 secretion inthe Pen2 cell line but little effect on the secretion of A�42 com-pared with the APP cell line. The A�42:A�40 ratio for the Pen2cell line was 0.29 and was 0.09 for the APP cell line (Fig. 2, rightpanel). The very similar results in both the cellular and in vitroassays strongly suggest that overproduction of Pen2 alters�-secretase activity for A�40 and A�42 production, which isreminiscent of the effect of PS1 and PS2 FAD mutations.Capture of the �-Secretase Complex with Biotinylated Active

Site-directed Inhibitors Depends on the Length of the BiotinLinker—To better understand the role of tagged Pen2 in theformation of �-secretase complexes, we set out to examine theactive �-secretase complexes present in the Pen2 and APP celllines. It is known that only a small percentage of PS is engaged incatalytically active complexes (35, 36). Therefore, traditionalWestern blotting and immunoprecipitation methods would beinadequate for our study because they fail to distinguishbetween catalytically active and inactive complexes. To over-come this, we attempted to develop small molecular affinityprobes that would allow us to capture and characterize theactive �-secretase complex under native conditions.L458 is a potent transition state analog that selectively binds

to catalytically active �-secretase, and its analogs have beenused to characterize �-secretase (17, 36) (Fig. 3a). We firstattempted to use L646, a biotinylated �-secretase inhibitor, toisolate the �-secretase complex (1). CHAPSO-solubilized

FIGURE 1. Overexpressed Pen2 is incorporated into the �-secretase com-plex and results in reduced expression of �-secretase components.a, Western blot (WB) showing overexpression of Pen2 as detected with anti-Pen2 and anti-Myc antibodies. b, Pen2 is associated with Nct. CHAPSO-solu-bilized membrane fractions were immunoprecipitated (IP) with anti-Nct andWestern blotted for Pen2 with anti-Myc. c, overexpression of Pen2 causes areduction in the protein levels of components of �-secretase but does notaffect the expression levels of the APP substrate. 10 �g of CHAPSO-solubi-lized membrane proteins were resolved by SDS-PAGE and Western blottedfor PS1-NTF, PS1-CTF, Nct, PS2-CTF, and APP.

FIGURE 2. Pen2 overexpression increases the A�42:A�40 ratio in both in vitro and cellular assays. For the in vitro assay (left panel), CHAPSO-solubilizedmembrane from the APP- or Pen2-expressing cell lines were assayed for A�40 and A�42 production using an APP transmembrane substrate. Background wasdefined as activity remaining in the presence of 1 �M L458. Values are the average of background-subtracted activity and are represented as units/min/�g(average � S.E., n � 3). For the cellular assay (middle panel), APP and Pen2 cells were grown in 96-well plates, and the amount of A�40 and A�42 secreted intothe medium was measured in the electrochemiluminescence (ECL) assay. Background was defined as the amount of A�40 and A�42 secreted when cells weregrown in the presence of 1 �M L458. The concentration of A�40 and A�42 was determined with peptide standard curves (average � S.E., n � 3). The A�42:A�40ratio for the APP (black bar) and Pen2 (gray bar) cell lines for both the in vitro and cellular (secreted A�) assays are shown in the right panel.

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membranes were incubated with L646 in the presence orabsence of excess L458, and the bound complexes were cap-tured with streptavidin-agarose, resolved by SDS-PAGE, andWestern blotted for the core components of �-secretase. Sur-prisingly L646was incapable of capturing PS1 under non-dena-turing condition even though it has been shown previously todirectly label PS1-NTF upon photoactivation (1) (Fig. 3b, lanes3 and 4). We reasoned that steric hindrance precluded L646from interacting with both streptavidin and the �-secretasecomplex under native conditions. Therefore, we designed andsynthesized a series of L458 analogs with varying linker lengths(Fig. 3a). In addition, L646, compound 1, and compound 3 alsocontain a benzophenone moiety that allows covalent photoin-corporation of these probes into the �-secretase complex. Ini-tially we determined their inhibitory potency against �-secre-tase and found that these compounds effectively block�-secretase activity with IC50 values in the low nanomolarrange, indicating that biotinylation did not adversely affect theactivity of the compounds (supplemental Table S1). We nextexamined the ability of these compounds to capture PS1. Wefound that only compound 3 and compound 4 were able tocapture both PS1-NTF and PS1-CTF (Fig. 3b). Because com-

pound 4 captured PS1with greater efficiency than compound 3,we determined whether compound 4 was able to capture theremaining components of �-secretase. Indeed compound 4wasalso able capture the remaining core components of active�-secretase: Pen2, Nct, and APH1a (Fig. 3c). Inclusion of excessnon-biotinylated L458 was able to completely block capture of�-secretase by both compounds 3 and 4, thereby indicating thatthe capture was specific in nature (Fig. 3, b and c, � L458).These studies suggest that probes that are able to interact withboth streptavidin-agarose and �-secretase require linkers of atleast 34Åbetween biotin and the L458 backbone. To verify this,we used twoof the photoreactive probes, compounds 1 and 3, todetermine whether they were capable of capturing �-secretaseunder denatured and native conditions following cross-linking.CHAPSO-solubilized HeLa membranes were incubated witheither compound 1 or 3 in the presence or absence of L458 andirradiated. Following photolysis, the labeled complexes werecaptured with streptavidin-agarose under either native(�RIPA) or denatured (�RIPA) conditions. First, we demon-strated that both compounds 1 and 3 were able to photoinsertinto PS1-NTF and that the labeled protein could be capturedunder denaturing conditions (�RIPA). Second, as predicted,

FIGURE 3. The capture of active �-secretase complexes relies on the length of linker. a, chemical structures of compounds used in this study. Thephotoreactive benzophenone group is marked with a dashed box. The linear distance of the linker between the parental compound backbone and the biotinmoiety is measured in Å as determined with 3D ChemDraw. b, PS1 can be captured by biotinylated compounds with linkers of at least 34 Å. Active PS1 wascaptured from CHAPSO-solubilized HeLa membrane with 20 nM biotinylated affinity probe in the presence (�) or absence (�) of 2 �M L458, isolated withstreptavidin-agarose, separated by SDS-PAGE, and Western blotted for PS1-NTF and PS1-CTF as indicated. c, compound 4 is able to capture the core compo-nents of �-secretase in addition to PS1. 20 nM compound 4 was incubated with CHAPSO-solubilized HeLa membrane in the presence (�) or absence (�) of 2�M L458 and isolated with streptavidin-agarose. The captured complexes were resolved by SDS-PAGE and Western blotted for the indicated �-secretasesubunits. Boc, t-butoxycarbonyl; Ph, phenyl.

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only compound 3 was able to capture PS1-NTF under native(�RIPA) conditions (Fig. 4a). In all cases, capture was com-pletely blocked by inclusion of excess L458, indicating specificcapture.These studies suggest that the biotin moiety of the ligand

becomes partly occluded by the protein interface of the activesite when compounds with short linkers, such as compound 1,bind to �-secretase under native non-denaturing conditions(Fig. 4a, �RIPA). This partial occlusion prevents streptavidin-agarose from binding to the biotin moiety of the ligand, andtherefore labeled �-secretase is not captured. However, dena-turing conditions destroy the �-secretase complex and therebyeliminate steric hindrance between the protein interface of theactive site and streptavidin-agarose allowing isolation of thelabeled components (Fig. 4a, �RIPA). To support this conclu-sion, we determined the inhibitory potency of the biotinylatedanalogs in the presence or absence of soluble streptavidin (Fig.4b and supplemental Table S1). Inclusion of soluble streptavi-din had no effect on the potency of L458 (Fig. 4b, left panel) but

dramatically increased the IC50 val-ues of L646, compound 1, and com-pound 2 (�220-fold) (Fig. 4c, mid-dle panel, and supplemental TableS1). However, inclusion of solublestreptavidin had much less of animpact on the potency of compound3 and compound 4 (20-fold) (Fig.4c, right panel, and supplementalTable S1). It appears that the effectof streptavidin on the interaction ofthese inhibitors with �-secretase isinversely correlated with the lengthof biotin linker. These data suggestthat the active site of �-secretase is afairly deep binding pocket, which isconsistent with studies that haveindicated that the active site of�-secretase is a hydrophilic pore20–40 Å in length within the lipidbilayer (37, 38). Furthermore thesedata also indicate that affinityprobes with linkers of at least 34 Åare required to capture �-secretaseunder native non-denaturing condi-tions (Fig. 4c).Overexpression of Pen2 Increases

the Formation of PS2-containingActive �-Secretase Complexes—After establishing that compound4 was able to fully capture ac-tive �-secretase complexes undernative conditions, we characterizedthe active �-secretase complexes inthe Pen2 and APP cell lines usingthis probe. First we assessed theaffinity of �-secretase for L458 fromboth cell lines. We determined thatthe IC50 values for inhibition of sol-

ubilized �-secretase from the Pen2 andAPP cells were 1.5� 0.1and 1.3� 0.3 nM, respectively, indicating that overexpression ofPen2 did not affect the affinity of �-secretase complexes forL458 (supplemental Fig. 1). We then used compound 4, basedon the L458 backbone, to analyze the �-secretase complexes inthe APP and Pen2 cell lines. Solubilized membrane fractionsfrom both cell lines were incubated with compound 4 in thepresence or absence of excess L458, and streptavidin-agarosewas then used to capture the compound 4��-secretase com-plexes. Bound complexeswerewashed, resolved by SDS-PAGE,and immunoblotted for �-secretase components: PS1-NTF,Nct, Pen2, and PS2-CTF (Fig. 5a). When we compared theactive �-secretase complexes from the two cell lines, we imme-diately noticed two remarkable features. First, Pen2 cells pos-sessed significantly more PS2-containing complexes but con-siderably fewer PS1 complexes than the APP cells even in lightof the fact that Pen2 cells express less total PS2 than APP cells(Figs. 5a and 1c). This finding further supports the assertionthat the total amount of �-secretase subunits in cell membrane

FIGURE 4. Steric hindrance between streptavidin and the active site of �-secretase prevents capture of�-secretase by compounds with short linkers. a, �-secretase can be captured in the native conformationwhen photolabeled with compound 3 but not compound 1. CHAPSO-solubilized HeLa membrane wascovalently photolabeled with 20 nM of either compound 1 or 3 in the presence (�) or absence (�) of 2 �M L458by UV activation of the photoreactive benzophenone group. Photolabeled complexes were captured withstreptavidin-agarose under either native (�RIPA) or denatured (�RIPA) conditions, resolved by SDS-PAGE, andWestern blotted for PS1-NTF. b, soluble streptavidin (SA) greatly increases the IC50 of compounds with biotinlinkers less than 25 Å. CHAPSO-solubilized HeLa membrane was treated with increasing concentrations of theindicated compound and assayed for A�40 production using the C100FLAG substrate in the presence (�) orabsence (�) of excess soluble streptavidin. Background is defined as activity remaining in the presence of 1 �M

compound. Activity is plotted as percentage of background-subtracted maximal (Max) activity. Curves weregenerated using a sigmoidal four-parameter logistic fit in SigmaPlot 8.0. (average � S.D., n � 4). c, schematicillustration of the interaction of the probes with the �-secretase complex and streptavidin.

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is not necessarily correlated with the level of protein engaged inthe active complexes. Therefore separation of the catalyticallyactive complexes from the non-enzymatic complexes helps toaccurately characterize the relationship between �-secretasecomplex composition and activity. These results suggest thatoverexpression of Pen2 alters the dynamics of PS1- and PS2-containing �-secretase complexes and favors the formation ofPS2-containing complexes. Second, Pen2 overexpressionseems to alter the relative stoichiometry of subunits within theactive �-secretase complex. Pen2 overexpression caused adecrease in the incorporation of Nct into the active complexesbut an increase in the incorporation of Pen2 (Fig. 5a). Althoughthe amount of each component that is associated with the PS1and PS2 complexes is unknown, it is clear that the relative stoi-chiometry of the �-secretase complexes is strikingly differentbetween the Pen2 cells and the APP cells. Quantification of therelative amounts of captured proteins revealed that the Pen2�-secretase complexes contain only �25–30% of PS1-NTF andNct but 250 and 400%, respectively, of Pen2 and PS2-CTF ascompared with the APP �-secretase complexes (Fig. 5b).Furthermore equivalent results were seen even when com-pound 4 was used at 100 nM, indicating that there was asufficient excess of compound 4 available for capture (datanot shown). Together these data indicate that the APP andPen2 cell lines display distinct �-secretase activity and pos-sess different �-secretase complexes and/or different ratiosof the components.Overexpression of PS1 FAD Mutants Causes a Shift in Equi-

librium from PS1-containing Complexes to PS2-containingComplexes—Mutations in PS1 linked to early onset AD areassociated with an increase in the A�42:A�40 ratio (31). This

prompted us to consider the pos-sibility that overexpression of PS1FAD mutants would alter thedynamics of PS1 and PS2 complexformation and mimic the effectseen with Pen2 overexpression.We performed analogous experi-ments as with the Pen2 cells usingestablished cell lines that expressedeither WT or mutated PS1. Wecharacterized N2a cell lines stablyexpressing either PS1 WT or PS1harboring the FAD mutationsM146L or C410Y. Cell membranesisolated from each cell line wereassayed for A�40 andA�42 produc-tion in the in vitro �-secretase assay(Fig. 6a, left panel) (31, 39). BothPS1 M146L and C410Y mutationscaused an increase in the A�42:A�40 ratio (0.20 and 0.36, respec-tively) compared with PS1 WT(0.08) (Fig. 6a, right panel) in our invitro assay; this is consistent withprevious cellular studies (31, 39).M146L slightly augmented A�40production (138% ofWT levels) and

to a much larger magnitude increased A�42 production (346%ofWT levels), whereas C410Y greatly decreased A�40 produc-tion (29% of WT levels) without significantly affecting A�42levels (128% of WT levels). Irrespective of the divergent effecton A�40 and A�42 production, the end result of overexpres-sion of either PS1 FAD mutant was an increase in the A�42:A�40 ratio.

Because the PS1 FADmutants affected the A�42:A�40 ratioin a manner similar to that of Pen2 overexpression, we charac-terized the active �-secretase complexes in the PS1 FADmutants compared with PS1WT.We first looked at expressionlevels of the known components of �-secretase by Westernblotting. Compared with the human WT PS1-expressing cells,the M146L-expressing cells exhibited a similar level of PS1,Pen2, andNct but had significantly higher amounts of PS2 (Fig.6b). Although overexpression of C410Y also resulted in higherlevels of PS2, therewas a decrease in expression of PS1,Nct, andPen2 (Fig. 6b). After we determined that �-secretase in thesecells exhibited the same affinity for L458 (data not shown), weassessed the relative amount of active PS1- versus PS2-contain-ing�-secretase complexes between the cell lines.We again usedcompound 4 to capture the active �-secretase complexes fromCHAPSO-solubilized membrane fractions. Clearly both FADPS1 and PS2 are capable of incorporating into the active�-secretase complex. Furthermore M146L and C410Y hadincreased amounts of PS2-containing �-secretase complexescompared withWT (Fig. 6c). M146L had slightly more PS1, butroughly equal amounts of Nct and Pen2 engaged in active com-plexes compared withWT, whereas C410Y had much less PS1,Nct, and Pen2. These data suggest that the amount of PS2-containing complexes is positively correlated with the A�42:

FIGURE 5. Pen2 overexpression causes a shift from PS1-containing active �-secretase complexes to PS2-containing complexes. a, the equilibrium of �-secretase complexes is altered in Pen2 cells compared with APPcells. Active �-secretase was captured from CHAPSO-solubilized membrane of APP or Pen2 cells with 20 nM

compound 4 in the presence (�) or absence (�) of 2 �M L458. Bound complexes were captured with strepta-vidin-agarose, resolved by SDS-PAGE, and Western blotted for the indicated components of �-secretase. b, rel-ative amounts of captured complex subunits indicate that the stoichiometry of the subunits is dynamic andcan be modulated by Pen2 overexpression. Quantification of captured components was calculated by meas-uring the relative band intensities from the representative blot shown in a using the gel analysis function inImageJ.

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A�40 ratio generated by these cell membranes. Additionallythese data, like the Pen2 overexpression data, suggest the pos-sibility of differential stoichiometries of subunits of the variousactive �-secretase complexes. For example,M146L overexpres-sion resulted in a gross increase in PS2-containing active com-plexes but did not affect the levels of active PS1-containingcomplexes nor did it alter the incorporation of the critical sub-units Nct and Pen2 into active complexes. Clearly the stoichi-ometry of subunits in the active �-secretase complexes isdynamic.To verify the assertion that PS1 WT and PS1 FAD mutants

differentially affect the dynamics of the PS1 andPS2�-secretase

complexes, we conducted similar studies using three additionalPS1 FAD stable expressing N2a cell lines. The L286V, H163R,and E280A mutations reduced �-secretase-mediated A�40production to 15, 23, and 11%, respectively, of WT levels (sup-plemental Fig. 2a, upper panel). These FAD mutations alsocaused a reduction in the production of A�42 (58, 54, and 84%of WT production, respectively) (supplemental Fig. 2a, middlepanel). The net effect of thesemutations resulted in an increasein the A�42:A�40 ratio (0.32, 0.19, and 0.64 for L286V, H163Rand E280A, respectively, compared with 0.08 for WT) (supple-mental Fig. 2a, lower panel). We again used compound 4 tocharacterize the active PS1 and PS2 �-secretase complexes in

FIGURE 6. Overexpression of PS1 FAD mutants causes an increase in the A�42:A�40 ratio and shifts the equilibrium from PS1-containing active�-secretase complexes to PS2-containing complexes. a, PS1 FAD mutations increase the A�42:A�40 ratio. CHAPSO-solubilized membrane from PS1 FADmutant-overexpressing N2a cells was assayed for in vitro production of A�40 and A�42 (left panel) using an APP transmembrane substrate. The A�42:A�40ratios are shown in the right panel. Background was defined as activity remaining in the presence of 1 �M L458. Activity is graphed as background-subtractedunits/min/�g of membrane assayed. b, expression of �-secretase components is altered by expression of PS1 FAD mutants. CHAPSO-solubilized membranefrom PS1 WT and two PS1 FAD mutants (M146L and C410Y) were Western blotted for the indicated components of �-secretase. c, formation of PS2-containing�-secretase complexes is increased by expression of PS1 FAD mutants. Active �-secretase was captured from CHAPSO-solubilized membrane of PS1 WT, PS1M146L, and PS1 C410Y cells with 20 nM compound 4 in the presence (�) or absence (�) of 2 �M L458. Bound complexes were captured with streptavidin-agarose, resolved by SDS-PAGE, and blotted for the indicated components of �-secretase. ECL, electrochemiluminescence.

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these cell lines. Although similar amounts of PS1 were detectedin all four cell lines (supplemental Fig. 1b, upper panel), theamount of PS1 engaged in the active �-secretase complex isconsiderably different. WT- and L286V-expressing cells hadsimilar amounts of PS1-containing active �-secretase, whereasH163R and E280Ahadmuch fewer PS1-containing active com-plexes (supplemental Fig. 2b, lower panel). H163R and E280Acontained roughly the same amount of PS2 comparedwithWT,whereas L286V showed increased PS2 levels compared withWT (supplemental Fig. 2b, upper panel). However, all threeFAD mutants contained much more active PS2-containing�-secretase complexes compared with WT (supplemental Fig.2b, lower panel). Furthermore using these PS1 FAD mutantsand PS1 WT, we determined the relationship among 1) theratios of A�42:A�40 and the compound 4-captured PS2:PS1(referred to (PS2:PS1)captured), 2) the ratios of A�42:A�40 andthe total PS2:PS1 (referred to (PS2:PS1)total), and 3) the ratios of(PS2:PS1)captured and (PS2:PS1)total. We found that 1) the ratioof A�42:A�40 strongly correlates with the ratio of (PS2:PS1)captured (r2 � 0.906) but not (PS2:PS1)total (r2 � 0.018) and2) there is little correlation between (PS2:PS1)total and(PS2:PS1)captured (r2 � 0.041) (supplemental Fig. 3). These data dem-onstrate three critical points. First, the total amount of PS1 andPS2 protein does not always correlate with their incorporationinto active �-secretase complexes. Therefore, isolation of theactive �-secretase complex is necessary for understanding theformation and dynamics of the complexes. Second, PS1 WTand FAD mutants have distinct effects on the equilibrium ofPS1 and PS2 �-secretase complexes, supporting our previousconclusion that �-secretase complexes are dynamic and thatperturbations to complex equilibrium can affect enzyme activ-ity. Third, despite the different amounts of active PS1 and PS2present in different cell lines, it appears that an increased ratioof captured PS2:PS1 leads to an elevated ratio of A�42:A�40,which correlates with the amount of characteristic AD plaquesin mouse models (40, 41) and with the age of onset of familialAlzheimer disease (42). Therefore, these studies suggest that itis the relative amount of active PS1 and PS2 �-secretase com-plexes that plays a critical role in the determination of the ratioof A�42:A�40.FADKnock-inMouseModels of AD Show an Increase in PS2-

containing �-Secretase Complexes—To further validate ourconclusion that perturbations to the PS1 and PS2 complexequilibrium results in increased A�42:A�40 ratios, we deter-mined whether FAD knock-in mouse models also exhibited abiochemical phenotype similar to that seen in the cell models.Knock-in mouse models of AD have been shown to haveincreased A�42:A�40 ratios and accelerated AD plaque depo-sition compared with wild type controls (31, 43, 44). We chosetwo knock-in models that harbor PS1 mutations, M146V andE10, to validate our findings that PS1 mutations can cause ashift in the equilibrium of PS1- and PS2-containing �-secretasecomplexes. In previous studies, we have shown that E10 micehave altered �-secretase specificity for A�40 andA�42 produc-tion that leads to a 1.7-fold increase in the A�42:A�40 ratio(40). We determined that M146V mice also show a similarincrease in the A�42:A�40 ratio. Solubilized membrane fromWT or PS1 M146V brain was assayed for in vitro A�40 and

A�42 production using the APP transmembrane substrate asdone in the above cellular assays. M146V mice showeddecreased A�40 but increased A�42 production comparedwithWT (Fig. 7a) that led to an increase in theA�42:A�40 ratio(1.5-fold).We then examined the total amount of PS1 and PS2 in the

membrane fractions from total brain. We found that there wasvery little difference in the expression levels of PS1 or PS2between either of the knock-in mice and their respective wildtype controls (Fig. 7b).We next determined the relative ratio ofPS1- versus PS2-containing active �-secretase complexes inbrain from the knock-in mice. �-Secretase was captured fromCHAPSO-solubilized membrane fractions of brain with com-pound 4, and the amount of bound PS1 and PS2 was deter-mined byWestern blotting.M146Vmice showed an increase inboth PS1- and PS2-containing active �-secretase complexescompared with WT control (Fig. 7c). E10 mice showed nochange in PS1-containing complexes but a large increase inPS2-containing complexes (Fig. 7c). In both cases it was evidentthat the equilibriumbetween PS1- and PS2-containing�-secre-tase complexes was altered in the knock-in mice, and bothexhibited an increase in the A�42:A�40 ratio. These data fur-ther support a positive correlation between shifting the equilib-rium toward PS2-containing complexes at the expense of PS1-containing complexes and alteration of the A�42:A�40 ratio.

DISCUSSION

Three mutated genes (APP, PS1, and PS2) have been linkedto early onset AD. Elucidating the function of these proteinsand the effect of their mutations on �-secretase activity offers aunique opportunity to investigate the reaction mechanism of�-secretase and the molecular pathogenesis of AD. The smallmolecule approaches used in our present studies have providedcritical insights into the effect of PS1 FAD mutations on�-secretase activity and the dynamics of �-secretase complexformation.PS1 mutations that increase the ratio of A�42:A�40 in cell

and animal models suggest that they affect �-secretase activity.However, whether these cellular effects are attributed to�-secretase itself and/or other cellular factors remains to beinvestigated. In other words, can these cellular observations bebiochemically recapitulated in an in vitro system? This studyprovides biochemical evidence that PS1 mutations directlyalter the rate of �-secretase production of A�40 and A�42.Furthermore although there was a similar increase in the A�42:A�40 ratio, the PS1 mutations differentially affected �-secre-tase activity forA�40 andA�42 production.We observed threedistinct effects on A�40 and A�42 production by PS1 FADmutants: 1)M146L increased bothA�40 andA�42 production,2)C410Y reducedA�40 and increasedA�42 production, and 3)L286V, H163R, and E280A reduced both A�40 and A�42 pro-duction. Our studies suggest that these mutations mediate anincrease in the A�42:A�40 ratio through distinctive mecha-nisms. Our data also indicate that expression of C-terminallyMyc-tagged Pen2 increases the A�42:A�40 ratio in a mannersimilar to that of PS1 FADmutants and therefore represents yetanother distinctive mechanism by which �-secretase activitycan be modulated. Understanding how PS1 mutations and

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Pen2 overexpression alter �-secretase complex formation mayreveal a unifying factor for understanding their diverse effectson �-secretase activity.Our current findings reveal that expression of PS1 FAD

mutants or C-terminal Myc-tagged Pen2 results in increasedformation of active PS2 �-secretase complexes. These findingsclearly suggest that PS1 FADmutants have a reduced ability tocompete for the pool of shared obligatory subunits (Nct, Pen2,and Aph1) with PS2 and therefore lead to increased PS2�-secretase complex formation (Fig. 8). The precisemechanismof this reduced ability requires further investigation but poten-tially results from a reduced affinity for subunit interactionsbecause of conformational changes in PS1. Because of the com-plexity of �-secretase as a multisubunit membrane-boundenzyme complex, there has been a lack of both an in vitro recon-stitution system and high resolution structural information ofthe complex. This has made it extremely challenging to obtainkinetic data that would indicate exactly how PS1 FAD muta-tions affect subunit interactions and complex assembly. Fur-thermore the expression of C-terminal Myc-tagged Pen2 alsoled to an increase in PS2-containing complexes suggesting thatPS2 may normally have an increased ability to compete withPS1 for the shared cofactors when the formation and naturaldynamic of complex equilibrium are perturbed.PS1 and PS2 are highly homologous (67% identical) but are

engaged in mutually exclusive complexes (13, 35). Both PS1-

and PS2-containing complexes are catalytically active; how-ever, PS1-containing �-secretase complexes display consider-ably higher specific activity thanPS2 complexes (28, 35). There-fore, shifting the equilibrium toward an increase inPS2-containing �-secretase complex at the expense of PS1-containing complexes should result in a reduction in overall�-secretase activity; this hypothesis is supported by our currentobservations. Another critical question is how changing thecomplex equilibrium alters the ratio of A�42:A�40. Our pre-liminary studies indicating that the A�42:A�40 ratio displayeda strong positive correlation with the relative amount of activePS2:PS1 complexes suggest that PS2 �-secretase complexesmight be capable of processing the APP substrate with a higherA�42:A�40 ratio (Fig. 8, pathway 1). Concomitantly PS1-mu-tated �-secretase also has altered specificity for A�42 andA�40production (Fig. 8, pathway 2). Therefore, the alteration of�-secretase specificity for A�40 and A�42 production couldresult from a combination of the increase in PS2 complex for-mation and altered activity by the mutated PS1 complex.Indeed our previous study showed that the A�42:A�40 ratio inPS2-expressing cells was 1.4-fold higher than that in PS1-ex-pressing cells, but this was not seen in biochemical studies (35).Therefore, it is noteworthy to point out that investigation of therelationship between PS1- and PS2-mediated �-secretase activ-ity for A�40 and A�42 production is technically challenging.Utilizing a single form of PS (PS1 or PS2) in the absence of the

FIGURE 7. Two independent knock-in mouse models of FAD have increased A�42:A�40 ratios and show a shift toward PS2 containing active �-secre-tase complexes. a, M146V knock-in mice exhibit altered A�42:A�40 ratios compared with WT mice. CHAPSO-solubilized membrane of total brain from PS1M146V mice and its respective WT control were assayed for in vitro production of A�40 (black bar) or A�42 (gray bar) using an APP transmembrane substrate.Background was defined as activity remaining in the presence of 1 �M L458. Activity is graphed as background-subtracted units/min/�g of membrane assayed(average � S.E., n � 3). The A�42:A�40 ratios are shown below (average � S.E., n � 3). b, FAD knock-in mice have comparable basal expression of �-secretasesubunits as compared with WT. CHAPSO-solubilized membrane from total brain of PS1 M146V mice (left panel) and PS1 E10 (right panel) and their respectiveWT controls was Western blotted for expression of PS1-NTF and PS2-CTF. c, FAD knock-in mice favor an increase in PS2-containing �-secretase complexformation compared with WT. Active �-secretase was captured from CHAPSO-solubilized membrane of total brain from PS1 M146V mice (left panel) or PS1E10 mice (right panel) and their respective WT controls with 20 nM compound 4 in the presence (�) or absence (�) of 2 �M L458. Bound complexes werecaptured with streptavidin-agarose, resolved by SDS-PAGE, and Western blotted for PS1-NTF and PS2-CTF. ECL, electrochemiluminescence.

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other does not reflect the endogenous dynamics of PS1- andPS2-containing �-secretase complexes that compete for theknown shared cofactors (Nct, Aph1, and Pen2) when present inthe same cells (32). Therefore, the contribution of PS1 muta-tions to the production of A�42 and A�40 should be carefullyinterpreted with consideration to PS2 involvement in the for-mation of A� peptides. Alternatively PS1 �-secretase com-plexes may preferentially process A�40 peptides, whereas PS2complexes show no preference for A�40 and A�42 production(Fig. 8, pathway 3). A loss of PS1 �-secretase complexes becauseof an increase in PS2 �-secretase complexes would selectivelyreduce A�40 peptide production and thereby account for theobserved A�42:A�40 ratio increases we observed. Similarly aloss of A�40-generating PS1 complexes because of PS1 FADmutations would also increase the A�42:A�40 ratio in theabsence of PS2 expression. This is in fact supported by previousstudies that showed that expression of PS1 FAD mutations inPS1- and PS2-null cells was capable of elevating the ratio ofA�42 to A�40 (28).Taken together, these findings reveal a novel mechanism of

�-secretase regulation by dynamic alteration of the equilibriumof PS1- and PS2-containing �-secretase complexes (Fig. 8).

These data provide a possible mechanism for multiple “loss offunction” PS mutations distributed within different regions ofthe protein (25–27); these distinct mutations could exert theireffect on A�40 production by perturbation of the complexequilibrium. In other words, shifting the equilibrium from PS1�-secretase to PS2 �-secretase alters overall �-secretase activityand leads to an elevated ratio of A�42:A�40 (Fig. 8). In additionto favoring an increase in PS2-containing complexes, PS1 FADmutations also result in formation of amutated PS1 �-secretasecomplexwith altered specificity forA�40 andA�42 productionas well as leading to increased A�42:A�40 ratios (Fig. 8).Additionally the requirement of affinity probes with longer

linkers for capture of native �-secretase has indicated that thatthe active site is buried deeply within the hydrophobic mem-brane. This conclusion is in agreement with other biochemicaland structural studies (36–38) that have shown the active site of�-secretase resides in a hydrophilic pore 20–40 Å in lengthwithin the lipid bilayer. Moreover conjugation of L685,458 tobiotin by either hydrophobic or hydrophilic linkers had littleeffect on the inhibitory potency of L-685,458, suggesting thatthis inhibitor can easily access the active site of �-secretaseregardless of the biophysical properties of linkers. It is likelythat L-685,458 accesses the �-secretase active site through achannel-like mechanism. It is of note to point out that confor-mation of the �-secretase complex is dependent on detergentconcentration because �-secretase in CHAPSO at concentra-tions above the critical micelle concentration, in the presenceor absence of digitonin, can be captured by a transition stateinhibitor immobilized to solid support through a six-atomhydrophilic linker (15, 17). �-Secretase captured under highdetergent conditions such as these may represent a differentform of the complex. Therefore we believe our panel of affinityprobes with varying linker lengths is a valuable tool for thefunctional characterization of active and endogenous �-secre-tase and allows us to further examine the relationship between�-secretase specificity and endogenous PS1- and PS2-contain-ing �-secretase complexes in normal individuals and ADpatients. This ability will facilitate elucidation of the pathogen-esis of AD and aid in the development of therapeutics.

Acknowledgments—We thank Christopher C. Shelton for criticalreadings of the manuscripts, Dr. Min-tain Lai for PS1-NTF antibody,and Dr. Jan Naslund for anti-Pen2 antibodies.

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Pen2-myc PS1 FAD

or

1

2Increased Aβ42:Aβ40

Ratio3

FIGURE 8. Proposed mechanism for the relationship between �-secretasecomplex dynamics and A�42:A�40 ratios. Under physiological conditionsPS1 and PS2 compete for the shared cofactors Nct, Aph1, and Pen2, and thecomplexes are in dynamic equilibrium. PS1 complex formation results in ahigher overall �-secretase activity relative to PS2 and/or preferential process-ing of A�40 peptides. Overexpression of Pen2-Myc or PS1 FAD mutantsresults in favored formation of active PS2 �-secretase complexes (blue) andthe selective reduction in active PS1 �-secretase complexes (green). Overallthis shift in complex equilibrium results in a net increase in the A�42:A�40ratio via multiple interacting mechanisms. Pathway 1, the positive correlationbetween increased A�42:A�40 ratios and increased PS2-containing com-plexes suggests that PS2 �-secretase complexes may preferentially increaseA�42 production thereby increasing the A�42:A�40 ratio. Pathway 2, PS1FAD mutants also show altered cleavage specificity for A�42 and A�40 pro-duction, which on its own can lead to increased A�42:A�40 ratios. PS1 FADexpression also results in increased PS2 �-secretase complex formation that,in concert with PS1 FAD altered specificity, can contribute to increased A�42:A�40. Pathway 3, perturbations to complex equilibrium that favor the forma-tion of PS2 �-secretase complexes may deplete A�40-generating PS1 com-plexes and result in increased A�42:A�40 ratios.

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Kim, Hui Zheng, Sangram S. Sisodia and Yue-Ming LiLisa Placanica, Leonid Tarassishin, Guangli Yang, Erica Peethumnongsin, Seong-Hun

-Secretase ComplexesγPresenilin-2 Pen2 and Presenilin-1 Modulate the Dynamic Equilibrium of Presenilin-1 and

doi: 10.1074/jbc.M807269200 originally published online November 25, 20082009, 284:2967-2977.J. Biol. Chem. 

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