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A faster migrating variant masquerades as NICD when performing in-vitro γ-secretase assays with bacterially expressed Notch substrates† ‡Department of Molecular Biology and Pharmacology and Department of Medicine, Division of Biology and Biomedical Sciences at Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8231, St. Louis, MO 63110. §Department of Biochemistry & Molecular Biophysics, Division of Biology and Biomedical Sciences at Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8231, St. Louis, MO 63110. _Department of Cell Biology and physiology, Division of Biology and Biomedical Sciences at Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8231, St. Louis, MO 63110. Neuroscience Program, Division of Biology and Biomedical Sciences at Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8231, St. Louis, MO 63110.5Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113-0033, Japan *Author for correspondence: Email: Kopan/at/wustl.edu, phone: 314-747-5520, fax: 314-362-7058 The publisher's final edited version of this article is available at Biochemistry.Abstract Intramembrane proteolysis is a new and rapidly growing field. In vitro assays utilizing recombinant substrates for γ-secretase, an intramembrane-cleaving enzyme, are critically important in order to characterize the biochemical properties of this unusual enzyme. Several recombinant Notch proteins of varying length are commonly used as in vitro substrates for CHAPSO-solubilized γ-secretase. Here we report that several recombinant Notch construct undergo limited or no proteolysis in vitro. Instead, upon incubation with or without γ-secretase, variants of the intact protein migrate during SDS-PAGE at the location expected for the γ-secretase specific cleavage products. In addition, we show that addition of aspartyl- and γ-secretase specific protease inhibitors are able to retard the formation of these variants independent of γ-secretase, which could lead to the erroneous conclusion that Notch cleavage by solubilized γ-secretase was achieved in vitro even when no proteolysis occurred. In contrast, substrates produced in mammalian or insect cells are cleaved efficiently in vitro. These observations suggest that in vitro studies reliant on recombinant, bacterially produced Notch TMD should be performed with the inclusion of additional controls able to differentiate between actual cleavage and this potential artifact. γ-Secretase, a multi-protein enzymatic complex with aspartyl-protease activity, is a member of a unique class of proteases classified as Intramembrane Cleavage Proteases (I-CliPs), which catalyze cleavage of substrate proteins within the hydrophobic lipid bilayer (1, 2). Clinical interest in γ-secretase arose because it is the enzyme responsible for hydrolysis of the Amyloid Precursor Protein (APP) thus generating the pathogenic Aβ42 peptide, the primary component of amyloid-plaques that are the hallmark pathology and likely cause of Alzheimer’s Disease (3, 4). γ-Secretase is also responsible for the cleavage of many other proteins, most notably Notch, which is critical not only for early embryonic development and adult immune system function, but is involved in stem cell maintenance and in several diseases including cancer, stroke, and multiple sclerosis (5, 6, 7, 8, 9, 10). Lastly, despite an intense interest in this enzyme as a therapeutic target (9–14), γ-secretase remains a member of a novel class of proteases whose catalytic properties are largely unknown (15) and thus an increasing number of laboratories will join in the effort to characterize this activity. Several groups have developed in vitro cleavage assays whereby the ability of partially purified γ-secretase, in CHAPSO-solubilized membrane extracts, to cleave recombinant Notch proteins is measured (16). While there are several variations reported for how to enrich membrane fractions with γ-secretase (17, 18), the size and complexity of this enzyme may preclude the determination of its high-resolution structure using current techniques. Nonetheless, a structural study of γ-secretase substrates would shed considerable light on the mechanism of cleavage until structural information for the entire enzyme becomes available. It has been established that truncated substrates retain all the properties for cleavage in their TMD (19) and are well suited for structural determination in a micellar environment using nuclear magnetic resonance (NMR) techniques (20, 21). A similar approach was previously used to determine the solution structure of the Aβ40 peptide (22). There are essentially two distinct sources of substrate: either the substrate is transfected into the same mammalian or insect cell culture from which the γ-secretase is solubilized (23), or substrate is separately expressed and purified from E. Coli and is added to the solubilized enzyme from membrane extract (18, 24). All Notch substrates contain the transmembrane domain (TMD) as well as one or more epitope tags to enable detection of the expected N-terminal (Nβ) and C-terminal (NICD) products generated by γ-secretase. Obtaining a biologically relevant result may depend upon retention of conditions that are compatible with both an in vitro γ-secretase assay and NMR analysis. The availability of a bacterially produced γ-secretase substrate opened the door for a variety of biophysical and structural measurements of Notch cleavage that were heretofore unattainable. Notch is a particularly attractive candidate for this analysis because there are several known single amino acid substitutions at the γ-secretase cleavage site (S3) that alter cleavage efficiency (19, 25, 26, 27). In addition, the structure of γ-secretase substrates is important for recognition and cleavage (19, 28, 29, 30). While other I-CliP (S2P, SPP and Rhomboids) substrates require helix-breaking residues for cleavage (31–33), mutations to Valine 1744 in mouse Notch 1 that substitute helix-breaking residues such as Glycine (G) have a surprising deleterious effect (25, 34) making them candidates for NMR studies. To our surprise we discovered that a recombinant Notch protein, HAN100Flag, was unsuitable for NMR studies because it was not structurally stable during incubation at 37°C resulting in the appearance of faster migrating “conformational variants” on SDS-PAGE gels. Because these variants are indistinguishable from the expected cleavage product(s), it became apparent to us that they might have confounding effects on the analysis of Notch cleavage in vitro, prompting the analysis reported here. We present alternative assays and controls capable of distinguishing cleavage from conformational variants. Experimental Procedures Membrane preparation and detergent solubilization of γ-secretase from mammalian cells γ-Secretase was isolated as described before (24) with slight modifications (16). Briefly, confluent Hek293 cells grown in T75 flasks were scraped into ice-cold lysis buffer (20mM HEPES, pH 7.0, 1mM EDTA) containing complete protease inhibitor cocktail (Roche) and homogenized. Lysate was centrifuged at 800g for 10 min to pellet unbroken cells and debris. The supernatent was subsequently centrifuged at 100,000g for 60 min. The resultant pellet was resuspended in lysis buffer and the centrifugation was repeated. The pellet was resuspended such that final total protein concentration was 12mg/ml and was stored at −80 C. Isolated membranes were diluted into 1% CHAPSO containing lysis buffer and 2.5mg/ml total protein and incubated for 1 hour at 4 C with rocking. Membranes were centrifuged at 100,000g for 1 hour and the supernatent fraction is considered solubilized γ-secretase. Solubilized γ-secretase was adjusted to 0.25% CHAPSO for cleavage reactions. Expression and purification of bacterially expressed Notch substrates HAN100Flag was purified as previously described (35). In short, BL21 (DE3) E. Coli bacterial cells (Stratagene) containing the HAN100Flag in the pET21a+ expression vector (Novagen) were grown in 1L LB flasks to an OD of 1.0 at 600nM. Expression was initiated with 1mM (final concentration) IPTG for 2 hours. The cells were pelleted in 1L centrifuge bottles and stored at −80 C. Frozen cell pellets were resuspended in lysis buffer (10mM Tris, pH 7.5, 200mM NaCl, 1%NP-40, 1mM EDTA, Complete Protease Inhibitor Cocktail (Roche) and passed 2X through a French Press. Cell lysates were centrifuged at 17K in a Sorvall SS34 rotor for 30 min and the soluble fraction was passed once over an M2-Flag affinity column (Sigma). Bound substrate was eluted using 100mM Glycine, pH 2.7 and 1% NP-40. Stable HAN100Flag was purified in the same buffers, with the following exceptions: no buffer contained NP-40 and protein was eluted from the M2-Flag column in 100mM Glycine, pH 3.5. Fractions were assayed for purity and stored in elution buffer at −80 C. All protein concentrations were determined using a commercially available BCA assay kit (Sigma). Expression and purification of N102FmH was described previously (36) with the exception that protein used for the in vitro reactions was obtained from the soluble fraction of E. Coli lysate. Cleavage reaction and detection for Hek293 cells or buffer only Purified substrate was added to a final concentration of 1uM in 50ul of solubilized γ-secretase or cleavage reaction buffer only. For 0 hour time points, substrate was added to each reaction and kept at −20 C for the duration of the assay. Cleavage reactions were stopped by addition of laemelli sample buffer and were either incubated at 65 C for 10 min or placed in boiling water for 5 min. No differences were observed between treatment at 65 C or in boiling water prior to loading on the gel. Samples from each reaction were loaded onto 4–20% Tris-Glycine pre-cast gels (BioRad or BioExpress) for SDS-PAGE and subsequently transferred to PVDF membranes (BioRad) for detection by chemiluminescence (Pico, Pierce). Antibodies used for detection are rabbit anti-mNotch1Val1744 (Cell Signaling), mouse anti-Flag M2 (Sigma), rabbit anti-HA (Ha.11; Babco) and mouse anti-c-myc (9B11; Cell Signaling Technology). Protein Sequencing Purified, recombinant HAN100Flag and variants were isolated using standard SDS-PAGE and transferred to PVDF membrane. The membrane was stained to detect transferred protein variants. Edman degradation protein sequencing was performed by Midwest Analytical, Inc. (11141 South Towne Square, Suite E, St. Louis, MO 63123). MALDI-TOF HAN100Flag was incubated in cleavage buffer (no enzyme) as described. The status of the protein was determined using SDS-PAGE and chemiluminescence. Representative samples were prepared for matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) by directly diluting protein samples in equal volumes of matrix prior to analysis. Samples were analyzed using a Voyager DE Pro spectrometer (Applied Biosystems, Foster City, Calif.). Baculovirus expression of γ-secretase and substrates γ-Secretase complex was reconstituted in Sf9 cells by the baculovirus expression system as described by (18) with the following changes. cDNAs that encode PS1-EGFP (PE) (37) or aspartate mutant PE together with HisXpress-Pen-2 (18, 38) are cloned into pFastBacDual (Invitrogen) to generate PS1/Pen-2 (PEHP or PEDNHP) recombinant baculovirus. Nct-V5His cDNA with polyhedrin promoter and polyA tail are inserted into pBlueBac4.5 with Aph-1a-mycHis (18) to generate Nct/Aph-1a (NA) recombinant baculovirus. Reconstitution of γ-secretase complex is achieved by coinfection of PEHP and NA viruses, which is confirmed by generation of PE fragments and coimmunoprecipitation analysis (data not shown). Infected Sf9 cells were homogenized and membranes were isolated. Membranes were dispersed in HEPES buffer (10mM HEPES, pH 7.4, 150mM NaCl) containing Complete protease inhibitor mixture (Roche Applied Science) and stored at −80 degrees until use. Membrane fraction containing N100FLAG substrate (39) was isolated from virally infected into Sf9 cells. The ΔICE substrate was stably transfected using retrovirus into mouse embryonic fibroblast double knock-out cells (MEF DKO), which lack presenilin 1 and 2. This construct has a C-terminal read-through error that increases its predicted weight by approximately a factor of 2. However, this does not affect its suitability as a substrate for γ-secretase. Baculovirus in vitro cleavage reaction and detection Doubleviruses or mock virus infected-Sf9 dispersed membranes were incubated for 16 hrs with HAN100Flag, ΔICE in MEF DKO membranes, or with N100FLAG (N100ppt) from virally infected Sf9 membranes in HEPES buffer containing Complete protease inhibitor cocktail and 0.25% CHAPSO. Cleavage reactions were performed in a volume of 500ul and terminated by boiling and trichloroacetic acid (TCA) precipitation of protein. Total TCA precipitate was loaded onto 13.5% Tris-Tricine gels for SDS-PAGE. Protein was transferred to PVDF membrane and boiled to enhance detection prior to blocking in 5% Milk. Chemiluminescence was otherwise the same as described (Fempto, Pierce). For the assay using N102FmH, we performed as reported (18), except for adding 0.1% Phosphatidylcholine (from porcine brain, Avanti polar lipids). Results The Notch TMD is cleaved twice during hydrolysis by γ-secretase; once near the inner leaflet (S3) that liberates the C-terminal NICD product from the plasma membrane, and a second near the outer leaflet (S4) that releases the amino-terminal Nβ product. HAN100Flag permits detection of both Nβ (with anti-HA) and NICD (with anti-Flag, Figure 1A
In order to analyze the NMR structure of HAN100Flag, we labored to identify suitable detergent-buffer conditions that are compatible with both an in vitro γ-secretase assay and NMR analysis. We initially set out to replicate the assay conditions that permit hydrolysis of HAN100Flag in vitro by γ-secretase (35). Upon addition of HAN100Flag to CHAPSO-solubilized γ-secretase, we observed the expected faster-migrating species corresponding to the expected product (NICD) using anti-Flag (Figure 1B Unexpectedly, we noticed that the same faster migrating band believed to represent the C-terminal NICD cleavage product (Figure 1B One possible explanation for the presence of a faster migrating, HA containing species (Figure 1B The detection of the putative “NICD” product with N-terminal HA opens the possibility that this faster migrating species was not the product of proteolysis. We noted that the aspartyl-protease inhibitor Pepstatin A could completely prevent the formation of the faster migrating species (Figure 1A
In an effort to explain these highly unusual observations, we next isolated each of the observed protein bands (Figure 1
We next sought to identify Notch substrates that are cleaved in vitro. We established a γ-secretase cleavage assay using the baculovirus system; γ-secretase purified in this way is reported to have a 10-fold greater activity than γ-secretase derived from mammalian cells (18). We assayed the activity of purified Sf9 γ-secretase using a baculovirus produced Notch substrates, N100ppt (43). N-terminal V1744 was readily detected in this assay with anti-V1744, and cleavage of N100ppt was completely inhibited by DAPT (Figure 4A
Next, we wished to determine if γ-secretase from Sf9 membranes could recognize and cleave a mammalian Notch protein produced by cells lacking γ-secretase. To accomplish that, we stably expressed the minimal Notch cleavage construct, ΔICE (19) in mouse embryonic fibroblast cells lacking both presenilin 1 and 2 (MEF PS1/2 DKO). These cells endogenously express APP; simultaneous cleavage of APP was observed in the same reaction (not shown). When CHAPSO-dispersed membranes from these substrate-containing cells are mixed and incubated with CHAPSO-dispersed membranes from γ-secretase producing Sf9 cells, generation of the NICD can be followed with anti-V1744 (Figure 4C Though we had been unable to detect any cleavage of HAN100Flag by γ-secretase from mammalian cells, we decided to determine if HAN100Flag could be cleaved using the more robust baculovirus system. We incubated this bacterially produced substrate with Sf9 cell membranes containing γ-secretase. Faster migrating species formed regardless of whether incubation was performed in buffer alone (Figure 4E We next sought to determine if other recombinant Notch substrates purified from bacteria underwent similar conformational changes, and if any are cleavable by γ-secretase. N102FmH is similar to HAN100Flag, and is reported to undergo cleavage in the baculovirus system (18). When incubated with CHAPSO-dispersed γ-secretase-containing Sf9 membranes, N102FmH does appear to undergo cleavage (Figure 5
Discussion The discovery of migration variants casts doubt on conclusions drawn from assays performed thus far. In reexamining previous reports using bacterially produced Notch substrates in vitro we noticed that in some, anti-Val1744 could not differentiate the substrate from the cleavage product (35), and that the putative NICD product also is visualized using anti-HA, suggesting that these were variants of the same (uncleaved) protein as described here. It was reported that recombinant Notch based substrates, including HAN100Flag, are cleaved efficiently in small reaction volumes and with relatively short incubation periods (35). Here we show that under such conditions, the “cleavage products” are a faster migrating variant. Cleavage does occur with other bacterial-produced substrates, but so inefficiently that extensive sample processing is required to detect the products and separate them from the faster migrating variants. One possible explanation for the difference observed between substrates that are pre-inserted into membranes (N100ppt, ΔICE) and bacterially produced substrates (HAN100Flag, N102FmH) could be that the long bacterial-produced substrate cannot efficiently integrate into the dispersed lipid membranes containing γ-secretase. Regardless, the presence of a non-cleaved protein that co-migrates with the cleaved “NICD” product (Figure 5 What is the chemical basis of this phenomenon? We were able to establish that inclusion of NP-40 in the buffer enhanced conformational variant formation with HAN100Flag. When NP-40 was excluded from the purification buffers, HAN100Flag was more stable, migrating as a single band when incubated under the common assay conditions described in Figure 1 Resolving how conformational variants are generated for any particular construct is perhaps less important then offering solutions to differentiate the artifact from actual cleavage. Future attempts to demonstrate γ-secretase mediated cleavage of Notch substrates in vitro must thus rely on definitive characterization of the substrates and their apparent cleavage products. As demonstrated here, bacterially expressed Notch substrates are cleaved much less efficiently than those produced in mammalian or insect cells, perhaps due to their tendency to form variants and/or aggregate, and one must question whether the residual cleavage observed in some substrates truly reflects the in vivo reaction. Despite the appearance of variants that mimic the expected “NICD” in assays conducted with different bacterially-expressed constructs, and the difficulty in properly identifying the actual cleavage product (see antibody comparison, Figure 5 Acknowledgment We wish to thank Dr. Robert Mecham for many helpful discussions, to the members of the Kopan lab for helpful suggestions and to John Monsey for expert technical advice and encouragement. Footnotes †PKC and RK are supported by Washington University and the national institutes of health grant P50 AG05681 1APP; Amyloid Precursor Protein; I-CliP, Intramembrane Cleavage Proteases; ICD, Notch Intracellular Domain; NMR, Nuclear Magnetic Resonance Spectroscopy; TMD, Transmembrane domain. DAPT: N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester. DMSO: Dimethyl sulfoxide CHAPSO: 3-([3-Cholamidopropyl]dimethylammonio)-2-hydroxy-1-propanesulfonate References 1. Haass C, Steiner H. Alzheimer disease gamma-secretase: a complex story of GxGD-type presenilin proteases. Trends Cell Biol. 2002;12:556–562. [PubMed] 2. Weihofen A, Martoglio B. Intramembrane-cleaving proteases: controlled liberation of proteins and bioactive peptides. Trends Cell Biol. 2003;13:71–78. [PubMed] 3. Iwatsubo T. The gamma-secretase complex: machinery for intramembrane proteolysis. Current Opinion in Neurobiology. 2004;14:379–383. [PubMed] 4. Wolfe MS. 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Trends Cell Biol. 2002 Dec; 12(12):556-62.
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[Biochemistry. 2004]J Biol Chem. 2004 Sep 3; 279(36):38040-6.
[J Biol Chem. 2004]J Biol Chem. 2004 Dec 3; 279(49):50864-73.
[J Biol Chem. 2004]Biochim Biophys Acta. 2000 Nov 23; 1508(1-2):164-81.
[Biochim Biophys Acta. 2000]Biochemistry. 1998 Aug 4; 37(31):11064-77.
[Biochemistry. 1998]J Biol Chem. 2004 Dec 3; 279(49):50864-73.
[J Biol Chem. 2004]J Neurochem. 2006 Jan; 96(1):228-35.
[J Neurochem. 2006]Nature. 2000 Jun 22; 405(6789):966-70.
[Nature. 2000]Nature. 1998 May 28; 393(6683):382-6.
[Nature. 1998]Mol Cell. 2000 Sep; 6(3):625-36.
[Mol Cell. 2000]Nature. 2000 Jun 8; 405(6787):689-94.
[Nature. 2000]Biochemistry. 2003 Jan 14; 42(1):137-44.
[Biochemistry. 2003]J Biol Chem. 2004 Sep 3; 279(36):38040-6.
[J Biol Chem. 2004]J Cell Biol. 2002 Aug 5; 158(3):551-61.
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[J Biol Chem. 2004]J Neurochem. 2006 Jan; 96(1):228-35.
[J Neurochem. 2006]Dev Cell. 2005 May; 8(5):677-88.
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[Biochemistry. 2003]J Neurochem. 2001 Jan; 76(1):173-81.
[J Neurochem. 2001]J Neurosci Res. 2000 Oct 15; 62(2):311-7.
[J Neurosci Res. 2000]Biochemistry. 2003 Jan 14; 42(1):137-44.
[Biochemistry. 2003]J Biol Chem. 2004 Sep 3; 279(36):38040-6.
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[Cell. 2005]J Biol Chem. 2004 Dec 3; 279(49):50864-73.
[J Biol Chem. 2004]J Biol Chem. 2004 Sep 3; 279(36):38040-6.
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