Intramembrane Aspartyl Protease Research Articles

A Presenilin-like protease associated with Plasmodium falciparum micronemes is involved in erythrocyte invasion

We describe identification of a Plasmodium falciparum microneme protease involved in RBC invasion. From the yeast two-hybrid screening of a P. falciparum cDNA library, we have identified a 47 kDa membrane protein that interacted with the 5ABC domain of human RBC band 3. This protein shared homology with a Presenilin-type aspartyl protease, the signal peptide peptidase (SPP). An antibody raised against a predicted exposed region of this protein reacted specifically to a single band of ∼47 kDa in the P. falciparum protein extract. Immunofluorescence microscopy suggested that this protein co-localized with the microneme protein EBA-175 in schizonts, and immunoelectron microscopy established that it is primarily localized to micronemes in merozoites. Functional characterization of Plasmodium falciparum signal peptide peptidase (PfSPP), demonstrates that an antibody to PfSPP blocks RBC invasion by P. falciparum in vitro. Native and recombinant PfSPP bound directly to the 5ABC domain of band 3 in solution and the binding of PfSPP to RBCs was chymotrypsin-sensitive, but trypsin and neuraminidase-resistant. Together, these results suggest that host band 3 interacts with PfSPP during RBC invasion presumably following parasite microneme discharge. PfSPP is the first microneme-associated intramembrane aspartyl protease identified in the apicomplexan parasites that interacts with a major transmembrane receptor on host erythrocytes.

Active γ-Secretase Complexes Contain Only One of Each Component

Gamma-secretase is an intramembrane aspartyl protease complex that cleaves type I integral membrane proteins, including the amyloid beta-protein precursor and the Notch receptor, and is composed of presenilin, Pen-2, nicastrin, and Aph-1. Although all four of these membrane proteins are essential for assembly and activity, the stoichiometry of the complex is unknown, with the number of presenilin molecules present being especially controversial. Here we analyze functional gamma-secretase complexes, isolated by immunoprecipitation from solubilized membrane fractions and able to produce amyloid beta-peptides and amyloid beta-protein precursor intracellular domain. We show that the active isolated protease contains only one presenilin per complex, which excludes certain models of the active site that require aspartate dyads formed between two presenilin molecules. We also quantified components in the isolated complexes by Western blot using protein standards and found that the amounts of Pen-2 and nicastrin were the same as that of presenilin. Moreover, we found that one Aph-1 was not co-immunoprecipitated with another in active complexes, evidence that Aph-1 is likewise present as a monomer. Taken together, these results demonstrate that the stoichiometry of gamma-components presenilin:Pen-2:nicastrin:Aph-1 is 1:1:1:1.

A C-terminal Region of Signal Peptide Peptidase Defines a Functional Domain for Intramembrane Aspartic Protease Catalysis

Intramembrane proteolysis is now firmly established as a prominent biological process, and structure elucidation is emerging as the new frontier in the understanding of these novel membrane-embedded enzymes. Reproducing this unusual hydrolysis within otherwise water-excluding transmembrane regions with purified proteins is a challenging prerequisite for such structural studies. Here we show the bacterial expression, purification, and reconstitution of proteolytically active signal peptide peptidase (SPP), a membrane-embedded enzyme in the presenilin family of aspartyl proteases. This finding formally proves that, unlike presenilin, SPP does not require any additional proteins for proteolysis. Surprisingly, the conserved C-terminal half of SPP is sufficient for proteolytic activity; purification and reconstitution of this engineered fragment of several SPP orthologues revealed that this region defines a functional domain for an intramembrane aspartyl protease. The discovery of minimal requirements for intramembrane proteolysis should facilitate mechanistic and structural analysis and help define general biochemical principles of hydrolysis in a hydrophobic environment.

Regulation of γ-Secretase Activity in Alzheimer's Disease

The gamma-secretase complex is an intramembrane aspartyl protease that cleaves its substrates along their transmembrane regions. Sequential proteolytic processing of amyloid precursor protein by beta- and gamma-secretase produces amyloid beta-peptides, which are the major components of amyloid plaques in the brains of Alzheimer's disease patients. The gamma-secretase complex is therefore believed to be critical in the pathogenesis of Alzheimer's disease. Here we review the range of factors found to affect the nature and degree of gamma-secretase complex activity; these include gamma-secretase complex assembly and activation, the integral regulatory subunit CD147, transient or weak binding partners, the levels of cholesterol and sphingolipids in cell membranes, and inflammatory cytokines. Integrated knowledge of the molecular mechanisms supporting the actions of these factors is expected to lead to a comprehensive understanding of the functional regulation of the gamma-secretase complex, and this, in turn, should facilitate the development of novel therapeutic strategies for the treatment of Alzheimer's disease.

Signal Peptide Peptidase: Biochemical Properties and Modulation by Nonsteroidal Antiinflammatory Drugs

Signal peptide peptidase (SPP) is an intramembrane aspartyl protease that cleaves remnant signal peptides after their release by signal peptidase. SPP contains active site motifs also found in presenilin, the catalytic component of the gamma-secretase complex of Alzheimer's disease. However, SPP has a membrane topology opposite that of presenilin, cleaves transmembrane substrates of opposite directionality, and does not require complexation with other proteins. Here we show that, upon isolation of membranes and solubilization with detergent, the biochemical characteristics of SPP are remarkably similar to gamma-secretase. The majority of the SPP-catalyzed cleavages occurred at a single site in a synthetic substrate based on the prolactin (Prl) signal sequence. However, as seen with cleavage of substrates by gamma-secretase, additional cuts at other minor sites are also observed. Like gamma-secretase, SPP is inhibited by helical peptidomimetics and apparently contains a substrate-binding site that is distinct from the active site. Surprisingly, certain nonsteroidal antiinflammatory drugs known to shift the site of proteolysis by gamma-secretase also alter the cleavage site of Prl by SPP. Together, these findings suggest that SPP and presenilin share certain biochemical properties, including a conserved drug-binding site for allosteric modulation of substrate proteolysis.

γ-Secretase Exists on the Plasma Membrane as an Intact Complex That Accepts Substrates and Effects Intramembrane Cleavage*

Research on Alzheimer's disease led to the identification of a novel proteolytic mechanism in all metazoans, the presenilin/gamma-secretase complex. This unique intramembrane-cleaving aspartyl protease is required for the normal processing of Notch, Jagged, beta-amyloid precursor protein (APP), E-cadherin, and many other receptor-like proteins. We recently provided indirect evidence of gamma-secretase activity at the cell surface in HeLa cells following inhibition of receptor-mediated endocytosis. Here, we directly identify and isolate gamma-secretase as an intact complex (Presenilin, Nicastrin, Aph-1, and Pen-2) from the plasma membrane, both in overexpressing cell lines and endogenously. Inhibition of its proteolytic activity allowed cell surface gamma-secretase to be captured in association with its plasma membrane-localized APP substrates (C83 and C99). Moreover, non-denaturing isolation of the intact enzyme complex revealed that cell surface gamma-secretase can specifically generate amyloid beta-protein from an APP substrate and similarly cleave a Notch substrate. These data directly establish the proteolytic function of gamma-secretase on the plasma membrane, independent of a hypothesized substrate trafficking role. We conclude that presenilin/gamma-secretase exists as a mature complex at the cell surface, where it interacts with and can cleave its substrates, consistent with an essential function in processing many adhesion molecules and receptors required for cell-cell interaction or intercellular signaling.

Cell biology of protein misfolding: The examples of Alzheimer's and Parkinson's diseases

The salutary intersection of fundamental cell biology with the study of disease is well illustrated by the emerging elucidation of neurodegenerative disorders. Novel mechanisms in cell biology have been uncovered through disease-orientated research; for example, the discovery of presenilin as an intramembrane aspartyl protease that processes many diverse proteins within the lipid bilayer. A common theme has arisen in this field: normally-soluble proteins accumulate, misfold and oligomerize, inducing cytotoxic effects that are particularly devastating in the post-mitotic milieu of the neuron.

S2-03-01 Presenilin as the active site of gamma-secretase, a novel intramembranous aspartyl protease

S2-03-01 Presenilin as the active site of gamma-secretase, a novel intramembranous aspartyl protease

P4-272 Presenilin-related putative intramembrane aspartyl-proteases

P4-272 Presenilin-related putative intramembrane aspartyl-proteases

Signal Peptide Peptidase Forms a Homodimer That Is Labeled by an Active Site-directed γ-Secretase Inhibitor

Presenilin (PS) is the presumptive catalytic component of the intramembrane aspartyl protease gamma-secretase complex. Recently a family of presenilin homologs was identified. One member of this family, signal peptide peptidase (SPP), has been shown to be a protease, which supports the hypothesis that PS and presenilin homologs are related intramembrane-cleaving aspartyl proteases. SPP has been reported as a glycoprotein of approximately 45 kDa. Our initial characterization of SPP isolated from human brain and cell lines demonstrated that SPP is primarily present as an SDS-stable approximately 95-kDa protein on Western blots. Upon heating or treatment of this approximately 95-kDa SPP band with acid, a approximately 45-kDa band could be resolved. Co-purification of two different epitope-tagged forms of SPP from a stably transfected cell line expressing both tagged versions demonstrated that the approximately 95-kDa band is a homodimer of SPP. Pulse-chase metabolic labeling studies demonstrated that the SPP homodimer assembles rapidly and is metabolically stable. In a glycerol velocity gradient, SPP sedimented from approximately 100-200 kDa. Significantly the SPP homodimer was specifically labeled by an active site-directed photoaffinity probe (III-63) for PS, indicating that the active sites of SPP and PS/gamma-secretase are similar and providing strong evidence that the homodimer is functionally active. Collectively these data suggest that SPP exists in vivo as a functional dimer.

Rhomboids

What are they? Rhomboids are a recently discovered family of serine proteases that cleave substrates within transmembrane domains. All rhomboids have multiple transmembrane domains (typically six or seven) and it is proposed that they work by forming the classical charge relaying catalytic triad – famous from serine proteases such as chymotrypsin – between their transmembrane domains. Hang on! Surely proteolysis can't work in the hydrophobic membrane bilayer…? Actually, the rhomboid family joins an exclusive club of proteases that appear to do just that. The presenilins and signal peptide peptidase are intramembrane aspartyl proteases; they cleave substrates including the Notch receptor and the amyloid precursor protein, which is implicated in Alzheimer's disease. The site-2 protease family are intramembrane metalloproteases; among other things, they regulate cholesterol biosynthesis. It's probably no coincidence that, although these families are unrelated, they all have multiple transmembrane domains: this may produce a hydrophilic microenvironment around the active site of hydrolysis. So all this can actually be seen in crystal structures? No, it's inferred from biochemistry and genetics. Nobody has yet succeeded in solving the structure of any of these proteins. But to be fair, the evidence for the basic model is pretty strong. Why the weird name? Blame the Drosophilists. Rhomboid's first recognition came as a mutant discovered in the genetic screens that won Christiane Nüsslein-Volhard and Eric Wieschaus a Nobel Prize in 1995. Mutant Drosophila embryos have rhomboid-shaped heads. How were they discovered to be proteases? Genetics indicated that Rhomboid-1 in flies – we now know that Drosophila has seven rhomboids – is a key activator of epidermal growth factor (EGF) receptor signalling, and that it works in the signal-sending cell. Subsequent biochemistry and cell biology showed that Rhomboid-1 cleaves and thereby activates three membrane-tethered EGF-like ligands. This occurs in the Golgi apparatus, where many eukaryotic rhomboids reside. Do they all control EGF receptor signalling? No. For one thing, rhomboids exist throughout evolution – from bacteria and archaea to humans – and most organisms which have rhomboids don't even have receptor tyrosine kinases, let alone EGF receptors. But, amazingly, the bacterium Providencia stuartii uses a rhomboid to release an intercellular signalling molecule – a mechanism apparently analagous to the activation of EGF ligands by rhomboids in Drosophila – implying a common signalling mechanism between bacteria and metazoans. But they all control intercellular signalling of some kind? No again. Although we know rather little about the roles of rhomboids in most species, they probably do a wide variety of things – connected only by the basic mechanism of releasing a protein from a mem brane by proteolysis of its trans membrane domain. For example, eukaryotes all have a mitochondrial rhomboid that, at least in yeast, controls membrane fusion by cleaving a dynamin-like GTPase. Can rhomboid cleavage sites be recognised? Not very efficiently, though current evidence suggests that all rhomboids recognise, as well as cleave, transmembrane domain sequences. There is a requirement for residues that destabilise transmembrane α helices, and substrate transmembrane domains must also be relatively hydrophilic near their luminal end. These requirements have allowed some prediction of rhomboid substrates. What's the difference between rhomboids and other intramembrane proteases? Apart from the catalytic mechanism – rhomboids are the only intramembrane serine proteases – one important difference is that all known rhomboids release extracellular or luminal domains from transmembrane domains. The others all release cytoplasmic domains, usually tethered transcription factors. By allowing intramembrane proteolysis to occur in the other direction, rhomboids therefore double the potential of intramembrane proteolysis to be a widespread signalling mechanism.

Presenilin, Notch, and the genesis and treatment of Alzheimer's disease.

Elucidation of the proteolytic processing of the amyloid beta-protein precursor (APP) has revealed that one of the two proteases (gamma-secretase) that cleave APP to release amyloid beta-protein (Abeta) is likely to be presenilin. Presenilin also mediates the gamma-secretase-like cleavage of Notch receptors to enable signaling by their cytoplasmic domains. Therefore, APP and Notch may be the first identified substrates of a unique intramembranous aspartyl protease that has presenilin as its active-site component. In view of the evidence for a central role of cerebral build-up of Abeta in the pathogenesis of Alzheimer's disease, this disorder appears to have arisen in the human population as a late-life consequence of the conservation of a critical developmental pathway.

Presenilins, β-amyloid precursor protein and the molecular basis of Alzheimer's disease

Progressive cerebral deposition of the 40- and 42-residue amyloid β-proteins is an early and invariant event in all forms of Alzheimer's disease (AD). Aβ proteins are generated from the β-amyloid precursor protein (APP) via two sequential cleavages by proteases designated β-secretase and γ-secretase and are constitutively secreted by essentially all cells throughout life. APP can undergo these cleavages during its secretory trafficking to the cell surface, yet much of Aβ appears to be generated after APP reaches the surface, i.e. in the endosomal pathway. Presenilin (PS) 1 and 2, homologous proteins with eight transmembrane (TM) domains, play a critical role in the γ-secretase cleavage of APP. Deletion of presenilin 1 (PS1) in mice markedly decreases Aβ production, whereas AD-causing PS1 mutations selectively increase Aβ 42 production, thereby markedly accelerating amyloid plaque formation, both in humans and transgenic mice. Small amounts of APP and PS can be co-immunoprecipitated from cells, suggesting a direct role of PS1 in the cleavage of APP by γ-secretase. We recently observed and mutated two unusual intramembranous aspartate residues in TM6 and TM7 of each presenilin, resulting in complete blockage of the γ-secretase cleavage of APP, with no detectable Aβ production by cells. Because our protease inhibitor studies suggest that γ-secretase is an aspartyl protease, we hypothesize that these two key aspartates serve as the active site of an unprecedented intramembranous aspartyl protease (i.e. γ-secretase). The recent discovery that Notch, a protein critical for cell fate determination during development, also undergoes an intramembranous cleavage mediated by PS suggests that presenilin may be a key regulatory enzyme for several vital proteolytic events. Thought of in this context, AD may arise late in the post-reproductive life of humans as an ancillary metabolic consequence of a proteolytic mechanism which confers strong evolutionary advantage. Specific and potent inhibitors of γ-secretase/presenilin or of the recently cloned β-secretase may well prove useful for the treatment and the prevention of AD.

Two transmembrane aspartates in presenilin-1 required for presenilin endoproteolysis and gamma-secretase activity.

Accumulation of the amyloid-beta protein (Abeta) in the cerebral cortex is an early and invariant event in the pathogenesis of Alzheimer's disease. The final step in the generation of Abeta from the beta-amyloid precursor protein is an apparently intramembranous proteolysis by the elusive gamma-secretase(s). The most common cause of familial Alzheimer's disease is mutation of the genes encoding presenilins 1 and 2, which alters gamma-secretase activity to increase the production of the highly amyloidogenic Abeta42 isoform. Moreover, deletion of presenilin-1 in mice greatly reduces gamma-secretase activity, indicating that presenilin-1 mediates most of this proteolytic event. Here we report that mutation of either of two conserved transmembrane (TM) aspartate residues in presenilin-1, Asp 257 (in TM6) and Asp 385 (in TM7), substantially reduces Abeta production and increases the amounts of the carboxy-terminal fragments of beta-amyloid precursor protein that are the substrates of gamma-secretase. We observed these effects in three different cell lines as well as in cell-free microsomes. Either of the Asp --> Ala mutations also prevented the normal endoproteolysis of presenilin-1 in the TM6 --> TM7 cytoplasmic loop. In a functional presenilin-1 variant (carrying a deletion in exon 9) that is associated with familial Alzheimer's disease and which does not require this cleavage, the Asp 385 --> Ala mutation still inhibited gamma-secretase activity. Our results indicate that the two transmembrane aspartate residues are critical for both presenilin-1 endoproteolysis and gamma-secretase activity, and suggest that presenilin 1 is either a unique diaspartyl cofactor for gamma-secretase or is itself gamma-secretase, an autoactivated intramembranous aspartyl protease.

Case of carcinoma of third part of duodenum.

<h3>Abstract</h3> Cleavage of Notch by the major intramembrane aspartyl protease complex γ-secretase is a central event in cell regulation and is also important to Alzheimer’s disease, with more than 200 mutations in the catalytic subunit of γ-secretase (PS1) causing severe early-onset forms of the disease. Recently, cryogenic electron microscopy (cryo-EM) has revealed the electron density of the protein-Notch complex in frozen solution, indicating major changes upon substrate binding and a possible helix unwinding to expose peptide bonds. In order understand the all-atom dynamics that cause this process, and to test the Notch binding in a membrane protein rather than solution, we developed an all-atom model of mature wild-type γ-secretase bound to Notch in a complete membrane-water system and studied the system using three independent 500-nanosecond molecular dynamics simulations. Our ensembles are in essential agreement with known cryo-EM data. As in previous simulations we find unusual β-strand transitions in exposed parts of PS1. We also observe the atomic helix motions that cause loss of helicity in bound Notch by direct comparison to corresponding 500 ns simulations of free Notch, in particular five residues to the N-terminal site of the primary cleavage site. Most importantly, we identify three conformation states, with two of them differing in the Notch-bound catalytic site. These dynamics produce a ping-pong relationship of positioning the S3 cleavage sites of Notch relative to the aspartates. These conformation states are not visible in the cryo-EM data; probably the density is an average snapshot of the two states. Our identified conformation states rationalize how Notch cleavage can be imprecise and yield multiple products. Our identified conformation states may aid efforts to develop conformation-selective drugs that target C99 and Notch cleavage differently. <h3>Statement of Significance</h3> The atomic dynamics underlying cleavage of Notch by γ-secretase in the membrane is of major biological importance. Electron microscopy has revealed the protein-Notch complex in frozen solution, showing major changes upon substrate binding and helix unwinding to expose peptide bonds, but does not explain why substrate cleavage is imprecise and produces several products. Our model of wild-type γ-secretase bound to Notch in a complete membrane-water system equilibrated by 3 × 500 nanoseconds of molecular dynamics strongly complements the electron microscopy data: We identify the specific loop and helix motions that cause the β-strand transitions in PS1 and the loss of helicity in specific residues of bound Notch. We identify different conformations of Notch, which importantly affect the S3 cleavage site; the open state may cause the imprecise cleavage with earlier release of products. Our identified states can aid development of conformation-selective drugs that target C99 and Notch cleavage differently.