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Entry into the Endoplasmic Reticulum: Protein Translocation, Folding and Quality Control

and *.

* * Corresponding Author: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA. Email:

Secretory proteins enter the ER after or concomitant with their synthesis on cytoplasmic ribosomes in a process known as translocation. In either case, nascent secretory proteins must be targeted to the translocation machinery at the ER membrane and must traverse the lipid bilayer of the ER through the translocation channel. Molecular chaperones in the cytosol and ER lumen assist translocation and facilitate protein folding and assembly in the lumen. Proteins that achieve their native conformation exit the ER and continue through the secretory pathway. Incompletely folded or unassembled proteins are recognized by a constitutively active quality control pathway in the ER that identifies aberrant proteins and targets them for destruction in the cytosol by the proteasome. This process is known as ER associated degradation (ERAD).


Due to their size and chemical heterogeneity, the transport of proteins into and across cellular membranes poses a number of challenges. First, proteins must be accurately targeted to their appropriate destinations after or during translation on cytoplasmic ribosomes, and then they must cross or insert into lipid bilayers without disturbing membrane integrity. This transport process is known as protein translocation. Second, protein translocation must be regulated to respond to dynamic cellular requirements. And third, cells must recognize and compensate for mutations or conditions that alter the trafficking of individual factors or the activities of components of the targeting and translocation machineries.

Although these challenges are common to all cell types and to most intra-cellular organelles, this chapter will focus on the translocation of proteins into the endoplasmic reticulum (ER). For proteins destined for extra-cellular secretion or for residence within the secretory pathway, protein translocation into the ER represents the first committed step in protein targeting. We will also discuss the quality control mechanism that monitors protein-folding efficiency in the ER. The reader is referred to other reviews that detail how the challenges of protein translocation are met by the plasma membrane in bacteria,1 chloroplasts,2 mitochondria,3 the nuclear envelope4 and the peroxisome,5 and that detail the similarities and differences between these systems.6 In the interest of space and due to the breadth of the primary literature, we have chosen to focus on selected areas of active research in this field.

Protein Translocation Across the ER Membrane

Protein translocation can occur either cotranslationally, during which insertion into the ER lumen or membrane occurs concomitant with protein synthesis, or post-translationally, in which translocation occurs after a polypeptide has been completely synthesized. In either mechanism, the translocation reaction involves: (a) the identification and targeting of proteins to the ER, (b) the association of proteins with the ER translocation machinery, including a pore through which proteins enter the ER, (c) the energy-dependent import of proteins into the ER lumen or membrane, and (d) protein folding and maturation in the ER (see fig. 1).

Figure 1. Translocation into the ER.

Figure 1

Translocation into the ER. Post- and cotranslational translocation requires four steps. 1) Targeting to the ER membrane, which can be SRP-dependent or independent. Post-translationally translocated preproteins require molecular chaperones to maintain (more...)

Secreted Protein Identification and Targeting

Most soluble secreted proteins contain an amino-terminal signal sequence that interacts with cytoplasmic targeting factors and the ER-resident translocation machinery.7 Upon entry into the ER, signal sequences on “preproteins” form a hairpin structure and are usually cleaved by signal peptidase, a protease complex residing at the lumenal face of the ER membrane. The removed signal peptide itself is broken-down by a recently-discovered signal peptide peptidase. 8 In some integral membrane proteins, the first transmembrane domain functions as an ER-targeting signal sequence and is not cleaved, possibly because of its residence within the translocation pore relative to the signal peptidase.9 While there is not a clear consensus for ER-targeting signal sequences, they are typically 11-27 amino acids, contain a central hydrophobic core flanked by positively charged residues, and are thought to form an α-helix. The relative hydrophobicity of the core controls whether preproteins are translocated cotranslationally or post-translationally in yeast such that more hydrophobic sequences target preproteins into the post-translational translocation pathway.10 Signal sequences may also dictate the “priority” by which different substrates are translocated.11

Cotranslational translocation occurs when membrane-bound ribosomes insert growing nascent polypeptide chains directly into an ER translocation pore. The targeting of cytoplasmic ribosomes translating signal sequence-containing polypeptides to the ER is mediated by the signal recognition particle (SRP). SRP is a cytoplasmic, 11S ribonucleoprotein particle comprised of 6 proteins and a single 7S RNA.12 Recent structural studies on SRP constituents suggest that the highly conserved RNA in this particle mediates SRP assembly and signal sequence recognition.13-16 SRP binds to a signal sequence emerging from the ribosome and slows protein synthesis, which is thought to allow time for a ribosome-nascent chain complex to diffuse to the ER membrane. If translation were not slowed, the premature folding of a secreted protein in the cytoplasm would preclude its translocation. Upon arriving at the ER membrane SRP interacts with the SRP receptor (SR), SRP is released, and translation resumes. The docking and release of SRP at the ER membrane requires GTP (see below). Overall, this cycle guarantees that translation is tightly coupled to translocation.

How does SRP discriminate between ribosomes translating cytosolic versus ER-targeted nascent chains? Current models predict that SRP binds to ribosomes and scans elongating nascent chains for the presence of a signal sequence. Recent measurements of SRP binding to ribosomes by Johnson and colleagues are consistent with this model. SRP interacts with nontranslating ribosomes with high affinity (Kd = 71 nM), indicating that much of the cytoplasmic pool of SRP is ribosome-bound, and this affinity increases when ribosomes initiate translation of cytosolic proteins (Kd = 8 nM) or, more dramatically, when translation of signal sequence containing polypeptides commences (Kd = 0.21 nM).17 Because these affinities were measured before the nascent signal sequence had emerged from the ribosome, the ribosome might undergo a conformational change that is nascent chain/signal sequence-specific. In addition, SRP-ribosome affinities are signal sequence-dependent.17 Thus, SRP distinguishes between translating and nontranslating ribosomes and amongst different ribosome-nascent chain complexes, subsequently directing only signal sequence-containing complexes to the ER membrane.

Is there another factor besides SRP that identifies ribosomes translating secreted proteins? The nascent chain associated complex (NAC) binds nascent chains before SRP and was originally thought to assist in ER targeting.18 However, because it was later shown that ribosome-nascent chain complexes target efficiently to the ER membrane regardless of whether NAC is present,19,20 the function of this factor during ER protein translocation is unclear.

How does SRP “know” how long to arrest translation, and how does it eventually hand-off the ribosome-nascent chain complex to the translocation machinery at the ER membrane? The answer lies in part through the observation that both SRP and SR are GTPases. SR54, the ~54 kDa component of SRP, and SRα a soluble constituent of SR, both belong to a structurally unique family of GTPases.21,22 GTP binding by SRP54 and SRα is required for the SR-dependent release of the signal sequence from SRP 23,24 and GTP hydrolysis by SRP54 and SRα must precede the subsequent dissociation of SRP from SR.24,25 Still controversial, however, is whether SRP interacts initially with ribosome-nascent chain complexes: (A) in a nucleotide-free state, which would require nucleotide binding and hydrolysis at the ER membrane upon SR interaction,24,26 (B) in the GDP state, which would require that the ribosome triggers nucleotide exchange prior to association with the SR,27 or (C) in the GTP-bound state, which would require that GTP hydrolysis is inhibited until SR docking occurs (see fig. 2).28 Rhis picture is complicated further by the fact that SRα is tethered to the ER membrane by the integral membrane SRβ subunit, which is also a GTPase; the nucleotide-bound state of SRβ controls whether SRα is free or attached to the ER membrane,29 and it has been suggested that a component of the translocation pore (see below) regulates nucleotide exchange on SRβ.30 Regardless, the targeting of ribosome-nascent chain complexes to the ER translocation machinery and the subsequent recycling of SRP are intimately regulated by the GTPase cycle of SRP54 and SRα/β.

Figure 2. Three models for the role of the SRP-SR complex GTPase cycle in SRP-dependent translocation.

Figure 2

Three models for the role of the SRP-SR complex GTPase cycle in SRP-dependent translocation. A) Nucleotide-free SRP binds the ribosome nascent chain complex (RNC) and targets the complex to the ER membrane. Cooperative binding of GTP to SRP54 and SRα (more...)

After ribosome-nascent chain complexes are targeted to the ER membrane by SRP, translation resumes and the translocation complex at the ER membrane engages the growing polypeptide (Table 1). Although several components of the translocation complex have been functionally characterized, the specific roles of others in the translocation reaction remain ill-defined. It is also unclear how the ribosome-nascent chain complex is captured by the translocation complex after its release from SRP. Putative ribosome receptors in the mammalian ER membrane have been identified that might help position the ribosome at the ER membrane during protein import;31 however, the translocation pore itself has been shown to be a high affinity (Kd = ~1 nM) ribosome receptor in both yeast and mammals (see below).32,33 Gilmore and colleagues have provided evidence that a component of the translocation pore regulates SRP's GTPase cycle, suggesting that the reinitiation of chain elongation, polypeptide transfer, and translocation through the channel are coupled.34 The molecular details underlying this coupling have not been determined.

Table 1. Factors involved in protein translocation into the ER.

Table 1

Factors involved in protein translocation into the ER.

A recent twist on the SRP paradigm is the proposal that mRNAs might contain ER localization sequences and that ribosomes engaged in secreted protein synthesis are predocked at the ER membrane and do not have to be targeted there.11 Both in vivo and in vitro evidence suggest that ribosomes remain bound to the ER membrane after completing preprotein translation and translocation, and these prebound ribosomes can reinitiate protein synthesis when an mRNA template encoding a secreted protein is encountered.35-37 If, instead, the prebound ER ribosomes are fed an mRNA encoding a cytosolic protein they dissociate from the ER membrane. Further support for this proposal is that several messages encoding secreted proteins were found associated with the ER membrane when the spectrum of ER microsome-associated mRNAs was examined by micro-array analysis.38 The appeal of this proposal is that the rapid synthesis and translocation of secreted proteins does not require SRP-mediated targeting/diffusion of ribosomes bearing nascent-chains from the cytoplasm to the ER membrane; instead, a single mRNA could be routed continuously through ribosomes already engaged at the membrane. This existence of ribosome spirals on the surface of the ER membrane39 might represent a snap-shot of this phenomenon. It is not certain whether all mRNAs encoding secreted proteins are actively routed to the ER, and more definitive support for this model will require that specific ER localization sequences in ER-targeted messages can be identified.

The translocation of every secreted protein in eukaryotes does not require SRP, and in fact budding yeast deleted for the genes encoding the SRP and SR subunits are viable.40-42 Instead, yeast and short (< 70 amino acids) mammalian preproteins can be targeted to and translocated into the ER post-translationally in vitro and in yeast.43,44 Because the diameter of the ER translocation pore is too small to permit passage of native proteins (see below), preproteins destined for post-translational translocation must remain in an unfolded or partially folded state. This is mediated by cytosolic Hsc70 and Hsp40 molecular chaperones and the TRiC/CCT chaperone complex,44-47 and can be mimicked in vitro by preprotein denaturation in urea.45,48,49 However, in addition to retaining preproteins in an unfolded conformation, the interaction between cytosolic Hsc70 and ER-tethered Hsp40 chaperones might facilitate the targeting of preproteins to the ER translocation machinery in vivo.50-52 Specific ER associated proteins in yeast—Sec62p, Sec71p and Sec72p—bind preproteins prior to their translocation and might also facilitate signal sequence recognition and preprotein docking at the ER membrane (see Table 1).53-57

Another SRP-independent route for translocation is exemplified by the insertion of carboxy-terminal “tail”-anchored proteins, such as some components of the ER translocation machinery and the SNAREs involved in vesicle fusion.58-60 A recent analysis of the yeast genome indicates that there are 55 such proteins in this organism.61 In lieu of a signal sequence, tail-anchored proteins contain a single hydrophobic membrane anchor located near the C-terminus of the protein. It is currently unknown how these proteins are targeted to and inserted distinctly into the ER and mitochondrial membranes, except that their insertion occurs independent of the translocation machinery and probably requires uncharacterized targeting and/or insertion factors.62

Preprotein Association with the Pore

That the translocation of preproteins into the ER proceeds through a specific membranous channel was first hypothesized by Blobel and Dobberstein.63 This channel must be tightly regulated and permit entry into the ER lumen or insertion into the ER membrane without compromising the permeability of the ER. This is necessary in order to: (1) maintain the oxidizing environment in the ER lumen that is critical for protein folding, and (2) maintain the high concentration of ER calcium that is critical for cellular signaling.

The translocation pore was identified genetically in yeast 64,65 and biochemically in yeast and mammalian cells.66-73 In both systems, the translocation pore consists of three proteins that form the Sec61 complex, Sec61α, β and γ in mammalian cells and Sec61p, Sbh1p and Sss1p in yeast. A second putative translocation complex exists in yeast that includes Ssh1p, Sbh2p and Sss1p (Table 1).74

Recent imaging of the Sec61 complex indicates that the pore is formed from 3-4 Sec61 trimers with an outer diameter of ~90-100 Å.75-77 Still controversial, however, are the exact dimensions of the inner channel of the pore. Using fluorescent probes inserted at specific sites in arrested, translocating preproteins the inner diameter of the pore was estimated at 40-60Å,78 whereas an inactive pore had a diameter of 9-15Å.79 In contrast, cryoelectron microscopy using purified components and 3-dimensional reconstruction studies suggested an asymetric pore with an inner diameter of 15 Å at the lumenal end and 35Å at the cytosolic end.77,80 These disparities may reflect the different experimental techniques employed and/or differences in the composition of channel-associated proteins and lipids. Alternatively, the Sec61 pore might be dynamic and exist in conformations besides “active” and “inactive”. In fact, a recent report describing the x-ray structure of the homologous Sec61 complex from an archaebacterium suggests that multiple, significant pore movements may occur during translocation.81 Although the diameter of the inner channel of the pore could accommodate limited secondary structure (e.g., an α-helix but not a β-sheet), recent data also suggest that significant protein folding does not occur within its confines.82

How is the Sec61 pore gated? A seminal study by Simon and Blobel83 determined that signal peptides open the bacterial plasma membrane pore. During cotranslational translocation, the permeability of the Sec61 channel is maintained through direct contact by a bound, translating ribosome,84 although data indicate that the tight seal between the ribosome and Sec61 might transiently flicker, exposing portions of the translocating polypeptide to the cytoplasm.85 Structural studies of ribosome-bound Sec61 channels indicate that the polypeptide exit site in the ribosome is aligned with the inner channel of the Sec61 complex,76,77,80 which should facilitate the direct insertion of the nascent chain into the channel without exposing the nascent chain or the pore to the cytosol. Formation of a tight seal between the ribosome and the pore also requires interaction of the Sec61 complex with a functional signal sequence.56,72 However, the concept of the tight seal was recently challenged by the discovery of a 10-20Å gap between the ribosome and the Sec61 complex. This gap might permit the lateral exit of cytosolic loops in transmembrane proteins76,77,80 and/or it might be required for the “pause transfer” mechanism employed by some preproteins, such as apolipoprotein B (ApoB).86-88 During pause-transfer, translocation is briefly arrested while translation proceeds, depositing a portion of the translocating protein in the cytoplasm. Pause-transfer modes of translocation might give hard-to-fold domains time to attain a native structure in the absence of translocation, or in the case of ApoB, might slow translocation so that lipid assembly onto the protein can occur efficiently. In any event, the gap might also function in the retrotranslocation of misfolded proteins back out of the ER (see below).

How then is the permeability barrier of the ER membrane maintained in light of this gap, and in the case of post-translational translocation, when the ribosome is absent from the cytoplasmic face of the pore? Studies on ribosome-free channels suggest that BiP, a lumenal hsp70, “plugs” the lumenal end of the pore.79 In addition, BiP directly or indirectly seals the channel during cotranslational translocation until the preprotein reaches a critical length of ~70 residues; because ~40 amino acids reside within the ribosome, ~30 amino acids are threaded through Sec61p and contact and release BiP, or trigger a conformational change within Sec61p that in turn induces BiP release.89,90

Reconstitution experiments have identified the minimal requirements for post-translational translocation in yeast cells73 and for cotranslational translocation in mammalian cells (see Table 1).91 In yeast, the Sec61 complex, the Sec63 complex, and BiP are required to translocate an in vitro synthesized substrate into proteoliposomes.73 The Sec63 complex includes two essential membrane proteins, Sec63p and Sec62p, which have also been identified in mammalian cells92,93 and two nonessential proteins, Sec71p and Sec72p.64,73,94-96 Sec62p, Sec71p, and Sec72p bind to preproteins in an ATP-independent reaction that facilitates docking at the ER membrane.55 Sec63p is a polytopic protein97 that interacts with Sec61p, Sec62p, Sec71p, Sec72p and BiP.53,98 The acidic cytosolic C-terminus and lumenal J domain of Sec63p might coordinate the ATP-dependent release of preproteins from Sec62p, Sec71p and Sec72p55 and transfer of signal sequence-containing preproteins to Sec61p56,72,99 with the unlocking of the pore by BiP.55,79

As mentioned above, the yeast Ssh1 complex is homologous to the Sec61 translocation complex (Table 1).74 There is no definitive proof that the Ssh1 complex is an active channel but it interacts with ribosomes, suggesting that it may function in cotranslational translocation.32 Consistent with this hypothesis, the growth of ssh1 Δ cells is severely compromised when the gene encoding an SRP subunit is disrupted in the same strain,100 and Ssh1p interacts with a subset of signal sequences that are not recognized by Sec62p.101 Taken together, these data implicate a role for the Ssh1p complex in SRP-dependent cotranslational translocation in yeast.

While not absolutely required, several accessory factors have been also identified that may participate in the translocation of specific substrates. For example, a polytopic glycoprotein in the mammalian ER required for the translocation of many but not all preproteins is known as the translocating chain-associated membrane protein (TRAM). The requirement for TRAM during translocation depends on the preprotein's signal sequence.70,102 TRAM may also facilitate insertion of transmembrane proteins into the lipid bilayer (also see below).103,104 Another factor, known as the translocon-associated protein complex (TRAP), stimulates the translocation of some preproteins. TRAP is tetramer that may stabilize the interaction between preproteins and the Sec61 complex. TRAP-dependence is also signal sequence-specific because sequences that interact weakly with Sec61 require TRAP for maximal translocation efficiency.105 Other factors include PAT-10, identified by its association with the first but not the second transmembrane domain of opsin,106 RAMP4,107 the signal peptidase complex,8,108 and the oligosaccharyltransferase complex.109 Overall, as the mechanism of translocation of additional, specific preproteins is dissected this list will undoubtedly grow, and combined with the use of powerful in vitro reconstitution assays that recapitulate protein translocation, their specific effects on the import reaction should become better defined.

Energy-Dependent Import

Upon their engagement to the translocation channel soluble preproteins may in principle be “pushed” or “pulled” into the ER lumen. Cotranslationally targeted proteins can be pushed into the lumen by the ribosome because polypeptide chain elongation is sufficient to drive translocation into reconstituted proteoliposomes lacking lumen factors.49,91 The lumenal Hsp70 and Hsp40 molecular chaperones, BiP and Sec63p, respectively, may provide a complementary force to pull cotranslationally and post-translationally translocated preproteins through the translocon. BiP, like other Hsp70s, is a soluble ATPase that binds hydrophobic patches in unfolded proteins in an ATP-dependent manner. Sec63p is a polytopic membrane protein with a lumenal J domain that interacts with BiP, anchoring it to the ER membrane and promoting BiP-peptide interactions by stimulating BiP ATP hydrolysis.97,110,111 Sec63p may also diversify the spectrum of polypeptides to which BiP can associate,112 an effect that might be important if this chaperone is necessary to promote the translocation of the spectrum of chemically diverse preproteins. Strains containing temperature sensitive mutations in the genes encoding either of these chaperones are defective in post-translational translocation in vivo,43,113 and in vitro.43,98,99,114

Two models have been proposed to explain the requirement for BiP and Sec63p in post-translational translocation. The Brownian ratchet model predicts that thermal oscillations by preproteins within the pore lead to exposure of the polypeptide in the ER lumen.49,115,116 Successive interactions with BiP prevent the retrograde movement of the preprotein from the ER, and as progressively longer segments of the protein enter the ER additional BiP molecules bind and “drive” translocation. In support of this model, substrate-specific antibodies reconstituted into yeast microsomes obviate the BiP requirement for the translocation of antigen,49 and recently, avidin incorporated in detergent-washed mammalian microsomes was shown to be sufficient to support the translocation of a biotinylated preprotein.117 These results suggest that antibody/polypeptide or avidin/biotin “ratcheting” is sufficient to prevent retrograde movement through the translocation pore. In contrast, the molecular motor model predicts a more active role for the Sec63p-BiP complex in pulling preproteins through the pore. Sec63p may anchor BiP at the ER membrane and enable it to grab and pull preproteins with diverse properties through the pore. The pulling force might be produced concomitant with an ATP-dependent conformational change in BiP. In support of this model, mutations in BiP or Sec63p that prevent their interaction or that prevent the ATP-dependent conformational change in BiP abrogate post-translational translocation.98,110,111,118 However, given that BiP plays a pivotal role in gating the translocation channel at the lumenal end (see above), the requirement for an active Sec63p-BiP complex might reflect the need for this complex to unlock the pore. Consistent with this possibility, BiP and Sec63p are required for both co and post-translational translocation in yeast,119,120 and thus it will be exciting to discover what roles the mammalian BiP and Sec63 homologues play during translocation.

The mechanism by which transmembrane segments are inserted into the lipid bilayer during translocation is still unclear. One model predicts that transmembrane sequences exit the translocon laterally into ER membrane in processes driven primarily by hydrophobic interactions between the nonpolar transmembrane sequence and membrane phospholipids with little influence by the translocon and its associated proteins. This model is supported by photocrosslinking studies demonstrating that transmembrane sequences are exposed to phospholipids immediately upon entry into the translocon.121-123 A second model contends that the translocon and associated proteins like TRAM and PAT-10 influence the orientation and lateral movement of transmembrane sequences into the membrane via protein-protein interactions. Using single photoreactive probes at different locations within a transmembrane sequence, Johnson and colleagues detected position- and substrate-dependent associations with Sec61α and TRAM that varied for different test substrates.124 This is consistent with previously observed interactions between some transmembrane sequences and the translocon, TRAM, or PAT-1069,103,106 These data suggest that the translocon and associated proteins may regulate and orient transmembrane sequences as they enter the pore. In addition, adjacent transmembrane segments in multi-spanning proteins may facilitate insertion into the lipid bilayer,125 and the orientation of the transmembrane segment may be dictated by its hydrophobicity, and/or by the charge distribution of amino acids flanking the transmembrane domain.126 Given the diversity of transmembrane proteins that enter the ER membrane, it seems likely that different membrane sequences may have unique requirements for proper membrane insertion.

Protein Folding in the ER

Both co and post-translationally translocated preproteins are thought to fold vectorially as they enter the lumen of the ER. Although short α helices can form within the Sec61 channel,127 the largely unfolded conformation of preproteins allows early, sequential recognition by the signal peptidase complex and the oligosaccharyltransferase complex (OST), which adds an N-linked, Glc3Man9GlcNAc2 glycan to asparagine in the Asn-X-Thr/Ser consensus sequence. 128-130 Addition of the glycan is required for the subsequent folding of many secreted proteins.131 Protein folding in the ER is facilitated by the oxidizing environment in the ER lumen that favors the formation of disulfide bonds, by the existence of specific enzymes that catalyze rate-limiting steps in the folding pathway (e.g., protein disfulfide isomerases and peptidyl prolyl cis-trans isomerases), and by molecular chaperones.132-135 ER lumenal chaperones not only prevent inappropriate inter-and intra-molecular interactions but also recognize terminally mis-folded proteins and target them for ER associated degradation (ERAD, see below). Molecular chaperones known to play a role in lumenal protein folding include the Hsp70 homologue BiP, a variety of Hsp40 homologues that serve as cochaperones for Hsp70, the Hsp90 homologue GRP94, and calnexin and calreticulin, which are lectins that recognize a mono-glucosylated, processed form of the core glycan. Many of these factors exist in a preformed multi-chaperone complex136 that may provide for coordinated catalysis of protein folding.

Recent studies suggest that N-linked glycans may play a pivotal role in directing the folding of glycoproteins. Rapidly following addition of Glc3Man9GlcNAc2 the two terminal glucoses on this moiety are removed by ER resident glucosidases to generate a mono-glucosylated glycan that is recognized by calnexin and calreticulin.137 Recognition by these chaperones retains glycoproteins in the ER and facilitates their folding by recruiting other chaperones, including a protein disulfide isomerase that assists in the formation and rearrangement of disulfide bonds.138 Calnexin and calreticulin dissociate from the glycoprotein when the final glucose is removed by glucosidase II.139 If the glycoprotein is correctly folded then it may exit the ER; however, nonnative glycoproteins may be specifically reglucosylated by another enzyme, known as UDP-glucose:glycoprotein glucosyltransferase (UGGT), which regenerates the monoglycosylated glycan.140-142 Because UGGT preferentially glucosylates nonnative proteins,143,144 it acts as a folding sensor by promoting the reassociation between incompletely folded glycoproteins and calnexin and calreticulin. This in turn retains aberrantly folded, secreted glycoproteins in the ER and prevents their transport to the Golgi. N-linked glycans may also promote correct folding when positioned near critical cysteines by recruiting calnexin and calreticulin to shield these residues from forming aberrant inter- or intra-molecular disulfide bonds.145 In addition, the location of glycans may dictate which molecular chaperones interact with a specific substrate. Viral proteins with glycans near the amino terminus interact preferentially with calnexin and calreticulin but those lacking glycans at this position bind instead to BiP.146

Folded proteins and properly assembled multimeric protein complexes leave the ER at specific exit sites, marked by membrane clusters that are coated with COPII coatomer proteins that drive vesicle budding from the ER.147-149 Nonnative proteins might be excluded from these exit sites because molecular chaperones, which are bound to incompletely folded proteins, might similarly be excluded. If wild type, ER resident proteins escape from the ER, they may be retrieved if they contain KDEL or KKXX (where X is any amino acid) amino acid motifs that mediate their interactions with Golgi-localized receptors. One of these receptors is a component of a vesicle coat protein complex (COPI) that targets its cargo back to the ER and binds directly to the di-lysine motif in the KKXX sequence.150 Another receptor, ERD2, binds KDEL and facilitates cargo loading into COPI-containing vesicles.151-153 Proteins may also be actively retained in the ER if they contain ER retention signals, like the RXR motif. The RXR motif is present in select proteins and is exposed when the protein has failed to assemble with partners, but becomes masked when the native, quaternary structure of a protein complex is achieved. This permits exit from the ER.154 Overall, the interplay between chaperone release and the sequestration of secreted proteins at ER exit sites is poorly understood.

Quality Control in the ER

When proteins are unable to achieve their native conformations they are recognized by a constitutively active quality control system in the ER. This process, known as ER associated protein degradation (ERAD),155 involves the selective recognition of aberrant proteins, the export or retrotranslocation of these proteins from the ER, and their subsequent degradation in the cytosol by the proteasome.135,156-158 In the event that mis-folded proteins accumulate in the ER, the unfolded protein response (UPR) is activated to induce the expression of factors required for ERAD, for folding aberrant proteins (e.g., chaperones), and for protein transport to other cellular compartments (see section IV below).159

Recognition of Nonnative Proteins in the ER

Because molecular chaperones play a pivotal role in protein folding, it is not surprising that they are intimately involved in the selection of ERAD substrates. Molecular chaperones facilitate protein folding by recognizing patches of hydrophobic amino acids that are exposed in unfolded proteins.160 The prolonged association with chaperones that results from aberrant or incomplete folding may prevent the exit of mis-folded proteins from the ER, thus retaining them as ERAD substrates. Consistent with this view, BiP,161,162 calnexin,155 and protein disulfide isomerase163 are required for the degradation of soluble ERAD substrates in yeast and release from these chaperones precedes substrate degradation in both yeast and mammals.163-168 Chaperones may also maintain ERAD substrates in a soluble conformation.169,170 This would not only prevent the potentially toxic aggregation of mis-folded proteins, but it would also facilitate egress of ERAD substrates back to the cytosol.

Given the structural diversity of proteins that enter the ER, it is remarkable that the ERAD system can distinguish inefficiently folding proteins from terminally mis-folded or unassembled proteins. In the case of glycoproteins, the constituents of N-linked glycans may define the time allotted for folding. As described above, calnexin binding and release is governed by the addition and removal of a terminal glucose. Further modification of the glycan by mannosidase cleavage (Glc3Man9GlcNAc2) appears to terminate the calnexin cycle because UGGT does not efficiently reglucosylate proteins with the Man8GlcNAc2 moiety (see fig. 3).140 A recently discovered mannosidase-like protein, EDEM in mammals171 and Htm1p/Mnl1p in yeast,172,173 lacks mannosidase activity but interacts with Man8GlcNAc-containing glycoproteins. Overexpression of EDEM accelerates ERAD in mammalian cells, possibly by promoting faster release of the glycoprotein from calnexin.174,175 Thus, EDEM-binding may terminate the calnexin quality control cycle and identify mis-folded glycoproteins as ERAD substrates.

Figure 3. The calnexin quality control cycle.

Figure 3

The calnexin quality control cycle. This figure illustrates one model for calnexin's role in the folding and quality control of glycoproteins in the ER. Upon entry into the ER lumen, a core oligosaccharide (Glc3Man9GlcNAc2; abbreviated as Glc3Man9) is (more...)

Despite the elucidation of this elegant timing mechanism for the folding and ERAD of glycoproteins, many questions remain regarding the recognition of ERAD substrates.176 For example, it is still unclear how the ER mannosidase that triggers EDEM binding competes with the glucosidase and UGGT. Mannosidase activity must be rate-limiting in this cycle to favor protein folding over ERAD targeting, and consistent with this view over-expression of the mannosidase enhances ERAD.177,178 In addition, nonglycosylated ERAD substrates exist. Although they may interact with BiP,146 PDI,163 and even calnexin,179 it is not known how these aberrant proteins are targeted for degradation. Moreover, some misfolded proteins escape ERAD and are targeted to the vacuole/lysosome for destruction.180-182 In one simple model, targeting to the vacuole/lysosome may occur if mis-folded proteins elude BiP-capture.181

Retrotranslocation of ERAD Substrates to the Cytoplasm

Once identified, ERAD substrates are retrotranslocated from the ER to the cytoplasm. Genetic and biochemical studies suggest that soluble and integral membrane ERAD substrates exit the ER through the Sec61 channel.161,183,184 ERAD-specific mutations in the genes encoding Sec61p and BiP imply that distinct mechanisms govern import and export through this channel.162,185,186 Moreover, examination of the ERAD requirements for soluble and transmembrane proteins in yeast indicates that multiple ERAD pathways may exist.135

These findings raise several questions that remain the topic of ongoing investigations. First, how are ERAD substrates within the ER targeted to the pore? By virtue of their transmembrane domains, calnexin and/or EDEM may tether ERAD substrates to the ER membrane, but direct targeting to the pore by these lectins has not been established. The question of targeting is further complicated by studies in yeast suggesting that some ERAD substrates may initially traffic to the Golgi before being returned to the ER for ERAD.187-189 Second, how is traffic through the Sec61 pore regulated to permit either the entry of translocating proteins or the exit retrotranslocating proteins? Given its role in gating the lumenal end of the channel during translocation BiP might dictate whether the channel is to operate in “forward” or “reverse”, 190 or as yet unidentified regulatory proteins or modifications might dedicate specific channels for export or import. Alternatively, retrotranslocation may occur through a subset of Sec61 channels that localize to the ER-Golgi intermediate compartment.191 In support of this hypothesis, UGGT preferentially localizes to this region.192 Third, how do transmembrane proteins reenter the channel prior to their retrotranslocation? It is not known what modifications of the channel might allow lateral entry of integral membrane domains. Finally, what is the driving force to pull or push ERAD substrates through the channel? Molecular chaperones might mediate export, but ubiquitination or direct extraction by the proteasome might also provide the driving force for protein extraction (see below).

Proteolysis of ERAD Substrates by Cytoplasmic Proteasomes

Once in the cytoplasm the proteasome degrades ERAD substrates, most of which require the addition of a polyubiquitin chain for proteasome recognition. Polyubiquitination is catalyzed by the sequential action of three enzymes: ubiquitin activating enzymes (E1), ubiquitin conjugating enzymes (E2), and ubiquitin ligases (E3).193 E3s transfer the activated ubiquitin from an E2 to the ε-amino group on a lysine. While there is only one known E1 in yeast and mammals, there are 11-18 E2s and probably a hundred E3s. Individual E3s may cooperate with multiple E2s to recognize specific ubiquitination signals in substrate proteins. For ERAD substrates, these ubiquitination signals most likely include exposed hydrophobic patches that are normally buried in native structures. However, the shear number of E3s implies that a great diversity of ubiquitination signals exists, and although a few E3s have been implicated in ERAD,194-198 this list is sure to grow.

It has been postulated that the successive addition of polyubiquitin chains onto ERAD substrates as they are retrotranslocating might provide sufficient force to ratchet them into the cytoplasm.199-201 Because polyubiquitinated species are rarely detected in the cytoplasm, degradation by the proteasome must occur rapidly after retrotranslocation. The proteasome consists of the 20S catalytic core and two 19S cap subunits that regulate access to the core.202 The 19S cap is a molecular chaperone that may help maintain ERAD substrates in an aggregation-free state via its 6 AAA chaperone-like ATPases.203,204 In addition, at least one polyubiquitin-binding protein resides in the 19S cap and might mediate recognition of ERAD substrates.205 However, some ERAD substrates are not ubiquitinated and it is not clear how they are recognized by the proteasome.

ERAD substrates may be targeted to the proteasome through multiple routes. One possibility is that proteasomes directly associated with the ER membrane interact with retrotranslocating polypeptides emerging from the Sec61-containing pore. Consistent with this scenario, proteasomes reside at the ER membrane206,207 and the 19S cap has been shown to be sufficient to retrotranslocate a soluble yeast ERAD protein in vitro.208 ER membrane-associated proteasomes might also extract integral membrane proteins.209 It is less obvious, however, whether the degradation of all integral membrane ERAD substrates occurs after their retrotranslocation back through the Sec61 complex: Proteasomes, which can clip polypeptide loops,210 might chew-away cytoplasmic domains of integral membrane proteins and the remaining transmembrane segments might then be degraded by other ER membrane-associated proteases, such as the signal pepide peptidase, or they too might be directly extracted by the proteasome.211 Cytosolic molecular chaperones, such as Hsp70 and Hsp90, might also help target ERAD substrates to proteasomes, maintaining them in an unfolded, aggregation-free state before degradation. 212 CHIP, an E3 ligase,194,213 BAG-1, a mammalian nucleotide exchange factor214 and the Cdc48-Ufd1-Npl4 complex215 are examples of factors that have been shown to link ubiquitination to the proteasomal destruction of ERAD substrates. The Cdc48 complex in particular plays an active, and direct role in the retrotranslocation of several ERAD substrates.156

The Unfolded Protein Response (UPR)

The UPR regulates protein trafficking into and out of the ER in response to environmental stress signals and/or mutations that may increase the load of unfolded or aberrant proteins in the ER lumen.159,216 Minimally, in yeast cells the UPR is a signaling cascade that up-regulates genes encoding factors involved in protein folding, ERAD and trafficking through the secretory pathway.217,218 In mammalian cells, the UPR also decreases global protein synthesis to reduce the amount of traffic thru the secretory pathway and may trigger apoptosis after prolonged periods.

In yeast cells, the lone sensor for induction of the UPR is Ire1p, an ER transmembrane protein with a lumenal dimerization domain and a cytosolic region with serine/threonine kinase and RNase activities.219 Activation of Ire1p occurs upon dimerization, which triggers its autophosphorylation in trans.220,221 Once activated, Ire1p recognizes and cleaves a noncanonical intron in the HAC1 mRNA.222 Only the spliced HAC1 mRNA is efficiently translated to yield a transcription factor that binds and activates a UPR responsive element (UPRE) in the promoter of UPR-responsive genes.223

As suggested above, the UPR is more complex in mammalian cells. There are two homologs to the yeast Ire1p, IREα and IREβ,224,225 that mediate the transcriptional up-regulation of UPR-responsive genes by cleaving the recently discovered mammalian Hac1p counterpart, XBP-1.226 In addition, PERK is another transmembrane kinase that upon activation by dimerization phosphorylates the α subunit of translation initiation factor 2 (eIF2α).227,228 This decreases translation initiation and leads to a global attenuation of protein synthesis. Finally, ATF6 is a transmembrane protein that upon ER stress redistributes to the Golgi where it is cleaved by S1P and S2P proteases to liberate an N-terminal, cytosolic leucine zipper transactivation domain that subsequently migrates to the nucleus and activates transcription of UPR-responsive genes.229,230

Interestingly, activation of Ire1p in yeast231 and IREα,IREβ,PERK, and ATF6 in mammalian cells is controlled by BiP, which binds to their lumenal domains.232,233 Current models predict that BiP prevents UPR induction under normal conditions by blocking the dimerization of IRE and PERK and holding ATF6 in the ER.232,233 However, upon ER stress, BiP is titrated from these factors by its preferential affinity for mis-folded proteins. Thus, IRE and PERK dimerize, ATF6 relocates to the Golgi, and the UPR is activated.

ER and Human Health

A growing number of human diseases are attributable to defects in ER-associated protein folding and trafficking (Table 2). For example Cystic Fibrosis (CF) results from a mutant protein that fails to fold efficiently in the ER and is subject to ERAD.234,235 Most cases of CF are caused by the deletion of phenylalanine at position 508 in the gene encoding the Cystic Fibrosis Transmembrane conductance Regulator (CFTR). Because nearly all of the CFTRΔ508 protein is degraded by ERAD, cells homozygous for this allele are phenotypically null. In other cases, such as juvenile Parkinson's disease, inefficient folding of a G protein-coupled receptor (Pae1) leads to its ER retention and aggregation, which triggers the unfolded protein response and apoptosis.236 Mutated, secreted proteins can also accumulate in the cytosol and subsequently aggregate. Cytosolic aggregation can be promoted by inefficient ERAD, as is the case for autosomal dominant retinitis pigmentosa, in which mutant rhodopsin is retrotranslocated from the ER and ubiquitinated in the cytosol. If the proteasome cannot keep-up with the production of the mutated protein, rhodopsin aggregation, cell death, and retinal degeneration occur.237 Other studies have revealed that PrP, the protein responsible for prion pathogenesis, accumulates in the cytoplasm upon proteasomal inhibition; as the concentration of the wild type protein rises in the cytoplasm, it spontaneously converts to the infectious, aggregated PrPSC-like form.238-240 Inefficient translocation of prePrP into the ER might result in the same phenomenon.241 In all cases, it is important to note that different mutant alleles or polymorphisms in the genome can lead to strikingly different presentations of the disease phenotype. Moreover, dominant and recessive forms of a specific disorder may arise from gain-of-function or loss-of function mutations in a single gene that affect the folding and trafficking of the corresponding protein differently.242

Table 2. Select examples of the ER in human health and disease.

Table 2

Select examples of the ER in human health and disease.

Because molecular chaperones are involved in protein folding and ERAD they are potential therapeutic targets for many of these disorders. Support for this approach stems from studies demonstrating that if the CFTRΔ508 conformation is stabilized by lowering the temperature or by chemical chaperones, such as trimethylamine oxide or glycerol, the protein can reach the plasma membrane and is at least transiently active.243-245 It is anticipated that pharmacological modulation of chaperone activities or cellular chaperone concentrations might ameliorate disease phenotypes by similar means.234,235

Several viruses and bacterial toxins have also coopted the ERAD pathway to evade detection by the immune system (Table 2). Human cytomegalovirus (HCMV) encodes two proteins, US2 and US11, that promote the rapid ERAD of MHC class I heavy chains, thus preventing the presentation of viral antigens on the surface of infected cells.246 Many bacterial toxins traffic to the ER following endocytosis and are recognized as ERAD substrates. Molecular chaperones in the ER may facilitate unfolding of the toxins so that they can retrotranslocate through the Sec61 pore to the cytoplasm where they exert their toxic effects. Investigation of cholera toxin trafficking, indicates that protein disulfide isomerae mediates unfolding of this toxin and may subsequently direct it to the pore for export.247

Concluding Remarks

As presented in this chapter, a combination of biochemical, genetic, and cell biological tools have aided significantly toward a deeper understanding of ER protein translocation and retrotranslocation. More recently, the three-dimensional structures of several of the components of the machineries involved in these processes have been visualized. As in most fields, each advance has met with a greater number of unanswered questions. For example, it is unknown whether and how translocation efficiency can be modulated, as might occur when the UPR is induced. Although it is becoming clear that cells adapt to defects in translocation or ERAD via UPR induction, and that the long and short term effects of these adaptations impact cellular physiology and can trigger apoptosis, the signaling pathways for these phenomena are ill-defined. Specific mechanistic questions also remain: How does Sec61 reengineer itself for translocation and retro-translocation and how is this channel gated? How does SRP release preproteins upon interacting with Sec61? How are ERAD substrates selected and actively transported to Sec61 and on to the cytoplasm? Indeed, most studies on protein translocation and quality control have utilized only a small number of “model” substrates, and thus the current cast of players is most likely missing many important actors. However, as a greater number of substrates are examined, and new biochemical assays and genetic tools become available, we anticipate that the rules and participants in the processes by which proteins are targeted, folded, and subjected to quality control in the ER will continue to become clearer.


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