3.A.16 The Endoplasmic Reticular Retrotranslocon (ER-RT or ERAD) Family
Misfolded proteins in the lumen of the endoplasmic reticulum (ER) are degraded in the cytoplasm of eukaryotic cells after translocation across the membrane by a retrotranslocon. The process involves recognition of a substrate in the ER lumen, translocation through the ER membrane, and binding to the cytosolic p97 ATPase (Cdc48 in yeast) which serves as a retrochaperone and maintains solubility of retrotranslocated substrates in the cytosol. p97 (Cdv48) may pull the misfolded protein through the membrane at the expense of ATP hydrolysis. In mammals, the p97-interacting membrane protein is Derlin-1 (Der1and Dfm1 in yeast). Derlin-1, an integral membrane protein with 5 or 6 TMSs, interacts with the substrate proteins as they move through the membrane. Inactivation of Derlin-1 in C. elegans causes ER stress. Derlin-1 interacts with a virally-encoded ER protein that targets MHC class I heavy chains for export from the ER as well as VIMP (selenoprotein S; VPC-interacting protein; a 1 TMS ER protein), which recruits P97 and its cofactor proteins, Ufd1 (ubiquitin fusion degradation 1 protein) and Npl4. Homologues of Derlin-1 are found in all types of eukaryotes and many contain multiple paralogues. Distant homologues may be present in bacteria. These homologues include the DNA internalization-related competence protein, ComEC of Enterococcus faecalis (AAO82165), homologous to the B. subtilis ComEC protein (TC #3.A.11.1.1). The ER-RT family is also called the ER-associated degradation (ERAD) transport apparatus (Bolte et al., 2011). TMS hydrophobicity is an energetic barrier during the retrotranslocation of transmembrane ERAD substrates (Guerriero et al. 2017).
The ER retrotranslocon interacts with the US11 protein of human cytomegalovirus (HCMV) to target newly synthesized major histocompatibility complex (MHC) class I heavy chains for retro-translocation. This allows the virus to selectively destroy cellular proteins required for immune defense of the host. Thus, the retrotranslocon is important for the establishment of viral infections. It plays a role in other human diseases as well.
Derlins (Derlin-1, Derlin-2, and Derlin-3) are functional components of ERAD for misfolded lumenal and membrane substrate proteins, and may act by forming a channel that allows the retrotranslocation of misfolded (glyco)proteins into the cytosol where they are ubiquitinated and degraded by the proteasome. They may mediate the interaction between VCP and misfolded glycoproteins (Lilley and Ploegh 2005, Oda et al. 2006). They may also be involved in ER stress-induced pre-emptive quality control, a mechanism that selectively attenuates the translocation of newly synthesized proteins into the endoplasmic reticulum and reroutes them to the cytosol for proteasomal degradation (Kadowaki et al. 2015). The involvement of derlins in protein translocation across the ER membrane has been confirmed after some controversy (Neal et al. 2018). The cryo-EM structure of the ERAD protein channel, formed by tetrameric human Derlin-1, has been solved (Rao et al. 2021). The structure shows that Derlin-1 forms a homotetramer that encircles a large tunnel traversing the ER membrane. The tunnel has a diameter of about 12 to 15 angstroms, large enough to allow an α-helix to pass through. The structure shows a lateral gate within the membrane, providing access of transmembrane proteins to the tunnel. Thus, Derlin-1 forms a protein channel for translocation of misfolded proteins. This structure is different from the monomeric yeast Derlin structure previously reported, which forms a semichannel with another protein (Rao et al. 2021).
A complex involving Derlin-1 and p97 mediates the retrotranslocation and endoplasmic reticulum (ER)-associated degradation of misfolded proteins in yeast and is used by certain viruses to promote host cell protein degradation (Romisch, 2005). Derlin-1 and p97 form complexes with non-ubiquitylated CFTR in human airway epithelial cells. Derlin-1 interacted with CFTR, whereas p97 associated with ubiquitylated CFTR. Exogenous expression of Derlin-1 led to its co-localization with CFTR in the ER where it reduced wild type (WT) CFTR expression and efficiently degraded the disease-associated CFTR folding mutants (>90%). Thus, Derlin-1 recognizes misfolded, non-ubiquitylated CFTR to initiate its dislocation and degradation early in the course of CFTR biogenesis, perhaps by detecting structural instability within the first transmembrane domain (Sun et al., 2006).
Cholera toxin (CT) intoxicates cells by using its receptor-binding B subunit (CTB) to traffic from the plasma membrane to the endoplasmic reticulum (ER). In this compartment, the catalytic A1 subunit (CTA1) is unfolded by protein disulfide isomerase (PDI) and retro-translocated to the cytosol where it triggers a signaling cascade leading to secretory diarrhea. Using a semipermeabilized-cell retro-translocation assay, Bernardi et al., (2007) demonstrated that a dominant-negative Derlin-1-YFP fusion protein attenuates the ER-to-cytosol transport of CTA1. Derlin-1 interacts with CTB and the ER chaperone PDI as assessed by coimmunoprecipitation experiments. An in vitro membrane-binding assay showed that CTB stimulated the unfolded CTA1 chain to bind to the ER membrane. Moreover, intoxication of intact cells with CTB stabilized the degradation of a Derlin-1-dependent substrate, suggesting that CT uses the Derlin-1 pathway. Thus, Derlin-1 facilitates the retro-translocation of CT. CTB may play a role in this process by targeting the holotoxin to Derlin-1, enabling the Derlin-1-bound PDI to unfold the A1 subunit and prepare it for transport (Bernardi et al., 2008).
Misfolded polytopic membrane proteins can be extracted from the ER, and the process involves the ER retrotranslocon. Chaperones play a role, and there is requirement for Ufd2p, a ubiquitin chain extension enzyme, during membrane protein quality control (Nakatsukasa et al., 2008).
The ERAD-machinery is well studied in Saccharomyces cerevisiae, where three different modes of ERAD complexes are utilized depending on the substrate (Carvalho et al. 2006; Bolte et al. 2011). Whereas the ERAD-L system is responsible for retro-translocation of soluble proteins and membrane proteins with misfolded lumenal regions, ERAD-M and ERAD-C mediate retro-translocation of membrane proteins possessing misfolded sections in transmembrane domains (ERAD-M) or in cytosolic domains (ERAD-C) of membrane proteins, respectively. For soluble ERAD-L substrates, a complete translocation from the ER lumen into the cytosol occurs.
Aberrant proteins are recognised within the ER lumen as ERAD-L substrates. Following recognition by a soluble receptor protein (such as Yos9p and Kar2p in the case of glycoproteins), this complex is bound by the membrane receptor protein Hrd3p - a protein with a large luminal domain comprising multiple TPR motifs. In the next step, the substrate is presumably inserted into a translocation channel, the identity of which was elusive in 2011. Prominent candidates for forming such a channel are the Sec61p complex, the transmembrane segments of the ubiquitin-ligases, Hrd1p andDoa10p, and the yeast membrane derlin protein, Der1p.
Once inserted into the channel, substrate translocation involves ubiquitination by E1, E2 and E3 enzymes on the cytosolic side. Ubiquitinated substrates are subsequently bound by the ATPase Cdc48p, which provides the energy for pulling the proteins out of the ERAD-L translocation channel (Fig. 1A in Bolte et al., 2011). A central player for substrate ubiquitination in the ERAD-L and ERAD-M pathways is the E3 enzyme Hrd1p, a RING-finger ubiquitin ligase with eight transmembrane helices. It has been shown to interact with the membrane receptor Hrd3p - required for Hrd1 stability and ubiquitination - and the membrane protein Usa1p - an adaptor for Hrd1p and Der1p interaction. The catalytic RING-H2 domain of Hrd1p is located on the cytoplasmic side of the ER and catalyses the transfer of ubiquitin to lysine residues of ERAD-L substrates. Prior activation of ubiquitin is mediated by the ubiquitin-activating protein Uba1p, followed by subsequent transfer to the ubiquitin conjugating enzymes, Ubc1p and Ubc7p. The ubiquitin ligase Hrd1p binds both the ERAD-substrate and the Ubc protein and catalyses the transfer of ubiquitin to the substrate. This ubiquitination process is essential for proteasomal degradation but, additionally, it is vital for the retro-translocation process. Ubiquitinated ERAD-L and ERAD-M substrates are specifically bound to and extracted by the cytosolic ATPase, called Cdc48p in yeast or p97 in mammals, thereby completing the process of retro-translocation. Cdc48p/p97 belongs to the AAA ATPase family. Together with the ERAD-specific co-factors Ufd1p and Npl4p, Cdc48p/p97 functions in the context of ERAD. The recruitment of the ATPase to the ER membrane is supported by the membrane protein Ubx2p, enabling Cdc48p/p97 to exert mechanical force for membrane release of ERAD-L and ERADM substrates. The ERAD-C substrates are recognized and ubiquitinated by the E3 ligase, Doa10p.
During endoplasmic reticulum-associated degradation (ERAD), misfolded lumenal and membrane proteins in the ER are recognized by the transmembrane Hrd1 ubiquitin ligase complex and retrotranslocated to the cytosol for ubiquitination and degradation. Substrates are believed to be delivered to the proteasome only after the ATPase Cdc48p/p97 acts. Nakatsukasa et al. 2013 provided evidence that inactivation of Cdc48p/p97 stalls retrotranslocation and triggers formation of a complex that contains the 26S proteasome, Cdc48p/p97, ubiquitinated substrates, select components of the Hrd1 complex, and the lumenal recognition factor, Yos9p. Possibly the actions of Cdc48p/p97 and the proteasome are tightly coupled during ERAD, and the Hrd1 complex links substrate recognition and degradation on opposite sides of the ER membrane.
Valosin-containing protein (VCP)/p97 is an AAA-ATPase that extracts polyubiquitinated substratesfrom multimeric macromolecular complexes and biological membranes for proteasomal degradation. During p97-mediated extraction, the substrate is largely deubiquitinated as it is threaded through the p97 central pore. Hu et al. 2020 reported that p97-extracted membrane proteins undergo a second round of ubiquitination catalyzed by the cytosolic ubiquitin ligase RNF126. RNF126 interacts with transmembrane-domain-specific chaperone BAG6, which captures p97-liberated substrates. RNF126 depletion in cells diminishes the ubiquitination of extracted membrane proteins, slows down their turnover, and dramatically stabilizes otherwise transient intermediates in the cytosol. Hu et al. 2020 reconstituted the reubiquitination of a p97-extracted, misfolded multispanning membrane protein with purified factors. Their results demonstrated that p97-extracted substrates need to rapidly engage ubiquitin ligase-chaperone pairs that rebuild the ubiquitin signal for proteasome targeting to prevent harmful accumulation of unfolded intermediates.
Maintaining the essential functions of mitochondria requires mechanisms to recognize and remove misfolded proteins (quality control pathways for misfolded mitochondrial proteins). Metzger et al. 2020 established temperature-sensitive (ts-) peripheral mitochondrial outer membrane (MOM) proteins as novel model QC substrates in Saccharomyces cerevisiae. The ts-proteins Sen2-1HA(ts) (P16658; 329 aas, 0 TMSs) and Sam35-2HA(ts) (P14693; 329 aas and 1 TMS) are degraded using the MOM-PD pathway (The Mitochondrial Outer Membrane-associated Protein Degradation Pathway) involving the ubiquitin-proteasome system. Ubiquitination of Sen2-1HA(ts) is mediated by the ubiquitin ligase (E3) Ubr1, while Sam35-2HA(ts) is ubiquitinated primarily by San1. Mitochondria-associated degradation (MAD) of both substrates requires the SSA family of Hsp70s (e.g., P10591; 642 aas and 0 TMSs) and the Hsp40 Sis1 (P25294; 352 aas and 0 TMSs), providing evidence for chaperone involvement in MOM-PD. In addition to a role for the Cdc48-Npl4-Ufd1 AAA-ATPase complex (see TC# 3.A.16.1.2), Doa1 and a mitochondrial pool of the transmembrane Cdc48 adaptor, Ubx2, are implicated in their degradation. Thus, a unique QC pathway comprised of a combination of cytosolic and mitochondrial factors distinguishes it from other cellular QC pathways (Metzger et al. 2020).
The reaction catalyzed by the ER-RT is:
misfolded protein (ER) → misfolded protein (cytosol)
Mammalian ER retrotranslocon. The Grp170 protein plays a role during ERAD, positioning this client-release factor at the retrotranslocation site, allowing a mechanism to couple client release from BiP and retrotranslocation (Inoue and Tsai, 2016). The cryo-EM structure of the ERAD protein channel, formed by tetrameric human Derlin-1, has been solved (Rao et al. 2021). The structure shows that Derlin-1 forms a homotetramer that encircles a large tunnel traversing the ER membrane. The tunnel has a diameter of about 12 to 15 angstroms, large enough to allow an α-helix to pass through. The structure shows a lateral gate within the membrane, providing access of transmembrane proteins to the tunnel. Thus, Derlin-1 forms a protein channel for translocation of misfolded proteins. This structure is different from the monomeric yeast Derlin structure previously reported, which forms a semichannel with another protein (Rao et al. 2021).
ER retrotranslocon of Homo sapiens
(1) p97 ATPase (valosin-containing protein, VCP) (P55072)
(2) Derlin-1 (NP_077271)
(3) VIMP (AAT46592)
(4) Ufd1 (Q541A5)
(5) Npl4 (Q8TAT6)
(6) gpUS11 (glycoprotein precursor) of HCMV (Q8UZK5)
ER retrotranslocon for misfolded luminal ER proteins. Uses the ERAD-associated E3 ubiquitin-protein ligase, Hrd1p, which promotes polypeptide movement through the ER membrane (Carvalho et al., 2010; Bolte et al., 2011). As determined by cryoEM, Hrd1 is an 8 TMS dimer that associates with Hrd3 on the luminal side of the ER membrane to seal the channel used for protein retrotranslocation (Schoebel et al., 2017). The protein-conducting channel, Hrd1, is a ubiquitin ligase that serves as the transmembrane channel (Wu and Rapoport, 2018). The Cdc48/p97 ATPase pulls the unfolded substrate through the channel, out of the membrane. Cdc48 has a central pore, and the substrate protein passes from the cis side to the trans side (Wu and Rapoport, 2018). Otu1, ubiquitin thio ligase, partially de-ubiquitinates the substrate protein. The E3 ubiquitin-protein ligase accepts ubiquitin specifically from endoplasmic reticulum-associated UBC6 and UBC7 E2 ligases, and transfers it to substrates, promoting their degradation. It mediates the degradation of a broad range of substrates, including endoplasmic reticulum membrane proteins, soluble nuclear proteins and soluble cytoplasmic proteins. The DOA10 ubiquitin ligase complex is part of the ERAD-C pathway responsible for the rapid degradation of membrane proteins with misfolded cytoplasmic domains (Ravid et al., 2006). The 3-D structure of the Hrd1 complex (including Hrd1, Hrd3, Der1, Usa1 and Yos9) has been solved (Wu et al. 2020). It mediates the retrotranslocation of the polypeptide into the cytosol, which it is polyubiqutinated, extracted from the membrane by the Cdc48 ATPase complex and degraded by a proteosome. The importance of Hrd1 complex integrity during ERAD, suggests that allosteric interactions between transmembrane domains regulate Hrd1 complex formation (Nakatsukasa et al. 2022).
ER retrotranslocon of Saccharomyces cerevisiae
(1) Cdc48 ATPase (NP_010157)
(2) Der1 (NP_009760)
(3) Npl4 (P33755)
(4) Hrd1p (ERAD-associated E2 ubiquitin-protein ligase) (5-6 N-terminal TMSs) (Q08109)
(5) 2TMS Hrd3p (Q05787)
(6) 3TMS Usa1p (E7KSD5)
(7) Uba1 (E7LWL7)
(8) Ubc1 (E7Q288)
(9) Ubc6 (E7NGV2)
(10) Ubc7 (C8ZEM9)
(11) Ufd1 (C8Z8U3)
(12) DOA10 (P40318)
(13) OTU1 (P43558
(14) OS-9 homolog (Q99220)
(15) Deerlin 1-like protein, Dfm1, rhomboid-like protein (Q12743).
ERAD system in the endoplasmic reticulum of the malaria parasite, Plasmodium falciparum (Spork et al. 2009)
The ERAD system of Plasmodium falciparum
Cdc48 (828aas) (C6KT34)
Der1-1 (212aas) (C7SP48)
Der1-2 (263aas) (Q8IJ82)
Hrd1 (510aas) (Q8ILM8)
Hrd3 (807aas) (O77341)
Nlp4 (531aas) (Q81426)
Ub (381aas) (Q7KQK2)
Uba1 (1,140aas) (Q815F9)
Uba2 (688aas) (Q81553)
Ubc (147aas) (Q81607)
Ufd1 (282aas) (Q8ILR6)
ERAD-L retrotranslocon system. SEL1L-dependent substrates require Derlin2/3 and Herp1/2 regardless of their soluble or transmembrane nature. The ERAD-L substrates take several routes to the cytosol. The HRD1-engaged route 1 requires SEL1L, Derlin2 or Derlin3, and Herp1 or Herp2 (Sugimoto et al. 2017). The nucleotide exchange factor, Grp170, a homolog of HSP70 proteins, plays a role in this ERAD pathway (Inoue and Tsai 2016).
ERAD-L of Homo sapiens
HRD1 (E3) - SYVN1 of 617 aas and 6 N-terminal TMSs (Q86TM6)
gp87 (E3) - G-protein coupled receptor 87, GPR87; GPR95 of 358 aas and 7 TMSs (Q9BY21)
SEL1L - protein Sel-1 homolog, a partner of HRD1 of 794 aas and 3 TMSs, 1 N-terminal and 2 C-terminal (Q9UBV2)
Grp170 - homologous to heat shock proteins, Hsp70 (TC# 1.A.33) (Q9Y4L1)
Derlin 2 (DRL2) of 239 aas and 4 - 5 TMSs (Q9GZP9)
Derlin 3 (DRL3) of 235 aas and 5 TMSs (Q96Q80)
HERP 1, 337 aas with a C-terminal hydrophobic region that could be transmembrane (Q9UBP5)
HERP 2, 304 aas with a C-terminal hydrophobic region that could be transmembrane (Q9Y5J3)
The ER-associated degradation (ERAD) pathway of 47 proteins (Liu and Li 2014).
ERAD of Arabidopsis thaliana
The yeast multicomponent mitochondrial outer membrane-associated protein degradation (MOM-PD) pathway. Maintaining the essential functions of mitochondria requires mechanisms to recognize and remove misfolded proteins (quality control pathways). Metzger et al. 2020 established temperature-sensitive (ts-) peripheral mitochondrial outer membrane (MOM) proteins as novel model QC substrates in Saccharomyces cerevisiae. The ts-proteins Sen2-1HA(ts) (P16658; 329 aas, 0 TMSs) and Sam35-2HA(ts) (P14693; 329 aas and 1 TMS) are degraded using the MOM-PD pathway involving the ubiquitin-proteasome system. Ubiquitination of Sen2-1HA(ts) is mediated by the ubiquitin ligase (E3) Ubr1, while Sam35-2HA(ts) is ubiquitinated primarily by San1. Mitochondria-associated degradation (MAD) of both substrates requires the SSA family of Hsp70s (e.g., P10591; 642 aas and 0 TMSs) and the Hsp40 Sis1 (P25294; 352 aas and 0 TMSs), providing evidence for chaperone involvement in MOM-PD. In addition to a role for the Cdc48-Npl4-Ufd1 AAA-ATPase complex (see TC# 3.A.16.1.2), Doa1 and a mitochondrial pool of the transmembrane Cdc48 adaptor, Ubx2, are implicated in their degradation. Thus, a unique QC pathway consists of a combination of cytosolic and mitochondrial factors and distinguishes it from other cellular QC pathways (Metzger et al. 2020). Nevertheless, most of the protein constituents have homologs in TC family 3.A.16.
MOM-PD of Saccharomyces cerevisiae
In addition to the Cdc48-Npl4-Ufd1 complex (see 3.A.16.1.2), the other consituents are:
The SSA family Hsp70 protein, P10591 of 642 aas, 0 TMSs
The Hsp40 homolog, Sis1 (P25294; 352 aas, 0 TMSs
The Doa1 (UFD3, ZZZ4) protein (P36037; 715 aas, 0 TMSs)
The ubiquitin ligase, Ubr1, Ptr1 (P19812; 1950 aas and 0-2 TMSs)
The Cdc48 adaptor, Ubx2 or Sel1 (Q04228; 584 aas and possibly 3 TMSs in a 1 + 2 TMS arrangement)
The San1 protein (P22470; 610 aas and 0 TMSs)