3.A.20 The Peroxisomal Protein Importer (PPI) Family
Proteins targeted to the peroxisome (in plants called glyoxisomes) are synthesized in the cytoplasm of the cell and are targeted to the peroxisome post-translationally, possibly via multiple pathways. Two peroxisomal targeting signals, PTS1 and PTS2, are recognized by separate sets of receptors. C-terminal PTS1 [(SAC)-(KRH)-(LM)] and N-terminal PTS2 [(RK)-(LIV)-X5-(HQ)-(LA)] targeting sequences are recognized by Pex5p and Pex7p, respectively, which may shuttle with the substrate protein to the peroxisomal lumen. Over two dozen proteins involved in protein import and membrane insertion, peroxins, encoded by PEX genes, have been characterized. Peroxisomal import appears to have features unique to this organelle. Many mechanistic features and protein constituents are still ill defined. An ATP requirement for import of some but not other proteins has been demonstrated. Import of these proteins probably does not require unfolding. Intact folded proteins and even oligomeric proteins can be transported. Note: Family PPI shares some constituents with the PPI2 family (TC# 9.A.17), their functions may overlap.
The importance of peroxisomes for human life is highlighted by severe inherited diseases which are caused by defects of peroxins, encoded by PEX genes. As of 2011, 32 peroxins were known to be involved in different aspects of peroxisome biogenesis. Rucktäschel et al. (2011) addresses two of these aspects, the translocation of soluble proteins into the peroxisomal matrix and the biogenesis of the peroxisomal membrane. The import tranlocon is formed transiently (Wolf et al., 2010). Ma et al. (2011) have reviewed the processes by which matrix and membrane proteins are incorporated into the peroxysome. The peroxisomal protein import machinery, which shares similarities with chloroplasts, is unique in transporting folded and large (up to 10 nm in diameter) protein complexes into peroxisomes. A large pore is formed by transmembrane proteins. In the budding yeast Saccharomyces cerevisiae, the minimal transport machinery includes the membrane proteins Pex13 and Pex14 and the cargo-protein-binding transport receptor, Pex5. Pex13 undergoes liquid-liquid phase separation (LLPS) with Pex5-cargo. Intrinsically disordered regions in Pex13 and Pex5 resemble those found in nuclear pore complex proteins. Peroxisomal protein import depends on both the number and pattern of aromatic residues in these intrinsically disordered regions, consistent with their roles as 'stickers' in associative polymer models of LLPS(5,6) (Ravindran et al. 2023). Imaging fluorescence cross-correlation spectroscopy showed that cargo import correlates with transient focusing of GFP-Pex13 and GFP-Pex14 on the peroxisome membrane. Pex13 and Pex14 form foci in distinct time frames, suggesting that they may form channels at different saturating concentrations of Pex5-cargo. This suggests a model in which LLPS of Pex5-cargo with Pex13 and Pex14 results in transient protein transport channels (Ravindran et al. 2023).
The translocon is believed to consist of several subcomplexes. The membrane bound docking subcomplex includes several Pex proteins, Pex13p, 14p and 17p. Pex5p, the PTS1 receptor, is known to bind to the integral Pex13p and/or Pex17p and the peripheral Pex14p. Pex4p is a membrane protein that may facilitate cycling of Pex5p back to the cytosol. Pex7p, the PTS2 receptor, interacts with Pex14p which interacts with Pex13p. Thus, the core translocon includes Pex13p, and Pex14p recognizes the receptors, Pex5p and Pex7p with nanomolar affinity. PEX14 is a bona fide intrinsic membrane protein with a Nin -Cout topology, and that PEX13 adopts a Nout -Cin topology, thus exposing its carboxy-terminal Src homology 3 [SH3] domain to theorganelle matrix (Barros-Barbosa et al. 2018). Pex5p and Pex7p have been shown to traverse the membrane (Kerssen et al., 2006). Chaperone proteins (Hsp70; DnaJ; Hsp40) may play a role in the overall process, but their roles are not defined. Thirty two peroxins perform functions in peroxisome biogenesis that are conserved from yeast to man (Girzalsky et al., 2010).
Another subcomplex is called the importomer which in addition to the docking subcomplex contains Pex8p and three RING finger peroxins, Pex2p, Pex10p and Pex12p. This subcomplex also exists in the peroxisome membrane. The ATP-dependent dislocation of the PTS1 receptor from the peroxisomal membrane into the cytosol is mediated by the AAA peroxins Pex1p and Pex6p (Platta et al., 2005). The two AAA (ATPase associated with various cellular activities) peroxins, Pex1p and Pex6p, are the causal genes for CG (complementation group) 1 and CG4 PBDs respectively. Pex26p is the recruiter of Pex1p-Pex6p complexes to peroxisomes. AAA peroxins are involved in the export from peroxisomes of Pex5p, the PTS1 (peroxisome-targeting signal type 1) receptor.
Most peroxisomal membrane proteins do not have PTS1 or PTS2, and insertion requires several peroxins distinct from those required for import of soluble matrix proteins. The membrane proteins may be sorted directly to peroxisomes from the cytosol or may go via the endoplasmic reticulum. The direct sorting mechanism is probably mediated by chaperones, and the two step binding and insertion process is temperature-dependent but ATP-independent. ATP is required downstream of the protein translocation step to reset the Pex5p-mediated transport system (Oliveira et al., 2003). Targeting signals for the membrane proteins, called mPTSs, include a cluster of basic residues and may be in loops between two TMSs or elsewhere. It therefore seems that at least 4 pathways are used for the import of matrix and membrane proteins into peroxisomes. Neuspiel et al. (2008) have identified a link between mitochondria and proxisomes. Mitochondria-derived vesicles (MDVs), appear to fuse with a fraction of pre-existing peroxisomes in mammalian cells. This may play a role in the exchange of metabolites and/or macromolecules between these compartments (Schumann and Subramani, 2008).
Pex7p, the peroxisome-targeting signal type 2 (PTS2) receptor, transports PTS2 proteins to peroxisomes from the cytosol. Miyata et al., 2009 developed a cell-free Pex7p translocation system. In assays using post-nuclear supernatant fractions, each from wild-type CHO-K1 and pex7 ZPG207 cells, 35S-labeled Pex7p was imported into peroxisomes. 35S-Pex7p import was also evident using rat liver peroxisomes. 35S-Pex7p was not imported into peroxisomal remnants from a pex5 ZPG231 defective in PTS2 import and pex2 Z65. When the import of 35S-Pex5pL was inhibited with an excess amount of recombinant Pex5pS, 35S-Pex7p import was concomitantly abrogated, suggesting that Pex5pL is a transporter for Pex7p. 35S-Pex7p as well as 35S-Pex5p is imported in an ATP-independent manner, whilst the import of PTS1 and PTS2 cargo-proteins is ATP-dependent. ATP-independent import of Pex7p implied that Pex5p export, requiring ATP hydrolysis, is not limiting for cargo recruitment to peroxisomes. PTS1 protein import is indeed insensitive to N-ethylmaleimide, whereas Pex5p export is N-ethylmaleimide-sensitive. Taken together, the cargo-protein translocation through peroxisomal membrane more likely involves an ATP-requiring step in addition to the Pex5p export. Upon concurrent import into peroxisomes, 35S-Pex5pL and 35S-Pex7p can be detected at mutually distinct ratios in the immunoprecipitates each of the import machinery peroxins, Pex14p, Pex13p, and Pex2p, suggesting that Pex7p as well as Pex5p were translocated from the initial docking complex to the RING complex on peroxisomes (Miyata et al., 2009).
Peroxin 13 (PEX13) is one of the components of a peroxisomal membrane complex involved in import of proteins into the matrix of the organelles. Trypanosomatids (Trypanosoma, Leishmania), protozoan parasites having peroxisome-like organelles designated glycosomes, possess an unusual PEX13 which shares very low sequence identity with others and lacks some typical PEX13 characteristics. It has multiple YGx motifs present in a glycine-rich N-terminal region of low sequence complexity. Like other PEX13s, it contains predicted transmembrane segments and a SH3 domain in its C-terminal half. PEX13 in T. brucei is in the glycosomal membrane. The C-terminal half of the protein was shown to interact with the third of three pentapeptide repeats of the previously characterized PEX5, the receptor of glycosomal proteins with a type 1 peroxisome-targeting signal, and with PEX14, another component of the same peroxisomal protein import complex in the membrane. PEX13 is essential for the parasite; depletion by RNA interference results in mislocalization of glycosomal proteins and death of the parasites.
Tail-anchored (TA) proteins are embedded into their corresponding membrane via a single transmembrane segment at their C-terminus whereas the majority of the protein is facing the cytosol. Using budding yeast as a model system, Cichocki et al. 2018 identified the cytosolic Hsp70 chaperone Ssa1 and the peroxisome import factor Pex19 as import mediators for a subset of mitochondrial TA proteins. Deletion of PEX19 results in: (i) a growth defect under respiratory conditions; (ii) alteration in mitochondrial morphology; (iii) reduced steady-state levels of the mitochondrial TA proteins Fis1 and Gem1; and (iv) hampered in organello import of the TA proteins Fis1 and Gem1 to which Pex19 can bind directly (Cichocki et al. 2018).
The peroxisomal protein import machinery differs fundamentally from most known translocons (endoplasmic reticulum, mitochondria, chloroplasts, bacteria) as it allows membrane passage of folded, oligomerized proteins similar to the Tat systems. A proteinaceous peroxisomal importomer enables docking of the cytosolic cargo-loaded receptors, cargo translocation and receptor recycling. Remarkably, the cycling import receptor Pex5p changes its topology from a soluble cytosolic form to an integral membrane-bound form. According to the transient pore hypothesis, the membrane-bound receptor forms the core component of the peroxisomal import pore. Meinecke et al. (2010) demonstrated that the membrane-associated import receptor Pex5p together with its docking partner Pex14p forms a gated ion-conducting channel which can be opened to a diameter of about 9 nm by the cytosolic receptor-cargo complex. The pore shows striking dynamics, as expected for an import machinery translocating proteins of variable sizes.
Cargo recognition and binding takes place in the cytosol, where two receptor proteins, Pex5 and Pex7, recognise and bind their cargo proteins, which either possess a C-terminal peroxisomal targeting signal 1 (PTS1) for transport via the Pex5 receptor or a peroxisomal targeting signal 2 (PTS2) that is located in the N-terminal part and is recognized by Pex7.
According to the transient pore model, and in the case of PTS1-harbouring proteins, the Pex5 cargo-loaded import receptors become part of the translocation apparatus. Pex5 proteins interact with the docking/translocation membrane protein complex, which consists of the receptor docking proteins Pex13 and Pex14 and the RING-finger ubiquitin ligases Pex2, Pex10 and Pex12. Recently, it has been revealed that Pex5 proteins form a gated ion-conducting channel together with the docking partner Pex14. Pex5 possesses several tetratrico peptide repeats (TPR) for substrate interaction, comparable to the central receptor protein Hrd3p of the ERAD-L system. Hrd3p proteins are permanently integrated in the ER membrane, but Pex5 proteins change their topology from soluble to integral to become part of the translocation apparatus in the peroxisomal membrane. Cargo release in the peroxisomal matrix may be initiated by intra-peroxisomal factors.
Before returning to the cytosol, Pex5 must be labelled to initiate its release from the peroxisomal membrane. This proceeds mechanistically similar to substrate extraction in the ERAD system (3.A.16). Thus, membrane integrated Pex5 proteins are ubiquitinated on their cytosolic parts. Ubiquitination is mediated by the ubiquitin conjugating enzymes (Pex4 and Ubc4), as well as three different ubiquitin ligases (Pex2, Pex10 and Pex12, Fig. 1A in Bolte et al.(2011). Comparable to the ERAD-L specific ubiquitin-ligase Hrd1p, Pex-specific ligases contain a catalytic RING-finger domain on the cytosolic side. For extraction from the peroxisomal membrane, the proteins are bound by hexameric AAA-ATPases and mobilised during ATP-hydrolysis, mediated by the ATPases, Pex1 and Pex6, which are anchored to the peroxisomal membrane by Pex15 in yeast or Pex26 in mammals.
Peroxysomal biogenesis is surprisingly complex and involves specialized proteins, termed peroxins, which mediate targeting and insertion of peroxisomal membrane proteins (PMPs) into the peroxisomal bilayer, and the import of soluble proteins into the protein-dense matrix of the organelle. The long-standing paradigm that all peroxisomal proteins are imported directly into preexisting peroxisomes has been challenged by the detection of PMPs inside the endoplasmic reticulum (ER) (Mayerhofer 2016). New models suggest that the ER originates peroxisomal biogenesis by mediating PMP trafficking to the peroxisomes via budding vesicles. However, the relative contribution of this ER-derived pathway is not known.
Peroxisomal biogenesis factor PEX26 is a membrane anchor for the multi-subunit PEX1-PEX6 protein complex that controls ubiquitination and dislocation of PEX5 cargo receptors for peroxisomal matrix protein import. PEX26 associates with the peroxisomal translocation pore via PEX14 and a splice variant (PEX26Deltaex5) of unknown function has been reported. Guder et al. 2018 demonstrated PEX26 homooligomerization mediated by two heptad repeat domains adjacent to the transmembrane domain. They showed that isoform-specific domain organization determines PEX26 oligomerization and impacts peroxisomal beta-oxidation and proliferation. PEX26 and PEX26Deltaex5 displayed different patterns of interaction with PEX2-PEX10 or PEX13-PEX14 complexes, which relate to distinct pre-peroxisomes in the de novo synthesis pathway. These results support an alternative PEX14-dependent mechanism of peroxisomal membrane association for the splice variant, which lacks a transmembrane domain (Guder et al. 2018).
ER domains in S. cerevisiae containing the reticulon homology domain (RHD) protein Pex30 are regions where preperoxisomal vesicles (PPVs) form (Joshi et al. 2018). Pex30 domains are also sites where most nascent lipid droplets (LDs) form. Mature LDs usually remain associated with Pex30 subdomains, and the same Pex30 subdomain simultaneously associate with a LD and a PPV or peroxisome. In higher eukaryotes, multiple C2 domain containing transmembrane protein (MCTP2) is similar to Pex30: it contains an RHD and resides in ER domains where most nascent LD biogenesis occurs, often associate with peroxisomes. Thus, most LDs and PPVs form and remain associated with conserved ER subdomains. There may be a link between LD and peroxisome biogenesis (Joshi et al. 2018).
The ER is shaped by a class of membrane proteins containing reticulon homology domains (RHDs), the conserved hydrophobic domain encompassing two short hairpin transmembrane domains. RHD resides in the outer leaflet of the ER membrane, generating high-curvature ER membrane (Yamamoto and Sakisaka 2018). Most of the membrane proteins destined to enter the secretory pathway are cotranslationally targeted and inserted into the ER. Yamamoto and Sakisaka 2018 showed that RHD-containingproteins can be posttranslationally targeted to the ER membrane. PEX19, a cytosolic peroxin, selectively recognizes the nascent RHD-containing proteins and mediates their posttranslational targeting in cooperation with PEX3, a membrane peroxin. Thus, these peroxisome biogenesis factors provide an alternative posttranslational route for membrane insertion of the RHD-containing proteins, implying that ER membrane shaping and peroxisome biogenesis may be coordinated by the posttranslational membrane insertion.
The reactions catalyzed by PPI systems are:
protein (cytoplasm) → protein (peroxisomal matrix),
protein (cytoplasm) → protein (peroxisomal membrane)
The peroxisomal importing translocon with receptors: Pex5p and Pex7p; and receptor facilitator: Pex4p. Peroxisomal biogenesis factor PEX26 is a membrane anchor for the multi-subunit PEX1-PEX6 protein complex that controls ubiquitination and dislocation of PEX5 cargo receptors for peroxisomal matrix protein import. PEX26 associates with the peroxisomal translocation pore via PEX14 (Guder et al. 2018). Luminal peroxisomal proteins are imported from the cytosol by mobile receptors, which then recycle back to the cytosol by a poorly understood process (Feng et al. 2022). Recycling requires receptor modification by a membrane-embedded ubiquitin ligase complex comprising three RING finger domain-containing proteins (Pex2, Pex10 and Pex12). Feng et al. 2022 reported a cryo-EM structure of the ligase complex, which together with biochemical and in vivo experiments reveals its function as a retrotranslocation channel for peroxisomal import receptors. Each subunit of the complex contributes five transmembrane segments that co-assemble into an open channel. The three ring finger domains form a cytosolic tower, with ring finger 2 (RF2) positioned above the channel pore. The N terminus of a recycling receptor is inserted from the peroxisomal lumen into the pore and monoubiquitylated by RF2 to enable extraction into the cytosol. If recycling is compromised, receptors are polyubiquitylated by the concerted action of RF10 and RF12 and degraded. This polyubiquitylation pathway also maintains the homeostasis of other peroxisomal import factors. Thus, a crucial step during peroxisomal protein import is clarified, and it explains why mutations in the ligase complex cause human disease (Feng et al. 2022).
The peroxisomal translocon of Homo sapiens
Pex1p (Peroxisomal AAA-type ATPase) (O43933)
Pex2p (Peroxisome assembly factor 1, PAF1; RING finger protein) (P28328)
Pex4p (183 aas; 0-1 TMS) (P29340) (Saccharomyces cerevisiae)
Pex5p (639 aas; 0-1 TMS) (O09012) (mouse)
Pex6p (Peroxisomal AAA-type ATPase) (Q13608)
Pex7p (323 aas; 0-2 TMSs) (O00628)
Pex10p (326 aas; 3-5 TMSs) (O60683)
Pex12p (359 aas; 2-4 TMSs) (O00623)
Pex13p (403 aas; 1-2 TMSs) (Q92968)
Pex14p (377 aas; 0-1 TMS) (O75381)
Pex26 (305 aas; 5-6 TMSs) (Q7Z412)
Uba1 (Ubc9; UbcE9; Ube21) (158aas; 0 TMSs) (P63279)
Ubc4 (UbD2/E2) (147aas; 0 TMSs) (P62837)
The peroxin complex for the import of proteins into the matrix of peroxisomes (Prestele et al., 2010). Note: PexII has five paralogues, PexIIA-E.
Peroxin (PEX) complex of Arabidopsis thaliana
Glycosomal membrane protein insertion apparatus. Two proteins included in the system are PEX14 and PEX19 which target to the peroxisome in several other organisms, but in T. brucei, they target to the glycosome. By contrast, PEX10 and PEX12 are involved in targetting to the peroxisome (Saveria et al. 2007). Altogether, PEX1, 2, 5, 6, 10, 11, 12, 14, 16, and 19 have been identified in T. brucei and are listed here. Inhibitors of PEX14 block protein import into glycosomes and kill Trypanosma parasites (Dawidowski et al. 2017). The glycosomal membrane-associated Leishmania donovani protein PEX14, which plays a crucial role in protein import from the cytosol to the glycosomal matrix, consists of three domains: an N-terminal domain where the signalling molecule binds, a transmembrane domain and an 84-residue coiled-coil domain (CC) that is responsible for oligomerization. CCs are versatile domains that participate in a variety of functions including supramolecular assembly, cellular signalling and transport (Shakya and Pratap 2020). Bioinformatic analyses indicate that the N-terminal region of TbPEX11 contains an amphiphilic helix and several putative TOM20 recognition motifs. Thus, the extreme N-terminal region of TbPEX11 contains a cryptic N-terminal signal that directs PEX11 to the mitochondrion if its glycosomal transport is blocked (Krishna et al. 2023).
Peroxisome/glycosome protein insertion apparatus of Trypanosoma brucei brucei
Pex1, 911 aas
Pex2, 332 aas
Pex5, 655 aas
Pex6, 982 aas
Pex10, 298 aas
Pex11, 218 aas
Pex12, 395 aas
Pex14, 366 aas
Pex16, 453 aas
Pex19, 285 aas
The peroxysomal protein import translocon
Peroxysomal protein import translocon of Leishmania major
Glycosome import protein (Q4Q9L4)
Peroxisomal targeting signal-2 receptor (Q4VQ66)
Putative peroxin 13 (Q4QDL4)
Putative peroxin 14 (Q4QBZ9)
Putative peroxisome assembly protein (Q4QD90)
RING finger protein (Q95ZB8)
Putative glycosomal membrane protein (Q4Q838)
The peroxisome complex for protein import into peroxisomes (Kiel et al. 2006).
Peroxin complex of Saccharomyces cerevisiae