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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 are 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 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)

This family belongs to the: AAA-ATPase Superfamily.

References associated with 3.A.20 family:

Agarraberes, F.A. and J.F. Dice. (2001). Protein translocation across membranes. Biochim. Biophys. Acta 1513: 1-24. 11427190
Barros-Barbosa, A., M.J. Ferreira, T.A. Rodrigues, A.G. Pedrosa, C.P. Grou, M.P. Pinto, M. Fransen, T. Francisco, and J.E. Azevedo. (2018). Membrane topologies of PEX13 and PEX14 provide new insights on the mechanism of protein import into peroxisomes. FEBS J. [Epub: Ahead of Print] 30414318
Bolte, K., N. Gruenheit, G. Felsner, M.S. Sommer, U.G. Maier, and F. Hempel. (2011). Making new out of old: recycling and modification of an ancient protein translocation system during eukaryotic evolution. Mechanistic comparison and phylogenetic analysis of ERAD, SELMA and the peroxisomal importomer. Bioessays 33: 368-376. 21425305
Cichocki, B.A., K. Krumpe, D.G. Vitali, and D. Rapaport. (2018). Pex19 is involved in importing dually targeted tail-anchored proteins to both mitochondria and peroxisomes. Traffic 19: 770-785. 30033679
Dawidowski, M., L. Emmanouilidis, V.C. Kalel, K. Tripsianes, K. Schorpp, K. Hadian, M. Kaiser, P. Mäser, M. Kolonko, S. Tanghe, A. Rodriguez, W. Schliebs, R. Erdmann, M. Sattler, and G.M. Popowicz. (2017). Inhibitors of PEX14 disrupt protein import into glycosomes and kill Trypanosoma parasites. Science 355: 1416-1420. 28360328
Feng, P., X. Wu, S.K. Erramilli, J.A. Paulo, P. Knejski, S.P. Gygi, A.A. Kossiakoff, and T.A. Rapoport. (2022). A peroxisomal ubiquitin ligase complex forms a retrotranslocation channel. Nature 607: 374-380. 35768507
Fujiki, Y., N. Miyata, N. Matsumoto, and S. Tamura. (2008). Dynamic and functional assembly of the AAA peroxins, Pex1p and Pex6p, and their membrane receptor Pex26p involved in shuttling of the PTS1 receptor Pex5p in peroxisome biogenesis. Biochem. Soc. Trans. 36: 109-113. 18208396
Girzalsky W., Saffian D. and Erdmann R. (2010). Peroxisomal protein translocation. Biochim Biophys Acta. 1803(6):724-31. 20079383
Guder, P., A.S. Lotz-Havla, M. Woidy, D.D. Reiß, M.K. Danecka, U.A. Schatz, M. Becker, R. Ensenauer, P. Pagel, L. Büttner, A.C. Muntau, and S.W. Gersting. (2018). Isoform-specific domain organization determines conformation and function of the peroxisomal biogenesis factor PEX26. Biochim. Biophys. Acta. Mol. Cell Res. [Epub: Ahead of Print] 30366024
Itoh, R. and Y. Fujiki. (2006). Functional domains and dynamic assembly of the peroxin Pex14p, the entry site of matrix proteins. J. Biol. Chem. 281: 10196-10205. 16459329
Joshi, A.S., B. Nebenfuehr, V. Choudhary, P. Satpute-Krishnan, T.P. Levine, A. Golden, and W.A. Prinz. (2018). Lipid droplet and peroxisome biogenesis occur at the same ER subdomains. Nat Commun 9: 2940. 30054481
Kerssen, D., E, Hambruch, W. Klaas, H.W. Platta, B. de Kruijff, R. Erdmann, W.H. Kunau, and W. Schliebs. (2006). Membrane association of the cycling peroxisome import receptor Pex5p. J. Biol. Chem. 281: 27003-27015. 16849337
Kiel, J.A., M. Veenhuis, and I.J. van der Klei. (2006). PEX genes in fungal genomes: common, rare or redundant. Traffic 7: 1291-1303. 16978390
Ma, C., G. Agrawal, and S. Subramani. (2011). Peroxisome assembly: matrix and membrane protein biogenesis. J. Cell Biol. 193: 7-16. 21464226
Mayerhofer, P.U. (2016). Targeting and insertion of peroxisomal membrane proteins: ER trafficking versus direct delivery to peroxisomes. Biochim. Biophys. Acta. 1863: 870-880. 26392202
Meinecke, M., C. Cizmowski, W. Schliebs, V. Krüger, S. Beck, R. Wagner, and R. Erdmann. (2010). The peroxisomal importomer constitutes a large and highly dynamic pore. Nat. Cell Biol. 12: 273-277. 20154681
Miyata, N., K. Hosoi, S. Mukai, and Y. Fujiki. (2009). In vitro import of peroxisome-targeting signal type 2 (PTS2) receptor Pex7p into peroxisomes. Biochim. Biophys. Acta. 1793: 860-870. 19264098
Mullen, R.T. and R.N. Trelease. (2000). The sorting signals for peroxisomal membrane-bound ascorbate peroxidase are within its C-terminal tail. J. Biol. Chem. 275: 16337-16344. 10748009
Mullen, R.T., C.R. Flynn, and R.N. Trelease. (2001). How are peroxisomes formed? The role of the endoplasmic reticulum and peroxins. Trends Plant Sci. 6: 256-261. 11378467
Neuspiel, M., A.C. Schauss, E. Braschi, R. Zunino, P. Rippstein, R.A. Rachubinski, M.A. Andrade-Navarro, and H.M. McBride. (2008). Cargo-selected transport from the mitochondria to peroxisomes is mediated by vesicular carriers. Curr. Biol. 18: 102-108. 18207745
Oliveira, M.E., A.M. Gouveia, R.A. Pinto, C. Sá-Miranda, and J.E. Azevedo. (2003). The energetics of Pex5p-mediated peroxisomal protein import. J. Biol. Chem. 278: 39483-39488. 12885776
Platta, H.W., S. Grunau, K. Rosenkranz, W. Girzalsky, and R. Erdmann. (2005). Functional role of the AAA peroxins in dislocation of the cycling PTS1 receptor back to the cytosol. Nat Cell Biol. 7: 817-822. 16007078
Purdue, P.E. and P.B. Lazarow. (1994). Peroxisomal biogenesis: multiple pathways of protein import. J. Biol. Chem. 269: 30065-30068. 7982905
Rucktäschel, R., W. Girzalsky, and R. Erdmann. (2011). Protein import machineries of peroxisomes. Biochim. Biophys. Acta. 1808: 892-900. 20659419
Saveria, T., A. Halbach, R. Erdmann, R. Volkmer-Engert, C. Landgraf, H. Rottensteiner, and M. Parsons. (2007). Conservation of PEX19-binding motifs required for protein targeting to mammalian peroxisomal and trypanosome glycosomal membranes. Eukaryot. Cell. 6: 1439-1449. 17586720
Schumann, U. and S. Subramani. (2008). Special delivery from mitochondria to peroxisomes. Trends Cell Biol. 18: 253-256. 18468897
Shakya, A.K. and J.V. Pratap. (2020). The coiled-coil domain of glycosomal membrane-associated Leishmania donovani PEX14: cloning, overexpression, purification and preliminary crystallographic analysis. Acta Crystallogr F Struct Biol Commun 76: 464-468. 33006573
Smith, M.D. and D.J. Schnell. (2001). Peroxisomal protein import: the paradigm shifts. Cell 105: 293-296. 11348588
Sparkes, I.A. and A. Baker. (2002). Peroxisome biogenesis and protein import in plants, animals and yeasts: enigma and variations? Mol. Mem. Biol. 19: 171-185. 12463717
Subramani, S. (1998). Components involved in peroxisome import, biogenesis, proliferation, turnover and movement. Physiol. Rev. 78: 171-188. 9457172
Subramani, S., A. Koller, and W.B. Snyder. (2000). Import of peroxisomal matrix and membrane proteins. Annu. Rev. Biochem. 69: 399-418. 10966464
Wolf, J., W. Schliebs, and R. Erdmann. (2010). Peroxisomes as dynamic organelles: peroxisomal matrix protein import. FEBS J. 277: 3268-3278. 20629744
Yamamoto, Y. and T. Sakisaka. (2018). The peroxisome biogenesis factors posttranslationally target reticulon homology domain-containing proteins to the endoplasmic reticulum membrane. Sci Rep 8: 2322. 29396426