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Peroxisomal matrix protein import: the transient pore model

Abstract

Peroxisomes import folded, even oligomeric, proteins, which distinguishes the peroxisomal translocation machinery from the well-characterized translocons of other organelles. How proteins are transported across the peroxisomal membrane is unclear. Here, we propose a mechanistic model that conceptually divides the import process into three consecutive steps: the formation of a translocation pore by the import receptor, the ubiquitylation of the import receptors, and pore disassembly/receptor recycling.

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Figure 1: Membrane protein complexes of the peroxisomal protein-import machinery.
Figure 2: The transient pore model.

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References

  1. Brown, L. A. & Baker, A. Peroxisome biogenesis and the role of protein import. J. Cell. Mol. Med. 7, 388–400 (2003).

    Article  CAS  Google Scholar 

  2. Eckert, J. H. & Erdmann, R. Peroxisome biogenesis. Rev. Physiol. Biochem. Pharmacol. 147, 75–121 (2003).

    Article  CAS  Google Scholar 

  3. Vizeacoumar, F. J., Torres-Guzman, J. C., Bouard, D., Aitchison, J. D. & Rachubinski, R. A. Pex30p, Pex31p, and Pex32p form a family of peroxisomal integral membrane proteins regulating peroxisome size and number in Saccharomyces cerevisiae. Mol. Biol. Cell 15, 665–677 (2004).

    Article  CAS  Google Scholar 

  4. Vizeacoumar, F. J., Torres-Guzman, J. C., Tam, Y. Y., Aitchison, J. D. & Rachubinski, R. A. YHR150w and YDR479c encode peroxisomal integral membrane proteins involved in the regulation of peroxisome number, size, and distribution in Saccharomyces cerevisiae. J. Cell Biol. 161, 321–332 (2003).

    Article  CAS  Google Scholar 

  5. Schnell, D. J. & Hebert, D. N. Protein translocons: multifunctional mediators of protein translocation across membranes. Cell 112, 491–505 (2003).

    Article  CAS  Google Scholar 

  6. Gouveia, A. M., Reguenga, C., Oliveira, M. E., Sa-Miranda, C. & Azevedo, J. E. Characterization of peroxisomal Pex5p from rat liver. Pex5p in the Pex5p–Pex14p membrane complex is a transmembrane protein. J. Biol. Chem. 275, 32444–32451 (2000).

    Article  CAS  Google Scholar 

  7. Kikuchi, M. et al. Proteomic analysis of rat liver peroxisome: presence of peroxisome-specific isozyme of Lon protease. J. Biol. Chem. 279, 421–428 (2004).

    Article  CAS  Google Scholar 

  8. Gouveia, A. M. et al. Characterization of the peroxisomal cycling receptor Pex5p import pathway. Adv. Exp. Med. Biol. 544, 219–220 (2003).

    Article  Google Scholar 

  9. Huhse, B. et al. Pex17p of Saccharomyces cerevisiae is a novel peroxin and component of the peroxisomal protein translocation machinery. J. Cell Biol. 140, 49–60 (1998).

    Article  CAS  Google Scholar 

  10. Agne, B. et al. Pex8p: an intraperoxisomal organizer of the peroxisomal import machinery. Mol. Cell 11, 635–646 (2003).

    Article  CAS  Google Scholar 

  11. Chang, C. C., Warren, D. S., Sacksteder, K. A. & Gould, S. J. PEX12 interacts with PEX5 and PEX10 and acts downstream of receptor docking in peroxisomal matrix protein import. J. Cell Biol. 147, 761–774 (1999).

    Article  CAS  Google Scholar 

  12. Schliebs, W. et al. Recombinant human peroxisomal targeting signal receptor PEX5. Structural basis for interaction of PEX5 with PEX14. J. Biol. Chem. 274, 5666–5673 (1999).

    Article  CAS  Google Scholar 

  13. Gatto, G. J., Geisbrecht, B. V., Gould, S. J. & Berg, J. M. Peroxisomal targeting signal-1 recognition by the TPR domains of human PEX5. Nature Struct. Biol. 7, 1091–1095 (2000).

    Article  CAS  Google Scholar 

  14. Eckert, J. H. & Johnsson, N. Pex10p links the ubiquitin conjugating enzyme Pex4p to the protein import machinery of the peroxisome. J. Cell Sci. 116, 3623–3634 (2003).

    Article  CAS  Google Scholar 

  15. Reguenga, C., Oliveira, M. E., Gouveia, A. M., Sa-Miranda, C. & Azevedo, J. E. Characterization of the mammalian peroxisomal import machinery: Pex2p, Pex5p, Pex12p, and Pex14p are subunits of the same protein assembly. J. Biol. Chem. 276, 29935–29942 (2001).

    Article  CAS  Google Scholar 

  16. Dalla Serra, M. & Menestrina, G. Liposomes in the study of pore-forming toxins. Methods Enzymol. 372, 99–124 (2003).

    Article  CAS  Google Scholar 

  17. Gouaux, E. Channel-forming toxins: tales of transformation. Curr. Opin. Struct. Biol. 7, 566–573 (1997).

    Article  CAS  Google Scholar 

  18. Oliveira, M. E., Gouveia, A. M., Pinto, R. A., Sa-Miranda, C. & Azevedo, J. E. The energetics of Pex5p-mediated peroxisomal protein import. J. Biol. Chem. 278, 39483–39488 (2003).

    Article  CAS  Google Scholar 

  19. Salomons, F. A., Kiel, J. A., Faber, K. N., Veenhuis, M. & van der Klei, I. J. Overproduction of Pex5p stimulates import of alcohol oxidase and dihydroxyacetone synthase in a Hansenula polymorpha Pex14 null mutant. J. Biol. Chem. 275, 12603–12611 (2000).

    Article  CAS  Google Scholar 

  20. Nair, D. M., Purdue, P. E. & Lazarow, P. B. Pex7p translocates in and out of peroxisomes in Saccharomyces cerevisiae. J. Cell Biol. 167, 599–604 (2004).

    Article  CAS  Google Scholar 

  21. Purdue, P. E., Yang, X. & Lazarow, P. B. Pex18p and Pex21p, a novel pair of related peroxins essential for peroxisomal targeting by the PTS2 pathway. J. Cell Biol. 143, 1859–1869 (1998).

    Article  CAS  Google Scholar 

  22. Schäfer, A., Kerssen, D., Veenhuis, M., Kunau, W. H. & Schliebs, W. Functional similarity between the peroxisomal PTS2 receptor binding protein Pex18p and the N-terminal half of the PTS1 receptor Pex5p. Mol. Cell. Biol. 24, 8895–8906 (2004).

    Article  Google Scholar 

  23. van Roermund, C. W., Elgersma, Y., Singh, N., Wanders, R. J. & Tabak, H. F. The membrane of peroxisomes in Saccharomyces cerevisiae is impermeable to NAD(H) and acetyl-CoA under in vivo conditions. EMBO J. 14, 3480–3486 (1995).

    Article  CAS  Google Scholar 

  24. van Roermund, C. W. et al. The peroxisomal lumen in Saccharomyces cerevisiae is alkaline. J. Cell Sci. 117, 4231–4237 (2004).

    Article  CAS  Google Scholar 

  25. Lasorsa, F. M. et al. The yeast peroxisomal adenine nucleotide transporter: characterization of two transport modes and involvement in ΔpH formation across peroxisomal membranes. Biochem. J. 381, 581–585 (2004).

    Article  CAS  Google Scholar 

  26. Erdmann, R. et al. PAS1, a yeast gene required for peroxisome biogenesis, encodes a member of a novel family of putative ATPases. Cell 64, 499–510 (1991).

    Article  CAS  Google Scholar 

  27. Lupas, A. N. & Martin, J. AAA proteins. Curr. Opin. Struct. Biol. 12, 746–753 (2002).

    Article  CAS  Google Scholar 

  28. Sauer, R. T. et al. Sculpting the proteome with AAA+ proteases and disassembly machines. Cell 119, 9–18 (2004).

    Article  CAS  Google Scholar 

  29. Ogura, T. & Wilkinson, A. J. AAA+ superfamily ATPases: common structure — diverse function. Genes Cells 6, 575–597 (2001).

    Article  CAS  Google Scholar 

  30. Arnold, I. & Langer, T. Membrane protein degradation by AAA proteases in mitochondria. Biochim. Biophys. Acta 1592, 89–96 (2002).

    Article  CAS  Google Scholar 

  31. Kihara, A., Akiyama, Y. & Ito, K. Dislocation of membrane proteins in FtsH-mediated proteolysis. EMBO J. 18, 2970–2981 (1999).

    Article  CAS  Google Scholar 

  32. Jarosch, E., Lenk, U. & Sommer, T. Endoplasmic reticulum-associated protein degradation. Int. Rev. Cytol. 223, 39–81 (2003).

    Article  CAS  Google Scholar 

  33. Ye, Y., Meyer, H. H. & Rapoport, T. A. Function of the p97–Ufd1–Npl4 complex in retrotranslocation from the ER to the cytosol: dual recognition of nonubiquitinated polypeptide segments and polyubiquitin chains. J. Cell Biol. 162, 71–84 (2003).

    Article  CAS  Google Scholar 

  34. Collins, C. S., Kalish, J. E., Morrell, J. C., McCaffery, J. M. & Gould, S. J. The peroxisome biogenesis factors Pex4p, Pex22p, Pex1p, and Pex6p act in the terminal steps of peroxisomal matrix protein import. Mol. Cell. Biol. 20, 7516–7526 (2000).

    Article  CAS  Google Scholar 

  35. Birschmann, I. et al. Pex15p of Saccharomyces cerevisiae provides a molecular basis for recruitment of the AAA peroxin Pex6p to peroxisomal membranes. Mol. Biol. Cell 14, 2226–2236 (2003).

    Article  CAS  Google Scholar 

  36. Matsumoto, N., Tamura, S. & Fujiki, Y. The pathogenic peroxin Pex26p recruits the Pex1p–Pex6p AAA ATPase complexes to peroxisomes. Nature Cell Biol. 5, 454–460 (2003).

    Article  CAS  Google Scholar 

  37. Purdue, P. E. & Lazarow, P. B. Pex18p is constitutively degraded during peroxisome biogenesis. J. Biol. Chem. 276, 47684–47689 (2001).

    Article  CAS  Google Scholar 

  38. Platta, H. W., Girzalsky, W. & Erdmann, R. Ubiquitination of the peroxisomal import receptor Pex5p. Biochem. J. 384, 37–45 (2004).

    Article  CAS  Google Scholar 

  39. Kiel, J. A., Emmrich, K., Meyer, H. E. & Kunau, W. H. Ubiquitination of the peroxisomal targeting signal type 1 receptor, Pex5p, suggests the presence of a quality control mechanism during peroxisomal matrix protein import. J. Biol. Chem. 280, 1921–1930 (2005).

    Article  CAS  Google Scholar 

  40. Kragt, A., Voorn-Brouwer, T. M., Van den Berg, M. & Distel, B. The Saccharomyces cerevisiae peroxisomal import receptor Pex5p is monoubiquitinated in wild type cells. J. Biol. Chem. 280, 7867–7874 (2005).

    Article  CAS  Google Scholar 

  41. Koller, A. et al. Pex22p of Pichia pastoris, essential for peroxisomal matrix protein import, anchors the ubiquitin-conjugating enzyme, Pex4p, on the peroxisomal membrane. J. Cell Biol. 146, 99–112 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Crane, D. I., Kalish, J. E. & Gould, S. J. The Pichia pastoris PAS4 gene encodes a ubiquitin-conjugating enzyme required for peroxisome assembly. J. Biol. Chem. 269, 21835–21844 (1994).

    CAS  PubMed  Google Scholar 

  43. van der Klei, I. J. et al. The ubiquitin-conjugating enzyme Pex4p of Hansenula polymorpha is required for efficient functioning of the PTS1 import machinery. EMBO J. 17, 3608–3618 (1998).

    Article  CAS  Google Scholar 

  44. Wiebel, F. F. & Kunau, W. -H. The PAS2 protein essential for peroxisome biogenesis is related to ubiquitin-conjugating enzymes. Nature 359, 73–76 (1992).

    Article  CAS  Google Scholar 

  45. Joazeiro, C. A. & Weissman, A. M. RING finger proteins: mediators of ubiquitin ligase activity. Cell 102, 549–552 (2000).

    Article  CAS  Google Scholar 

  46. Xie, Y. & Varshavsky, A. The E2–E3 interaction in the N-end rule pathway: the RING-H2 finger of E3 is required for the synthesis of multiubiquitin chain. EMBO J. 18, 6832–6844 (1999).

    Article  CAS  Google Scholar 

  47. Bellu, A. R., Komori, M., van Der Klei, I. J., Kiel, J. A. & Veenhuis, M. Peroxisome biogenesis and selective degradation converge at Pex14p. J. Biol. Chem. 276, 44570–44574 (2001).

    Article  CAS  Google Scholar 

  48. Titorenko, V. I. & Rachubinski, R. A. Peroxisomal membrane fusion requires two AAA family ATPases, Pex1p and Pex6p. J. Cell Biol. 150, 881–886 (2000).

    Article  CAS  Google Scholar 

  49. Tolbert, N. E. & Essner, E. Microbodies: peroxisomes and glyoxysomes. J. Cell Biol. 91, 271–283 (1981).

    Article  CAS  Google Scholar 

  50. van den Bosch, H., Schutgens, R. B., Wanders, R. J. & Tager, J. M. Biochemistry of peroxisomes. Annu. Rev. Biochem. 61, 157–197 (1992).

    Article  CAS  Google Scholar 

  51. Wanders, R. J. Metabolic and molecular basis of peroxisomal disorders: a review. Am. J. Med. Genet. A 126, 355–375 (2004).

    Article  Google Scholar 

  52. Michels, P. A., Hannaert, V. & Bringaud, F. Metabolic aspects of glycosomes in trypanosomatidae — new data and views. Parasitol. Today 16, 482–489 (2000).

    Article  CAS  Google Scholar 

  53. Opperdoes, F. R. & Borst, P. Localization of nine glycolytic enzymes in a microbody-like organelle in Trypanosoma brucei: the glycosome. FEBS Lett. 80, 360–364 (1977).

    Article  CAS  Google Scholar 

  54. Veenhuis, M., van der Klei, I. J., Titorenko, V. & Harder, W. Hansenula polymorpha: an attractive model organism for molecular studies of peroxisome biogenesis and function. FEMS Microbiol. Lett. 79, 393–403 (1992).

    Article  Google Scholar 

  55. Marzioch, M., Erdmann, R., Veenhuis, M. & Kunau, W. -H. PAS7 encodes a novel yeast member of the WD-40 protein family essential for import of 3-oxoacyl-CoA thiolase, a PTS2-containing protein, into peroxisomes. EMBO J. 13, 4908–4918 (1994).

    Article  CAS  Google Scholar 

  56. Dodt, G. & Gould, S. J. Multiple PEX genes are required for proper subcellular distribution and stability of Pex5p, the PTS1 receptor: evidence that PTS1 protein import is mediated by a cycling receptor. J. Cell Biol. 135, 1763–1774 (1996).

    Article  CAS  Google Scholar 

  57. Dammai, V. & Subramani, S. The human peroxisomal targeting signal receptor, Pex5p, is translocated into the peroxisomal matrix and recycled to the cytosol. Cell 105, 187–196 (2001).

    Article  CAS  Google Scholar 

  58. Kunau, W. Peroxisomes: the extended shuttle to the peroxisome matrix. Curr. Biol. 11, 659–662 (2001).

    Article  Google Scholar 

  59. Gould, S. J. & Collins, C. S. Peroxisomal-protein import: is it really that complex? Nature Rev. Mol. Cell Biol. 3, 382–389 (2002).

    Article  CAS  Google Scholar 

  60. Azevedo, J. E., Costa-Rodrigues, J., Guimaraes, C. P., Oliveira, M. E. & Sa-Miranda, C. Protein translocation across the peroxisomal membrane. Cell Biochem. Biophys. 41, 451–468 (2004).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank W.-H. Kunau and H. Rottensteiner for critically reading this manuscript. We gratefully acknowledge M. Veenhuis for kindly sharing electron micrographs. Work in our laboratories is supported by grants from the Deutsche Forschungsgemeinschaft, the European Union and the Fonds der Chemischen Industrie. We apologize to the many researchers whose work we could not cite due to space limitations.

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Correspondence to Ralf Erdmann.

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DATABASES

Swiss-Prot

Pex1

Pex2

Pex5

Pex6

Pex7

Pex8

Pex10

Pex12

Pex13

Pex14

Pex17

Pex22

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Erdmann, R., Schliebs, W. Peroxisomal matrix protein import: the transient pore model. Nat Rev Mol Cell Biol 6, 738–742 (2005). https://doi.org/10.1038/nrm1710

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