Skip to main content
The EMBO Journal logoLink to The EMBO Journal
. 1998 Jun 1;17(11):2982–2993. doi: 10.1093/emboj/17.11.2982

The Vps4p AAA ATPase regulates membrane association of a Vps protein complex required for normal endosome function.

M Babst 1, B Wendland 1, E J Estepa 1, S D Emr 1
PMCID: PMC1170638  PMID: 9606181

Abstract

Vps4p is an AAA-type ATPase required for efficient transport of biosynthetic and endocytic cargo from an endosome to the lysosome-like vacuole of Saccharomyces cerevisiae. Vps4p mutants that do not bind ATP or are defective in ATP hydrolysis were characterized both in vivo and in vitro. The nucleotide-free or ADP-bound form of Vps4p existed as a dimer, whereas in the ATP-locked state, Vps4p dimers assembled into a decameric complex. This suggests that ATP hydrolysis drives a cycle of association and dissociation of Vps4p dimers/decamers. Nucleotide binding also regulated the association of Vps4p with an endosomal compartment in vivo. This membrane association required the N-terminal coiled-coil motif of Vps4p, but deletion of the coiled-coil domain did not affect ATPase activity or oligomeric assembly of the protein. Membrane association of two previously uncharacterized class E Vps proteins, Vps24p and Vps32p/Snf7p, was also affected by mutations in VPS4. Upon inactivation of a temperature-conditional vps4 mutant, Vps24p and Vps32p/Snf7p rapidly accumulated in a large membrane-bound complex. Immunofluorescence indicated that both proteins function with Vps4p at a common endosomal compartment. Together, the data suggest that the Vps4 ATPase catalyzes the release (uncoating) of an endosomal membrane-associated class E protein complex(es) required for normal morphology and sorting activity of the endosome.

Full Text

The Full Text of this article is available as a PDF (419.2 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Arlt H., Tauer R., Feldmann H., Neupert W., Langer T. The YTA10-12 complex, an AAA protease with chaperone-like activity in the inner membrane of mitochondria. Cell. 1996 Jun 14;85(6):875–885. doi: 10.1016/s0092-8674(00)81271-4. [DOI] [PubMed] [Google Scholar]
  2. Babst M., Sato T. K., Banta L. M., Emr S. D. Endosomal transport function in yeast requires a novel AAA-type ATPase, Vps4p. EMBO J. 1997 Apr 15;16(8):1820–1831. doi: 10.1093/emboj/16.8.1820. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Becherer K. A., Rieder S. E., Emr S. D., Jones E. W. Novel syntaxin homologue, Pep12p, required for the sorting of lumenal hydrolases to the lysosome-like vacuole in yeast. Mol Biol Cell. 1996 Apr;7(4):579–594. doi: 10.1091/mbc.7.4.579. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Beckers C. J., Block M. R., Glick B. S., Rothman J. E., Balch W. E. Vesicular transport between the endoplasmic reticulum and the Golgi stack requires the NEM-sensitive fusion protein. Nature. 1989 Jun 1;339(6223):397–398. doi: 10.1038/339397a0. [DOI] [PubMed] [Google Scholar]
  5. Beyer A. Sequence analysis of the AAA protein family. Protein Sci. 1997 Oct;6(10):2043–2058. doi: 10.1002/pro.5560061001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bock J. B., Klumperman J., Davanger S., Scheller R. H. Syntaxin 6 functions in trans-Golgi network vesicle trafficking. Mol Biol Cell. 1997 Jul;8(7):1261–1271. doi: 10.1091/mbc.8.7.1261. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Burd C. G., Mustol P. A., Schu P. V., Emr S. D. A yeast protein related to a mammalian Ras-binding protein, Vps9p, is required for localization of vacuolar proteins. Mol Cell Biol. 1996 May;16(5):2369–2377. doi: 10.1128/mcb.16.5.2369. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Burd C. G., Peterson M., Cowles C. R., Emr S. D. A novel Sec18p/NSF-dependent complex required for Golgi-to-endosome transport in yeast. Mol Biol Cell. 1997 Jun;8(6):1089–1104. doi: 10.1091/mbc.8.6.1089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Cereghino J. L., Marcusson E. G., Emr S. D. The cytoplasmic tail domain of the vacuolar protein sorting receptor Vps10p and a subset of VPS gene products regulate receptor stability, function, and localization. Mol Biol Cell. 1995 Sep;6(9):1089–1102. doi: 10.1091/mbc.6.9.1089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Christianson T. W., Sikorski R. S., Dante M., Shero J. H., Hieter P. Multifunctional yeast high-copy-number shuttle vectors. Gene. 1992 Jan 2;110(1):119–122. doi: 10.1016/0378-1119(92)90454-w. [DOI] [PubMed] [Google Scholar]
  11. Confalonieri F., Duguet M. A 200-amino acid ATPase module in search of a basic function. Bioessays. 1995 Jul;17(7):639–650. doi: 10.1002/bies.950170710. [DOI] [PubMed] [Google Scholar]
  12. Daro E., Sheff D., Gomez M., Kreis T., Mellman I. Inhibition of endosome function in CHO cells bearing a temperature-sensitive defect in the coatomer (COPI) component epsilon-COP. J Cell Biol. 1997 Dec 29;139(7):1747–1759. doi: 10.1083/jcb.139.7.1747. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Dieckmann C. L., Tzagoloff A. Assembly of the mitochondrial membrane system. CBP6, a yeast nuclear gene necessary for synthesis of cytochrome b. J Biol Chem. 1985 Feb 10;260(3):1513–1520. [PubMed] [Google Scholar]
  14. Finken-Eigen M., Röhricht R. A., Köhrer K. The VPS4 gene is involved in protein transport out of a yeast pre-vacuolar endosome-like compartment. Curr Genet. 1997 Jun;31(6):469–480. doi: 10.1007/s002940050232. [DOI] [PubMed] [Google Scholar]
  15. Fröhlich K. U., Fries H. W., Peters J. M., Mecke D. The ATPase activity of purified CDC48p from Saccharomyces cerevisiae shows complex dependence on ATP-, ADP-, and NADH-concentrations and is completely inhibited by NEM. Biochim Biophys Acta. 1995 Nov 15;1253(1):25–32. doi: 10.1016/0167-4838(95)00136-i. [DOI] [PubMed] [Google Scholar]
  16. Graham T. R., Emr S. D. Compartmental organization of Golgi-specific protein modification and vacuolar protein sorting events defined in a yeast sec18 (NSF) mutant. J Cell Biol. 1991 Jul;114(2):207–218. doi: 10.1083/jcb.114.2.207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Gruenberg J., Maxfield F. R. Membrane transport in the endocytic pathway. Curr Opin Cell Biol. 1995 Aug;7(4):552–563. doi: 10.1016/0955-0674(95)80013-1. [DOI] [PubMed] [Google Scholar]
  18. Hanson P. I., Roth R., Morisaki H., Jahn R., Heuser J. E. Structure and conformational changes in NSF and its membrane receptor complexes visualized by quick-freeze/deep-etch electron microscopy. Cell. 1997 Aug 8;90(3):523–535. doi: 10.1016/s0092-8674(00)80512-7. [DOI] [PubMed] [Google Scholar]
  19. Hay J. C., Scheller R. H. SNAREs and NSF in targeted membrane fusion. Curr Opin Cell Biol. 1997 Aug;9(4):505–512. doi: 10.1016/s0955-0674(97)80026-9. [DOI] [PubMed] [Google Scholar]
  20. Hicke L., Zanolari B., Pypaert M., Rohrer J., Riezman H. Transport through the yeast endocytic pathway occurs through morphologically distinct compartments and requires an active secretory pathway and Sec18p/N-ethylmaleimide-sensitive fusion protein. Mol Biol Cell. 1997 Jan;8(1):13–31. doi: 10.1091/mbc.8.1.13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Horazdovsky B. F., Emr S. D. The VPS16 gene product associates with a sedimentable protein complex and is essential for vacuolar protein sorting in yeast. J Biol Chem. 1993 Mar 5;268(7):4953–4962. [PubMed] [Google Scholar]
  22. Ito H., Fukuda Y., Murata K., Kimura A. Transformation of intact yeast cells treated with alkali cations. J Bacteriol. 1983 Jan;153(1):163–168. doi: 10.1128/jb.153.1.163-168.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Jones E. W. Proteinase mutants of Saccharomyces cerevisiae. Genetics. 1977 Jan;85(1):23–33. doi: 10.1093/genetics/85.1.23. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Komada M., Kitamura N. Regulatory role of major tyrosine autophosphorylation site of kinase domain of c-Met receptor (scatter factor/hepatocyte growth factor receptor). J Biol Chem. 1994 Jun 10;269(23):16131–16136. [PubMed] [Google Scholar]
  25. Komada M., Masaki R., Yamamoto A., Kitamura N. Hrs, a tyrosine kinase substrate with a conserved double zinc finger domain, is localized to the cytoplasmic surface of early endosomes. J Biol Chem. 1997 Aug 15;272(33):20538–20544. doi: 10.1074/jbc.272.33.20538. [DOI] [PubMed] [Google Scholar]
  26. Lenhard J. M., Kahn R. A., Stahl P. D. Evidence for ADP-ribosylation factor (ARF) as a regulator of in vitro endosome-endosome fusion. J Biol Chem. 1992 Jun 25;267(18):13047–13052. [PubMed] [Google Scholar]
  27. Lupas A., Van Dyke M., Stock J. Predicting coiled coils from protein sequences. Science. 1991 May 24;252(5009):1162–1164. doi: 10.1126/science.252.5009.1162. [DOI] [PubMed] [Google Scholar]
  28. Muhlberg A. B., Warnock D. E., Schmid S. L. Domain structure and intramolecular regulation of dynamin GTPase. EMBO J. 1997 Nov 17;16(22):6676–6683. doi: 10.1093/emboj/16.22.6676. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Mukhopadhyay A., Funato K., Stahl P. D. Rab7 regulates transport from early to late endocytic compartments in Xenopus oocytes. J Biol Chem. 1997 May 16;272(20):13055–13059. doi: 10.1074/jbc.272.20.13055. [DOI] [PubMed] [Google Scholar]
  30. Nagiec E. E., Bernstein A., Whiteheart S. W. Each domain of the N-ethylmaleimide-sensitive fusion protein contributes to its transport activity. J Biol Chem. 1995 Dec 8;270(49):29182–29188. doi: 10.1074/jbc.270.49.29182. [DOI] [PubMed] [Google Scholar]
  31. Novick P., Zerial M. The diversity of Rab proteins in vesicle transport. Curr Opin Cell Biol. 1997 Aug;9(4):496–504. doi: 10.1016/s0955-0674(97)80025-7. [DOI] [PubMed] [Google Scholar]
  32. Patel S., Latterich M. The AAA team: related ATPases with diverse functions. Trends Cell Biol. 1998 Feb;8(2):65–71. [PubMed] [Google Scholar]
  33. Peters J. M., Walsh M. J., Franke W. W. An abundant and ubiquitous homo-oligomeric ring-shaped ATPase particle related to the putative vesicle fusion proteins Sec18p and NSF. EMBO J. 1990 Jun;9(6):1757–1767. doi: 10.1002/j.1460-2075.1990.tb08300.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Piper R. C., Cooper A. A., Yang H., Stevens T. H. VPS27 controls vacuolar and endocytic traffic through a prevacuolar compartment in Saccharomyces cerevisiae. J Cell Biol. 1995 Nov;131(3):603–617. doi: 10.1083/jcb.131.3.603. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Périer F., Coulter K. L., Liang H., Radeke C. M., Gaber R. F., Vandenberg C. A. Identification of a novel mammalian member of the NSF/CDC48p/Pas1p/TBP-1 family through heterologous expression in yeast. FEBS Lett. 1994 Sep 5;351(2):286–290. doi: 10.1016/0014-5793(94)00879-5. [DOI] [PubMed] [Google Scholar]
  36. Raymond C. K., Howald-Stevenson I., Vater C. A., Stevens T. H. Morphological classification of the yeast vacuolar protein sorting mutants: evidence for a prevacuolar compartment in class E vps mutants. Mol Biol Cell. 1992 Dec;3(12):1389–1402. doi: 10.1091/mbc.3.12.1389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Rieder S. E., Banta L. M., Köhrer K., McCaffery J. M., Emr S. D. Multilamellar endosome-like compartment accumulates in the yeast vps28 vacuolar protein sorting mutant. Mol Biol Cell. 1996 Jun;7(6):985–999. doi: 10.1091/mbc.7.6.985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Robinson J. S., Klionsky D. J., Banta L. M., Emr S. D. Protein sorting in Saccharomyces cerevisiae: isolation of mutants defective in the delivery and processing of multiple vacuolar hydrolases. Mol Cell Biol. 1988 Nov;8(11):4936–4948. doi: 10.1128/mcb.8.11.4936. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Robinson L. J., Aniento F., Gruenberg J. NSF is required for transport from early to late endosomes. J Cell Sci. 1997 Sep;110(Pt 17):2079–2087. doi: 10.1242/jcs.110.17.2079. [DOI] [PubMed] [Google Scholar]
  40. Rodriguez L., Stirling C. J., Woodman P. G. Multiple N-ethylmaleimide-sensitive components are required for endosomal vesicle fusion. Mol Biol Cell. 1994 Jul;5(7):773–783. doi: 10.1091/mbc.5.7.773. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Rothman J. H., Howald I., Stevens T. H. Characterization of genes required for protein sorting and vacuolar function in the yeast Saccharomyces cerevisiae. EMBO J. 1989 Jul;8(7):2057–2065. doi: 10.1002/j.1460-2075.1989.tb03614.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Rybin V., Ullrich O., Rubino M., Alexandrov K., Simon I., Seabra M. C., Goody R., Zerial M. GTPase activity of Rab5 acts as a timer for endocytic membrane fusion. Nature. 1996 Sep 19;383(6597):266–269. doi: 10.1038/383266a0. [DOI] [PubMed] [Google Scholar]
  43. Sarkar G., Edery I., Sonenberg N. Photoaffinity labeling of the cap-binding protein complex with ATP/dATP. Differential labeling of free eukaryotic initiation factor 4A and the eukaryotic initiation factor 4A component of the cap-binding protein complex with [alpha-32P]ATP/dATP. J Biol Chem. 1985 Nov 5;260(25):13831–13837. [PubMed] [Google Scholar]
  44. Shirahama K., Noda T., Ohsumi Y. Mutational analysis of Csc1/Vps4p: involvement of endosome in regulation of autophagy in yeast. Cell Struct Funct. 1997 Oct;22(5):501–509. doi: 10.1247/csf.22.501. [DOI] [PubMed] [Google Scholar]
  45. Südhof T. C. The synaptic vesicle cycle: a cascade of protein-protein interactions. Nature. 1995 Jun 22;375(6533):645–653. doi: 10.1038/375645a0. [DOI] [PubMed] [Google Scholar]
  46. Takei K., McPherson P. S., Schmid S. L., De Camilli P. Tubular membrane invaginations coated by dynamin rings are induced by GTP-gamma S in nerve terminals. Nature. 1995 Mar 9;374(6518):186–190. doi: 10.1038/374186a0. [DOI] [PubMed] [Google Scholar]
  47. Tu J., Vallier L. G., Carlson M. Molecular and genetic analysis of the SNF7 gene in Saccharomyces cerevisiae. Genetics. 1993 Sep;135(1):17–23. doi: 10.1093/genetics/135.1.17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Ullrich O., Reinsch S., Urbé S., Zerial M., Parton R. G. Rab11 regulates recycling through the pericentriolar recycling endosome. J Cell Biol. 1996 Nov;135(4):913–924. doi: 10.1083/jcb.135.4.913. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Warnock D. E., Hinshaw J. E., Schmid S. L. Dynamin self-assembly stimulates its GTPase activity. J Biol Chem. 1996 Sep 13;271(37):22310–22314. doi: 10.1074/jbc.271.37.22310. [DOI] [PubMed] [Google Scholar]
  50. Whiteheart S. W., Rossnagel K., Buhrow S. A., Brunner M., Jaenicke R., Rothman J. E. N-ethylmaleimide-sensitive fusion protein: a trimeric ATPase whose hydrolysis of ATP is required for membrane fusion. J Cell Biol. 1994 Aug;126(4):945–954. doi: 10.1083/jcb.126.4.945. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Whitney J. A., Gomez M., Sheff D., Kreis T. E., Mellman I. Cytoplasmic coat proteins involved in endosome function. Cell. 1995 Dec 1;83(5):703–713. doi: 10.1016/0092-8674(95)90183-3. [DOI] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES