Yeast Ysl2p, Homologous to Sec7 Domain Guanine Nucleotide Exchange Factors, Functions in Endocytosis and Maintenance of Vacuole Integrity and Interacts with the Arf-Like Small GTPase Arl1p

REFERENCES

• Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389–3402.
   PubMed Web of Science ®Google Scholar
• Amor, J. C., J. R. Horton, X. Zhu, Y. Wang, C. Sullards, D. Ringe, X. Cheng, and R. A. Kahn. 2001. Structures of yeast ARF2 and ARL1. J. Biol. Chem. 276: 42477–42484.
   PubMedGoogle Scholar
• Barik, S., and M. Galinski. 1991. “Megaprimer”method of PCR: increased template concentration improves yield. BioTechniques 10: 489–490.
   PubMedGoogle Scholar
• Beraud-Dufour, S., S. Robineau, P. Chardin, S. Paris, M. Chabre, J. Cherfils, and B. Antonny. 1998. A glutamic finger in the guanine nucleotide exchange factor ARNO displaces Mg2+ and the beta-phosphate to destabilize GDP on ARF1. EMBO J. 17: 3651–3659.
   PubMedGoogle Scholar
• Beraud-Dufour, S., and W. E. Balch. 2001. Structural and functional organization of ADP-ribosylation factor (ARF) proteins. Methods Enzymol. 329: 245–247.
   PubMedGoogle Scholar
• Bourne, H. R., D. A. Sanders, and F. McCormick. 1991. The GTPase superfamily: conserved structure and molecular mechanism. Nature 349: 117–127.
   PubMed Web of Science ®Google Scholar
• Chardin, P., S. Paris, B. Antonny, S. Robineau, S. Beraud-Dufour, C. L. Jackson, and M. Chabre. 1996. A human exchange factor for ARF contains Sec7- and pleckstrin-homology domains. Nature 384: 481–484.
   PubMedGoogle Scholar
• Cherfils, J., J. Menetrey, M. Mathieu, G. Le Bras, S. Robineau, S. Beraud-Dufour, and B. Antonny. 1998. Structure of the Sec7 domain of the Arf exchange factor ARNO. Nature 392: 101–105.
   PubMedGoogle Scholar
• Claros, M. G., and G. von Heijne. 1994. TopPred II: an improved software for membrane protein structure predictions. Comput. Appl. Biosci. 10: 685–686.
   PubMedGoogle Scholar
• Dulic, V., M. Egerton, I. Elguindi, S. Raths, B. Singer, and H. Riezman. 1991. Yeast endocytosis assays. Methods Enzymol. 194: 679–710.
   Google Scholar
• Eddy, S. R. 1996. Hidden Markov models. Curr. Opin. Struct. Biol. 6: 361–365.
   PubMed Web of Science ®Google Scholar
• Franzusoff, A., and R. Schekman. 1989. Functional compartments of the yeast Golgi apparatus are defined by the sec7 mutation. EMBO J. 8: 2695–2702.
   PubMed Web of Science ®Google Scholar
• Gaynor, E. C., C. Y. Chen, S. D. Emr, and T. R. Graham. 1998. ARF is required for maintenance of yeast Golgi and endosome structure and function. Mol. Biol. Cell 9: 653–670.
   PubMed Web of Science ®Google Scholar
• Gerrard, S. R., N. J. Bryant, and T. H. Stevens. 2000. VPS21 controls entry of endocytosed and biosynthetic proteins into the yeast prevacuolar compartment. Mol. Biol. Cell 11: 613–626.
   PubMed Web of Science ®Google Scholar
• Goldstein, A., and J. O. Lampen. 1975. Beta-D-fructofuranoside fructohydolase from yeast. Methods Enzymol. 42: 504–511.
   PubMedGoogle Scholar
• Guarente, L. 1983. Yeast promoters and lacZ fusions designed to study expression of cloned genes in yeast. Methods Enzymol. 101: 181–191.
   PubMed Web of Science ®Google Scholar
• Haas, A., B. Conradt, and W. Wickner. 1994. G-protein ligands inhibit in vitro reactions of vacuole inheritance. J. Cell Biol. 126: 87–97.
   PubMed Web of Science ®Google Scholar
• Hicke, L., and H. Riezman. 1996. Ubiquitination of a yeast plasma membrane receptor signals its ligand-stimulated endocytosis. Cell 84: 277–287.
   PubMed Web of Science ®Google Scholar
• Hillig, R. C., M. Hanzal-Bayer, M. Linari, J. Becker, A. Wittinghofer, and L. Renault. 2000. Structural and biochemical properties show ARL3-GDP as a distinct GTP binding protein. Struct. Fold. Des. 8: 1239–1245.
   Google Scholar
• Hohenberg, H., K. Mannweiler, and M. Müller. 1994. High-pressure freezing of cell suspensions in cellulose capillary tubes. J. Microsc. 175: 34–43.
   PubMed Web of Science ®Google Scholar
• Horazdovsky, B. F., G. Busch, and S. D. Emr. 1994. VPS21 encodes a rab5-like GTP binding protein that is required for the sorting of yeast vacuolar proteins. EMBO J. 13: 1297–1309.
   PubMed Web of Science ®Google Scholar
• Jackson, C. L., and J. E. Casanova. 2000. Turning on ARF: the Sec7 family of guanine-nucleotide-exchange factors. Trends Cell Biol. 10: 60–67.
   PubMed Web of Science ®Google Scholar
• Jones, S., G. Jedd, R. A. Kahn, A. Franzusoff, F. Bartolini, and N. Segev. 1999. Genetic interactions in yeast between Ypt GTPases and Arf guanine nucleotide exchangers. Genetics 152: 1543–1556.
   PubMed Web of Science ®Google Scholar
• Kahn, R. A., and A. G. Gilman. 1984. ADP-ribosylation of Gs promotes the dissociation of its alpha and beta subunits. J. Biol. Chem. 259: 6235–6240.
   PubMed Web of Science ®Google Scholar
• Kahn, R. A., P. Randazzo, T. Serafini, O. Weiss, C. Rulka, J. Clark, M. Amherdt, P. Roller, L. Orci, and J. E. Rothman. 1992. J. Biol. Chem. 267: 13039–13046.
   PubMedGoogle Scholar
• Kahn, R. A. 1995. The Arf subfamily. Oxford University Press, Oxford, United Kingdom.
   Google Scholar
• Klausner, R. D., J. G. Donaldson, and J. Lippincott-Schwartz. 1992. Brefeldin A: insights into the control of membrane traffic and organelle structure. J. Cell Biol. 116: 1071–1080.
   PubMed Web of Science ®Google Scholar
• Lee, F. J. S., C. F. Huang, W. L. Yu, L. M. Buu, C. Y. Lin, M. C. Huang, J. Moss, and M. Vaughan. 1997. Characterization of an ADP-ribosylation factor-like 1 protein in Saccharomyces cerevisiae. J. Biol. Chem. 272: 30998–31005.
   PubMed Web of Science ®Google Scholar
• Letourneur, F., E. C. Gaynor, S. Hennecke, C. Demolliere, R. Duden, S. D. Emr, H. Riezman, and P. Cosson. 1994. Coatomer is essential for retrieval of dilysine-tagged proteins to the endoplasmic reticulum. Cell 79: 1199–1207.
   PubMed Web of Science ®Google Scholar
• Longtine, M. S., A. McKenzie, D. J. Demarini, N. G. Shah, A. Wach, A. Brachat, P. Philippsen, and J. R. Pringle. 1998. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14: 953–961.
   PubMed Web of Science ®Google Scholar
• Mansour, S. J., J. Skaug, X. H. Zhao, J. Giordano, S. Scherer, and P. Melancon. 1999. p200 ARF-GEP1: a Golgi-localized guanine nucleotide exchange protein whose Sec7 domain is targeted by the drug brefeldin A. Proc. Natl. Acad. Sci. USA 96: 7968–7973.
   PubMed Web of Science ®Google Scholar
• McGuffin, L. J., K. Bryson, and D. T. Jones. 2000. The PSIPRED protein structure prediction server. Bioinformatics 16: 404–405.
   PubMed Web of Science ®Google Scholar
• Morinaga, N., R. Adamik, J. Moss, and M. Vaughan. 1999. Brefeldin A inhibited activity of the Sec7 domain of p200, a mammalian guanine nucleotide-exchange protein for ADP-ribosylation factors. J. Biol. Chem. 274: 17417–17423.
   PubMedGoogle Scholar
• Moss, J., and M. Vaughan. 1998. Molecules in the ARF orbit. J. Biol. Chem. 273: 21431–21434.
   PubMedGoogle Scholar
• Mossessova, E., J. M. Gulbis, and J. Goldberg. 1998. Structure of the guanine nucleotide exchange factor of the Sec7 domain of human Arno and analysis of the interaction with ARF GTPase. Cell 92: 415–423.
   PubMedGoogle Scholar
• Muhlrad, D., R. Hunter, and R. Parker. 1992. A rapid method for localized mutagenesis of yeast genes. Yeast 8: 79–82.
   PubMed Web of Science ®Google Scholar
• Novick, P., S. Ferro, and R. Schekman. 1981. Order of events in the yeast secretory pathway. Cell 25: 461–469.
   PubMedGoogle Scholar
• Peyroche, A., S. Paris, and C. L. Jackson. 1996. Nucleotide exchange on ARF mediated by yeast Geal protein. Nature 384: 479–481.
   PubMedGoogle Scholar
• Peyroche, A., B. Antonny, S. Robineau, J. Acker, J. Cherfils, and C. L. Jackson. 1999. Brefeldin A acts to stabilize an abortive ARF-GDP-Sec7 domain protein complex: involvement of specific residues of the Sec7 domain. Mol. Cell 3: 275–285.
   PubMed Web of Science ®Google Scholar
• Piper, R. C., A. A. Cooper, H. Yang, and T. H. Stevens. 1995. VPS27 controls vacuolar and endocytic traffic through a prevacuolar compartment in Saccharomyces cerevisiae. J. Cell Biol. 131: 603–617.
   PubMedGoogle Scholar
• Prescianotto-Baschong, C., and H. Riezman. 2002. Ordering of compartments in the yeast endocytic pathway. Traffic 3: 37–49.
   PubMedGoogle Scholar
• Rost, B., P. Fariselli, and R. Casadio. 1996. Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci. 5: 1704–1718.
   PubMed Web of Science ®Google Scholar
• Schandel, K. A., and D. D. Jenness. 1994. Direct evidence for ligand-induced internalization of the yeast a-factor pheromone receptor. Mol. Cell. Biol. 14: 7245–7255.
   PubMed Web of Science ®Google Scholar
• Schultz, J., R. R. Copley, T. Doerks, C. P. Ponting, and P. Bork. 2000. SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res. 28: 231–234.
   PubMed Web of Science ®Google Scholar
• Sharer, J. D., and R. A. Kahn. 1999. The ARF-like 2 (ARL2)-binding protein, BART. Purification, cloning, and initial characterization. J. Biol. Chem. 274: 27553–27561.
   PubMedGoogle Scholar
• Singer-Krüger, B., R. Frank, F. Crausaz, and H. Riezman. 1993. Partial purification and characterization of early and late endosomes from yeast. J. Biol. Chem. 268: 14376–14386.
   PubMedGoogle Scholar
• Singer-Krüger, B., H. Stenmark, A. Düsterhöft, P. Philippsen, J.-S. Yoo, D. Gallwitz, and M. Zerial. 1994. Role of three rab5-like GTPases, Ypt51p, Ypt52p, and Ypt53p, in the endocytic and vacuolar protein sorting pathways of yeast. J. Cell Biol. 125: 283–298.
   PubMed Web of Science ®Google Scholar
• Singer-Krüger, B., H. Stenmark, and M. Zerial. 1995. Yeast Ypt51p and mammalian Rab5: counterparts with similar function in the early endocytic pathway. J. Cell Sci. 108: 3509–3521.
   PubMed Web of Science ®Google Scholar
• Singer-Krüger, B., and S. Ferro-Novick. 1997. Use of a synthetic lethal screen to identify yeast mutants impaired in endocytosis, vacuolar protein sorting and the organization of the cytoskeleton. Eur. J. Cell Biol. 74: 365–375.
   PubMed Web of Science ®Google Scholar
• Sonnhammer, E. L., G. von Heijne, and A. Krogh. 1998. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6: 175–182.
   PubMedGoogle Scholar
• Stearns, T., R. A. Kahn, D. Botstein, and M. A. Hoyt. 1990. ADP ribosylation factor is an essential protein in Saccharomyces cerevisiae and is encoded by two genes. Mol. Cell. Biol. 10: 6690–6699.
   PubMed Web of Science ®Google Scholar
• Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673–4680.
   PubMed Web of Science ®Google Scholar
• Togawa, A., N. Morinaga, M. Ogasawara, J. Moss, and M. Vaughan. 1999. Purification and cloning of a brefeldin A-inhibited guanine nucleotide-exchange protein for ADP-ribosylation factors. J. Biol. Chem. 274: 12308–12315.
   PubMedGoogle Scholar
• Van Valkenburgh, H., J. F. Shern, J. D. Sharer, X. Zhu, and R. A. Kahn. 2001. ADP-ribosylation factors (ARFs) and ARF-like 1 (ARL1) have both specific and shared effectors: characterizing ARL1 binding proteins. J. Biol. Chem. 276: 22826–22837.
   PubMed Web of Science ®Google Scholar
• Vida, T. A., and S. D. Emr. 1995. A new vital stain for visualizing vacuolar membrane dynamics and endocytosis in yeast. J. Cell Biol. 128: 779–792.
   PubMed Web of Science ®Google Scholar
• Wach, A., A. Brachat, R. Pohlmann, and P. Philippsen. 1994. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10: 1793–1808.
   PubMed Web of Science ®Google Scholar
• Yahara, N., T. Ueda, K. Sato, and A. Nakano. 2001. Multiple roles of Arf1 GTPase in the yeast exocytic and endocytic pathways. Mol. Biol. Cell 12: 221–238.
   PubMedGoogle Scholar
• Zerial, M., and H. McBride. 2001. Rab proteins as membrane organizers. Nat. Rev. Mol. Cell Biol. 2: 107–117.
   PubMed Web of Science ®Google Scholar
• Zheng, Y., A. Bender, and R. A. Cerione. 1995. Interactions among proteins involved in bud-site selection and bud-site assembly in Saccharomyces cerevisiae. J. Biol. Chem. 270: 626–630.
   PubMedGoogle Scholar
• Zhu, X., A. L. Boman, J. Kuai, W. Cieplak, and R. A. Kahn. 2000. Effectors increase the affinity of ADP-ribosylation factor for GTP to increase binding. J. Biol. Chem. 275: 13465–13475.
   PubMedGoogle Scholar