The eisosome core is composed of BAR domain proteins

Molecular Biology of the Cell

Volumn 22, Issue 13, 2011, Pages 2360-2372

  Olivera Couto, Agustina ^a   Graña, Martin ^a   Harispe, Laura ^a   Aguilar, Pablo S ^a  

^a INSTITUT PASTEUR DE MONTEVIDEO   (Uruguay)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOPLASM PROTEIN; EISOSOME; PROTEIN BAR; PROTEIN LSP1; PROTEIN PIL1; PROTEIN SLM1; PROTEIN SLM2; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; CELL MEMBRANE; MEMBRANE BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; SACCHAROMYCES CEREVISIAE; SITE DIRECTED MUTAGENESIS; STRUCTURAL HOMOLOGY;

ANIMALS; CARRIER PROTEINS; CELL MEMBRANE; CERCOPITHECUS AETHIOPS; COMPUTATIONAL BIOLOGY; COS CELLS; CYTOPLASM; LIPOSOMES; MEMBRANE LIPIDS; MEMBRANE PROTEINS; MODELS, MOLECULAR; PHOSPHOPROTEINS; PROTEIN STRUCTURE, TERTIARY; RNA-BINDING PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

MAMMALIA; SACCHAROMYCES CEREVISIAE;

EID: 79959907600     PISSN: 10591524     EISSN: 19394586     Source Type: Journal    
DOI: 10.1091/mbc.E10-12-1021     Document Type: Article

References (61)

1. Abascal F, Zardoya R, Posada D (2005). ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21, 2104-2105. (Pubitemid 40668057)
2. Aguilar PS et al. (2010). A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking. Nat Struct Mol Biol 17, 901-908.
3. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402. (Pubitemid 27359211)
4. Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG (2008). Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 36, D419-D425. (Pubitemid 351149760)
5. Aronova S, Wedaman K, Aronov PA, Fontes K, Ramos K, Hammock BD, Powers T (2008). Regulation of ceramide biosynthesis by TOR complex 2. Cell Metab 7, 148-158.
6. Audhya A, Loewith R, Parsons AB, Gao L, Tabuchi M, Zhou H, Boone C, Hall MN, Emr SD (2004). Genome-wide lethality screen identifies new PI4,5P2 effectors that regulate the actin cytoskeleton. EMBO J 23, 3747-3757. (Pubitemid 39389706)
7. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001). Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 98, 10037-10041.
8. Berchtold D, Walther TC (2009). TORC2 plasma membrane localization is essential for cell viability and restricted to a distinct domain. Mol Biol Cell 20, 1565-1575.
9. Berman H, Henrick K, Nakamura H, Markley JL (2007). The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35, D301-303.
10. Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, Holstege FC, Weissman JS, Krogan NJ (2007). Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics 6, 439-450. (Pubitemid 46554539)
11. Davies RB (1987). Hypothesis testing when a nuisance parameter is present only under the alternative. Biometrika 74, 33-43.
12. Deng C, Xiong X, Krutchinsky AN (2009). Unifying fluorescence microscopy and mass spectrometry for studying protein complexes in cells. Mol Cell Proteomics 8, 1413-1423.
13. Emsley P, Cowtan K (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, 2126-2132. (Pubitemid 41742764)
14. Fadri M, Daquinag A, Wang S, Xue T, Kunz J (2005). The pleckstrin homology domain proteins Slm1 and Slm2 are required for actin cytoskeleton organization in yeast and bind phosphatidylinositol-4,5-bisphosphate and TORC2. Mol Biol Cell 16, 1883-1900. (Pubitemid 40471957)
15. Finn RD et al. (2010). The Pfam protein families database. Nucleic Acids Res 38, D211-D222.
16. Frohlich F, Moreira K, Aguilar PS, Hubner NC, Mann M, Walter P, Walther TC (2009). A genome-wide screen for genes affecting eisosomes reveals Nce102 function in sphingolipid signaling. J Cell Biol 185, 1227-1242.
17. Frost A, Perera R, Roux A, Spasov K, Destaing O, Egelman EH, De Camilli P, Unger VM (2008). Structural basis of membrane invagination by F-BAR domains. Cell 132, 807-817. (Pubitemid 351320580)
18. Frost A, Unger VM, De Camilli P (2009). The BAR domain superfamily: membrane-molding macromolecules. Cell 137, 191-196.
19. Grossmann G, Malinsky J, Stahlschmidt W, Loibl M, Weig-Meckl I, Frommer WB, Opekarova M, Tanner W (2008). Plasma membrane microdomains regulate turnover of transport proteins in yeast. J Cell Biol 183, 1075-1088.
20. Grossmann G, Opekarova M, Malinsky J, Weig-Meckl I, Tanner W (2007). Membrane potential governs lateral segregation of plasma membrane proteins and lipids in yeast. EMBO J 26, 1-8. (Pubitemid 46094694)
21. Guindon S, Gascuel O (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52, 696-704. (Pubitemid 37365050)
22. Ho Y et al. (2002). Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183. (Pubitemid 34059520)
23. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y (2001). A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 98, 4569-4574. (Pubitemid 32295017)
24. Itoh T, Erdmann KS, Roux A, Habermann B, Werner H, De Camilli P (2005). Dynamin and the actin cytoskeleton cooperatively regulate plasma membrane invagination by BAR and F-BAR proteins. Dev Cell 9, 791-804. (Pubitemid 41724107)
25. Johannes L, Mayor S (2010). Induced domain formation in endocytic invagination, lipid sorting, and scission. Cell 142, 507-510.
26. Jones DT, Taylor WR, Thornton JM (1992). The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8, 275-282.
27. Krogan NJ et al. (2006). Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643.
28. Lee E, Marcucci M, Daniell L, Pypaert M, Weisz OA, Ochoa GC, Farsad K, Wenk MR, De Camilli P (2002). Amphiphysin 2 (Bin1) and T-tubule biogenesis in muscle. Science 297, 1193-1196. (Pubitemid 36193356)
29. Lingwood D, Simons K (2010). Lipid rafts as a membrane-organizing principle. Science 327, 46-50.
30. Longtine MS, McKenzie A 3rd, Demarini DJ, Shah NG, Wach A, Brachat A, Philippsen P, Pringle JR (1998). Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14, 953-961. (Pubitemid 28328001)
31. Luo G, Gruhler A, Liu Y, Jensen ON, Dickson RC (2008). The sphingolipid long-chain base-Pkh1/2-Ypk1/2 signaling pathway regulates eisosome assembly and turnover. J Biol Chem 283, 10433-10444.
32. Malinska K, Malinsky J, Opekarova M, Tanner W (2003). Visualization of protein compartmentation within the plasma membrane of living yeast cells. Mol Biol Cell 14, 4427-4436. (Pubitemid 37444645)
33. Mann HB, Whitney DR (1947). On a test of whether one of two random variables is stochastically larger than the other. Ann Math Stat 18, 50-60.
34. Marchler-Bauer A et al. (2007). CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res 35, D237-D240. (Pubitemid 46056206)
35. Markin VS (1981). Lateral organization of membranes and cell shapes. Biophys J 36, 1-19.
36. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A (2000). Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29, 291-325. (Pubitemid 30599596)
37. Masuda M, Mochizuki N (2010). Structural characteristics of BAR domain superfamily to sculpt the membrane. Semin Cell Dev Biol 21, 391-398.
38. Moreira KE, Walther TC, Aguilar PS, Walter P (2009). Pil1 controls eisosome biogenesis. Mol Biol Cell 20, 809-818.
39. Munro S (2003). Lipid rafts: elusive or illusive? Cell 115, 377-388.
40. Notredame C, Higgins DG, Heringa J (2000). T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302, 205-217.
41. Pandit SB, Gosar D, Abhiman S, Sujatha S, Dixit SS, Mhatre NS, Sowdhamini R, Srinivasan N (2002). SUPFAM - a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes. Nucleic Acids Res 30, 289-293. (Pubitemid 34679566)
42. Peter BJ, Kent HM, Mills IG, Vallis Y, Butler PJ, Evans PR, McMahon HT (2004). BAR domains as sensors of membrane curvature: the amphiphysin BAR structure. Science 303, 495-499. (Pubitemid 38120842)
43. Phair RD, Gorski SA, Misteli T (2004). Measurement of dynamic protein binding to chromatin in vivo, using photobleaching microscopy. Methods Enzymol 375, 393-414. (Pubitemid 38124881)
44. Poveda JA, Fernandez AM, Encinar JA, Gonzalez-Ros JM (2008). Protein-promoted membrane domains. Biochim Biophys Acta 1778, 1583-1590.
45. Roux A, Cuvelier D, Nassoy P, Prost J, Bassereau P, Goud B (2005). Role of curvature and phase transition in lipid sorting and fission of membrane tubules. EMBO J 24, 1537-1545. (Pubitemid 40646444)
46. Russell RB, Barton GJ (1992). Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins 14, 309-323.
47. Sadreyev RI, Baker D, Grishin NV (2003). Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein Sci 12, 2262-2272.
48. Sircar A, Chaudhury S, Kilambi KP, Berrondo M, Gray JJ (2010). A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19. Proteins 78, 3115-3123.
49. Soding J (2005). Protein homology detection by HMM-HMM comparison. Bioinformatics 21, 951-960.
50. Stimpson HE, Toret CP, Cheng AT, Pauly BS, Drubin DG (2009). Early-arriving Syp1p and Ede1p function in endocytic site placement and formation in budding yeast. Mol Biol Cell 20, 4640-4651.
51. Stradalova V, Stahlschmidt W, Grossmann G, Blazikova M, Rachel R, Tanner W, Malinsky J (2009). Furrow-like invaginations of the yeast plasma membrane correspond to membrane compartment of Can1. J Cell Sci 122, 2887-2894.
52. Tabuchi M, Audhya A, Parsons AB, Boone C, Emr SD (2006). The phosphatidylinositol 4,5-biphosphate and TORC2 binding proteins Slm1 and Slm2 function in sphingolipid regulation. Mol Cell Biol 26, 5861-5875. (Pubitemid 44134340)
53. Takei K, Slepnev VI, Haucke V, De Camilli P (1999). Functional partnership between amphiphysin and dynamin in clathrin-mediated endocytosis. Nat Cell Biol 1, 33-39. (Pubitemid 129495007)
54. Tanos B, Rodriguez-Boulan E (2008). The epithelial polarity program: machineries involved and their hijacking by cancer. Oncogene 27, 6939-6957.
55. Walther TC, Aguilar PS, Frohlich F, Chu F, Moreira K, Burlingame AL, Walter P (2007). Pkh-kinases control eisosome assembly and organization. EMBO J 26, 4946-4955. (Pubitemid 350261294)
56. Walther TC, Brickner JH, Aguilar PS, Bernales S, Pantoja C, Walter P (2006). Eisosomes mark static sites of endocytosis. Nature 439, 998-1003. (Pubitemid 43292420)
57. Youn JY et al. (2010). Dissecting BAR domain function in the yeast amphiphysins Rvs161 and Rvs167 during endocytosis. Mol Biol Cell 21, 3054-3069.
58. Young ME, Karpova TS, Brugger B, Moschenross DM, Wang GK, Schneiter R, Wieland FT, Cooper JA (2002). The Sur7p family defines novel cortical domains in Saccharomyces cerevisiae, affects sphingolipid metabolism, and is involved in sporulation. Mol Cell Biol 22, 927-934. (Pubitemid 34053069)
59. Yu H et al. (2008). High-quality binary protein interaction map of the yeast interactome network. Science 322, 104-110.
60. Yu JW, Mendrola JM, Audhya A, Singh S, Keleti D, DeWald DB, Murray D, Emr SD, Lemmon MA (2004). Genome-wide analysis of membrane targeting by S. cerevisiae pleckstrin homology domains. Mol Cell 13, 677-688. (Pubitemid 38368125)
61. Zhang X, Lester RL, Dickson RC (2004). Pil1p and Lsp1p negatively regulate the 3-phosphoinositide-dependent protein kinase-like kinase Pkh1p and downstream signaling pathways Pkc1p and Ypk1p. J Biol Chem 279, 22030-22038. (Pubitemid 38679394)