Intracellular Parcel Service: Current Issues in Intracellular Membrane Trafficking

  • Johannes M. Herrmann
  • Anne Spang
Part of the Methods in Molecular Biology book series (MIMB, volume 1270)


Eukaryotic cells contain a multitude of membrane structures that are connected through a highly dynamic and complex exchange of their constituents. The vibrant instability of these structures challenges the classical view of defined, static compartments that are connected by different types of vesicles. Despite this astonishing complexity, proteins and lipids are accurately transported into the different intracellular membrane systems. Over the past few decades many factors have been identified that either mediate or regulate intracellular membrane trafficking. Like in a modern parcel sorting system of a logistics center, the cargo typically passes through several sequential sorting stations until it finally reaches the location that is specified by its individual address label. While each membrane system employs specific sets of factors, the transport processes typically operate on common principles. With the advent of genome- and proteome-wide screens, the availability of mutant collections, exciting new developments in microscope technology and sophisticated methods to study their dynamics, the future promises a broad and comprehensive picture of the processes by which eukaryotic cells sort their proteins.

Key words

Membrane trafficking Protein sorting Protein translocation Vesicular transport 


  1. 1.
    Palade G (1975) Intracellular aspects of the process of protein synthesis. Science 189:347–358CrossRefPubMedGoogle Scholar
  2. 2.
    Novikoff PM, Novikoff AB, Quintana N, Hauw JJ (1971) Golgi apparatus, GERL, and lysosomes of neurons in rat dorsal root ganglia, studied by thick section and thin section cytochemistry. J Cell Biol 50:859–886CrossRefPubMedCentralPubMedGoogle Scholar
  3. 3.
    Sengupta P, Van Engelenburg S, Lippincott-Schwartz J (2012) Visualizing cell structure and function with point-localization superresolution imaging. Dev Cell 23:1092–1102CrossRefPubMedCentralPubMedGoogle Scholar
  4. 4.
    Leis A, Rockel B, Andrees L, Baumeister W (2009) Visualizing cells at the nanoscale. Trends Biochem Sci 34:60–70CrossRefPubMedGoogle Scholar
  5. 5.
    Wickner W, Schekman R (2005) Protein translocation across biological membranes. Science 310:1452–1456CrossRefPubMedGoogle Scholar
  6. 6.
    Schatz G, Dobberstein B (1996) Common principles of protein translocation across membranes. Science 271:1519–1526CrossRefPubMedGoogle Scholar
  7. 7.
    Saito K, Chen M, Bard F, Chen S, Zhou H, Woodley D, Polischuk R, Schekman R, Malhotra V (2009) TANGO1 facilitates cargo loading at endoplasmic reticulum exit sites. Cell 136:891–902CrossRefPubMedGoogle Scholar
  8. 8.
    Kurokawa K, Okamoto M, Nakano A (2014) Contact of cis-Golgi with ER exit sites executes cargo capture and delivery from the ER. Nat Commun 5:3653CrossRefPubMedCentralPubMedGoogle Scholar
  9. 9.
    Dancourt J, Barlowe C (2010) Protein sorting receptors in the early secretory pathway. Annu Rev Biochem 79:777–802CrossRefPubMedGoogle Scholar
  10. 10.
    van der Zand A, Gent J, Braakman I, Tabak HF (2012) Biochemically distinct vesicles from the endoplasmic reticulum fuse to form peroxisomes. Cell 149:397–409CrossRefPubMedGoogle Scholar
  11. 11.
    Walter P, Gilmore R, Blobel G (1984) Protein translocation across the endoplasmic reticulum. Cell 38:5–8CrossRefPubMedGoogle Scholar
  12. 12.
    Wild K, Halic M, Sinning I, Beckmann R (2004) SRP meets the ribosome. Nat Struct Mol Biol 11:1049–1053CrossRefPubMedGoogle Scholar
  13. 13.
    Johnson AE, van Waes MA (1999) The translocon: a dynamic gateway at the ER membrane. Annu Rev Cell Dev Biol 15:799–842CrossRefPubMedGoogle Scholar
  14. 14.
    von Heijne G (1990) Protein targeting signals. Curr Opin Cell Biol 2:604–608CrossRefGoogle Scholar
  15. 15.
    Oh E, Becker AH, Sandikci A, Huber D, Chaba R, Gloge F, Nichols RJ, Typas A, Gross CA, Kramer G, Weissman JS, Bukau B (2011) Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell 147:1295–1308CrossRefPubMedCentralPubMedGoogle Scholar
  16. 16.
    Reid DW, Nicchitta CV (2012) Primary role for endoplasmic reticulum-bound ribosomes in cellular translation identified by ribosome profiling. J Biol Chem 287:5518–5527CrossRefPubMedCentralPubMedGoogle Scholar
  17. 17.
    Zhang D, Sweredoski MJ, Graham RL, Hess S, Shan SO (2012) Novel proteomic tools reveal essential roles of SRP and importance of proper membrane protein biogenesis. Mol Cell Proteomics 11(M111):011585PubMedGoogle Scholar
  18. 18.
    Willmund F, del Alamo M, Pechmann S, Chen T, Albanese V, Dammer EB, Peng J, Frydman J (2013) The cotranslational function of ribosome-associated Hsp70 in eukaryotic protein homeostasis. Cell 152:196–209CrossRefPubMedCentralPubMedGoogle Scholar
  19. 19.
    Sheffield WP, Shore GC, Randall SK (1990) Mitochondrial precursor protein. Effects of 70-kD heat shock protein on polypeptide folding, aggregation, and import competence. J Biol Chem 265:11069–11076PubMedGoogle Scholar
  20. 20.
    Brodsky JL, Hamamoto S, Feldheim D, Schekman R (1993) Reconstitution of protein translocation from solubilized yeast membranes reveals topologically distinct roles for BiP and cytosolic Hsc70. J Cell Biol 120:95–102CrossRefPubMedGoogle Scholar
  21. 21.
    Young JC, Hoogenraad NJ, Hartl FU (2003) Molecular chaperones Hsp90 and Hsp70 deliver preproteins to the mitochondrial import receptor Tom70. Cell 112:41–50CrossRefPubMedGoogle Scholar
  22. 22.
    Kikuchi S, Bedard J, Hirano M, Hirabayashi Y, Oishi M, Imai M, Takase M, Ide T, Nakai M (2013) Uncovering the protein translocon at the chloroplast inner envelope membrane. Science 339:571–574CrossRefPubMedGoogle Scholar
  23. 23.
    Kikuchi S, Oishi M, Hirabayashi Y, Lee DW, Hwang I, Nakai M (2009) A 1-megadalton translocation complex containing Tic20 and Tic21 mediates chloroplast protein import at the inner envelope membrane. Plant Cell 21:1781–1797CrossRefPubMedCentralPubMedGoogle Scholar
  24. 24.
    Schliebs W, Girzalsky W, Erdmann R (2010) Peroxisomal protein import and ERAD: variations on a common theme. Nat Rev Mol Cell Biol 11:885–890CrossRefPubMedGoogle Scholar
  25. 25.
    Bonifacino JS, Glick BS (2004) The mechanisms of vesicle budding and fusion. Cell 116:153–166CrossRefPubMedGoogle Scholar
  26. 26.
    Fromme JC, Schekman R (2005) COPII-coated vesicles: flexible enough for large cargo? Curr Opin Cell Biol 17:345–352CrossRefPubMedGoogle Scholar
  27. 27.
    Lippincott-Schwartz J, Liu W (2006) Insights into COPI coat assembly and function in living cells. Trends Cell Biol 16:e1–e4CrossRefPubMedGoogle Scholar
  28. 28.
    Spang A (2004) Vesicle transport: a close collaboration of Rabs and effectors. Curr Biol 14:R33–R34CrossRefPubMedGoogle Scholar
  29. 29.
    Henry AG, Hislop JN, Grove J, Thorn K, Marsh M, von Zastrow M (2012) Regulation of endocytic clathrin dynamics by cargo ubiquitination. Dev Cell 23:519–532CrossRefPubMedCentralPubMedGoogle Scholar
  30. 30.
    Zanetti G, Prinz S, Daum S, Meister A, Schekman R, Bacia K, Briggs JA (2013) The structure of the COPII transport-vesicle coat assembled on membranes. Elife 2:e00951CrossRefPubMedCentralPubMedGoogle Scholar
  31. 31.
    Duran JM, Campelo F, van Galen J, Sachsenheimer T, Sot J, Egorov MV, Rentero C, Enrich C, Polishchuk RS, Goni FM, Brugger B, Wieland F, Malhotra V (2012) Sphingomyelin organization is required for vesicle biogenesis at the Golgi complex. EMBO J 31:4535–4546CrossRefPubMedCentralPubMedGoogle Scholar
  32. 32.
    Faini M, Prinz S, Beck R, Schorb M, Riches JD, Bacia K, Brugger B, Wieland FT, Briggs JA (2012) The structures of COPI-coated vesicles reveal alternate coatomer conformations and interactions. Science 336:1451–1454CrossRefPubMedGoogle Scholar
  33. 33.
    Contreras FX, Ernst AM, Haberkant P, Bjorkholm P, Lindahl E, Gonen B, Tischer C, Elofsson A, von Heijne G, Thiele C, Pepperkok R, Wieland F, Brugger B (2012) Molecular recognition of a single sphingolipid species by a protein’s transmembrane domain. Nature 481:525–529Google Scholar
  34. 34.
    Farsad K, Ringstad N, Takei K, Floyd SR, Rose K, De Camilli P (2001) Generation of high curvature membranes mediated by direct endophilin bilayer interactions. J Cell Biol 155:193–200CrossRefPubMedCentralPubMedGoogle Scholar
  35. 35.
    Matsuoka K, Orci L, Amherdt M, Bednarek SY, Hamamoto S, Schekman R, Yeung T (1998) COPII-coated vesicle formation reconstituted with purified coat proteins and chemically defined liposomes. Cell 93:263–275CrossRefPubMedGoogle Scholar
  36. 36.
    Spang A, Matsuoka K, Hamamoto S, Schekman R, Orci L (1998) Coatomer, Arf1p, and nucleotide are required to bud coat protein complex I-coated vesicles from large synthetic liposomes. Proc Natl Acad Sci U S A 95:11199–11204CrossRefPubMedCentralPubMedGoogle Scholar
  37. 37.
    Bremser M, Nickel W, Schweikert M, Ravazzola M, Amherdt M, Hughes CA, Sollner TH, Rothman JE, Wieland FT (1999) Coupling of coat assembly and vesicle budding to packaging of putative cargo receptors. Cell 96:495–506CrossRefPubMedGoogle Scholar
  38. 38.
    Takei K, Haucke V, Slepnev V, Farsad K, Salazar M, Chen H, De Camilli P (1998) Generation of coated intermediates of clathrin-mediated endocytosis on protein-free liposomes. Cell 94:131–141CrossRefPubMedGoogle Scholar
  39. 39.
    Daumke O, Roux A, Haucke V (2014) BAR domain scaffolds in dynamin-mediated membrane fission. Cell 156:882–892CrossRefPubMedGoogle Scholar
  40. 40.
    Shnyrova AV, Bashkirov PV, Akimov SA, Pucadyil TJ, Zimmerberg J, Schmid SL, Frolov VA (2013) Geometric catalysis of membrane fission driven by flexible dynamin rings. Science 339:1433–1436CrossRefPubMedCentralPubMedGoogle Scholar
  41. 41.
    Hinshaw JE (2000) Dynamin and its role in membrane fission. Annu Rev Cell Dev Biol 16:483–519CrossRefPubMedGoogle Scholar
  42. 42.
    Roux A, Uyhazi K, Frost A, De Camilli P (2006) GTP-dependent twisting of dynamin implicates constriction and tension in membrane fission. Nature 441:528–531CrossRefPubMedGoogle Scholar
  43. 43.
    Antonny B, Bigay J, Casella JF, Drin G, Mesmin B, Gounon P (2005) Membrane curvature and the control of GTP hydrolysis in Arf1 during COPI vesicle formation. Biochem Soc Trans 33:619–622CrossRefPubMedGoogle Scholar
  44. 44.
    Spang A (2002) ARF1 regulatory factors and COPI vesicle formation. Curr Opin Cell Biol 14:423–427CrossRefPubMedGoogle Scholar
  45. 45.
    Tanigawa G, Orci L, Amherdt M, Ravazzola M, Helms JB, Rothman JE (1993) Hydrolysis of bound GTP by ARF protein triggers uncoating of Golgi-derived COP-coated vesicles. J Cell Biol 123:1365–1371CrossRefPubMedGoogle Scholar
  46. 46.
    Kirchhausen T (2000) Three ways to make a vesicle. Nat Rev Mol Cell Biol 1:187–198CrossRefPubMedGoogle Scholar
  47. 47.
    Salama NR, Schekman RW (1995) The role of coat proteins in the biosynthesis of secretory proteins. Curr Opin Cell Biol 7:536–543CrossRefPubMedGoogle Scholar
  48. 48.
    Andag U, Neumann T, Schmitt HD (2001) The coatomer-interacting protein Dsl1p is required for Golgi-to-endoplasmic reticulum retrieval in yeast. J Biol Chem 276:39150–39160CrossRefPubMedGoogle Scholar
  49. 49.
    Behnia R, Barr FA, Flanagan JJ, Barlowe C, Munro S (2007) The yeast orthologue of GRASP65 forms a complex with a coiled-coil protein that contributes to ER to Golgi traffic. J Cell Biol 176:255–261CrossRefPubMedCentralPubMedGoogle Scholar
  50. 50.
    Diefenbacher M, Thorsteinsdottir H, Spang A (2011) The Dsl1 tethering complex actively participates in soluble NSF (N-ethylmaleimide-sensitive factor) attachment protein receptor (SNARE) complex assembly at the endoplasmic reticulum in Saccharomyces cerevisiae. J Biol Chem 286:25027–25038CrossRefPubMedCentralPubMedGoogle Scholar
  51. 51.
    Cai H, Yu S, Menon S, Cai Y, Lazarova D, Fu C, Reinisch K, Hay JC, Ferro-Novick S (2007) TRAPPI tethers COPII vesicles by binding the coat subunit Sec23. Nature 445:941–944CrossRefPubMedGoogle Scholar
  52. 52.
    Söllner T, Whiteheart SW, Brunner M, Erdjument-Bromage H, Geromanos S, Tempst P, Rothman JE (1993) SNAP receptors implicated in vesicle targeting and fusion. Nature 362:318–324CrossRefPubMedGoogle Scholar
  53. 53.
    Sollner T, Bennett MK, Whiteheart SW, Scheller RH, Rothman JE (1993) A protein assembly-disassembly pathway in vitro that may correspond to sequential steps of synaptic vesicle docking, activation, and fusion. Cell 75:409–418Google Scholar
  54. 54.
    Jahn R, Scheller RH (2006) SNAREs–engines for membrane fusion. Nat Rev Mol Cell Biol 7:631–643CrossRefPubMedGoogle Scholar
  55. 55.
    Sudhof TC (2004) The synaptic vesicle cycle. Annu Rev Neurosci 27:509–547CrossRefPubMedGoogle Scholar
  56. 56.
    Singh P, Jorgacevski J, Kreft M, Grubisic V, Stout RF Jr, Potokar M, Parpura V, Zorec R (2014) Single-vesicle architecture of synaptobrevin2 in astrocytes. Nat Commun 5:3780PubMedGoogle Scholar
  57. 57.
    Min D, Kim K, Hyeon C, Cho YH, Shin YK, Yoon TY (2013) Mechanical unzipping and rezipping of a single SNARE complex reveals hysteresis as a force-generating mechanism. Nat Commun 4:1705CrossRefPubMedCentralPubMedGoogle Scholar
  58. 58.
    Weber T, Zemelman BV, McNew JA, Westermann B, Gmachl M, Parlati F, Söllner TH, Rothman JE (1998) SNAREpins: minimal machinery for membrane fusion. Cell 92:759–772CrossRefPubMedGoogle Scholar
  59. 59.
    Witte K, Schuh AL, Hegermann J, Sarkeshik A, Mayers JR, Schwarze K, Yates JR 3rd, Eimer S, Audhya A (2011) TFG-1 function in protein secretion and oncogenesis. Nat Cell Biol 13:550–558CrossRefPubMedCentralPubMedGoogle Scholar
  60. 60.
    Bevis BJ, Hammond AT, Reinke CA, Glick BS (2002) De novo formation of transitional ER sites and Golgi structures in Pichia pastoris. Nat Cell Biol 4:750–756CrossRefPubMedGoogle Scholar
  61. 61.
    Kondylis V, Rabouille C (2003) A novel role for dp115 in the organization of tER sites in Drosophila. J Cell Biol 162:185–198CrossRefPubMedCentralPubMedGoogle Scholar
  62. 62.
    Miller EA, Beilharz TH, Malkus PN, Lee MC, Hamamoto S, Orci L, Schekman R (2003) Multiple cargo binding sites on the COPII subunit Sec24p ensure capture of diverse membrane proteins into transport vesicles. Cell 114:497–509CrossRefPubMedGoogle Scholar
  63. 63.
    Rein U, Andag U, Duden R, Schmitt HD, Spang A (2002) ARF-GAP-mediated interaction between the ER-Golgi v-SNAREs and the COPI coat. J Cell Biol 157:395–404CrossRefPubMedCentralPubMedGoogle Scholar
  64. 64.
    Springer S, Spang A, Schekman R (1999) A primer on vesicle budding. Cell 97:145–148CrossRefPubMedGoogle Scholar
  65. 65.
    Seeley ES, Kato M, Margolis N, Wickner W, Eitzen G (2002) Genomic analysis of homotypic vacuole fusion. Mol Biol Cell 13:782–794CrossRefPubMedCentralPubMedGoogle Scholar
  66. 66.
    Sickmann A, Reinders J, Wagner Y, Joppich C, Zahedi R, Meyer HE, Schonfisch B, Perschil I, Chacinska A, Guiard B, Rehling P, Pfanner N, Meisinger C (2003) The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci U S A 100:13207–13212CrossRefPubMedCentralPubMedGoogle Scholar
  67. 67.
    Vögtle FN, Wortelkamp S, Zahedi RP, Becker D, Leidhold C, Gevaert K, Kellermann J, Voos W, Sickmann A, Pfanner N, Meisinger C (2009) Global analysis of the mitochondrial N-proteome identifies a processing peptidase critical for protein stability. Cell 139:428–439CrossRefPubMedGoogle Scholar
  68. 68.
    Vögtle FN, Burkhart JM, Rao S, Gerbeth C, Hinrichs J, Martinou JC, Chacinska A, Sickmann A, Zahedi RP, Meisinger C (2012) Intermembrane space proteome of yeast mitochondria. Mol Cell Proteomics 11:1840–1852CrossRefPubMedCentralPubMedGoogle Scholar
  69. 69.
    Andersen JS, Mann M (2006) Organellar proteomics: turning inventories into insights. EMBO Rep 7:874–879CrossRefPubMedCentralPubMedGoogle Scholar
  70. 70.
    Eisenstein M (2006) Exploring how the organelles are organized. Nat Methods 3:420–421Google Scholar
  71. 71.
    Simpson JC, Pepperkok R (2006) The subcellular localization of the mammalian proteome comes a fraction closer. Genome Biol 7:222CrossRefPubMedCentralPubMedGoogle Scholar
  72. 72.
    Yates JR 3rd, Gilchrist A, Howell KE, Bergeron JJ (2005) Proteomics of organelles and large cellular structures. Nat Rev Mol Cell Biol 6:702–714CrossRefPubMedGoogle Scholar
  73. 73.
    Millar AH, Whelan J, Small I (2006) Recent surprises in protein targeting to mitochondria and plastids. Curr Opin Plant Biol 9:610–615CrossRefPubMedGoogle Scholar
  74. 74.
    Rhee HW, Zou P, Udeshi ND, Martell JD, Mootha VK, Carr SA, Ting AY (2013) Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. Science 339:1328–1331CrossRefPubMedCentralPubMedGoogle Scholar
  75. 75.
    Pagliarini DJ, Calvo SE, Chang B, Sheth SA, Vafai SB, Ong SE, Walford GA, Sugiana C, Boneh A, Chen WK, Hill DE, Vidal M, Evans JG, Thorburn DR, Carr SA, Mootha VK (2008) A mitochondrial protein compendium elucidates complex I disease biology. Cell 134:112–123CrossRefPubMedCentralPubMedGoogle Scholar
  76. 76.
    Mootha VK, Bunkenborg J, Olsen JV, Hjerrild M, Wisniewski JR, Stahl E, Bolouri MS, Ray HN, Sihag S, Kamal M, Patterson N, Lander ES, Mann M (2003) Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 115:629–640CrossRefPubMedGoogle Scholar
  77. 77.
    Van den Berg B, Clemons WM Jr, Collinson I, Modis Y, Hartmann E, Harrison SC, Rapoport TA (2004) X-ray structure of a protein-conducting channel. Nature 427:36–44CrossRefPubMedGoogle Scholar
  78. 78.
    Gogala M, Becker T, Beatrix B, Armache JP, Barrio-Garcia C, Berninghausen O, Beckmann R (2014) Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion. Nature 506:107–110CrossRefPubMedGoogle Scholar
  79. 79.
    Brandt F, Carlson LA, Hartl FU, Baumeister W, Grunewald K (2010) The three-dimensional organization of polyribosomes in intact human cells. Mol Cell 39:560–569CrossRefPubMedGoogle Scholar
  80. 80.
    Pfeffer S, Dudek J, Gogala M, Schorr S, Linxweiler J, Lang S, Becker T, Beckmann R, Zimmermann R, Forster F (2014) Structure of the mammalian oligosaccharyl-transferase complex in the native ER protein translocon. Nat Commun 5:3072CrossRefPubMedGoogle Scholar
  81. 81.
    Stagg SM, Gurkan C, Fowler DM, LaPointe P, Foss TR, Potter CS, Carragher B, Balch WE (2006) Structure of the Sec13/31 COPII coat cage. Nature 439:234–238CrossRefPubMedGoogle Scholar
  82. 82.
    Bi X, Corpina RA, Goldberg J (2002) Structure of the Sec23/24-Sar1 pre-budding complex of the COPII vesicle coat. Nature 419:271–277CrossRefPubMedGoogle Scholar
  83. 83.
    Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelsen TS, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F (2014) Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343:84–87CrossRefPubMedCentralPubMedGoogle Scholar
  84. 84.
    Wang T, Wei JJ, Sabatini DM, Lander ES (2014) Genetic screens in human cells using the CRISPR-Cas9 system. Science 343:80–84CrossRefPubMedCentralPubMedGoogle Scholar
  85. 85.
    Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152:1173–1183CrossRefPubMedCentralPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Cell BiologyUniversity of KaiserslauternKaiserslauternGermany
  2. 2.Growth & Development, BiozentrumUniversity of BaselBaselSwitzerland

Personalised recommendations