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Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers
  1. 1.

    Takamori, S. et al. Molecular anatomy of a trafficking organelle. Cell 127, 831–846 (2006).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  2. 2.

    Yu, I. M. & Hughson, F. M. Tethering factors as organizers of intracellular vesicular traffic. Annu. Rev. Cell Dev. Biol. 26, 137–156 (2010).

    CAS  Article  Google Scholar 

  3. 3.

    Gillingham, A. K. & Munro, S. Transport carrier tethering—how vesicles are captured by organelles. Curr. Opin. Cell Biol. 59, 140–146 (2019).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  4. 4.

    Witkos, T. M. & Lowe, M. Recognition and tethering of transport vesicles at the Golgi apparatus. Curr. Opin. Cell Biol. 47, 16–23 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  5. 5.

    Witkos, T. M. & Lowe, M. The golgin family of coiled-coil tethering proteins. Front Cell Dev. Biol. 3, 86 (2015).

    PubMed  PubMed Central  Google Scholar 

  6. 6.

    Muschalik, N. & Munro, S. Golgins. Curr. Biol. 28, R374–R376 (2018).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  7. 7.

    Gillingham, A. K. & Munro, S. Finding the Golgi: golgin coiled-coil proteins show the way. Trends Cell Biol. 26, 399–408 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  8. 8.

    Pfeffer, S. R. Entry at the trans-face of the Golgi. Cold Spring Harb. Perspect. Biol. 3, a005272 (2011).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  9. 9.

    Goud, B. & Gleeson, P. A. TGN golgins, Rabs and cytoskeleton: regulating the Golgi trafficking highways. Trends Cell Biol. 20, 329–336 (2010).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  10. 10.

    Lowe, M. The physiological functions of the golgin vesicle tethering proteins. Front Cell Dev. Biol. 7, 94 (2019).

    ADS  PubMed  PubMed Central  Article  Google Scholar 

  11. 11.

    Wong, M. & Munro, S. Membrane trafficking. The specificity of vesicle traffic to the Golgi is encoded in the golgin coiled-coil proteins. Science 346, 1256898 (2014).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  12. 12.

    Gillingham, A. K., Bertram, J., Begum, F. & Munro, S. In vivo identification of GTPase interactors by mitochondrial relocalization and proximity biotinylation. eLife 8, e45916 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  13. 13.

    Wong, M., Gillingham, A. K. & Munro, S. The golgin coiled-coil proteins capture different types of transport carriers via distinct N-terminal motifs. BMC Biol. 15, 3 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  14. 14.

    Shin, J. J. H., Gillingham, A. K., Begum, F., Chadwick, J. & Munro, S. TBC1D23 is a bridging factor for endosomal vesicle capture by golgins at the trans-Golgi. Nat. Cell Biol. 19, 1424–1432 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  15. 15.

    Navarro Negredo, P., Edgar, J. R., Manna, P. T., Antrobus, R. & Robinson, M. S. The WDR11 complex facilitates the tethering of AP-1-derived vesicles. Nat. Commun. 9, 596 (2018).

    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

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    Borner, G. H. et al. Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein-protein interactions. Mol. Biol. Cell 25, 3178–3194 (2014).

    PubMed  PubMed Central  Article  Google Scholar 

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    McNally, K. E. & Cullen, P. J. Endosomal retrieval of cargo: retromer Is not alone. Trends Cell Biol. 28, 807–822 (2018).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

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    Wang, J. et al. Endosomal receptor trafficking: retromer and beyond. Traffic 19, 578–590 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

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    Cullen, P. J. & Steinberg, F. To degrade or not to degrade: mechanisms and significance of endocytic recycling. Nat. Rev. Mol. Cell Biol. 19, 679–696 (2018).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

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    Christoforou, A., Arias, A. M. & Lilley, K. S. Determining protein subcellular localization in mammalian cell culture with biochemical fractionation and iTRAQ 8-plex quantification. Methods Mol. Biol. 1156, 157–174 (2014).

    CAS  PubMed  Article  Google Scholar 

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    Itzhak, D. N. et al. A mass spectrometry-based approach for mapping protein subcellular localization reveals the spatial proteome of mouse primary neurons. Cell Rep. 20, 2706–2718 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

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    Itzhak, D. N., Tyanova, S., Cox, J. & Borner, G. H. Global, quantitative and dynamic mapping of protein subcellular localization. eLife 5, e16590 (2016).

    Article  CAS  Google Scholar 

  23. 23.

    Geladaki, A. et al. Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics. Nat. Commun. 10, 331 (2019).

    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

  24. 24.

    Trotter, M. W., Sadowski, P. G., Dunkley, T. P., Groen, A. J. & Lilley, K. S. Improved sub-cellular resolution via simultaneous analysis of organelle proteomics data across varied experimental conditions. Proteomics 10, 4213–4219 (2010).

    CAS  PubMed  Article  Google Scholar 

  25. 25.

    Crook, O. M., Mulvey, C. M., Kirk, P. D. W., Lilley, K. S. & Gatto, L. A Bayesian mixture modelling approach for spatial proteomics. PLoS Comput. Biol. 14, e1006516 (2018).

    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

  26. 26.

    Crook, O. M., Smith, T., Elzek, M. & Lilley, K. S. Moving profiling spatial proteomics beyond discrete classification. Proteomics e1900392 (2020).

  27. 27.

    Crook, O. M., Lilley, K. S., Gatto, L. & Kirk, P. D. W. Semi-supervised non-parametric Bayesian modelling of spatial proteomics. Preprint at https://arxiv.org/abs/1903.02909 (2020).

  28. 28.

    Crook, O. M. et al. A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection. PLoS Comput. Biol. 16, e1008288 (2020).

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    Christoforou, A. et al. A draft map of the mouse pluripotent stem cell spatial proteome. Nat. Commun. 7, 8992 (2016).

    PubMed  Article  CAS  Google Scholar 

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    Thomas, G. Furin at the cutting edge: from protein traffic to embryogenesis and disease. Nat. Rev. Mol. Cell Biol. 3, 753–766 (2002).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

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    Judith, D. et al. ATG9A shapes the forming autophagosome through Arfaptin 2 and phosphatidylinositol 4-kinase IIIbeta. J. Cell Biol. 218, 1634–1652 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

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    Naslavsky, N. & Caplan, S. The enigmatic endosome—sorting the ins and outs of endocytic trafficking. J. Cell Sci. 131, jcs216499 (2018).

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    Hierro, A., Gershlick, D. C., Rojas, A. L. & Bonifacino, J. S. Formation of tubulovesicular carriers from endosomes and their fusion to the trans-Golgi network. Int. Rev. Cell Mol. Biol. 318, 159–202 (2015).

    CAS  PubMed  Article  Google Scholar 

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    Hirst, J. et al. Distinct and overlapping roles for AP-1 and GGAs revealed by the “knocksideways” system. Curr. Biol. 22, 1711–1716 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

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    CAS  PubMed  PubMed Central  Article  Google Scholar 

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    Navarro Negredo, P. et al. Contribution of the clathrin adaptor AP-1 subunit μ1 to acidic cluster protein sorting. J. Cell Biol. 216, 2927–2943 (2017).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

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    Stein, I. S., Gottfried, A., Zimmermann, J. & Fischer von Mollard, G. TVP23 interacts genetically with the yeast SNARE VTI1 and functions in retrograde transport from the early endosome to the late Golgi. Biochem. J. 419, 229–236 (2009).

    CAS  PubMed  Article  Google Scholar 

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    Gendre, D. et al. Conserved Arabidopsis ECHIDNA protein mediates trans-Golgi-network trafficking and cell elongation. Proc. Natl Acad. Sci. USA 108, 8048–8053 (2011).

    ADS  CAS  PubMed  Article  Google Scholar 

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    PubMed  PubMed Central  Google Scholar 

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Original Text (This is the original text for your reference.)

  1. 1.

    Takamori, S. et al. Molecular anatomy of a trafficking organelle. Cell 127, 831–846 (2006).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  2. 2.

    Yu, I. M. & Hughson, F. M. Tethering factors as organizers of intracellular vesicular traffic. Annu. Rev. Cell Dev. Biol. 26, 137–156 (2010).

    CAS  Article  Google Scholar 

  3. 3.

    Gillingham, A. K. & Munro, S. Transport carrier tethering—how vesicles are captured by organelles. Curr. Opin. Cell Biol. 59, 140–146 (2019).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  4. 4.

    Witkos, T. M. & Lowe, M. Recognition and tethering of transport vesicles at the Golgi apparatus. Curr. Opin. Cell Biol. 47, 16–23 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  5. 5.

    Witkos, T. M. & Lowe, M. The golgin family of coiled-coil tethering proteins. Front Cell Dev. Biol. 3, 86 (2015).

    PubMed  PubMed Central  Google Scholar 

  6. 6.

    Muschalik, N. & Munro, S. Golgins. Curr. Biol. 28, R374–R376 (2018).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  7. 7.

    Gillingham, A. K. & Munro, S. Finding the Golgi: golgin coiled-coil proteins show the way. Trends Cell Biol. 26, 399–408 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  8. 8.

    Pfeffer, S. R. Entry at the trans-face of the Golgi. Cold Spring Harb. Perspect. Biol. 3, a005272 (2011).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  9. 9.

    Goud, B. & Gleeson, P. A. TGN golgins, Rabs and cytoskeleton: regulating the Golgi trafficking highways. Trends Cell Biol. 20, 329–336 (2010).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  10. 10.

    Lowe, M. The physiological functions of the golgin vesicle tethering proteins. Front Cell Dev. Biol. 7, 94 (2019).

    ADS  PubMed  PubMed Central  Article  Google Scholar 

  11. 11.

    Wong, M. & Munro, S. Membrane trafficking. The specificity of vesicle traffic to the Golgi is encoded in the golgin coiled-coil proteins. Science 346, 1256898 (2014).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  12. 12.

    Gillingham, A. K., Bertram, J., Begum, F. & Munro, S. In vivo identification of GTPase interactors by mitochondrial relocalization and proximity biotinylation. eLife 8, e45916 (2019).

    PubMed  PubMed Central  Article  Google Scholar 

  13. 13.

    Wong, M., Gillingham, A. K. & Munro, S. The golgin coiled-coil proteins capture different types of transport carriers via distinct N-terminal motifs. BMC Biol. 15, 3 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  14. 14.

    Shin, J. J. H., Gillingham, A. K., Begum, F., Chadwick, J. & Munro, S. TBC1D23 is a bridging factor for endosomal vesicle capture by golgins at the trans-Golgi. Nat. Cell Biol. 19, 1424–1432 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  15. 15.

    Navarro Negredo, P., Edgar, J. R., Manna, P. T., Antrobus, R. & Robinson, M. S. The WDR11 complex facilitates the tethering of AP-1-derived vesicles. Nat. Commun. 9, 596 (2018).

    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

  16. 16.

    Borner, G. H. et al. Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein-protein interactions. Mol. Biol. Cell 25, 3178–3194 (2014).

    PubMed  PubMed Central  Article  Google Scholar 

  17. 17.

    McNally, K. E. & Cullen, P. J. Endosomal retrieval of cargo: retromer Is not alone. Trends Cell Biol. 28, 807–822 (2018).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  18. 18.

    Wang, J. et al. Endosomal receptor trafficking: retromer and beyond. Traffic 19, 578–590 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  19. 19.

    Cullen, P. J. & Steinberg, F. To degrade or not to degrade: mechanisms and significance of endocytic recycling. Nat. Rev. Mol. Cell Biol. 19, 679–696 (2018).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  20. 20.

    Christoforou, A., Arias, A. M. & Lilley, K. S. Determining protein subcellular localization in mammalian cell culture with biochemical fractionation and iTRAQ 8-plex quantification. Methods Mol. Biol. 1156, 157–174 (2014).

    CAS  PubMed  Article  Google Scholar 

  21. 21.

    Itzhak, D. N. et al. A mass spectrometry-based approach for mapping protein subcellular localization reveals the spatial proteome of mouse primary neurons. Cell Rep. 20, 2706–2718 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  22. 22.

    Itzhak, D. N., Tyanova, S., Cox, J. & Borner, G. H. Global, quantitative and dynamic mapping of protein subcellular localization. eLife 5, e16590 (2016).

    Article  CAS  Google Scholar 

  23. 23.

    Geladaki, A. et al. Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics. Nat. Commun. 10, 331 (2019).

    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

  24. 24.

    Trotter, M. W., Sadowski, P. G., Dunkley, T. P., Groen, A. J. & Lilley, K. S. Improved sub-cellular resolution via simultaneous analysis of organelle proteomics data across varied experimental conditions. Proteomics 10, 4213–4219 (2010).

    CAS  PubMed  Article  Google Scholar 

  25. 25.

    Crook, O. M., Mulvey, C. M., Kirk, P. D. W., Lilley, K. S. & Gatto, L. A Bayesian mixture modelling approach for spatial proteomics. PLoS Comput. Biol. 14, e1006516 (2018).

    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

  26. 26.

    Crook, O. M., Smith, T., Elzek, M. & Lilley, K. S. Moving profiling spatial proteomics beyond discrete classification. Proteomics e1900392 (2020).

  27. 27.

    Crook, O. M., Lilley, K. S., Gatto, L. & Kirk, P. D. W. Semi-supervised non-parametric Bayesian modelling of spatial proteomics. Preprint at https://arxiv.org/abs/1903.02909 (2020).

  28. 28.

    Crook, O. M. et al. A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection. PLoS Comput. Biol. 16, e1008288 (2020).

  29. 29.

    Christoforou, A. et al. A draft map of the mouse pluripotent stem cell spatial proteome. Nat. Commun. 7, 8992 (2016).

    PubMed  Article  CAS  Google Scholar 

  30. 30.

    Thomas, G. Furin at the cutting edge: from protein traffic to embryogenesis and disease. Nat. Rev. Mol. Cell Biol. 3, 753–766 (2002).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  31. 31.

    Judith, D. et al. ATG9A shapes the forming autophagosome through Arfaptin 2 and phosphatidylinositol 4-kinase IIIbeta. J. Cell Biol. 218, 1634–1652 (2019).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  32. 32.

    Naslavsky, N. & Caplan, S. The enigmatic endosome—sorting the ins and outs of endocytic trafficking. J. Cell Sci. 131, jcs216499 (2018).

  33. 33.

    Hierro, A., Gershlick, D. C., Rojas, A. L. & Bonifacino, J. S. Formation of tubulovesicular carriers from endosomes and their fusion to the trans-Golgi network. Int. Rev. Cell Mol. Biol. 318, 159–202 (2015).

    CAS  PubMed  Article  Google Scholar 

  34. 34.

    Hirst, J. et al. Distinct and overlapping roles for AP-1 and GGAs revealed by the “knocksideways” system. Curr. Biol. 22, 1711–1716 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  35. 35.

    Hirst, J. et al. Contributions of epsinR and gadkin to clathrin-mediated intracellular trafficking. Mol. Biol. Cell 26, 3085–3103 (2015).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  36. 36.

    Navarro Negredo, P. et al. Contribution of the clathrin adaptor AP-1 subunit μ1 to acidic cluster protein sorting. J. Cell Biol. 216, 2927–2943 (2017).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  37. 37.

    Stein, I. S., Gottfried, A., Zimmermann, J. & Fischer von Mollard, G. TVP23 interacts genetically with the yeast SNARE VTI1 and functions in retrograde transport from the early endosome to the late Golgi. Biochem. J. 419, 229–236 (2009).

    CAS  PubMed  Article  Google Scholar 

  38. 38.

    Gendre, D. et al. Conserved Arabidopsis ECHIDNA protein mediates trans-Golgi-network trafficking and cell elongation. Proc. Natl Acad. Sci. USA 108, 8048–8053 (2011).

    ADS  CAS  PubMed  Article  Google Scholar 

  39. 39.

    Wang, A. L. et al. Role of FAM18B in diabetic retinopathy. Mol. Vis. 20, 1146–1159 (2014).

    PubMed  PubMed Central  Google Scholar 

  40. 40.

    Davies, A. K. et al. AP-4 vesicles contribute to spatial control of autophagy via RUSC-dependent peripheral delivery of ATG9A. Nat. Commun. 9, 3958 (2018).

    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

  41. 41.

    Rosa, A. et al. HIV-1 Nef promotes infection by excluding SERINC5 from virion incorporation. Nature 526, 212–217 (2015).

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  42. 42.

    Usami, Y., Wu, Y. & Gottlinger, H. G. SERINC3 and SERINC5 restrict HIV-1 infectivity and are counteracted by Nef. Nature 526, 218–223 (2015).

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  43. 43.

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