Structural characterization of coatomer in its cytosolic state

Shengliu Wang, Yujia Zhai, Xiaoyun Pang, Tongxin Niu, Yue-He Ding, Meng-Qiu Dong, Victor W. Hsu, Zhe Sun, Fei Sun

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Protein Cell ›› 2016, Vol. 7 ›› Issue (8) : 586-600. DOI: 10.1007/s13238-016-0296-z
RESEARCH ARTICLE
RESEARCH ARTICLE

Structural characterization of coatomer in its cytosolic state

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Abstract

Studies on coat protein I (COPI) have contributed to a basic understanding of how coat proteins generate vesicles to initiate intracellular transport. The core component of the COPI complex is coatomer, which is a multimeric complex that needs to be recruited from the cytosol to membrane in order to function in membrane bending and cargo sorting. Previous structural studies on the clathrin adaptors have found that membrane recruitment induces a large conformational change in promoting their role in cargo sorting. Here, pursuing negative-stain electron microscopy coupled with singleparticle analyses, and also performing CXMS (chemical cross-linking coupled with mass spectrometry) for validation, we have reconstructed the structure of coatomer in its soluble form. When compared to the previously elucidated structure of coatomer in its membrane-bound form we do not observe a large conformational change. Thus, the result uncovers a key difference between how COPI versus clathrin coats are regulated by membrane recruitment.

Keywords

coatomer / COPI / human / single-particle electron microscopy / membrane trafficking

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Shengliu Wang, Yujia Zhai, Xiaoyun Pang, Tongxin Niu, Yue-He Ding, Meng-Qiu Dong, Victor W. Hsu, Zhe Sun, Fei Sun. Structural characterization of coatomer in its cytosolic state. Protein Cell, 2016, 7(8): 586‒600 https://doi.org/10.1007/s13238-016-0296-z

References

[1]
Bai XC, Rajendra E, Yang GH, Shi YG, Scheres SHW (2015) Sampling the conformational space of the catalytic subunit of human gamma-secretase. eLife4
[2]
Beck R, Sun Z, Adolf F, Rutz C, Bassler J, Wild K, Sinning I, Hurt E, Brugger B, Bethune J (2008) Membrane curvature induced by Arf1-GTP is essential for vesicle formation. Proc Natl Acad Sci USA 105:11731–11736
CrossRef Google scholar
[3]
Beck R, Adolf F, Weimer C, Bruegger B, Wieland FT (2009) ArfGAP1 Activity and COPIVesicle Biogenesis. Traffic 10:307–315
CrossRef Google scholar
[4]
Bharat TA, Russo CJ, Lowe J, Passmore LA, Scheres SH (2015) Advances in single-particle electron cryomicroscopy structure determination applied to sub-tomogram averaging. Structure 23:1743–1753
CrossRef Google scholar
[5]
Bielli A, Haney CJ, Gabreski G, Watkins SC, Bannykh SI, Aridor M (2005) Regulation of Sar1 NH2 terminus by GTP binding and hydrolysis promotes membrane deformation to control COPII vesicle fission. J Cell Biol 171:919–924
CrossRef Google scholar
[6]
Bigay J, Gounon P, Robineau S, Antonny B (2003) Lipid packing sensed by ArfGAP1 couples COPI coat disassembly to membrane bilayer curvature. Nature 426:563–566
CrossRef Google scholar
[7]
Bonifacino JS, Glick BS (2004) The mechanisms of vesicle budding and fusion. Cell 116:153–166
CrossRef Google scholar
[8]
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 96:495–506
CrossRef Google scholar
[9]
Brugger B, Sandhoff R, Wegehingel S, Gorgas K, Malsam J, Helms JB, Lehmann WD, Nickel W, Wieland FT (2000) Evidence for segregation ofsphingomyelin and cholesterol during formation of COPI-coated vesicles. J cell biol 151:507–518
CrossRef Google scholar
[10]
Collins BM, McCoy AJ, Kent HM, Evans PR, Owen DJ (2002) Molecular architecture and functional model of the endocytic AP2 complex. Cell 109:523–535
CrossRef Google scholar
[11]
Cosson P, Letourneur F (1994) Coatomer interaction with di-lysine endoplasmic reticulum retention motifs. Science 263:1629–1631
CrossRef Google scholar
[12]
Cukierman E, Huber I, Rotman M, Cassel D (1995) The ARF1GTPase-activating protein: Zinc finger motif and Golgi complex localization. Science 270:1999–2002
CrossRef Google scholar
[13]
Deng Y, Golinelli-Cohen MP, Smirnova E, Jackson CL (2009) A COPI coat subunit interacts directly with an early-Golgi localized Arf exchange factor. EMBO Rep 10:58–64
CrossRef Google scholar
[14]
Ding Y, Fan S, Li S, Feng B, Gao N, Ye K, He S-M, Dong M-Q (2016) Increasing the depth of mass spectrometry-based structural analysis of protein complexes through the use of multiple cross-linkers. Anal Chem 88(8):4461–4469
[15]
Dodonova SO, Diestelkoetter-Bachert P, von Appen A, Hagen WJ, Beck R, Beck M, Wieland F, Briggs JA (2015) VESICULAR TRANSPORT.A structure of the COPI coat and the role of coat proteins in membrane vesicle assembly. Science 349:195–198
CrossRef Google scholar
[16]
Donaldson JG, Cassel D, Kahn RA, Klausner RD (1992) ADPribosylation factor, a small GTP-binding protein, is required for binding of the coatomer protein beta-COP to Golgi membranes. Proc Natl Acad Sci USA 89:6408–6412
CrossRef Google scholar
[17]
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 336:1451–1454
CrossRef Google scholar
[18]
Faini M, Beck R, Wieland FT, Briggs JA (2013) Vesicle coats: structure, function, and general principles of assembly. Trends Cell Biol 23:279–288
CrossRef Google scholar
[19]
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 155:193–200
CrossRef Google scholar
[20]
Fiedler K, Veit M, Stamnes MA, Rothman JE (1996) Bimodal interaction of coatomer with the p24 family of putative cargo receptors. Science 273:1396–1399
CrossRef Google scholar
[21]
Franco M, Chardin P, Chabre M, Paris S (1996) Myristoylationfacilitated binding of the G protein ARF1(GDP) to membrane phospholipidsis requiredforits activationby a soluble nucleotide exchange factor. J Biol Chem 271:1573–1578
CrossRef Google scholar
[22]
Goldberg J (1999) Structural and functional analysis of the ARF1ARFGAP complex reveals a role for coatomer in GTP hydrolysis. Cell 96:893–902
CrossRef Google scholar
[23]
Han R, Wang L, Liu Z, Sun F, Zhang F (2015) Anovel fully automatic scheme for fiducial marker-based alignment in electron tomography. J Struct Biol 192:403–417
CrossRef Google scholar
[24]
Hara-Kuge S, Kuge O, Orci L, Amherdt M, Ravazzola M, Wieland FT, Rothman JE (1994) En bloc incorporation of coatomer subunits during the assembly of COP-coated vesicles [published erratum appears in J Cell Biol 1994 Jul; 126(2):589]. J Cell Biol 124:883–892
CrossRef Google scholar
[25]
Hariri H, Bhattacharya N, Johnson K, Noble AJ, Stagg SM (2014) Insights into the mechanisms ofmembrane curvature and vesicle scission by the small GTPase Sar1 in the early secretory pathway. J Mol Biol 426:3811–3826
CrossRef Google scholar
[26]
Heldwein EE, Macia E, Wang J, Yin HL, Kirchhausen T, Harrison SC (2004) Crystal structure of the clathrin adaptor protein 1 core. Proc Natl Acad Sci USA 101:14108–14113
CrossRef Google scholar
[27]
Hsu VW, Lee SY, Yang JS (2009) The evolving understanding of COPI vesicle formation. Nat Rev Mol Cell Biol 10:360–364
CrossRef Google scholar
[28]
Jackson LP (2014) Structure and mechanism of COPI vesicle biogenesis. Curr Opin Cell Biol 29:67–73
CrossRef Google scholar
[29]
Jackson LP, Kelly BT, McCoy AJ, Gaffry T, James LC, Collins BM, Honing S, Evans PR, Owen DJ (2010) A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex. Cell 141:1220–1229
CrossRef Google scholar
[30]
Jackson LP, Lewis M, Kent HM, Edeling MA, Evans PR, Duden R, Owen DJ (2012) Molecular basis for recognition of dilysine trafficking motifs by COPI. Dev Cell 23:1255–1262
CrossRef Google scholar
[31]
Jia, X., Weber, E., Tokarev, A., Lewinski, M., Rizk, M., Suarez, M., Guatelli, J., and Xiong, Y. (2014). Structural basis of HIV-1 Vpumediated BST2 antagonism via hijacking of the clathrin adaptor protein complex 1. eLife 3, e02362
[32]
Krauss M, Jia JY, Roux A, Beck R, Wieland FT, De Camilli P, Haucke V (2008) Arf1-GTP-induced tubule formation suggests a function of Arf family proteins in curvature acquisition at sites of vesicle budding. J Biol Chem 283:27717–27723
CrossRef Google scholar
[33]
Kremer JR, Mastronarde DN, McIntosh JR (1996) Computer visualization of three-dimensional image data using IMOD. J Struct Biol 116:71–76
CrossRef Google scholar
[34]
Langer JD, Roth CM, Bethune J, Stoops EH, Brugger B, Herten DP, Wieland FT (2008)Aconformational change in the alpha-subunit of coatomer induced by ligand binding to gamma-COP revealed by single-pair FRET. Traffic 9:597–607
CrossRef Google scholar
[35]
Lee C, Goldberg J (2010) Structureof coatomer cage proteins and the relationship among COPI, COPII, and clathrin vesicle coats. Cell 142:123–132
CrossRef Google scholar
[36]
Lee MC, Orci L, Hamamoto S, Futai E, Ravazzola M, Schekman R (2005a) Sar1p N-terminal helix initiates membrane curvature and completes the fission of a COPII vesicle. Cell 122:605–617
[37]
Lee SY, Yang JS, Hong W, Premont RT, Hsu VW (2005b) ARFGAP1 plays a central role in coupling COPI cargo sorting with vesicle formation. J Cell Biol 168, 281–290
[38]
Leitner A, Walzthoeni T, Aebersold R (2014) Lysine-specific chemical cross-linking ofprotein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline. Nat Protoc 9:120–137
[39]
Lundmark R, Doherty GJ, Vallis Y, Peter BJ, McMahon HT (2008)Arf family GTP loading is activated by, and generates, positive membrane curvature. BiochemJ 414:189–194
CrossRef Google scholar
[40]
Ma W, Goldberg J (2013) Rules for the recognition of dilysine retrieval motifsby coatomer. EMBOJ 32:926–937
CrossRef Google scholar
[41]
Malhotra V, Serafini T, Orci L, Shepherd JC, Rothman JE (1989) Purification of a novel class of coated vesicles mediating biosynthetic protein transport through the Golgi stack. Cell 58:329–336
CrossRef Google scholar
[42]
Mastronarde DN (2005) Automated electron microscope tomography using robust predictionof specimen movements. JStruct Biol 152:36–51
CrossRef Google scholar
[43]
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 93:263–275
CrossRef Google scholar
[44]
McMahon HT, Gallop JL (2005) Membrane curvatureandmechanisms of dynamiccellmembrane remodelling. Nature 438:590–596
[45]
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
CrossRef Google scholar
[46]
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF chimera-A visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612
CrossRef Google scholar
[47]
Politis A, Stengel F, Hall Z, Hernandez H, Leitner A, Walzthoeni T, Robinson CV, Aebersold R (2014) A mass spectrometry-based hybrid method for structural modeling of protein complexes. Nat Methods 11:403–406
CrossRef Google scholar
[48]
Pucadyil TJ, Schmid SL (2009) Conserved functions of membrane active GTPases in coated vesicle formation. Science 325:1217–1220
CrossRef Google scholar
[49]
Reinhard C, Harter C, Bremser M, Brugger B, Sohn K, Helms JB, Wielan dF (1999) Receptor-induced polymerization of coatomer. Proc Natl Acad Sci USA 96:1224–1228
CrossRef Google scholar
[50]
Ren X, Farias GG, Canagarajah BJ, Bonifacino JS, Hurley JH (2013) Structural basis for recruitment and activation ofthe AP-1 clathrin adaptor complex by Arf1. Cell 152:755–767
CrossRef Google scholar
[51]
Rosenthal PB, Henderson R (2003) Optimal determinationof particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J Mol Biol 333:721–745
CrossRef Google scholar
[52]
Sahlmuller MC, Strating JR, Beck R, Eckert P, Popoff V, Haag M, Hellwig A, Berger I, Brugger B, Wieland FT (2011) Recombinant heptameric coatomer complexes: novel tools to study isoformspecific functions. Traffic 12:682–692
CrossRef Google scholar
[53]
Šali A, Potterton L, Yuan F, van Vlijmen H, Karplus M (1995) Evaluation of comparative protein modeling by MODELLER. Proteins: Structure. Funct Bioinform 23:318–326
CrossRef Google scholar
[54]
Scheres SHW (2012) RELION: Implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol 180:519–530
CrossRef Google scholar
[55]
Serafini T, Orci L, Amherdt M, Brunner M, Kahn RA, Rothman JE (1991a) ADP-ribosylation factor is a subunit of the coat of Golgiderived COP-coated vesicles: a novel role for a GTP-binding protein. Cell 67:239–253
[56]
Serafini T, Stenbeck G, Brecht A, Lottspeich F, Orci L, Rothman JE, Wieland FT (1991b) Acoat subunit of Golgi-derived non-clathrincoated vesicles with homology to the clathrin-coated vesicle coat protein beta-adaptin. Nature 349:215–220
[57]
Shan H, Wang Z, Zhang F, Xiong Y, Yin CC, Sun F (2016) A localoptimizationrefinementalgorithminsingle particleanalysisformacromolecularcomplexwith multiple rigidmodules. Protein Cell 7:46–62
[58]
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 USA 95:11199–11204
CrossRef Google scholar
[59]
Suckling RJ, Poon PP, Travis SM, Majoul IV, Hughson FM, Evans PR, Duden R, Owen DJ (2015) Structural basis for the binding of tryptophan-based motifs by delta-COP. Proc Natl Acad Sci USA 112:14242–14247
CrossRef Google scholar
[60]
Takei K, Haucke V, Slepnev V, Farsad K, Salazar M, Chen H, De Camilli P (1998) Generation of coated intermediates of clathrinmediated endocytosis on protein-free liposomes. Cell 94:131–141
CrossRef Google scholar
[61]
van Meer G (1998) Lipids of the Golgi membrane. Trends Cell Biol 8:29–33
CrossRef Google scholar
[62]
van Meer G, Voelker DR, Feigenson GW (2008) Membrane lipids: where they are and how they behave. Nat Rev Mol Cell Biol 9:112–124
CrossRef Google scholar
[63]
Waters MG, Serafini T, Rothman JE (1991) ‘Coatomer’: a cytosolic protein complex containing subunits of non-clathrin-coated Golgi transport vesicles. Nature 349:248–251
CrossRef Google scholar
[64]
Yang JS, Lee SY, Gao M, Bourgoin S, Randazzo PA, Premont RT, Hsu VW (2002) ARFGAP1 promotes the formation of COPI vesicles, suggesting functionasa componentof the coat. J Cell Biol 159:69–78
CrossRef Google scholar
[65]
Yang B, Wu YJ, Zhu M, Fan SB, Lin J, Zhang K, Li S, Chi H, Li YX, Chen HF (2012) Identification of cross-linked peptides from complex samples. Nat Methods 9:904–906
CrossRef Google scholar
[66]
Yip CK, Walz T (2011) Molecular structure andflexibility of the yeast coatomer as revealed by electron microscopy. J Mol Biol 408:825–831
CrossRef Google scholar
[67]
Yu X, Breitman M, Goldberg J (2012) Astructure-based mechanism for Arf1-dependent recruitment of coatomer to membranes. Cell 148:530–542
CrossRef Google scholar
[68]
Zhang K (2016) Gctf: Real-time CTF determination and correction. J Struct Biol 193:1–12
CrossRef Google scholar

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2016 The Author(s) 2016. This article is published with open access at Springerlink.com and journal.hep.com.cn
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