Molecular architecture of the endocytic TPLATE complex
Status PubMed-not-MEDLINE Jazyk angličtina Země Spojené státy americké Médium electronic-print
Typ dokumentu časopisecké články, práce podpořená grantem
Grantová podpora
682436
European Research Council - International
PubMed
33637534
PubMed Central
PMC7909872
DOI
10.1126/sciadv.abe7999
PII: 7/9/eabe7999
Knihovny.cz E-zdroje
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Eukaryotic cells rely on endocytosis to regulate their plasma membrane proteome and lipidome. Most eukaryotic groups, except fungi and animals, have retained the evolutionary ancient TSET complex as an endocytic regulator. Unlike other coatomer complexes, structural insight into TSET is lacking. Here, we reveal the molecular architecture of plant TSET [TPLATE complex (TPC)] using an integrative structural approach. We identify crucial roles for specific TSET subunits in complex assembly and membrane interaction. Our data therefore generate fresh insight into the differences between the hexameric TSET in Dictyostelium and the octameric TPC in plants. Structural elucidation of this ancient adaptor complex represents the missing piece in the coatomer puzzle and vastly advances our functional as well as evolutionary insight into the process of endocytosis.
Department of Biochemistry and Microbiology Ghent University 9052 Ghent Belgium
VIB Center for Inflammation Research 9052 Ghent Belgium
VIB Center for Plant Systems Biology Technologiepark 71 9052 Ghent Belgium
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Dacks J. B., Field M. C., Evolution of the eukaryotic membrane-trafficking system: Origin, tempo and mode. J. Cell Sci. 120, 2977–2985 (2007). PubMed
Field M. C., Sali A., Rout M. P., Evolution: On a bender–BARs, ESCRTs, COPs, and finally getting your coat. J. Cell Biol. 193, 963–972 (2011). PubMed PMC
Rout M. P., Field M. C., The evolution of organellar coat complexes and organization of the eukaryotic cell. Annu. Rev. Biochem. 86, 637–657 (2017). PubMed
Béthune J., Wieland F. T., Assembly of COPI and COPII vesicular coat proteins on membranes. Annu. Rev. Biophys. 47, 63–83 (2018). PubMed
Beacham G. M., Partlow E. A., Hollopeter G., Conformational regulation of AP1 and AP2 clathrin adaptor complexes. Traffic 20, 741–751 (2019). PubMed PMC
Hirst J., Schlacht A., Norcott J. P., Traynor D., Bloomfield G., Antrobus R., Kay R. R., Dacks J. B., Robinson M. S., Characterization of TSET, an ancient and widespread membrane trafficking complex. eLife 3, e02866 (2014). PubMed PMC
More K., Klinger C. M., Barlow L. D., Dacks J. B., Evolution and natural history of membrane trafficking in eukaryotes. Curr. Biol. 30, R553–R564 (2020). PubMed
Gadeyne A., Sánchez-Rodríguez C., Vanneste S., Di Rubbo S., Zauber H., Vanneste K., Van Leene J., De Winne N., Eeckhout D., Persiau G., Van De Slijke E., Cannoot B., Vercruysse L., Mayers J. R., Adamowski M., Kania U., Ehrlich M., Schweighofer A., Ketelaar T., Maere S., Bednarek S. Y., Friml J., Gevaert K., Witters E., Russinova E., Persson S., De Jaeger G., Van Damme D., The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants. Cell 156, 691–704 (2014). PubMed
Dodonova S. O., Diestelkoetter-Bachert P., von Appen A., Hagen W. J. H., Beck R., Beck M., Wieland F., Briggs J. A. G., VESICULAR TRANSPORT. A structure of the COPI coat and the role of coat proteins in membrane vesicle assembly. Science 349, 195–198 (2015). PubMed
Collins B. M., McCoy A. J., Kent H. M., Evans P. R., Owen D. J., Molecular architecture and functional model of the endocytic AP2 complex. Cell 109, 523–535 (2002). PubMed
Ren X., Farías G. G., Canagarajah B. J., Bonifacino J. S., Hurley J. H., Structural basis for recruitment and activation of the AP-1 clathrin adaptor complex by Arf1. Cell 152, 755–767 (2013). PubMed PMC
Yperman K., Papageorgiou A. C., Merceron R., De Munck S., Bloch Y., Eeckhout D., Tack P., Evangelidis T., Van Leene J., Vincze L., Vandenabeele P., Potocký M., De Jaeger G., Savvides S. N., Tripsianes K., Pleskot R., Van Damme D., Distinct EH domains of the endocytic TPLATE complex confer lipid and protein binding. bioRxiv 2020.05.29.122911, (2020). PubMed PMC
Sánchez-Rodríguez C., Shi Y., Kesten C., Zhang D., Sancho-Andrés G., Ivakov A., Lampugnani E. R., Sklodowski K., Fujimoto M., Nakano A., Bacic A., Wallace I. S., Ueda T., Van Damme D., Zhou Y., Persson S., The cellulose synthases are cargo of the TPLATE adaptor complex. Mol. Plant 11, 346–349 (2018). PubMed
Wang P., Pleskot R., Zang J., Winkler J., Wang J., Yperman K., Zhang T., Wang K., Gong J., Guan Y., Richardson C., Duckney P., Vandorpe M., Mylle E., Fiserova J., van Damme D., Hussey P. J., Plant AtEH/Pan1 proteins drive autophagosome formation at ER-PM contact sites with actin and endocytic machinery. Nat. Commun. 10, 5132 (2019). PubMed PMC
Arora D., Abel N. B., Liu C., van Damme P., Yperman K., Eeckhout D., Vu L. D., Wang J., Tornkvist A., Impens F., Korbei B., Van Leene J., Goossens A., De Jaeger G., Ott T., Moschou P. N., Van Damme D., Establishment of proximity-dependent biotinylation approaches in different plant model systems. Plant Cell 32, 3388–3407 (2020). PubMed PMC
Platre M. P., Noack L. C., Doumane M., Bayle V., Simon M. L. A., Maneta-Peyret L., Fouillen L., Stanislas T., Armengot L., Pejchar P., Caillaud M. C., Potocký M., Čopič A., Moreau P., Jaillais Y., A combinatorial lipid code shapes the electrostatic landscape of plant endomembranes. Dev. Cell 45, 465–480.e11 (2018). PubMed
Rout M. P., Sali A., Principles for integrative structural biology studies. Cell 177, 1384–1403 (2019). PubMed PMC
Russel D., Lasker K., Webb B., Velázquez-Muriel J., Tjioe E., Schneidman-Duhovny D., Peterson B., Sali A., Putting the pieces together: Integrative modeling platform software for structure determination of macromolecular assemblies. PLOS Biol. 10, e1001244 (2012). PubMed PMC
Kozakov D., Hall D. R., Xia B., Porter K. A., Padhorny D., Yueh C., Beglov D., Vajda S., The ClusPro web server for protein–protein docking. Nat. Protoc. 12, 255–278 (2017). PubMed PMC
Viswanath S., Chemmama I. E., Cimermancic P., Sali A., Assessing exhaustiveness of stochastic sampling for integrative modeling of macromolecular structures. Biophys. J. 113, 2344–2353 (2017). PubMed PMC
Winkler J., Mylle E., De Meyer A., Pavie B., Merchie J., Grones P., Van Damme D., Visualizing protein-protein interactions in plants by rapamycin-dependent delocalization. Plant Cell 33, (in press) (2021). PubMed PMC
Wang J., Mylle E., Johnson A., Besbrugge N., De Jaeger G., Friml J., Pleskot R., Van Damme D., High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiol. 183, 986–997 (2020). PubMed PMC
Henne W. M., Boucrot E., Meinecke M., Evergren E., Vallis Y., Mittal R., McMahon H. T., FCHo proteins are nucleators of clathrin-mediated endocytosis. Science 328, 1281–1284 (2010). PubMed PMC
Reider A., Barker S. L., Mishra S. K., Im Y. J., Maldonado-Báez L., Hurley J. H., Traub L. M., Wendland B., Syp1 is a conserved endocytic adaptor that contains domains involved in cargo selection and membrane tubulation. EMBO J. 28, 3103–3116 (2009). PubMed PMC
Jackson L. P., Lewis M., Kent H. M., Edeling M. A., Evans P. R., Duden R., Owen D. J., Molecular basis for recognition of dilysine trafficking motifs by COPI. Dev. Cell 23, 1255–1262 (2012). PubMed PMC
Yamamoto E., Domański J., Naughton F. B., Best R. B., Kalli A. C., Stansfeld P. J., Sansom M. S. P., Multiple lipid binding sites determine the affinity of PH domains for phosphoinositide-containing membranes. Sci. Adv. 6, eaay5736 (2020). PubMed PMC
Furt F., König S., Bessoule J.-J., Sargueil F., Zallot R., Stanislas T., Noirot E., Lherminier J., Simon-Plas F., Heilmann I., Mongrand S., Polyphosphoinositides are enriched in plant membrane rafts and form microdomains in the plasma membrane. Plant Physiol. 152, 2173–2187 (2010). PubMed PMC
Simon M. L. A., Platre M. P., Marquès-Bueno M. M., Armengot L., Stanislas T., Bayle V., Caillaud M.-C., Jaillais Y., A PtdIns(4)P-driven electrostatic field controls cell membrane identity and signalling in plants. Nat. Plants 2, 16089 (2016). PubMed PMC
van Damme D., Coutuer S., De Rycke R., Bouget F.-Y., Inzé D., Geelen D., Somatic cytokinesis and pollen maturation in Arabidopsis depend on TPLATE, which has domains similar to coat proteins. Plant Cell 18, 3502–3518 (2006). PubMed PMC
Gronnier J., Crowet J.-M., Habenstein B., Nasir M. N., Bayle V., Hosy E., Platre M. P., Gouguet P., Raffaele S., Martinez D., Grelard A., Loquet A., Simon-Plas F., Gerbeau-Pissot P., Der C., Bayer E. M., Jaillais Y., Deleu M., Germain V., Lins L., Mongrand S., Structural basis for plant plasma membrane protein dynamics and organization into functional nanodomains. eLife 6, e26404 (2017). PubMed PMC
Dodonova S. O., Aderhold P., Kopp J., Ganeva I., Röhling S., Hagen W. J. H., Sinning I., Wieland F., Briggs J. A. G., 9Å structure of the COPI coat reveals that the Arf1 GTPase occupies two contrasting molecular environments. eLife 6, e26691 (2017). PubMed PMC
Kovtun O., Dickson V. K., Kelly B. T., Owen D. J., Briggs J. A. G., Architecture of the AP2/clathrin coat on the membranes of clathrin-coated vesicles. Sci. Adv. 6, eaba8381 (2020). PubMed PMC
Paraan M., Mendez J., Sharum S., Kurtin D., He H., Stagg S. M., The structures of natively assembled clathrin-coated vesicles. Sci. Adv. 6, eaba8397 (2020). PubMed PMC
Ma L., Umasankar P. K., Wrobel A. G., Lymar A., McCoy A. J., Holkar S. S., Jha A., Pradhan-Sundd T., Watkins S. C., Owen D. J., Traub L. M., Transient Fcho1/2·Eps15/R·AP-2 nanoclusters prime the AP-2 clathrin adaptor for cargo binding. Dev. Cell 37, 428–443 (2016). PubMed PMC
van Damme D., Bouget F.-Y., Van Poucke K., Inzé D., Geelen D., Molecular dissection of plant cytokinesis and phragmoplast structure: A survey of GFP-tagged proteins. Plant J. 40, 386–398 (2004). PubMed
Karimi M., Bleys A., Vanderhaeghen R., Hilson P., Building blocks for plant gene assembly. Plant Physiol. 145, 1183–1191 (2007). PubMed PMC
Van Leene J., Eeckhout D., Cannoot B., De Winne N., Persiau G., Van De Slijke E., Vercruysse L., Dedecker M., Verkest A., Vandepoele K., Martens L., Witters E., Gevaert K., De Jaeger G., An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes. Nat. Protoc. 10, 169–187 (2015). PubMed
Van Leene J., Han C., Gadeyne A., Eeckhout D., Matthijs C., Cannoot B., De Winne N., Persiau G., Van De Slijke E., Van de Cotte B., Stes E., Van Bel M., Storme V., Impens F., Gevaert K., Vandepoele K., De Smet I., De Jaeger G., Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase. Nat. Plants 5, 316–327 (2019). PubMed
Cox J., Mann M., MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008). PubMed
Chen Z.-L., Meng J.-M., Cao Y., Yin J.-L., Fang R.-Q., Fan S.-B., Liu C., Zeng W.-F., Ding Y.-H., Tan D., Wu L., Zhou W.-J., Chi H., Sun R.-X., Dong M.-Q., He S.-M., A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides. Nat. Commun. 10, 3404 (2019). PubMed PMC
Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J., Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997). PubMed PMC
Katoh K., Rozewicki J., Yamada K. D., MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization. Brief. Bioinform. 20, 1160–1166 (2019). PubMed PMC
Waterhouse A. M., Procter J. B., Martin D. M. A., Clamp M., Barton G. J., Jalview Version 2—A multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009). PubMed PMC
Šali A., Blundell T. L., Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779–815 (1993). PubMed
Zimmermann L., Stephens A., Nam S.-Z., Rau D., Kübler J., Lozajic M., Gabler F., Söding J., Lupas A. N., Alva V., A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J. Mol. Biol. 430, 2237–2243 (2018). PubMed
Källberg M., Wang H., Wang S., Peng J., Wang Z., Lu H., Xu J., Template-based protein structure modeling using the RaptorX web server. Nat. Protoc. 7, 1511–1522 (2012). PubMed PMC
Buchan D. W. A., Jones D. T., The PSIPRED Protein Analysis Workbench: 20 years on. Nucleic Acids Res. 47, W402–W407 (2019). PubMed PMC
Bryson K., Cozzetto D., Jones D. T., Computer-assisted protein domain boundary prediction using the DomPred server. Curr. Protein Pept. Sci. 8, 181–188 (2007). PubMed
Jones D. T., Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195–202 (1999). PubMed
Jones D. T., Cozzetto D., DISOPRED3: Precise disordered region predictions with annotated protein-binding activity. Bioinformatics 31, 857–863 (2014). PubMed PMC
Algret R., Fernandez-Martinez J., Shi Y., Kim S. J., Pellarin R., Cimermancic P., Cochet E., Sali A., Chait B. T., Rout M. P., Dokudovskaya S., Molecular architecture and function of the SEA Complex, a modulator of the TORC1 pathway. Mol. Cell. Proteomics 13, 2855–2870 (2014). PubMed PMC
Sparkes I. A., Runions J., Kearns A., Hawes C., Rapid, transient expression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants. Nat. Protoc. 1, 2019–2025 (2006). PubMed
de Jong D. H., Singh G., Bennett W. F. D., Arnarez C., Wassenaar T. A., Schäfer L. V., Periole X., Tieleman D. P., Marrink S. J., Improved parameters for the Martini coarse-grained protein force field. J. Chem. Theory Comput. 9, 687–697 (2013). PubMed
Monticelli L., Kandasamy S. K., Periole X., Larson R. G., Tieleman D. P., Marrink S.-J., The MARTINI coarse-grained force field: Extension to proteins. J. Chem. Theory Comput. 4, 819–834 (2008). PubMed
Marrink S. J., Risselada H. J., Yefimov S., Tieleman D. P., de Vries A. H., The MARTINI force field: Coarse grained model for biomolecular simulations. J. Phys. Chem. B. 111, 7812–7824 (2007). PubMed
Periole X., Cavalli M., Marrink S.-J., Ceruso M. A., Combining an elastic network with a coarse-grained molecular force field: Structure, dynamics, and intermolecular recognition. J. Chem. Theory Comput. 5, 2531–2543 (2009). PubMed
Ingólfsson H. I., Melo M. N., van Eerden F. J., Arnarez C., Lopez C. A., Wassenaar T. A., Periole X., de Vries A. H., Tieleman D. P., Marrink S. J., Lipid organization of the plasma membrane. J. Am. Chem. Soc. 136, 14554–14559 (2014). PubMed
Hsu P.-C., Bruininks B. M. H., Jefferies D., de Souza P. C. T., Lee J., Patel D. S., Marrink S. J., Qi Y., Khalid S., Im W., CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. J. Comput. Chem. 38, 2354–2363 (2017). PubMed PMC
Abraham M. J., Murtola T., Schulz R., Páll S., Smith J. C., Hess B., Lindahl E., GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015).
De Rybel B., Möller B., Yoshida S., Grabowicz I., Barbier de Reuille P., Boeren S., Smith R. S., Borst J. W., Weijers D., A bHLH complex controls embryonic vascular tissue establishment and indeterminate growth in Arabidopsis. Dev. Cell 24, 426–437 (2013). PubMed
Micsonai A., Wien F., Bulyáki É., Kun J., Moussong É., Lee Y.-H., Goto Y., Réfrégiers M., Kardos J., BeStSel: A web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra. Nucleic Acids Res. 46, W315–W322 (2018). PubMed PMC
Kooijman E. E., Tieleman D. P., Testerink C., Munnik T., Rijkers D. T. S., Burger K. N. J., de Kruijff B., An electrostatic/hydrogen bond switch as the basis for the specific interaction of phosphatidic acid with proteins. J. Biol. Chem. 282, 11356–11364 (2007). PubMed
Herberich E., Sikorski J., Hothorn T., A robust procedure for comparing multiple means under heteroscedasticity in unbalanced designs. PLOS ONE 5, e9788 (2010). PubMed PMC
Mravec J., Petrášek J., Li N., Boeren S., Karlova R., Kitakura S., Pařezová M., Naramoto S., Nodzyński T., Dhonukshe P., Bednarek S. Y., Zažímalová E., de Vries S., Friml J., Cell plate restricted association of DRP1A and PIN proteins is required for cell polarity establishment in Arabidopsis. Curr. Biol. 21, 1055–1060 (2011). PubMed
Pettersen E. F., Goddard T. D., Huang C. C., Couch G. S., Greenblatt D. M., Meng E. C., Ferrin T. E., UCSF Chimera—A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004). PubMed
Goddard T. D., Huang C. C., Meng E. C., Pettersen E. F., Couch G. S., Morris J. H., Ferrin T. E., UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2017). PubMed PMC
Humphrey W., Dalke A., Schulten K., VMD: Visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996). PubMed
Grimm M., Zimniak T., Kahraman A., Herzog F., xVis: A web server for the schematic visualization and interpretation of crosslink-derived spatial restraints. Nucleic Acids Res. 43, W362–W369 (2015). PubMed PMC
Bashline L., Li S., Zhu X., Gu Y., The TWD40-2 protein and the AP2 complex cooperate in the clathrin-mediated endocytosis of cellulose synthase to regulate cellulose biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 112, 12870–12875 (2015). PubMed PMC
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