دورية أكاديمية

Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum.

التفاصيل البيبلوغرافية
العنوان: Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum.
المؤلفون: González A; Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany., Covarrubias-Pinto A; Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany., Bhaskara RM; Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany.; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany., Glogger M; Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany., Kuncha SK; Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany.; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany., Xavier A; Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany.; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany., Seemann E; Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany., Misra M; Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany.; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany., Hoffmann ME; Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany., Bräuning B; Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany., Balakrishnan A; Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany., Qualmann B; Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany., Dötsch V; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt, Germany., Schulman BA; Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany., Kessels MM; Institute of Biochemistry I, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany., Hübner CA; Institute of Human Genetics, University Hospital Jena, Friedrich Schiller University, Jena, Germany., Heilemann M; Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany., Hummer G; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.; Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany., Dikić I; Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany. dikic@biochem2.uni-frankfurt.de.; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany. dikic@biochem2.uni-frankfurt.de.; Fraunhofer Institute of Translational Medicine and Pharmacology, Frankfurt am Main, Germany. dikic@biochem2.uni-frankfurt.de.
المصدر: Nature [Nature] 2023 Jun; Vol. 618 (7964), pp. 394-401. Date of Electronic Publication: 2023 May 24.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 0410462 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1476-4687 (Electronic) Linking ISSN: 00280836 NLM ISO Abbreviation: Nature Subsets: MEDLINE
أسماء مطبوعة: Publication: Basingstoke : Nature Publishing Group
Original Publication: London, Macmillan Journals ltd.
مواضيع طبية MeSH: Autophagy*/physiology , Endoplasmic Reticulum*/metabolism , Endoplasmic Reticulum Stress* , Ubiquitination*, Intracellular Signaling Peptides and Proteins/metabolism ; Ubiquitins/metabolism ; Microtubule-Associated Proteins/metabolism ; Receptors, Autocrine Motility Factor/metabolism
مستخلص: The endoplasmic reticulum (ER) undergoes continuous remodelling via a selective autophagy pathway, known as ER-phagy 1 . ER-phagy receptors have a central role in this process 2 , but the regulatory mechanism remains largely unknown. Here we report that ubiquitination of the ER-phagy receptor FAM134B within its reticulon homology domain (RHD) promotes receptor clustering and binding to lipidated LC3B, thereby stimulating ER-phagy. Molecular dynamics (MD) simulations showed how ubiquitination perturbs the RHD structure in model bilayers and enhances membrane curvature induction. Ubiquitin molecules on RHDs mediate interactions between neighbouring RHDs to form dense receptor clusters that facilitate the large-scale remodelling of lipid bilayers. Membrane remodelling was reconstituted in vitro with liposomes and ubiquitinated FAM134B. Using super-resolution microscopy, we discovered FAM134B nanoclusters and microclusters in cells. Quantitative image analysis revealed a ubiquitin-mediated increase in FAM134B oligomerization and cluster size. We found that the E3 ligase AMFR, within multimeric ER-phagy receptor clusters, catalyses FAM134B ubiquitination and regulates the dynamic flux of ER-phagy. Our results show that ubiquitination enhances RHD functions via receptor clustering, facilitates ER-phagy and controls ER remodelling in response to cellular demands.
(© 2023. The Author(s).)
References: Gubas, A. & Dikic, I. ER remodeling via ER-phagy. Mol. Cell 82, 1492–1500 (2022). (PMID: 354526179098120)
Chino, H. & Mizushima, N. ER-phagy: quality and quantity control of the endoplasmic reticulum by autophagy. Cold Spring Harb. Perspect. Biol. 15, a041256 (2023). (PMID: 35940904)
Khaminets, A. et al. Regulation of endoplasmic reticulum turnover by selective autophagy. Nature 522, 354–358 (2015). (PMID: 26040720)
Bhaskara, R. M. et al. Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy. Nat. Commun. 10, 2370 (2019). (PMID: 311475496542808)
Reggio, A. et al. Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER-phagy, and collagen quality control. EMBO Rep. 22, e52289 (2021). (PMID: 343384058447607)
Siggel, M., Bhaskara, R. M., Moesser, M. K., Dikic, I. & Hummer, G. FAM134B-RHD protein clustering drives spontaneous budding of asymmetric membranes. J. Phys. Chem. Lett. 12, 1926–1931 (2021). (PMID: 335917708028312)
Jiang, X. et al. FAM134B oligomerization drives endoplasmic reticulum membrane scission for ER-phagy. EMBO J. 39, e102608 (2020). (PMID: 319307417049798)
Chino, H., Hatta, T., Natsume, T. & Mizushima, N. Intrinsically disordered protein TEX264 mediates ER-phagy. Mol. Cell 74, 909–921.e906 (2019). (PMID: 31006538)
Sauer, M. & Heilemann, M. Single-molecule localization microscopy in eukaryotes. Chem. Rev. 117, 7478–7509 (2017). (PMID: 28287710)
Schnitzbauer, J., Strauss, M. T., Schlichthaerle, T., Schueder, F. & Jungmann, R. Super-resolution microscopy with DNA-PAINT. Nat. Protoc. 12, 1198–1228 (2017). (PMID: 28518172)
Levet, F. et al. SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data. Nat. Methods 12, 1065–1071 (2015). (PMID: 26344046)
Ester, M., Kriegel, H.P., Sander, J., Xu, X. A density-based algorithm for discovering clusters in large spatial databases with noise. In Proceedings of the 2nd International Conference on Knowledge Discovery and Data Mining (AAAI Press, 1996).
Jungmann, R. et al. Quantitative super-resolution imaging with qPAINT. Nat. Methods 13, 439–442 (2016). (PMID: 270185804941813)
Croucher, D. R. et al. Bimolecular complementation affinity purification (BiCAP) reveals dimer-specific protein interactions for ERBB2 dimers. Sci. Signal. 9, ra69 (2016). (PMID: 27405979)
Grumati, P. et al. Full length RTN3 regulates turnover of tubular endoplasmic reticulum via selective autophagy. eLife 6, e25555 (2017). (PMID: 286172415517149)
Gubas, A. & Dikic, I. A guide to the regulation of selective autophagy receptors. FEBS J. 289, 75–89 (2022). (PMID: 33730405)
Chen, Z., Du, S. & Fang, S. gp78: A multifaceted ubiquitin ligase that integrates a unique protein degradation pathway from the endoplasmic reticulum. Curr. Protein Pept. Sci. 13, 414–424 (2012). (PMID: 22812524)
Li, W. et al. Mechanistic insights into active site-associated polyubiquitination by the ubiquitin-conjugating enzyme Ube2g2. Proc. Natl Acad. Sci. USA 106, 3722–3727 (2009). (PMID: 192235792644258)
Foronda, H. et al. Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy. Nature https://doi.org/10.1038/s41586-023-06090-9 (2023). (PMID: 10.1038/s41586-023-06090-937225994)
Liang, J. R. et al. A genome-wide ER-phagy screen highlights key roles of mitochondrial metabolism and ER-resident UFMylation. Cell 180, 1160–1177.e20 (2020). (PMID: 321605267197389)
Hubner, C. A. & Dikic, I. ER-phagy and human diseases. Cell Death Differ. 27, 833–842 (2020). (PMID: 31659280)
Gordon, W. R. et al. Effects of S1 cleavage on the structure, surface export, and signaling activity of human Notch1 and Notch2. PLoS ONE4, e6613 (2009).
Izadi, M. et al. Cobl-like promotes actin filament formation and dendritic branching using only a single WH2 domain. J. Cell Biol. 217, 211–230 (2018). (PMID: 292338635748978)
Chaudhary, S., Pak, J. E., Gruswitz, F., Sharma, V. & Stroud, R. M. Overexpressing human membrane proteins in stably transfected and clonal human embryonic kidney 293S cells. Nat. Protoc. 7, 453–466 (2012). (PMID: 223222183613139)
Schneider, K. et al. ProSAP1 and membrane nanodomain-associated syndapin I promote postsynapse formation and function. J. Cell Biol. 205, 197–215 (2014). (PMID: 247515384003247)
Seemann, E. et al. Deciphering caveolar functions by syndapin III KO-mediated impairment of caveolar invagination. eLife 6, e29854 (2017). (PMID: 292029285716666)
Wolf, D. et al. Ankyrin repeat-containing N-Ank proteins shape cellular membranes. Nat. Cell Biol. 21, 1191–1205 (2019). (PMID: 31548610)
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). (PMID: 19029910)
Tyanova, S. et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods 13, 731–740 (2016). (PMID: 27348712)
Elias, J. E. & Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207–214 (2007). (PMID: 17327847)
Cox, J. et al. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol. Cell. Proteomics 13, 2513–2526 (2014). (PMID: 249427004159666)
Deutsch, E. W. et al. The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. Nucleic Acids Res. 45, D1100–D1106 (2017). (PMID: 27924013)
Perez-Riverol, Y. et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 47, D442–D450 (2019). (PMID: 30395289)
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). (PMID: 17569554)
Monticelli, L. et al. The MARTINI coarse-grained force field: extension to proteins. J. Chem. Theory Comput. 4, 819–834 (2008). (PMID: 26621095)
Wassenaar, T. A., Ingolfsson, H. I., Bockmann, R. A., Tieleman, D. P. & Marrink, S. J. Computational lipidomics with insane: a versatile tool for generating custom membranes for molecular simulations. J. Chem. Theory Comput. 11, 2144–2155 (2015). (PMID: 26574417)
Jones, D. T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195–202 (1999). (PMID: 10493868)
Kabsch, W. & Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637 (1983). (PMID: 6667333)
Nosé, S. A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 52, 255–268 (1984).
Nosé, S. A unified formulation of the constant temperature molecular dynamics methods. J. Chem. Phys. 81, 511–519 (1984).
Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling through velocity rescaling. J. Chem. Phys. 126, 014101 (2007). (PMID: 17212484)
Parrinello, M. & Rahman, A. Polymorphic transitions in single crystals: a new molecular dynamics method. J. Appl. Phys. 52, 7182–7190 (1981).
Abraham, M. J. et al. GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1, 19–25 (2015).
Pronk, S. et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29, 845–854 (2013). (PMID: 234073583605599)
Daura, X. et al. Peptide folding: when simulation meets experiment. Angew. Chem. Int. Ed. 38, 236–240 (1999).
Durrant, J. D. & Amaro, R. E. LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry. PLoS Comput. Biol. 10, e1003720 (2014).
Benayad, Z., von Bulow, S., Stelzl, L. S. & Hummer, G. Simulation of FUS protein condensates with an adapted coarse-grained model. J. Chem. Theory Comput. 17, 525–537 (2021). (PMID: 33307683)
Schroder, M. S. et al. Imaging the fibroblast growth factor receptor network on the plasma membrane with DNA-assisted single-molecule super-resolution microscopy. Methods 193, 38–45 (2021). (PMID: 32389748)
Jungmann, R. et al. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nat. Methods 11, 313–318 (2014). (PMID: 244875834153392)
Edelstein, A. D. et al. Advanced methods of microscope control using muManager software. J. Biol. Methods 1, e10 (2014). (PMID: 25606571)
Endesfelder, U., Malkusch, S., Fricke, F. & Heilemann, M. A simple method to estimate the average localization precision of a single-molecule localization microscopy experiment. Histochem. Cell Biol. 141, 629–638 (2014). (PMID: 24522395)
Glogger, M., Spahn, C., Enderlein, J. & Heilemann, M. Multi-color, bleaching-resistant super-resolution optical fluctuation imaging with oligonucleotide-based exchangeable fluorophores. Angew. Chem. Int. Ed.60, 6310–6313 (2021).
El Beheiry, M. & Dahan, M. ViSP: representing single-particle localizations in three dimensions. Nat. Methods 10, 689–690 (2013). (PMID: 23900246)
Jayasinghe, I. et al. True molecular scale visualization of variable clustering properties of ryanodine receptors. Cell Rep. 22, 557–567 (2018). (PMID: 293207485775502)
المشرفين على المادة: 0 (Intracellular Signaling Peptides and Proteins)
0 (Ubiquitins)
0 (Microtubule-Associated Proteins)
EC 2.3.2.27 (Receptors, Autocrine Motility Factor)
تواريخ الأحداث: Date Created: 20230524 Date Completed: 20230613 Latest Revision: 20230613
رمز التحديث: 20230614
مُعرف محوري في PubMed: PMC10247366
DOI: 10.1038/s41586-023-06089-2
PMID: 37225996
قاعدة البيانات: MEDLINE